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WO2008042867A2 - Modulators of multiple kinases - Google Patents

Modulators of multiple kinases Download PDF

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Publication number
WO2008042867A2
WO2008042867A2 PCT/US2007/080113 US2007080113W WO2008042867A2 WO 2008042867 A2 WO2008042867 A2 WO 2008042867A2 US 2007080113 W US2007080113 W US 2007080113W WO 2008042867 A2 WO2008042867 A2 WO 2008042867A2
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signaling
hydrogen
induces cell
induces
optionally substituted
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WO2008042867A3 (en
Inventor
Dale E. Johnson
Jagarlapudi A. R. P. Sarma
Duvvuri Subrahmanyam
Sucha Sudarsanam
Francine Grant
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Emiliem Inc
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Emiliem Inc
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D498/00—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms
    • C07D498/02—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms in which the condensed system contains two hetero rings
    • C07D498/04—Ortho-condensed systems
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D213/00—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members
    • C07D213/02—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members
    • C07D213/04—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom
    • C07D213/60—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
    • C07D213/62—Oxygen or sulfur atoms
    • C07D213/63—One oxygen atom
    • C07D213/68—One oxygen atom attached in position 4
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
    • C07D401/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
    • C07D401/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings linked by a chain containing hetero atoms as chain links
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
    • C07D401/14—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing three or more hetero rings

Definitions

  • the invention relates to compounds and compound structures representing modulators of multiple kinases. These compounds exhibit kinase activity modulation patterns over a multiplicity of kinases contributing to various medical conditions.
  • Phosphorylation and dephosphorylation are processes by which phosphate groups are added or removed from a target molecule, typically a protein.
  • the process of reversible phosphorylation is a key feature of cellular regulation, including signal transduction, gene expression, cell cycle regulation, cytoskeletal regulation and apoptosis. See, e.g., Roberts (2003) "Protein phosphorylation” The Engineer 17:12-13; and Hunter (2000) “Signaling-2000 and beyond" Cell 100:113-127.
  • kinases add phosphate groups and phosphatases remove phosphate groups from substrates.
  • the substrates are proteins whose enzymatic activity is modulated thereby.
  • Signal transduction is one example of a process involving protein phosphorylation that is critical for cellular regulation. After an extracellular stimulatory factor (such as a ligand) binds to its recognized cell surface receptor, signal transduction is initiated, often mediated by a specific set of cellular protein kinases. These kinases subsequently phosphorylate the target molecule, resulting in an altered activity and a continued cellular response to the signal. See, e.g., Nishizuka (1986) "Studies and perspectives of protein kinase C" Science 233:305-312.
  • kinases act in signaling for a large number of biological functions. For example, in the context of cancer, kinases are largely responsible for signaling whether cells should continue to grow, remain dormant, or proceed to cell death. To stop cells from growing without control, thereby leading to tumor progression, the signaling activities of certain kinases can be inhibited.
  • the present invention provides compounds which are designed to modulate kinase targets in a selected pattern, which pattern of modulation will act synergistically in effecting modulation of signal transduction, either at a set time point, or over a temporal window. It is expected that the compounds can be applied to address various medical areas, including the oncology area, as well as many others caused by an inappropriate pattern of kinase signals. It is expected that treatments will be matched appropriately, e.g., according to tumor type, location, stage of disease, molecular definition, and others. [0011] The present invention provides structures, compounds and methods for modulating a pattern of kinase signaling useful in therapeutic applications.
  • the pattern incorporates effects on multiple kinases, in contrast to drugs designed to modulate a single kinase target.
  • the pattern will affect a plurality of kinases, e.g., a defined pattern of kinase effects.
  • An attractive pattern might be selected to selectively modulate certain kinase pathways while exhibiting minimal effect on others, and may target multiple points in a signal pathway.
  • Another attractive pattern may target modulating kinases in alternative or parallel signaling pathways, and the signal is modulated by affecting alternative signals. In another case, both strategies may be applied, depending upon the clinical context.
  • the invention further identifies chemical scaffolds and compounds capable of achieving the desired pattern of selective modulation of kinase pathways, e.g., by acting on specified kinases in the specified direction.
  • the present invention also provides methods for analyzing data and identifying important patterns of kinase inhibition useful in therapeutic applications. In some cases, the various kinases will function in the same pathways and inhibition may be at multiple points in a signal process. In other cases, the various kinases will function in alternative or parallel signaling pathways, and the signal is modulated by affecting alternative signals. And in other cases, both strategies may be applied, depending upon the clinical context.
  • the invention further identifies chemical scaffolds and compounds capable of achieving desired patterns of inhibition of kinase pathways, e.g., by acting on specified kinases.
  • the invention provides a method comprising identifying a therapeutically valuable profile inhibition of a plurality of kinases, the profile capable of being effected by a group of compounds sharing a chemical scaffold.
  • the method provides effects on one or more pathways important in development or maintenance of an oncogenic state of cells.
  • the compounds number at least 5.
  • the pathways number at least 2.
  • the pathways include cell division signal, metastasis, angiogenesis, and apoptosis.
  • Direct means of modulation may make use of antibodies which interact specifically with defined kinases, or nucleic acid sequence based methods may be used, e.g., antisense or RNAi means to modulate gene expression.
  • various combinations of structural segments are screened computationally for modulation of a plurality of kinases, preferably in patterns as described.
  • Specific attractive modulation patterns have been identified, and means to achieve such are provided.
  • the means include antibody based methods or transcription regulation methods. Both make use of sequences specific for the identified kinases, e.g., or of genetic, developmental, or resistance variants thereof.
  • Other means to achieve desired patterns of kinase modulation are effected by various small molecule scaffold structures, whether combinations or single compounds.
  • Those patterns of modulation of kinases may be effected by combinations with antibody or nucleic acid anti-sense reagents, e.g., based upon sequences of the described kinases.
  • the invention further provides structures and methods for modulating relevant patterns of kinase signaling useful in therapeutic applications.
  • the patterns incorporate effects on multiple kinases, in contrast to drugs designed to inhibit a single kinase target.
  • the pattern will affect a plurality of kinases, e.g., a defined or desired pattern of kinase effects.
  • An attractive pattern may target modulating kinases in alternative or parallel signaling pathways, and the signal is modulated by affecting alternative signals.
  • both strategies may be applied, depending upon the clinical context.
  • the invention further identifies chemical scaffolds and compounds capable of achieving the desired pattern of selective modulation of kinase pathways, e.g., by acting on specified kinases in the specified direction. In some cases, the pattern will include inhibition of various kinases with little effect on others.
  • the compound binds to the designated kinases in a pattern as described below, and/or modulates a biological activity modulated by the designated kinases in a pattern as described below.
  • the compounds further provide methods of modulating the biochemical activity of the designated kinases described in Table 1, the method comprising exposing those kinases to a compound as described herein at an effective concentration, e.g., less than about 1 mM, 100 nM, 10 nM, or 1 nM.
  • the pattern of selectivity exhibits at least about 0.5 log unit of specificity for said designated kinase effect relative to certain others.
  • the pathways include cell division signal, metastasis, angiogenesis, and apoptosis.
  • One embodiment provides a compound of Formula (I) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
  • X is O or NH; Z is CH or N;
  • A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R 1 substituents;
  • B is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R 7 substituents;
  • R 2 and R 8 are independently selected from hydrogen, halogen, hydroxy, OR 9 , CN, amino, NHR 9 or C 1-6 alkyl;
  • R 1 and R 7 are independently selected from hydrogen, halogen, OR 9 , Cl-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF 3 , nitro, CF 3 , CN, aryl, heteroaryl, COOR 9 , CON(R 9 ) 2 , NHR 9 , N(R ⁇ 2 , COR 9 , C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, CCMalkylheterocyclyl, CN, amino, NHCOR 9 , hydroxy, Cl-6alkoxy, OC(O)R 9 , -OC0-4alkylaryl, OC0-4alkylhetero
  • R 3 and R 4 are independently selected from hydrogen, halogen, CF 3 , CN, hydroxy, NO 2 , amino, NHAryl, NHR 9 , COOH, OR 9 , COOR 9 , CONHR 9 , or CON(R 9 ) 2 ; R 3 and R 4 may together form a 5-membered or 6- membered aryl or heteroaryl ring; R 5 and R 6 are independently selected from hydrogen, Cl-6 alkyl and optionally may be joined to form a 3-10 membered cycloalkyl;
  • R 9 is selected from hydrogen, Cl-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.
  • One embodiment provides a compound selected from:
  • Another embodiment provides a compound of Formula (II) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
  • Y is O or NH
  • Z is CH or N
  • A is an optionally substituted heteroaryl ring having between 6 and 12 members and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R 1 substituents;
  • R 7 is selected from hydrogen or Cl-6 alkyl
  • R 5 is selected from hydrogen, halogen, hydroxy, OR 8 , CN, amino, NHR 8 or Cl-6 alkyl;
  • R 1 and R 4 are independently selected from hydrogen, halogen, OR 8 , Cl-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, OCF 3 , nitro, CF 3 , CN, aryl, heteroaryl, COOR 8 , CON(R 8 ) 2 , NHR 8 , N(R 8 ) 2> COR 8 , C0-4alkylC3-10cycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR 8 , hydroxy, Cl-6alkoxy, OC(O)R 8 , -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0
  • R 8 is selected from hydrogen, Cl -6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl.
  • One embodiment provides a compound selected from: l-(4-(oxazolo[5,4-b]pyridin-7-yloxy)phenyl)-3-(5-(5-(trifluoromethyl)pyridin-2-yl)oxazol-2-yl)urea; l-(4-(oxazolo[5,4-b]pyridin-7-yloxy)phenyl)-3-(5-(4-(trifluoromethyl)phenyl)oxazol-2-yl)urea; l-(4-(quinazolin-4-yloxy)phenyl)-3-(5-(5-(trifluoromethyl)pyridin-2-yl)oxazol-2-yl)urea; N-methyl-4-(4-(3-(5-
  • Yet another embodiment provides a compound of Formula (III) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
  • X is O or NH; Z is CH or N;
  • A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R 1 substituents;
  • B is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R 7 substituents;
  • R 2 and R 8 are independently selected from hydrogen, halogen, hydroxy, OR 9 , CN, amino, NHR 9 or C 1-6 alkyl;
  • R 1 and R 7 are independently selected from hydrogen, halogen, OR 9 , C 1-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF 3 , nitro, CF 3 , CN, aryl, heteroaryl, COOR 9 , CON(R 9 ) 2 , NHR 9 , N(R 9 ) 2 , COR 9 , C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, CO ⁇ alkylheterocyclyl, CN, amino, NHCOR 9 , hydroxy, C 1 -6alkoxy, OC(O)R 9 , -OC0-4alkylaryl,
  • OC0-4alkylheteroaryl -OC0-4alkylC3-10cycloalkyl, NHCOOR 9 , OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR 9 , NR 9 COOR 9 , OCONR 9 , or NR 9 COR 9 ;
  • R 3 and R 4 are independently selected from hydrogen, halogen, CF 3 , CN, hydroxy, NO 2 , amino, NHAryl, NHR 9 ,
  • R 3 and R 4 may together form a 5-membered or 6- membered aryl or heteroaryl ring;
  • R 5 and R 6 are independently selected from hydrogen or C 1-6 alkyl
  • R 9 is selected from hydrogen, Cl -6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.
  • Still another embodiment provides a compound selected from: N-(4-(6-chloropyridin-3-yl)phenyl-N'-(4-(pyridin-4-yloxy)phenyl)-sulfamide; N-(4-(6-chloropyridin-3-yl)phenyl-N'-(4-(oxazolo[5,4-b]pyridin-7-yloxy)phenyl)-sulfamide; or N-(4-(6-chloropyridin-3-yl)phenyl-N'-(4-(quinazolin-4-yloxy)phenyl)-sulfamide.
  • Yet another embodiment provides a compound of Formula (IV) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
  • X is O or NH
  • Y is O, NH, -OCH 2 - or -CH 2 O-
  • Z is CH or N
  • A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R' substituents;
  • R 1 and R 4 are independently selected from hydrogen, halogen, OR 9 , Cl-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF 3 , nitro, CF 3 , CN, aryl, heteroaryl, COOR 9 , CONCR 9 ) ⁇ NHR 9 , N(R 9 ) 2 , COR 9 , C0-4a!kylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR 9 , hydroxy, Cl-6
  • R 2 and R 3 are independently selected from hydrogen, halogen, CF 3 , CN, hydroxy, NO 2 , amino, NHAryl, NHR 9 , COOH, OR 9 , COOR 9 , CONHR 9 , or CON(R 9 ) 2 ; R 2 and R 3 may together form a 5-membered or 6- membered aryl or heteroaryl ring; R 5 is selected from hydrogen, halogen, hydroxy, OR 9 , CN, amino, NHR 9 or Cl-6 alkyl;
  • R 6 and R 7 are independently selected from hydrogen, Cl-6 alkyl and optionally may be joined to form a 3-10 membered cycloalkyl;
  • R 8 is selected from hydrogen or Cl-6 alkyl
  • R 9 is selected from hydrogen, Cl-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.
  • the compound binds to the designated kinases in a particular pattern; and/or modulates a biological activity modulated by the designated kinases in such a pattern.
  • Embodiments further provide methods of modulating the biochemical activity of the designated kinases, the method comprising exposing those kinases to a compound of Claim 1 at an effective concentration, e.g., less than about 1 mM, 100 nM, 10 nM, or 1 nM.
  • the pattern of selectivity exhibits at least about 0.5 log unit of specificity for said designated kinase effect relative to certain others.
  • the pathways include cell division signal, metastasis, angiogenesis, and apoptosis.
  • Figure 1-10 illustrate embodiments according to the invention for the design of modulators of panels of multiple kinases.
  • the present invention provides structures, compounds and methods for modulating a pattern of kinase signaling useful in therapeutic applications.
  • the pattern incorporates effects on multiple kinases, in contrast to drugs designed to modulate a single kinase target.
  • the pattern will affect a plurality of kinases, e.g., a defined pattern of kinase effects.
  • An attractive pattern might be selected to selectively modulate certain kinase pathways while exhibiting minimal effect on others, and may target multiple points in a signal pathway.
  • Another attractive pattern may target modulating kinases in alternative or parallel signaling pathways, and the signal is modulated by affecting alternative signals. In another case, both strategies may be applied, depending upon the clinical context.
  • the invention further identifies chemical scaffolds and compounds capable of achieving the desired pattern of selective modulation of kinase pathways, e.g., by acting on specified kinases in the specified direction.
  • FIG. 1-10 The compound design and screening approach of the present invention are summarized in Figures 1-10. These methods are based on the identification of a set of validated kinases. Crystal structures of known kinases are solved through X-ray crystallography, NMR based methods or other protein structure elucidation methods. The binding sites of the kinases are analyzed and scaffolds of potential modulators are generated. Lead compounds are designed based on the scaffolds and tested both in silico and through experimental methods to identify lead compounds for further development. Derivatives of the lead compounds are synthesized and tested for their kinase modulatory activity across selected kinase profiles. Details of the methods and compounds described herein are set forth below.
  • a foundation of the approach is a comprehensive understanding of the signaling network of individual kinases and their roles in physiologic and pathologic conditions. This provides the basis to identify targets for pharmaceutical intervention in various human diseases and conditions.
  • the invention teaches how to identify simultaneously sets of kinases (relevant multi-kinase profiles) and chemical starting points (scaffolds) to modulate multi-kinases.
  • the invention provides processes that lead to the synthesis of kinase modulators with predetermined multi-kinase profiles in a timely manner.
  • a pathway is a series of linked biochemical steps, with a beginning and an end; activity within a pathway takes the form of flux, or flow, of molecules, e.g., substrates.
  • the network of pathways forms the biochemical repertoire or potential phenotypes of a biological system.
  • a profile is a combination of kinases that together modulate one or more biological pathways whose coordinated inhibition leads to a desired physiological effect.
  • the profile involves at least two, three, four or more target kinases. This in effect amounts to combination therapies, for example, a "cocktail" of selective drugs.
  • our combination strategy can be combined with other therapy leading to multiple therapeutic modalities.
  • the difference will preferably be a one log difference in effect on binding specificity or biological activity across the kinases, for example in terms of molar concentrations.
  • the differences for a similar effect on a plurality of kinases will typically be small at an appropriate pharmacological concentration, e.g., less than about 1.3, 1, or 0.3 log units difference in molar concentrations.
  • the differences will typically be large at an appropriate pharmacological concentration, e.g., more than about 1, 1.3, 2, 2.3, 3 or more log units difference in molar concentrations.
  • a profile which inhibits kinases A and B, but not C will preferably have similar amounts of inhibition of the A and B kinases at the appropriate pharmacological concentration, while much less (e.g., about 2 logs) less effect on kinase C.
  • the assay will have biochemical components, e.g., kinases at concentrations analogous to physiological conditions.
  • the concentrations of compound necessary to effect the desired modulatory effects on kinases may be at least about 10, 30, 100, 300, or more on different kinases.
  • kinases A and B may be effected by similar concentrations of compound, while kinase C may be unaffected until much higher concentrations of compound are reached. Conversely, the sensitivity of kinase C may low, while much lower amounts of compound may modulate kinases A and B. Additional effects of kinases D, E, and so on may also be combined into these compounds using various SAR or pharmacophore models directed to the additional kinases. Alternatively, appropriate selective entities modulating kinases D and E (but not A, B, and C) may be used in combination to extend the selectivity of the combined treatment.
  • kinase signal pathways are relevant in cell-cell interactions, in regulation of organ metabolism and physiology, and thereby aspects of organ physiology and systems biology. These may be either in the context of normal growth or development, or in abnormal contexts. In particular, many diseases or disorders may be caused by or cause aberrant interactions within an organism.
  • Kinases have been implicated in various cancer conditions, and a number of drugs have been developed which target specific kinases. See Wanebo, et al. (2006) “Targeting growth factors and angiogenesis; using small molecules in malignancy” Cancer Metastasis Rev. 25:279-92, PMID: 16770540; Adjei and Hidalgo (2005) "Intracellular signal transduction pathway proteins as targets for cancer therapy” J. Clin.
  • Protein kinases regulate multiple cellular processes that contribute to tumor development and progression, including cell growth, differentiation, migration, and programmed cell death (apoptosis). Inappropriate activity of protein kinases has been implicated in a variety of human diseases such as cancer, diabetes, and autoimmunity. In cancer model systems, perturbation of tyrosine kinase signaling can result in malignant transformation. For tumors whose growth is driven by activated kinases caused by genetic alterations, targeted drugs can potentially modulate or reverse malignant progression.
  • tyrosine kinase modulators are safe and therapeutically active in selected populations of cancer patients.
  • Several of these drugs are now part of the standard treatment regimen for specific tumor types. Modulating the abnormal activity of kinases with small molecules has demonstrated significant clinical benefit in patients, as in the case of the Bcr/Abl tyrosine kinase modulator Gleevec, the first marketed small molecule (SM) protein kinase modulator approved for treatment of chronic myelogenous leukemia (CML).
  • SM small molecule
  • CML chronic myelogenous leukemia
  • Other drugs such as Tarceva, Nexavar and Sutent, have followed the success of Gleevec. Judging from the efficacy of these drugs and results from ongoing clinical studies, protein kinases have been firmly established as targets for oncology therapeutics. The era of the so-called targeted therapies for cancer is arriving, supplanting cytotoxic drugs.
  • Protein kinases are classified according to major groups and families, which are denominated TK, TKL, STE, CMGC, CAMK, and AGC. Kinases share a catalytic domain, but otherwise have diverse domain architecture. The common catalytic domain is where ATP binds and transfer of a phosphate group to a substrate takes place.
  • Kinase assays may be performed by many standard and other methodologies, and assay services are commercially available. See Giordano and Romano (eds. 2004) Cell Cycle Control and Dvsregulation Protocols: Cvclins. Cvclin-Dependent Kinases, and Other Factors (Methods in Molecular Biology) Humana Press, ISBN: 0896039498; Terrian (ed.
  • IQ technology utilizes an iron compound that acts as a dark quencher upon specific binding to the phosphoryl group of a fluorescent dye-labeled phosphorylated peptide.
  • the binding event results in a decrease in the observed fluorescence intensity of the dye- labeled peptide after it becomes phosphorylated by the kinase.
  • Systems biology analyses and techniques are described, e.g., in Klipp, et al. (2005) Systems Biology in Practice: Concepts. Implementation and Application Wiley, ISBN: 3527310789; Kitano (ed. 2001) Foundations of Systems Biology MIT Press, ISBN: 0262112663; Bower and Bolouri (eds.
  • the human genome encodes some 518 protein kinases that share a catalytic domain conserved in structure, but which notably differ in how their catalysis is regulated.
  • the ATP binding pocket is between the two lobes of the kinase fold. This ATP binding site, together with less conserved hydrophobic surrounding pockets, has been the focus of modulator design that has exploited differences in kinase structure and pliability in order to achieve selectivity.
  • Drugs are in clinical trials that target all stages of signal transduction. These range from the receptor tyrosine kinases that initiate intracellular signaling through second-messenger generators and kinases involved in signaling cascades to the kinases that regulate the cell cycle that governs cellular fate.
  • cancer is one indication for which kinases have been validated as targets for therapeutic intervention
  • many other medical conditions will similarly be sensitive to the fundamental signal pathways regulated by these same kinases.
  • other medical conditions will be susceptible to treatment by the compounds of the invention, including inflammation, developmental abnormalities, aging processes, and the like.
  • Particular target medical conditions include those in which modulation of a process such as angiogenesis, cell cycle progression, cell division, cell growth, cell migration, cell mobility, cell motility, cell proliferation, cell survival, oncogenesis, p53 degradation, general proliferation, tumorigenesis, apoptosis, or metastasis are likely processes contributing to the symptoms or condition.
  • PK related disorder As used herein, "PK related disorder,” "PK driven disorder,” and “abnormal PK activity” all refer to a condition characterized by inappropriate; i.e., under or, more commonly, over, PK catalytic activity, where the particular PK can be an RTK, a CTK or an STK. Inappropriate catalytic activity can arise as the result of one of: (1) PK expression in cells which normally do not express PKs; (2) increased PK expression leading to unwanted cell proliferation, differentiation and/or growth; or (3) decreased PK expression leading to unwanted reductions in cell proliferation, differentiation, and/or growth.
  • Over-activity of a PK refers to either amplification of the gene encoding a particular PK or production of a level of PK activity which can correlate with a cell proliferation, differentiation, and/or growth disorder (that is, as the level of the PK increases, the severity of one or more of the symptoms of the cellular disorder increases). Under-activity is, of course, the converse, wherein the severity of one or more symptoms of a cellular disorder increase as the level of the PK activity decreases.
  • the term "therapeutically effective amount” as used herein refers to that amount of the compound being administered which will relieve to some extent one or more of the symptoms of the disorder being treated.
  • a therapeutically effective amount refers to that amount which has the effect of (1) reducing the size of the tumor; (2) modulating (that is, slowing to some extent, preferably stopping) tumor metastasis; (3) modulating to some extent (that is, slowing to some extent, preferably stopping) tumor growth; and/or (4) relieving to some extent (or, preferably, eliminating) one or more symptoms associated with the cancer.
  • the above-referenced protein kinase related disorder is selected from the group consisting of a receptor protein kinase related disorder, a cellular kinase disorder, and a serine-threonine kinase related disorder.
  • the protein kinase related disorder is a cancer selected from the group consisting of squamous cell carcinoma, astrocytoma, glioblastoma, lung cancer, bladder cancer, head and neck cancer, melanoma, ovarian cancer, prostate cancer, breast cancer, small-cell lung cancer, and glioma in a further aspect of this invention.
  • the compounds of this invention may modulate the activity of protein phosphatases which are enzymes which remove phosphate groups from phosphorylated proteins.
  • the compounds disclosed herein may also represent a new generation of therapeutic compounds for diseases and disorders associated with abnormal phosphatase activity (such as, without limitation, cell proliferation disorders and inflammatory disorders).
  • the terms defined herein with respect to PKs would be understood by one skilled in the art to have the same or similar meaning with regard to phosphatases. IV. Medicinal Chemistry
  • references on assays and approaches include Moore and Kliewer (2000) Toxicology 153: 1-10;
  • Parameters on compounds screened by in silico screening include services and software available from
  • the cytochrome P450 system is a significant component of modulating toxicity of proposed therapeutic compounds. See, e.g., Park, et al. (2005) "The role of metabolic activation in drug-induced hepatotoxicity” Ann- Rev. Pharmacology and Toxicology 45:177-202. Ann. Revs. Pr. and Coon (2005) "Cytochrome P450: Nature's Most Versatile Biological Catalyst” Ann. Rev. Pharmacology and Toxicology 45: 1-25.
  • Various cytochrome P450 isoforms, in decreasing order of importance, is typically P450 isoforms 3A4 » 2D6 > 2C9, 2C19 » 1 A2, 2El.
  • Such effects are not limited to drug induced effects on pharmacology, but may similarly be induced by environmental effects, e.g., diet, specific food intake, and other physiological effects, e.g., status of the immune or nervous system, presence of infectious agents, general health status, etc.
  • Xenobiotic transporters are expressed in several tissues including the intestine, liver, kidney, and brain, and play key roles in drug absorption, distribution, and excretion. Functional characteristics of transporters provide important information allowing improvements in drug delivery or drug design through targeting or avoiding specific transporter proteins.
  • Optimizing drugs based on transporter interaction offers the possibility of delivering a drug to a target organ, avoiding distribution to other organs (thereby reducing the chance of toxic side effects), controlling the elimination process, and/or improving oral bioavailability. It is useful to select a lead compound that may or may not interact with transporters, depending on whether such an interaction is desirable.
  • the expression system of transporters is an efficient tool for screening the activity of individual transport processes.
  • the changes in pharmacokinetics due to genetic polymorphisms and drug-drug interactions involving transporters can often have a direct and adverse effect on the therapeutic safety and efficacy of many important drugs.
  • ABLl GeneID 25; see MIM 189980; described functions include ATP binding, DNA binding; nucleotide binding, protein C-terminus binding, protein-tyrosine kinase activity, and transferase activity; indicated function pathways dependent upon gene include DNA damage response (signal transduction resulting in induction of apoptosis), S-phase-specific transcription in mitotic cell cycle, intracellular signaling cascade, mismatch repair, protein amino acid phosphorylation, regulation of progression through cell cycle, and regulation of transcription (DNA-dependent).
  • AKTl GeneID 207 (NCBI); see MIM 164730; described functions include ATP binding, identical protein binding, nucleotide binding; protein kinase activity, receptor signaling protein serine/threonine kinase activity, sugar porter activity, and transferase activity; indicated function pathways dependent upon gene include G-protein coupled receptor protein signaling pathway, anti-apoptosis, apoptosis, carbohydrate metabolism, glucose metabolism, glycogen biosynthesis, insulin receptor signaling pathway, insulin-like growth factor receptor signaling pathway, nitric oxide biosynthesis, protein amino acid phosphorylation, protein amino acid phosphorylation, regulation of translation, response to heat, signal transduction, and transport.
  • AURKA GeneID 6790; see MIM 164920; described functions include ATP binding, nucleotide binding, protein binding, protein binding, protein kinase activity, protein serine/threonine kinase activity, and transferase activity, indicated functional pathways dependent upon gene include cell cycle, mitosis, phosphoinositide- mediated signaling, protein amino acid phosphorylation, protein amino acid phosphorylation, regulation of protein stability, spindle organization, and biogenesis.
  • BRAF GeneID 673; see MIM 164757; described functions include ATP binding, diacylglycerol binding, metal ion binding, nucleotide binding, protein serine/threonine kinase activity, receptor signaling protein activity, transferase activity, zinc ion binding; indicated functional pathways dependent upon gene include anti-apoptosis, intracellular signaling cascade, organ morphogenesis, protein amino acid phosphorylation.
  • CDC2 GeneED 983 (NCBI); see MIM 116940; described functions include ATP binding, cyclin- dependent protein kinase activity, nucleotide binding, protein binding, and transferase activity; indicated function pathways dependent upon gene include anti-apoptosis, cell cycle, cell division, mitosis, protein amino acid phosphorylation, regulation of progression through cell cycle, and traversing start control point of mitotic cell cycle.
  • EGFR GeneID 1956 (NCBI); see MIM 131550; described functions include ATP binding, MAP/ERK kinase kinase activity, actin filament binding, double-stranded DNA binding, epidermal growth factor receptor activity, epidermal growth factor receptor activity, identical protein binding, nitric-oxide synthase regulator activity, nucleotide binding, protein heterodimerization activity, transferase activity, and transmembrane receptor activity; indicated function pathways dependent upon gene include calcium-dependent phospholipase A2 activation, cell cycle, cell proliferation, cell surface receptor linked signal transduction, cell-cell adhesion, epidermal growth factor receptor signaling pathway, negative regulation of progression through cell cycle, ossification, phospholipase C activation, positive regulation of MAPK activity, positive regulation of cell migration, positive regulation of epithelial cell proliferation, positive regulation of nitric oxide biosynthesis, positive regulation of phosphorylation, protein amino acid phosphorylation, protein insertion into membrane
  • ERBB2 GeneID 2064 (NCBI); see MIM 164870 (also designated HER2); described functions include ATP binding, ErbB-3 class receptor binding, electron carrier activity, epidermal growth factor receptor activity, epidermal growth factor receptor activity, iron ion binding, non-membrane spanning protein tyrosine kinase activity, nucleotide binding, protein heterodimerization activity, protein heterodimerization activity, protein- tyrosine kinase activity, receptor activity, receptor signaling protein tyrosine kinase activity, and transferase activity; indicated function pathways dependent upon gene include cell proliferation, electron transport, heart development, mammary gland development, nervous system development, phosphoinositide-mediated signaling, positive regulation of MAPK activity, positive regulation of epithelial cell proliferation, protein amino acid phosphorylation, protein amino acid phosphorylation, regulation of angiogenesis, transmembrane receptor protein tyrosine kinase signaling pathway, and trans
  • FRAPl GeneID 2475 (NCBI); see MIM 601231; described functions include binding, kinase activity, phosphoprotein binding, phosphotransferase activity (alcohol group as acceptor), and transferase activity, indicated function pathways dependent upon gene include cell growth, phosphorylation, protein catabolism, regulation of progression through cell cycle, regulation of translation, response to nutrient, and signal transduction.
  • JAK3 GeneID 3718 (NCBl); see MIM 600173; described functions include ATP binding, Janus kinase activity, nucleotide binding, protein binding, protein-tyrosine kinase activity, protein-tyrosine kinase activity, and transferase activity, indicated function pathways dependent upon gene include intracellular signaling cascade, mesoderm development, protein amino acid phosphorylation, and protein amino acid phosphorylation.
  • KDR GeneID 3791 (NCBI); see MIM 191306; described functions include ATP binding, nucleotide binding, receptor activity, transferase activity, vascular endothelial growth factor receptor activity; indicated functional pathways dependent upon gene include angiogenesis, cell differentiation, protein amino acid phosphorylation, and transmembrane receptor protein tyrosine kinase signaling pathway.
  • KIT GeneID 3815 (NCBI); see MIM 164920; described functions include ATP binding, nucleotide binding, receptor activity, receptor signaling protein tyrosine kinase activity, transferase activity, and vascular endothelial growth factor receptor activity; indicated functional pathways dependent upon gene include protein amino acid dephosphorylation, protein amino acid phosphorylation, signal transduction, and transmembrane receptor protein tyrosine kinase signaling pathway.
  • LCK GeneID 3932 (NCBI); see MIM 153390; described functions include ATP binding, ATPase binding, CD4 receptor binding, CD8 receptor binding, SH2 domain binding, SH2 domain binding, glycoprotein binding, nucleotide binding, phosphoinositide 3-kinase binding, protein C-terminus binding, protein kinase binding, protein serine/threonine phosphatase activity, protein-tyrosine kinase activity, protein-tyrosine kinase activity, and transferase activity; indicated functional pathways dependent upon gene include Ras protein signal transduction, T cell differentiation, caspase activation, hemopoiesis, induction of apoptosis, intracellular signaling cascade, positive regulation of T cell activation, positive regulation of T cell receptor signaling pathway, protein amino acid phosphorylation, regulation of lymphocyte activation, regulation of progression through cell cycle, release of sequestered calcium ion into cytosol, response to drug, and zinc ion homeost
  • MAP2Kl GeneID 5604 (NCBI); see MIM 176872; described functions include ATP binding, MAP kinase kinase activity, nucleotide binding, protein binding, protein serine/threonine kinase activity, protein- tyrosine kinase activity, and transferase activity; indicated functional pathways dependent upon gene include cell motility, chemotaxis, protein amino acid phosphorylation, and signal transduction.
  • MAPKl GeneID 5594 (NCBI); see MIM 176948; described functions include ATP binding, MAP kinase activity, nucleotide binding, protein serine/threonine kinase activity, and transferase activity; indicated functional pathways dependent upon gene include cell cycle, chemotaxis, induction of apoptosis, protein amino acid phosphorylation, response to stress, signal transduction, and synaptic transmission.
  • PDGFRB GeneID 5159; see MIM 173410; described functions include ATP binding, nucleotide binding, platelet activating factor receptor activity, platelet-derived growth factor receptor activity, protein binding, receptor activity, and transferase activity; indicated functional pathways dependent upon gene include vascular endothelial growth factor receptor activity, protein amino acid phosphorylation, signal transduction, and transmembrane receptor protein tyrosine kinase signaling pathway.
  • PIK3CG GeneID 5294 (NCBI); see MIM 601232; described functions include inositol or phosphatidylinositol kinase activity, phosphatidylinositol 3-kinase activity, phosphatidylinositol-4,5-bisphosphate 3-kinase activity, and transferase activity; indicated functional pathways dependent upon gene include G-protein coupled receptor protein signaling pathway.
  • SRC GeneID 6714 (NCBI); see MIM 190090; described functions include ATP binding, SH2 domain binding, SH3/SH2 adaptor activity, nucleotide binding, protein binding, protein-tyrosine kinase activity, protein- tyrosine kinase activity, and transferase activity; indicated functional pathways dependent upon gene include protein amino acid phosphorylation, protein kinase cascade, and signal complex formation.
  • Non-human species counterparts will be useful in many contexts including testing in other species and evaluation of in vitro and in vivo animal models. Other activities and pathways related to a species counterpart may often be adapted to a human counterpart.
  • Binding pockets of all known kinase crystal structures are classified and interacting residues identified.
  • binding pockets are clustered according to shape similarities.
  • a two-way clustering of kinases and IC50 of compounds are performed. In addition, clustering of compounds by themselves is performed. This yields sets of profiles for which Quantitative Structure Activity Relationship (QSAR) and Quantitative Structure Property Relationship (QSPR) are modeled.
  • QSAR Quantitative Structure Activity Relationship
  • QSPR Quantitative Structure Property Relationship
  • the binding sites of the kinases are analyzed and scaffolds of potential modulators are generated.
  • Lead compounds are designed based on the scaffolds and tested both in silico and through experimental methods to identify lead compounds for further development. Derivatives of the lead compounds are synthesized and tested for their kinase inhibitory activity across selected kinase profiles. Details of the methods and compounds described herein are set forth below.
  • a "Structure Target Activity” is generated from: (i) all known kinase modulators ; (ii) known kinase crystal structures; (iii) novel chemical scaffolds generated from analysis of kinase modulators and crystal structures; and (iv) kinase biology, which provides as the basis for selectivity based on the foregoing information.
  • the process bypasses key steps in the conventional drug discovery. The approach moves the starting point of drug discovery to the lead-optimization stage and results in both time and cost savings.
  • drug-like properties e.g., the ADMETox, and simplicity of synthesis and susceptibility to patent protection.
  • Pharmacophore models have been applied, e.g., GOLD and GLIDE, for predicting the activities against various kinases, e.g., KDR or PDGFRB.
  • animal models will further confirm appropriate response in an organismal context.
  • Table 1 lists biological pathways relevant to diseases. These pathways include kinases as important mediators.
  • Kinase refers to official gene symbol (according to Human Genome Organization, HUGO).
  • NCBI refers to unique numeric identifier for the kinase as designated by NCBI.
  • Pathway refers to specific biological pathway as it is commonly understood.
  • Class refers to specific biological function mediated by the pathway. [00111] .
  • GSK3A, GSK3B (2931, 2932) » Activation of cAMP-Dependent PKA » Induces oncogenesis MAP2K1 , MAP2K2 (5604, 5605) » Activation of cAMP-Dependent PKA » Induces cell survival
  • PRKCA PRKCBl
  • PRKCD PRKCE
  • PRKCH PRKCG
  • PRKCI PRKDl
  • PRKD3 PRKCQ
  • PRKCZ (5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 23683, 5588, 5590) » Activation of PKC through GPCR » Induces cell survival
  • EPHB4 (2050 » Akt Signaling » Induces cell cycle progression EPHB4 (2050 » Akt Signaling » Inhibits apoptosis EPHB5 (2051 » Akt Signaling » Induces cell cycle progression EPHB5 (2051 » Akt Signaling » Inhibits apoptosis EPOR (2057 » Akt Signaling » Induces cell cycle progression EPOR (2057 » Akt Signaling » Inhibits apoptosis ERBB2 (2064) » Akt Signaling » Induces cell cycle progression ERBB2 (2064) » Akt Signaling » Inhibits apoptosis ERBB4 (2066) » Akt Signaling » Induces cell cycle progression ERBB4 (2066) » Akt Signaling » Inhibits apoptosis ERBB4 (2066) » Akt Signaling » Induces cell cycle progression ERBB4 (2066) » Akt Signaling » Inhibits apoptosis apoptosis ERBB4 (2066) » Akt
  • Akt Signaling Inhibits apoptosis PDKl (5163) » Akt Signaling » Induces cell cycle progression
  • Akt Signaling Inhibits apoptosis PRKDC (5591) » Akt Signaling » Induces cell cycle progression
  • CDK5 (1020) » Dopamine-DARPP32 Feedback onto cAMP Pathway » Induces cell survival PRKACA, PRKACB, PRKACG, PRKARlA, PRKARlB, PRKAR2B, PRKAR2A (5566, 5567, 5568, 5573, 5575, 5577, 5576) » Dopamine-DARPP32 Feedback onto cAMP Pathway » Induces cell survival PRKCA, PRKCBl, PRKCD, PRKCE, PRKCH, PRKCG, PRKCI, PRKDl, PRKCQ (5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 5588) » Dopamine-DARPP32 Feedback onto cAMP Pathway » Induces cell survival
  • PAK6 (56924) » FAKl Signaling » Induces cell proliferation
  • PTK2 (5747) » FAKl Signaling » Metastasis RAFl (5894) » FAKl Signaling » Induces cell proliferation
  • BTK (695) » Fas Signaling » Induces cell proliferation
  • MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6 (5604, 5605, 5606, 6416, 5608) » FLT3 Signaling » Induces cell division
  • MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6 (5604, 5605, 5606, 6416, 5608) » JAK/STAT Pathway » Induces cell division
  • PAK3 (5063) » JNK Pathway » Induces tumorigenesis
  • PAK4 (10298) » JNK Pathway » Induces cell migration
  • CDK2 (1017) » p53 Signaling » Induces cell cycle progression
  • CDK4 ( 1019) » p53 Signaling » Induces cell cycle progression
  • MAP2K1; MAP2K2; MAP2K3; MAP2K4; MAP2K5; MAP2K6 (5604; 5605; 5606; 6416; 5607; 5608) » p70S6K Signaling » Induces cell survival MAPKl; MAPK3; MAPK4; MAPK6; MAPK7; MAPK8; MAPK9; MAPKlO; MAPK14; MAPKl 1; MAPK12; MAPK13 (5594; 5595; 5596; 5597; 5598; 5599; 5601; 5602; 1432; 5600; 6300; 5603) » p70S6K Signaling » Induces cell growth
  • PRKCD (5580) » p70S6K Signaling » Induces cell growth PRKCD (5580) » p70S6K Signaling » Induces cell motility
  • PAK2 (5062) » PAK pathway » Induces cell survival
  • PAK3 (5063) » PAK pathway » Induces cell survival
  • PAK6 (56924) » PAK pathway » Induces cell survival
  • PRKCBl (5579) » PBK Signaling » Induces cell proliferation PRKCD (5580) » PBK Signaling » Induces cell growth PRKCD (5580) » PDK Signaling » Induces cell proliferation PRKCE (5581) » PBK Signaling » Induces cell growth PRKCE (5581) » PBK Signaling » Induces cell proliferation PRKCG (5582) » PBK Signaling » Induces cell growth PRKCG (5582) » PBK Signaling » Induces cell proliferation PRKCH (5583) » PBK Signaling » Induces cell growth PRKCH (5583) » PBK Signaling » Induces cell proliferation PRKCI (5584) » PBK Signaling » Induces cell growth
  • MAP2K1 » PDK Signaling in B-Lymphocyte » Induces cell growth MAP2K2 (5605) » PDK Signaling in B-Lymphocyte » Induces cell growth MAPKl (5594) » PDK Signaling in B-Lymphocyte » Induces cell growth MAPKlO (5602) » PDK Signaling in B-Lymphocyte » Induces cell growth MAPKl 1 (5600) » PBK Signaling in B-Lymphocyte » Induces cell growth MAPK12 (6300) » PBK Signaling in B-Lymphocyte » Induces cell growth MAPK 13 (5603) » PBK Signaling in B-Lymphocyte » Induces cell growth MAPK14 (1432) » PBK Signaling in B-Lymphocyte » Induces cell growth MAPK3 (5595) » PBK Signaling in B-Lymphocyte » Induces cell growth MAPK4 (5596) » PBK Signaling in B-Lymphocyte » Induces cell growth MA
  • MAPK9 (5601) » PDK Signaling in B-Lymphocyte » Induces cell growth
  • PK.3CA (5290) » PDK Signaling in B-Lymphocyte » Induces cell growth
  • PIK3CB (5291) » PDK Signaling in B-Lymphocyte » Induces cell growth
  • PIK3CG (5294) » PDK Signaling in B-Lymphocyte » Induces cell growth
  • PRKCA PRKCBl
  • PRKCD PRKCE
  • PRKCH PRKCG;PRKD3; PRKDl; PRKCQ; PRKCI; PRKCZ(5578;
  • AKTl (207 » S-IP Stimulated Signaling » Inhibits apoptosis
  • MAPK6 [or ERK3] (5597) » S-IP Stimulated Signaling » Inhibits apoptosis
  • MAP2K1, MAP2K2 (5604, 5605) » TGF-Beta Pathway » Induces angiogenesis
  • MAP2K1, MAP2K2 (5604, 5605) » TGF-Beta Pathway » Induces cell growth
  • MAP2K1, MAP2K2 (5604, 5605) » TGF-Beta Pathway » Induces cell mobility
  • MAP2K1, MAP2K2 (5604, 5605) » TGF-Beta Pathway » Induces tumorigenesis MAP2K4 (6416) » TGF-Beta Pathway » Induces angiogenesis
  • MAP3K7 (6885) » TGF-Beta Pathway » Induces angiogenesis MAP3K7 (6885) » TGF-Beta Pathway » Induces cell growth
  • MAP3K1; MAP3K2; MAP3K3; MAP3K4; MAP3K5 (4214; 10746; 4215; 4216; 4217) » TNF Signaling »
  • MAPK3; MAPKl; MAPK4; MAPK6; MAPK12 (5595; 5594; 5596; 5597; 6300) » TNF Signaling » Induces cell survival
  • MAP2K1; MAP2K2; MAP2K3; MAP2K4; MAP2K5; MAP2K6 (5604; 5605; 5606; 6416; 5607; 5608) » TNF- Induced Apoptosis Implicating Sphingolipids » Induces proliferation
  • MAP3K1 (5595) » TNFRl Pathway » Induces cell survival
  • MAP3K7 (6885) » TNFRl Pathway » Induces cell survival
  • MAPK8 (5599) » TNFRl Pathway » Induces cell survival
  • PRKCI (5584) » UVC-Induced MAPK Signaling » Induces tumorigenesis PRKCQ (5588) » UVC-Induced MAPK Signaling » Induces cell proliferation
  • PRKDl (5587) » UVC-Induced MAPK Signaling » Induces cell proliferation PRKDl (5587) » UVC-Induced MAPK Signaling » Induces tumorigenesis
  • MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6 (5604, 5605, 5606, 6416, 5608) » VEGF and S-IP Signaling » Induces angiogenesis
  • MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6 (5604, 5605, 5606, 6416, 5608) » VEGF and S-IP Signaling » Induces cell proliferation
  • PRKCA PRKCBl
  • PRKCD PRKCE
  • PRKCH PRKCG
  • PRKCI PRKDl
  • PRKD3 PRKCQ
  • PRKCZ (5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 23683, 5588, 5590) » VEGF and S-IP Signaling » Induces angiogenesis
  • PRKCA PRKCBl
  • PRKCD PRKCE
  • PRKCH PRKCG
  • PRKCI PRKDl
  • PRKD3 PRKCQ
  • PRKCZ 5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 23683, 5588, 5590
  • VEGF Pathway Induces cell survival MAP2K1 , MAP2K2 (5604, 5605) » VEGF Pathway » Induces angiogenesis
  • MAP2K1, MAP2K2 (5604, 5605) » VEGF Pathway » Induces cell proliferation
  • MAP2K3, MAP2K6 (5595, 5608) » VEGF Pathway » Induces angiogenesis
  • MAPKAPK2, MAPKAPK3 (9261, 7867) » VEGF Pathway » Induces angiogenesis
  • PRKCA PRKCBl
  • PRKCD PRKCE
  • PRKCH PRKCG
  • PRKCI PRKDl
  • PRKD3 PRKCQ
  • PRKCZ (5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 23683, 5588, 5590) » VEGF Pathway » Induces angiogenesis
  • PRKCA PRKCBl
  • PRKCD PRKCE
  • PRKCH PRKCG
  • PRKCI PRKDl
  • PRKD3 PRKCQ
  • PRKCZ (5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 23683, 5588, 5590) » VEGF Pathway » Induces cell proliferation
  • AKTl (207), AKT2 (208), AKT3 (10000)
  • 20 AURKA (6790), CDC2 (983), CDK2 (1017), CDK5 (1020), GSK3B (2932)
  • CDK2 (1017), CDK4 (1019), EGFR (1956), HER2 (2064),
  • PK3CA FRAPl (2475), PK3CA (5290), PIK3CB (5291), PDC3CD (5293), PDC3CG (5294), PIK3CG (5294)
  • IRAKI (3654), IRAK2 (3656), IRAK3 (11213), IRAK4 (51135), MAP3K5 (4217), PIK3CA (5290),
  • the invention features a pharmaceutical composition
  • a pharmaceutical composition comprising (i) a physiologically acceptable carrier, diluent, or excipient; and (ii) a compound as described herein.
  • the receptor or cellular protein kinase whose catalytic activity is selectively modulated (to an appropriate amount, e.g., about 1.0, 1.3, 2, or 2.3 log units) by a compound of this invention at a pharmaceutically acceptable concentration.
  • the target kinase to be selectively inhibited is selected from the group consisting of two or more (e.g., 3, 4, or more) among ABL,
  • selected profiles may include inhibition of select subsets of specific kinases, e.g., at nanomolar range concentrations, while lack of inhibition of other select subsets of kinases at similar or higher concentration, e.g., tens, hundreds or thousands of times higher , e.g., sub or micromolar concentrations, or substantially different quantitative effects at similar concentrations.
  • a protein kinase natural binding partner can bind to a protein kinase's intracellular region with high affinity. High affinity represents an equilibrium binding constant on the order of 10E-6 M or less.
  • a natural binding partner can also transiently interact with a protein kinase intracellular region and chemically modify it.
  • Protein kinase natural binding partners are chosen from a group that includes, but is not limited to, SRC homology 2 (SH2) or 3 (SH3) domains, other phosphoryl tyrosine binding (PTB) domains, guanine nucleotide exchange factors, protein phosphatases, and other protein kinases.
  • the compounds of the invention preferably modulate the activity of the protein kinase in vitro. These compounds preferably show positive results in one or more in vitro assays for an activity described.
  • the invention also features a method of identifying compounds that modulate the function of protein kinase, comprising the following steps: (a) contacting cells expressing the protein kinase with the compound; and (b) monitoring an effect upon the cells.
  • the effect upon the cells is preferably a change or an absence of a change in cell phenotype, more preferably it is a change or an absence of a change in cell proliferation or other physiological response, and even more preferably it is a change or absence of a change in the catalytic activity of the protein kinase.
  • the invention features a method for identifying the compounds of the invention, comprising the following steps: (a) lysing the cells to render a lysate comprising protein kinase; (b) adsorbing the protein kinase to an antibody; (c)incubating the adsorbed protein kinase with a substrate or substrates; and (d) adsorbing the substrate or substrates to a solid support or antibody; where the step of monitoring the effect on the cells comprises measuring the phosphate concentration of the substrate or substrates.
  • the invention features a method for treating a disease related to unregulated kinase signal transduction, where the method includes the step of administering to a subject in need thereof a therapeutically effective amount of a compound of the invention as described herein.
  • the invention also features a method of regulating kinase signal transduction comprising administering to a subject a therapeutically effective amount of a compound of the invention as described herein.
  • the invention features a method of preventing or treating an abnormal condition in an organism, where the abnormal condition is associated with an aberration in a signal transduction pathway characterized by an interaction between a protein kinase and a binding partner, e.g., substrate homolog, where the method comprises the following steps: (a) administering a compound of the invention as described herein; and (b) promoting or disrupting the abnormal interaction.
  • the organism is preferably a mammal and the abnormal condition is preferably cancer or other proliferative condition.
  • Compounds synthesized will be purified for testing in biochemical assays.
  • the assays may measure the binding capability to the designated target, compound to target binding "on-off ' kinetic rates, substrate site occupancy or competitive interaction, biologically relevant concentrations at the reactive site, "optimal biological concentrations to elicit the desired pharmacological effect", the ability to modulate the natural enzymatic reaction catalyzed by the kinase, and other such parameters.
  • Assays will be preferably evaluated in conditions similar to those found physiologically, e.g., temperature, concentration of targets, ion and salt concentrations, pH, and the like. The extent of kinase effect is determined and compared to the selectivity profile desired to confirm whether the structures have a profile of selective effects as described.
  • the correlation of structural features of the compounds is compared to the measured effect on the enzymes to determine whether the structural features of compounds match the predicted pattern of kinase effects.
  • the modulation of the panel of kinases is compared to the predicted to establish the accuracy of the algorithms used to validate particular pharmacophore models.
  • the models are further used to design additional variant structures which retain the desired pattern of modulation of kinase activity while minimizing the negative pharmacological problems.
  • the cycles of activity testing and correlation to structural features of structurally similar compounds are repeated to refine the predictive methods to prioritize the likelihood of compounds in exhibiting balance of properties of enzyme interaction and pharmacology.
  • the compounds may also be used in animal model systems to evaluate relevance of animal test systems and their relationship to corresponding human conditions.
  • QSAR and QSPR models generated are applied to scaffolds to create multiple compounds with desired binding pattern characteristics for kinase profiles.
  • Compounds are synthesized and purified using appropriate technologies. Binding pattern characteristics of compounds from these steps are confirmed using a panel of kinases and their variants (including common or relevant mutants and splice variants). In the context, e.g., of oncology, mutants and splice variants can play a role in resistance selection and ultimate drug efficacy and toxicity in a clinical setting.
  • synthesized compounds are screened against a panel of kinases, or variants thereof, found among kinases listed in selected kinase profiles. These include, for example, ABLl, ABLl E255K, ABLl G250E, ABLl T315I, ABLl Y253F, ABL2 (Arg), AKTl (PKB alpha), AKT2 (PKB beta), AKT3 (PKB gamma), AURKA (Aurora A), AURKB (Aurora B), AURKC (Aurora C), BRAF, BRAF V599E, CSNK2A1 (CK2 alpha 1), CSNK2A2 (CK2 alpha 2), EGFR (ErbBl), ERBB2 (HER2), FGFRl, FGFR2, FGFR3, FGFR3 K650E, FGFR4, FLTl (VEGFRl), FLT3, FLT3 D835Y, FLT4 (VEGFR3),
  • Pattern of inhibition of compounds is matched to a desired profile, which may be inhibition or lack of inhibition of a designated kinase recited in a profile.
  • a desired profile which may be inhibition or lack of inhibition of a designated kinase recited in a profile.
  • synthesized compounds are specific structures exhibiting desired modulation patterns, e.g., of inhibition and lack of inhibition. Data collected, both lack of inhibition and inhibition indicates that the design process described herein provides a tool that allows design of novel compounds and prediction of their activity or lack of activity across panel of kinases or kinase profile.
  • analogs of compounds can be synthesized, e.g. as described, and evaluated for structure activity relationship leading to desired patterns of inhibition. Patterns of inhibition will be useful in a therapeutic context, using a described compound with another compatible entity providing a desired pattern of kinase modulation.
  • Goal Identification of lead structures modulating a profile of multiple kinase targets.
  • Ring system A was selected from the group of 79 in table 7a;
  • Ring system B was selected from the group of 32 in table 7b;
  • L is a linker selected from the group of 24 shown in table 7c;
  • Xi is a functional group selected from the group of 13 shown in table 7d; Ri is functional group or ring system.
  • a total of 57,600 possible scaffolds were generated in silico from combinatorial assortment of 24 linkers, 79 ring system A fragments, and 32 ring system B fragments and some examples are shown in table 7e.
  • one embodiment provides a compound of Formula (I) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
  • X is O or NH;
  • Z is CH or N;
  • A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R 1 substituents;
  • B is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R 7 substituents;
  • R 2 and R 8 are independently selected from hydrogen, halogen, hydroxy, OR 9 , CN, amino, NHR 9 or C 1-6 alkyl;
  • R 1 and R 7 are independently selected from hydrogen, halogen, OR 9 , C 1-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF 3 , nitro, CF 3 , CN, aryl, heteroaryl, COOR 9 , CON(R 9 ) 2 , NHR 9 , N(R 9 ) 2 , COR 9 , C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, CO ⁇ alkylheterocyclyl, CN, amino, NHCOR 9 , hydroxy, Cl-6alkoxy, OC(O)R 9 , -OC0-4alkylaryl,
  • OC0-4alkylheteroaryl -OC0-4alkylC3-10cycloalkyl, NHCOOR 9 , OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR 9 , NR 9 COOR 9 , OCONR 9 , or NR 9 COR 9 ;
  • R 3 and R 4 are independently selected from hydrogen, halogen, CF 3 , CN, hydroxy, NO 2 , amino, NHAryl, NHR 9 ,
  • R 3 and R 4 may together form a 5-membered or 6- membered aryl or heteroaryl ring;
  • R 5 and R 6 are independently selected from hydrogen, Cl-6 alkyl and optionally may be joined to form a 3-10 membered cycloalkyl;
  • R 9 is selected from hydrogen, C 1-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.
  • Another embodiment provides a compound of Formula (II) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
  • A is an optionally substituted heteroaryl ring having between 6 and 12 members and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1 -3 R 1 substituents; R 7 is selected from hydrogen or C 1 -6 al kyl ;
  • R 5 is selected from hydrogen, halogen, hydroxy, OR 8 , CN, amino, NHR 8 or C 1-6 alkyl;
  • R 1 and R 4 are independently selected from hydrogen, halogen, OR 8 , C 1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, OCF 3 , nitro, CF 3 , CN, aryl, heteroaryl, COOR 8 , CON(R 8 ) 2 , NHR 8 , N(R 8 ) 2 , COR 8 , C0-4alkylC3-10cycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, CCMalkylheterocyclyl, CN, amino, NHCOR 8 , hydroxy, Cl - ⁇ alkoxy, OC(O)R 8 , -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OCO ⁇ alkylCS-lOcycloalkyl, NHCOOR 8 , OC0-4alkylC3-10he
  • R 8 is selected from hydrogen, C 1-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl.
  • Illustrative structures according to Formula II include:
  • Yet another embodiment provides a compound of Formula (III) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
  • X is O or NH; Z is CH or N;
  • A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R 1 substituents;
  • B is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R 7 substituents;
  • R 2 and R 8 are independently selected from hydrogen, halogen, hydroxy, OR 9 , CN, amino, NHR 9 or Cl-6 alkyl;
  • R 1 and R 7 are independently selected from hydrogen, halogen, OR 9 , Cl-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF 3 , nitro, CF 3 , CN, aryl, heteroaryl, COOR 9 , CON(R 9 ) 2 , NHR 9 , N(R 9 ) 2 , COR 9 , C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR 9 , hydroxy, Cl-6alkoxy, OC(O)R 9 , -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR 9 , OC0-4alkylC3-10
  • R 5 and R 6 are independently selected from hydrogen or Cl-6 alkyl
  • R 9 is selected from hydrogen, Cl-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.
  • Yet another embodiment provides a compound of Formula (IV) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
  • Y is O, NH, -OCH 2 - or -CH 2 O- Z is CH or N;
  • A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R' substituents;
  • R 1 and R 4 are independently selected from hydrogen, halogen, OR 9 , Cl-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl,
  • OCF 3 nitro, CF 3 , CN, aryl, heteroaryl, COOR 9 , CON(R 9 ) 2> NHR 9 , N(R 9 ) 2 , COR 9 , C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl,
  • C0-4alkylheterocyclyl CN, amino, NHCOR 9 , hydroxy, Cl-6alkoxy, OC(O)R 9 , -OC0-4alkylaryl, OCO ⁇ alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR 9 , OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR 9 , OCONR 9 , or NR 9 COR 9 ;
  • R 2 and R 3 are independently selected from hydrogen, halogen, CF 3 , CN, hydroxy, NO 2 , amino, NHAryl, NHR 9 , COOH, OR 9 , COOR 9 , CONHR 9 , or CON(R 9 ) 2 ; R 2 and R 3 may together form a 5-membered or 6- membered aryl or heteroaryl ring;
  • R 5 is selected from hydrogen, halogen, hydroxy, OR 9 , CN, amino, NHR 9 or Cl-6 alkyl;
  • R 6 and R 7 are independently selected from hydrogen, Cl-6 alkyl and optionally may be joined to form a 3-10 membered cycloalkyl;
  • R 8 is selected from hydrogen or Cl-6 alkyl
  • R 9 is selected from hydrogen, Cl-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.
  • Structures of Formula IV include:
  • Cell lines and other cellular systems appropriate for testing the effect of modulators in a cell context include, e.g., 32D cell line; 3T3 cell line; 3T3 Ll cell line; 4Tl cell line; A2780 cell line; A375 cell line; A43 cell line; A431 cell line; A459 cell line; A549 cell line; Aortic smooth muscle cells; ARH-77 cell line; B cells; B 16 cell line; Ba/F3 cell line; Ba/F3-TEL-FGFR3 cell line; BALB/c3T3 cell line; BALB/MK cell line; BT-20 cell line; BT-474 tumor cell line; BT-549 cell line; BxPC3 cell line; C26 cell line; C6 cell line; CaCo-2 cell line; CaIu- 3 cell line; CCRF-CEM cell line; CHO cell line; CHO-HIRc cells; COLO 201 cell line; COLO 205 cell line; Diploid fibroblast cells; DLD-I cell line; D
  • the effect of a compound on the plurality of kinases desired in the pattern is evaluated in a cell.
  • the effects may be using kinase-specific reagents compatible with a selected cell line, or by evaluating multiple kinases in that cell line.
  • Antibody reagents may be useful to allow simultaneous measurement of the impact of the compound on the different kinases together.
  • prostate cancer mouse models at /prostate_models/rnouse_rninireview ; gastrointestinal cancer animal models at /gastro_models ; hematopoietic cancer models at /hema_models ; lung cancer models at /lung_models ; mammary gland cancer models at /mammary_models ; ovarian cancer models at /ovarian_models/animal_models ; skin cancer models at
  • bladder cancer models bladder cancer models; cervical cancer models; endometrial cancer models; gastrointestinal cancer models; genitourinary cancer models; head and neck cancer models; hematopoietic cancer models; kidney cancer models; lung cancer models; mammary gland cancer models; melanoma models; myeloma models; nervous system cancer models; oral cancer models; ovarian cancer models; pancreatic cancer models; prostate cancer models; sarcoma cancer models; and skin cancer models.
  • Other disease models, or counterparts in other species may be found by search in the PubMed and patent literature databases.
  • DC Structures Exhibiting Desired Pattern of Kinase Modulation
  • the tables below disclose a selected profile desired for therapeutic compound(s) useful for treating various cancers, as well as other medical conditions. These conditions typically share mechanisms or effects with cancer, development, aging, and other similar cell processes. These compounds are lead compounds around which synthesis and further activity testing will generate a structure activity relationship dataset. This SAR can be used to generate various predictive pharmacophore models based on structural and other features for predicting similar variant structure compounds which may possess advantageous pharmacological features while retaining the desired pattern of kinase effect. Of particular importance in the selection of useful variants will be those optimized for adsorption, distribution, metabolism, excretion, toxicity, and manufacturability.
  • Tables 3a, 4a, 5a and 6a disclose selected profiles desired for therapeutic compounds useful for treating various cancers, as well as other medical conditions. These conditions typically share mechanisms or effects with cancer, development, aging, and other similar cell processes. These compounds are lead compounds around which synthesis and further activity testing will generate a structure activity relationship dataset. This SAR can be used to generate various predictive pharmacophore models based on structural and other features for predicting similar variant structure compounds which may possess advantageous pharmacological features while retaining the desired pattern of kinase effect. Of particular importance in the selection of useful variants will be those optimized for adsorption, distribution, metabolism, excretion, toxicity, and manufacturability.
  • Profile One Table 3a Profile one description: compounds selected to have the combination of high binding affinity and ability to inhibit the kinases KDR and PDGFR-B while having minimal binding affinity and ability to modulate the kinase KIT.
  • the targets are preferably human, but the combination is relevant for other species, typically mammals.
  • Six lead structures are provided.
  • the predicted ICso's derived from the KDR and PDGFR-B pharmacophore models are given in Table 3b.
  • Indications for use of compounds which exhibit a profile one modulation pattern include hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, and similar neoplastic conditions.
  • Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, anorexia, macular degeneration, diabetic retinopathy, retinal vein occlusion, and retinopathy of prematurity, scleroderma, cardiofaciocutaneous syndrome, chronic myeloid leukemia, androgen independent prostate cancer cells, head and neck squamous cell carcinoma, cervical cancer, and similar neoplastic conditions.
  • Profile Two Table 4a Profile 2 description: compounds selected to have the combination of high binding affinity and ability to inhibit the kinases BRAF (wild type and V600E variant), KDR and PDGFR-B while having minimal binding affinity and ability to modulate the kinase KIT.
  • the targets are preferably human, but the combination is relevant for other species, typically mammals.
  • Nine lead structures are provided.
  • the predicted IC 50 1 S derived from the BRAF, KDR, PDGFR-B and KIT pharmacophore models are given in Table 4b.
  • Indications for use of compounds exhibiting a profile two modulation pattern include hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, melanoma, thyroid carcinoma, neuroendocrine gastroenteropancreatic tumors, lymphoblastic leukemia and similar neoplastic conditions.
  • Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, macular degeneration, diabetic retinopathy, retinal vein occlusion, retinopathy of prematurity, scleroderma, cardiofaciocutaneous syndrome.
  • Table 4a Profile Two Inhibitors of BRAF, KDR, PDGFR-B but not KIT
  • Profile Three Table 5a Profile three description: compounds selected to have the combination of high binding affinity and ability to inhibit the kinases AURORA, KDR, and PDGFR-B, while having minimal binding affinity and ability to modulate the kinase KIT.
  • the targets are preferably human, but the combination is relevant for other species, typically mammals.
  • Six lead structures are provided.
  • the predicted IC 50 's derived from the AURORA, KDR, PDGFR-B and KIT pharmacophore models are given in Table 5b.
  • Indications for use of compounds exhibiting a profile three modulation pattern include hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, esophageal squamous cell carcinoma, breast carcinoma, glioma, laryngeal carcinoma, ovarian cancer, prostate cancer, and similar neoplastic conditions.
  • Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, macular degeneration, diabetic retinopathy, retinal vein occlusion, retinopathy of prematurity, scleroderma, and cardiofaciocutaneous syndrome.
  • Profile Four Table 6a Profile four description: compounds selected to have the combination of high binding affinity and ability to inhibit the kinases PI3K and mTOR (FRAPl), while having minimal binding affinity and ability to modulate the kinase KIT.
  • the targets are preferably human, but the combination is relevant for other species, typically mammals.
  • Six lead structures are provided.
  • the predicted IC 50 's derived from the PI3K, mTOR (FRAPl) and KIT pharmacophore models are given in Table 6b.
  • Indications for use of compounds exhibiting a profile four modulation pattern include chronic myeloid leukemia, androgen independent prostate cancer cells, head and neck squamous cell carcinoma, cervical cancer, and similar neoplastic conditions. Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, and anorexia. Table 6a. Profile Four Inhibitors of PI3K and mTOR (FRAPl) but not KIT
  • Reagents a) 4-chbroqulnazollne, CS2CO3, DMF. 150C b) NaBH4, MeOH, OC c) SOCI2 d) Na2SO3, " IHRwaler, reflux e) CI2. H2O 0 ArNH2, Pr2NEt DCM
  • Phenol 1 may be contacted with an equivalent of 4-chloroquinazoline in the presence of a base such as potassium carbonate, sodium carbonate or cesium carbonate, in a solvent such as N.N-dimethylformamide or dimethylsulfoxide at temperatures ranging from 100 0 C to 160 0 C and may lead to aryloxy 2.
  • a base such as potassium carbonate, sodium carbonate or cesium carbonate
  • a solvent such as N.N-dimethylformamide or dimethylsulfoxide
  • Transformation into 4 may take place using neat thionyl chloride at temperatures ranging from 0 0 C to 60 0 C.
  • the resulting optionally substituted 4 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification.
  • Formation of the sulfonic acid 5 may take place in a protic solvent such as water, or a combination of water- tetrahydrofuran, at temperatures ranging from 20 0 C to 90 0 C, with a stoichiometric amount or excess of sodium sulfate.
  • Sulfonyl chloride 6 may be obtained by treatment of 5 with a chlorinating agent such as phosphorus pentachloride or phosphorus oxide trichloride, at temperatures ranging from 0 0 C to 60 0 C, for 1 to 12 hours.
  • sulfonyl chloride 6 Treatment of sulfonyl chloride 6 with an appropriately substituted aniline will provide sulfonamide 7 in the presence of a tertiary base such as triethylamine or Hunig's base, in a solvent system such as dichloromethane or the like, at temperatures ranging from 15 0 C to 40 0 C. Upon completion of the reaction, 7 is recovered by conventional methods including neutralization, extraction, chromatography and the like.
  • boronic acid 8 may be used in a Suzuki coupling with commercially available 4- bromoaniline to afford biaryl 9, in the presence of a base such as potassium carbonate or cesium carbonate, in a solvent such as dioxane, dimethoxyethane or tetrahydrofuran, at temperatures ranging from 25 0 C to 90 0 C, for 1 to 12 hours, with a source of palladium (0) such as for example Pd 2 (dba) 3 .
  • iodo pyridine 10 may be coupled to commercially available 4-aminophenyl boronic acid via a Suzuki coupling using conditions described above to provide biaryl 9.
  • the resulting optionally substituted 9 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification.
  • Sulfonamide 11 can be prepared as described in Scheme 1-2 and can be transformed into 12 through the use of a stoichiometric equivalent of a reducing agent such as tin chloride (II) in a protic solvent such as ethanol or the like. Alternatively, this reduction could take place with zinc powder in a solvent such as acetic acid.
  • the resulting optionally substituted 12 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without isolation.
  • Ring formation from 12 into 13 can take place with the use of a stoichiometric equivalent or slight excess of trimethyl orthoformate or the like, in a solvent system such as N,N-dimethylformamide or dimethylsulfoxide, for 1 to 12 hours, at temperatures ranging from 25 0 C to 100 0 C.
  • a solvent system such as N,N-dimethylformamide or dimethylsulfoxide
  • Reagents a) s-BuLi/HCON(M ⁇ )2 b) NBS, CCW c) NaN3, DMF d)TrtNCS, PPti3, dioxane 100C e) HO, dioxane
  • An aryl bromide or heteroaryl bromide 1 can be converted to a corresponding methyl ketone 2 by treatment with 1 to 2 equivalents of sec-butyl lithium (sec-BuLi) or n-BuLi at temperatures ranging from -80 0 C to -50 0 C, for about 1 to 5 hours, in a solvent such as dry ethyl ether, followed by addition of 1 to 2 equivalents of N,N-dimethylacetamide, and gradual increase of the temperature to 0 0 C.
  • sec-butyl lithium sec-butyl lithium
  • n-BuLi sec-butyl lithium
  • Methyl ketone 2 may be converted to an alpha bromo ketone 3 upon treatment with 1 to 1.5 equivalents of N- bromosuccinimide (NBS), in a solvent such as carbon tetrachloride (CCl 4 ), for 5 to 12 hours at temperatures ranging from 20 0 C to 55 0 C.
  • NBS N- bromosuccinimide
  • CCl 4 carbon tetrachloride
  • the acyl azide 4 can be prepared under conventional methods by contacting 3 with a stoichiometric equivalent or a slight excess of sodium azide in an anhydrous solvent such as N,N- dimethylformamide (DMF) or the like, at temperatures ranging from 25 0 C to 90 0 C, for 2 to 7 hours.
  • the resulting optionally substituted 4 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification or isolation.
  • Construction of the amino oxazole ring 5 takes place by mixing 4 with a stoichiometric amount of commercially available tritylisothiocyanate, in the presence of reducing agent triphenylphosphine, in a solvent such as dioxane or tetrahydrofuran (THF), at temperatures ranging from 20 0 C to 100 0 C for 1 to 12 hours. Removal of the protecting group under standard conditions such as treatment with a saturated solution of HCl (g) in dioxane at room temperature leads to the desired substituted amino oxazole 6.
  • SCHEME 2-2 SCHEME 2-2
  • Reagents 1) KOH, AgNO 3 , H 2 O b) Br 2 , CCI 4 c) ArB(OH) 2 , Pd(O), aq. K 2 CO 3 , PhH Or ArSnBu 3 , Pd(O), LiCI, DMF d)TFA, CH 2 CI 2
  • carboxylic acid 7 may be converted to the corresponding silver salt by treatment with a stoichiometric amount of potassium hydroxide (KOH) or the like, and silver nitrate (AgNO 3 ) preferably in a solvent such as water.
  • KOH potassium hydroxide
  • AgNO 3 silver nitrate
  • Bromooxazole 8 is obtained by directly heating the above silver salt in the presence of a stoichiometric amount of bromine (Br 2 ), at temperatures ranging from 30 °C to 75 0 C, in solvents such as carbon tetrachloride (CCl 4 ) for 2 to 8 hours.
  • Br 2 bromine
  • CCl 4 carbon tetrachloride
  • a palladium (O) catalyst such as tetrakistriphenylphosphine palladium (O) or the like
  • a deoxygenated solvent such as benzene, dimethoxyethane (DME), dioxane and the like
  • a palladium (O) catalyst such as tetrakistriphenylphosphine palladium (0) or the like in a deoxygenated solvent such as dimethoxyethane, N,N-dirnethylformamide
  • Reagents a) 1 - HSR 1 , HATU, ET3N, CH3CN 2- AB(OH)2. CuTc b) TFA, DCM
  • Boc-glycine 10 may be transformed into the corresponding aryl or heteroaryl ketone 11 via a Liebeskind-Srogl coupling using conditions described in J. Am. Chem. Soc. 2000, 122, 11260- 11261.
  • Deprotection under acidic conditions such as trifluoroacetic acid (TFA) in dichloromethane (DCM) at temperatures ranging from 0 0 C to 40 0 C, for 1 to 12 hours, leads to amino ketone 12 in quantitative yield.
  • Ketone 12 can then be treated with commercially available tritylisothiocyanate as shown in Scheme 2-1 using steps d and e to give 6.
  • Reagents a) 4-chloro quinazoline, KOtBu, K2CO3, DMF, 8OC or quinazo.n-4-ylboronlc acid, Cu(OAC)2, DME, K2CO3.
  • 4-nitro phenol 13 can be contacted with commercially available 4- chloroquinazoline in the presence of a base such as potassium tert-butoxide or the like (KOtBu) and a freshly ground base such as potassium carbonate (K 2 CO 3 ) or cesium carbonate (Cs 2 CO 3 ), in a solvent such as N,N- dimethylformamide (DMF) or tetrahydrofuran (THF), at temperatures ranging from 30 0 C to 80 0 C, for a period of 1 to 9 hours and obtain aryloxy 14.
  • a base such as potassium tert-butoxide or the like (KOtBu) and a freshly ground base such as potassium carbonate (K 2 CO 3 ) or cesium carbonate (Cs 2 CO 3 )
  • a solvent such as N,N- dimethylformamide (DMF) or tetrahydrofuran (THF)
  • Reagents a) 4-hydroxy quinazoline,Cu(OAC)2, DME, K2CO3, RT
  • Reagents a) phosgene, EON. CH2CI2 b) 6. Et3N, CH3CN c) p-NO2 phenyl chloroformate, Et3N, CH2CI2 d) 6, DIEA, CH2CI2
  • Aniline 14 may be reacted with a stoichiometric amount to a slight excess of phosgene in the presence of a tertiary base such as triethylamine (Et 3 N) or Hunig's base (DIEA), in a solvent such as dichloromethane or the like, at temperatures ranging from 0 0 C to 25 0 C, to lead isocyanate 15.
  • a tertiary base such as triethylamine (Et 3 N) or Hunig's base (DIEA)
  • Et 3 N triethylamine
  • DIEA Hunig's base
  • the resulting optionally substituted 15 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification.
  • Condensation of 14 with 6 takes place in a solvent such as dichloromethane, N,N-dimethylformamide, or acetonitrile, in the presence of a stoichiometric amount of tertiary base such as triethylamine or Hunig's base, at room temperature for 1 to 12 hours, and leads to urea 16.
  • a solvent such as dichloromethane, N,N-dimethylformamide, or acetonitrile
  • aniline 14 can be activated to its corresponding 4-nitrophenyl carbamate 17 by contact with a stoichiometric amount to slight excess of 4-nitrophenyl chloroformate or other phenyl chloroformate, in the presence of a base such as triethylamine or Hunig's base, in a solvent such as dichloromethane, at temperatures ranging from 0 0 C to 55 0 C, for 1 to 12 hours.
  • the resulting optionally substituted 17 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification.
  • Nitro pyridone 18 can be reduced to the corresponding aniline 19 using a reducing agent such as tin chloride in a solvent such as ethanol or the like, for 1 to 12 hours.
  • a reducing agent such as tin chloride in a solvent such as ethanol or the like
  • other reducing agents such as zinc powder or iron could be used instead of tin chloride.
  • Cyclization of 19 into oxazole 20 can be obtained with one stoichiometric equivalent of trimethylorthoformate in a solvent system such as N,N-dimethylformamide of the like, at temperatures ranging from 20 0 C to 90 0 C, for 1 to 12 hours.
  • the resulting optionally substituted 17 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification.
  • Reagents a) 2-bramoethanol, chlorosulfonyl isocyanate, Et 3 N, DCM b)4-(quinazolin-4-yloxy)aniline, Et 3 N, CH 3 CN.
  • the burgundy colored solution was flushed with nitrogen and then sealed with the cap.
  • the reaction mixture was heated to 100 0 C for 18 hours with very vigorous stirring.
  • the reaction mixture was cooled to room temperature and filtered through a short pad of silica gel washing with ethyl acetate.
  • the mixture was dried over sodium sulfate, filtered and the solvent concentrated in vacuo affording a yellow semisolid material. This was then pre- absorbed onto silica gel and applied to a 70 g Biotage column packed with silica gel which had been preconditioned with 3:7 ethyl acetatexhloroform. The column was eluted with the same solvent system.
  • Step A Synthesis of N-[4-(6-Chloro-3-pyridinyl)phenyI]-2-oxo-l,3-oxazolidine-3-sulfonamide (22). Chlorosulfonyl isocyanate (0.17 mL, 1.9 mmole) was dissolved in dry dichloromethane (6 mL) in a dry flask under a nitrogen stream.
  • Step B Synthesis of N-[4-(6-Chloro-3-pyridinyl)phenyl]-N'-[4-(4-quinazolinyIoxy)phenyl]sulfamide (23).
  • Compound 22 (90.2 mg, 0.255 mmole) and 4-(4-quinazolinyloxy)aniline hydrochloride (63 mg, 0.23 mmole) were taken up into 4 mL of acetonitrile. Triethylamine (0.081 mL, 0.58 mmole) was added and the reaction mixture was heated to 8O 0 C for 3 hours.
  • Reagents a) cyanoaceticacid, EDC, DMAP, DCM b) hydroxylamine hydrochloride, Et 3 N c) Iron, hydrochloric acid d) 2-bromo-1-(pyridin-3-yl)ethanone, NaHCO 3 , H 2 O, THF.
  • the hot reaction mixture was filtered through Celite ® 545, washed with ethanol (20 mL), and the solvent concentrated in vacuo. The residue was taken up in water (50 mL) and then acidified to pH 4 with 10% hydrochloric acid. The aqueous layer was extracted with ether (50 mL), ethyl acetate (50 inL), toluene (50 mL) and then was brought to pH 9 using sodium bicarbonate. The aqueous layer was extracted with methylene chloride (5 x 40 mL) and the combined organic layers were stripped to a dark solid.
  • 3-Bromoacetylpyridine hydrobromide (32.9 mg, 0.12 mmole) was taken up in a 2:1 mixture of tetrahydrofiiran: water (1.5 mL) and was added in portions over a 35 minute period to the bicarbonate mixture. After 5 hours, the reaction mixture was removed from the oil bath and cooled to room temperature. The reaction mixture was diluted with ethyl acetate (30 mL) and washed with water (3 x 10 mL) and 0. IN hydrochloric acid (30 mL). The organic layer was dried over sodium sulfate, filtered and the solvent concentrated in vacuo affording a dark brown solid (50 mg).
  • the methods of the invention are advantageous in conditions involving immunosuppression, autoimmune conditions, inflammatory conditions, cerebral vasospasm, diabetic retinopathy, rheumatoid arthritis, or neurodegeneration.
  • Drugs that modulate kinase activities will be combined with companion efficacy and safety biomarkers for efficient and accelerated clinical development in targeted patient populations.
  • Biomarkers are objective, measurable biochemical parameters that faithfully reflect the status of a critical pathway to a disease or a critical pathway that predisposes to a disease.
  • Biomarkers in ultimate or proximal critical pathways can be direct measures of the progression or reversal of a fundamental underlying disease process.
  • a clinical development strategy will be focused on developing kinase modulator drugs, e.g., in the oncology arena, and establishing proprietary biomarkers that identify patients most likely to respond to treatment and those at risk for adverse drug reactions.
  • biomarker strategy By incorporating a biomarker strategy at the beginning, the drug candidates will be favorably positioned. This strategy increases the likelihood of drug development success and reduces the drug failure rate common within the industry.
  • Biomarkers have enormous potential to predict who will develop cancer and/or to detect the disease at an early stage. The anticipated benefit in this setting is based on the assumption that interventions exist that either prevent cancer in high-risk individuals or more effectively eradicate cancer when individuals are diagnosed at a time of low tumor burden.
  • Biomarkers can guide treatment decisions.
  • Biomarkers provide an opportunity to identify subpopulations of patients who are most likely to respond to a given therapy. This application will allow more informed decisions about modifying and adapting treatment protocols to subpopulations and also help guide patient enrollment into clinical trials.
  • Cancer biomarkers exist in many different forms, including physiologic (patient performance status), images (mammograms), specific molecules (prostate-specific antigen, PSA), genetic alterations (BRCA mutations), gene or protein expression profiles (serum protein electrophoresis for detection of monoclonal gammopathies), and cell-based markers (circulating tumor cells), among others.
  • physiologic patient performance status
  • images mammograms
  • specific molecules prostate-specific antigen, PSA
  • BRCA mutations genetic alterations
  • gene or protein expression profiles gene or protein electrophoresis for detection of monoclonal gammopathies
  • cell-based markers circulating tumor cells
  • biomarker hypothesis states that changes in levels of blood or tissue proteins, individually or multiplexed, are highly and specifically characteristic of disease states and therapeutic outcomes.
  • the basis of this hypothesis is that biological systems are adaptive and that challenges to homeostasis affect characteristic levels of proteins.
  • Biomarker development occurs in a multi-step process of discovery, followed by replication in independent cohorts, validation of diagnostic sensitivity and specificity, and, finally, translation into a clinical diagnostic test or surrogate endpoint in a clinical study.
  • Candidate biomarkers are triaged at each stage of development.
  • a biomarker can be a single protein, such as prostate-specific antigen, a panel of proteins or genes or a combination of one or more proteins, genes, and other clinical measures, together with an algorithm that integrates these into an individual profile.
  • these compounds will comprise significant therapeutic application.
  • these compounds should modulate appropriate kinase signaling and the biological effects associated therewith. More specifically, these compounds should selectively modulate cell proliferation and/or differentiation and/or promote apoptosis especially of cancer and other neoplastic cells. Pathways affected by the inhibition of the various kinases should be as indicated.
  • Description of formulation and compounding include, e.g., Johnston (2005) Compounding: The Pharmacy Technician Series Prentice Hall, ISBN: 0131147609; Rowe, et al. (eds.
  • the compounds produced according to the invention will be used to treat conditions wherein the pattern of inhibition of the various kinase signaling pathways is therapeutically beneficial.
  • This will include conditions that involve abnormal cell growth and/or differentiation such as cancers and other neoplastic conditions.
  • the subject compounds may be used to treat other conditions involving abnormal cell proliferation and/or differentiation such as neoplastic conditions and disorders.
  • the selected indication is often cancer, especially cancers involving abnormal levels of expression of the relevant kinase(s) or close relatives, cancers that express variant or mutant relatives, or cancers which comprise genetic translocation or deletion of the kinase(s).
  • the subject therapies will comprise administration of at least one compound according to the invention in an amount sufficient to elicit a therapeutic response, e.g., inhibition of one or more of tumor cell proliferation, differentiation, metastasis, mutagenesis, or promotion of apoptosis.
  • the compound may be administered alone, or may be targeted by various means, including liposomes, targeted liposomes, antibody targeting mechanisms, localized activation methods, targeting conjugates, conjugates with site activatable active components, and the like.
  • One embodiment provides a method of treating an indication selected from hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, and similar neoplastic conditions.
  • Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, anorexia, macular degeneration, diabetic retinopathy, retinal vein occlusion, and retinopathy of prematurity, scleroderma, cardiofaciocutaneous syndrome, chronic myeloid leukemia, androgen independent prostate cancer cells, head and neck squamous cell carcinoma, cervical cancer, and similar neoplastic conditions; the method comprising administering to a subject a compound of Formula I or a compound of Formula in.
  • Another embodiment provides a method of treating an indication selected from hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, melanoma, thyroid carcinoma, neuroendocrine gastroenteropancreatic tumors, lymphoblastic leukemia and similar neoplastic conditions.
  • Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, macular degeneration, diabetic retinopathy, retinal vein occlusion, retinopathy of prematurity, scleroderma, cardiofaciocutaneous syndrome; the method comprising administering to a subject a compound of Formula II or a compound of Formula FV.
  • the invention described herein includes a pharmaceutical composition which is comprised of a compound of the indicated formulae, including a pharmaceutically acceptable salt or hydrate thereof in combination with a carrier.
  • the terms “pharmaceutically acceptable salts” and “hydrates” refer to those salts and hydrated forms of the compound which would be apparent to the pharmaceutical chemist, i.e., those which favorably affect the physical or pharmacokinetic properties of the compound, such as solubility, palatability, absorption, distribution, metabolism and excretion.
  • pharmaceutical chemist i.e., those which favorably affect the physical or pharmacokinetic properties of the compound, such as solubility, palatability, absorption, distribution, metabolism and excretion.
  • Other factors, more practical in nature, which are also of interest in the selection are the cost of the raw materials, ease of crystallization, yield, stability, solubility, hygroscopicity, and flowability of the resulting bulk drug.
  • a compound When a compound is present as a salt or hydrate which is non-pharmaceutically acceptable, this can be converted to a salt or hydrate form which is pharmaceutically acceptable in accordance with the present invention.
  • a counterion e.g., an alkali metal cation such as sodium or potassium.
  • suitable counterions include calcium, magnesium, zinc, ammonium, or alkylammonium cations such as tetramethylammonium, tetrabutylammonium, choline, triethylhydroammonium, meglumine, triethanolhydroammonium, etc.
  • An appropriate number of counterions is associated with the molecule to maintain overall charge neutrality.
  • the compound is positively charged, e.g., protonated, an appropriate number of negatively charged counterions is present to maintain overall charge neutrality.
  • Pharmaceutically acceptable salts also include acid addition salts.
  • the compound can be used in the form of salts derived from inorganic or organic acids or bases. Examples include acetate, adipate, alginate, aspartate, benzoate, benzenesulfonate, bisulfate, butyrate, citrate, camphorate, camphorsulfonate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, glucoheptanoate, glycerophosphate, hemisulfate, heptanoate, hexanoate, hydrochloride, hydrobromide, hydroiodide, 2- hydroxyethanesulfonate, lactate, maleate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, oxalate, pamoate, pectinate, pers
  • Base salts include ammonium salts, alkali metal salts such as sodium and potassium salts, alkaline earth metal salts such as calcium and magnesium salts, salts with organic bases such as dicyclohexylamine salts, N-methyl-D-glucamine, and salts with amino acids such as arginine, lysine, and so forth.
  • the basic nitrogen-containing groups may be quaternized with such agents as lower alkyl halides, such as methyl, ethyl, propyl, and butyl chloride, bromides and iodides; dialkyl sulfates like dimethyl, diethyl, dibutyl; and diamyl sulfates, long chain halides such as decyl, lauryl, myristyl and stearyl chlorides, bromides and iodides, aralkyl halides like benzyl and phenethyl bromides and others.
  • Other pharmaceutically acceptable salts include the sulfate salt ethanolate and sulfate salts.
  • the compounds of the present invention may have asymmetric centers and occur as racemates, racemic mixtures and as individual diastereomers, or enantiomers with all isomeric forms being included in the present invention.
  • any variable e.g., aryl, heterocyle, Rl, etc.
  • its definition on each occurence is independent of its definition at every other occurrence, unless otherwise stated.
  • a therapeutically effective dose of a kinase modulator is administered to a patient.
  • therapeutically effective dose herein is meant a dose that produces effects for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using acceptable techniques (e.g., Ansel et al., Pharmaceutical Dosage Forms and Drug Delivery, Lippincott, Williams & Wilkins Publishers, ISBN:0683305727; Lieberman (1992) Pharmaceutical Dosage Forms (vols.
  • a "patient” for the purposes of the present invention includes both humans and other animals, particularly mammals. Thus the methods are applicable to both human therapy and veterinary applications.
  • the patient is a mammal, preferably a primate, and in one embodiment the patient is human.
  • the administration of the modulators of the present invention can be done in a variety of ways, either systemic or local, including, but not limited to, orally, subcutaneously, intravenously, intranasally, transdermally, intraperitoneally, intramuscularly, intrapulmonary, vaginally, rectally, intraocularly, or directly onto a mucosal surface.
  • the compounds of the invention can be formulated in a pharmaceutical composition by combining the compound with a pharmaceutically acceptable carrier. Examples of such compositions and carriers are set forth below.
  • the subject compounds will be typically be administered in a pharmaceutically acceptable formulation or composition.
  • compositions include injectable solutions, tablets, milk, or suspensions, creams, oil-in-water and water-in-oil emulsions, microcapsules, and microvesicles.
  • the pharmaceutical compositions are in a water soluble form, such as being present as pharmaceutically acceptable salts, which is meant to include both acid and base addition salts.
  • “Pharmaceutically acceptable acid addition salt” refers to those salts that retain the biological effectiveness of the free bases and that are not biologically or otherwise undesirable, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, and organic acids such as acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid and the like.
  • inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like
  • organic acids such as acetic acid, propionic acid, glycolic acid, pyruvic acid,
  • “Pharmaceutically acceptable base addition salts” include those derived from inorganic bases such as sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Salts of interest include the ammonium, potassium, sodium, calcium, and magnesium salts. Salts derived from pharmaceutically acceptable organic non-toxic bases include salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, and ethanolamine.
  • the compounds may be employed in powder or crystalline form, in solution or in suspension. They may be administered orally, parenterally (intravenously or intramuscularly), topically, transdermally or by inhalation.
  • the carrier employed may be, for example, either a solid or liquid.
  • solid carriers include lactose, terra alba, sucrose, talc, gelatin, agar, pectin, acacia, magnesium stearate, stearic acid and the like.
  • liquid carriers include syrup, peanut oil, olive oil, water and the like.
  • the carrier for oral use may include time delay material well known in the art, such as glyceryl monostearate or glyceryl distearate alone or with a wax.
  • the pharmaceutical compositions may also include one or more of the following: carrier proteins such as serum albumin; buffers; fillers such as microcrystalline cellulose, lactose, corn and other starches; binding agents; sweeteners and other flavoring agents; coloring agents; and polyethylene glycol.
  • carrier proteins such as serum albumin
  • buffers such as microcrystalline cellulose, lactose, corn and other starches
  • binding agents such as microcrystalline cellulose, lactose, corn and other starches
  • binding agents such as microcrystalline cellulose, lactose, corn and other starches
  • binding agents such as microcrystalline cellulose, lactose, corn and other starches
  • binding agents such as microcrystalline cellulose, lactose, corn and other starches
  • sweeteners and other flavoring agents such as microcrystalline cellulose, lactose, corn and other starches
  • oral solid dosage forms include tablets, capsules, troches, lozenges and the like. The size of the dosage form will vary widely, but preferably will be from about 25 mg to about 500 mg.
  • oral liquid dosage forms include solutions, suspensions, syrups, emulsions, soft gelatin capsules and the like.
  • injectable dosage forms include sterile injectable liquids, e.g., solutions, emulsions and suspensions. Examples of injectable solids would include powders which are reconstituted, dissolved or suspended in a liquid prior to injection.
  • unit dosage forms suitable for oral administration include, but are not limited to, powder, tablets, pills, capsules and lozenges.
  • kinase modulators e.g., small organic molecules, etc.
  • This is typically accomplished either by complexing the molecule(s) with a composition to render it resistant to acidic and enzymatic hydrolysis, or by packaging the molecule(s) in an appropriately resistant carrier, such as a liposome or a protection barrier.
  • Means of protecting agents from digestion are well known in the art.
  • Topical applications may be formulated in carriers such as hydrophobic or hydrophilic bases to form ointments, creams, lotions, in aqueous, oleaginous or alcoholic liquids to form paints or in dry diluents to form powders.
  • Such topical formulations can be used to treat ocular diseases as well as inflammatory diseases such as rheumatoid arthritis, psoriasis, contact dermatitis, delayed hypersensitivity reactions and the like.
  • the carrier is typically comprised of sterile water, saline or another injectable liquid, e.g., peanut oil for intramuscular injections. Also, various buffering agents, preservatives and the like can be included.
  • a typical pharmaceutical composition for intravenous administration would be about 0.1 to 10 mg per patient per day. Dosages from 0.1 up to about 100 mg per patient per day may be used, particularly when the drug is administered to a secluded site and not into the blood stream, such as into a body cavity or into a lumen of an organ. Substantially higher dosages are possible in direct or topical administration. Actual methods for preparing parenterally administrable compositions will be known or apparent to those skilled in the art, e.g., Remington's Pharmaceutical Science and Goodman and Gillman, The Pharmacological Basis of Therapeutics, supra.
  • compositions will typically comprise conventional pharmaceutical excipients and carriers used in drug formulations, e.g., water, saline solutions, such as phosphate buffered saline, buffers, and surfactants.
  • saline solutions such as phosphate buffered saline, buffers, and surfactants.
  • the subject compounds may be free or entrapped in microcapsules, in colloidal drug delivery systems such as liposomes, microemulsions, and macroemulsions.
  • solid formulations containing the subject compounds such as tablets, and capsule formulations, may be prepared.
  • Suitable examples thereof include semipermeable materials of solid hydrophobic polymers containing the subject compound which may be in the form of shaped articles, e.g., films or microcapsules, as well as various other polymers and copolymers known in the art.
  • the dosage effective amount of compounds according to the invention will vary depending upon factors including the particular compound, toxicity, and inhibitory activity, the condition treated, and whether the compound is administered alone or with other therapies. Typically a dosage effective amount will range from about 0.0001 mg/kg to 1500 mg/kg, more preferably 1 to 1000 mg/kg, more preferably from about 1 to 150 mg/kg of body weight, and most preferably about 50 to 100 mg/kg of body weight.
  • the subjects treated will typically comprise warm blooded species, such as mammals, and most preferably will be primate subjects, e.g., human cancer subjects.
  • the compounds of the invention may be used alone or in combination. Additionally, the treated compounds may be utilized with other types of treatments, e.g., cancer treatments. For example, the subject compounds may be used with other chemo- or other therapies, e.g., tamoxifen, taxol, methotrexate, biologicals, such as antibodies, growth factors, lymphokines, or radiation, RNAi, etc. Combination therapies may result in synergistic results.
  • chemo- or other therapies e.g., tamoxifen, taxol, methotrexate
  • biologicals such as antibodies, growth factors, lymphokines, or radiation, RNAi, etc.
  • Combination therapies may result in synergistic results.
  • dosages can be varied depending upon the overall condition of the patient, the nature of the illness being treated and other factors.
  • An example of a suitable oral dosage range is from about 0.1 to about 80 mg/kg per day, in single or divided doses.
  • An example of a suitable parenteral dosage range is often from about 0.1 to about 80 mg/kg per day, in single or divided dosages, administered by intravenous or intramuscular injection.
  • An example of a topical dosage range is from about 0.1 mg to about 150 mg, applied externally from about one to four times a day.
  • An example of an inhalation dosage range is from about 0.01 mg/kg to about 1 mg/kg per day.
  • compositions containing kinase modulators can be administered for therapeutic or prophylactic treatments. In therapeutic applications, compositions are administered to a patient suffering from a disease (e.g., a cancer) in an amount sufficient to cure or at least partially delay or arrest the disease and its complications.
  • a disease e.g., a cancer
  • a therapeutically effective dose An amount adequate to accomplish this is defined as a "therapeutically effective dose.” Amounts effective for this use will depend upon the severity of the disease and the general state of the patient's health. Single or multiple administrations of the compositions may be administered depending on the dosage and frequency as required and tolerated by the patient. In any event, the composition should provide a sufficient quantity of the agents of this invention to effectively treat the patient.
  • An amount of modulator that is capable of preventing or slowing the development of cancer in a mammal is referred to as a "prophylactically effective dose.” The particular dose required for a prophylactic treatment will depend upon the medical condition and history of the mammal, the particular cancer being prevented, as well as other factors such as age, weight, gender, administration route, efficiency, etc.
  • Such prophylactic treatments may be used, e.g., in a mammal who has previously had cancer to prevent a recurrence of the cancer, or in a mammal who is suspected of having a significant likelihood of developing cancer.
  • the compounds may be administered using targeted adjuncts; delivery systems; antibody linkages, localized activation, and other means to provide localized effect.
  • the present kinase-modulating compounds can be administered alone or in combination with additional modulating compounds or with other therapeutic agent, e.g., other anti-cancer agents or treatments.

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Abstract

Compound structures are provided which should modulate various selected kinases thereby regulating the corresponding kinase signal pathways. These pathways have been shown to regulate biological functions. The compounds, and similar variants, will be useful in therapeutic or diagnostic methods related to said kinases. In particular, improved effects on functional pathways mediated by kinases can be achieved by modulating selected combinations of kinases.

Description

MODULATORS OF MULTIPLE KINASES
RELATED APPLICATIONS
[0001] This application claims priority to the following US Provisional Applications: 60/827,676, filed on September 29, 2006; 60/864,586, filed on November 6, 2006; 60/866,588, filed on November 20, 2006; 60/866,594, filed on November 20, 2006; 60/866,597, filed on November 20, 2006; and 60/866,596, filed November 20, 2006. The contents of all provisional applications are incorporated herein by reference in their entirety.
FIELD OF THE INVENTION
[0002] The invention relates to compounds and compound structures representing modulators of multiple kinases. These compounds exhibit kinase activity modulation patterns over a multiplicity of kinases contributing to various medical conditions.
BACKGROUND OF THE INVENTION
[0003] Phosphorylation and dephosphorylation are processes by which phosphate groups are added or removed from a target molecule, typically a protein. The process of reversible phosphorylation is a key feature of cellular regulation, including signal transduction, gene expression, cell cycle regulation, cytoskeletal regulation and apoptosis. See, e.g., Roberts (2003) "Protein phosphorylation" The Scientist 17:12-13; and Hunter (2000) "Signaling-2000 and beyond" Cell 100:113-127. Principally, two classes of enzymes modulate reversible protein phosphorylation: kinases add phosphate groups and phosphatases remove phosphate groups from substrates. Often the substrates are proteins whose enzymatic activity is modulated thereby. [0004] Signal transduction is one example of a process involving protein phosphorylation that is critical for cellular regulation. After an extracellular stimulatory factor (such as a ligand) binds to its recognized cell surface receptor, signal transduction is initiated, often mediated by a specific set of cellular protein kinases. These kinases subsequently phosphorylate the target molecule, resulting in an altered activity and a continued cellular response to the signal. See, e.g., Nishizuka (1986) "Studies and perspectives of protein kinase C" Science 233:305-312.
[0005] Serine, threonine, and tyrosine amino acid residues are the most common sites of phosphorylation in eukaryotic cells. See, e.g., Guy, et al. (1994) "Analysis of Cellular Phosphoproteins by Two-Dimensional Gel Electrophoresis: Applications for Cell Signaling in Normal and Cancer Cells" Electrophoresis 15:417-440. However, other molecules have been shown to be phosphorylated, including lipids, which may also be involved in signal transduction pathways.
[0006] Kinases act in signaling for a large number of biological functions. For example, in the context of cancer, kinases are largely responsible for signaling whether cells should continue to grow, remain dormant, or proceed to cell death. To stop cells from growing without control, thereby leading to tumor progression, the signaling activities of certain kinases can be inhibited.
[0007] Especially in complex systems, and where cells differentiate and specialize, communication and regulation of processes among different cells and cell types are relevant. In differentiation, kinases are involved in regulating developmental pathways. See Vivekanand and Rebay (2006) "Intersection of Signal Transduction Pathways and Development" Ann. Rev. Genetics. PMID: 16771628.
[0008] While modulators of kinases have been recognized to block certain signaling pathways, often the leakage through a single block point, or alternative signal mechanisms exist or become relevant. For this reason, modulators of single kinases are often ineffective in maintaining the signal blockage. The means to block at multiple defined points in the signal transduction pathway will often be far more effective than blockage at single target sites. Thus, the ability to identify and recognize appropriate multiple kinases which synergistically can block signal transduction will be of interest. Conversely, other pathways should remain active, and the unintentional inhibition of one pathway may induce other problems or counteract the inhibition of another kinase pathway. [0009] In the specific area of oncology therapeutics alone, e.g., there are currently 25 million people afflicted with cancer worldwide, and the World Health Organization (WHO) predicts that cancer rates may increase by 50% from 2000 to 2015. The Association for International Cancer Research (AICR) estimates that by 2020, there will be 10 million deaths from cancer per year. Even in developed nations, approximately 50% of patients diagnosed with cancer will eventually die of this disease. The rate of growth in non-U.S. countries is highlighted by statistics in Asia where the cancer market is increasing rapidly, with current rates of growth outstripping the average growth rate of the previous five years.
SUMMARY OF THE INVENTION
[0010] The present invention provides compounds which are designed to modulate kinase targets in a selected pattern, which pattern of modulation will act synergistically in effecting modulation of signal transduction, either at a set time point, or over a temporal window. It is expected that the compounds can be applied to address various medical areas, including the oncology area, as well as many others caused by an inappropriate pattern of kinase signals. It is expected that treatments will be matched appropriately, e.g., according to tumor type, location, stage of disease, molecular definition, and others. [0011] The present invention provides structures, compounds and methods for modulating a pattern of kinase signaling useful in therapeutic applications. The pattern incorporates effects on multiple kinases, in contrast to drugs designed to modulate a single kinase target. The pattern will affect a plurality of kinases, e.g., a defined pattern of kinase effects. An attractive pattern might be selected to selectively modulate certain kinase pathways while exhibiting minimal effect on others, and may target multiple points in a signal pathway. Another attractive pattern may target modulating kinases in alternative or parallel signaling pathways, and the signal is modulated by affecting alternative signals. In another case, both strategies may be applied, depending upon the clinical context. [0012] The invention further identifies chemical scaffolds and compounds capable of achieving the desired pattern of selective modulation of kinase pathways, e.g., by acting on specified kinases in the specified direction. [0013] The present invention also provides methods for analyzing data and identifying important patterns of kinase inhibition useful in therapeutic applications. In some cases, the various kinases will function in the same pathways and inhibition may be at multiple points in a signal process. In other cases, the various kinases will function in alternative or parallel signaling pathways, and the signal is modulated by affecting alternative signals. And in other cases, both strategies may be applied, depending upon the clinical context. The invention further identifies chemical scaffolds and compounds capable of achieving desired patterns of inhibition of kinase pathways, e.g., by acting on specified kinases.
[0014] In one embodiment, the invention provides a method comprising identifying a therapeutically valuable profile inhibition of a plurality of kinases, the profile capable of being effected by a group of compounds sharing a chemical scaffold. The method provides effects on one or more pathways important in development or maintenance of an oncogenic state of cells. In one embodiment, the compounds number at least 5. In another embodiment, the pathways number at least 2.
[0015] In yet another embodiment, the pathways include cell division signal, metastasis, angiogenesis, and apoptosis. Direct means of modulation may make use of antibodies which interact specifically with defined kinases, or nucleic acid sequence based methods may be used, e.g., antisense or RNAi means to modulate gene expression.
[0016] In another embodiment, various combinations of structural segments are screened computationally for modulation of a plurality of kinases, preferably in patterns as described. Specific attractive modulation patterns have been identified, and means to achieve such are provided. The means include antibody based methods or transcription regulation methods. Both make use of sequences specific for the identified kinases, e.g., or of genetic, developmental, or resistance variants thereof. Other means to achieve desired patterns of kinase modulation are effected by various small molecule scaffold structures, whether combinations or single compounds. Those patterns of modulation of kinases may be effected by combinations with antibody or nucleic acid anti-sense reagents, e.g., based upon sequences of the described kinases. [0017] The invention further provides structures and methods for modulating relevant patterns of kinase signaling useful in therapeutic applications. The patterns incorporate effects on multiple kinases, in contrast to drugs designed to inhibit a single kinase target. The pattern will affect a plurality of kinases, e.g., a defined or desired pattern of kinase effects. An attractive pattern may target modulating kinases in alternative or parallel signaling pathways, and the signal is modulated by affecting alternative signals. In another case, both strategies may be applied, depending upon the clinical context. The invention further identifies chemical scaffolds and compounds capable of achieving the desired pattern of selective modulation of kinase pathways, e.g., by acting on specified kinases in the specified direction. In some cases, the pattern will include inhibition of various kinases with little effect on others.
[0018] In various embodiments, the compound binds to the designated kinases in a pattern as described below, and/or modulates a biological activity modulated by the designated kinases in a pattern as described below. The compounds further provide methods of modulating the biochemical activity of the designated kinases described in Table 1, the method comprising exposing those kinases to a compound as described herein at an effective concentration, e.g., less than about 1 mM, 100 nM, 10 nM, or 1 nM. In certain embodiments, the pattern of selectivity exhibits at least about 0.5 log unit of specificity for said designated kinase effect relative to certain others. In yet another embodiment, the pathways include cell division signal, metastasis, angiogenesis, and apoptosis.
[0019] One embodiment provides a compound of Formula (I) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000005_0001
Formula (I) wherein, X is O or NH; Z is CH or N; A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R1 substituents; B is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R7 substituents;
R2 and R8 are independently selected from hydrogen, halogen, hydroxy, OR9, CN, amino, NHR9 or C 1-6 alkyl; R1 and R7 are independently selected from hydrogen, halogen, OR9, Cl-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR9, CON(R9)2, NHR9, N(R^2, COR9, C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, CCMalkylheterocyclyl, CN, amino, NHCOR9, hydroxy, Cl-6alkoxy, OC(O)R9, -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR9, OC0-4alkylC3-10heterocycloalkyl,
OC0-4alkylNR9, NR9COOR9, OCONR9, or NR9COR9;
R3 and R4 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, NHAryl, NHR9, COOH, OR9, COOR9, CONHR9, or CON(R9)2; R3 and R4 may together form a 5-membered or 6- membered aryl or heteroaryl ring; R5 and R6 are independently selected from hydrogen, Cl-6 alkyl and optionally may be joined to form a 3-10 membered cycloalkyl;
R9 is selected from hydrogen, Cl-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.
[0020] One embodiment provides a compound selected from:
N-(4-(6-chloropyridin-3-yl)phenyl)-l-(4-(oxazolo[5,4-b]pyridin-7-yloxy)phenyl)methanesulfonamide; or N-(4-(6-chloropyridin-3-yl)phenyl)- 1 -(4-(quinazolin-4-yloxy)phenyl)methanesulfonarnide.
Another embodiment provides a compound of Formula (II) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000006_0001
Formula (II) wherein, X is O, S or NH;
Y is O or NH;
Z is CH or N;
A is an optionally substituted heteroaryl ring having between 6 and 12 members and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R1 substituents;
R7 is selected from hydrogen or Cl-6 alkyl;
R5 is selected from hydrogen, halogen, hydroxy, OR8, CN, amino, NHR8 or Cl-6 alkyl; R1 and R4 are independently selected from hydrogen, halogen, OR8, Cl-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR8, CON(R8)2, NHR8, N(R8)2> COR8, C0-4alkylC3-10cycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR8, hydroxy, Cl-6alkoxy, OC(O)R8, -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR8, OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR8, NR8COOR8, OCONR8, or NR8COR8; R2 and R3 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, aminoaryl, NHR8, COOH, OR8, COOR8, CONHR8, CON(R8)2; R2 and R3 may together form a 5-membered or 6- membered heteroaryl ring;
R8 is selected from hydrogen, Cl -6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl. [0021] One embodiment provides a compound selected from: l-(4-(oxazolo[5,4-b]pyridin-7-yloxy)phenyl)-3-(5-(5-(trifluoromethyl)pyridin-2-yl)oxazol-2-yl)urea; l-(4-(oxazolo[5,4-b]pyridin-7-yloxy)phenyl)-3-(5-(4-(trifluoromethyl)phenyl)oxazol-2-yl)urea; l-(4-(quinazolin-4-yloxy)phenyl)-3-(5-(5-(trifluoromethyl)pyridin-2-yl)oxazol-2-yl)urea; N-methyl-4-(4-(3-(5-(5-(trifluoromethyl)pyridin-2-yl)oxazol-2-yl)ureido)phenoxy)picolinamide; N-methyl-4-(4-(3-(5-(4-(trifluoromethyl)phenyl)oxazol-2-yl)ureido)phenoxy)picolinamide; or l-(4-(quinazolin-4-yloxy)phenyl)-3-(5-(4-(trifluoromethyl)phenyl)oxazol-2-yl)urea.
[0022] Yet another embodiment provides a compound of Formula (III) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000007_0001
wherein, X is O or NH; Z is CH or N; A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R1 substituents; B is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R7 substituents; R2 and R8 are independently selected from hydrogen, halogen, hydroxy, OR9, CN, amino, NHR9 or C 1-6 alkyl;
R1 and R7 are independently selected from hydrogen, halogen, OR9, C 1-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR9, CON(R9)2, NHR9, N(R9)2, COR9, C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, CO^alkylheterocyclyl, CN, amino, NHCOR9, hydroxy, C 1 -6alkoxy, OC(O)R9, -OC0-4alkylaryl,
OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR9, OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR9, NR9COOR9, OCONR9, or NR9COR9;
R3 and R4 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, NHAryl, NHR9,
COOH, OR9, COOR9, CONHR9, or CON(R9)2; R3 and R4 may together form a 5-membered or 6- membered aryl or heteroaryl ring;
R5 and R6 are independently selected from hydrogen or C 1-6 alkyl;
R9 is selected from hydrogen, Cl -6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.
[0023] Still another embodiment provides a compound selected from: N-(4-(6-chloropyridin-3-yl)phenyl-N'-(4-(pyridin-4-yloxy)phenyl)-sulfamide; N-(4-(6-chloropyridin-3-yl)phenyl-N'-(4-(oxazolo[5,4-b]pyridin-7-yloxy)phenyl)-sulfamide; or N-(4-(6-chloropyridin-3-yl)phenyl-N'-(4-(quinazolin-4-yloxy)phenyl)-sulfamide.
[0024] Yet another embodiment provides a compound of Formula (IV) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000008_0001
Formula (IV) wherein,
X is O or NH;
Y is O, NH, -OCH2- or -CH2O-
Z is CH or N;
A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R' substituents; R1 and R4 are independently selected from hydrogen, halogen, OR9, Cl-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR9, CONCR9)^ NHR9, N(R9)2, COR9, C0-4a!kylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR9, hydroxy, Cl-6alkoxy, OC(O)R9, -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR9, OC0-4alkylC3-10heterocycloalkyl,
OC0-4alkylNR9, NR9COOR9, OCONR9, or NR9COR9;
R2 and R3 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, NHAryl, NHR9, COOH, OR9, COOR9, CONHR9, or CON(R9)2; R2 and R3 may together form a 5-membered or 6- membered aryl or heteroaryl ring; R5 is selected from hydrogen, halogen, hydroxy, OR9, CN, amino, NHR9 or Cl-6 alkyl;
R6 and R7 are independently selected from hydrogen, Cl-6 alkyl and optionally may be joined to form a 3-10 membered cycloalkyl;
R8 is selected from hydrogen or Cl-6 alkyl;
R9 is selected from hydrogen, Cl-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl. [0025] Still a further embodiment provides a compound selected from:
N-(4-(quinolin-4-ylmethoxy)phenyl)-2-(5-(6-(trifluoromethyl)pyridin-3-yl)-lH-imidazol-2-yl)acetamide;
N-(4-(pyridin-4-ylmethoxy)phenyl)-2-(5-(6-(trifiuoromethyl)pyridin-3-yl)-lH-imidazol-2-yl)acetamide; 2-(5-(pyridin-3-yl)-lH-imidazol-2-yl)-N-(4-(pyridin-4-ylmethoxy)phenyl)acetamide; or 2-(5-(pyridin-3-yl)-lH-imidazol-2-yl)-N-(4-(quinolin-4-ylmethoxy)phenyl)acetamide. [0026] [0027]
[0028] In various embodiments, the compound binds to the designated kinases in a particular pattern; and/or modulates a biological activity modulated by the designated kinases in such a pattern. [0029] Embodiments further provide methods of modulating the biochemical activity of the designated kinases, the method comprising exposing those kinases to a compound of Claim 1 at an effective concentration, e.g., less than about 1 mM, 100 nM, 10 nM, or 1 nM. In certain embodiments, the pattern of selectivity exhibits at least about 0.5 log unit of specificity for said designated kinase effect relative to certain others. In yet another embodiment, the pathways include cell division signal, metastasis, angiogenesis, and apoptosis. BRIEF DESCRIPTION OF THE DRAWINGS
[0030) Figure 1-10 illustrate embodiments according to the invention for the design of modulators of panels of multiple kinases.
DETAILED DESCRIPTION OF THE INVENTION OUTLINE
I. Introduction
II. Kinase Pathways and Systems Biology
III. Regulating Combinations of Kinase Pathways IV. Medicinal Chemistry
V. Biochemical Assay
VI. Structure Activity Relationship; Pharmacophore Models
VII. In vitro and in vivo disease models VICE In vitro/in vivo testing DC. Structures Exhibiting Desired Pattern of Kinase Modulation
X. Efficacy and Safety Biomarkers
XI. Formulation Xn. Therapy
I. Introduction
[0031] As indicated above, the present invention provides structures, compounds and methods for modulating a pattern of kinase signaling useful in therapeutic applications. The pattern incorporates effects on multiple kinases, in contrast to drugs designed to modulate a single kinase target. The pattern will affect a plurality of kinases, e.g., a defined pattern of kinase effects. An attractive pattern might be selected to selectively modulate certain kinase pathways while exhibiting minimal effect on others, and may target multiple points in a signal pathway. Another attractive pattern may target modulating kinases in alternative or parallel signaling pathways, and the signal is modulated by affecting alternative signals. In another case, both strategies may be applied, depending upon the clinical context. The invention further identifies chemical scaffolds and compounds capable of achieving the desired pattern of selective modulation of kinase pathways, e.g., by acting on specified kinases in the specified direction.
[0032] The compound design and screening approach of the present invention are summarized in Figures 1-10. These methods are based on the identification of a set of validated kinases. Crystal structures of known kinases are solved through X-ray crystallography, NMR based methods or other protein structure elucidation methods. The binding sites of the kinases are analyzed and scaffolds of potential modulators are generated. Lead compounds are designed based on the scaffolds and tested both in silico and through experimental methods to identify lead compounds for further development. Derivatives of the lead compounds are synthesized and tested for their kinase modulatory activity across selected kinase profiles. Details of the methods and compounds described herein are set forth below. [0033] Kinase signal pathways have been identified as a common means for signal transduction making pathway modulation a theme in the regulation of biological systems. See, e.g., Heineke and Molkentin (2006) "Regulation of cardiac hypertrophy by intracellular signalling pathways" Nat. Rev. MoI. Cell Biol. 7:589-600, PMID: 16936699; Cashin, et al. (2006) "Contrasting signal transduction mechanisms in bacterial and eukaryotic gene transcription" FEMS Microbiol. Lett. 261:155-64, PMID: 16907715; and Sawyer, et al. (2005) "Protein phosphorylation and signal transduction modulation: chemistry perspectives for small-molecule drug discovery" Med. Chem. 1:293-319, PMID: 16787325.
[0034] A foundation of the approach is a comprehensive understanding of the signaling network of individual kinases and their roles in physiologic and pathologic conditions. This provides the basis to identify targets for pharmaceutical intervention in various human diseases and conditions. The invention teaches how to identify simultaneously sets of kinases (relevant multi-kinase profiles) and chemical starting points (scaffolds) to modulate multi-kinases. The invention provides processes that lead to the synthesis of kinase modulators with predetermined multi-kinase profiles in a timely manner. [0035] A pathway is a series of linked biochemical steps, with a beginning and an end; activity within a pathway takes the form of flux, or flow, of molecules, e.g., substrates. The network of pathways forms the biochemical repertoire or potential phenotypes of a biological system.
[0036] A profile is a combination of kinases that together modulate one or more biological pathways whose coordinated inhibition leads to a desired physiological effect. Typically the profile involves at least two, three, four or more target kinases. This in effect amounts to combination therapies, for example, a "cocktail" of selective drugs. In certain contexts, our combination strategy can be combined with other therapy leading to multiple therapeutic modalities.
[0037J In a pattern combining both inhibition of certain defined kinases and having minimal effect on others, the difference will preferably be a one log difference in effect on binding specificity or biological activity across the kinases, for example in terms of molar concentrations. The differences for a similar effect on a plurality of kinases will typically be small at an appropriate pharmacological concentration, e.g., less than about 1.3, 1, or 0.3 log units difference in molar concentrations. Where a different effect on kinases is desired, the differences will typically be large at an appropriate pharmacological concentration, e.g., more than about 1, 1.3, 2, 2.3, 3 or more log units difference in molar concentrations. For example, a profile which inhibits kinases A and B, but not C will preferably have similar amounts of inhibition of the A and B kinases at the appropriate pharmacological concentration, while much less (e.g., about 2 logs) less effect on kinase C. Typically, the assay will have biochemical components, e.g., kinases at concentrations analogous to physiological conditions. [0038] In other embodiments, the concentrations of compound necessary to effect the desired modulatory effects on kinases may be at least about 10, 30, 100, 300, or more on different kinases. For example to modulate kinases A and B may be effected by similar concentrations of compound, while kinase C may be unaffected until much higher concentrations of compound are reached. Conversely, the sensitivity of kinase C may low, while much lower amounts of compound may modulate kinases A and B. Additional effects of kinases D, E, and so on may also be combined into these compounds using various SAR or pharmacophore models directed to the additional kinases. Alternatively, appropriate selective entities modulating kinases D and E (but not A, B, and C) may be used in combination to extend the selectivity of the combined treatment. [0039J Descriptions of pharmacology and the pharmaceutical sciences are provided, e.g., in Atkinson, et al. (eds. 2006) Principles of Clinical Pharmacology (2d ed.) Academic Pr., ISBN: 0123694175; Holland and Adams (2006) Core Concepts in Pharmacology (2d ed.) Prentice Hall, ISBN: 0131714732; DiPiro, et al. (eds. 2005) Pharmacotherapy (6th ed.) McGraw-Hill Medical, ISBN: 0071416137; Sinko (2005) Martin's Physical Pharmacy and Pharmaceutical Sciences (5th ed.) Lippincott Williams & Wilkins, ISBN: 078175027X; Trissel 2005) Trissel's Stability of Compounded Formulations (3d ed.) APhA Pub., ISBN: 1582120676; University of the
Sciences in Philadelphia (eds. 2005) Remington: The Science and Practice of Pharmacy (Remington the Science and Practice of Pharmacy, 21st ed.) Lippincott Williams & Wilkins, ISBN: 0781746736; Ghosh and Jasti (eds. 2004) Theory and Practice of Contemporary Pharmaceutics (2d ed.) CRC, ISBN: 0415288630; Golan, et al. (eds. 2004) Principles of Pharmacology: The Pathophysiologic Basis of Drug Therapy Lippincott Williams & Wilkins, ISBN: 078174678; Hitner and Nagle (2004) Pharmacology: An Introduction (5th ed.) McGraw-Hill, ISBN: 0073122750; Winter (2003) Basic Clinical Pharmacokinetics (4th ed.) Lippincott Williams & Wilkins, ISBN: 0781741475; Walker and Edwards (2002) Clinical Pharmacy and Therapeutics (3d ed.) Churchill Livingstone, ISBN: 0443071373; Dressman (2000) Oral Drug Absorption (Drugs and the Pharmaceutical Sciences: a Series of Textbooks and Monographs) Informa Healthcare, ISBN: 0824702727; van de Waterbeemd, et al. (eds. 2003) Drug Bioavailability: Estimation of Solubility. Permeability. Absorption and Bioavailability (Methods and
Principles in Medicinal Chemistry) Wiley- VCH, ISBN: 352730438X; and references cited therein, and similar or related publications.
[0040] General description of the field of oncology is provided in, e.g., Debatin and Fulda (eds. 2006) Apoptosis and Cancer Therapy: From Cutting-edge Science to Novel Therapeutic Concepts Wiley & Sons, ISBN: 3527312374; Khan and Pelengaris (eds. 2006) The Molecular Biology of Cancer Blackwell Pub., ISBN:
1405118148; Schwab (ed. 2006) Encyclopedic Reference of Cancer Springer, ISBN: 3540334432; Stillman and Stewart (eds. 2006) Molecular Approaches to Controlling Cancer (CSHSQB) CSH Pr., ISBN: 0879697741; Chabner and Longo (2005) Cancer Chemotherapy and Biotherapy: Principles and Practice (4th ed.) Lippincott Williams & Wilkins, ISBN: 0781756286; Pecorino (2005) Molecular Biology of Cancer: Mechanisms. Targets. and Therapeutics Oxford Univ. Pr., ISBN: 0199264724; Abeloff, et al. (2004) Clinical Oncology (3d ed.) Churchill Livingstone, ISBN: 0443066299; Alison (ed. 2004) The Cancer Handbook Wiley & Sons. ISBN: 0470025069; Casciato (2004) Manual of Clinical Oncology (5th ed.) Lippincott Williams & Wilkins, ISBN: 0781747414; De Vita, et al. (2004) Cancer: Principles & Practice Of Oncology (7th ed. 2 Vol. bk and CDR) Lippincott Williams & Wilkins, ISBN: 0781748658; Harris, et al. (2004) Diseases of the Breast (3d ed.) Lippincott Williams & Wilkins, ISBN: 0781746191 ; Hoffman, et al. (2004) Hematology: Basic Principles and Practice (4th ed.) Churchill Livingstone, ISBN: 0443066280; Kasper, et al. (2004) Harrison's Principles of Internal Medicine (16th ed.) McGraw-Hill Professional, ISBN: 0071402357; Kumar, et al. (2004) Robbins & Cotran Pathologic Basis of Disease (7th ed.) Saunders ISBN: 0721601871; Prendergast (ed. 2004) Molecular Cancer Therapeutics: Strategies for Drug Discovery and Development Wiley-Liss, ISBN: 0471432024; Ross and Hortobagyi (eds. 2004) Molecular Oncology of Breast Cancer Jones & Bartlett Pub., ISBN: 0763748102; Fischer, et al. (2003) The Cancer Chemotherapy Handbook (6th ed.) Mosby, ISBN: 0323018904; Skeel (2003) Handbook of Cancer Chemotherapy (6th ed.) Lippincott Williams & Wilkins, ISBN: 0781736293; Bartone (2002) Cancer Encyclopedia: Collections of Anti-Cancer & Anti-Carcinogenic Agents. Chemicals. Drugs and Substances: Index of New Information and Guide-Book for Consumers. Reference and Research Abbe Pub Assn of Wash DC, ISBN: 0788326511; Bertino (ed. 2002) Encyclopedia of Cancer (2d ed. 4 vol. set) Acad. Pr., ISBN: 0122275551; Kelsen, et al. (2001) Gastrointestinal Oncology: Principles and Practice Lippincott Williams & Wilkins, ISBN: 0781722306; Thompson, et al. (eds. 2001) Textbook of Melanoma Taylor & Francis, ISBN: 1901865657; and references cited therein and the like, including specific types or organ sites of the diseases or tumors. [0041] The US National Cancer Institute list of prevalent cancer types includes prostate, breast, lung, colorectal, lymphoma, bladder, melanoma, endometrial, head/neck, kidney, leukemia, pancreas, ovarian, and esophagus. The Pan American Health organization lists the major cancers in men are lung, stomach, liver, colorectal, esophagus, and prostate. In women, the major cancers are breast, lung, stomach, colorectal, and cervical. Other types and categories into which cancers can be grouped will be found within the general oncology references. Specific animal models have been described herein for melanoma and myeloma, and bladder, cervical, endometrial, gastrointestinal, genitourinary, head and neck, hematopoietic, kidney, lung, mammary gland, nervous system, oral, ovarian, pancreatic, prostate, sarcoma, or skin cancers. See also http://eniice.nci.nih.gov/eniice/mouse_models/mouse_publications .
II. Kinase Pathways and Systems Biology
[0042] Kinase signals control central aspects of cellular physiology, metabolism, and function.
Moreover, kinase signal pathways are relevant in cell-cell interactions, in regulation of organ metabolism and physiology, and thereby aspects of organ physiology and systems biology. These may be either in the context of normal growth or development, or in abnormal contexts. In particular, many diseases or disorders may be caused by or cause aberrant interactions within an organism. Kinases have been implicated in various cancer conditions, and a number of drugs have been developed which target specific kinases. See Wanebo, et al. (2006) "Targeting growth factors and angiogenesis; using small molecules in malignancy" Cancer Metastasis Rev. 25:279-92, PMID: 16770540; Adjei and Hidalgo (2005) "Intracellular signal transduction pathway proteins as targets for cancer therapy" J. Clin. Oncol. 23:5386-403, PMBD: 15983388; and Kondapalli, et al. (2005) "The promise of molecular targeted therapies: protein kinase modulators in the treatment of cutaneous malignancies" J. Am. Acad. Dermatol. 53:291-302, PMID: 16021125. Other disorders, including imbalances in the function of the immune system, neural system, and other organ systems have been shown, or are suspected, to result from inappropriate regulation mediated by kinase signal pathways. [0043] In some circumstances, drugs targeting particular multiple kinases have been reported to be more effective than drugs targeting single kinases. See Faivre, et al. (2006) "New paradigms in anticancer therapy: targeting multiple signaling pathways with kinase modulators " Semin. Oncol. 33:407-20, PMID: 16890796. This may be because tumors are often driven or promoted by multiple pathways involving kinases. [0044] A major challenge in the drug development industry over the last decade has been to design drugs with the most highly desired multi-kinase profile that will target specific types of tumors. Typically, research efforts target a single kinase and the resulting lead therapeutic compounds directed to that kinase also have specificity for other kinases that are not necessarily the most desired set of kinases or effects.
[0045] During the past decade, perceptions about cancer biology and therapeutic interventions have changed. Understanding the genetic and biochemical mechanisms by which cancers arise and behave is now widely believed to portend improvements in the way the medical profession will detect, classify, monitor, and treat these diseases. This message has been driven home, gradually, but effectively, by a variety of new and less toxic agents for treating cancers — hormones, antibodies, and enzyme-inhibitory drugs, and, especially, by the arrival of imatinib (Gleevec), and other new targeted therapies described above. [0046] Targeting protein kinases in human cancer is now part of the standard treatment regimen for specific tumor types. Protein kinases are enzymes that modulate the amount of phosphorylation on specific proteins within cells in response to external stimuli. Kinases regulate multiple cellular processes that contribute to tumor development and progression, including cell growth, differentiation, migration, and programmed cell death (apoptosis). Inappropriate activity of protein kinases has been implicated in a variety of human diseases such as cancer, diabetes, and autoimmunity. In cancer model systems, perturbation of tyrosine kinase signaling can result in malignant transformation. For tumors whose growth is driven by activated kinases caused by genetic alterations, targeted drugs can potentially modulate or reverse malignant progression.
[0047] Clinical studies conducted over the past decade have established that tyrosine kinase modulators are safe and therapeutically active in selected populations of cancer patients. Several of these drugs are now part of the standard treatment regimen for specific tumor types. Modulating the abnormal activity of kinases with small molecules has demonstrated significant clinical benefit in patients, as in the case of the Bcr/Abl tyrosine kinase modulator Gleevec, the first marketed small molecule (SM) protein kinase modulator approved for treatment of chronic myelogenous leukemia (CML). Other drugs, such as Tarceva, Nexavar and Sutent, have followed the success of Gleevec. Judging from the efficacy of these drugs and results from ongoing clinical studies, protein kinases have been firmly established as targets for oncology therapeutics. The era of the so-called targeted therapies for cancer is arriving, supplanting cytotoxic drugs.
[0048] Taking advantage of the completed human genome sequence, a comprehensive analysis of protein kinases in human and other species was carried out by a team in Sugen/Pharmacia. For the first time, this analysis revealed the total number of protein kinases as well as enabled evolutionary comparisons to make functional inference. The human complement of protein kinases was dubbed as the "Human Kinome." This classification served as the launching platform for research on protein kinases.
[0049] Protein kinases are classified according to major groups and families, which are denominated TK, TKL, STE, CMGC, CAMK, and AGC. Kinases share a catalytic domain, but otherwise have diverse domain architecture. The common catalytic domain is where ATP binds and transfer of a phosphate group to a substrate takes place.
[0050] Clinical evidence indicates that multiple processes, such as tumorigenesis, tumor maintenance, and tumor growth should be modulated to achieve both efficacy and to overcome drug resistance. Overlapping pathways involving multiple kinases control these processes. In chemical terms, this translates into engineering small molecules modulating multiple kinases. Some time ago it was speculated that lack of specificity might lead to less efficacious and perhaps toxic drugs; however, it is increasingly clear that multi-kinase modulators are required for modulating all aspects of cancer.
[0051) Clinical data recently confirms that drugs targeting multiple-kinases are more effective than the ones targeting single kinases. "Most of us feel that except for in very rare instances, tumors are driven by multiple pathways, and therefore it makes sense that a multi-targeted approach makes most sense," said Mark Socinski, Associate Professor of Medicine at the University of North Carolina at Chapel Hill.
[0052] Methods for genetic analysis are well known, especially in the era of microarray analysis of genes. Specific evaluation of the full intact sequence of alleles is also common, which may include full sequencing, hybridization to selected probes, PCR analysis, and others. General methods of molecular biology are well known. See, e.g., Ausubel (ed.), et al. (2002) Short Protocols in Molecular Biology (Short Protocols in Molecular Biology; 5th ed.) Current Protocols, ISBN: 0471250929); Sambrook, et al. (2001) Molecular Cloning: A Laboratory Manual (vol. 1-3) CSH Lab. Pr. and affiliated www.MolecularCloning.com site that is evolving into an on-line laboratory manual; Cutler (ed. 2004) Protein Purification Protocols (Methods in Molecular Biology; 2d ed.) Humana Press, ISBN: 1588290670; Coligan, et al. (2001) Current Protocols in Protein Science Wiley, ISBN: 0471356808; Dickson and Mendenhall (eds. 2004) Signal Transduction Protocols (Methods in Molecular Biology; 2d ed.) Humana Press, ISBN: 1588292452; Waldman (ed. 2004) Genetic Recombination: Reviews and Protocols (Methods in Molecular Biology) Humana Press, ISBN: 1588292363; Schneider (ed. 2000) Chaperonin Protocols (Methods in Molecular Biology) Humana Press, ISBN: 0896037398; van de Heuvel (ed. 1997) PCR Protocols in Molecular Toxicology CRC-Press, ISBN: 084933344X; Fan (ed. 2002) Molecular Cytogenetics: Protocols and Applications (Methods in Molecular Biology) Humana Press, ISBN: 1588290069; Selinsky (ed. 2003) Membrane Protein Protocols: Expression. Purification, and Characterization (Methods in Molecular Biology) Humana Press, ISBN: 1588291243; Theophilus, et al. (2002) PCR Mutation Detection Protocols: Methods in Molecular Biology (Methods in Molecular Biology) Humana Press, ISBN: 0896036170; Wise (ed. 2002) Epithelial Cell Culture Protocols (Methods in Molecular Biology) Humana Press, ISBN: 0896038939; Brownstein and Khodursky (eds. 2003) Functional Genomics: Methods and Protocols (Methods in Molecular Biology) Humana Press, ISBN: 1588292916; Aguilar (ed. 2004) HPLC of Peptides and Proteins: Methods and Protocols (Methods in Molecular Biology) Humana Press, ISBN: 0896039773; Helfrich and Ralson (eds. 2003) Bone Research Protocols (Methods in Molecular Medicine) Humana Press, ISBN: 1588290441; Janzen (ed. 2002) High Throughput Screening: Methods and Protocols (Methods in Molecular Biology) Humana Press, ISBN: 0896038890; Killeen (ed. 2001) Molecular Pathology Protocols Humana Press, ISBN: 0896036812; Sioud (ed. 2004) Ribozvmes and siRNA Protocols (Methods in Molecular Biology; 2d ed.) Humana Press, ISBN:
1588292266; and other volumes in the Humana Press Methods in Molecular Biology/Molecular Medicine series (see www.humanapress.com; or BioMedProtocols.com'): in the Methods in Enzvmology series; in the periodical "Nature Methods"; or the like. [0053] Kinase assays may be performed by many standard and other methodologies, and assay services are commercially available. See Giordano and Romano (eds. 2004) Cell Cycle Control and Dvsregulation Protocols: Cvclins. Cvclin-Dependent Kinases, and Other Factors (Methods in Molecular Biology) Humana Press, ISBN: 0896039498; Terrian (ed. 2002) Cancer Cell Signaling: Methods and Protocols (Methods in Molecular Biology) Humana Press, ISBN: 1588290751, and other volumes in the Methods in Molecular Biology series. Many of these assays make use of labeled substrates, e.g., fluorescent, or antibodies which are specific for phosphorylated forms of peptides segments, or quenching methods. One example is the Pierce Iron Quenching (IQ) Kinase Assay platform, providing fast, high throughput analysis of protein kinases. The assays are homogeneous and universal so no antibody is required. Since detection is based on fluorescence intensity quenching, any plate fluorometer can be used. The assays can be performed in 96-, 384- or 1536- well formats. IQ technology utilizes an iron compound that acts as a dark quencher upon specific binding to the phosphoryl group of a fluorescent dye-labeled phosphorylated peptide. The binding event results in a decrease in the observed fluorescence intensity of the dye- labeled peptide after it becomes phosphorylated by the kinase. See Perbio Science N. V., Belgium. [0054] Systems biology analyses and techniques are described, e.g., in Klipp, et al. (2005) Systems Biology in Practice: Concepts. Implementation and Application Wiley, ISBN: 3527310789; Kitano (ed. 2001) Foundations of Systems Biology MIT Press, ISBN: 0262112663; Bower and Bolouri (eds. 2001) Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology) MIT Press, ISBN: 0262024810; Voit (2000) Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists (with CD-ROM) Cambridge Univ. Pr., ISBN: 0521785790; and other materials used in leading academic or professional school departments teaching courses in this area. Fundamental principles may include, e.g., coordinate regulation suggesting functional relationship, and others which are based upon information theory and mathematics of complex systems, of which biology is one of the most complex.
[0055] Other references relevant to the subject matter of the present invention include, e.g., Babine, et al. (2004) Protein Crystallography in Drug Discovery (Methods and Principles in Medicinal Chemistry) Wiley, ISBN: 3527306781; Kumar, et al. (2004) Robbins and Cotran: Pathologic Basis of Disease (7th ed. with CD) Saunders Co., ISBN: 0721601871; Kubinyi, et al. (2004) Chemogenomics in Drug Discovery: A Medicinal Chemistry Perspective (Methods and Principles in Medicinal Chemistry) Wiley, ISBN: 352730987X; Block, et al. (2004) Wilson and Gisvold's Textbook of Organic Medicinal and Pharmaceutical Chemistry (1 lth ed.) Lippincott Williams and Wilkins, ISBN: 0781734819; Bδhm, et al. (2003) Protein-Ligand Interactions: From Molecular Recognition to Drug Design (Methods and Principles in Medicinal Chemistry) Wiley, ISBN: 3527305211 ; Seydel, et al. (2002) Drug-Membrane Interactions: Analysis. Drug Distribution. Modeling (Methods and Principles in Medicinal Chemistry, Volume 15) Wiley-VCH, ISBN: 3527304274; Smith, et al (2000) Pharmacokinetics and Metabolism in Drug Design (Methods and Principles in Medicinal Chemistry) Wiley-VCH, ISBN: 3527301976; Wolff (ed. 1997) Therapeutic Agents. Volume 4. Burger's Medicinal Chemistry and Drug Discovery (5th ed.) Wiley-Interscience, ISBN: 0471575593; and Kennewell (1991) Comprehensive Medicinal Chemistry: General Principals Pergamon Pr., ISBN: 0080370578. Additional references of general medical relevance include, e.g., Berkow (ed.) The Merck Manual of Diagnosis and Therapy Merck and Co., Rahway, N.J.; Thorn, et al. Harrison's Principles of Internal Medicine McGraw-Hill, N. Y.; and Weatherall, et al. (eds.) Oxford Textbook of Medicine Oxford Univ. Press, Oxford. III. Regulating Combinations of Kinase Pathways [0056] A number of diseases, including cancer, diabetes, and inflammation, are linked to perturbation of protein kinase-mediated cell signaling pathways. The human genome encodes some 518 protein kinases that share a catalytic domain conserved in structure, but which notably differ in how their catalysis is regulated. [0057] The ATP binding pocket is between the two lobes of the kinase fold. This ATP binding site, together with less conserved hydrophobic surrounding pockets, has been the focus of modulator design that has exploited differences in kinase structure and pliability in order to achieve selectivity. Drugs are in clinical trials that target all stages of signal transduction. These range from the receptor tyrosine kinases that initiate intracellular signaling through second-messenger generators and kinases involved in signaling cascades to the kinases that regulate the cell cycle that governs cellular fate.
[0058] Although cancer is one indication for which kinases have been validated as targets for therapeutic intervention, many other medical conditions will similarly be sensitive to the fundamental signal pathways regulated by these same kinases. As such, other medical conditions will be susceptible to treatment by the compounds of the invention, including inflammation, developmental abnormalities, aging processes, and the like. Particular target medical conditions include those in which modulation of a process such as angiogenesis, cell cycle progression, cell division, cell growth, cell migration, cell mobility, cell motility, cell proliferation, cell survival, oncogenesis, p53 degradation, general proliferation, tumorigenesis, apoptosis, or metastasis are likely processes contributing to the symptoms or condition. Most of these processes are implicated in most cancers, and typically are considered to have effect by, e.g., specific inhibition or lack thereof, depending upon the medical circumstances. [0059] As used herein, "PK related disorder," "PK driven disorder," and "abnormal PK activity" all refer to a condition characterized by inappropriate; i.e., under or, more commonly, over, PK catalytic activity, where the particular PK can be an RTK, a CTK or an STK. Inappropriate catalytic activity can arise as the result of one of: (1) PK expression in cells which normally do not express PKs; (2) increased PK expression leading to unwanted cell proliferation, differentiation and/or growth; or (3) decreased PK expression leading to unwanted reductions in cell proliferation, differentiation, and/or growth. Over-activity of a PK refers to either amplification of the gene encoding a particular PK or production of a level of PK activity which can correlate with a cell proliferation, differentiation, and/or growth disorder (that is, as the level of the PK increases, the severity of one or more of the symptoms of the cellular disorder increases). Under-activity is, of course, the converse, wherein the severity of one or more symptoms of a cellular disorder increase as the level of the PK activity decreases. [0060] The term "therapeutically effective amount" as used herein refers to that amount of the compound being administered which will relieve to some extent one or more of the symptoms of the disorder being treated. In reference to the treatment of cancer, a therapeutically effective amount refers to that amount which has the effect of (1) reducing the size of the tumor; (2) modulating (that is, slowing to some extent, preferably stopping) tumor metastasis; (3) modulating to some extent (that is, slowing to some extent, preferably stopping) tumor growth; and/or (4) relieving to some extent (or, preferably, eliminating) one or more symptoms associated with the cancer. [0061] It is an aspect of this invention that the above-referenced protein kinase related disorder is selected from the group consisting of a receptor protein kinase related disorder, a cellular kinase disorder, and a serine-threonine kinase related disorder. In certain embodiments, the protein kinase related disorder is a cancer selected from the group consisting of squamous cell carcinoma, astrocytoma, glioblastoma, lung cancer, bladder cancer, head and neck cancer, melanoma, ovarian cancer, prostate cancer, breast cancer, small-cell lung cancer, and glioma in a further aspect of this invention. [0062] In addition to modulating PK activity, the compounds of this invention may modulate the activity of protein phosphatases which are enzymes which remove phosphate groups from phosphorylated proteins. Thus the compounds disclosed herein may also represent a new generation of therapeutic compounds for diseases and disorders associated with abnormal phosphatase activity (such as, without limitation, cell proliferation disorders and inflammatory disorders). The terms defined herein with respect to PKs would be understood by one skilled in the art to have the same or similar meaning with regard to phosphatases. IV. Medicinal Chemistry
[0063] Principles of organic chemistry, medicinal chemistry, and drug design are described, e.g., in the Methods and Principles in Medicinal Chemistry series published by Wiley-VCH, about 25 volumes by 2005; and the Progress in Medicinal Chemistry series published by Elsevier Science, about 45 volumes by 2006. More general descriptions are provided, e.g., in Bannwarth, et al. (2006) Combinatorial Chemistry: From Theory to Application (Methods and Principles in Medicinal Chemistry) (2d ed.) Wiley & Sons, ISBN: 3527306935; Dewick (2006) Essentials of Organic Chemistry: For Students of Pharmacy. Medicinal Chemistry and Biological Chemistry Wiley & Sons, ISBN: 0470016655; Ishar (2006) Syntheses of Organic Medicinal Compounds Alpha Science Intl Ltd, ISBN: 184265280X; Park and Mrsny (eds. 2006) Controlled Drug Delivery (ACS Symposium Series)
Oxford Univ. Pr., ISBN: 0841236259; Copeland (2005) Evaluation of Enzyme Modulators in Drug Discovery: A Guide for Medicinal Chemists and Pharmacologists (Methods of Biochemical Analysis) Wiley-Interscience, ISBN: 0471686964; Kappe, et al. (eds. 2005) Methods and Principles in Medicinal Chemistry: Microwaves in Organic and Medicinal Chemistry Wiley & Sons, ISBN: 3527312102; Dingermann, et al. (2004) Molecular Biology in Medicinal Chemistry (Methods and Principles in Medicinal Chemistry) Wiley, ISBN: 3527304312; Shargel, et al. (eds. 2004) Applied Biopharmaceutics & Pharmacokinetics (5th ed.) McGraw-Hill Medical, ISBN: 0071375503; Silverman (2004) The Organic Chemistry of Drug Design and Drug Action (2d ed.) Academic Pr., ISBN: 0126437327; Swarbrick (2004) Encyclopedia of Pharmaceutical Technology (2d ed.) 2004 Update Supplement, Informa Healthcare, ISBN: 0824721527; Abraham (ed. 2003) Burger's Medicinal Chemistry and Drug Discovery (6 VoIs. on Drug Discovery; Drug Discovery and Drug Development; Autocoids, Diagnostics, and Drugs from New Biology; Cardiovascular Agents and Endocrines; Chemotherapeutic Agents; and Nervous System Agents) Wiley-Interscience, ISBN: 0471370320; Abraham (ed. 2003) Burger's Medicinal Chemistry and Drug Discovery. Drug Discovery and Drug Development (6th ed.) Wiley-Interscience, ISBN: 0471370282; Bδhm, et al. (eds. 2003) Protein-Ligand Interactions: From Molecular Recognition to Drug Design (Methods and Principles in Medicinal Chemistry) Wiley & Sons, ISBN: 3527305211; Bultinck, et al. (eds. 2003) Computational Medicinal Chemistry for Drug Discovery CRC, ISBN: 0824747747; Lemke (2003) Review of Organic Functional Groups: Introduction to Medicinal Organic Chemistry (4th ed. book and CDRom) Lippincott Williams & Wilkins, ISBN: 0781743818; Thomas (2003) Fundamentals of Medicinal Chemistry Wiley & Sons, ISBN: 0470843071; Wermuth (ed. 2003) The Practice of Medicinal Chemistry (2d ed.) Academic Press; ISBN: 0127444815; King, et al. (eds. 2002) Progress in Medicinal Chemistry Vol. 40 (Progress in Medicinal Chemistry) Elsevier Science Pub., ISBN: 0444510540; Rrogsgaard-Larsen, et al. (eds. 2002) Textbook of Drug Design and Discovery (3d ed.) CRC, ISBN: 0415282888; Williams, et al. (eds. 2002) Fove's Principles of Medicinal Chemistry (5th ed.) Lippincott Williams & Wilkins, ISBN: 0683307371; Patrick (2001) An Introduction to Medicinal Chemistry (2d ed.) Oxford Univ. Pr., ISBN: 0198505337; Smith, et al (2000) Pharmacokinetics and Metabolism in Drug Design (Methods and Principles in Medicinal Chemistry) Wiley- VCH, ISBN: 3527301976; Thomas (2000) Medicinal Chemistry: An Introduction Wiley & Sons, ISBN: 0471489352; Cannon (1999) Pharmacology for Chemists (ACS Professional Reference Book) ACS Pub., ISBN: 0841235244; Dickson (1998) Medicinal Chemistry Laboratory Manual: Investigations in Biological and Pharmaceutical Chemistry CRC Press, ISBN: 0849318882; King (1994) Medicinal Chemistry: Principles and Practice Springer-Verlag, ISBN: 0851864945; references cited therein, and similar or related publications.
[0064] Description of drug optimization chemistry strategies is reviewed in Rodrigues (2004) "Inhibition and Induction of Enzymes (Cytochromes P450): Rational Approaches To Anticipate and Minimize Drug-Drug Interactions" at AAPS Workshop, September 2004 on Optimizing Drug-Like Properties During Lead Optimization. There is described a general four step strategy of the steps of: (1) understand drivers of drug-drug interactions and the pharmacokinetic models that have been developed to describe known clinical drug interactions; (2) establish early (discovery) higher-throughput in vitro screens for the relevant parameters; (3) relate in vitro human P450 data to the observed (animal), or predicted (human), in vivo efficacy data to place P450 data in the appropriate context; and (4) use preclinical P450 data to prioritize "mechanistic" clinical drug interaction studies, and apply the results of these studies to govern the prioritization of, and need for, additional interaction studies.
[0065] Useful references cited therein include Lin and Lu (1997) Pharmacological Reviews 49:403-449; Bonnabry, et al. (2001) Clin. Pharmacokin. 40:631-640; White (2000) Ann. Rev. Pharmacol. Toxicol. 40:133- 157; Yao and Levy (2002) J. Pharm. Sci. 91:1923-1935; Wienkers (2002) Eur. J. Pharm. Sci. 15:239-242; Rodrigues and Lin (2001) Curr. Opin. Chem. Bio. 15:396-401; Erhardt (ed. 1999) Drug Metabolism: Databases and High-Throughput Testing During Drug Design and Development Blackwell Sciences. ISBN 0-632-05342-9; Testa, et al. (eds. 2000) Pharmacokinetic Optimization in Drug Research: Biological. Phvsicochemical and Computational Strategies Wiley- Verlag; Woolf (ed. 1999) Handbook of Drug Metabolism Marcel Dekker. ISBN 0-8247-0229-8; Rodrigues (ed. 2002) Drug-Drug Interactions Marcel Dekker. ISBN 0-8247-0283-2; Levy, et al. (eds. 2000) Metabolic Drug-Drug Interactions Lippincott Williams and Wilkins. ISBN 0-7817-1441-9; Li and Sugiyama (eds. 2002) Preclinical and Clinical Evaluations of Drug-Drug Interactions ISE Press
(www.isebooks.com); Lin (2000) Curr. Drug Metab. 1:305-331; Ito, et al. (1998) Pharm. Revs. 50:387-411; Huang, et al. (1999) J. Clin. Pharmacol. 39:1006-1014; Davit, et al. (1999) J. Clin. Pharmacol. 39:899-910; Yuan, et al. (1999) Clin. Pharmacol. Then 66:9-15; Yuan, et al. (2002) Drug Metab. Dispos. 30:1311-1319; Bradley, et al. (2000) Drug Metab. Dispos. 28:1031-1037; Marroum, et al. (2000) Clin. Pharmacol. Ther. 68:280-285; Tucker, et al. (2001) Clin. Pharmacol. Ther. 70:103-114; references cited therein, and similar or related references.
[0066] Also, references on assays and approaches include Moore and Kliewer (2000) Toxicology 153: 1-10;
Crespi (1999) Curr. Opin. Drug Disc. Devel. 2:15-19; Dierks, et al. (2001) Drug Metab. Dispos. 29:23-29; McGinnity, et al. (2000) Drug Metab. Dispos. 28:1327-1334; Favreau, et al. (1999) Drug Metab. Dispos. 27:436-
439; Chauret, et al. (1999) Anal. Biochem. 276:215-226; Moody, et al. (1999) Xenobiotica 29:53-75; El-Sankary, et al. (2000) Drue Metab. Dispos. 28:493-496; Yin, et al. (2000) Xenobiotica 30:141-154; Shibata, et al. (2000)
Drug Metab. Dispos. 28:1518-1523; Bu, et al. (2000) Rapid Commun. Mass Spec. 14:1619-1624; Crespi, et al.
(1997) Anal. Biochem. 248:188-190; Rodrigues, et al. (1997) Drug Metab. Dispos. 25:1097-1100; Draper, et al. (1998) Drug Metab. Dispos. 26:299-304; Stresser, et al. (2000) Drug Metab. Dispos. 28: 1440-1448; Bowen, et al.
(2000) Drug Metab. Dispos. 28:781-788; Delaporte and Rodrigues (2001) Current Protocols in Pharmacology
3.9:1-32; Gibbs, et al. (1999) Drug Metab. Dispos. 27:596-599; Gibbs, et al. (1999) Drug Metab. Dispos. 27:180-
187; Takahashi, et al. (1999) Drug Metab. Dispos. 27:1179-1186; Kohl and Steinkellner (2000) Drug Metab.
Dispos. 28:161-168; Yamano, et al. (19991 Drug Metab. Dispos. 27:395-402: Yamano. et al. (2001) Drug Metab. Dispos. 29:443-452; Kunze, et al. (1996) Drug Metab. Dispos. 24:414-421, 422-428, and 429-435; Tran, et al.
(2002) Drug Metab. Dispos. 30:1441-1445; references cited therein, and similar or related references.
[0067] Parameters on compounds screened by in silico screening include services and software available from
MDL, Accelrys, or Tripos, at http://www.simulations-pkis.com/ or http://www.goldenlielix.com/about.html .
Kulkarni, et al. (2005) "In silico techniques for the study and prediction of xenobiotic metabolism: A review" Xenobiotica 35:955-973 reviews computational toxicity prediction. Other references on in silico and computational approaches include, e.g., Ertl, et al. (2000) J. Med. Chem.43: 3714-3717; Yoshida and Topliss
(2000) J. Med. Chem. 43:2575-2585; Egan, et al. (2000) J. Med. Chem. 43:3867-3877; Lewis, et al. (1999) Drug Metab. Drug Inter. 15:1-49; Lewis (2000) Biochem. Pharmacol. 60:293-306; de Groot, et al. (1999) J. Med. Chem. 42:4062-4070; Schneider, et al. (1999) J. Med. Chem. 42:5072-5076; Ekins, et al. (1999) J. Pharmacol. Exp. Ther. 290:429-438; Ekins and Obach (2000) J. Pharmacol. Exp. Ther. 295:463-473; Rao, et al. (2000) L Med. Chem. 43:2789-2796; Ekins, et al. (2000) Drug Metab. Dispos. 28:994-1002; Ekins, et al. (1999) Pharmacogenetics 9:477-489; Podlogar, et al. (2001) Curr. Opin. Drug Disc. Devel. 4:102-109; Chatuverdi, et al.
(2001) Curr. Opin. Chem. Biol. 5:452-463; van de Waterbeemd, et al. (2001) J. Med. Chem. 44:1313-1333; Ekins, et al. (2001) Drug Metab. Dispos. 29:936-944; Jones, et al. (2002) Drug Metab. Dispos. 30:7-12; De Groot and Ekins (2002) Advanced Drug Del. Res. 54:367-383; Kirton, et al. (2002) Advanced Drug Del. Res. 54:385- 406; references cited therein, and similar or related references.
[0068] The cytochrome P450 system is a significant component of modulating toxicity of proposed therapeutic compounds. See, e.g., Park, et al. (2005) "The role of metabolic activation in drug-induced hepatotoxicity" Ann- Rev. Pharmacology and Toxicology 45:177-202. Ann. Revs. Pr. and Coon (2005) "Cytochrome P450: Nature's Most Versatile Biological Catalyst" Ann. Rev. Pharmacology and Toxicology 45: 1-25. Various cytochrome P450 isoforms, in decreasing order of importance, is typically P450 isoforms 3A4 » 2D6 > 2C9, 2C19 » 1 A2, 2El. However, specific isoforms are recognized to have different activities on different substrate classes, and the differential expression levels or kinetics of isoforms among different groups, e.g., racial, developmental, sex, etc., often will affect sensitivity or tolerability to specific doses of particular drugs. In addition, coadministration of particular drugs may induce or repress activity of specific isoforms, which may increase or decrease metabolism rates and affect pharmacology of another drug entity. Thus drug-drug interactions often are caused by effects of one drug on the pharmacology of the other through the cytochrome P450 effects induced, or other mechanisms affecting pharmacology. Reports on known interactions of drugs are often made and catalogued, e.g., see http://medicine.iupui.edu/flockhart/table.htm . Such effects are not limited to drug induced effects on pharmacology, but may similarly be induced by environmental effects, e.g., diet, specific food intake, and other physiological effects, e.g., status of the immune or nervous system, presence of infectious agents, general health status, etc.
[0069] Clearly another significant component affecting pharmacology of a compound is its transport into cells. Among the transporters recognized to be relevant is the hERG potassium channel. See, e.g., Dubus, et al. (2006) "In Silico Classification of hERG Channel Blockers: a Knowledge-Based Strategy" Chem. Med. Chem. 1 :622- 630; Song and Clark (2006) "Development and Evaluation of an in Silico Model for hERG Binding" J. Chem. Inf. Model 46:392-400; Thomas, et al. (2006) Curr. Pharm. Pes. 12:2271-2283; and Sanguinetti and Tristani-Firouzi (2006) Nature 440:463-469; and related or similar publications. Thus, often drug screening programs consider the biochemistry of the interaction of a drug candidate with transporters such as these. [00701 Xenobiotic transporters are expressed in several tissues including the intestine, liver, kidney, and brain, and play key roles in drug absorption, distribution, and excretion. Functional characteristics of transporters provide important information allowing improvements in drug delivery or drug design through targeting or avoiding specific transporter proteins. [0071] Optimizing drugs based on transporter interaction offers the possibility of delivering a drug to a target organ, avoiding distribution to other organs (thereby reducing the chance of toxic side effects), controlling the elimination process, and/or improving oral bioavailability. It is useful to select a lead compound that may or may not interact with transporters, depending on whether such an interaction is desirable. The expression system of transporters is an efficient tool for screening the activity of individual transport processes. The changes in pharmacokinetics due to genetic polymorphisms and drug-drug interactions involving transporters can often have a direct and adverse effect on the therapeutic safety and efficacy of many important drugs.
[0072] Transporters, along with their function, classification, and use in optimizing drug structures are discussed in Mizuno, et al (2003) "Impact of Drug Transporter Studies on Drug Discovery and Development" Pharmacol. Rev. 55:425-461. V. Biochemical Assay [0073] Compounds synthesized will be evaluated using standard kinase phosphorylation assays as described below. A panel of kinases will be used to evaluate predicted selectivity of compounds. In particular, variants of the specified kinases may also be evaluated to determine the "common" variants found in the relevant medical conditions and likely to provide resistance to the modulators of the invention. Thus, for certain cancers, particular variants may arise which provide resistance of the variants to the treatment methods. Means for testing the various kinases are well established in the art, and are available from commercial sources. [0074J Assays for the appropriate kinases can be performed according to Shah (2006) "How to Choose an In Vitro Kinase Assay" Drug Discovery and Development: or according to methods which can be based on commercial methods available from InVitrogen or Millipore. [00751 GeneID provides sequence, alternative designations, other features, and further references. MEM provides additional references, information, gene function (useful for binding or activity screening), and animal models (useful for pathway effect validation).
[0076] ABLl=GeneID 25; see MIM 189980; described functions include ATP binding, DNA binding; nucleotide binding, protein C-terminus binding, protein-tyrosine kinase activity, and transferase activity; indicated function pathways dependent upon gene include DNA damage response (signal transduction resulting in induction of apoptosis), S-phase-specific transcription in mitotic cell cycle, intracellular signaling cascade, mismatch repair, protein amino acid phosphorylation, regulation of progression through cell cycle, and regulation of transcription (DNA-dependent). [0077] AKTl=GeneID 207 (NCBI); see MIM 164730; described functions include ATP binding, identical protein binding, nucleotide binding; protein kinase activity, receptor signaling protein serine/threonine kinase activity, sugar porter activity, and transferase activity; indicated function pathways dependent upon gene include G-protein coupled receptor protein signaling pathway, anti-apoptosis, apoptosis, carbohydrate metabolism, glucose metabolism, glycogen biosynthesis, insulin receptor signaling pathway, insulin-like growth factor receptor signaling pathway, nitric oxide biosynthesis, protein amino acid phosphorylation, protein amino acid phosphorylation, regulation of translation, response to heat, signal transduction, and transport.
[0078] AURKA=GeneID 6790; see MIM 164920; described functions include ATP binding, nucleotide binding, protein binding, protein binding, protein kinase activity, protein serine/threonine kinase activity, and transferase activity, indicated functional pathways dependent upon gene include cell cycle, mitosis, phosphoinositide- mediated signaling, protein amino acid phosphorylation, protein amino acid phosphorylation, regulation of protein stability, spindle organization, and biogenesis.
[0079] BRAF=GeneID 673; see MIM 164757; described functions include ATP binding, diacylglycerol binding, metal ion binding, nucleotide binding, protein serine/threonine kinase activity, receptor signaling protein activity, transferase activity, zinc ion binding; indicated functional pathways dependent upon gene include anti-apoptosis, intracellular signaling cascade, organ morphogenesis, protein amino acid phosphorylation. [0080] CDC2=GeneED 983 (NCBI); see MIM 116940; described functions include ATP binding, cyclin- dependent protein kinase activity, nucleotide binding, protein binding, and transferase activity; indicated function pathways dependent upon gene include anti-apoptosis, cell cycle, cell division, mitosis, protein amino acid phosphorylation, regulation of progression through cell cycle, and traversing start control point of mitotic cell cycle.
[0081] EGFR=GeneID 1956 (NCBI); see MIM 131550; described functions include ATP binding, MAP/ERK kinase kinase activity, actin filament binding, double-stranded DNA binding, epidermal growth factor receptor activity, epidermal growth factor receptor activity, identical protein binding, nitric-oxide synthase regulator activity, nucleotide binding, protein heterodimerization activity, transferase activity, and transmembrane receptor activity; indicated function pathways dependent upon gene include calcium-dependent phospholipase A2 activation, cell cycle, cell proliferation, cell surface receptor linked signal transduction, cell-cell adhesion, epidermal growth factor receptor signaling pathway, negative regulation of progression through cell cycle, ossification, phospholipase C activation, positive regulation of MAPK activity, positive regulation of cell migration, positive regulation of epithelial cell proliferation, positive regulation of nitric oxide biosynthesis, positive regulation of phosphorylation, protein amino acid phosphorylation, protein insertion into membrane, regulation of nitric-oxide synthase activity, regulation of peptidyl-tyrosine phosphorylation, and response to stress.
[0082] ERBB2=GeneID 2064 (NCBI); see MIM 164870 (also designated HER2); described functions include ATP binding, ErbB-3 class receptor binding, electron carrier activity, epidermal growth factor receptor activity, epidermal growth factor receptor activity, iron ion binding, non-membrane spanning protein tyrosine kinase activity, nucleotide binding, protein heterodimerization activity, protein heterodimerization activity, protein- tyrosine kinase activity, receptor activity, receptor signaling protein tyrosine kinase activity, and transferase activity; indicated function pathways dependent upon gene include cell proliferation, electron transport, heart development, mammary gland development, nervous system development, phosphoinositide-mediated signaling, positive regulation of MAPK activity, positive regulation of epithelial cell proliferation, protein amino acid phosphorylation, protein amino acid phosphorylation, regulation of angiogenesis, transmembrane receptor protein tyrosine kinase signaling pathway, and transmembrane receptor protein tyrosine kinase signaling pathway. [0083] FRAPl=GeneID 2475 (NCBI); see MIM 601231; described functions include binding, kinase activity, phosphoprotein binding, phosphotransferase activity (alcohol group as acceptor), and transferase activity, indicated function pathways dependent upon gene include cell growth, phosphorylation, protein catabolism, regulation of progression through cell cycle, regulation of translation, response to nutrient, and signal transduction.
[0084] JAK3=GeneID 3718 (NCBl); see MIM 600173; described functions include ATP binding, Janus kinase activity, nucleotide binding, protein binding, protein-tyrosine kinase activity, protein-tyrosine kinase activity, and transferase activity, indicated function pathways dependent upon gene include intracellular signaling cascade, mesoderm development, protein amino acid phosphorylation, and protein amino acid phosphorylation. [0085] KDR=GeneID 3791 (NCBI); see MIM 191306; described functions include ATP binding, nucleotide binding, receptor activity, transferase activity, vascular endothelial growth factor receptor activity; indicated functional pathways dependent upon gene include angiogenesis, cell differentiation, protein amino acid phosphorylation, and transmembrane receptor protein tyrosine kinase signaling pathway. [0086] KIT=GeneID 3815 (NCBI); see MIM 164920; described functions include ATP binding, nucleotide binding, receptor activity, receptor signaling protein tyrosine kinase activity, transferase activity, and vascular endothelial growth factor receptor activity; indicated functional pathways dependent upon gene include protein amino acid dephosphorylation, protein amino acid phosphorylation, signal transduction, and transmembrane receptor protein tyrosine kinase signaling pathway.
[0087] LCK=GeneID 3932 (NCBI); see MIM 153390; described functions include ATP binding, ATPase binding, CD4 receptor binding, CD8 receptor binding, SH2 domain binding, SH2 domain binding, glycoprotein binding, nucleotide binding, phosphoinositide 3-kinase binding, protein C-terminus binding, protein kinase binding, protein serine/threonine phosphatase activity, protein-tyrosine kinase activity, protein-tyrosine kinase activity, and transferase activity; indicated functional pathways dependent upon gene include Ras protein signal transduction, T cell differentiation, caspase activation, hemopoiesis, induction of apoptosis, intracellular signaling cascade, positive regulation of T cell activation, positive regulation of T cell receptor signaling pathway, protein amino acid phosphorylation, regulation of lymphocyte activation, regulation of progression through cell cycle, release of sequestered calcium ion into cytosol, response to drug, and zinc ion homeostasis.
[0088] MAP2Kl=GeneID 5604 (NCBI); see MIM 176872; described functions include ATP binding, MAP kinase kinase activity, nucleotide binding, protein binding, protein serine/threonine kinase activity, protein- tyrosine kinase activity, and transferase activity; indicated functional pathways dependent upon gene include cell motility, chemotaxis, protein amino acid phosphorylation, and signal transduction. [0089] MAPKl=GeneID 5594 (NCBI); see MIM 176948; described functions include ATP binding, MAP kinase activity, nucleotide binding, protein serine/threonine kinase activity, and transferase activity; indicated functional pathways dependent upon gene include cell cycle, chemotaxis, induction of apoptosis, protein amino acid phosphorylation, response to stress, signal transduction, and synaptic transmission. [0090] PDGFRB=GeneID 5159; see MIM 173410; described functions include ATP binding, nucleotide binding, platelet activating factor receptor activity, platelet-derived growth factor receptor activity, protein binding, receptor activity, and transferase activity; indicated functional pathways dependent upon gene include vascular endothelial growth factor receptor activity, protein amino acid phosphorylation, signal transduction, and transmembrane receptor protein tyrosine kinase signaling pathway. [0091] PIK3CG=GeneID 5294 (NCBI); see MIM 601232; described functions include inositol or phosphatidylinositol kinase activity, phosphatidylinositol 3-kinase activity, phosphatidylinositol-4,5-bisphosphate 3-kinase activity, and transferase activity; indicated functional pathways dependent upon gene include G-protein coupled receptor protein signaling pathway.
100921 SRC=GeneID 6714 (NCBI); see MIM 190090; described functions include ATP binding, SH2 domain binding, SH3/SH2 adaptor activity, nucleotide binding, protein binding, protein-tyrosine kinase activity, protein- tyrosine kinase activity, and transferase activity; indicated functional pathways dependent upon gene include protein amino acid phosphorylation, protein kinase cascade, and signal complex formation.
[0093] Non-human species counterparts will be useful in many contexts including testing in other species and evaluation of in vitro and in vivo animal models. Other activities and pathways related to a species counterpart may often be adapted to a human counterpart. VI. Structure Activity Relationship; Pharmacophore Models
[0094] Binding pockets of all known kinase crystal structures are classified and interacting residues identified.
Further, binding pockets are clustered according to shape similarities.
[0095] A two-way clustering of kinases and IC50 of compounds are performed. In addition, clustering of compounds by themselves is performed. This yields sets of profiles for which Quantitative Structure Activity Relationship (QSAR) and Quantitative Structure Property Relationship (QSPR) are modeled.
[0096] Taken together, these two clustering steps yield kinase and compound sets and QSAR models. Using scaffold hopping and other types of virtual modeling and screening, novel scaffolds are designed for specified sets of kinases. Additional novel scaffolds are designed using ATP binding pocket classification.
[0097] Virtual screening and docking methodologies are used to identify scaffolds for further evaluation. [0098] The compound design and screening approach of the present invention are summarized in Figures 1-10.
These methods are based on the identification of a set of validated kinases. Crystal structures of known kinases are solved through X-ray crystallography, NMR based methods or other protein structure elucidation methods.
The binding sites of the kinases are analyzed and scaffolds of potential modulators are generated. Lead compounds are designed based on the scaffolds and tested both in silico and through experimental methods to identify lead compounds for further development. Derivatives of the lead compounds are synthesized and tested for their kinase inhibitory activity across selected kinase profiles. Details of the methods and compounds described herein are set forth below.
[0099] The results of structural studies have identified the properties of the protein kinase ATP binding site that are exploited by the relatively potent and selective subset of modulators that are showing promise in clinical trials. Although conserved in architecture, the ATP-binding site presents distinct features. From such structures, the sites of different kinases that are potential drug targets can be classified on the basis of shape and amino acid composition. There are a number of examples where inferred routes to kinase selectivity are representative of the action of families of clinically tested modulators of protein kinase signaling.
[00100] The ability to engineer molecules that target a common functional domain on all kinases, yet exhibit selectivity through their specific interactions with unique amino acid residues within the different ATP binding pockets, represents a powerful approach for the discovery of kinase modulator drugs. The conventional approach to kinase drug discovery involves: (1) target validation; (2) high-throughput screening; (3) hits-to-lead; and (4) lead-optimization.
[00101] Ongoing research in kinase biology and clinical experience with kinase targets has resulted in a rich set of available information on biological consequences of modulating kinases with small molecule modulators.
[00102] Expression profiles of kinases in normal and cancer tissues, mutation profiles of kinases in various cancers, and chromosomal amplification of kinases are described in available published information, which includes descriptions of 368,000 kinase modulators. Although not all of these 368,000 have comprehensive biological data, they serve as templates for further advances in kinase modulator design. [00103] All available information on protein kinases, including biological, structural, and activity of small molecule modulators, has been used to design novel molecules effective against clinically validated kinases.
[00104] A "Structure Target Activity" is generated from: (i) all known kinase modulators ; (ii) known kinase crystal structures; (iii) novel chemical scaffolds generated from analysis of kinase modulators and crystal structures; and (iv) kinase biology, which provides as the basis for selectivity based on the foregoing information. By using available chemical, biological, and clinical evidence, the process bypasses key steps in the conventional drug discovery. The approach moves the starting point of drug discovery to the lead-optimization stage and results in both time and cost savings.
[00105] Based upon the collation of data, as described, certain patterns of inhibition of specific kinases become readily achievable, while others may not appear. However, based upon the data, the structures which achieve desired patterns, determined by the etiology of disease or condition, can be selected and appropriate structural scaffolds corresponding to such patterns are provided. The structures which provide the desired pattern of target kinases modulation correspond to the RingA-Linker-RingB type structure described. Thus, the computational screening was performed to identify the 370 compound.
[00106] These scaffolds then serve as the starting structures and motifs for rounds of medicinal chemistry to generate variants with desired characteristics. Typical desired characteristics include the standard aspects of
"drug-like" properties, e.g., the ADMETox, and simplicity of synthesis and susceptibility to patent protection.
[00107] Pharmacophore models have been applied, e.g., GOLD and GLIDE, for predicting the activities against various kinases, e.g., KDR or PDGFRB.
VII. In vitro and in vivo disease models [00108] A panel of cell lines expressing appropriate combinations of kinases and exhibiting appropriate biological responses will be used to further evaluate and confirm that a compound elicits the appropriate physiological response.
[00109] Similarly, animal models will further confirm appropriate response in an organismal context.
[00110] Table 1 lists biological pathways relevant to diseases. These pathways include kinases as important mediators. "Kinase" refers to official gene symbol (according to Human Genome Organization, HUGO). "NCBI" refers to unique numeric identifier for the kinase as designated by NCBI. "Pathway" refers to specific biological pathway as it is commonly understood. "Class" refers to specific biological function mediated by the pathway. [00111] .
Table 1
Kinase(s) (NCBI) » Pathway or Function »Class
BRAF (673) » Activation of cAMP-Dependent PKA » Induces cell survival
GSK3A, GSK3B (2931, 2932) » Activation of cAMP-Dependent PKA » Induces oncogenesis MAP2K1 , MAP2K2 (5604, 5605) » Activation of cAMP-Dependent PKA » Induces cell survival
RAFl (5894) » Activation of cAMP-Dependent PKA » Induces cell survival
BRAF (673) » Activation of PKA through GPCR » Induces cell survival
MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAP2K6 (5604, 5605, 5606, 6416, 5607, 5608) »
Activation of PKA through GPCR » Induces cell survival PQGCA, PIK3CG, PIK3CB (5290), (5294), (5291) » Activation of PKA through GPCR » Induces cell survival
RAFl, BRAF, ARAF (5894), (673), (369) » Activation of PKA through GPCR » Induces cell survival
PRKCA, PRKCBl, PRKCD, PRKCE, PRKCH, PRKCG, PRKCI, PRKDl, PRKD3, PRKCQ, PRKCZ (5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 23683, 5588, 5590) » Activation of PKC through GPCR » Induces cell survival
RAFl (5894) » Activation of PKC through GPCR » Induces cell survival
AATK (9625) » Akt Signaling » Induces cell cycle progression
AATK (9625) » Akt Signaling » Inhibits apoptosis
AKTl (207) » Akt Signaling » Induces cell cycle progression AKT2 (208) » Akt Signaling » Induces cell cycle progression
AKT2 (208) » Akt Signaling » Inhibits apoptosis
AKT3 (10000) » Akt Signaling » Induces cell cycle progression
AKT3 (10000) » Akt Signaling » Inhibits apoptosis
ALK (238) » Akt Signaling » Induces cell cycle progression ALK (238) » Akt Signaling » Inhibits apoptosis
AXL (558) » Akt Signaling » Induces cell cycle progression
AXL (558) » Akt Signaling » Inhibits apoptosis
CSFlR (1436) » Akt Signaling » Induces cell cycle progression
CSFlR (1436) » Akt Signaling » Inhibits apoptosis DDRl (780) » Akt Signaling » Induces cell cycle progression
DDRl (780) » Akt Signaling » Inhibits apoptosis
DDR2 (4921) » Akt Signaling » Induces cell cycle progression
DDR2 (4921) » Akt Signaling » Inhibits apoptosis
EGFR (1956) » Akt Signaling » Induces cell cycle progression EGFR (1956) » Akt Signaling » Inhibits apoptosis
EPHA (2045) » Akt Signaling » Induces cell cycle progression
EPHA (2045) » Akt Signaling » Inhibits apoptosis
EPHAl (2041) » Akt Signaling » Induces cell cycle progression
EPHAl (2041) » Akt Signaling » Inhibits apoptosis EphA2 (1969) » Akt Signaling » Induces cell cycle progression
EphA2 (1969) » Akt Signaling » Inhibits apoptosis
EPHA3 (2042) » Akt Signaling » Induces cell cycle progression
EPHA3 (2042) » Akt Signaling » Inhibits apoptosis
EPHA4 (2043) » Akt Signaling » Induces cell cycle progression EPHA4 (2043) » Akt Signaling » Inhibits apoptosis EPHA5 (2044) » Akt Signaling » Induces cell cycle progression EPHA5 (2044) » Akt Signaling » Inhibits apoptosis EPHB (2046) » Akt Signaling » Induces cell cycle progression EPHB (2046) » Akt Signaling » Inhibits apoptosis EPHB 1 (2047) » Akt Signaling » Induces cell cycle progression EPHBl (2047) » Akt Signaling » Inhibits apoptosis EPHB2 (2048 » Akt Signaling » Induces cell cycle progression EPHB2 (2048 » Akt Signaling » Inhibits apoptosis EPHB3 (2049 » Akt Signaling » Induces cell cycle progression EPHB3 (2049 » Akt Signaling » Inhibits apoptosis
EPHB4 (2050 » Akt Signaling » Induces cell cycle progression EPHB4 (2050 » Akt Signaling » Inhibits apoptosis EPHB5 (2051 » Akt Signaling » Induces cell cycle progression EPHB5 (2051 » Akt Signaling » Inhibits apoptosis EPOR (2057 » Akt Signaling » Induces cell cycle progression EPOR (2057 » Akt Signaling » Inhibits apoptosis ERBB2 (2064) » Akt Signaling » Induces cell cycle progression ERBB2 (2064) » Akt Signaling » Inhibits apoptosis ERBB4 (2066) » Akt Signaling » Induces cell cycle progression ERBB4 (2066) » Akt Signaling » Inhibits apoptosis
FGFRl (2260) » Akt Signaling » Induces cell cycle progression FGFRl (2260) » Akt Signaling » Inhibits apoptosis FGFR2 (2263) » Akt Signaling » Induces cell cycle progression FGFR2 (2263) » Akt Signaling » Inhibits apoptosis FGFR3 (2261) » Akt Signaling » Induces cell cycle progression FGFR3 (2261) » Akt Signaling » Inhibits apoptosis FLTl (2321) » Akt Signaling » Induces cell cycle progression FLTl (2321) » Akt Signaling » Inhibits apoptosis FLT3 (2322) » Akt Signaling » Induces cell cycle progression FLT3 (2322) » Akt Signaling » Inhibits apoptosis
FLT4 (2324) » Akt Signaling » Induces cell cycle progression FLT4 (2324) » Akt Signaling » Inhibits apoptosis FRAPl (2475) » Akt Signaling » Induces cell growth GSK3A (2931) » Akt Signaling » Induces cell cycle progression GSK3B (2932) » Akt Signaling » Induces cell cycle progression IGFRl (3480) » Akt Signaling » Induces cell cycle progression IGFRl (3480) » Akt Signaling » Inhibits apoptosis ILK (3611) » Akt Signaling » Induces cell cycle progression ILK (3611) » Akt Signaling » Induces cell growth ILK (3611) » Akt Signaling » Induces cell survival
ILK (3611) » Akt Signaling » Induces p53 degradation ILK (3611) » Akt Signaling » Inhibits apoptosis JAKl (3716) » Akt Signaling » Induces cell cycle progression JAKl (3716) » Akt Signaling » Induces cell growth JAKl (3716) » Akt Signaling » Induces cell survival
JAKl (3716) » Akt Signaling » Induces p53 degradation JAKl (3716) » Akt Signaling » Inhibits apoptosis KDR (3791) » Akt Signaling » Induces cell cycle progression KDR (3791) » Akt Signaling » Inhibits apoptosis KIT (3815) » Akt Signaling » Induces cell cycle progression KIT (3815) » Akt Signaling » Inhibits apoptosis MERTK (10461) » Akt Signaling » Induces cell cycle progression MERTK (10461) » Akt Signaling » Inhibits apoptosis
MET (4233) » Akt Signaling » Induces cell cycle progression
MET (4233) » Akt Signaling » Inhibits apoptosis
NTRKl (4914) » Akt Signaling » Induces cell cycle progression NTRKl (4914) » Akt Signaling » Inhibits apoptosis
Pl 3K (5290, 5291, 5293, 5294) » Akt Signaling » Induces cell cycle progression
P13K (5290, 5291, 5293, 5294) » Akt Signaling » Induces cell growth
P13K (5290, 5291, 5293, 5294) » Akt Signaling » Induces cell survival
Pl 3K (5290, 5291, 5293, 5294) » Akt Signaling » Induces p53 degradation P13K (5290, 5291, 5293, 5294) » Akt Signaling » Inhibits apoptosis
PDGFRA (5156) » Akt Signaling » Induces cell cycle progression
PDGFRA (5156) » Akt Signaling » Inhibits apoptosis
PDGFRB (5159) » Akt Signaling » Induces cell cycle progression
PDGFRB (5159) » Akt Signaling » Inhibits apoptosis PDKl (5163) » Akt Signaling » Induces cell cycle progression
PDKl (5163) » Akt Signaling » Induces cell growth
PDKl (5163) » Akt Signaling » Induces cell survival
PDKl (5163) » Akt Signaling » Induces p53 degradation
PDKl (5163) » Akt Signaling » Inhibits apoptosis PRKDC (5591) » Akt Signaling » Induces cell cycle progression
PRKDC (5591) » Akt Signaling » Induces cell growth
PRKDC (5591) » Akt Signaling » Induces cell survival
PRKDC (5591) » Akt Signaling » Induces p53 degradation
PRKDC (5591) » Akt Signaling » Inhibits apoptosis PTK2 (5747) » Akt Signaling » Induces cell cycle progression
PTK2 (5747) » Akt Signaling » Induces cell growth
PTK2 (5747) » Akt Signaling » Induces cell survival
PTK2 (5747) » Akt Signaling » Induces p53 degradation
PTK2 (5747) » Akt Signaling » Inhibits apoptosis PTK2B (2185) » Akt Signaling » Induces cell cycle progression
PTK2B (2185) » Akt Signaling » Inhibits apoptosis
PTK2B (2185) » Akt Signaling » Induces cell cycle progression
PTK2B (2185) » Akt Signaling » Induces cell growth
PTK2B (2185) » Akt Signaling » Induces cell survival PTK2B (2185) » Akt Signaling » Induces p53 degradation
PTK2B (2185) » Akt Signaling » Inhibits apoptosis
RPS6KB1 (6198) » Akt Signaling » Induces cell growth
SYK (6850) » Akt Signaling » Induces cell cycle progression
SYK (6850) » Akt Signaling » Induces cell growth SYK (6850) » Akt Signaling » Induces cell survival
SYK (6850) » Akt Signaling » Induces p53 degradation
SYK (6850) » Akt Signaling » Inhibits apoptosis
AKTl (207) » AMPK Enzyme Complex Pathway » Induces angiogenesis
INSR (3643) » AMPK Enzyme Complex Pathway » Induces angiogenesis PRKACA, PRKACB, PRKACG (5566, 5567, 5568) » AMPK Enzyme Complex Pathway » Induces angiogenesis
SRC (6714) » AMPK Enzyme Complex Pathway » Induces angiogenesis
PTK2 (5747) » Angiopoietin-TIE2 Signaling » Induces angiogenesis
PTK2 (5747) » Angiopoietin-TIE2 Signaling » Induces cell migration TIE2 (7010) » Angiopoietin-TIE2 Signaling » Induces angiogenesis
TIE2 (7010) » Angiopoietin-TIE2 Signaling » Induces cell migration
CDC2 (983) » ATM Pathway » Induces cell cycle progression CDK2 (1017) » ATM Pathway » Induces cell cycle progression CHEKl (1111) » ATM Pathway » Induces cell cycle progression CHEK2 (11200) » ATM Pathway » Induces cell cycle progression
MAPK8; MAPK14; MAPKIl; MAPK12; MAPK13 (5599; 1432; 5600; 6300; 5603) » ATM Pathway » Induces cell survival
AKTl (207) » BAD Phosphorylation » Induces cell survival AKTl (207) » BAD Phosphorylation » Inhibits apoptosis EGFR (1956) » BAD Phosphorylation » Induces cell survival EGFR (1956) » BAD Phosphorylation » Inhibits apoptosis IGFRl (3480) » BAD Phosphorylation » Induces cell survival IGFRl (3480) » BAD Phosphorylation » Inhibits apoptosis MAP2K1; MAP2K2 (5604; 5605) » BAD Phosphorylation » Induces cell survival MAP2K1; MAP2K2 (5604; 5605) » BAD Phosphorylation » Inhibits apoptosis MAPK3; MAPKl (5595; 5594) » BAD Phosphorylation » Induces cell survival MAPK3; MAPKl (5595; 5594) » BAD Phosphorylation » Inhibits apoptosis RAFl (5894) » BAD Phosphorylation » Induces cell survival RAFl (5894) » BAD Phosphorylation » Inhibits apoptosis RPS6KB1 (6198) » BAD Phosphorylation » Induces cell survival RPS6KB1 (6198) » BAD Phosphorylation » Inhibits apoptosis CDC2 (983) » BRCAl Pathway » Induces cell cycle progression
CHEK2 (11200) » BRCAl Pathway » Induces cell cycle progression
PLKl (5347) » BRCAl Pathway » Induces cell cycle progression
CDC2 (983) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression
CDK2 (1017) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression CDK4 (1019) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression CDK6 (1021) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression CSK (1445) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression CSK (1445) » Calpain Protease Regulates Cellular Mechanics » Metastasis EGFR (1956) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression EGFR (1956) » Calpain Protease Regulates Cellular Mechanics » Metastasis
MAPKl (5594) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression MAPKl (5594) » Calpain Protease Regulates Cellular Mechanics » Metastasis MAPK 12 (6300) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression MAPK3 (5595) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression MAPK3 (5595) » Calpain Protease Regulates Cellular Mechanics » Metastasis
MAPK4 (5596) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression MAPK4 (5596) » Calpain Protease Regulates Cellular Mechanics » Metastasis MAPK7 (5598) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression MAPK7 (5598) » Calpain Protease Regulates Cellular Mechanics » Metastasis PTK2 (5747) » Calpain Protease Regulates Cellular Mechanics » Metastasis PTK2B (2185) » Calpain Protease Regulates Cellular Mechanics » Metastasis SRC (6714) » Calpain Protease Regulates Cellular Mechanics » Induces cell cycle progression SRC (6714) » Calpain Protease Regulates Cellular Mechanics » Metastasis PAKl (5058) » Caspase Cascade » Induces cell survival CDC2 (983) » Cell Cycle Control by BTG Proteins » Induces cell cycle progression CDK4 (1019) » Cell Cycle Control by BTG Proteins » Induces cell proliferation AKTl (207) » Ceramide Pathway » Inhibits apoptosis CERK (64781) » Ceramide Pathway » Inhibits apoptosis MAP2K1 (5604) » Ceramide Pathway » Inhibits apoptosis RAFl (5894) » Ceramide Pathway » Inhibits apoptosis
ATM (472) » Checkpoint Comparative Pathways » Induces cell cycle progression ATR (545) » Checkpoint Comparative Pathways » Induces cell cycle progression CDC2 (983) » Checkpoint Comparative Pathways » Induces cell cycle progression CDK2 (1017) » Checkpoint Comparative Pathways » Induces cell cycle progression CHEKl (1111) » Checkpoint Comparative Pathways » Induces cell cycle progression CHEK2 (11200) » Checkpoint Comparative Pathways » Induces cell cycle progression ATM (472) » Chks in Checkpoint Regulation » Induces cell cycle progression ATR (545) » Chks in Checkpoint Regulation » Induces cell cycle progression CDC2 (983) » Chks in Checkpoint Regulation » Induces cell cycle progression CHEKl (1111) » Chks in Checkpoint Regulation » Induces cell cycle progression CHEK2 (11200) » Chks in Checkpoint Regulation » Induces cell cycle progression LCK (3932) » CTLA4 Signaling » Inhibits apoptosis PDPKl (5170) » CTLA4 Signaling » Inhibits apoptosis
ATM (472) » Cyclins and Cell Cycle Regulation » Induces cell cycle progression ATR (545) » Cyclins and Cell Cycle Regulation » Induces cell cycle progression CDC2 (983) » Cyclins and Cell Cycle Regulation » Induces cell cycle progression CDK2 (1017) » Cyclins and Cell Cycle Regulation » Induces cell cycle progression
CDK4; CDK6 (1019; 1021) » Cyclins and Cell Cycle Regulation » Induces cell cycle progression CDK7 (1022) » Cyclins and Cell Cycle Regulation » Induces cell cycle progression RAFl (5894) » Cyclins and Cell Cycle Regulation » Induces cell cycle progression CAMK4 (814) » Dopamine-DARPP32 Feedback onto cAMP Pathway » Induces cell survival CAMKK 1 , CAMKK2 (84254, 10645) » Dopamine-DARPP32 Feedback onto cAMP Pathway » Induces cell survival
CDK5 (1020) » Dopamine-DARPP32 Feedback onto cAMP Pathway » Induces cell survival PRKACA, PRKACB, PRKACG, PRKARlA, PRKARlB, PRKAR2B, PRKAR2A (5566, 5567, 5568, 5573, 5575, 5577, 5576) » Dopamine-DARPP32 Feedback onto cAMP Pathway » Induces cell survival PRKCA, PRKCBl, PRKCD, PRKCE, PRKCH, PRKCG, PRKCI, PRKDl, PRKCQ (5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 5588) » Dopamine-DARPP32 Feedback onto cAMP Pathway » Induces cell survival
CDC2 (983) » Estrogen-mediated S-Phase Entry » Induces cell cycle progression CDK2 (1017) » Estrogen-mediated S-Phase Entry » Induces cell cycle progression CDK4 (1019) » Estrogen-mediated S-Phase Entry » Induces cell cycle progression AKTl (207) » FAKl Signaling » Induces cell survival BRAF (673) » FAKl Signaling » Induces cell proliferation EGFR (1956) » FAKl Signaling » Induces cell proliferation MAP2K1 (5604) » FAKl Signaling » Induces cell proliferation MAP2K2 (5605) » FAKl Signaling » Induces cell proliferation MAP2K3 (5606) » FAKl Signaling » Induces cell proliferation MAP2K4 (6416) » FAKl Signaling » Induces cell proliferation MAP2K5 (5607) » FAKl Signaling » Induces cell proliferation MAP2K6 (5608) » FAKl Signaling » Induces cell proliferation MAPKl (5594) » FAKl Signaling » Induces cell proliferation MAPK3 (5595) » FAKl Signaling » Induces cell proliferation PAKl (5058) » FAKl Signaling » Induces cell proliferation PAK2 (5062) » FAKl Signaling » Metastasis PAK3 (5063) » FAKl Signaling » Induces cell proliferation PAK4 (10298) » FAKl Signaling » Metastasis
PAK6 (56924) » FAKl Signaling » Induces cell proliferation PAK6; PAK7 (56924; 57144) » FAKl Signaling » Metastasis PDKl (5163) » FAKl Signaling » Induces cell survival PTK2 (5747) » FAKl Signaling » Metastasis RAFl (5894) » FAKl Signaling » Induces cell proliferation BTK (695) » Fas Signaling » Induces cell proliferation
CHUK; IKBKB; IKBKE; IKBKG (1147; 3551; 9641; 8517) » Fas Signaling » Induces cell proliferation MAP2K1 (5604) » Fas Signaling » Induces cell proliferation
MAPK3 (5595) » Fas Signaling » Induces cell proliferation
RAFl (5894) » Fas Signaling » Induces cell proliferation
AKTl (207) » FLT3 Signaling » Induces cell division FRAPl (2475) » FLT3 Signaling » Induces cell division
MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6 (5604, 5605, 5606, 6416, 5608) » FLT3 Signaling » Induces cell division
PDPKl (5170) » FLT3 Signaling » Induces cell division
RAFl, BRAF, ARAF (5894, 673, 369) » FLT3 Signaling » Induces cell division RPS6KA1, RPS6KA3, RPS6KA2, RPS6KA6, RPS6KA4 (6195, 6197, 6196, 27330, 8986) » FLT3 Signaling » Induces cell division
RPS6KA1, RPS6KA3, RPS6KA2, RPS6KA6, RPS6KA4, RPS6KA5, RPS6KB1, RPS6KB2, RPS6KC1 (6195, 6197, 6196, 27330, 8986, 9252, 6198, 6199, 26750) » FLT3 Signaling » Induces cell division
ATM (472) » Gl-S Phase Transition » Induces cell cycle progression ATR (545) » G 1 -S Phase Transition » Induces cell cycle progression
CDC2 (983) » Gl-S Phase Transition » Induces cell cycle progression
CDK2 (1017) » Gl-S Phase Transition » Induces cell cycle progression
CDK4; CDK6 (1019; 1021) » Gl-S Phase Transition » Induces cell cycle progression
ATM (472) » G2-M Phase Transition » Induces cell cycle progression ATR (545) » G2-M Phase Transition » Induces cell cycle progression
CDC2 (983) » G2-M Phase Transition » Induces cell cycle progression
CHEKl (1111) » G2-M Phase Transition » Induces cell cycle progression
CHEK2 (11200) » G2-M Phase Transition » Induces cell cycle progression
AKTl (207) » IGFlR Signaling » Induces cell survival AKT2 (208) » IGFlR Signaling » Induces cell survival
AKT3 (10000) » IGFlR Signaling » Induces cell survival
ARAFl (369) » IGFlR Signaling » Induces cell survival
BRAF (673) » IGFlR Signaling » Induces cell survival
CHUK (1147) » IGFlR Signaling » Induces cell survival IGFRl (3480) » IGFlR Signaling » Induces cell survival
IKBKB (3551) » IGFlR Signaling » Induces cell survival
MAP2K1 (5604) » IGFlR Signaling » Induces cell survival
MAP2K2 (5605) » IGFlR Signaling » Induces cell survival
MAPKl (5594) » IGFlR Signaling » Induces cell survival MAPK3 (5595) » IGFlR Signaling » Induces cell survival
RAFl (5894) » IGFlR Signaling » Induces cell survival
JAKl, JAK2 (3716, 3717) » JAK/STAT Pathway » Induces cell division
JAK2 (3717) » JAK/STAT Pathway » Induces cell division
MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6 (5604, 5605, 5606, 6416, 5608) » JAK/STAT Pathway » Induces cell division
RAFl, BRAF (5894, 673) » JAK/STAT Pathway » Induces cell division
GCK (2645) » JNK Pathway » Induces cell migration
GCK (2645) » JNK Pathway » Induces tumorigenesis
MAP2K4 (6416) » JNK Pathway » Induces cell migration MAP2K4 (6416) » JNK Pathway » Induces tumorigenesis
MAP2K7 (5609) » JNK Pathway » Induces cell migration
MAP2K7 (5609) » JNK Pathway » Induces tumorigenesis
MAP3K1 (4214) » JNK Pathway » Induces cell migration
MAP3K1 (4214) » JNK Pathway » Induces tumorigenesis MAP3K10 (4294) » JNK Pathway » Induces cell migration
MAP3K10 (4294) » JNK Pathway » Induces tumorigenesis
MAP3K11 (4296) » JNK Pathway » Induces cell migration MAP3K11 (4296) » JNK Pathway » Induces tumorigenesis
MAP3K4 (4216) » JNK Pathway » Induces cell migration
MAP3K4 (4216) » JNK Pathway » Induces tumorigenesis
MAP3K5 (4217) » JNK Pathway » Induces cell migration MAP3K5 (4217) » JNK Pathway » Induces tumorigenesis
MAP3K7 (6885) » JNK Pathway » Induces cell migration
MAP3K7 (6885) » JNK Pathway » Induces tumorigenesis
MAP3K9 (4293) » JNK Pathway » Induces cell migration
MAP3K9 (4293) » JNK Pathway » Induces tumorigenesis MAP4K1 (11184) » JNK Pathway » Induces cell migration
MAP4K1 (11184) » JNK Pathway » Induces tumorigenesis
MAP4K3 (8491) » JNK Pathway » Induces cell migration
MAP4K3 (8491) » JNK Pathway » Induces tumorigenesis
MAP4K4 (9448) » JNK Pathway » Induces cell migration MAP4K4 (9448) » JNK Pathway » Induces tumorigenesis
MAPKlO (5602) » JNK Pathway » Induces cell migration
MAPKlO (5602) » JNK Pathway » Induces tumorigenesis
MAPK8 (5599) » JNK Pathway » Induces cell migration
MAPK8 (5599) » JNK Pathway » Induces tumorigenesis MAPK9 (5601) » JNK Pathway » Induces cell migration
MAPK9 (5601) » JNK Pathway » Induces tumorigenesis
P 13K (isoforms 5290, 5291, 5293, 5294) » JNK Pathway » Induces cell migration
P13K (isoforms 5290, 5291, 5293, 5294) » JNK Pathway » Induces tumorigenesis
PAKl (5058) » JNK Pathway » Induces cell migration PAKl (5058) » JNK Pathway » Induces tumorigenesis
PAK2 (5062) » JNK Pathway » Induces cell migration
PAK2 (5062) » JNK Pathway » Induces tumorigenesis
PAK3 (5063) » JNK Pathway » Induces cell migration
PAK3 (5063) » JNK Pathway » Induces tumorigenesis PAK4 (10298) » JNK Pathway » Induces cell migration
PAK4 (10298) » JNK Pathway » Induces tumorigenesis
PAK5/6 (56924) » JNK Pathway » Induces cell migration
PAK5/6 (56924) » JNK Pathway » Induces tumorigenesis
RAFl (5894) » JNK Pathway » Induces cell migration RAF 1 (5894) » JNK Pathway » Induces tumorigenesis
CDC2 (983) » Mitotic Roles of Polo-Like Kinase » Induces cell cycle progression
PLKl (5347) » Mitotic Roles of Polo-Like Kinase » Induces cell cycle progression
PLKl (5347) » Mitotic Roles of Polo-Like Kinase » Induces cell division
EGFR (1956) » Mucosal Healing through Trefoil Factors » Induces cell migration ERBB2 (2064) » Mucosal Healing through Trefoil Factors » Induces cell migration
MAPKl (5594) » Mucosal Healing through Trefoil Factors » Induces cell migration
MAPK12 (6300) » Mucosal Healing through Trefoil Factors » Induces cell migration
MAPK3 (5595) » Mucosal Healing through Trefoil Factors » Induces cell migration
MAPK4 (5596) » Mucosal Healing through Trefoil Factors » Induces cell migration ROCKl (6093) » Mucosal Healing through Trefoil Factors » Metastasis
ROCK2 (9475) » Mucosal Healing through Trefoil Factors » Metastasis
PRKARlA; PRKARlB; PRKAR2A; PRKAR2B; PRKACA; PRKACB; PRKACG (5573; 5575; 5576; 5577; 5566; 5567; 5568) » Nuclear Receptor Activation by Vitamin-A » Induces cell proliferation
CDK2 (1017) » p53 Signaling » Induces cell cycle progression CDK4 ( 1019) » p53 Signaling » Induces cell cycle progression
AKTl (207) » p70S6K Signaling » Induces cell growth
AKTl (207) » p70S6K Signaling » Induces cell motility AKTl (207) » p70S6K Signaling » Induces cell survival
FRAPl (2475) » p70S6K Signaling » Induces cell growth
FRAPl (2475) » p70S6K Signaling » Induces cell motility
FRAPl (2475) » p70S6K Signaling » Induces cell survival INSR (3643) » p70S6K Signaling » Induces cell growth
INSR (3643) » p70S6K Signaling » Induces cell motility
INSR (3643) » p70S6K Signaling » Induces cell survival
JAKl (3716) » p70S6K Signaling » Induces cell growth
JAKl (3716) » p70S6K Signaling » Induces cell motility JAKl (3716) » p70S6K Signaling » Induces cell survival
JAK2 (3717) » p70S6K Signaling » Induces cell growth
JAK2 (3717) » p70S6K Signaling » Induces cell motility
JAK2 (3717) » p70S6K Signaling » Induces cell survival
MAP2K1; MAP2K2; MAP2K3; MAP2K4; MAP2K5; MAP2K6 (5604; 5605; 5606; 6416; 5607; 5608) » p70S6K Signaling » Induces cell growth
MAP2K1; MAP2K2; MAP2K3; MAP2K4; MAP2K5; MAP2K6 (5604; 5605; 5606; 6416; 5607; 5608) » p70S6K Signaling » Induces cell motility
MAP2K1; MAP2K2; MAP2K3; MAP2K4; MAP2K5; MAP2K6 (5604; 5605; 5606; 6416; 5607; 5608) » p70S6K Signaling » Induces cell survival MAPKl; MAPK3; MAPK4; MAPK6; MAPK7; MAPK8; MAPK9; MAPKlO; MAPK14; MAPKl 1; MAPK12; MAPK13 (5594; 5595; 5596; 5597; 5598; 5599; 5601; 5602; 1432; 5600; 6300; 5603) » p70S6K Signaling » Induces cell growth
MAPKl; MAPK3; MAPK4; MAPK6; MAPK7; MAPK8; MAPK9; MAPKlO; MAPK14; MAPKl 1; MAPK12; MAPK13 (5594; 5595; 5596; 5597; 5598; 5599; 5601; 5602; 1432; 5600; 6300; 5603) » p70S6K Signaling » Induces cell survival
PDKl (5163) » p70S6K Signaling » Induces cell growth
PDKl (5163) » p70S6K Signaling » Induces cell motility
PDKl (5163) » p70S6K Signaling » Induces cell survival
PRKCD (5580) » p70S6K Signaling » Induces cell growth PRKCD (5580) » p70S6K Signaling » Induces cell motility
PRKCD (5580) » p70S6K Signaling » Induces cell survival
PRKCZ (5590) » p70S6K Signaling » Induces cell growth
PRKCZ (5590) » p70S6K Signaling » Induces cell motility
PRKCZ (5590) » p70S6K Signaling » Induces cell survival RAFl (5894) » p70S6K Signaling » Induces cell growth
RAFl (5894) » p70S6K Signaling » Induces cell motility
RAFl (5894) » p70S6K Signaling » Induces cell survival
RPS6KB1 (6198) » p70S6K Signaling » Induces cell growth
RPS6KB1 (6198) » p70S6K Signaling » Induces cell motility RPS6KB 1 (6198) » p70S6K Signaling » Induces cell survival
IKBKE (9641) » PAK pathway » Induces cell survival
IKBKG (8517) » PAK pathway » Induces cell survival
PAKl (5058) » PAK pathway » Induces cell survival
PAK2 (5062) » PAK pathway » Induces cell survival PAK3 (5063) » PAK pathway » Induces cell survival
PAK4 (10298) » PAK pathway » Induces cell survival
PAK6 (56924) » PAK pathway » Induces cell survival
PAK6; PAK7 (56924; 57144) » PAK pathway » Induces cell survival
PDGFRA (5156) » PAK pathway » Induces cell survival PDGFRB (5159) » PAK pathway » Induces cell survival
AKTl (207) » PI3K Signaling » Induces angiogenesis
AKTl (207) » PI3K Signaling » Induces cell growth AKTl (207) » PDK Signaling » Induces cell survival AKT2 (208) » PI3K Signaling » Induces angiogenesis AKT2 (208) » PDK Signaling » Induces cell cycle progression AKT2 (208) » PDK Signaling » Induces cell growth AKT3 (10000) » PDK Signaling » Induces angiogenesis
AKT3 (10000) » PDK Signaling » Induces cell cycle progression AKT3 (10000) » PDK Signaling » Induces cell growth BLK (640) » PDK Signaling » Induces cell cycle progression BLK (640) » PDK Signaling » Induces cell proliferation EGFR (1956) » PDK Signaling » Induces cell cycle progression EGFR (1956) » PDK Signaling » Induces cell proliferation ERBB2 (2064) » PDK Signaling » Induces cell cycle progression ERBB2 (2064) » PDK Signaling » Induces cell proliferation ERBB4 (2066) » PDK Signaling » Induces cell cycle progression ERBB4 (2066) » PDK Signaling » Induces cell proliferation
FGFRl (2260) » PDK Signaling » Induces cell cycle progression FGFRl (2260) » PDK Signaling » Induces cell proliferation FGFR2 (2263) » PDK Signaling » Induces cell cycle progression FGFR2 (2263) » PDK Signaling » Induces cell proliferation FGFR3 (2261) » PDK Signaling » Induces cell cycle progression FGFR3 (2261) » PDK Signaling » Induces cell proliferation FLTl (2321) » PDK Signaling » Induces cell cycle progression FLTl (2321) » PDK Signaling » Induces cell proliferation FLT3 (2322) » PDK Signaling » Induces cell cycle progression FLT3 (2322) » PDK Signaling » Induces cell proliferation
FLT4 (2324) » PDK Signaling » Induces cell cycle progression FLT4 (2324) » PDK Signaling » Induces cell proliferation FRAPl (2475) » PDK Signaling » Induces cell growth FYN (2534) » PDK Signaling » Induces cell cycle progression FYN (2534) » PDK Signaling » Induces cell survival
GLGl (2734) » PDK Signaling » Induces cell cycle progression GLGl (2734) » PDK Signaling » Induces cell proliferation GSK3A (2931) » PDK Signaling » Induces cell cycle progression GSK3B (2932) » PDK Signaling » Induces cell cycle progression HBEGF (1839) » PDK Signaling » Induces cell cycle progression HBEGF (1839) » PDK Signaling » Induces cell proliferation IGF2R (3482) » PDK Signaling » Induces cell cycle progression IGF2R (3482) » PDK Signaling » Induces cell proliferation IGFRl (3480) » PDK Signaling » Induces cell cycle progression IGFRl (3480) » PDK Signaling » Induces cell proliferation
IL2RA (3559) » PDK Signaling » Induces cell cycle progression IL2RA (3559) » PDK Signaling » Induces cell proliferation JAKl (3716) » PDK Signaling » Induces cell cycle progression JAKl (3716) » PDK Signaling » Induces cell proliferation JAK2 (3717) » PDK Signaling » Induces cell cycle progression JAK2 (3717) » PDK Signaling » Induces cell proliferation JAK3 (3718) » PDK Signaling » Induces cell cycle progression JAK3 (3718) » PDK Signaling » Induces cell proliferation KDR (3791) » PDK Signaling » Induces cell cycle progression KDR (3791) » PDK Signaling » Induces cell proliferation
KIT (3815) » PDK Signaling » Induces cell cycle progression KIT (3815) » PDK Signaling » Induces cell proliferation LCK (3932) » PI3K Signaling » Induces cell cycle progression LCK (3932) » PI3K Signaling » Induces cell survival MAP2K1 (5604) » PI3K Signaling » Induces cell cycle progression MAP2K2 (5605) » PI3K Signaling » Induces cell cycle progression MAP2K3 (5606) » PI3K Signaling » Induces cell cycle progression MAP2K4 (6416) » PI3K Signaling » Induces cell cycle progression MAP2K5 (5607) » PI3K Signaling » Induces cell cycle progression MAP2K6 (5608) » PBK Signaling » Induces cell cycle progression MAP2K7 (5609) » PBK Signaling » Induces cell cycle progression MAP3K1 (4214) » PBK Signaling » Induces cell cycle progression MAP3K2 (10746) » PBK Signaling » Induces cell cycle progression MAP3K3 (4215) » PBK Signaling » Induces cell cycle progression MAP3K4 (4216) » PBK Signaling » Induces cell cycle progression MAP3K5 (4217) » PBK Signaling » Induces cell cycle progression MAP3K6 (9064) » PBK Signaling » Induces cell cycle progression MAPKl (5594) » PBK Signaling » Induces cell cycle progression MAPKlO (5602) » PBK Signaling » Induces cell proliferation MAPKIl (5600) » PBK Signaling » Induces cell proliferation MAPK12 (6300) » PBK Signaling » Induces cell cycle progression MAPK12 (6300) » PBK Signaling » Induces cell proliferation MAPKl 3 (5603) » PBK Signaling » Induces cell proliferation MAPK14 (1432) » PBK Signaling » Induces cell proliferation MAPK3 (5595) » PBK Signaling » Induces cell cycle progression MAPK4 (5596) » PBK Signaling » Induces cell cycle progression MAPK7 (5598) » PBK Signaling » Induces cell cycle progression MAPK9 (5601) » PBK Signaling » Induces cell proliferation MERTK (10461) » PBK Signaling » Induces cell cycle progression MERTK (10461) » PBK Signaling » Induces cell proliferation MET (4233) » PBK Signaling » Induces cell cycle progression MET (4233) » PBK Signaling » Induces cell proliferation
NGFR (4804) » PBK Signaling » Induces cell cycle progression NGFR (4804) » PBK Signaling » Induces cell proliferation NRPl (8829) » PBK Signaling » Induces cell cycle progression NRPl (8829) » PBK Signaling » Induces cell proliferation NRP2 (8828) » PBK Signaling » Induces cell cycle progression NRP2 (8828) » PBK Signaling » Induces cell proliferation NTRKl (4914) » PBK Signaling » Induces cell cycle progression NTRKl (4914) » PBK Signaling » Induces cell proliferation NTRK2 (4915) » PBK Signaling » Induces cell cycle progression NTRK2 (4915) » PBK Signaling » Induces cell proliferation
NTRK3 (4916) » PBK Signaling » Induces cell cycle progression NTRK3 (4916) » PBK Signaling » Induces cell proliferation OGFR (11054) » PBK Signaling » Induces cell cycle progression OGFR (11054) » PBK Signaling » Induces cell proliferation PAKl (5058) » PBK Signaling » Induces cell proliferation PAK2 (5062) » PBK Signaling » Induces cell proliferation PAK3 (5063) » PBK Signaling » Induces cell proliferation PAK4 (10298) » PBK Signaling » Induces cell proliferation PAK6 (56924) » PBK Signaling » Induces cell proliferation PAK6; PAK7 (56924; 57144) » PBK Signaling » Induces cell proliferation PDGFRA (5156) » PBK Signaling » Induces cell cycle progression PDGFRA (5156) » PBK Signaling » Induces cell proliferation PDGFRB (5159) » PBK Signaling » Induces cell cycle progression PDGFRB (5159) » PDK Signaling » Induces cell proliferation PRKCA (5578) » PBK Signaling » Induces cell growth PRKCA (5578) » PDK Signaling » Induces cell proliferation PRKCBl (5579) » PBK Signaling » Induces cell growth
PRKCBl (5579) » PBK Signaling » Induces cell proliferation PRKCD (5580) » PBK Signaling » Induces cell growth PRKCD (5580) » PDK Signaling » Induces cell proliferation PRKCE (5581) » PBK Signaling » Induces cell growth PRKCE (5581) » PBK Signaling » Induces cell proliferation PRKCG (5582) » PBK Signaling » Induces cell growth PRKCG (5582) » PBK Signaling » Induces cell proliferation PRKCH (5583) » PBK Signaling » Induces cell growth PRKCH (5583) » PBK Signaling » Induces cell proliferation PRKCI (5584) » PBK Signaling » Induces cell growth
PRKCI (5584) » PBK Signaling » Induces cell proliferation PRKCQ (5588) » PBK Signaling » Induces cell growth PRKCQ (5588) » PBK Signaling » Induces cell proliferation PRKCZ (5590) » PBK Signaling » Induces cell growth PRKCZ (5590) » PBK Signaling » Induces cell proliferation PRKDl (5587) » PBK Signaling » Induces cell growth PRKDl (5587) » PBK Signaling » Induces cell proliferation PRKD3 (23683) » PBK Signaling » Induces cell growth PRKD3 (23683 » PBK Signaling » Induces cell proliferation PTK2 (5747) » PDK Signaling » Induces cell cycle progression PTK2 (5747) » PDK Signaling » Metastasis PTK2B (2185) » PDK Signaling » Induces cell cycle progression PTK2B (2185) » PBK Signaling » Metastasis RAFl (5894) » PBK Signaling » Induces cell cycle progression RAFl (5894) » PBK Signaling » Induces cell proliferation SRC (6714) » PBK Signaling » Induces cell cycle progression SRC (6714) » PBK Signaling » Induces cell proliferation SYK (6850) » PBK Signaling » Induces cell cycle progression SYK (6850) » PBK Signaling » Induces cell survival TGFBRl (7046) » PBK Signaling » Induces cell cycle progression TGFBRl (7046) » PBK Signaling » Induces cell proliferation TGFBR3 (7049) » PBK Signaling » Induces cell cycle progression TGFBR3 (7049) » PBK Signaling » Induces cell proliferation ZAP70 (7535) » PBK Signaling » Induces cell cycle progression ZAP70 (7535) » PDK Signaling » Induces cell proliferation
MAP2K1 (5604) » PDK Signaling in B-Lymphocyte » Induces cell growth MAP2K2 (5605) » PDK Signaling in B-Lymphocyte » Induces cell growth MAPKl (5594) » PDK Signaling in B-Lymphocyte » Induces cell growth MAPKlO (5602) » PDK Signaling in B-Lymphocyte » Induces cell growth MAPKl 1 (5600) » PBK Signaling in B-Lymphocyte » Induces cell growth MAPK12 (6300) » PBK Signaling in B-Lymphocyte » Induces cell growth MAPK 13 (5603) » PBK Signaling in B-Lymphocyte » Induces cell growth MAPK14 (1432) » PBK Signaling in B-Lymphocyte » Induces cell growth MAPK3 (5595) » PBK Signaling in B-Lymphocyte » Induces cell growth MAPK4 (5596) » PBK Signaling in B-Lymphocyte » Induces cell growth MAPK6 (5597) » PDK Signaling in B-Lymphocyte » Induces cell growth MAPK7 (5598) » PDK Signaling in B-Lymphocyte » Induces cell growth MAPK8 (5599) » PDK Signaling in B-Lymphocyte » Induces cell growth
MAPK9 (5601) » PDK Signaling in B-Lymphocyte » Induces cell growth
PK.3CA (5290) » PDK Signaling in B-Lymphocyte » Induces cell growth
PIK3CB (5291) » PDK Signaling in B-Lymphocyte » Induces cell growth PIK3CG (5294) » PDK Signaling in B-Lymphocyte » Induces cell growth
PRKCI (5584) » PDK Signaling in B-Lymphocyte » Induces cell growth
PRKCZ (5590) » PDK Signaling in B-Lymphocyte » Induces cell growth
RAFl (5894) » PDK Signaling in B-Lymphocyte » Induces cell growth
AKTl; AKT2; AKT3 (207; 208; 10000) » PTEN Pathway » Induces cell survival MAP2K1; MAP2K2 (5604; 5605) » PTEN Pathway » Induces cell survival
MAPK3; MAPKl (5595; 5594) » PTEN Pathway » Induces cell survival
PDKl (5163) » PTEN Pathway » Induces cell survival
PRKCA; PRKCBl; PRKCD; PRKCE; PRKCH; PRKCG;PRKD3; PRKDl; PRKCQ; PRKCI; PRKCZ(5578;
5579; 5580; 5581; 5583; 5582; 23683; 5587; 5588; 5584; 5590) » PTEN Pathway » Induces cell survival RAFl ; ARAF; BRAF (5894; 369; 673) » PTEN Pathway » Induces cell survival
AKTl (207 » Relaxin Pathway » Induces angiogenesis
PRKACA, PKAC-beta, gamma, (5566) » Relaxin Pathway » Induces angiogenesis
AKTl (207 » S-IP Stimulated Signaling » Inhibits apoptosis
MAPKl [or ERK2] (5594) » S-IP Stimulated Signaling » Inhibits apoptosis MAPK12 [or ERK)) (6300) » S-IP Stimulated Signaling » Inhibits apoptosis
MAPK3 [or ERKl] (5595) » S-IP Stimulated Signaling » Inhibits apoptosis
MAPK6 [or ERK3] (5597) » S-IP Stimulated Signaling » Inhibits apoptosis
MAPK7 [or ERK5] (5598) » S-IP Stimulated Signaling » Inhibits apoptosis
PIK3CA (5290) » S-IP Stimulated Signaling » Inhibits apoptosis P1K3CB (5291) » S-IP Stimulated Signaling » Inhibits apoptosis
PIK3CD (5293) » S-IP Stimulated Signaling » Inhibits apoptosis
PIK3CG (5294) » S-IP Stimulated Signaling » Inhibits apoptosis
PTK2 (5747) » S-IP Stimulated Signaling » Induces cell migration
PTK2B (2185) » S-IP Stimulated Signaling » Induces cell migration PTK2B (2185) » S-IP Stimulated Signaling » Inhibits apoptosis
MAP2K1, MAP2K2 (5604, 5605) » TGF-Beta Pathway » Induces angiogenesis
MAP2K1, MAP2K2 (5604, 5605) » TGF-Beta Pathway » Induces cell growth
MAP2K1, MAP2K2 (5604, 5605) » TGF-Beta Pathway » Induces cell mobility
MAP2K1, MAP2K2 (5604, 5605) » TGF-Beta Pathway » Induces tumorigenesis MAP2K4 (6416) » TGF-Beta Pathway » Induces angiogenesis
MAP2K4 (6416) » TGF-Beta Pathway » Induces cell growth
MAP2K4 (6416) » TGF-Beta Pathway » Induces cell mobility
MAP2K4 (6416) » TGF-Beta Pathway » Induces tumorigenesis
MAP3K7 (6885) » TGF-Beta Pathway » Induces angiogenesis MAP3K7 (6885) » TGF-Beta Pathway » Induces cell growth
MAP3K7 (6885) » TGF-Beta Pathway » Induces cell mobility
MAP3K7 (6885) » TGF-Beta Pathway » Induces tumorigenesis
MAPK3 (5595) » TGF-Beta Pathway » Induces angiogenesis
MAPK3 (5595) » TGF-Beta Pathway » Induces cell growth MAPK3 (5595) » TGF-Beta Pathway » Induces cell mobility
MAPK3 (5595) » TGF-Beta Pathway » Induces tumorigenesis
MAPK8 (5599) » TGF-Beta Pathway » Induces angiogenesis
MAPK8 (5599) » TGF-Beta Pathway » Induces cell growth
MAPK8 (5599) » TGF-Beta Pathway » Induces cell mobility MAPK8 (5599) » TGF-Beta Pathway » Induces tumorigenesis πCBKB (3553) » Thrombin Signaling through PARs » Induces cell division
IKBKB (3552) » Thrombin Signaling through PARs » Induces cell growth MAP2K2 (5605) » Thrombin Signaling through PARs » Induces cell growth
MAP2K3 (5606) » Thrombin Signaling through PARs » Induces cell division
PRKCD (5582) » Thrombin Signaling through PARs » Induces cell division
PRKCD (5581) » Thrombin Signaling through PARs » Induces cell growth PRKCZ (5592) » Thrombin Signaling through PARs » Induces cell division
PRKCZ (5591) » Thrombin Signaling through PARs » Induces cell growth
RAFl (5896) » Thrombin Signaling through PARs » Induces cell division
RAFl (5895) » Thrombin Signaling through PARs » Induces cell growth
RPS6KB1 (6198) » Thrombin Signaling through PARs » Induces cell division RPS6KB 1 (6198) » Thrombin Signaling through PARs » Induces cell growth
CHUK; DCBKB; IKBKE; IKBKG (1147; 3551; 9641; 8517) » TNF Signaling » Induces cell survival
MAP2K4 (6416) » TNF Signaling » Induces cell survival
MAP3K1; MAP3K2; MAP3K3; MAP3K4; MAP3K5 (4214; 10746; 4215; 4216; 4217) » TNF Signaling »
Induces cell survival MAP3K7 (6885) » TNF Signaling » Induces cell survival
MAPK14; MAPKl 1; MAPK12; MAPK13 (1432; 5600; 6300; 5603) » TNF Signaling » Induces cell survival
MAPK3; MAPKl; MAPK4; MAPK6; MAPK12 (5595; 5594; 5596; 5597; 6300) » TNF Signaling » Induces cell survival
MAPK8 (5599) » TNF Signaling » Induces cell survival CERK (64781) » TNF-Induced Apoptosis Implicating Sphingolipids » Induces proliferation
MAP2K1; MAP2K2; MAP2K3; MAP2K4; MAP2K5; MAP2K6 (5604; 5605; 5606; 6416; 5607; 5608) » TNF- Induced Apoptosis Implicating Sphingolipids » Induces proliferation
MAPK3; MAPKl; MAPK4; MAPK6; MAPK12 (5595; 5594; 5596; 5597; 6300) » TNF-Induced Apoptosis
Implicating Sphingolipids » Induces proliferation RAFl (5894) » TNF-Induced Apoptosis Implicating Sphingolipids » Induces proliferation
CHUK; DCBKB; DCBKE; DCBKG (1147; 3551; 9641; 8517) » TNFRl Pathway » Induces cell survival
MAP2K4 (6416) » TNFRl Pathway » Induces cell survival
MAP3K1 (5595) » TNFRl Pathway » Induces cell survival
MAP3K7 (6885) » TNFRl Pathway » Induces cell survival MAPK8 (5599) » TNFRl Pathway » Induces cell survival
PAKl (5058) » TNFRl Pathway » Induces cell survival
PAK2 (5062) » TNFRl Pathway » Induces cell survival
CHUK; DCBKB; DCBKE; DCBKG (1147; 3551; 9641; 8517) » TNFR2 Pathway » Induces cell survival
MAPK8; MAPK9; MAPKlO (5599; 5601; 5602) » TNFR2 Pathway » Induces cell survival CHUK; DCBKB; DCBKE; DCBKG (1147; 3551; 9641; 8517) » Toll-Like Receptors Pathway » Induces cell survival
AKTl (207) » TRAF Pathway » Induces cell survival
AKT2 (208) » TRAF Pathway » Induces cell survival
AKT3 (10000) » TRAF Pathway » Induces cell survival DlAKl (3654) » TRAF Pathway » Induces cell survival
DIAK2 (3656) » TRAF Pathway » Induces cell survival
DIAK3 (11213) » TRAF Pathway » Induces cell survival
DIAK4 (51135) » TRAF Pathway » Induces cell survival
MAP3K5 (4217) » TRAF Pathway » Induces cell survival PDC3CA (5290) » TRAF Pathway » Induces cell survival
PDC3CB (5291) » TRAF Pathway » Induces cell survival
PDC3CD (5293) » TRAF Pathway » Induces cell survival
PDC3CG (5294) » TRAF Pathway » Induces cell survival
SRC (6714) » TRAF Pathway » Induces cell survival CHUK (1147) » TRAIL Pathway » Induces cell survival
DCBKB (3551) » TRAIL Pathway » Induces cell survival
DCBKE (9641) » TRAIL Pathway » Induces cell survival CHUK (1147) » TWEAK Pathway » Induces cell survival CHUK (1147) » TWEAK Pathway » Inhibits apoptosis IKBKB (3551) » TWEAK Pathway » Induces cell survival πCBKB (3551) » TWEAK Pathway » Inhibits apoptosis IKBKE (9641) » TWEAK Pathway » Induces cell survival IKBKE (9641) » TWEAK Pathway » Inhibits apoptosis MAP3K14 (9020) » TWEAK Pathway » Induces cell survival MAP3K14 (9020) » TWEAK Pathway » Inhibits apoptosis ATM (472) » UVA-Induced MAPK Signaling » Induces cell proliferation ATM (472) » UVA-Induced MAPK Signaling » Induces tumorigenesis
EGFR (1956) » UVA-Induced MAPK Signaling » Induces cell proliferation
EGFR (1956) » UVA-Induced MAPK Signaling » Induces proliferation
EGFR (1956) » UVA-Induced MAPK Signaling » Inhibits apoptosis
MAPKl [or ERK2] (5594) » UVA-Induced MAPK Signaling » Induces proliferation MAPKl [or ERK2] (5594) » UVA-Induced MAPK Signaling » Inhibits apoptosis MAPKlO (5602) » UVA-Induced MAPK Signaling » Induces cell proliferation MAPKlO (5602) » UVA-Induced MAPK Signaling » Induces tumorigenesis MAPKl 1 (5600) » UVA-Induced MAPK Signaling » Inhibits apoptosis MAPK12 (6300) » UVA-Induced MAPK Signaling » Inhibits apoptosis MAPK 13 (5603) » UVA-Induced MAPK Signaling » Inhibits apoptosis MAPK14 (1432) » UVA-Induced MAPK Signaling » Inhibits apoptosis MAPK3 [or ERKl] (5595) » UVA-Induced MAPK Signaling » Induces proliferation MAPK3 [or ERKl] (5595) » UVA-Induced MAPK Signaling » Inhibits apoptosis MAPK8 (5599) » UVA-Induced MAPK Signaling » Induces cell proliferation MAPK8 (5599) » UVA-Induced MAPK Signaling » Induces tumorigenesis MAPK9 (5601) » UVA-Induced MAPK Signaling » Induces cell proliferation MAPK9 (5601) » UVA-Induced MAPK Signaling » Induces tumorigenesis PIK3CA (5290) » UVA-Induced MAPK Signaling » Induces proliferation PIK3CB (5291) » UVA-Induced MAPK Signaling » Induces proliferation PIK3CD (5293) » UVA-Induced MAPK Signaling » Induces proliferation PIK3CG (5294) » UVA-Induced MAPK Signaling » Induces proliferation PRKCA (5578) » UVA-Induced MAPK Signaling » Induces proliferation PRKCA (5578) » UVA-Induced MAPK Signaling » Inhibits apoptosis RPS6KA1 (6195) » UVA-Induced MAPK Signaling » Induces proliferation RPS6KA2 (6196) » UVA-Induced MAPK Signaling » Induces proliferation RPS6KA3 (6197) » UVA-Induced MAPK Signaling » Induces proliferation RPS6KA4 (8986) » UVA-Induced MAPK Signaling » Induces proliferation RPS6KA5 (9252) » UVA-Induced MAPK Signaling » Induces proliferation RPS6KA6 (27330) » UVA-Induced MAPK Signaling » Induces proliferation MAP2K1 (5604) » UVB-Induced MAPK Signaling » Induces cell proliferation MAP2K1 (5604) » UVB-Induced MAPK Signaling » Induces tumorigenesis MAPKl [or ERK2] (5594) » UVB-Induced MAPK Signaling » Induces cell proliferation MAPKl [or ERK2) (5594) » UVB-Induced MAPK Signaling » Induces tumorigenesis MAPKlO (5602) » UVB-Induced MAPK Signaling » Induces cell proliferation MAPKl 0 (5602) » UVB-Induced MAPK Signaling » Induces tumorigenesis
MAPK3 [orERKl] (5595) » UVB-Induced MAPK Signaling » Induces cell proliferation MAPK3 [or ERKl) (5595) » UVB-Induced MAPK Signaling » Induces tumorigenesis MAPK8 (5599) » UVB-Induced MAPK Signaling » Induces cell proliferation MAPK8 (5599) » UVB-Induced MAPK Signaling » Induces tumorigenesis MAPK9 (5601) » UVB-Induced MAPK Signaling » Induces cell proliferation MAPK9 (5601) » UVB-Induced MAPK Signaling » Induces tumorigenesis PIK3CA (5290) » UVB-Induced MAPK Signaling » Induces cell proliferation PDC3CA (5290) » UVB-Induced MAPK Signaling » Induces tumorigenesis PIK3CB (5291) » UVB-Induced MAPK Signaling » Induces cell proliferation PIK3CB (5291) » UVB-Induced MAPK Signaling » Induces tumorigenesis PIK3CD (5293) » UVB-Induced MAPK Signaling » Induces cell proliferation PIK3CD (5293) » UVB-Induced MAPK Signaling » Induces tumorigenesis PDC3CG (5294) » UVB-Induced MAPK Signaling » Induces cell proliferation PIK3CG (5294) » UVB-Induced MAPK Signaling » Induces tumorigenesis PRKCA (5578) » UVB-Induced MAPK Signaling » Induces cell proliferation PRKCA (5578) » UVB-Induced MAPK Signaling » Induces tumorigenesis PRKCB 1 (5579) » UVB-Induced MAPK Signaling » Induces cell proliferation PRKCBl (5579) » UVB-Induced MAPK Signaling » Induces tumorigenesis PRKCD (5580) » UVB-Induced MAPK Signaling » Induces cell proliferation PRKCD (5580) » UVB-Induced MAPK Signaling » Induces tumorigenesis PRKCE (5581) » UVB-Induced MAPK Signaling » Induces cell proliferation PRKCE (5581) » UVB-Induced MAPK Signaling » Induces tumorigenesis PRKCG (5582) » UVB-Induced MAPK Signaling » Induces cell proliferation PRKCG (5582) » UVB-Induced MAPK Signaling » Induces tumorigenesis PRKCH (5583) » UVB-Induced MAPK Signaling » Induces cell proliferation PRKCH (5583) » UVB-Induced MAPK Signaling » Induces tumorigenesis PRKCI (5584) » UVB-Induced MAPK Signaling » Induces cell proliferation PRKCI (5584) » UVB-Induced MAPK Signaling » Induces tumorigenesis PRKCQ (5588) » UVB-Induced MAPK Signaling » Induces cell proliferation PRKCQ (5588) » UVB-Induced MAPK Signaling » Induces tumorigenesis PRKCZ (5590) » UVB-Induced MAPK Signaling » Induces cell proliferation PRKCZ (5590) » UVB-Induced MAPK Signaling » Induces tumorigenesis PRKDl (5587) » UVB-Induced MAPK Signaling » Induces cell proliferation PRKDl (5587) » UVB-Induced MAPK Signaling » Induces tumorigenesis PRKD3 (23683) » UVB-Induced MAPK Signaling » Induces cell proliferation PRKD3 (23683) » UVB-Induced MAPK Signaling » Induces tumorigenesis ARAF (369) » UVC-Induced MAPK Signaling » Induces cell proliferation ARAF (369) » UVC-Induced MAPK Signaling » Induces tumorigenesis BRAF (673) » UVC-Induced MAPK Signaling » Induces cell proliferation BRAF (673) » UVC-Induced MAPK Signaling » Induces tumorigenesis MAP2K1 (5604) » UVC-Induced MAPK Signaling » Induces cell proliferation MAP2K1 (5604) » UVC-Induced MAPK Signaling » Induces tumorigenesis MAP2K2 (5605) » UVC-Induced MAPK Signaling » Induces cell proliferation MAP2K2 (5605) » UVC-Induced MAPK Signaling » Induces tumorigenesis MAPKl [or ERK2] (5594) » UVC-Induced MAPK Signaling » Induces cell proliferation MAPKl [or ERK2] (5594) » UVC-Induced MAPK Signaling » Induces tumorigenesis MAPKlO (5602) » UVC-Induced MAPK Signaling » Induces cell proliferation MAPKlO (5602) » UVC-Induced MAPK Signaling » Induces tumorigenesis MAPK3 [or ERKl] (5595) » UVC-Induced MAPK Signaling » Induces cell proliferation MAPK3 [or ERKl] (5595) » UVC-Induced MAPK Signaling » Induces tumorigenesis MAPK8 (5599) » UVC-Induced MAPK Signaling » Induces cell proliferation MAPK8 (5599) » UVC-Induced MAPK Signaling » Induces tumorigenesis MAPK9 (5601) » UVC-Induced MAPK Signaling » Induces cell proliferation MAPK9 (5601) » UVC-Induced MAPK Signaling » Induces tumorigenesis PRKCA (5578) » UVC-Induced MAPK Signaling » Induces cell proliferation PRKCA (5578) » UVC-Induced MAPK Signaling » Induces tumorigenesis PRKCBl (5579) » UVC-Induced MAPK Signaling » Induces cell proliferation PRKCBl (5579) » UVC-Induced MAPK Signaling » Induces tumorigenesis PRKCD (5580) » UVC-Induced MAPK Signaling » Induces cell proliferation PRKCD (5580) » UVC-Induced MAPK Signaling » Induces tumorigenesis
PRKCE (5581) » UVC-Induced MAPK Signaling » Induces cell proliferation
PRKCE (5581) » UVC-Induced MAPK Signaling » Induces tumorigenesis
PRKCG (5582) » UVC-Induced MAPK Signaling » Induces cell proliferation PRKCG (5582) » UVC-Induced MAPK Signaling » Induces tumorigenesis
PRKCH (5583) » UVC-Induced MAPK Signaling » Induces cell proliferation
PRKCH (5583) » UVC-Induced MAPK Signaling » Induces tumorigenesis
PRKCI (5584) » UVC-Induced MAPK Signaling » Induces cell proliferation
PRKCI (5584) » UVC-Induced MAPK Signaling » Induces tumorigenesis PRKCQ (5588) » UVC-Induced MAPK Signaling » Induces cell proliferation
PRKCQ (5588) » UVC-Induced MAPK Signaling » Induces tumorigenesis
PRKCZ (5590) » UVC-Induced MAPK Signaling » Induces cell proliferation
PRKCZ (5590) » UVC-Induced MAPK Signaling » Induces tumorigenesis
PRKDl (5587) » UVC-Induced MAPK Signaling » Induces cell proliferation PRKDl (5587) » UVC-Induced MAPK Signaling » Induces tumorigenesis
PRKD3 (23683) » UVC-Induced MAPK Signaling » Induces cell proliferation
PRKD3 (23683) » UVC-Induced MAPK Signaling » Induces tumorigenesis
RAFl (5894) » UVC-Induced MAPK Signaling » Induces cell proliferation
RAFl (5894) » UVC-Induced MAPK Signaling » Induces tumorigenesis SRC (6714) » UVC-Induced MAPK Signaling » Induces cell proliferation
SRC (6714) » UVC-Induced MAPK Signaling » Induces tumorigenesis
MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6 (5604, 5605, 5606, 6416, 5608) » VEGF and S-IP Signaling » Induces angiogenesis
MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6 (5604, 5605, 5606, 6416, 5608) » VEGF and S-IP Signaling » Induces cell proliferation
PRKCA, PRKCBl, PRKCD, PRKCE, PRKCH, PRKCG, PRKCI, PRKDl, PRKD3, PRKCQ, PRKCZ (5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 23683, 5588, 5590) » VEGF and S-IP Signaling » Induces angiogenesis
PRKCA, PRKCBl, PRKCD, PRKCE, PRKCH, PRKCG, PRKCI, PRKDl, PRKD3, PRKCQ, PRKCZ (5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 23683, 5588, 5590) » VEGF and S-IP Signaling » Induces cell proliferation
RAFl, BRAF (5894, 673) » VEGF and S-IP Signaling » Induces angiogenesis
RAFl, BRAF (5894, 673) » VEGF and S-IP Signaling » Induces cell proliferation
SRC (6714) » VEGF and S-IP Signaling » Induces angiogenesis SRC (6714) » VEGF and S-IP Signaling » Induces cell migration
SRC (6714) » VEGF and S-IP Signaling » Induces cell proliferation
SRC (6714) » VEGF and S-IP Signaling » Induces cell survival
AKTl (207) » VEGF Pathway » Induces angiogenesis
AKTl (207) » VEGF Pathway » Induces cell survival MAP2K1 , MAP2K2 (5604, 5605) » VEGF Pathway » Induces angiogenesis
MAP2K1, MAP2K2 (5604, 5605) » VEGF Pathway » Induces cell proliferation
MAP2K3, MAP2K6 (5595, 5608) » VEGF Pathway » Induces angiogenesis
MAPKAPK2, MAPKAPK3 (9261, 7867) » VEGF Pathway » Induces angiogenesis
PRKCA, PRKCBl, PRKCD, PRKCE, PRKCH, PRKCG, PRKCI, PRKDl, PRKD3, PRKCQ, PRKCZ (5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 23683, 5588, 5590) » VEGF Pathway » Induces angiogenesis
PRKCA, PRKCBl, PRKCD, PRKCE, PRKCH, PRKCG, PRKCI, PRKDl, PRKD3, PRKCQ, PRKCZ (5578, 5579, 5580, 5581, 5583, 5582, 5584, 5587, 23683, 5588, 5590) » VEGF Pathway » Induces cell proliferation
PTK2 (5747) » VEGF Pathway » Induces angiogenesis PTK2 (5747) » VEGF Pathway » Induces cell migration
RAFl (5894) » VEGF Pathway » Induces angiogenesis
RAFl (5894) » VEGF Pathway » Induces cell proliferation [00112] Table 2 lists profiles relevant to diseases including cancer. "Profile" refers to useful combinations of kinases relevant to diseases and particular combinations relevant to therapeutic treatments. "Kinase" refers to official gene symbol (according to Human Genome Organization, HUGO). "NCBI" refers to unique numeric identifier for the kinase as designated by NCBI. "Pathway" refers to specific biological pathway as it is commonly understood. Table 2: Profile=Kinases (NCBI):
1 = JAKl (3716), KDR (3791), KIT (3815), PDGFRB (5159)
2 = EGFR (1956), HER2 (2064), SRC (6714)
3 = ABL (25), KIT (3815), LCK (3932), PDGFRB (5159), SRC (6714)
4 = BRAF (673), KDR (3791), PDGFRB (5159) 5 = CDC2 (983), CDK2 (1017), CDK4 (1019)
6 = AKTl (207), BRAF (673), MAP3K1 (4214)
7 = FLTl (2321), FLT4 (2324), KDR (3791), PDGFRB (5159), RET (5979)
8 = FRAPl (2475), KDR (3791), PDGFRB (5159), PIK3CG (5294)
9 = EGFR (1956), FRAPl (2475), KDR (3791) 10 = AURKA (6790), KDR (3791), PDGFRB (5159)
11 = PLKl (5347), PLK2 (10769), PLK3 (1263), PLK4 (10733)
12 = AKTl (207), PDBKl (5170), PIK3CG (5294)
13 = JAKl (3716), JAK3 (3718), KDR (3791), PDGFRB (5159)
14 = KDR (3791), PDGFRB (5159) 15 = KDR (3791), LCK (3932), SRC (6714), TEK (7010)
16 = EGFR (1956), FYN (2534), HER2 (2064)
17 = ABL (25), EGFR (1956), HER2 (2064), LCK (3932), PDGFRB (5159), SRC (6714)
18 = EGFR (1956), HER2 (2064), JAK3 (3718)
19 = AKTl (207), AKT2 (208), AKT3 (10000) 20 = AURKA (6790), CDC2 (983), CDK2 (1017), CDK5 (1020), GSK3B (2932)
21 = BRAF (673), MAPKlO (5602), MAPK8 (5599), MAPK9 (5595)
22 = ABL (25), KDR (3791), LCK (3932), SRC (6714)
23 = FGFRl (2263), FGFR2 (2263), KDR (3791), KIT (3815), PDGFRA (5156), PDGFRB (5159)
24 = FLTl (2321), FLT3 (2322), FLT4 (2324), KDR (3791), MAP3K10 (4294), MAP3K12 (7786), MAP3K9 (4293), PDGFRB (5159)
25 = CDC2 (983), CDK2 (1017), CDK4 (1019), EGFR (1956), HER2 (2064),
26 = ABL (25), LCK (3932), SRC (6714), YES (7525)
27 = ABL (25), HER2 (2064), IGFlR (3480), JAK3 (3718), LCK (3932), SRC (6714), ZAP70 (7535)
28 = EGFR (1956), FYN (2534), LCK (3932), SRC (6714), ZAP70 (7535) 29 = EGFR (1956), HER2 (2064), KDR (3791), PDGFRB (5159), SRC (6714)
30 = CHEK2 (11200), CSNKlD (1453), MAP2K1 (5604), PRKCA (5578)
31 = BTK (695), KDR (3791), LYN (4067), PDGFRB (5159), SRC (6714), ZAP70 (7535)
32 = FRAPl (2475), PK3CA (5290), PIK3CB (5291), PDC3CD (5293), PDC3CG (5294), PIK3CG (5294)
33 = ABL (25), EGFR (1956), FGFRl (2260), FLT3 (2322), HER2 (2064), KIT (3815), PDGFRB (5159), PDGFRB (5159), SRC (6714)
34 = AURKA (6790), MAP2K1 (5604), MAP2K2 (5605), MAP3K1 (4214), MAPKl (5594)
35 = AURKA (6790), MAPKl (5594), MAPKl 1 (5600), MAPK14 (1432), MAPK8 (5599), MAPK9 (5595),
SRC (6714)
36 = ABL (25), EGFR (1956), HER2 (2064), LCK (3932), MAPKl (5594), MAPK14 (1432) 37 = HGK (9448), MINK (50488), TNIK (23043)
38 = HGK (9448), PAK4 (10298), PAK5 (56924)
39 = STLK3 (27347), STLK6 (55437)
40 = BRAF (673), GSK3A (2931), GSK3B (2932), MAP2K1 (5604), MAP2K2 (5605), RAFl (5894)
41 = BRAF (673), EGFR (1956), HER2 (2064), KDR (3791) 42 = PAKl (5058), PAK2 (5062), PAK3 (5063), PAK4 (10298), PAK5 (56924), PIK3CG (5294), RAFl (5894) 43 = CDC2 (983), PLKl (5347), PLKl (5347)
44 = EGFR (1956), HER2 (2064), MAPKl (5594), MAPK12 (6300), MAPK3 (5595), MAPK4 (5596)
45 = IRAKI (3654), IRAK2 (3656), IRAK3 (11213), IRAK4 (51135), MAP3K5 (4217), PIK3CA (5290),
PDC3CB (5291), PIK3CD (5293), PIK3CG (5294) 46 = AKTl (207), MAP2K1 (5604), MAP2K2 (5605), MAP2K3 (5595), MAP2K6 (5608)
47 = PDC3CG (5294), RPS6KA1 (6195), RPS6KA2 (6196), RPS6KA3 (6197), RPS6KA4 (8986), RPS6KA5
(9252), RPS6KA6 (27330)
48 = NTRKl (4914), NTRK2 (4915), NTRK3 (4916)
49 = ATM (473), CHEKl (1111), CHEK2 (11200) 50 = FRAPl (2475), JAKl (3716), JAK2 (3717), JAK3 (3718)
[00113] The invention features a pharmaceutical composition comprising (i) a physiologically acceptable carrier, diluent, or excipient; and (ii) a compound as described herein. Typically, the receptor or cellular protein kinase whose catalytic activity is selectively modulated (to an appropriate amount, e.g., about 1.0, 1.3, 2, or 2.3 log units) by a compound of this invention at a pharmaceutically acceptable concentration. Preferably the target kinase to be selectively inhibited is selected from the group consisting of two or more (e.g., 3, 4, or more) among ABL,
AKTl, AURKA, BRAF, CDC2, EGFR, FRAPl, HER2, JAK3, KDR, KIT, LCK, MAP2K1, MAPKl, PDGFRB, PDC3CG, and SRC. While positive effect is relevant, specific absence of effect on one or more particular kinases may also be of interest. Thus, selected profiles may include inhibition of select subsets of specific kinases, e.g., at nanomolar range concentrations, while lack of inhibition of other select subsets of kinases at similar or higher concentration, e.g., tens, hundreds or thousands of times higher , e.g., sub or micromolar concentrations, or substantially different quantitative effects at similar concentrations.
[00114] A protein kinase natural binding partner can bind to a protein kinase's intracellular region with high affinity. High affinity represents an equilibrium binding constant on the order of 10E-6 M or less. In addition, a natural binding partner can also transiently interact with a protein kinase intracellular region and chemically modify it. Protein kinase natural binding partners are chosen from a group that includes, but is not limited to, SRC homology 2 (SH2) or 3 (SH3) domains, other phosphoryl tyrosine binding (PTB) domains, guanine nucleotide exchange factors, protein phosphatases, and other protein kinases. Methods of determining changes in interactions between protein kinases and their natural binding partners are readily available in the art. [00115] The compounds of the invention preferably modulate the activity of the protein kinase in vitro. These compounds preferably show positive results in one or more in vitro assays for an activity described.
[00116] The invention also features a method of identifying compounds that modulate the function of protein kinase, comprising the following steps: (a) contacting cells expressing the protein kinase with the compound; and (b) monitoring an effect upon the cells. The effect upon the cells is preferably a change or an absence of a change in cell phenotype, more preferably it is a change or an absence of a change in cell proliferation or other physiological response, and even more preferably it is a change or absence of a change in the catalytic activity of the protein kinase. [00117] In a selected embodiment, the invention features a method for identifying the compounds of the invention, comprising the following steps: (a) lysing the cells to render a lysate comprising protein kinase; (b) adsorbing the protein kinase to an antibody; (c)incubating the adsorbed protein kinase with a substrate or substrates; and (d) adsorbing the substrate or substrates to a solid support or antibody; where the step of monitoring the effect on the cells comprises measuring the phosphate concentration of the substrate or substrates. [00118] In yet another aspect, the invention features a method for treating a disease related to unregulated kinase signal transduction, where the method includes the step of administering to a subject in need thereof a therapeutically effective amount of a compound of the invention as described herein.
[00119] The invention also features a method of regulating kinase signal transduction comprising administering to a subject a therapeutically effective amount of a compound of the invention as described herein. [00120] Furthermore, the invention features a method of preventing or treating an abnormal condition in an organism, where the abnormal condition is associated with an aberration in a signal transduction pathway characterized by an interaction between a protein kinase and a binding partner, e.g., substrate homolog, where the method comprises the following steps: (a) administering a compound of the invention as described herein; and (b) promoting or disrupting the abnormal interaction. The organism is preferably a mammal and the abnormal condition is preferably cancer or other proliferative condition. [00121] Compounds synthesized will be purified for testing in biochemical assays. The assays may measure the binding capability to the designated target, compound to target binding "on-off ' kinetic rates, substrate site occupancy or competitive interaction, biologically relevant concentrations at the reactive site, "optimal biological concentrations to elicit the desired pharmacological effect", the ability to modulate the natural enzymatic reaction catalyzed by the kinase, and other such parameters. Assays will be preferably evaluated in conditions similar to those found physiologically, e.g., temperature, concentration of targets, ion and salt concentrations, pH, and the like. The extent of kinase effect is determined and compared to the selectivity profile desired to confirm whether the structures have a profile of selective effects as described.
[00122] The correlation of structural features of the compounds is compared to the measured effect on the enzymes to determine whether the structural features of compounds match the predicted pattern of kinase effects. The modulation of the panel of kinases is compared to the predicted to establish the accuracy of the algorithms used to validate particular pharmacophore models. The models are further used to design additional variant structures which retain the desired pattern of modulation of kinase activity while minimizing the negative pharmacological problems. [00123]The cycles of activity testing and correlation to structural features of structurally similar compounds are repeated to refine the predictive methods to prioritize the likelihood of compounds in exhibiting balance of properties of enzyme interaction and pharmacology.
[00124] The compounds may also be used in animal model systems to evaluate relevance of animal test systems and their relationship to corresponding human conditions. [00125] QSAR and QSPR models generated are applied to scaffolds to create multiple compounds with desired binding pattern characteristics for kinase profiles. Compounds are synthesized and purified using appropriate technologies. Binding pattern characteristics of compounds from these steps are confirmed using a panel of kinases and their variants (including common or relevant mutants and splice variants). In the context, e.g., of oncology, mutants and splice variants can play a role in resistance selection and ultimate drug efficacy and toxicity in a clinical setting. [00126] As described below, synthesized compounds are screened against a panel of kinases, or variants thereof, found among kinases listed in selected kinase profiles. These include, for example, ABLl, ABLl E255K, ABLl G250E, ABLl T315I, ABLl Y253F, ABL2 (Arg), AKTl (PKB alpha), AKT2 (PKB beta), AKT3 (PKB gamma), AURKA (Aurora A), AURKB (Aurora B), AURKC (Aurora C), BRAF, BRAF V599E, CSNK2A1 (CK2 alpha 1), CSNK2A2 (CK2 alpha 2), EGFR (ErbBl), ERBB2 (HER2), FGFRl, FGFR2, FGFR3, FGFR3 K650E, FGFR4, FLTl (VEGFRl), FLT3, FLT3 D835Y, FLT4 (VEGFR3), FRAPl (mTOR), JAK2, JAK2 JHl JH2, JAK2 JHl JH2 V617F, KDR (VEGFR2), KIT, KIT T670I, PDGFRA (PDGFR alpha), PDGFRA D842V, PDGFRA T674I, PDGFRB (PDGFR beta), RAFl (cRAF) Y340D Y341D, TEK (Tie2). Pattern of inhibition of compounds is matched to a desired profile, which may be inhibition or lack of inhibition of a designated kinase recited in a profile. [00127] Among synthesized compounds are specific structures exhibiting desired modulation patterns, e.g., of inhibition and lack of inhibition. Data collected, both lack of inhibition and inhibition indicates that the design process described herein provides a tool that allows design of novel compounds and prediction of their activity or lack of activity across panel of kinases or kinase profile. [00128] As further illustrated below, analogs of compounds can be synthesized, e.g. as described, and evaluated for structure activity relationship leading to desired patterns of inhibition. Patterns of inhibition will be useful in a therapeutic context, using a described compound with another compatible entity providing a desired pattern of kinase modulation.
[00129] Illustration of the methods of compounds described herein is provided below. [00130] Particular scaffolds which modulate desired patterns of kinase inhibition result from the SAR data collection and analyses. These structures can be evaluated using medicinal chemistry, described below, as starting structures to generate compound structure diversity. Provided below are examples of virtual screening methodology according to the present invention.
[00131] Goal: Identification of lead structures modulating a profile of multiple kinase targets.
Procedure: [00132] The designed molecules were assembled in silico from fragments and fit the general motif shown below:
Figure imgf000047_0001
Wherein
Ring system A was selected from the group of 79 in table 7a;
Ring system B was selected from the group of 32 in table 7b; L is a linker selected from the group of 24 shown in table 7c;
Xi is a functional group selected from the group of 13 shown in table 7d; Ri is functional group or ring system.
[00133] A total of 57,600 possible scaffolds were generated in silico from combinatorial assortment of 24 linkers, 79 ring system A fragments, and 32 ring system B fragments and some examples are shown in table 7e.
[00134]From this group, 6864 scaffolds were selected and variation of Ri and Xi on these scaffolds produced 7530 molecules after in silico optimization of drug-likeness, docking and affinity scoring against enzymes of the profile. Some examples lead molecules with drug-like properties and affinity for KDR and PDGFR-B are shown in table 7f.
Table
Figure imgf000049_0001
Figure imgf000049_0002
Figure imgf000049_0003
Figure imgf000050_0001
Table 7b Ring System B Fragments
Figure imgf000050_0002
O
Figure imgf000050_0003
Table 7c Linker Units
Figure imgf000051_0001
1 2 3 4
Figure imgf000051_0002
8 10
Figure imgf000051_0003
11 12 13 14 15
Figure imgf000051_0004
16 17 18 19
Figure imgf000051_0005
20 21 22 23 24
Table 7d Xj Functional Groups
≡N o— O=N V- α Br OEt
Λ"F
N-H N —
K lsopropyl Table 7e 157 scaffolds
Figure imgf000052_0001
Figure imgf000053_0001
Figure imgf000054_0001
Figure imgf000055_0001
Figure imgf000056_0001
Figure imgf000057_0001
Figure imgf000058_0001
Figure imgf000059_0001
Figure imgf000059_0002
Figure imgf000059_0004
Figure imgf000059_0003
Figure imgf000059_0005
Figure imgf000060_0001
Examples of Selected Scaffolds Produced During in silico Fragment-based Design
Figure imgf000061_0001
Lead Molecules with Drug-like Properties and Affinity for KDR and PDGFR-B
Figure imgf000062_0001
Figure imgf000062_0002
Figure imgf000062_0004
Figure imgf000062_0003
Figure imgf000062_0005
Figure imgf000062_0007
Figure imgf000062_0009
Figure imgf000062_0006
Figure imgf000062_0008
[00135] Thus, one embodiment provides a compound of Formula (I) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000063_0001
Formula (I) wherein, X is O or NH; Z is CH or N; A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R1 substituents;
B is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R7 substituents;
R2 and R8 are independently selected from hydrogen, halogen, hydroxy, OR9, CN, amino, NHR9 or C 1-6 alkyl;
R1 and R7 are independently selected from hydrogen, halogen, OR9, C 1-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR9, CON(R9)2, NHR9, N(R9)2, COR9, C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, CO^alkylheterocyclyl, CN, amino, NHCOR9, hydroxy, Cl-6alkoxy, OC(O)R9, -OC0-4alkylaryl,
OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR9, OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR9, NR9COOR9, OCONR9, or NR9COR9;
R3 and R4 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, NHAryl, NHR9,
COOH, OR9, COOR9, CONHR9, or CON(R9)2; R3 and R4 may together form a 5-membered or 6- membered aryl or heteroaryl ring;
R5 and R6 are independently selected from hydrogen, Cl-6 alkyl and optionally may be joined to form a 3-10 membered cycloalkyl; R9 is selected from hydrogen, C 1-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl. [00136] Structures according to Formula I are illustrated below:
Figure imgf000064_0001
[00137] Another embodiment provides a compound of Formula (II) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000064_0002
(II) wherein, X is O, S or NH; Y is O or NH; Z is CH or N;
A is an optionally substituted heteroaryl ring having between 6 and 12 members and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1 -3 R1 substituents; R7 is selected from hydrogen or C 1 -6 al kyl ;
R5 is selected from hydrogen, halogen, hydroxy, OR8, CN, amino, NHR8 or C 1-6 alkyl;
R1 and R4 are independently selected from hydrogen, halogen, OR8, C 1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR8, CON(R8)2, NHR8, N(R8)2, COR8, C0-4alkylC3-10cycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, CCMalkylheterocyclyl, CN, amino, NHCOR8, hydroxy, Cl -όalkoxy, OC(O)R8, -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OCO^alkylCS-lOcycloalkyl, NHCOOR8, OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR8, NR8COOR8, OCONR8, Or NR8COR8; R2 and R3 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, aminoaryl, NHR8,
COOH, OR8, COOR8, CONHR8, CON(R8)2; R2 and R3 may together form a 5-membered or 6- membered heteroaryl ring;
R8 is selected from hydrogen, C 1-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl.
[00138] Illustrative structures according to Formula II include:
Figure imgf000066_0001
Figure imgf000066_0002
Figure imgf000066_0003
Figure imgf000066_0004
[00139] Yet another embodiment provides a compound of Formula (III) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000067_0001
Formula (III) wherein, X is O or NH; Z is CH or N; A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R1 substituents; B is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R7 substituents;
R2 and R8 are independently selected from hydrogen, halogen, hydroxy, OR9, CN, amino, NHR9 or Cl-6 alkyl;
R1 and R7 are independently selected from hydrogen, halogen, OR9, Cl-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR9, CON(R9)2, NHR9, N(R9)2, COR9, C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR9, hydroxy, Cl-6alkoxy, OC(O)R9, -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR9, OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR9, NR9COOR9, OCONR9, or NR9COR9; R3 and R4 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, NHAryl, NHR9, COOH, OR9, COOR9, CONHR9, or CON(R9)2; R3 and R4 may together form a 5-membered or 6- membered aryl or heteroaryl ring;
R5 and R6 are independently selected from hydrogen or Cl-6 alkyl;
R9 is selected from hydrogen, Cl-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl. [00140] Structures according to FormulaIII include:
Figure imgf000068_0001
[00141] Yet another embodiment provides a compound of Formula (IV) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000068_0002
Formula (IV) wherein, X is O or NH;
Y is O, NH, -OCH2- or -CH2O- Z is CH or N; A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R' substituents;
R1 and R4 are independently selected from hydrogen, halogen, OR9, Cl-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl,
OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR9, CON(R9)2> NHR9, N(R9)2, COR9, C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl,
C0-4alkylheterocyclyl, CN, amino, NHCOR9, hydroxy, Cl-6alkoxy, OC(O)R9, -OC0-4alkylaryl, OCO^alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR9, OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR9, NR9COOR9, OCONR9, or NR9COR9;
R2 and R3 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, NHAryl, NHR9, COOH, OR9, COOR9, CONHR9, or CON(R9)2; R2 and R3 may together form a 5-membered or 6- membered aryl or heteroaryl ring;
R5 is selected from hydrogen, halogen, hydroxy, OR9, CN, amino, NHR9 or Cl-6 alkyl; R6 and R7 are independently selected from hydrogen, Cl-6 alkyl and optionally may be joined to form a 3-10 membered cycloalkyl;
R8 is selected from hydrogen or Cl-6 alkyl;
R9 is selected from hydrogen, Cl-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl. [00142] Structures of Formula IV include:
Figure imgf000069_0001
Figure imgf000069_0002
Vm. In vitro/in vivo testing
[00143] Cell lines and other cellular systems appropriate for testing the effect of modulators in a cell context include, e.g., 32D cell line; 3T3 cell line; 3T3 Ll cell line; 4Tl cell line; A2780 cell line; A375 cell line; A43 cell line; A431 cell line; A459 cell line; A549 cell line; Aortic smooth muscle cells; ARH-77 cell line; B cells; B 16 cell line; Ba/F3 cell line; Ba/F3-TEL-FGFR3 cell line; BALB/c3T3 cell line; BALB/MK cell line; BT-20 cell line; BT-474 tumor cell line; BT-549 cell line; BxPC3 cell line; C26 cell line; C6 cell line; CaCo-2 cell line; CaIu- 3 cell line; CCRF-CEM cell line; CHO cell line; CHO-HIRc cells; COLO 201 cell line; COLO 205 cell line; Diploid fibroblast cells; DLD-I cell line; DMS-114 cell line; DU145 cell line; Endothelial cells; F/L-HERC cell line; GH3 cell line; H 1299 cell line; H16N-2 cell line; H209 cell line; H29 cell line; H460 cell line; H526 cell line; HaCat cell line; HB4a cell line ; HCT-116 cell line; HCT-15 cell line; HDF-3 cell line; HEK-293 cell line; HeLa cell line; HeLa S3 cell line; HepG2 cell line; HFF cell line; HL60 cell line; HMEC cell line; HMVECd cell line; HN5 cell line; HOP-62 cell line; HP75 cell line; HPBM cells ; HT29 cell line; HUVEC cell line; IMR-90 cell line; INS-IE beta-cell line; ITD-BaF3 cell line; Jurkat cell line; Jurkat T cell line; Jurkat T-cell; K-562 cell line; KARPAS-299 cell line; KB tumour cell line; KM12L4A cell line; KU812 cell line; L1210 cell line; LNCaP cell line; LoVo cell line; LOX cell line; LS174T cell line; M-14 cell line; Mast cells; MC26 cell line; MCF-7 cell line; MDA-MB-231 cell line; MDA-MB-435 cell line; MDA-MB-453 cell line; MDA-MB-468 cell line; MES/SA cell line; MIA PaCa-2 cell line; MK cell line; M-NFS-60 cell line; MO7E cell line; MOLT4 cell line; Mononuclear cells; MRC-5 cell line; MT-4 cell line; Mv.l.Lu cell line; MV4-11 cell line; MV522 cell line; N87 cell line; NIH-3T3 cell line; OVCAR-3 cell line; P388 cell line; PBM cells; PBMN cell line; PC3 cell line; PC-3P cell line; PMBC cells; PrEC cell line; RBL cell line; RBL-2H3 cell line; RKO cell line; RS4;11 cell line; RXF 393 cell line; SA0S2 cell line; SK-BR-3 cell line; SK-MEL 2 cell line; SK-MEL 28 cell line; SK0V3 cell line; SKUT-I cell line; SKUT-IB cell line; SR cell line; SW-1353 cell line; SW-480 cell line; SW-620 cell line; T cells; T-24 cell line; T-47D cell line; T98G cell line; TF-I cell line; THP 1 cell line; Tumor cell line; U-1242 MG cell line; U2OS cell line; U397 MG cell line; U87 MG cell line; U937 cell line; UACC-62 cell line; WiDr cell line; ZR-75-1 cell line; and many others. Many of these may be available from the ATCC or other cell line depositories or commercial sources. [00144] Preferably the effect of a compound on the plurality of kinases desired in the pattern is evaluated in a cell. The effects may be using kinase-specific reagents compatible with a selected cell line, or by evaluating multiple kinases in that cell line. Antibody reagents may be useful to allow simultaneous measurement of the impact of the compound on the different kinases together.
[00145] With selected structures exhibiting desired patterns of kinase modulation, the physiological effects of the compound are evaluated in systems analogous to the normal or disease context. Many different in vitro or in situ models exist for cancer or other selected disease.
[00146] In vivo models for oncology indications are described at http://emice.nci. nih.gov/emice/mouse_models/organ_niodels. For example, prostate cancer mouse models at /prostate_models/rnouse_rninireview ; gastrointestinal cancer animal models at /gastro_models ; hematopoietic cancer models at /hema_models ; lung cancer models at /lung_models ; mammary gland cancer models at /mammary_models ; ovarian cancer models at /ovarian_models/animal_models ; skin cancer models at
/skin_models ; and nervous system cancer models at /cns_models . Other models may be available upon a search of PubMed or patent searches for test systems. [00147] Several (1300+) reviews on mouse cancer models are found at http://emice.nci.nih.gov/emice/mouse_models/ and links to Mouse Models of Cancer Publications, which lead to Mouse Models of Cancer (Review). Over 8,000 publications (primary publications) at Mouse Models of Cancer Publications are at: http://emice.nci.nih.gov/emice/mouse_models/mouse_publications . These publications are separated (as of the filing date) into the following categories: bladder cancer models; cervical cancer models; endometrial cancer models; gastrointestinal cancer models; genitourinary cancer models; head and neck cancer models; hematopoietic cancer models; kidney cancer models; lung cancer models; mammary gland cancer models; melanoma models; myeloma models; nervous system cancer models; oral cancer models; ovarian cancer models; pancreatic cancer models; prostate cancer models; sarcoma cancer models; and skin cancer models. Other disease models, or counterparts in other species, may be found by search in the PubMed and patent literature databases. DC. Structures Exhibiting Desired Pattern of Kinase Modulation
[00148] The tables below disclose a selected profile desired for therapeutic compound(s) useful for treating various cancers, as well as other medical conditions. These conditions typically share mechanisms or effects with cancer, development, aging, and other similar cell processes. These compounds are lead compounds around which synthesis and further activity testing will generate a structure activity relationship dataset. This SAR can be used to generate various predictive pharmacophore models based on structural and other features for predicting similar variant structure compounds which may possess advantageous pharmacological features while retaining the desired pattern of kinase effect. Of particular importance in the selection of useful variants will be those optimized for adsorption, distribution, metabolism, excretion, toxicity, and manufacturability. [00149] Tables 3a, 4a, 5a and 6a disclose selected profiles desired for therapeutic compounds useful for treating various cancers, as well as other medical conditions. These conditions typically share mechanisms or effects with cancer, development, aging, and other similar cell processes. These compounds are lead compounds around which synthesis and further activity testing will generate a structure activity relationship dataset. This SAR can be used to generate various predictive pharmacophore models based on structural and other features for predicting similar variant structure compounds which may possess advantageous pharmacological features while retaining the desired pattern of kinase effect. Of particular importance in the selection of useful variants will be those optimized for adsorption, distribution, metabolism, excretion, toxicity, and manufacturability.
[00150] Profile One Table 3a: Profile one description: compounds selected to have the combination of high binding affinity and ability to inhibit the kinases KDR and PDGFR-B while having minimal binding affinity and ability to modulate the kinase KIT. The targets are preferably human, but the combination is relevant for other species, typically mammals. Six lead structures are provided. The predicted ICso's derived from the KDR and PDGFR-B pharmacophore models are given in Table 3b.
[00151] Indications for use of compounds which exhibit a profile one modulation pattern include hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, and similar neoplastic conditions. Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, anorexia, macular degeneration, diabetic retinopathy, retinal vein occlusion, and retinopathy of prematurity, scleroderma, cardiofaciocutaneous syndrome, chronic myeloid leukemia, androgen independent prostate cancer cells, head and neck squamous cell carcinoma, cervical cancer, and similar neoplastic conditions. Table 3a. Profile One Inhibitors of KDR, PDGFR-B but not KIT
Figure imgf000072_0001
P1-1 P1-2
Figure imgf000072_0002
P1-3 P1-4
Figure imgf000072_0003
P1-5 P1-6
Table 3b. Predicted IC50 of Profile One Modulators
Figure imgf000072_0004
[00152] Profile Two Table 4a: Profile 2 description: compounds selected to have the combination of high binding affinity and ability to inhibit the kinases BRAF (wild type and V600E variant), KDR and PDGFR-B while having minimal binding affinity and ability to modulate the kinase KIT. The targets are preferably human, but the combination is relevant for other species, typically mammals. Nine lead structures are provided. The predicted IC50 1S derived from the BRAF, KDR, PDGFR-B and KIT pharmacophore models are given in Table 4b. [00153] Indications for use of compounds exhibiting a profile two modulation pattern include hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, melanoma, thyroid carcinoma, neuroendocrine gastroenteropancreatic tumors, lymphoblastic leukemia and similar neoplastic conditions. Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, macular degeneration, diabetic retinopathy, retinal vein occlusion, retinopathy of prematurity, scleroderma, cardiofaciocutaneous syndrome. Table 4a. Profile Two Inhibitors of BRAF, KDR, PDGFR-B but not KIT
Figure imgf000073_0001
P2-1 P2-2
Figure imgf000073_0002
P2-3 P2-4
Figure imgf000073_0003
P2-9
Figure imgf000074_0001
[00154] Profile Three Table 5a: Profile three description: compounds selected to have the combination of high binding affinity and ability to inhibit the kinases AURORA, KDR, and PDGFR-B, while having minimal binding affinity and ability to modulate the kinase KIT. The targets are preferably human, but the combination is relevant for other species, typically mammals. Six lead structures are provided. The predicted IC50's derived from the AURORA, KDR, PDGFR-B and KIT pharmacophore models are given in Table 5b. [00155] Indications for use of compounds exhibiting a profile three modulation pattern include hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, esophageal squamous cell carcinoma, breast carcinoma, glioma, laryngeal carcinoma, ovarian cancer, prostate cancer, and similar neoplastic conditions. Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, macular degeneration, diabetic retinopathy, retinal vein occlusion, retinopathy of prematurity, scleroderma, and cardiofaciocutaneous syndrome.
Table 5a. Profile Three Inhibitors of AURORA, KDR, PDGFR-B but not KIT
Figure imgf000075_0001
Table 5b. Predicted IC50 of Profile Three Modulators
Figure imgf000075_0002
[00156] Profile Four Table 6a: Profile four description: compounds selected to have the combination of high binding affinity and ability to inhibit the kinases PI3K and mTOR (FRAPl), while having minimal binding affinity and ability to modulate the kinase KIT. The targets are preferably human, but the combination is relevant for other species, typically mammals. Six lead structures are provided. The predicted IC50's derived from the PI3K, mTOR (FRAPl) and KIT pharmacophore models are given in Table 6b.
[00157] Indications for use of compounds exhibiting a profile four modulation pattern include chronic myeloid leukemia, androgen independent prostate cancer cells, head and neck squamous cell carcinoma, cervical cancer, and similar neoplastic conditions. Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, and anorexia. Table 6a. Profile Four Inhibitors of PI3K and mTOR (FRAPl) but not KIT
Figure imgf000076_0001
P4-5 P4-6
Table 6b. Predicted IC50 of Profile Four Modulators
Figure imgf000076_0002
General Synthesis of Compounds of the Formula (I)
[00158] Compounds of Formula (I) can be synthesized as exemplified in Schemes 1-1, 1-2 and 1-3. When appropriate, protecting groups are used prior to performing the reaction outlined below, and may or may not be removed upon completion of the synthesis. The individual starting materials are synthesized according to methods known in the art (or described herein) or are commercially available. SCHEME 1-1
Figure imgf000077_0001
Figure imgf000077_0002
Reagents: a) 4-chbroqulnazollne, CS2CO3, DMF. 150C b) NaBH4, MeOH, OC c) SOCI2 d) Na2SO3, "IHRwaler, reflux e) CI2. H2O 0 ArNH2, Pr2NEt DCM
[00159] Phenol 1 may be contacted with an equivalent of 4-chloroquinazoline in the presence of a base such as potassium carbonate, sodium carbonate or cesium carbonate, in a solvent such as N.N-dimethylformamide or dimethylsulfoxide at temperatures ranging from 100 0C to 1600C and may lead to aryloxy 2. Upon completion of the reaction, 2 is recovered by conventional methods including neutralization, extraction, chromatography and the like. Reduction of the aldehyde with a reducing agent such as a stoichiometric amount of sodium borohydride or another hydride source in a protic solvent such as methanol, ethanol or the like, at temperatures ranging from -10 0C to 00C, for 1 to 5 hours will afford primary alcohol 3. [00160] Transformation into 4 may take place using neat thionyl chloride at temperatures ranging from 00C to 60 0C. The resulting optionally substituted 4 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification. Formation of the sulfonic acid 5 may take place in a protic solvent such as water, or a combination of water- tetrahydrofuran, at temperatures ranging from 20 0C to 90 0C, with a stoichiometric amount or excess of sodium sulfate. Sulfonyl chloride 6 may be obtained by treatment of 5 with a chlorinating agent such as phosphorus pentachloride or phosphorus oxide trichloride, at temperatures ranging from 00C to 600C, for 1 to 12 hours. Treatment of sulfonyl chloride 6 with an appropriately substituted aniline will provide sulfonamide 7 in the presence of a tertiary base such as triethylamine or Hunig's base, in a solvent system such as dichloromethane or the like, at temperatures ranging from 15 0C to 400C. Upon completion of the reaction, 7 is recovered by conventional methods including neutralization, extraction, chromatography and the like. SCHEME 1-2
Figure imgf000078_0001
Reagents: a)4-bromo aniline, K2CO3, Pd2(dba)3, THF b) p-amlno phenyl boronicadd, Pd(PPh3μ, dioxane, K2CO3 [00161] Commercially available boronic acid 8 may be used in a Suzuki coupling with commercially available 4- bromoaniline to afford biaryl 9, in the presence of a base such as potassium carbonate or cesium carbonate, in a solvent such as dioxane, dimethoxyethane or tetrahydrofuran, at temperatures ranging from 25 0C to 900C, for 1 to 12 hours, with a source of palladium (0) such as for example Pd2(dba)3. Alternatively, commercially available iodo pyridine 10 may be coupled to commercially available 4-aminophenyl boronic acid via a Suzuki coupling using conditions described above to provide biaryl 9. The resulting optionally substituted 9 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification. SCHEME 1-3
Figure imgf000078_0002
11 12
Figure imgf000078_0003
13
Reagents: a)SnCI2, EtOH b) HC(OMe)3, DMF, reflux
[00162] Sulfonamide 11 can be prepared as described in Scheme 1-2 and can be transformed into 12 through the use of a stoichiometric equivalent of a reducing agent such as tin chloride (II) in a protic solvent such as ethanol or the like. Alternatively, this reduction could take place with zinc powder in a solvent such as acetic acid. The resulting optionally substituted 12 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without isolation. Ring formation from 12 into 13 can take place with the use of a stoichiometric equivalent or slight excess of trimethyl orthoformate or the like, in a solvent system such as N,N-dimethylformamide or dimethylsulfoxide, for 1 to 12 hours, at temperatures ranging from 25 0C to 1000C. [00163] According to the procedures of Scheme 1-1, 1-2 and 1 -3 the following compounds were prepared:
Figure imgf000079_0001
[00164] Synthesis of N-^δ-ChloroO-pyridinyOphenylJ-l-phenylmethanesuIfonamide. 4-(6-Chloro-3- pyridinyl)aniline (51.0 mg, 0.249 mmole) was taken up in dry dichloromethane (1.5 mL) in a round-bottomed flask under a stream of nitrogen. Triethylamine (0.042 mL, 0.30 mmole) was added at room temperature followed by the addition of benzylsulfonyl chloride (49.9 mg, 0.262 mmole). The reaction mixture was stirred at room temperature for 2 hours. Pyridine (0.2 mL) was added in addition more benzylsulfonyl chloride (20mg). The reaction mixture was stirred for 2 days at room temperature. The reaction was worked up by pouring into a separatory funnel with ethyl acetate. The organic layer was washed sequentially with water (5 mL), IN hydrochloric acid (5 mL), dipotassium phosphate/potassium carbonate (5 mL, pH 8), and brine (5 mL). The organic layer was dried over sodium sulfate, filtered and the solvent removed in vacuo affording a white foam. The residue was applied directly to 2 10 x 20cm 0.25 mm analytical TLC plates and eluted once with ethyl acetatexhloroform (3:17). The appropriate spot was scraped off of the plates, extracted into ethyl acetate, filtered and the solvent removed in vacuo affording the title compound as an off-white solid (65.1 mg). MS (ESI+) for C18H15ClN2O2S m/z 359.1 (M+H)+.
General Synthesis of Compounds of the Formula (II)
[00165] Compounds of Formula (H) can be synthesized as exemplified in Schemes 2-1 thru 2-7. When appropriate, protecting groups are used prior to performing the reaction outlined below, and may or may not be removed upon completion of the synthesis. The individual starting materials are synthesized according to methods known in the art (or described herein) or are commercially available.
SCHEME 2-1
Figure imgf000080_0001
Reagents: a) s-BuLi/HCON(Mθ)2 b) NBS, CCW c) NaN3, DMF d)TrtNCS, PPti3, dioxane 100C e) HO, dioxane
[00166] An aryl bromide or heteroaryl bromide 1 can be converted to a corresponding methyl ketone 2 by treatment with 1 to 2 equivalents of sec-butyl lithium (sec-BuLi) or n-BuLi at temperatures ranging from -800C to -500C, for about 1 to 5 hours, in a solvent such as dry ethyl ether, followed by addition of 1 to 2 equivalents of N,N-dimethylacetamide, and gradual increase of the temperature to 00C. Upon completion of the reaction, 2 is recovered by conventional methods including neutralization, extraction, chromatography and the like. Methyl ketone 2 may be converted to an alpha bromo ketone 3 upon treatment with 1 to 1.5 equivalents of N- bromosuccinimide (NBS), in a solvent such as carbon tetrachloride (CCl4), for 5 to 12 hours at temperatures ranging from 20 0C to 55 0C. The acyl azide 4 can be prepared under conventional methods by contacting 3 with a stoichiometric equivalent or a slight excess of sodium azide in an anhydrous solvent such as N,N- dimethylformamide (DMF) or the like, at temperatures ranging from 25 0C to 900C, for 2 to 7 hours. The resulting optionally substituted 4 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification or isolation. Construction of the amino oxazole ring 5 takes place by mixing 4 with a stoichiometric amount of commercially available tritylisothiocyanate, in the presence of reducing agent triphenylphosphine, in a solvent such as dioxane or tetrahydrofuran (THF), at temperatures ranging from 200C to 1000C for 1 to 12 hours. Removal of the protecting group under standard conditions such as treatment with a saturated solution of HCl (g) in dioxane at room temperature leads to the desired substituted amino oxazole 6. SCHEME 2-2
Figure imgf000081_0001
Reagents: 1) KOH, AgNO3, H2O b) Br2, CCI4 c) ArB(OH)2, Pd(O), aq. K2CO3, PhH Or ArSnBu3, Pd(O), LiCI, DMF d)TFA, CH2CI2
[00167] Commercially available carboxylic acid 7 may be converted to the corresponding silver salt by treatment with a stoichiometric amount of potassium hydroxide (KOH) or the like, and silver nitrate (AgNO3) preferably in a solvent such as water. Bromooxazole 8 is obtained by directly heating the above silver salt in the presence of a stoichiometric amount of bromine (Br2), at temperatures ranging from 30 °C to 75 0C, in solvents such as carbon tetrachloride (CCl4) for 2 to 8 hours. Upon completion of the reaction, 8 is recovered by conventional methods including neutralization, extraction, chromatography and the like. Suzuki coupling of 8 with a substituted aryl or heteroaryl boronic acid in the presence of a palladium (O) catalyst such as tetrakistriphenylphosphine palladium (O) or the like, in a deoxygenated solvent such as benzene, dimethoxyethane (DME), dioxane and the like, at temperatures ranging from 20 °C to 85 0C, for 2 to 12 hours with an aqueous solution of potassium carbonate or sodium carbonate leads to biaryl 9. Alternatively, a Stille coupling of 8 with an aryl or heteroaryl stannane in the presence of a palladium (O) catalyst such as tetrakistriphenylphosphine palladium (0) or the like in a deoxygenated solvent such as dimethoxyethane, N,N-dirnethylformamide, at temperatures ranging from 200C to 90 0C, for 2 to 13 hours, with a freshly ground base such as potassium carbonate, cesium carbonate or potassium phosphonate, in the presence of lithium chloride will lead to 9. Deprotection under acidic conditions such as trifluoroacetic acid (TFA) in a solvent like dichloromethane (DCM) or HCl (g) in a solvent such as ethyl acetate will lead to amino oxazole 6. SCHEME 2-3:
BocHN
Figure imgf000081_0002
Reagents: a) 1 - HSR1, HATU, ET3N, CH3CN 2- AB(OH)2. CuTc b) TFA, DCM
[00168] Commercially available Boc-glycine 10 may be transformed into the corresponding aryl or heteroaryl ketone 11 via a Liebeskind-Srogl coupling using conditions described in J. Am. Chem. Soc. 2000, 122, 11260- 11261. Deprotection under acidic conditions such as trifluoroacetic acid (TFA) in dichloromethane (DCM) at temperatures ranging from 00C to 40 0C, for 1 to 12 hours, leads to amino ketone 12 in quantitative yield. Ketone 12 can then be treated with commercially available tritylisothiocyanate as shown in Scheme 2-1 using steps d and e to give 6. SCHEME 2-4
Figure imgf000082_0001
Reagents: a) 4-chloro quinazoline, KOtBu, K2CO3, DMF, 8OC or quinazo.n-4-ylboronlc acid, Cu(OAC)2, DME, K2CO3. RT b) H2, Pd/C, 10 psi, MeOH
[00169] Commercially available 4-nitro phenol 13 can be contacted with commercially available 4- chloroquinazoline in the presence of a base such as potassium tert-butoxide or the like (KOtBu) and a freshly ground base such as potassium carbonate (K2CO3) or cesium carbonate (Cs2CO3), in a solvent such as N,N- dimethylformamide (DMF) or tetrahydrofuran (THF), at temperatures ranging from 30 0C to 80 0C, for a period of 1 to 9 hours and obtain aryloxy 14. Upon completion of the reaction, 14 is recovered by conventional methods including neutralization, extraction, chromatography and the like. Alternatively, a Chan-Lam coupling {Tetrahedron Letters, 1998, 39, 2937-2940) can be used to transform 13 into 14, in the presence of commercially available quinazolin-4-yl boronic acid. Hydrogenation of 14 with a catalyst such as 10% Pd on C at room temperature, in a solvent such as methanol, ethanol or water, under 5 to 10 psi, will lead to aniline 15. Upon completion of the reaction, 15 is recovered by conventional methods including neutralization, extraction, chromatography and the like. SCHEME 2-5
Figure imgf000082_0002
Reagents: a) 4-hydroxy quinazoline,Cu(OAC)2, DME, K2CO3, RT
[00170] Commercially available boronic acid 16 can be treated with commercially available 4- hydroxyquinazoline using a Chan-Lam coupling (Tetrahedron Letters, 1998, 39, 2937-2940) to give nitro aryl 14. SCHEME 2-6
Figure imgf000083_0001
14 15 16
17
Reagents: a) phosgene, EON. CH2CI2 b) 6. Et3N, CH3CN c) p-NO2 phenyl chloroformate, Et3N, CH2CI2 d) 6, DIEA, CH2CI2
[00171] Aniline 14 may be reacted with a stoichiometric amount to a slight excess of phosgene in the presence of a tertiary base such as triethylamine (Et3N) or Hunig's base (DIEA), in a solvent such as dichloromethane or the like, at temperatures ranging from 00C to 25 0C, to lead isocyanate 15. The resulting optionally substituted 15 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification. Condensation of 14 with 6 takes place in a solvent such as dichloromethane, N,N-dimethylformamide, or acetonitrile, in the presence of a stoichiometric amount of tertiary base such as triethylamine or Hunig's base, at room temperature for 1 to 12 hours, and leads to urea 16. [00172J Alternatively, aniline 14 can be activated to its corresponding 4-nitrophenyl carbamate 17 by contact with a stoichiometric amount to slight excess of 4-nitrophenyl chloroformate or other phenyl chloroformate, in the presence of a base such as triethylamine or Hunig's base, in a solvent such as dichloromethane, at temperatures ranging from 00C to 55 0C, for 1 to 12 hours. The resulting optionally substituted 17 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification. Condensation of 17 with 6 takes place in a solvent such as dichloromethane, N,N-dimethylformamide, or acetonitrile, in the presence of a stoichiometric amount of tertiary base such as triethylamine or Hunig's base, at room temperature for 1 to 12 hours, and leads to urea 16. SCHEME 2-7
Figure imgf000084_0001
Reagents: a) SnCI2, EtOH b) HC(OMe)3, DMF, reflux
Figure imgf000084_0002
[00173] Nitro pyridone 18 can be reduced to the corresponding aniline 19 using a reducing agent such as tin chloride in a solvent such as ethanol or the like, for 1 to 12 hours. Alternatively, other reducing agents such as zinc powder or iron could be used instead of tin chloride. Cyclization of 19 into oxazole 20 can be obtained with one stoichiometric equivalent of trimethylorthoformate in a solvent system such as N,N-dimethylformamide of the like, at temperatures ranging from 200C to 90 0C, for 1 to 12 hours. The resulting optionally substituted 17 can be recovered by conventional methods such as neutralization, chromatography, filtration, crystallization and the like or can be used in the next step without purification. General Synthesis of Compounds of the Formula (III)
[00174] Compounds of Formula (EI) can be synthesized as exemplified in Scheme 3-1. When appropriate, protecting groups are used prior to performing the reaction outlined below, and may or may not be removed upon completion of the synthesis. The individual starting materials are synthesized according to methods known in the art (or described herein) or are commercially available.
Figure imgf000085_0001
Reagents: a) 2-bramoethanol, chlorosulfonyl isocyanate, Et3N, DCM b)4-(quinazolin-4-yloxy)aniline, Et3N, CH3CN.
[00175J Synthesis of 4-(6-Chloro-3-pyridinyl)aniIine. p-Bromoaniline (1.1 g, 6.4 mmole), (6-chloro-3- pyridinyl)boronic acid (1.1 g, 7.0 mmole), tris(dibenzylideneacetone)dipalladium (0) (60 mg, 0.06 mmole), and tricyclohexylphosphine (43 mg, 0.15 mmole) were all added to a 25 mL pressure tube. Dioxane (15 mL) was added followed by potassium phosphate (2.3 g, 11 mmole) which had been dissolved in 8.25 mL of water. The burgundy colored solution was flushed with nitrogen and then sealed with the cap. The reaction mixture was heated to 1000C for 18 hours with very vigorous stirring. The reaction mixture was cooled to room temperature and filtered through a short pad of silica gel washing with ethyl acetate. The mixture was dried over sodium sulfate, filtered and the solvent concentrated in vacuo affording a yellow semisolid material. This was then pre- absorbed onto silica gel and applied to a 70 g Biotage column packed with silica gel which had been preconditioned with 3:7 ethyl acetatexhloroform. The column was eluted with the same solvent system. The appropriate fractions were collected and the solvent concentrated in vacuo affording 1 g of the title compound, aniline 21, as a pale yellow solid. MS (ESI+) for CnH9ClN2 m/z 205.2 (M+H)+. [00176] Step A - Synthesis of N-[4-(6-Chloro-3-pyridinyl)phenyI]-2-oxo-l,3-oxazolidine-3-sulfonamide (22). Chlorosulfonyl isocyanate (0.17 mL, 1.9 mmole) was dissolved in dry dichloromethane (6 mL) in a dry flask under a nitrogen stream. The clear solution was cooled to 00C and then 2-bromoethanol (0.14 mL, 1.9 mmole) was added. The reaction mixture was stirred at 00C for 1 hour. Aniline 21 (426 mg, 2.08 mmole) was taken up into dry dichloromethane (6 mL), triethylamine (0.53 mL, 3.8 mmole) was added and the resultant clear yellow solution was then added slowly to the sulfonyl chloride solution. The reaction mixture was stirred at 0 0C for 15 minutes and then warmed to room temperature for 1.5 hours. The reaction mixture was worked up by the addition of 10% hydrochloric acid (8 mL), the mixture stirred, and the aqueous layer decanted off. The same sequence was followed using first 10 mL of 1% hydrochloric acid and then 10 mL of water. Another 10 mL of water was added and the solvent was removed in vacuo, keeping the bath temperature below 250C, affording 467 mg of compound 22 as a yellow solid. MS (ESI+) for Ci4Hi2ClN3O4S m/z 354.1 (M+H)+. [00177] Synthesis of 4-[(4-Nitrophenyl)oxy]quinazoline. 4-Quinazolinol (2.64 g, 18.1 mmole) was taken up in 25 mL of dry dimethylformamide. l-Fluoro-4-nitrobenzene (1.92 mL, 18.1 mmole) was added followed by potassium carbonate (4.99 g, 36.1 mmole). The reaction slurry was heated to 1500C and heated overnight. The reaction mixture was cooled to room temperature, poured into 150 mL of water and the mixture stirred for 1 hour. The solids were removed by filtration washing with water. Air drying afforded 4.65 g of the title compound as a greenish yellow solid. MS (ESI+) for C4H9N3O3 m/z 268.1 (M+H)+.
[00178] Synthesis of 4-(4-Quinazolinyloxy)aniline hydrochloride. 4-[(4-Nitrophenyl)oxy]quinazoline (1.00 g, 3.74 mmole) was taken up in 8 mL of 1 : 1 ethanol:water. Iron (325 mesh, 0.627 g, 11.2 mmole) was added to the reaction flask and the resultant slurry was vigorously stirred while being heated at reflux. Concentrated hydrogen chloride (0.2 mL) was added to 1 mL of 1 : 1 ethanol:water and the acidic solution was added slowly to the iron mixture (vigorous reaction). After the addition was complete, the reaction mixture was refluxed for 30 minutes. The reaction mixture was poured hot through a fritted funnel filled with Celite®545 and the solids were washed with 95% ethanol. An additional 1 mL of concentrated hydrochloric acid was added to the filtrate causing immediate precipitation of large quantities of solids. The solids were filtered washing with a minimal amount of 95% ethanol affording, after drying, the title compound as an off-white solid (720 mg). MS (ESI+) for C14H11N3O m/z 238.3 (M+H)+.
[00179] Step B - Synthesis of N-[4-(6-Chloro-3-pyridinyl)phenyl]-N'-[4-(4-quinazolinyIoxy)phenyl]sulfamide (23). Compound 22 (90.2 mg, 0.255 mmole) and 4-(4-quinazolinyloxy)aniline hydrochloride (63 mg, 0.23 mmole) were taken up into 4 mL of acetonitrile. Triethylamine (0.081 mL, 0.58 mmole) was added and the reaction mixture was heated to 8O0C for 3 hours. An additional 50 mg of the product from 4-(4- quinazolinyloxy)aniline hydrochloride was added in addition to 0.15 mL more of triethylamine and the reaction mixture heated at reflux for 8h. The reaction mixture was cooled to ambient temperature and then pre-absorbed directly onto silica gel. The material was flash chromatographed on a 20 g silica gel column which had been preconditioned with 3:7 ethyl acetatexhloroform. The solvent polarity was increased from 3:7 to 2:3 ethyl acetatexhloroform. The appropriate fractions were combined affording 70 mg of a white foam. The material was taken up into chloroform from which solids precipitated. The solvent was decanted and the solids rinsed twice with chloroform. This afforded 3 mg of the title compound 23 as a white solid. MS (ESI+) for C25Hi8ClN5O3S m/z 504.0 (M+H)+. [00180] According to the procedures of Scheme 3-1 the following compounds were prepared: N-[4-(6-Chloro-3-pyridinyl)phenyl]-N'-[4-(methyloxy)phenyl]sulfamide
Figure imgf000087_0001
[00181] Synthesis of N-[4-(Methyloxy)phenyl]-2-oxo-l,3-oxazolidine-3-sulfonamide. Chlorosulfonyl isocyanate (0.308 mL, 3.53 mmole) was taken up in 5mL of dichloromethane in a round-bottomed flask and cooled to 0 0C under a stream of nitrogen. 2-Bromoethanol (0.25 mL, 3.53 mmole) was added slowly. After the addition is complete, the reaction mixture is stirred at 0 0C for an additional 1 hour. para-Anisidine (0.478 g, 3.88 mmole) and triethylamine (0.985 mL, 7.06 mmole) were both taken up in 1.5 mL of dichloromethane. This dark solution was then added slowly to the chlorosulfonyl solution. The reaction mixture was stirred at 0 0C for 30 minutes and then warmed to room temperature for 1.5 hours. The reaction mixture was worked up by the addition of 10% hydrochloric acid (8 mL), the mixture stirred, and the aqueous layer decanted off. Next, 10 mL of 1% hydrochloric acid was added, the mixture stirred and the aqueous layer decanted off. The same sequence was followed using first 10 mL of 1% hydrochloric acid and then 10 mL of water. Another 10 mL of water was added and the solvent was removed in vacuo, keeping the bath temperature below 25 0C, affording 950 mg of the title compound as a purple solid. MS (ESI-) for Ci0H12N2O5S m/z 271.2 (M-H)". [00182] Synthesis of N-[4-(6-Chloro-3-pyridinyl)phenyl]-N'-[4-(methyloxy)phenyl]sulfamide. The product from N-[4-(methyloxy)phenyl]-2-oxo-l,3-oxazolidine-3-sulfonamide (99 mg, 0.36 mmole) and the product from 4-(6-chloro-3-pyridinyl)aniline (60 mg, 0.3 mmole) were added to a round-bottomed flask and then acetonitrile (4 mL) was added. Triethylamine (0.14 mL, 1.0 mmole) is added causing the purple color to dissipate and then the reaction was heated to reflux for 30 minutes. More of the sulfonamide (10 mg) was added and the reaction heated at reflux for an additional 30 minutes. The reaction was cooled to ambient temperature and the solvent was removed in vacuo affording a dark colored solid. The mixture was taken up into ethyl acetate and washed with water. The organic layer was dried with sodium sulfate, filtered and the solvent removed in vacuo. The solids were taken back up into chloroform and applied directly to 220x20cm 2mm thick TLC plates and the plates were eluted twice with 3:7 ethyl acetatexhloroform. The desired band was scraped off the plate, the silica gel was extracted with ethyl acetate, filtered and the solvent removed in vacuo affording 90 mg of the title compound as a pale purplish foam. MS (ESI+) for C18Hi6ClN3O3S m/z 390.1 (M+H)+.
[00183] N-[4-(6-Chloro-3-pyridinyl)phenyl]-N'-[4-(4-pyridinyloxy)phenyl]sulfamide
Figure imgf000088_0001
[00184] Synthesis of 4-[(4-Nitrophenyl)oxy]pyridine. 4-Pyridinol (2.15 g, 21.5 mmole) was taken up in dry dimethylformamide (25 mL). l-Fluoro-4-nitrobenzene (2.28 mL, 21.5 mmole) was added followed by potassium carbonate (5.94 g, 43.0 mmole). The reaction slurry was heated at 1650C for 24 hours. The reaction mixture was cooled to room temperature where it sets to a solid mass. The solid was transferred to a 250 mL Erlenmeyer flask filled with 120 mL of water using water to transfer the solids out of the flask. After stirring for about 30 minutes, the solids was filtered on a Bϋchner funnel and washed with water. The solids were air dried affording the title compound as a yellow solid (4.06 g). MS (ESI+) for CnH8N2O3 m/z 217.2 (M+H)+. [00185] Synthesis of 4-(4-Pyridinyloxy)aniline hydrochloride. 4-[(4-Nitrophenyl)oxy]pyridine (1.02 g, 4.72 mmole) was taken up in 1:1 ethanohwater (8 mL). Iron (325 mesh, 0.790 g, 14.2 mmole) was added and the blackish grey reaction mixture heated to boiling with vigorous stirring. Concentrated hydrogen chloride acid (0.2 mL) was added to 2 mL of 1 : 1 ethanokwater and the resultant solution is added slowly drop-wise to the hot iron solution (vigorous reaction). After the complete addition, the reaction mixture was refluxed for 30 minutes. The reaction mixture was filtered hot through a pad of Celite® 545 and rinsed with 95% ethanol. Concentrated hydrochloric acid (1 mL) is added to filtrate causing immediate precipitation of solids. The solvent is removed in vacuo affording the title compounds as a pale yellow solid (1.04 g). MS (ESI+) for CuHi0N2O m/z 187.3 (M+H)+.
[00186] Synthesis of N-[4-(6-Chloro-3-pyridinyI)phenyll-N'-[4-(4-pyridinyloxy)phenyI]suIfamide. N-[4-(6- Chloro-3-pyridinyl)phenyl]-2-oxo-l,3-oxazolidine-3-sulfonamide (139.6 mg, 0.395 mmole) and the product of 4- (4-Pyridinyloxy)aniline hydrochloride (156 mg, 0.700 mmole) were taken up in acetonitrile (4 mL).
Triethylamine (0.275 mL, 1.97 mmole) was added at ambient temperature. The reaction mixture was heated to 80 0C for 3 hours before being cooled to room temperature. The reaction mixture was poured into a separatory funnel and the flask was rinsed with ethyl acetate. The reaction mixture is washed with water (3 x 10 mL) and the organic layer dried over sodium sulfate. The mixture is filtered and the solvent concentrated in vacuo affording a dark yellow solid. The title compound was re-crystallized from chlorofornrmethanol affording material which was about 85% pure. A second re-crystallization from chlorofornrmethanol affords the desired title product as a white solid (8 mg). MS (ESI+) for C22H17ClN4O3S m/z 453.0 (M+H)+. General Synthesis of Compounds of the Formula (TV)
[00187] Compounds of Formula (TV) can be synthesized as exemplified in Scheme 4-1. When appropriate, protecting groups are used prior to performing the reaction outlined below, and may or may not be removed upon completion of the synthesis. The individual starting materials are synthesized according to methods known in the art (or described herein) or are commercially available.
SCHEME 4-1
Figure imgf000089_0001
Reagents: a) cyanoaceticacid, EDC, DMAP, DCM b) hydroxylamine hydrochloride, Et3N c) Iron, hydrochloric acid d) 2-bromo-1-(pyridin-3-yl)ethanone, NaHCO3, H2O, THF.
[00188] Synthesis of 4-[(4-Nitrophenoxy)methyl]quinoline. Quinolin-4-ylmethanol (4.34 g, 0.027 mole) was taken up in tetrahydrofuran (50 mL). Potassium hydroxide (2.2 g, 0.033 mole, partially pulverized with a mortar and pestle) was added at room temperature. After 5 minutes, 4-fluoronitrobenzene (3.8 mL, 0.035 mole) was added, the mixture soon becoming a yellow slurry. More tetrahydrofuran (6 mL) was added and the reaction mixture stirred overnight. An additional amount of potassium hydroxide (0.30 g, 0.005 mole) was added and stirred for 3 more hours. The reaction mixture was stirred with water (50 mL), the solids filtered and washed with water (5 x 10 mL) to give 7.1 g of the title compound as a white solid. MS (ESI+) for C16H12N2O3 mJz 281.2 (M+H)+.
[00189] 4-(Quinolin-4-ylmethoxy)aniline hydrochloride (24). 4-[(4-Nitrophenoxy)methyl]quinoline (2.74 g, 9.79 mmole) and iron (3.28 g, 0.058 mole) were taken up into a 1:1 mixture of ethanol: water (20 mL). This stirring mixture was placed in an oil bath (1040C) and heated to reflux. A hydrochloric acid solution (0.2 mL of concentrated hydrochloric acid in 3 ml of 1 : 1 ethanol:water) was added to the reaction mixture over a period of 1 minute. The reaction mixture was stirred for an additional 60 minutes. The hot reaction mixture was filtered through Celite® 545, washed with ethanol (20 mL), and the solvent concentrated in vacuo. The residue was taken up in water (50 mL) and then acidified to pH 4 with 10% hydrochloric acid. The aqueous layer was extracted with ether (50 mL), ethyl acetate (50 inL), toluene (50 mL) and then was brought to pH 9 using sodium bicarbonate. The aqueous layer was extracted with methylene chloride (5 x 40 mL) and the combined organic layers were stripped to a dark solid. The solid was mixed with methanol (5 mL), filtered and then washed with methanol (3 x 2 mL) to give the title compound 24 as an off-white solid (1.08 g). MS (ESI+) for Ci6Hi4N2O m/z 251.1 (M+H)+.
[00190] 2-Cyano-N-[4-(quinolin-4-ylmethoxy)phenyl]acetamide (25). 4-(Quinolin-4-ylmethoxy)aniline hydrochloride (24) in water (100 mL) was brought to pH 11 using aqueous sodium hydroxide and then the mixture was shaken with a 1:1 toluene:ether (3 x 30 mL) and the combined organic layers stripped in vacuo to an off white solid. The resultant 4-(quinolin-4-ylmethoxy)aniline (0.39 g, 1.57 mmole) was mixed with cyanoacetic acid (0.15 g, 1.78 mmole) and toluene (30 mL) and stripped to dryness. The toluene stripping was repeated once more and to the flask was added N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (0.34 g, 1.78 mmole), 4-dimethylaminopyridine (0.02 g, 0.2 mmole), dichloromethane (5 mL, forming a slurry) and finally triethylamine (0.24 mL, 1.74 mmole). The reaction mixture was stirred overnight. The reaction mixture was diluted with dichloromethane (200 mL), shaken with water (3 x 80 mL) and the organic layer dried over sodium sulfate. Filtration and concentration of the solvent in vacuo afforded an off white solid (0.44 g). The solid was triturated with dichloromethane (2 x 4 mL) and dried giving the title compound 25 as an off white solid (0.43 g). MS (ESI+) for C19Hi5N3O2 m/z 318.2 (M+H)+.
[00191] 3-(Hydroxyamino)-3-imino-N-[4-(quinolin-4-yImethoxy)phenyl]propanamide (26). 2-Cyano-N-[4- (quinolin-4-ylmethoxy)phenyl]acetamide (25) (0.26 g, 0.82 mmole) was taken up in anhydrous methanol (15 mL). Hydroxylamine hydrochloride (0.25 g, 3.60 mmole) was added followed by the addition of triethylamine (0.50 mL, 3.60 mmole). The reaction mixture was stirred at room temperature for 4 days. The reaction mixture was filtered and the solids washed with methanol (3 x 2 mL). The filtered solid was air dried affording the title compound 26 as a white solid (0.18 g). MS (ESI+) for C20H19N3O3 m/z 350.2 (M+H)+. [00192] 3-Amino-3-imino-N-[4-(quinolin-4-ylmethoxy)phenyJJpropanamide hydrochloride (27). 3- (Hydroxyamino)-3-imino-N-[4-(quinolin-4-ylmethoxy)phenyl]propanamide (26) (0.12 g, 0.351 mmole) and iron (325 mesh, 0.12 g, 2.11 mmole) was taken up a 1:1 mix of ethanol:water (5 mL). The reaction mixture was placed in an oil bath (104 0C) and heated. A mixture of IN hydrochloric acid (0.86 mL) in 1:1 ethanol:water (2 mL) was added slowly drop-wise to the iron mixture. After addition has been completed, the reaction mixture was stirred for an additional 30 minutes. The reaction mixture was filtered hot through Celite® 545, washed with ethanol and the solvent concentrated in vacuo affording the title compound 27 as a light brown solid (0.14 g). MS (ESI+) for C19H18N4O2 m/z 335.2 (M+H)+.
[00193] 2-(5-Pyridin-3-yI-lH-imidazol-2-yl)-N-[4-(quinoli n-4-ylmethoxy)phenyl]acetamide (28). 3-Amino- 3-imino-N-[4-(quinolin-4-ylmethoxy)phenyl]propanamide hydrochloride (27) (45.7 mg, 0.12 mmole) and sodium bicarbonate (54.9 mg, 0.654 mmole) was taken up in tetrahydrofuran (20 mL) and water (5 mL) The reaction mixture was placed in an oil bath (700C). 3-Bromoacetylpyridine hydrobromide (32.9 mg, 0.12 mmole) was taken up in a 2:1 mixture of tetrahydrofiiran: water (1.5 mL) and was added in portions over a 35 minute period to the bicarbonate mixture. After 5 hours, the reaction mixture was removed from the oil bath and cooled to room temperature. The reaction mixture was diluted with ethyl acetate (30 mL) and washed with water (3 x 10 mL) and 0. IN hydrochloric acid (30 mL). The organic layer was dried over sodium sulfate, filtered and the solvent concentrated in vacuo affording a dark brown solid (50 mg). This material was dissolved in water (20 mL) and chromatographed on areverse phase C18 column using an acetonitrile:water gradient (1:9 - 100:0). The appropriate fractions were combined and the solvent removed in vacuo. The resultant residue was made basic with saturated aqueous sodium bicarbonate and the resultant precipitate was filtered and the solids washed with water (5 x 5 mL). The solid was dried under high vacuum affording the title compound 28 as tan solid (12 mg). MS (ESI+) for C26H21N5O2 m/z 436.2 (M+H)+. X. Efficacy and Safety Biomarkers
[00194] Currently, e.g., cancer therapies are still essentially "one size fits all," with virtually all patients within a given diagnostic category, typically based on tumor type and stage of disease — receiving the same treatment despite the biological heterogeneity known to exist from patient to patient. [00195J The present invention allows for identifying efficacy and safety biomarkers, based in part upon in vitro and in vivo data collated from publicly available reports. It is expected that one or more such biomarkers will be useful in identifying appropriate target individuals susceptible to effective treatment with identified drug candidates. This may lead to an ability to combine a drug product with a companion biomarker. [00196] In oncology therapeutics, toxicities from traditional chemotherapies are the major dose-limiting and regimen-limiting factors in the treatment of cancer patients. While chemotherapy will remain a mainstay of cancer treatment for many years, it will be used increasingly in combination with targeted therapies. A major thrust of clinical oncology research in medical centers is expected to focus on the mechanisms by which these drugs assist one another while reducing the toxicity of the conventional chemotherapeutic. Understanding these mechanisms will lead to improvements in the efficacy of combination therapies and may increase cost effectiveness. Combination drug strategies are a potential approach for prolonging tumor responses and to delay the onset of resistance to chemotherapeutic drugs. The methods of the invention are beneficial in a number of indications. For example, the methods of the invention are advantageous in conditions involving immunosuppression, autoimmune conditions, inflammatory conditions, cerebral vasospasm, diabetic retinopathy, rheumatoid arthritis, or neurodegeneration. [00197] Drugs that modulate kinase activities will be combined with companion efficacy and safety biomarkers for efficient and accelerated clinical development in targeted patient populations. Biomarkers are objective, measurable biochemical parameters that faithfully reflect the status of a critical pathway to a disease or a critical pathway that predisposes to a disease. Biomarkers in ultimate or proximal critical pathways can be direct measures of the progression or reversal of a fundamental underlying disease process. [00198] A clinical development strategy will be focused on developing kinase modulator drugs, e.g., in the oncology arena, and establishing proprietary biomarkers that identify patients most likely to respond to treatment and those at risk for adverse drug reactions. By incorporating a biomarker strategy at the beginning, the drug candidates will be favorably positioned. This strategy increases the likelihood of drug development success and reduces the drug failure rate common within the industry.
[00199] Efforts to identify biomarkers encompass genetic, gene expression, post-translational function, metabolomic, and organ specific or organ shared evaluations. Both efficacy and safety biomarkers will lead to efficient and accelerated clinical development in targeted patient populations, because they will identify patients most likely to respond to treatment and those at risk for adverse drug reactions. [00200] Biomarkers have enormous potential to predict who will develop cancer and/or to detect the disease at an early stage. The anticipated benefit in this setting is based on the assumption that interventions exist that either prevent cancer in high-risk individuals or more effectively eradicate cancer when individuals are diagnosed at a time of low tumor burden. [00201] Biomarkers can guide treatment decisions. For example, cancer patients with biomarkers that predict a poor outcome could be selected for aggressive treatments to increase their chance of survival, whereas patients with biomarkers predicting a good outcome could be spared unnecessary and potentially debilitating treatments. [00202] Biomarkers provide an opportunity to identify subpopulations of patients who are most likely to respond to a given therapy. This application will allow more informed decisions about modifying and adapting treatment protocols to subpopulations and also help guide patient enrollment into clinical trials. [00203] Cancer biomarkers exist in many different forms, including physiologic (patient performance status), images (mammograms), specific molecules (prostate-specific antigen, PSA), genetic alterations (BRCA mutations), gene or protein expression profiles (serum protein electrophoresis for detection of monoclonal gammopathies), and cell-based markers (circulating tumor cells), among others. With recent technological advances in molecular biology, the range of cancer biomarkers has expanded dramatically to encompass identification of single-nucleotide polymorphisms (SNPs), genomic profiling, transcriptome analysis, splice differences, and proteomic analysis.
[00204] As applied to drug development, the biomarker hypothesis states that changes in levels of blood or tissue proteins, individually or multiplexed, are highly and specifically characteristic of disease states and therapeutic outcomes. The basis of this hypothesis is that biological systems are adaptive and that challenges to homeostasis affect characteristic levels of proteins. Biomarker development occurs in a multi-step process of discovery, followed by replication in independent cohorts, validation of diagnostic sensitivity and specificity, and, finally, translation into a clinical diagnostic test or surrogate endpoint in a clinical study. Candidate biomarkers are triaged at each stage of development. A biomarker can be a single protein, such as prostate-specific antigen, a panel of proteins or genes or a combination of one or more proteins, genes, and other clinical measures, together with an algorithm that integrates these into an individual profile. XI. Formulation
[00205] Based on the results obtained with the compounds synthesized, it is contemplated that these compounds will comprise significant therapeutic application. In particular, these compounds should modulate appropriate kinase signaling and the biological effects associated therewith. More specifically, these compounds should selectively modulate cell proliferation and/or differentiation and/or promote apoptosis especially of cancer and other neoplastic cells. Pathways affected by the inhibition of the various kinases should be as indicated. [00206] Description of formulation and compounding include, e.g., Johnston (2005) Compounding: The Pharmacy Technician Series Prentice Hall, ISBN: 0131147609; Rowe, et al. (eds. 2005) Handbook of Pharmaceutical Excipients (5th ed.) APhA Pub., ISBN: 1582120587; Allen, et al. (eds. 2004) Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems (8th ed.) Lippincott Williams & Wilkins, ISBN: 0781746124; Allen (2002) The Art. Science, and Technology of Pharmaceutical Compounding (2d ed.) APhA Pub., ISBN: 1582120358; Stahl and Wermuth (eds. 2002) Handbook of Pharmaceutical Salts: Properties. Selection, and Use Wiley-VCH, ISBN: 3906390268; Gibson (2001) Pharmaceutical Preformulation and Formulation: A Practical Guide from Candidate Drug Selection to Commercial Dosage Form CRC, ISBN: 1574911201; Carstensen (1998) Pharmaceutical Preformulation CRC, ISBN: 1566766907; references cited therein, and similar or related publications.
[00207] Thus, the compounds produced according to the invention will be used to treat conditions wherein the pattern of inhibition of the various kinase signaling pathways is therapeutically beneficial. This will include conditions that involve abnormal cell growth and/or differentiation such as cancers and other neoplastic conditions. Also, the subject compounds may be used to treat other conditions involving abnormal cell proliferation and/or differentiation such as neoplastic conditions and disorders. The selected indication is often cancer, especially cancers involving abnormal levels of expression of the relevant kinase(s) or close relatives, cancers that express variant or mutant relatives, or cancers which comprise genetic translocation or deletion of the kinase(s). [00208] The subject therapies will comprise administration of at least one compound according to the invention in an amount sufficient to elicit a therapeutic response, e.g., inhibition of one or more of tumor cell proliferation, differentiation, metastasis, mutagenesis, or promotion of apoptosis. The compound may be administered alone, or may be targeted by various means, including liposomes, targeted liposomes, antibody targeting mechanisms, localized activation methods, targeting conjugates, conjugates with site activatable active components, and the like.
[00209] One embodiment provides a method of treating an indication selected from hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, and similar neoplastic conditions. Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, anorexia, macular degeneration, diabetic retinopathy, retinal vein occlusion, and retinopathy of prematurity, scleroderma, cardiofaciocutaneous syndrome, chronic myeloid leukemia, androgen independent prostate cancer cells, head and neck squamous cell carcinoma, cervical cancer, and similar neoplastic conditions; the method comprising administering to a subject a compound of Formula I or a compound of Formula in. [00210] Another embodiment provides a method of treating an indication selected from hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, melanoma, thyroid carcinoma, neuroendocrine gastroenteropancreatic tumors, lymphoblastic leukemia and similar neoplastic conditions. Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, macular degeneration, diabetic retinopathy, retinal vein occlusion, retinopathy of prematurity, scleroderma, cardiofaciocutaneous syndrome; the method comprising administering to a subject a compound of Formula II or a compound of Formula FV. [00211] The invention described herein includes a pharmaceutical composition which is comprised of a compound of the indicated formulae, including a pharmaceutically acceptable salt or hydrate thereof in combination with a carrier. As used herein the terms "pharmaceutically acceptable salts" and "hydrates" refer to those salts and hydrated forms of the compound which would be apparent to the pharmaceutical chemist, i.e., those which favorably affect the physical or pharmacokinetic properties of the compound, such as solubility, palatability, absorption, distribution, metabolism and excretion. Other factors, more practical in nature, which are also of interest in the selection, are the cost of the raw materials, ease of crystallization, yield, stability, solubility, hygroscopicity, and flowability of the resulting bulk drug.
[00212] When a compound is present as a salt or hydrate which is non-pharmaceutically acceptable, this can be converted to a salt or hydrate form which is pharmaceutically acceptable in accordance with the present invention. When the compound is negatively charged, it is balanced by a counterion, e.g., an alkali metal cation such as sodium or potassium. Other suitable counterions include calcium, magnesium, zinc, ammonium, or alkylammonium cations such as tetramethylammonium, tetrabutylammonium, choline, triethylhydroammonium, meglumine, triethanolhydroammonium, etc. An appropriate number of counterions is associated with the molecule to maintain overall charge neutrality. Likewise when the compound is positively charged, e.g., protonated, an appropriate number of negatively charged counterions is present to maintain overall charge neutrality.
[00213] Pharmaceutically acceptable salts also include acid addition salts. Thus, the compound can be used in the form of salts derived from inorganic or organic acids or bases. Examples include acetate, adipate, alginate, aspartate, benzoate, benzenesulfonate, bisulfate, butyrate, citrate, camphorate, camphorsulfonate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, glucoheptanoate, glycerophosphate, hemisulfate, heptanoate, hexanoate, hydrochloride, hydrobromide, hydroiodide, 2- hydroxyethanesulfonate, lactate, maleate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, oxalate, pamoate, pectinate, persulfate, 3-phenylpropionate, picrate, pivalate, propionate, succinate, tartrate, thiocyanate, tosylate and undecanoate. Base salts include ammonium salts, alkali metal salts such as sodium and potassium salts, alkaline earth metal salts such as calcium and magnesium salts, salts with organic bases such as dicyclohexylamine salts, N-methyl-D-glucamine, and salts with amino acids such as arginine, lysine, and so forth. Also, the basic nitrogen-containing groups may be quaternized with such agents as lower alkyl halides, such as methyl, ethyl, propyl, and butyl chloride, bromides and iodides; dialkyl sulfates like dimethyl, diethyl, dibutyl; and diamyl sulfates, long chain halides such as decyl, lauryl, myristyl and stearyl chlorides, bromides and iodides, aralkyl halides like benzyl and phenethyl bromides and others. Other pharmaceutically acceptable salts include the sulfate salt ethanolate and sulfate salts.
[00214] The compounds of the present invention may have asymmetric centers and occur as racemates, racemic mixtures and as individual diastereomers, or enantiomers with all isomeric forms being included in the present invention. When any variable (e.g., aryl, heterocyle, Rl, etc.) occurs more than one time in any constituent or in Formula I, its definition on each occurence is independent of its definition at every other occurrence, unless otherwise stated. XII. Therapy
[00215] In one embodiment, a therapeutically effective dose of a kinase modulator is administered to a patient. By "therapeutically effective dose" herein is meant a dose that produces effects for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using acceptable techniques (e.g., Ansel et al., Pharmaceutical Dosage Forms and Drug Delivery, Lippincott, Williams & Wilkins Publishers, ISBN:0683305727; Lieberman (1992) Pharmaceutical Dosage Forms (vols. 1-3), Dekker, ISBN 0824770846, 082476918X, 0824712692, 0824716981; Lloyd (1999) The Art, Science and Technology of Pharmaceutical Compounding, Amer. Pharmaceutical Assn, ISBN 0917330889; and Pickar (1999) Dosage Calculations, Delmar Pub, ISBN 0766805042). As is known in the art, adjustments for physiologic degradation, systemic versus localized delivery, and rate of new kinase synthesis, as well as the age, body weight, general health, sex, diet, time of administration, drug interaction and the severity of the condition may be necessary, and will be ascertainable with routine experimentation by those skilled in the art.
[00216] A "patient" for the purposes of the present invention includes both humans and other animals, particularly mammals. Thus the methods are applicable to both human therapy and veterinary applications. In the selected embodiment the patient is a mammal, preferably a primate, and in one embodiment the patient is human.
[00217] The administration of the modulators of the present invention can be done in a variety of ways, either systemic or local, including, but not limited to, orally, subcutaneously, intravenously, intranasally, transdermally, intraperitoneally, intramuscularly, intrapulmonary, vaginally, rectally, intraocularly, or directly onto a mucosal surface. [00218] The compounds of the invention can be formulated in a pharmaceutical composition by combining the compound with a pharmaceutically acceptable carrier. Examples of such compositions and carriers are set forth below. The subject compounds will be typically be administered in a pharmaceutically acceptable formulation or composition. Examples of such formulations include injectable solutions, tablets, milk, or suspensions, creams, oil-in-water and water-in-oil emulsions, microcapsules, and microvesicles. In a selected embodiment, the pharmaceutical compositions are in a water soluble form, such as being present as pharmaceutically acceptable salts, which is meant to include both acid and base addition salts. "Pharmaceutically acceptable acid addition salt" refers to those salts that retain the biological effectiveness of the free bases and that are not biologically or otherwise undesirable, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, and organic acids such as acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid and the like. "Pharmaceutically acceptable base addition salts" include those derived from inorganic bases such as sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Salts of interest include the ammonium, potassium, sodium, calcium, and magnesium salts. Salts derived from pharmaceutically acceptable organic non-toxic bases include salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, and ethanolamine. [00219] The compounds may be employed in powder or crystalline form, in solution or in suspension. They may be administered orally, parenterally (intravenously or intramuscularly), topically, transdermally or by inhalation. [00220]Thus, the carrier employed may be, for example, either a solid or liquid. Examples of solid carriers include lactose, terra alba, sucrose, talc, gelatin, agar, pectin, acacia, magnesium stearate, stearic acid and the like. Examples of liquid carriers include syrup, peanut oil, olive oil, water and the like. Similarly, the carrier for oral use may include time delay material well known in the art, such as glyceryl monostearate or glyceryl distearate alone or with a wax. The pharmaceutical compositions may also include one or more of the following: carrier proteins such as serum albumin; buffers; fillers such as microcrystalline cellulose, lactose, corn and other starches; binding agents; sweeteners and other flavoring agents; coloring agents; and polyethylene glycol. [00221] Typically, oral administration or administration via injection is preferred. The subject compounds may be administered in a single dosage or chronically dependent upon the particular disease, condition of patient, toxicity of compound, and whether this compound is being utilized alone or in combination with other therapies. Chronic or repeated administration will likely be selected based on other chemotherapies, and sustained release modalities are contemplated. [00222] Examples of oral solid dosage forms include tablets, capsules, troches, lozenges and the like. The size of the dosage form will vary widely, but preferably will be from about 25 mg to about 500 mg. Examples of oral liquid dosage forms include solutions, suspensions, syrups, emulsions, soft gelatin capsules and the like. Examples of injectable dosage forms include sterile injectable liquids, e.g., solutions, emulsions and suspensions. Examples of injectable solids would include powders which are reconstituted, dissolved or suspended in a liquid prior to injection. For example, unit dosage forms suitable for oral administration include, but are not limited to, powder, tablets, pills, capsules and lozenges. It is recognized that kinase modulators (e.g., small organic molecules, etc.) when administered orally, should be protected from digestion. This is typically accomplished either by complexing the molecule(s) with a composition to render it resistant to acidic and enzymatic hydrolysis, or by packaging the molecule(s) in an appropriately resistant carrier, such as a liposome or a protection barrier. Means of protecting agents from digestion are well known in the art. [00223] Topical applications may be formulated in carriers such as hydrophobic or hydrophilic bases to form ointments, creams, lotions, in aqueous, oleaginous or alcoholic liquids to form paints or in dry diluents to form powders. Such topical formulations can be used to treat ocular diseases as well as inflammatory diseases such as rheumatoid arthritis, psoriasis, contact dermatitis, delayed hypersensitivity reactions and the like. [00224] In injectable compositions, the carrier is typically comprised of sterile water, saline or another injectable liquid, e.g., peanut oil for intramuscular injections. Also, various buffering agents, preservatives and the like can be included. A typical pharmaceutical composition for intravenous administration would be about 0.1 to 10 mg per patient per day. Dosages from 0.1 up to about 100 mg per patient per day may be used, particularly when the drug is administered to a secluded site and not into the blood stream, such as into a body cavity or into a lumen of an organ. Substantially higher dosages are possible in direct or topical administration. Actual methods for preparing parenterally administrable compositions will be known or apparent to those skilled in the art, e.g., Remington's Pharmaceutical Science and Goodman and Gillman, The Pharmacological Basis of Therapeutics, supra.
[00225] These compositions will typically comprise conventional pharmaceutical excipients and carriers used in drug formulations, e.g., water, saline solutions, such as phosphate buffered saline, buffers, and surfactants. [00226] The subject compounds may be free or entrapped in microcapsules, in colloidal drug delivery systems such as liposomes, microemulsions, and macroemulsions. Also, solid formulations containing the subject compounds, such as tablets, and capsule formulations, may be prepared.
[00227] Suitable examples thereof include semipermeable materials of solid hydrophobic polymers containing the subject compound which may be in the form of shaped articles, e.g., films or microcapsules, as well as various other polymers and copolymers known in the art. The dosage effective amount of compounds according to the invention will vary depending upon factors including the particular compound, toxicity, and inhibitory activity, the condition treated, and whether the compound is administered alone or with other therapies. Typically a dosage effective amount will range from about 0.0001 mg/kg to 1500 mg/kg, more preferably 1 to 1000 mg/kg, more preferably from about 1 to 150 mg/kg of body weight, and most preferably about 50 to 100 mg/kg of body weight. The subjects treated will typically comprise warm blooded species, such as mammals, and most preferably will be primate subjects, e.g., human cancer subjects.
[00228] The compounds of the invention may be used alone or in combination. Additionally, the treated compounds may be utilized with other types of treatments, e.g., cancer treatments. For example, the subject compounds may be used with other chemo- or other therapies, e.g., tamoxifen, taxol, methotrexate, biologicals, such as antibodies, growth factors, lymphokines, or radiation, RNAi, etc. Combination therapies may result in synergistic results.
[00229] For the methods of treatment disclosed herein, dosages can be varied depending upon the overall condition of the patient, the nature of the illness being treated and other factors. An example of a suitable oral dosage range is from about 0.1 to about 80 mg/kg per day, in single or divided doses. An example of a suitable parenteral dosage range is often from about 0.1 to about 80 mg/kg per day, in single or divided dosages, administered by intravenous or intramuscular injection. An example of a topical dosage range is from about 0.1 mg to about 150 mg, applied externally from about one to four times a day. An example of an inhalation dosage range is from about 0.01 mg/kg to about 1 mg/kg per day. [00230] The examples which follow illustrate the compounds that can be synthesized but they are not limited by the compounds in the tables nor by any particular substituents employed in the schemes for illustrative purposes. [00231] The compounds may be administered in conventional dosages as a single agent or in combination with other therapeutically active compounds. The non-limiting examples that follow are illustrations of the compounds of the instant invention and are not meant to limit the invention in any way. [00232] The compositions containing kinase modulators can be administered for therapeutic or prophylactic treatments. In therapeutic applications, compositions are administered to a patient suffering from a disease (e.g., a cancer) in an amount sufficient to cure or at least partially delay or arrest the disease and its complications. An amount adequate to accomplish this is defined as a "therapeutically effective dose." Amounts effective for this use will depend upon the severity of the disease and the general state of the patient's health. Single or multiple administrations of the compositions may be administered depending on the dosage and frequency as required and tolerated by the patient. In any event, the composition should provide a sufficient quantity of the agents of this invention to effectively treat the patient. An amount of modulator that is capable of preventing or slowing the development of cancer in a mammal is referred to as a "prophylactically effective dose." The particular dose required for a prophylactic treatment will depend upon the medical condition and history of the mammal, the particular cancer being prevented, as well as other factors such as age, weight, gender, administration route, efficiency, etc. Such prophylactic treatments may be used, e.g., in a mammal who has previously had cancer to prevent a recurrence of the cancer, or in a mammal who is suspected of having a significant likelihood of developing cancer. [00233] In certain embodiments, the compounds may be administered using targeted adjuncts; delivery systems; antibody linkages, localized activation, and other means to provide localized effect. [00234] It will be appreciated that the present kinase-modulating compounds can be administered alone or in combination with additional modulating compounds or with other therapeutic agent, e.g., other anti-cancer agents or treatments.
[00235] All references cited herein are incorporated herein by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference in its entirety for all purposes.
[00236] Many modifications and variations of this invention can be made without departing from its spirit and scope, as will be apparent to those skilled in the art. The invention has been described in terms of selected embodiments, but the skilled artisan will appreciate that various modifications, substitutions, omissions and changes may be made without departing from the spirit thereof. The specific embodiments described herein are offered by way of example and the invention is to be limited by the terms of the appended claims, along with the full scope of equivalents to which such claims are entitled.

Claims

CLAIMSWhat is claimed is:
1. A compound of Formula (I) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000100_0001
Formula (I) wherein, X is O or NH; Z is CH or N;
A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R1 substituents;
B is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R7 substituents; R2 and R8 are independently selected from hydrogen, halogen, hydroxy, OR9, CN, amino, NHR9 or C 1-6 alkyl;
R1 and R7 are independently selected from hydrogen, halogen, OR9, Cl-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR9, CON(R9)2, NHR9, N(R9)2, COR9, C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR9, hydroxy, Cl-6alkoxy, OC(O)R9, -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR9, OC0-4alkylC3-10heterocycloalkyl,
OC0-4alkylNR9, NR9COOR9, OCONR9, or NR9COR9; R3 and R4 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, NHAryl, NHR9, COOH, OR9, COOR9, CONHR9, or CON(R9)2; R3 and R4 may together form a 5-membered or 6- membered aryl or heteroaryl ring;
R5 and R6 are independently selected from hydrogen, C 1 -6 alkyl and optionally may be joined to form a 3-10 membered cycloalkyl; and
R9 is selected from hydrogen, C 1-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.
2. A compound of claim 1, wherein: X is O;
Z is CH or N; A is an optionally substituted aryl ring or an optionally substituted 6-membered heteroaryl ring having 1-4 ring heteroatoms selected from nitrogen or oxygen; said heterocyclic ring being monocyclic or polycyclic, optionally substituted with 1-3 R1 substituents;
B is an optionally substituted aryl ring or an optionally substituted 6-membered heteroaryl ring having 1-4 ring heteroatoms selected from nitrogen or oxygen; said heterocyclic ring being monocyclic or polycyclic, optionally substituted with 1-3 R7 substituents;
R2 and R8 are independently selected from hydrogen, halogen, hydroxy, OR9, CN, amino, NHR9 or Cl -6 alkyl; R1, R7 are independently selected from hydrogen, halogen, OR9, Cl-6 alkyl, nitro, CF3, CN, aryl, heteroaryl, COOR9, CON(R9)2, NHR9, N(R9)2, COR9, C0-4alkylC3-10cycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR9, hydroxy, Cl-6alkoxy, OC(O)R9, -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl,
NHCOOR9, OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR9, NR9COOR9, OCONR9, NR9COR9; R3 and R4 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, NHAryl, NHR9, COOH, OR9, COOR9, CONHR9, CON(R9J2; R3 and R4 may together form a 5-membered or 6- membered aryl or heteroaryl ring; R5 and R6 are hydrogen; and
R9 is selected from hydrogen, Cl-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl.
3. A compound selected from: N-(4-(6-chloropyridin-3-yl)phenyl)-l-(4-(oxazolo[5,4-b]pyridin-7-yloxy)phenyl)methanesulfonamide; or N-(4-(6-chloropyridin-3-yl)phenyl)-l-(4-(quinazolin-4-yloxy)phenyl)methanesulfonamide.
4. A compound of Formula (II) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000102_0001
a (II) wherein,
X is O, S or NH;
Y is O or NH; Z is CH or N;
A is an optionally substituted heteroaryl ring having between 6 and 12 members and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R1 substituents;
R7 is selected from hydrogen or Cl -6 alkyl;
R5 is selected from hydrogen, halogen, hydroxy, OR8, CN, amino, NHR8 or C 1-6 alkyl;
R1 and R4 are independently selected from hydrogen, halogen, OR8, Cl -6 alkyl, C2-6 alkenyl, C2-6 alkynyl, OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR8, CON(R8^, NHR8, N(R8)2, COR8,
C0-4alkylC3-10cycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR8, hydroxy, Cl-6alkoxy, OC(O)R8, -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR8, OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR8, NR8COOR8, OCONR8, or NR8COR8; R2 and R3 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, aminoaryl, NHR8, COOH, OR8, COOR8, CONHR8, CON(R8)2; R2 and R3 may together form a 5-membered or 6- membered heteroaryl ring; and
R8 is selected from hydrogen, Cl -6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl.
5. A compound of claim 4, wherein X is O;
Y is O; Z is CH;
A is a 6-membered heteroaryl ring with 1-3 R1 substitutents; R5 and R7 are hydrogen; R1 is selected from hydrogen, halogen, CF3, CN, NO2, CONHR8, CON(R8)2; R4 is selected from hydrogen, halogen, CF3, Cl-6 alkyl, aryl;
R2 and R3 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, CONHR8, CON(R8)2; R2 and R3 may together form a 5-membered or 6-membered heteroaryl ring; and R8 is selected from hydrogen, Cl-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl.
6. A compound selected from: l-(4-(oxazolo[5,4-b]pyridin-7-yloxy)phenyl)-3-(5-(5-(trifluoromethyl)pyridin-2-yl)oxazol-2-yl)urea; l-(4-(oxazolo[5,4-b]pyridin-7-yloxy)phenyl)-3-(5-(4-(trifluoromethyl)phenyl)oxazol-2-yl)urea; l-(4-(quinazolin-4-yloxy)phenyl)-3-(5-(5-(trifluoromethyl)pyridin-2-yl)oxazol-2-yl)urea;
N-methyl-4-(4-(3-(5-(5-(trifluoromethyl)pyridin-2-yl)oxazol-2-yl)ureido)phenoxy)picolinamide; N-methyl-4-(4-(3-(5-(4-(trifluoromethyl)phenyl)oxazol-2-yl)ureido)phenoxy)picolinamide; or l-(4-(quinazolin-4-yloxy)phenyl)-3-(5-(4-(trifluoromethyl)phenyl)oxazol-2-yl)urea.
7. A compound of Formula (HI) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000103_0001
Formula (III) wherein, X is O or NH; Z is CH or N;
A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R' substituents; B is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R7 substituents;
R2 and R8 are independently selected from hydrogen, halogen, hydroxy, OR9, CN, amino, NHR9 or C 1-6 alkyl; R1 and R7 are independently selected from hydrogen, halogen, OR9, Cl -6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR9, CON(R9)2, NHR9, N(R9)2, COR9, C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR9, hydroxy, Cl-6alkoxy, OC(O)R9, -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR9, OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR9, NR9COOR9, OCONR9, or NR9COR9;
R3 and R4 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, NHAryl, NHR9, COOH, OR9, COOR9, CONHR9, or CON(R9)2; R3 and R4 may together form a 5-membered or 6- membered aryl or heteroaryl ring;
R5 and R6 are independently selected from hydrogen or C 1-6 alkyl; and R9 is selected from hydrogen, Cl -6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.
8. A compound of claim 7, wherein
X is O;
Z is CH or N;
A is an optionally substituted aryl ring or an optionally substituted 6-membered heteroaryl ring having 1-4 ring heteroatoms selected from nitrogen or oxygen; said heterocyclic ring being monocyclic or polycyclic, optionally substituted with 1-3 R1 substituents;
B is an optionally substituted aryl ring or an optionally substituted 6-membered heteroaryl ring having 1-4 ring heteroatoms selected from nitrogen or oxygen; said heterocyclic ring being monocyclic or polycyclic, optionally substituted with 1-3 R7 substituents; R2 and R8 are independently selected from hydrogen, halogen, hydroxy, OR9, CN, amino, NHR9 or Cl -6 alkyl;
R1, R7 are independently selected from hydrogen, halogen, OR9, Cl-6 alkyl, nitro, CF3, CN, aryl, heteroaryl, COOR9, CON(R9)2, NHR9, N(R9)2, COR9, C0-4alkylC3-10cycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR9, hydroxy, Cl-6alkoxy, OC(O)R9, -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR9, OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR9, NR9COOR9, OCONR9, NR9COR9; R3 and R4 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, NHAryl, NHR9, COOH, OR9, COOR9, CONHR9,
Figure imgf000105_0001
R3 and R4 may together form a 5-membered or 6- membered aryl or heteroaryl ring;
R5 and R6 are hydrogen; and R9 is selected from hydrogen, Cl -6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl.
9. A compound selected from:
N-(4-(6-chloropyridin-3-yl)phenyl-N'-(4-(pyridin-4-yloxy)phenyl)-sulfamide; N-(4-(6-chloropyridin-3-yl)phenyl-N'-(4-(oxazolo[5,4-b]pyridin-7-yloxy)phenyl)-sulfamide; or N-(4-(6-chloropyridin-3-yl)phenyl-N'-(4-(quinazolin-4-yloxy)phenyl)-sulfamide.
10. A compound of Formula (IV) or pharmaceutically acceptable solvate, pharmaceutically acceptable salt, or pharmaceutically acceptable prodrug thereof:
Figure imgf000105_0002
Formula (IV) wherein, X is O or NH; Y is O, NH, -OCH2- or -CH2O- Z is CH or N; A is an optionally substituted aryl or optionally substituted heteroaryl ring, having 5 or 6 members, and 1-4 ring heteroatoms each independently selected from nitrogen, oxygen or sulfur; said ring being monocyclic or polycyclic, optionally substituted with 1-3 R1 substituents; R1 and R4 are independently selected from hydrogen, halogen, OR9, Cl-6 alkyl, C2-6 alkenyl, C2-C6 alkynyl, OCF3, nitro, CF3, CN, aryl, heteroaryl, COOR9, CON(R^2, NHR9, N(R9J2, COR9, C0-4alkylC3- lOcycloalkyl, C0-4alkylaryl, C0-4alkylheteroaryl, C2-4alkenylaryl, C2-4alkynylaryl, C0-4alkylheterocyclyl, CN, amino, NHCOR9, hydroxy, Cl-6alkoxy, OC(O)R9, -OC0-4alkylaryl, OC0-4alkylheteroaryl, -OC0-4alkylC3-10cycloalkyl, NHCOOR9, OC0-4alkylC3-10heterocycloalkyl, OC0-4alkylNR9, NR9COOR9, OCONR9, or NR9COR9;
R2 and R3 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, NO2, amino, NHAryl, NHR9, COOH, OR9, COOR9, CONHR9, or CON(R9)2; R2 and R3 may together form a 5-membered or 6- membered aryl or heteroaryl ring; R5 is selected from hydrogen, halogen, hydroxy, OR9, CN, amino, NHR9 or Cl-6 alkyl;
R6 and R7 are independently selected from hydrogen, Cl-6 alkyl and optionally may be joined to form a 3-10 membered cycloalkyl;
R8 is selected from hydrogen or Cl-6 alkyl; and R9 is selected from hydrogen, Cl-6 alkyl, C2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.
11. A compound of claim 10, wherein X is NH;
Y is -OCH2-; Z is CH; A is a 6-membered heteroaryl ring with 1-3 R1 substitutents;
R1 is selected from hydrogen, halogen, CF3, CN, NO2, CONHR8, CON(R8)2;
R2 and R3 are independently selected from hydrogen, halogen, CF3, CN, hydroxy, CONHR8, CON(R8)2; R2 and R3 may together form a 5-membered or 6-membered heteroaryl ring;
R4 is selected from hydrogen, halogen, CF3, Cl-6 alkyl, aryl; and R5, R6, R7, R8 are hydrogen.
12. A compound selected from:
N-(4-(quinolin-4-ylmethoxy)phenyl)-2-(5-(6-(trifluoromethyl)pyridin-3-yl)-lH-imidazol-2-yl)acetamide; N-(4-(pyridin-4-ylmethoxy)phenyl)-2-(5-(6-(trifluoromethyl)pyridin-3-yl)-lH-imidazol-2-yl)acetamide; 2-(5-(pyridin-3-yl)-lH-imidazol-2-yl)-N-(4-(pyridin-4-ylmethoxy)phenyl)acetamide; or 2-(5-(pyridin-3-yl)-lH-imidazol-2-yl)-N-(4-(quinolin-4-ylmethoxy)phenyl)acetamide.
13. A compound of any of the preceding claims, wherein said compound binds to the designated kinases in a pattern as described in Table 1.
14. compound of any of the preceding claims, wherein said compound modulates a biological activity modulated by the designated kinases in a pattern as described in Table 1.
15. . An antibody, antisense molecule, or RNAi molecule that modulates a biological activity modulated by the designated kinases in a pattern as described in Table 1.
16. A method of modulating the biochemical activity of a profile of kinases, said method comprising exposing said kinases to a compound of any of the preceding claims at an effective concentration.
17. The method of Claim 16, wherein said effective concentration is less than 1 mM.
18. The method of Claim 17, wherein said effective concentration is less than 100 nM.
19. The method of Claim 18, wherein said effective concentration is less than 10 nM.
20. The compound of Claim 1, wherein said pattern of selectivity exhibits at least about 0.5 log unit of specificity for said designated kinase effect.
21. A method of treating an indication selected from hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, and similar neoplastic conditions. Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, anorexia, macular degeneration, diabetic retinopathy, retinal vein occlusion, and retinopathy of prematurity, scleroderma, cardiofaciocutaneous syndrome, chronic myeloid leukemia, androgen independent prostate cancer cells, head and neck squamous cell carcinoma, cervical cancer, and similar neoplastic conditions; the method comprising administering to a subject a compound of Formula I or a compound of Formula III.
22. A method of treating an indication selected from hepatocellular carcinoma, anti-angiogenesis, chronic obstructive pulmonary disease, thyroid tumor, T-cell lymphoma, colorectal cancer, renal cell carcinoma, myeloid leukemia cells, gastrointestinal stromal carcinoma, non-Hodgkin lymphoma, juvenile hemangiomas, melanoma, thyroid carcinoma, neuroendocrine gastroenteropancreatic tumors, lymphoblastic leukemia and similar neoplastic conditions. Additional medical indications for use include autoimmune conditions, rheumatoid arthritis, inflammatory diseases, dermatological conditions, macular degeneration, diabetic retinopathy, retinal vein occlusion, retinopathy of prematurity, scleroderma, cardiofaciocutaneous syndrome; the method comprising administering to a subject a compound of Formula II or a compound of Formula IV.
23. A method according to Claim 21 or 22 further comprising administrering an antibody, an antisense or an
RNAi molecule that modulates a biological activity modulated by the designated kinases in a pattern as described in Table 1, in combination with said compound of Formula II or compound of Formula IV.
PCT/US2007/080113 2006-09-29 2007-10-01 Modulators of multiple kinases Ceased WO2008042867A2 (en)

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