[go: up one dir, main page]

US20150284422A1 - Inhibitors of protein methyltransferase dot1l and methods of use thereof - Google Patents

Inhibitors of protein methyltransferase dot1l and methods of use thereof Download PDF

Info

Publication number
US20150284422A1
US20150284422A1 US14/420,877 US201314420877A US2015284422A1 US 20150284422 A1 US20150284422 A1 US 20150284422A1 US 201314420877 A US201314420877 A US 201314420877A US 2015284422 A1 US2015284422 A1 US 2015284422A1
Authority
US
United States
Prior art keywords
amino
alkyl
compound
dot1l
halo
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Abandoned
Application number
US14/420,877
Other languages
English (en)
Inventor
Edward J. Olhava
Richard Chesworth
Roy M. Pollock
Lei Jin
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Epizyme Inc
Original Assignee
Epizyme Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Epizyme Inc filed Critical Epizyme Inc
Priority to US14/420,877 priority Critical patent/US20150284422A1/en
Assigned to Epizyme, Inc. reassignment Epizyme, Inc. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: OLHAVA, EDWARD J., JIN, LEI, POLLOCK, ROY M., CHESWORTH, RICHARD
Publication of US20150284422A1 publication Critical patent/US20150284422A1/en
Assigned to BIOPHARMA CREDIT PLC reassignment BIOPHARMA CREDIT PLC SECURITY INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: Epizyme, Inc.
Assigned to Epizyme, Inc. reassignment Epizyme, Inc. TERMINATION AND RELEASE OF SECURITY INTEREST IN PATENTS AT REEL/FRAME: 051057/0848 Assignors: BIOPHARMA CREDIT PLC
Abandoned legal-status Critical Current

Links

Images

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/16—Purine radicals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D473/00—Heterocyclic compounds containing purine ring systems
    • C07D473/26—Heterocyclic compounds containing purine ring systems with an oxygen, sulphur, or nitrogen atom directly attached in position 2 or 6, but not in both
    • C07D473/32—Nitrogen atom
    • C07D473/34—Nitrogen atom attached in position 6, e.g. adenine
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/14—Pyrrolo-pyrimidine radicals
    • C40B30/02—
    • G06F19/16—
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/30—Drug targeting using structural data; Docking or binding prediction
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/60—In silico combinatorial chemistry
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/60—In silico combinatorial chemistry
    • G16C20/64—Screening of libraries
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
    • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
    • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A61K31/7068—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
    • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A61K31/7068—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
    • A61K31/7072—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid having two oxo groups directly attached to the pyrimidine ring, e.g. uridine, uridylic acid, thymidine, zidovudine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
    • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A61K31/7076—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines containing purines, e.g. adenosine, adenylic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
    • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A61K31/7076—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines containing purines, e.g. adenosine, adenylic acid
    • A61K31/708—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines containing purines, e.g. adenosine, adenylic acid having oxo groups directly attached to the purine ring system, e.g. guanosine, guanylic acid

Definitions

  • the invention is based upon the discovery that a surprising conformational adaptation results in high-affinity inhibitor binding of aminonucleoside inhibitors of DOT1L to the enzyme and prolonged residence time.
  • the invention provides compounds useful for selectively inhibiting DOT1L.
  • the present invention also provides pharmaceutically acceptable salts, esters, and/or N-oxides, of these compounds.
  • the invention further features a method for designing, identifying, and/or optimizing a candidate DOT1L inhibitor.
  • the invention features a compound of Formula (I) below or a pharmaceutically acceptable salt or ester thereof:
  • Nuc is adenosine-like moiety or an analog or a derivative thereof
  • T is a linker group of a 6-10 carbon atoms, in which one or more carbon atoms are optionally replaced with a heteroatom and T is optionally substituted;
  • Nuc-T is capable of binding within the SAM binding pocket of human DOT1L which comprises amino acid residues 135-241 of SEQ ID NO: 1;
  • R 9 is a group such that R 9 induces a conformational adaptation in human DOT1L, wherein the conformational adaptation is the formation of a hydrophobic pocket domain which comprises amino acid residues 139-312 of SEQ ID NO: 1;
  • Nuc-T is capable of binding within the SAM binding pocket of human DOT1L which comprises amino acid residues 135-241 of SEQ ID NO: 1.
  • the invention features a method for designing and/or identifying a potential binding compound for protein DOT1L.
  • the method comprises:
  • the invention features a method for designing and/or identifying a potential binding compound for protein DOT1L, the method comprising computationally identifying a binding compound that binds to DOT1L using the atomic coordinates of Leu143, Met147, Phe239, and Tyr312 according to Table S1 or S2.
  • the invention features a method for designing and/or identifying a potential binding compound for protein DOT1L, the method comprising:
  • the invention also features a method of identifying a drug candidate for the treatment of a disease, the method comprising:
  • the invention features a DOT1L inhibitor having molecular dimensions compatible with the shape of a hydrophobic pocket domain of DOT1L characterized by the crystallography coordinates of human DOT1L amino acids Leu143, Met147, Phe239, and Tyr312, according to Table S1 or S2, wherein the compound has a biochemical IC 50 for DOT1L of less than 100 nM.
  • the invention also features a computer readable medium comprising the atomic coordinates of one or more DOT1L-Compound A2, DOT1L-Compound C1, DOT1L-Compound C118 and DOT1L-Compound D16.
  • the invention also features a method for designing, identifying, and/or optimizing a candidate DOT1L inhibitor compound or complex.
  • the method comprises:
  • the invention features a method for designing, identifying, and/or optimizing a candidate DOT1L inhibitor compound or complex that interacts with all or a part of a hydrophobic pocket domain which comprises amino acid residues 139-312 of SEQ ID NO: 1 and the SAM binding pocket of human DOT1L which comprises amino acid residues 135-241 of SEQ ID NO: 1.
  • the method includes
  • the invention also relates to a pharmaceutical composition of a compound of Formula (I) and a pharmaceutically acceptable carrier.
  • the invention also relates to a pharmaceutical composition
  • a pharmaceutical composition comprising a DOT1L inhibitor designed, identified, and/or optimized by the method disclosed herein and a pharmaceutically acceptable carrier.
  • the invention also relates to a pharmaceutical composition of a salt of a compound of Formula (I) or a salt of a DOT1L inhibitor designed, identified, and/or optimized by the method disclosed herein and a pharmaceutically acceptable carrier.
  • the invention also relates to a pharmaceutical composition of a hydrate of a compound of Formula (I) or a hydrate of a DOT1L inhibitor designed, identified, and/or optimized by the method disclosed herein and a pharmaceutically acceptable carrier.
  • the present invention provides methods of treating or preventing cancer.
  • the present invention provides methods of treating cancer.
  • the present invention also provides methods of preventing cancer.
  • the method includes administering to a subject in need thereof a therapeutically effective amount of the compound of Formula (I) or a therapeutically effective amount of a DOT1L inhibitor designed, identified, and/or optimized by the method disclosed herein.
  • the cancer can be a hematological cancer.
  • the cancer is leukemia. More preferably, the cancer is acute myeloid leukemia, acute lymphocytic leukemia or mixed lineage leukemia.
  • the present invention provides methods of treating or preventing a disease or disorder mediated by translocation of a gene on chromosome 11q23.
  • the present invention provides methods of treating a disease or disorder mediated by translocation of a gene on chromosome 11q23.
  • the present invention also provides methods of preventing a disease or disorder mediated by translocation of a gene on chromosome 11q23.
  • the method includes administering to a subject in need thereof a therapeutically effective amount of the compound of Formula (I) or a therapeutically effective amount of a DOT1L inhibitor designed, identified, and/or optimized by the method disclosed herein.
  • the present invention provides methods of treating or preventing a disease or disorder in which DOT1-mediated protein methylation plays a part or a disease or disorder mediated by DOT1-mediated protein methylation.
  • the present invention provides methods of treating a disease or disorder in which DOT1-mediated protein methylation plays a part or a disease or disorder mediated by DOT-mediated protein methylation.
  • the present invention also provides methods of preventing a disease or disorder in which DOT1-mediated protein methylation plays a part or a disease or disorder mediated by DOT1-mediated protein methylation.
  • the method includes administering to a subject in need thereof a therapeutically effective amount of the compound of Formula (I) or a therapeutically effective amount of a DOT1L inhibitor designed, identified, and/or optimized by the method disclosed herein.
  • the present invention provides methods of inhibiting DOT1L activity in a cell.
  • the method includes contacting the cell with an effective amount of one or more of the compound of Formula (I) or one or more of the DOT1L inhibitor designed, identified, and/or optimized by the method disclosed herein.
  • Still another aspect of the invention relates to a method of reducing the level of Histone H3 Lysine residue 79 (H3-K79) methylation in a cell.
  • the method includes contacting a cell with a compound of the present invention.
  • Such method can be used to ameliorate any condition which is caused by or potentiated by the activity of DOT1 through H3-K79 methylation.
  • the present invention relates to use of the compounds disclosed herein in preparation of a medicament for treating or preventing cancer.
  • the use includes a compound of Formula (I) for administration to a subject in need thereof in a therapeutically effective amount.
  • the cancer can be a hematological cancer.
  • the cancer is leukemia. More preferably, the cancer is acute myeloid leukemia, acute lymphocytic leukemia or mixed lineage leukemia.
  • the present invention provides use of the compounds disclosed herein in preparation of a medicament for treating or preventing a disease or disorder mediated by translocation of a gene on chromosome 11q23.
  • the use includes a compound of Formula (I) or a DOT1L inhibitor designed, identified, and/or optimized by the method disclosed herein for administration to a subject in need thereof in a therapeutically effective amount.
  • the present invention provides use of the compounds disclosed herein in preparation of a medicament for treating or preventing a disease or disorder in which DOT1-mediated protein methylation plays a part or a disease or disorder mediated by DOT1-mediated protein methylation.
  • the use includes a compound of Formula (I) or a DOT1L inhibitor designed, identified, and/or optimized by the method disclosed herein for administration to a subject in need thereof in a therapeutically effective amount.
  • the present invention provides use of the compounds disclosed herein for inhibiting DOT1L activity in a cell.
  • the use includes contacting the cell with an effective amount of one or more of the compound of Formula (I) and/or the DOT1L inhibitor designed, identified, and/or optimized by the method disclosed herein.
  • Still another aspect of the invention relates to a use of the compounds disclosed herein for reducing the level of Histone H3 Lysine residue 79 (H3-K79) methylation in a cell.
  • the use includes contacting a cell with a compound of the present invention.
  • Such use can ameliorate any condition which is caused by or potentiated by the activity of DOT1 through H3-K79 methylation.
  • the invention provides methods of synthesizing the foregoing compounds.
  • a therapeutically effective amount of one or more of the compounds can be formulated with a pharmaceutically acceptable carrier for administration to a mammal, particularly humans, for use in modulating an epigenetic enzyme.
  • the compounds of the present invention are useful for treating, preventing, or reducing the risk of cancer or for the manufacture of a medicament for treating, preventing, or reducing the risk of cancer.
  • the compounds or the formulations can be administered, for example, via oral, parenteral, otic, ophthalmic, nasal, or topical routes, to provide an effective amount of the compound to the mammal.
  • FIG. 1 is a plot showing that Compound A2 causes complete and sustained tumor regression in a MV4-11 nude rat xenograft model of MLL-rearranged leukemia.
  • FIG. 2 includes plots showing biochemical characterization of Compound D16 inhibition of DOT1L.
  • Compound D16 is a competitive inhibitor with respect to SAM.
  • the IC 50 of Compound D16 was determined as a function of SAM concentration relative to the K m of SAM ([SAM]/K m ) and found to display a linear relationship as expected for competitive inhibition.
  • Inset Michaelis-Menten plot of product formation as a function of SAM concentration at various concentrations of Compound D16. The data were fit globally to a general equation for enzyme inhibition (Copeland R A, Evaluation of enzyme inhibitors in drug discovery. A guide for medicinal chemists and pharmacologists .
  • Compound D16 is a noncompetitive inhibitor with respect to oligonucleosome (Nucl).
  • the IC 50 of Compound D16 was determined as a function of Nuc concentration relative to the K m of Nucl ([Nucl]/K m ) and found to be independent of [Nucl]/K m , as expected for noncompetitive inhibition.
  • Inset Michaelis-Menten plot of product formation as a function of Nuc concentration at various concentrations of Compound D16. The data were fit globally to a general equation for enzyme inhibition (Copeland, 2005) and yield values of alpha of 0.5 ⁇ 0.2 and K i of 0.3 ⁇ 0.02 nM.
  • FIG. 3 is a plot showing superposition of SAM and Compound C1 within the active site of DOT1L, demonstrating conservation of binding motif.
  • DOT1L-SAM co-crystal structure (PDB code: 3QOW): in line presentation (carbon atoms: light blue; oxygen: red; nitrogen: dark blue).
  • SAM stick presentation (carbon atoms: light blue; oxygen: red; nitrogen: dark blue, sulfur: yellow).
  • Compound C1 stick presentation (carbon atoms: maroon; oxygen: red; nitrogen: dark blue). Hydrogen bonds between SAM and DOT1L are labeled by dashed lines.
  • FIG. 4A shows key contacts between DOT1L protein and the urea moiety of Compound C118 in the DOT1L-Compound C118 co-crystal structure.
  • SAM is superimposed on to Compound C118.
  • the interactions for 5′-amino and urea of Compound C118 are labeled by dashed lines.
  • DOT1L protein of the DOT1L-Compound C118 co-crystal structure in line presentation (carbon atoms: green; oxygen: red; nitrogen: dark blue).
  • Compound C118 stick presentation (carbon atoms: green).
  • SAM stick presentation (carbon atoms: light blue)
  • FIG. 4B shows opening of the hydrophobic pocket within the DOT1L-Compound C118 co-crystal structure.
  • Superimposition of DOT1L-SAM and DOT1L-Compound C118 demonstrates the opening of the hydrophobic pocket by the tert-butyl phenyl group on Compound C118.
  • DOT1L structures are presented in Ca trace. The key residue side chains which open the pocket are displayed as in line presentation. Comparison of these residues in the DOT1L-SAM and DOT1L-Compound C118 structures shows the conformational change and resultant opening of the hydrophobic pocket upon the binding of Compound C118.
  • DOT1L protein in line presentation (carbon atoms: green for the DOT1L-Compound C118 structure and light blue for the DOT1L-SAM structure; oxygen: red; nitrogen: dark blue).
  • Compound C118 stick presentation (carbon atoms: green).
  • SAM stick presentation (carbon atoms: light blue)
  • FIG. 4C shows loop disorder induced by binding of Compound C118 to DOT1L.
  • Superimposition of DOT1L-SAM and DOT1L-Compound C118 shows the disorder in 130s' and 300s' loops upon the binding of Compound C118.
  • DOT1L protein in line presentation (carbon atoms: green for the DOT1L-Compound C118 structure and light blue for the DOT1L-SAM structure).
  • Compound C118 stick presentation (carbon atoms: green; oxygen: red; nitrogen: dark blue).
  • SAM stick presentation (carbon atoms: light blue; oxygen: red; nitrogen: dark blue; sulfur: yellow)
  • FIG. 5 is superimposition of Compound D16 and Compound C118 structures.
  • the DOT1L protein of DOT1L-Compound D16 is in surface presentation in grey.
  • Compound D16 carbon atoms: magenta
  • Compound C118 carbon atoms: green.
  • FIG. 6 is a ligand plot to show the binding pockets of DOT1L in complex with Compound A2.
  • FIG. 7 is a ligand plot to show the binding pockets of DOT1L in complex with Compound D16.
  • FIG. 8 is a ligand plot to show the binding pockets of DOT1L in complex with Compound D8.
  • FIG. 9 is a ligand plot to show the binding pockets of DOT1L in complex with Compound C118.
  • FIG. 10 is a series of images showing 2Fo-Fc maps for Compounds C1 (A), C118 (B) and D16 (C). All maps were contoured at 1 ⁇ .
  • Certain aspects of the present invention provide compounds that can be used to selectively modulate the aberrant action of an epigenetic enzyme. Further, the compounds can be used to treat or prevent a disease state in a mammal caused or mediated by aberrant action of an epigenetic enzyme.
  • the present invention includes pharmaceutically acceptable salts, esters, tautomers, and N-oxides of these compounds. Certain aspects of the present invention also provide methods of designing, identifying, and/or optimizing novel compounds as DOT1L inhibitors, synthetic methods for making the compounds, pharmaceutical compositions containing them and various uses of the compounds.
  • One aspect of the present invention relates to compounds that selectively modulate the activity of the histone methyltransferase DOT1L, an enzyme known to methylate lysine 79 of histone H3 (“H3K79”) in vivo (Feng et al. (2002) Curr. Biol. 12:1052-1058).
  • DOT1L contains a S-adenosylmethionine (SAM) binding site and uses SAM as a methyl donor.
  • SAM S-adenosylmethionine
  • the DOT1 polypeptides do not contain a SET domain.
  • DOT1L nucleic acid and polypeptides have previously been described (see, e.g., U.S. Patent Application Publication No. 2005-0048634 A1 (hereby incorporated by reference); Feng et al. (2002) Curr. Biol. 12:1052-1058; and Okada et al. (2005) Cell 121:167-78).
  • the sequences of the human nucleic acid and protein have been deposited under GenBank Accession No. AF509504, which is hereby incorporated by reference in its entirety. Only the approximately 360 N-terminal amino acids of hDOT1L share significant sequence similarity with the yeast DOT1.
  • DOT1 homologs from C. elegans GenBank Accession Nos.
  • NP510056 and CAA90610 Drosophila (GenBank Accession Nos. CG10272 and AAF54122), mouse (GenBank Accession No. XP125730), Anopheles gambiae (GenBank Accession No. EAA03558), and Neurospora crassa (GenBank Accession No. EAA33634) are available in public databases (the disclosures of which are incorporated by reference herein in their entireties). The SAM binding domain among these homologs is conserved (approximately 30-100% amino acid sequence identity and 50-100% amino acid similarity).
  • Various aspects of the present invention can be practiced with any DOT1L polypeptide or nucleic acid.
  • human DOT1L includes the protein comprising SEQ ID NO: 1 and variants thereof comprising at least about 70% amino acid sequence identity to SEQ ID NO: 1, or preferably 80%, 85%, 90% and 95% sequence identity to SEQ ID NO:1, or more preferably, at least about 95% or more sequence identity to SEQ ID NO:1.
  • hDOT1L plays an important role in MLL-AF10-mediated leukemogenesis (Okada et al. (2005) Cell 121:167-78). It was also shown that mistargeting of hDOT1L to the Hoxa9 gene by MLL-AF10 results in H3K79 methylation and Hoxa9 upregulation which contributes to leukemic transformation (Okada et al. (2005) Cell 121:167-78). It was further demonstrated that the hDOT1L and MLL-AF10 interaction involves the OM-LZ (octapeptide motif-leucine zipper) region of AF10, required for MLL-AF10-mediated leukemic transformation (DiMartino et al.
  • OM-LZ octapeptide motif-leucine zipper
  • CALM-AF10 fusion appears to be both necessary and sufficient to mediate leukemogenesis in vitro and in vivo; that hDOT1L and its H3K79 methyltransferase activity are implicated in CALM-AF10-mediated leukemic transformation; and that the Hoxa5 gene is involved in CALM-AF10-mediated transformation (U.S. Patent Application Publication No. 2009-0061443 A1, which is hereby incorporated by reference in its entirety). Aberrant recruitment of DOT1L leading to deregulated gene expression may be a common feature of many other oncogenic MLL-fusion proteins.
  • the MLL fusion partners ENL, AF4, and AF9 are normally found in nuclear complexes with DOT1L (Bitoun et al. (2007) Hum. Mol. Genet. 16:92-106, Mueller et al. (2007) Blood 110:4445-54, Zhang et al. (2006) J. Biol. Chem . 281:18059-68), and altered H3K79 methylation profiles are a feature of murine and human MLL-AF4 leukemias (Krivstov et al. (2008) Cancer Cell 14:355-368).
  • the present disclosure presents the design and optimization of a series of aminonucleoside inhibitors of the PKMT DOT1L.
  • Using the crystal structures of various aminonucleoside inhibitors bound to human DOT1L the key recognition elements of ligand binding to the enzymatic active site have been systematically defined. Conformational adaptation is a common feature of enzyme catalysis and of high-affinity ligand interactions with enzymes. This is clearly the case with the potent aminonucleoside inhibitors of DOT1L.
  • a novel hydrophobic pocket, immediately adjacent to the SAM binding site of the enzyme has been discovered by the applicants. It was opened up to accommodate the extended aminonucleoside compounds that had been originally designed to engage the lysine binding channel of the contiguous enzyme active site.
  • This structural adaptation results in very high-affinity binding of aminonucleosides to the enzyme and provided new directions for inhibitor optimization.
  • the conformational adaptation mechanism of inhibitor binding demonstrated for the aminonucleosides also results in extended residence time for the optimized members of this inhibitor series.
  • D16 displays a DOT1L enzyme residence time of sixty minutes, as measured by surface plasmon resonance.
  • a long residence time on PMT targets, such as DOT1L may prove to be of value in demonstrating durable pharmacology in patients.
  • the invention features a method of designing, identifying, and/or optimizing an inhibitor of DOT1L, e.g., an aminonucleoside DOT1L inhibitor.
  • the designing of inhibitors can be initiated using mechanism-guided design principles, based on the DOT1L enzymatic reaction mechanism, and optimized through structure-guided approaches using iterative enzyme-inhibitor complex crystal structures.
  • conformational adaptation of the enzyme active site attends potent inhibitor binding and this observation can be taken into account to develop a cogent structure-activity relationship (SAR) for active site-directed DOT1L inhibition.
  • SAR cogent structure-activity relationship
  • this optimization process results in Compound D16, which is a picomolar inhibitor of DOT1L with extraordinar selectivity for its target enzyme.
  • Compound D16 has been shown to demonstrate potent and selective killing of MLL-rearranged leukemic cells, both in cell culture and in a highly aggressive disseminated mouse model of this disease.
  • the methods described herein provide ways to identify, design, or optimize potent, selective small molecule inhibitors of DOT1L to affect selective killing of MLL-rearranged leukemias.
  • the method of the invention includes:
  • step (b) identifying amino acid residues forming an hydrophobic pocket site in the three-dimensional structure of DOT1L from step (a), wherein the hydrophobic pocket domain of DOT1L is characterized by the crystallography coordinates of human DOT1L amino acids Leu143, Met147, Phe239, and Tyr312 according to Table S1 or S2;
  • the method can further include contacting the identified candidate inhibitor with the DOT1L in order to determine the effect of the inhibitor on DOT1L enzymatic activity, e.g., by evaluating the residence time, K i value, or in an in vivo study.
  • the invention also features a method of identifying a drug candidate for the treatment of a disease, the method comprising:
  • the invention also features a method for designing, identifying, and/or optimizing a candidate DOT1L inhibitor compound or complex.
  • the method comprises:
  • the invention features a method of locating a binding site of a candidate DOT1L inhibitor compound or complex that modulates the activity of human DOT1L.
  • the method comprises:
  • step (c) subtracting the X-ray diffraction data obtained in step (a) from the X-ray diffraction data obtained in step (b) to obtain the difference in the X-ray diffraction data;
  • step (d) obtaining phases that correspond to X-ray diffraction data obtained in step (a);
  • step (e) utilizing the phases obtained in step (d) and the difference in the X-ray diffraction data obtained in step (c) to compute a difference Fourier image of the candidate inhibitor;
  • step (f) locating the binding site of the candidate inhibitor to human DOT1L based on the computations obtained in step (e).
  • the crystal in step (a) includes human DOT1L in complex with SAM or SAH, or Compound D16 or A2.
  • the DOT1L-inhibitor complex in step (b) comprises the hydrophobic pocket domain which comprises amino acid residues 139-312 of SEQ ID NO: 1 and the SAM binding pocket which comprises amino acid residues 135-241 of SEQ ID NO: 1.
  • the invention features a method for designing, identifying, and/or optimizing a candidate DOT1L inhibitor compound or complex that interacts with all or a part of a hydrophobic pocket domain which comprises amino acid residues 139-312 of SEQ ID NO: 1 and the SAM binding pocket of human DOT1L which comprises amino acid residues 135-241 of SEQ ID NO: 1.
  • the method includes
  • the SAM binding pocket of human DOT1L is characterized by the crystallography coordinates of human DOT1L amino acids Asp161, Gly163, Glu 186, Asp222, and Asn241.
  • the crystallography coordinates are within about a root mean square deviation of not more than about 3 ⁇ (e.g., not more than about 2.5 ⁇ , not more than about 2 ⁇ , or not more than about 1.5 ⁇ ) from the backbone atoms of the amino acids according to Table S1 or S2.
  • the SAM binding pocket of human DOT1L is characterized by the crystallography coordinates of human DOT1L amino acids Val135, Thr139, Asp161, Gly163, Gln168, Glu 186, Asp222, and Asn241.
  • the crystallography coordinates are within about a root mean square deviation of not more than about 3 ⁇ (e.g., not more than about 2.5 ⁇ , not more than about 2 ⁇ , or not more than about 1.5 ⁇ ) from the backbone atoms of the amino acids according to Table S1 or S2.
  • the SAM binding pocket of human DOT1L is further characterized by the crystallography coordinates of human DOT1L amino acid Phe223, for example, the crystallography coordinates are within about a root mean square deviation of not more than about 3 ⁇ (e.g., not more than about 2.5 ⁇ , not more than about 2 ⁇ , or not more than about 1.5 ⁇ ) from the backbone atoms of the amino acid according to Table S1 or S2.
  • the hydrophobic pocket domain of human DOT1L is characterized by the crystallography coordinates of human DOT1L amino acids Leu143, Met147, Phe239, and Tyr 312, for example, the crystallography coordinates are within about a root mean square deviation of not more than about 3 ⁇ (e.g., not more than about 2.5 ⁇ , not more than about 2 ⁇ , or not more than about 1.5 ⁇ ) from the backbone atoms of the amino acids according to Table S1 or S2.
  • the hydrophobic pocket domain of human DOT1L is further characterized by the crystallography coordinates of human DOT1L amino acid Thr139, Val144, Val169, Phe239, Val240, Asn241, Val267, Ser268, or Ser269, or combination thereof, for example, the crystallography coordinates are within about a root mean square deviation of not more than about 3 ⁇ (e.g., not more than about 2.5 ⁇ , not more than about 2 ⁇ , or not more than about 1.5 ⁇ ) from the backbone atoms of the amino acid according to Table S1 or S2.
  • the SAM binding pocket or the hydrophobic pocket domain of human DOT1L is characterized by the ligand plot as shown in any of FIGS. 6-9 .
  • the binding affinity (K i ) of the compound to human DOT1L is not greater than 50 ⁇ M, not greater than 10 ⁇ M, not greater than 5 ⁇ M, not greater than 2.5 ⁇ M, or not greater than 1 ⁇ M.
  • association refers to a condition of proximity between a chemical entity or compound, or portions thereof, and a binding pocket or binding site on a protein.
  • the association may be non-covalent, wherein the juxtaposition is energetically favored by hydrogen bonding, hydrophobic, van der Waals or electrostatic interactions, or it may be covalent.
  • binding pocket or “binding site” of DOT1L refers to a region of DOT1L or a molecular complex comprising DOT1L that, as a result of the primary amino acid sequence of human DOT1L and/or its three-dimensional shape, favorably associates with another chemical entity.
  • the term “pocket” includes, but is not limited to, a cleft, channel or site.
  • the shape of a binding pocket may be largely pre-formed before binding of a chemical entity, may be formed simultaneously with binding of a chemical entity, or may be formed by the binding of another chemical entity to a different binding pocket of the molecule, which in turn induces a change in shape of the binding pocket.
  • chemical entity refers to chemical compounds, complexes of at least two chemical compounds, and fragments of such compounds or complexes.
  • the chemical entity can be, for example, a ligand, substrate, nucleotide triphosphate, nucleotide diphosphate, phosphate, nucleotide, agonist, antagonist, inhibitor, antibody, peptide, protein or drug.
  • the chemical entity is an inhibitor or substrate for the active site.
  • DOT1L complex refers to a molecular complex formed by associating the DOT1L protein with a chemical entity, for example, a ligand, a substrate, nucleotide triphosphate, nucleotide diphosphate, phosphate, an agonist or antagonist, inhibitor, antibody, drug or compound.
  • a chemical entity for example, a ligand, a substrate, nucleotide triphosphate, nucleotide diphosphate, phosphate, an agonist or antagonist, inhibitor, antibody, drug or compound.
  • an inhibitor complex refers to an association of two or more chemical compounds which can inhibit DOT1L activity.
  • an inhibitor complex is a complex of a compound having the adenosine-like moiety and another compound having a R 9 group and the complex does not have the linker group T.
  • root mean square deviation means the square root of the arithmetic mean of the squares of the deviations from the mean.
  • hydrophilic atoms either O or N
  • hydrogen bond refers to two hydrophilic atoms (either O or N), which share a hydrogen that is covalently bonded to only one atom, while interacting with the other.
  • hydrophobic interaction refers to interactions made by two hydrophobic residues or atoms (such as carbon).
  • crystal coordinates or “structure coordinates” refers to mathematical coordinates that describe the positions of atoms in crystals of hDOT1L in Protein Data Bank (PDB) format, including X, Y, Z and B, for each atom.
  • the diffraction data obtained from the crystals are used to calculate an electron density map of the repeating unit of the crystal.
  • the electron density maps may be used to establish the positions (i.e. coordinates X, Y and Z) of the individual atoms within the crystal.
  • ligand refers to any molecule, or chemical entity, which binds with or to DOT1L, a subunit of DOT1L, a domain of DOT1L, a target structural motif of DOT1L, or a fragment of DOT1L.
  • ligands include, but are not limited to, modulators of DOT1L activity such as small molecule inhibitors, small molecule agonists, and small molecule inverse agonists, for example.
  • small molecule inhibitor refers to ligands useful in the present invention having the ability to modulate a measurable amount of DOT1L activity.
  • a small molecule inhibitor has MW of less than 10,000 Daltons, and preferably less than 5,000 Daltons.
  • the term “homolog” refers to the DOT1L protein molecule or the nucleic acid molecule which encodes the protein, or a functional domain from said protein from a first source having at least about 70% or 75% sequence identity, or at least about 80% sequence identity, or more preferably at least about 85% sequence identity, or even more preferably at least about 90% sequence identity, and most preferably at least about 95%, 97% or 99% sequence identity, with the amino acid sequence of the protein, the encoding nucleic acid molecule, or any functional domain thereof, from a second source.
  • the second source may be a version of the molecule from the first source that has been genetically altered by any available means to change the primary amino acid or nucleotide sequence or may be from the same or a different species than that of the first source.
  • active site refers to regions on DOT1L or a structural motif of DOT1L that are directly involved in the function or activity of human DOT1L.
  • part of a binding pocket refers to less than all of the amino acid residues that define the binding pocket.
  • the structure coordinates of amino acid residues that constitute part of a binding pocket may be specific for defining the chemical environment of the binding pocket, or useful in designing fragments of an inhibitor that may interact with those residues.
  • the portion of amino acid residues may be key residues that play a role in ligand binding, or may be residues that are spatially related and define a three-dimensional compartment of the binding pocket.
  • the amino acid residues may be contiguous or non-contiguous in primary sequence.
  • part of the binding pocket has at least two amino acid residues, preferably at least three, six, eight, ten, fourteen or fifteen amino acid residues.
  • a candidate which can be identified or optimized as a DOT1L inhibitor by the method of the invention is a compound of Formula (I) below or a pharmaceutically acceptable salt or ester thereof:
  • Nuc is a nucleoside moiety (e.g., an adenosine-like moiety) or an analog or a derivative thereof,
  • T is a linker group of a 6-10 carbon atoms, in which one or more carbon atoms are optionally replaced with a heteroatom and T is optionally substituted;
  • Nuc-T is capable of binding within the SAM binding pocket of human DOT1L which comprises amino acid residues 135-241 of SEQ ID NO: 1;
  • R 9 is a group such that R 9 induces a conformational adaptation in human DOT1L, wherein the conformational adaptation is the formation of a hydrophobic pocket domain which comprises amino acid residues 139-312 of SEQ ID NO: 1
  • the compound of Formula (I) may include one or more of the following features:
  • R 9 is a group such that R 9 induces a residence time of the compound greater than 20 seconds in a complex formed of the compound and human DOT1L.
  • R 9 is a group such that R 9 induces a conformational adaptation in human DOT1L, wherein the conformational adaptation is the formation of a hydrophobic pocket domain which is characterized by the crystallography coordinates of human DOT1L amino acids Leu143, Met147, Phe239, and Tyr312, wherein the crystallography coordinates are within about a root mean square deviation of not more than about 2 ⁇ from the backbone atoms of the amino acids according to Table S1 or S2;
  • Nuc is an adenosine-like moiety.
  • the adenosine-like moiety can be any suitable adenosine-like moiety.
  • the adenosine-like moiety can be any adenosine-like moiety.
  • A is O or CH 2 ;
  • each of G and J independently, is H, halo, C(O)OH, C(O)O—C 1 -C 6 alkyl or OR a , R a being H, C 1 -C 6 alkyl, C(O)—C 1 -C 6 alkyl, or silyl, wherein C(O)O—C 1 -C 6 alkyl, C 1 -C 6 alkyl or C(O)—C 1 -C 6 alkyl is optionally substituted with one or more substituents selected from the group consisting of halo, cyano hydroxyl, carboxyl, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, and C 3 -C 8 cycloalkyl;
  • each of R 1 and R 2 independently is H, halo, hydroxyl, carboxyl, cyano, or R S2 , R S2 being amino, C 1 -C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, or C 3 -C 8 cycloalkyl, and each R S2 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, and 5 to 6-membered heteroaryl;
  • R 8 is H, halo or R S3 , R S3 being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and R S3 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano amino, C 1 -C 6 alkoxyl, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, and C 3 -C 5 cycloalkyl; and
  • Q is H, NH 2 , NHR b , NR b R c , R b , ⁇ O, OH, or OR b , in which each of R b and R c independently is C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 10-membered heteroaryl, or -M 1 -T 1 in which M 1 is a bond or C 1 -C 6 alkyl linker optionally substituted with halo, cyano, hydroxyl or C 1 -C 6 alkoxyl and T 1 is C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 10-membered heteroaryl, or R b and R c , together with
  • the adenosine-like moiety is adenosine-like moiety
  • the residence time of the compound in the DOT1L-compound complex is ⁇ 50 seconds, ⁇ 100 seconds, ⁇ 2 minutes, ⁇ 10 minutes, ⁇ 30 minutes, ⁇ 1 hr, ⁇ 5 hr, ⁇ 10 hr, ⁇ 20 hr, or ⁇ 30 hr.
  • the compound has a residence time in the DOT1L-compound complex not shorter than that of Compound D16.
  • the compound has a residence time in the DOT1L-compound complex not shorter than that of Compound A2.
  • the SAM binding pocket of human DOT1L is characterized by the crystallography coordinates of human DOT1L amino acids Asp161, Gly163, Glu 186, Asp222, and Asn241.
  • the crystallography coordinates are within about a root mean square deviation of not more than about 3 ⁇ (e.g., not more than about 2.5 ⁇ , not more than about 2 ⁇ , or not more than about 1.5 ⁇ ) from the backbone atoms of the amino acids according to Table S1 or S2.
  • the SAM binding pocket of human DOT1L is characterized by the crystallography coordinates of human DOT1L amino acids Val135, Thr139, Asp161, Gly163, Gln168, Glu 186, Asp222, and Asn241.
  • the crystallography coordinates are within about a root mean square deviation of not more than about 3 ⁇ (e.g., not more than about 2.5 ⁇ , not more than about 2 ⁇ , or not more than about 1.5 ⁇ ) from the backbone atoms of the amino acids according to Table S1 or S2.
  • the SAM binding pocket of human DOT1L is further characterized by the crystallography coordinates of human DOT1L amino acid Phe223.
  • the crystallography coordinates are within about a root mean square deviation of not more than about 3 ⁇ (e.g., not more than about 2.5 ⁇ , not more than about 2 ⁇ , or not more than about 1.5 ⁇ ) from the backbone atoms of the amino acid according to Table S1 or S2.
  • the hydrophobic pocket domain of human DOT1L is characterized by the crystallography coordinates of human DOT1L amino acids Leu143, Met147, Phe239, and Tyr 312.
  • the crystallography coordinates are within about a root mean square deviation of not more than about 3 ⁇ (e.g., not more than about 2.5 ⁇ , not more than about 2 ⁇ , or not more than about 1.5 ⁇ ) from the backbone atoms of the amino acids according to Table S1 or S2.
  • the hydrophobic pocket domain of human DOT1L is further characterized by the crystallography coordinates of human DOT1L amino acid Thr139, Val144, Val169, Phe239, Val240, Asn241, Val267, Ser268, or Ser269, or combination thereof, for example, the crystallography coordinates are within about a root mean square deviation of not more than about 3 ⁇ (e.g., not more than about 2.5 ⁇ , not more than about 2 ⁇ , or not more than about 1.5 ⁇ ) from the backbone atoms of the amino acid according to Table S1 or S2.
  • the SAM binding pocket or the hydrophobic pocket domain of human DOT1L is characterized by the ligand plot as shown in any of FIGS. 6-9 .
  • the binding affinity (K i ) of the compound to human DOT1L is not greater than 50 ⁇ M, not greater than 10 ⁇ M, not greater than 5 ⁇ M, not greater than 2.5 ⁇ M, or not greater than 1 ⁇ M.
  • R 9 comprises C 6 -C 10 aryl or 5 to 10-membered heteroaryl optionally substituted with one or more substituents selected from the group consisting of unsubstituted or substituted t-butyl, CF 3 , cyclohexyl, C 6 -C 10 aryl, and 5 to 10-membered heteroaryl.
  • R 9 is selected from the group consisting of
  • the compound is of Formula (II):
  • A is O or CH 2 ;
  • each of G and J independently, is H, halo, C(O)OH, C(O)O—C 1 -C 6 alkyl or OR a , R a being H, C 1 -C 6 alkyl, C(O)—C 1 -C 6 alkyl, or silyl, wherein C(O)O—C 1 -C 6 alkyl, C 1 -C 6 alkyl or C(O)—C 1 -C 6 alkyl is optionally substituted with one or more substituents selected from the group consisting of halo, cyano hydroxyl, carboxyl, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, and C 3 -C 8 cycloalkyl;
  • each X independently is N or CR x , in which R x is H, halo, hydroxyl, carboxyl, cyano, or R S1 , R S1 being amino, C 1 -C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and R S1 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalky
  • each of R 1 and R 2 independently is H, halo, hydroxyl, carboxyl, cyano, or R S2 , R S2 being amino, C 1 -C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, or C 3 -C 8 cycloalkyl, and each R S2 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, and 5 to 6-membered heteroaryl;
  • R 8 is H, halo or R S3 , R S3 being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and R S3 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano amino, C 1 -C 6 alkoxyl, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, and C 3 -C 5 cycloalkyl; and
  • Q is H, NH 2 , NHR b , NR b R c , R b , ⁇ O, OH, or OR b , in which each of R b and R c independently is C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 10-membered heteroaryl, or -M 1 -T 1 in which M 1 is a bond or C 1 -C 6 alkyl linker optionally substituted with halo, cyano, hydroxyl or C 1 -C 6 alkoxyl and T 1 is C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 10-membered heteroaryl, or R b and R c , together with
  • T is —CH 2 -L 1 -L 2 -L 3 -, with L 3 connected to R 9 , wherein:
  • L 1 is N(Y), S, SO, or SO 2 ;
  • L 2 is CO or absent when L 1 is N(Y), or L 2 is absent when L 1 is S, SO, or SO 2 , in which Y is H, R d , SO 2 R d , or COR d when L 2 is absent, or Y is H or R d when L 2 is CO, R d being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and R d being optionally substituted with one or more substituents selected from the group consisting of C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, halo, carboxyl, cyano, C 1 -C 6 alkoxyl, C 1 -C 6 alkylsulfony
  • L 3 is —(CR 4 R 5 ) n (CR 6 R 7 ) m — or —(CR 4 R 5 ) n -unsubstituted or substituted C 3 -C 8 cycloalkyl-(CR 6 R 7 ) m —, with (CR 6 R 7 ) m connected to R 9 ;
  • each of R 4 , R 5 , R 6 , and R 7 is H, halo, hydroxyl, carboxyl, cyano, or R S2 , R S2 being amino, C 1 -C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and each R S2 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, and 5 to 6-membered heteroaryl; or two geminal R 4 and R 5 or two geminal R 6 and R 7 taken together are ethylene, propylene or buty
  • n 0, 1, or 2;
  • n 0, 1, or 2.
  • R 9 is
  • each of R e , R f , R g , and R h independently is -M 2 -T 2 , in which M 2 is a bond, SO 2 , SO, S, CO, CO 2 , O, O—C 1 -C 4 alkyl linker, C 1 -C 4 alkyl linker, NH, or N(R t ), R t being C 1 -C 6 alkyl, and T 2 is H, halo, or R S4 , R S4 being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 8-membered heterocycloalkyl, or 5 to 10-membered heteroaryl, and each of O—C 1 -C 4 alkyl linker, C 1 -C 4 alkyl linker, R t , and R S4 being optionally substituted
  • D is O, NR j , or CR j R k , each of R j and R k independently being H or C 1 -C 6 alkyl, or R j and R k taken together, with the carbon atom to which they are attached, form a C 3 -C 10 cycloalkyl ring
  • E is -M 3 -T 3
  • M 3 being a bond or C 1 -C 6 alkyl linker optionally substituted with halo or cyano
  • T 3 being C 3 -C 14 carbocycle or 4 to 14-membered heterocycle
  • T 3 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, thiol, carboxyl, cyano, nitro, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 1 -C 6 alkoxyl, C 1 -C 6 haloalkyl,
  • the compound is of formula (IIIa) or (IIIb):
  • R 3 is H, halo, hydroxyl, carboxyl, cyano, or R S2 , and q is 0, 1, 2, 3, or 4.
  • the compound is of formula (IIIa) and R 9 is
  • the compound is of formula (IIIb) and R 9 is
  • Compounds that are identified as DOT1L inhibitors by the method described herein can also include those of Formula (IIa) or (IIb)
  • A is O or CH 2 ;
  • each of G and J independently, is H, halo, C(O)OH, C(O)O—C 1 -C 6 alkyl or OR a , R a being H, C 1 -C 6 alkyl or C(O)—C 1 -C 6 alkyl, wherein C(O)O—C 1 -C 6 alkyl, C 1 -C 6 alkyl or C(O)—C 1 -C 6 alkyl is optionally substituted with one or more substituents selected from the group consisting of halo, cyano hydroxyl, carboxyl, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, and C 3 -C 8 cycloalkyl;
  • Q is H, NH 2 , NHR b , NR b R c , R b , ⁇ O, OH, or OR b , in which each of R b and R c independently is C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 10-membered heteroaryl, or -M 1 -T 1 in which M 1 is a bond or C 1 -C 6 alkyl linker optionally substituted with halo, cyano, hydroxyl or C 1 -C 6 alkoxyl and T 1 is C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 10-membered heteroaryl, or R b and R c , together with
  • X is N or CR x , in which R x is H, halo, hydroxyl, carboxyl, cyano, or R S1 , R S1 being amino, C 1 -C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and R S1 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl,
  • L 1 is N(Y), S, SO, or SO 2 ;
  • L 2 is CO or absent when L 1 is N(Y) or L 2 is absent when L 1 is S, SO, or SO 2 , in which Y is H, R d , SO 2 R d , or COR d when L 2 is absent, or Y is H or R d when L 2 is CO, R d being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and R d being optionally substituted with one or more substituents selected from the group consisting of C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, C 1 -C 6 alkyls
  • each of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , and R 7 is H, halo, hydroxyl, carboxyl, cyano, R S2 , R S2 being amino, C 1 -C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and each R S2 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, and 5 to 6-membered heteroaryl;
  • R 8 is H, halo or R S3 , R S3 being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and R S3 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano amino, C 1 -C 6 alkoxyl, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, and C 3 -C 5 cycloalkyl;
  • each of R e , R f , R g , and R h independently is -M 2 -T 2 , in which M 2 is a bond, SO 2 , SO, S, CO, CO 2 , O, O—C 1 -C 4 alkyl linker, C 1 -C 4 alkyl linker, NH, or N(R t ), R t being C 1 -C 6 alkyl, and T 2 is H, halo, or R S4 , R S4 being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 8-membered heterocycloalkyl, or 5 to 10-membered heteroaryl, and each of O—C 1 -C 4 alkyl linker, C 1 -C 4 alkyl linker, R t , and R S4 being optionally
  • q 0, 1, 2, 3, or 4;
  • n 0, 1, or 2;
  • n 0, 1, or 2.
  • the sum of m and n is at least 1.
  • n 1 or 2 and n is 0.
  • n is 0
  • A is CH 2 .
  • A is O.
  • L 1 is N(Y).
  • L 1 is SO or SO 2 .
  • Y is R d .
  • R d is C 1 -C 6 alkyl.
  • L 2 is absent.
  • each of G and J independently is OR a .
  • R a is H.
  • R 9 is
  • R 9 is
  • R e , R f , R g , and R h is halo (such as F, Cl, and Br), C 1 -C 6 alkoxyl optionally substituted with one or more halo (such as OCH 3 , OCH 2 CH 3 , O-iPr, and OCF 3 ), C 1 -C 6 alkylsulfonyl optionally substituted with one or more halo (such as SO 2 CF 3 ), or C 1 -C 6 alkyl optionally substituted with one or more halo (such as CH 3 , i-propyl, n-butyl, and CF 3 ).
  • halo such as F, Cl, and Br
  • C 1 -C 6 alkylsulfonyl optionally substituted with one or more halo
  • SO 2 CF 3 such as SO 2 CF 3
  • R i is H or C 1 -C 6 alkyl (e.g., methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, s-pentyl and n-hexyl).
  • R 9 is
  • D is O.
  • D is NR j .
  • R j is H.
  • D is CR j R k .
  • each of R j and R k is H.
  • E is -M 3 -T 3 , in which M 3 is a bond or C 1 -C 3 alkyl linker, T 3 is phenyl, naphthyl, thienyl, cyclopropyl, or cyclohexyl, and T 3 is optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, thiol, carboxyl, cyano, nitro, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 1 -C 6 alkoxyl, C 1 -C 6 haloalkyl, C 1 -C 6 haloalkoxyl, C 1 -C 6 alkylthio, C 1 -C 6 alkylsulfonyl, C 1 -C 6 alkylcarbonyl, C 1 -C 6 alkoxycarbonyl, oxo, amino, mono-C 1 -C
  • T 3 is phenyl optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, nitro, C 1 -C 6 alkyl (e.g., methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, s-pentyl and n-hexyl), C 1 -C 6 alkoxyl, C 1 -C 6 haloalkyl, C 1 -C 6 haloalkoxyl, C 1 -C 6 alkylsulfonyl, C 6 -C 10 aryl (e.g., phenyl or naphthyl), and C 6 -C 10 aryloxyl, and C 7 -C 14 alkylaryl.
  • substituents selected from the group consisting of halo, hydroxyl, carboxy
  • X is N.
  • X is CRY.
  • X is CH.
  • Q is NH 2 or NHR b , in which R b is -M 1 -T 1 , M 1 being a bond or C 1 -C 6 alkyl linker and T being C 3 -C 5 cycloalkyl.
  • Q is H.
  • R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 are each H.
  • R 8 is halo and is attached to the same carbon atom as J, then J is not hydroxyl.
  • R 8 is halo and is attached to the same carbon atom as G, then G is not hydroxyl.
  • T 2 is not halo when M 2 is SO 2 , SO, S, CO or O.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a heteroatom.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a N atom.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a C atom.
  • the compound of Formula (II) include those of Formula (IIIa), or (IIIb):
  • A is O or CH 2 ;
  • Q is H, NH 2 , NHR b , NR b R c , R b , ⁇ O, OH, or OR b , in which each of R b and R c independently is C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 10-membered heteroaryl, or -M 1 -T 1 in which M 1 is a bond or C 1 -C 6 alkyl linker optionally substituted with halo, cyano, hydroxyl, or C 1 -C 6 alkoxyl and T 1 is C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 10-membered heteroaryl, or R b and R c , together
  • X is N or CR x , in which R x is H, halo, hydroxyl, carboxyl, cyano, or R S1 , R S1 being amino, C 1 -C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and R S1 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl,
  • L 1 is N(Y), S, SO, or SO 2 ;
  • L 2 is CO or absent when L 1 is N(Y) or L 2 is absent when L 1 is S, SO, or SO 2 , in which Y is H, R d , SO 2 R d , or COR d when L 2 is absent, or Y is H or R d when L 2 is CO, R d being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and R d being optionally substituted with one or more substituents selected from the group consisting of C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, C 1 -C 6 alkyls
  • each of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , and R 7 is H, halo, hydroxyl, carboxyl, cyano, R S2 , R S2 being amino, C 1 -C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and each R S2 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, and 5 to 6-membered heteroaryl;
  • R 8 is H, halo or R S3 , R S3 being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and R S3 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano amino, C 1 -C 6 alkoxyl, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, and C 3 -C 8 cycloalkyl;
  • each of R e , R f , R g , and R h independently is -M 2 -T 2 , in which M 2 is a bond, SO 2 , SO, S, CO, CO 2 , O, O—C 1 -C 4 alkyl linker, C 1 -C 4 alkyl linker, NH, or N(R t ), R t being C 1 -C 6 alkyl, and T 2 is H, halo, or R S4 , R S4 being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 8-membered heterocycloalkyl, or 5 to 10-membered heteroaryl, and each of O—C 1 -C 4 alkyl linker, C 1 -C 4 alkyl linker, R t , and R S4 being optionally
  • q 0, 1, 2, 3, or 4;
  • n 0, 1, or 2;
  • n 0, 1, or 2.
  • the sum of m and n is at least 1.
  • n 1 or 2 and n is 0.
  • n is 0
  • A is CH 2 .
  • A is O.
  • L 1 is N(Y).
  • L 1 is SO or SO 2 .
  • Y is R d .
  • R d is C 1 -C 6 alkyl.
  • L 2 is absent.
  • R 9 is
  • R 9 is
  • R e , R f , R g , and R h is halo (such as F, Cl, and Br), C 1 -C 6 alkoxyl optionally substituted with one or more halo (such as OCH 3 , OCH 2 CH 3 , O-iPr, and OCF 3 ), C 1 -C 6 alkylsulfonyl optionally substituted with one or more halo (such as SO 2 CF 3 ), or C 1 -C 6 alkyl optionally substituted with one or more halo (such as CH 3 , i-propyl, n-butyl, and CF 3 ).
  • halo such as F, Cl, and Br
  • C 1 -C 6 alkylsulfonyl optionally substituted with one or more halo
  • SO 2 CF 3 such as SO 2 CF 3
  • R i is H or C 1 -C 6 alkyl (e.g., methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, s-pentyl or n-hexyl).
  • R 9 is
  • D is O.
  • D is NR j .
  • R j is H.
  • D is CR j R k .
  • each of R j and R k is H.
  • E is -M 3 -T 3 , in which M 3 is a bond or C 1 -C 3 alkyl linker, T 3 is phenyl, naphthyl, thienyl, cyclopropyl, or cyclohexyl, and T 3 is optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, thiol, carboxyl, cyano, nitro, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 1 -C 6 alkoxyl, C 1 -C 6 haloalkyl, C 1 -C 6 haloalkoxyl, C 1 -C 6 alkylthio, C 1 -C 6 alkylsulfonyl, C 1 -C 6 alkylcarbonyl, C 1 -C 6 alkoxycarbonyl, oxo, amino, mono-C 1 -C
  • T 3 is phenyl optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, nitro, C 1 -C 6 alkyl (e.g., methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, s-pentyl and n-hexyl), C1-C 6 alkoxyl, C 1 -C 6 haloalkyl, C 1 -C 6 haloalkoxyl, C 1 -C 6 alkylsulfonyl, C 6 -C 10 aryl (e.g., phenyl or naphthyl), and C 6 -C 10 aryloxyl, and C 7 -C 14 alkylaryl.
  • substituents selected from the group consisting of halo, hydroxyl, carboxyl
  • X is N.
  • X is CR x .
  • X is CH.
  • Q is NH 2 or NHR b , in which R b is -M 1 -T 1 , M 1 being a bond or C 1 -C 6 alkyl linker and T 1 being C 3 -C 5 cycloalkyl.
  • Q is H.
  • R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 are each H.
  • R 8 is halo and is attached to the same carbon atom as J, then J is not hydroxyl.
  • R 8 is halo and is attached to the same carbon atom as G, then G is not hydroxyl.
  • T 2 is not halo when M 2 is SO 2 , SO, S, CO or O.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a heteroatom.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a N atom.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a C atom.
  • the present invention provides the compounds of Formula (IVa), (IVb), (IVd), or (IVe):
  • A is O or CH 2 ;
  • each of G and J independently, is H, halo, C(O)OH, C(O)O—C 1 -C 6 alkyl or OR a , R a being H, C 1 -C 6 alkyl or C(O)—C 1 -C 6 alkyl, wherein C(O)O—C 1 -C 6 alkyl, C 1 -C 6 alkyl or C(O)—C 1 -C 6 alkyl is optionally substituted with one or more substituents selected from the group consisting of halo, cyano hydroxyl, carboxyl, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, and C 3 -C 5 cycloalkyl;
  • Q is H, NH 2 , NHR b , NR b R c , R b , ⁇ O, OH, or OR b , in which each of R b and R c independently is C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 10-membered heteroaryl, or -M 1 -T 1 in which M 1 is a bond or C 1 -C 6 alkyl linker optionally substituted with halo, cyano, hydroxyl or C 1 -C 6 alkoxyl and T 1 is C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 10-membered heteroaryl, or R b and R c , together with
  • X is N or CR x , in which R x is H, halo, hydroxyl, carboxyl, cyano, or R S1 , R S1 being amino, C 1 -C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and R S1 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl,
  • L 1 is N(Y), S, SO, or SO 2 ;
  • L 2 is CO or absent when L 1 is N(Y) or L 2 is absent when L 1 is S, SO, or SO 2 , in which Y is H, R d , SO 2 R d , or COR d when L 2 is absent, or Y is H or R d when L 2 is CO, R d being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and R d being optionally substituted with one or more substituents selected from the group consisting of C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, C 1 -C 6 alkyls
  • each of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , and R 7 is H, halo, hydroxyl, carboxyl, cyano, R S2 , R S2 being amino, C 1 -C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and each R S2 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, and 5 to 6-membered heteroaryl;
  • R 8 is H, halo or R S3 , R S3 being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and R S3 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano amino, C 1 -C 6 alkoxyl, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, and C 3 -C 8 cycloalkyl;
  • each of R e , R f , R g , and R h independently is -M 2 -T 2 , in which M 2 is a bond, SO 2 , SO, S, CO, CO 2 , O, O—C 1 -C 4 alkyl linker, C 1 -C 4 alkyl linker, NH, or N(R t ), R t being C 1 -C 6 alkyl, and T 2 is H, halo, or R S4 , R S4 being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 8-membered heterocycloalkyl, or 5 to 10-membered heteroaryl, and each of O—C 1 -C 4 alkyl linker, C 1 -C 4 alkyl linker, R t , and R S4 being optionally substituted
  • R i is H or C 1 -C 6 alkyl optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, and 5 to 6-membered heteroaryl;
  • q 0, 1, 2, 3, or 4;
  • n 0, 1, or 2;
  • n 0, 1, or 2.
  • the sum of m and n is at least 1.
  • n 1 or 2 and n is 0.
  • n is 0
  • A is CH 2 .
  • A is O.
  • L 1 is N(Y).
  • L 1 is SO or SO 2 .
  • Y is R d .
  • R d is C 1 -C 6 alkyl.
  • L 2 is absent.
  • each of G and J independently is OR a .
  • R a is H.
  • R e , R f , R g , and R h is halo (such as F, Cl, and Br), C 1 -C 6 alkoxyl optionally substituted with one or more halo (such as OCH 3 , OCH 2 CH 3 , O-iPr, and OCF 3 ), C 1 -C 6 alkylsulfonyl optionally substituted with one or more halo (such as SO 2 CF 3 ), or C 1 -C 6 alkyl optionally substituted with one or more halo (such as CH 3 , i-propyl, n-butyl, and CF 3 ).
  • halo such as F, Cl, and Br
  • C 1 -C 6 alkylsulfonyl optionally substituted with one or more halo
  • SO 2 CF 3 such as SO 2 CF 3
  • R i is H or C 1 -C 6 alkyl (e.g., methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, s-pentyl and n-hexyl).
  • X is N.
  • X is CR x .
  • X is CH.
  • Q is NH 2 or NHR b , in which R b is -M 1 -T 1 , M 1 being a bond or C 1 -C 6 alkyl linker and T 1 being C 3 -C 8 cycloalkyl.
  • Q is H.
  • R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 are each H.
  • R 8 is halo and is attached to the same carbon atom as J, then J is not hydroxyl.
  • R 8 is halo and is attached to the same carbon atom as G, then G is not hydroxyl.
  • T 2 is not halo when M 2 is SO 2 , SO, S, CO or O.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a heteroatom.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a N atom.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a C atom.
  • the present invention provides the compounds of Formula (IVc) or (IVf):
  • A is O or CH 2 ;
  • each of G and J independently, is H, halo, C(O)OH, C(O)O—C 1 -C 6 alkyl or OR a , R a being H, C 1 -C 6 alkyl or C(O)—C 1 -C 6 alkyl, wherein C(O)O—C 1 -C 6 alkyl, C 1 -C 6 alkyl or C(O)—C 1 -C 6 alkyl is optionally substituted with one or more substituents selected from the group consisting of halo, cyano hydroxyl, carboxyl, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, and C 3 -C 8 cycloalkyl;
  • Q is H, NH 2 , NHR b , NR b R c , R b , ⁇ O, OH, or OR b , in which each of R b and R c independently is C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 10-membered heteroaryl, or -M 1 -T 1 in which M 1 is a bond or C 1 -C 6 alkyl linker optionally substituted with halo, cyano, hydroxyl or C 1 -C 6 alkoxyl and T 1 is C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 10-membered heteroaryl, or R b and R c , together with
  • X is N or CR x , in which R x is H, halo, hydroxyl, carboxyl, cyano, or R S1 , R S1 being amino, C 1 -C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and R S1 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl,
  • L 1 is N(Y), S, SO, or SO 2 ;
  • L 2 is CO or absent when L 1 is N(Y) or L 2 is absent when L 1 is S, SO, or SO 2 , in which Y is H, R d , SO 2 R d , or COR d when L 2 is absent, or Y is H or R d when L 2 is CO, R d being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and R d being optionally substituted with one or more substituents selected from the group consisting of C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, C 1 -C 6 alkyls
  • each of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , and R 7 is H, halo, hydroxyl, carboxyl, cyano, R S2 , R S2 being amino, C1-C 6 alkoxyl, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and each R S2 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, C 1 -C 6 alkoxyl, amino, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, and 5 to 6-membered heteroaryl;
  • R 8 is H, halo or R S3 , R S3 being C 1 -C 6 alkyl, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and R S3 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano amino, C 1 -C 6 alkoxyl, mono-C 1 -C 6 alkylamino, di-C 1 -C 6 alkylamino, and C 3 -C 5 cycloalkyl;
  • D is O, NR j , or CR j R k , each of R j and R k independently being H or C 1 -C 6 alkyl, or R j and R k taken together, with the carbon atom to which they are attached, form a C 3 -C 10 cycloalkyl ring;
  • E is -M 3 -T 3 , M 3 being a bond or C 1 -C 6 alkyl linker optionally substituted with halo or cyano, T 3 being C 3 -C 10 cycloalkyl, C 6 -C 10 aryl, 5 to 10-membered heteroaryl, or 4 to 10-membered heterocycloalkyl, and T 3 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, thiol, carboxyl, cyano, nitro, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 1 -C 6 alkoxyl, C 1 -C 6 haloalkyl, C 1 -C 6 haloalkoxyl, C 1 -C 6 alkylthio, C 1 -C 6 alkylsulfonyl, C 1 -C 6 haloalkylsulfon
  • q 0, 1, 2, 3, or 4;
  • n 0, 1, or 2;
  • n 0, 1, or 2.
  • the sum of m and n is at least 1.
  • n 1 or 2 and n is 0.
  • n is 0
  • A is CH 2 .
  • A is O.
  • L 1 is N(Y).
  • L 1 is SO or SO 2 .
  • Y is R d .
  • R d is C1-C 6 alkyl.
  • L 2 is absent.
  • each of G and J independently is OR a .
  • R a is H.
  • D is O.
  • D is NR j .
  • R j is H.
  • D is CR j R k .
  • each of R j and R k is H.
  • E is -M 3 -T 3 , in which M 3 is a bond or C 1 -C 3 alkyl linker, T 3 is phenyl, naphthyl, thienyl, cyclopropyl, or cyclohexyl, and T 3 is optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, thiol, carboxyl, cyano, nitro, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 1 -C 6 alkoxyl, C 1 -C 6 haloalkyl, C 1 -C 6 haloalkoxyl, C 1 -C 6 alkylthio, C 1 -C 6 alkylsulfonyl, C 1 -C 6 alkylcarbonyl, C 1 -C 6 alkoxycarbonyl, oxo, amino, mono-C 1 -C
  • T 3 is phenyl optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, carboxyl, cyano, nitro, C1-C 6 alkyl (e.g., methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, s-pentyl and n-hexyl), C 1 -C 6 alkoxyl, C 1 -C 6 haloalkyl, C 1 -C 6 haloalkoxyl, C 1 -C 6 alkylsulfonyl, C 6 -C 10 aryl (e.g., phenyl or naphthyl), and C 6 -C 10 aryloxyl, and C 7 -C 14 alkylaryl.
  • substituents selected from the group consisting of halo, hydroxyl, carboxyl
  • X is N.
  • X is CR x .
  • X is CH.
  • Q is NH 2 or NHR b , in which R b is -M 1 -T 1 , M 1 being a bond or C 1 -C 6 alkyl linker and T 1 being C 3 -C 8 cycloalkyl.
  • Q is H.
  • R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 are each H.
  • R 8 is halo and is attached to the same carbon atom as J, then J is not hydroxyl.
  • R 8 is halo and is attached to the same carbon atom as G, then G is not hydroxyl.
  • T 2 is not halo when M 2 is SO 2 , SO, S, CO or O.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a heteroatom.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a N atom.
  • T 2 is a 4-8 membered heterocycloalkyl which is bound to M 2 via a C atom.
  • the invention also relates to a compound of Formula (IV) or its N-oxide or a pharmaceutically acceptable salt thereof:
  • A is O or CH 2 ;
  • Q is H, NH 2 , NHR b , NR b R c , R b , ⁇ O, OH, or OR b , in which each of R b and R c independently is C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 3 -C 5 cycloalkyl, C 6 -C 10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 10-membered heteroaryl, or -M 1 -T 1 in which M 1 is a bond or C 1 -C 6 alkyl linker optionally substituted with halo, cyano, hydroxyl or C 1 -C 6 alkoxyl and T 1 is C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, 4 to 6-membered heterocycloalkyl, or 5 to 10-membered heteroaryl, or R
  • A is O.
  • A is O and m is 2.
  • X is N.
  • Q is NH 2 or NHR b , in which R b is -M 1 -T 1 , M 1 being a bond or C 1 -C 6 alkyl linker and T 1 being C 3 -C 5 cycloalkyl
  • R 1 and R 2 are each H.
  • Y is R d .
  • R d is C 1 -C 6 alkyl optionally substituted with C 3 -C 8 cycloalkyl or halo.
  • R d is C 3 -C 8 cycloalkyl optionally substituted with C 1 -C 6 alkyl or halo.
  • the invention also relates to a compound of Formula (IV), wherein at least one of R e , R f , R g , and R h is halo, C 1 -C 6 alkoxyl optionally substituted with one or more halo; C 1 -C 6 alkylsulfonyl optionally substituted with one or more halo; C 1 -C 6 alkyl optionally substituted with one or more substituents selected from CN, halo, C 3 -C 5 cycloalkyl, hydroxy, and C 1 -C 6 alkoxyl; C 3 -C 8 cycloalkyl optionally substituted with one or more C 1 -C 6 alkyl or CN; or 4 to 8-membered heterocycloalkyl optionally substituted with one or more substituents selected from CN, halo, hydroxy, C 1 -C 6 alkyl and C 1 -C 6 alkoxyl.
  • the compound of Formula (IV) has at least one of R e , R f , R g , and R h selected from F; Cl; Br; CF 3 ; OCF 3 ; SO 2 CF 3 ; oxetanyl optionally substituted with one or more substituents selected from CN, halo, hydroxy, C 1 -C 6 alkyl and C 1 -C 6 alkoxyl; C 3 -C 8 cycloalkyl optionally substituted with one or more substituents selected from C 1 -C 4 alkyl; and C 1 -C 4 alkyl optionally substituted with one or more substituents selected from halo, C 3 -C 5 cycloalkyl, hydroxy and C 1 -C 6 alkoxyl.
  • the invention relates to compounds of Formula (IV) where at least one of R f and R g is alkyl, optionally substituted with hydroxyl.
  • the invention relates to compounds where at least one of R f and R g is t-butyl substituted with hydroxyl.
  • the invention relates to a compound selected from Tables 1-4.
  • the invention also relates to a salt of a compound selected from Tables 1-4.
  • the invention also relates to an N-oxide of compound selected from Tables 1-4.
  • the invention also relates to a salt of an N-oxide of compound selected from Tables 1-4.
  • the invention relates to a compound selected from Compounds A1-A7, A9-A109, and A111-A140.
  • the invention also relates to a pharmaceutical composition of a therapeutically effective amount of a compound of any of the Formulae disclosed herein and a pharmaceutically acceptable carrier.
  • the invention also relates to a pharmaceutical composition of a therapeutically effective amount of a salt of a compound of any of the Formulae disclosed herein and a pharmaceutically acceptable carrier.
  • the invention also relates to a pharmaceutical composition of a therapeutically effective amount of a hydrate of a compound of any of the Formulae disclosed herein and a pharmaceutically acceptable carrier.
  • the invention also relates to a pharmaceutical composition of a therapeutically effective amount of a compound selected from Tables 1-4 and a pharmaceutically acceptable carrier.
  • the invention also relates to a pharmaceutical composition of a therapeutically effective amount of a salt of a compound selected from Tables 1-4 and a pharmaceutically acceptable carrier.
  • the invention also relates to a pharmaceutical composition of a therapeutically effective amount of an N-oxide of a compound selected from Tables 1-4 and a pharmaceutically acceptable carrier.
  • the invention also relates to a pharmaceutical composition of a therapeutically effective amount of an N-oxide of salt of a compound selected from Tables 1-4 and a pharmaceutically acceptable carrier.
  • the invention also relates to a pharmaceutical composition of a therapeutically effective amount of a hydrate of a compound selected from Tables 1-4 and a pharmaceutically acceptable carrier.
  • the present invention provides methods of treating or preventing cancer.
  • the present invention provides methods of treating cancer.
  • the present invention also provides methods of preventing cancer.
  • the method includes administering to a subject in need thereof a therapeutically effective amount of the compound of any of the Formulae disclosed herein.
  • the cancer can be a hematological cancer.
  • the cancer is leukemia. More preferably, the cancer is acute myeloid leukemia, acute lymphocytic leukemia or mixed lineage leukemia.
  • the present invention provides methods of treating or preventing a disease or disorder mediated by translocation of a gene on chromosome 11q23.
  • the present invention provides methods of treating a disease or disorder mediated by translocation of a gene on chromosome 11q23.
  • the present invention also provides methods of preventing a disease or disorder mediated by translocation of a gene on chromosome 11q23.
  • the method includes administering to a subject in need thereof a therapeutically effective amount of the compound of any of the Formulae disclosed herein.
  • the present invention provides methods of treating or preventing a disease or disorder in which DOT -mediated protein methylation plays a part or a disease or disorder mediated by DOT1-mediated protein methylation.
  • the present invention provides methods of treating a disease or disorder in which DOT1-mediated protein methylation plays a part or a disease or disorder mediated by DOT1-mediated protein methylation.
  • the present invention also provides methods of preventing a disease or disorder in which DOT1-mediated protein methylation plays a part or a disease or disorder mediated by DOT1-mediated protein methylation.
  • the method includes administering to a subject in need thereof a therapeutically effective amount of the compound of any of the Formulae disclosed herein.
  • the present invention provides methods of inhibiting DOT1L activity in a cell.
  • the method includes contacting the cell with an effective amount of one or more of the compound of any of the Formulae disclosed herein.
  • Still another aspect of the invention relates to a method of reducing the level of Histone H3 Lysine residue 79 (H3-K79) methylation in a cell.
  • the method includes contacting a cell with a compound of the present invention.
  • Such method can be used to ameliorate any condition which is caused by or potentiated by the activity of DOT1 through H3-K79 methylation.
  • the present invention relates to use of the compounds disclosed herein in preparation of a medicament for treating or preventing cancer.
  • the use includes a compound of any of the Formulae disclosed herein for administration to a subject in need thereof in a therapeutically effective amount.
  • the cancer can be a hematological cancer.
  • the cancer is leukemia. More preferably, the cancer is acute myeloid leukemia, acute lymphocytic leukemia or mixed lineage leukemia.
  • the present invention provides use of the compounds disclosed herein in preparation of a medicament for treating or preventing a disease or disorder mediated by translocation of a gene on chromosome 11q23.
  • the use includes a compound of any of the Formulae disclosed herein for administration to a subject in need thereof in a therapeutically effective amount.
  • the present invention provides use of the compounds disclosed herein in preparation of a medicament for treating or preventing a disease or disorder in which DOT1-mediated protein methylation plays a part or a disease or disorder mediated by DOT1-mediated protein methylation.
  • the use includes a compound of any of the Formulae disclosed herein for administration to a subject in need thereof in a therapeutically effective amount.
  • the present invention provides use of the compounds disclosed herein for inhibiting DOT1L activity in a cell.
  • the use includes contacting the cell with an effective amount of one or more of the compound of any of the Formulae disclosed herein.
  • Still another aspect of the invention relates to a use of the compounds disclosed herein for reducing the level of Histone H3 Lysine residue 79 (H3-K79) methylation in a cell.
  • the use includes contacting a cell with a compound of the present invention.
  • Such use can ameliorate any condition which is caused by or potentiated by the activity of DOT1 through H3-K79 methylation.
  • the invention provides methods of synthesizing the foregoing compounds.
  • a therapeutically effective amount of one or more of the compounds can be formulated with a pharmaceutically acceptable carrier for administration to a mammal, particularly humans, for use in modulating an epigenetic enzyme.
  • the compounds of the present invention are useful for treating, preventing, or reducing the risk of cancer or for the manufacture of a medicament for treating, preventing, or reducing the risk of cancer.
  • the compounds or the formulations can be administered, for example, via oral, parenteral, otic, ophthalmic, nasal, or topical routes, to provide an effective amount of the compound to the mammal.
  • Representative compounds of the present invention include compounds listed in Tables 1-4.
  • alkyl As used herein, “alkyl”, “C 1 , C 2 , C 3 , C 4 , C 5 or C 6 alkyl” or “C 1 -C 6 alkyl” is intended to include C 1 , C 2 , C 3 , C 4 , C 5 or C 6 straight chain (linear) saturated aliphatic hydrocarbon groups and C 3 , C 4 , C 5 or C 6 branched saturated aliphatic hydrocarbon groups.
  • cycloalkyl refers to a saturated or unsaturated nonaromatic hydrocarbon mono- or multi-ring system having 3 to 30 carbon atoms (e.g., C 3 -C 10 ).
  • examples of cycloalkyl include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl, cyclopentenyl, cyclohexenyl, cycloheptenyl, and adamantyl.
  • heterocycloalkyl refers to a saturated or unsaturated nonaromatic 5-8 membered monocyclic, 8-12 membered bicyclic, or 11-14 membered tricyclic ring system having one or more heteroatoms (such as O, N, S, or Se).
  • heterocycloalkyl groups include, but are not limited to, piperazinyl, pyrrolidinyl, dioxanyl, morpholinyl, and tetrahydrofuranyl.
  • optionally substituted alkyl refers to unsubstituted alkyl or alkyl having designated substituents replacing one or more hydrogen atoms on one or more carbons of the hydrocarbon backbone.
  • substituents can include, for example, alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamin
  • arylalkyl or an “aralkyl” moiety is an alkyl substituted with an aryl (e.g., phenylmethyl (benzyl)).
  • alkylaryl moiety is an aryl substituted with an alkyl (e.g., methylphenyl).
  • alkyl linker is intended to include C 1 , C 2 , C 3 , C 4 , C 5 or C 6 straight chain (linear) saturated divalent aliphatic hydrocarbon groups and C 3 , C 4 , C 5 or C 6 branched saturated aliphatic hydrocarbon groups.
  • C1-C6 alkyl linker is intended to include C 1 , C 2 , C 3 , C 4 , C 5 and C 6 alkyl linker groups.
  • Alkenyl includes unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double bond.
  • Alkynyl includes unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but which contain at least one triple bond.
  • optionally substituted moieties include both the unsubstituted moieties and the moieties having one or more of the designated substituents.
  • Aryl includes groups with aromaticity, including “conjugated,” or multicyclic systems with at least one aromatic ring and do not contain any heteroatom in the ring structure. Examples include phenyl, benzyl, 1,2,3,4-tetrahydronaphthalenyl, etc.
  • Heteroaryl groups are aryl groups, as defined above, except having from one to four heteroatoms in the ring structure, and may also be referred to as “aryl heterocycles” or “heteroaromatics.”
  • the term “heteroaryl” is intended to include a stable 5- or 6-membered monocyclic or 7-, 8-, 9-, 10-, 11- or 12-membered bicyclic aromatic heterocyclic ring which consists of carbon atoms and one or more heteroatoms, e.g., 1 or 1-2 or 1-3 or 1-4 or 1-5 or 1-6 heteroatoms, or e.g. 1, 2, 3, 4, 5, or 6 heteroatoms, independently selected from the group consisting of nitrogen, oxygen and sulfur.
  • the nitrogen atom may be substituted or unsubstituted (i.e., N or NR wherein R is H or other substituents, as defined).
  • heteroaryl groups include pyrrole, furan, thiophene, thiazole, isothiazole, imidazole, triazole, tetrazole, pyrazole, oxazole, isoxazole, pyridine, pyrazine, pyridazine, pyrimidine, and the like.
  • aryl and heteroaryl include multicyclic aryl and heteroaryl groups, e.g., tricyclic, bicyclic, e.g., naphthalene, benzoxazole, benzodioxazole, benzothiazole, benzoimidazole, benzothiophene, methylenedioxyphenyl, quinoline, isoquinoline, naphthrydine, indole, benzofuran, purine, benzofuran, deazapurine, indolizine.
  • the rings In the case of multicyclic aromatic rings, only one of the rings needs to be aromatic (e.g., 2,3-dihydroindole), although all of the rings may be aromatic (e.g., quinoline).
  • the second ring can also be fused or bridged.
  • “carbocycle” or “carbocyclic ring” is intended to include any stable monocyclic, bicyclic or tricyclic ring having the specified number of carbons, any of which may be saturated, unsaturated, or aromatic.
  • a C 3 -C 14 carbocycle is intended to include a monocyclic, bicyclic or tricyclic ring having 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 carbon atoms.
  • carbocycles include, but are not limited to, cyclopropyl, cyclobutyl, cyclobutenyl, cyclopentyl, cyclopentenyl, cyclohexyl, cycloheptenyl, cycloheptyl, cycloheptenyl, adamantyl, cyclooctyl, cyclooctenyl, cyclooctadienyl, fluorenyl, phenyl, naphthyl, indanyl, adamantyl and tetrahydronaphthyl.
  • Bridged rings are also included in the definition of carbocycle, including, for example, [3.3.0]bicyclooctane, [4.3.0]bicyclononane, [4.4.0]bicyclodecane and [2.2.2]bicyclooctane.
  • a bridged ring occurs when one or more carbon atoms link two non-adjacent carbon atoms.
  • bridge rings are one or two carbon atoms. It is noted that a bridge always converts a monocyclic ring into a tricyclic ring. When a ring is bridged, the substituents recited for the ring may also be present on the bridge. Fused (e.g., naphthyl, tetrahydronaphthyl) and spiro rings are also included.
  • heterocycle includes any ring structure (saturated or partially unsaturated) which contains at least one ring heteroatom (e.g., N, O or S).
  • heterocycles include, but are not limited to, morpholine, pyrrolidine, tetrahydrothiophene, piperidine, piperazine and tetrahydrofuran.
  • heterocyclic groups include, but are not limited to, acridinyl, azocinyl, benzimidazolyl, benzofuranyl, benzothiofuranyl, benzothiophenyl, benzoxazolyl, benzoxazolinyl, benzthiazolyl, benztriazolyl, benztetrazolyl, benzisoxazolyl, benzisothiazolyl, benzimidazolinyl, carbazolyl, 4aH-carbazolyl, carbolinyl, chromanyl, chromenyl, cinnolinyl, decahydroquinolinyl, 2H,6H-1,5,2-dithiazinyl, dihydrofuro[2,3-b]tetrahydrofuran, furanyl, furazanyl, imidazolidinyl, imidazolinyl, imidazolyl, 1H-indazolyl, indol,
  • substituted means that any one or more hydrogen atoms on the designated atom is replaced with a selection from the indicated groups, provided that the designated atom's normal valency is not exceeded, and that the substitution results in a stable compound.
  • a substituent is oxo or keto (i.e., ⁇ O)
  • Keto substituents are not present on aromatic moieties.
  • Ring double bonds as used herein, are double bonds that are formed between two adjacent ring atoms (e.g., C ⁇ C, C ⁇ N or N ⁇ N).
  • “Stable compound” and “stable structure” are meant to indicate a compound that is sufficiently robust to survive isolation to a useful degree of purity from a reaction mixture, and formulation into an efficacious therapeutic agent.
  • any variable e.g., R 1
  • its definition at each occurrence is independent of its definition at every other occurrence.
  • R 1 at each occurrence is selected independently from the definition of R 1 .
  • substituents and/or variables are permissible, but only if such combinations result in stable compounds.
  • N-oxides can be converted to N-oxides by treatment with an oxidizing agent (e.g., 3-chloroperoxybenzoic acid (mCPBA) and/or hydrogen peroxides) to afford other compounds of the present invention.
  • an oxidizing agent e.g., 3-chloroperoxybenzoic acid (mCPBA) and/or hydrogen peroxides
  • mCPBA 3-chloroperoxybenzoic acid
  • hydrogen peroxides hydrogen peroxides
  • all shown and claimed nitrogen-containing compounds are considered, when allowed by valency and structure, to include both the compound as shown and its N-oxide derivative (which can be designated as N ⁇ O or N + —O ⁇ ).
  • the nitrogens in the compounds of the present invention can be converted to N-hydroxy or N-alkoxy compounds.
  • N-hydroxy compounds can be prepared by oxidation of the parent amine by an oxidizing agent such as m-CPBA.
  • nitrogen-containing compounds are also considered, when allowed by valency and structure, to cover both the compound as shown and its N-hydroxy (i.e., N—OH) and N-alkoxy (i.e., N—OR, wherein R is substituted or unsubstituted C 1 -C 6 alkyl, C 1 -C 6 alkenyl, C 1 -C 6 alkynyl, 3-14-membered carbocycle or 3-14-membered heterocycle) derivatives.
  • N—OH N-hydroxy
  • N-alkoxy i.e., N—OR, wherein R is substituted or unsubstituted C 1 -C 6 alkyl, C 1 -C 6 alkenyl, C 1 -C 6 alkynyl, 3-14-membered carbocycle or 3-14-membered heterocycle
  • the structural formula of the compound represents a certain isomer for convenience in some cases, but the present invention includes all isomers, such as geometrical isomers, optical isomers based on an asymmetrical carbon, stereoisomers, tautomers, and the like.
  • a crystal polymorphism may be present for the compounds represented by the formula. It is noted that any crystal form, crystal form mixture, or anhydride or hydrate thereof is included in the scope of the present invention. Furthermore, so-called metabolite which is produced by degradation of the present compound in vivo is included in the scope of the present invention.
  • “Isomerism” means compounds that have identical molecular formulae but differ in the sequence of bonding of their atoms or in the arrangement of their atoms in space. Isomers that differ in the arrangement of their atoms in space are termed “stereoisomers.” Stereoisomers that are not mirror images of one another are termed “diastereoisomers,” and stereoisomers that are non-superimposable mirror images of each other are termed “enantiomers” or sometimes optical isomers. A mixture containing equal amounts of individual enantiomeric forms of opposite chirality is termed a “racemic mixture.”
  • compounds of Formula (II) include those of the following chiral isomers and geometric isomers.
  • atropic isomers are a type of stereoisomer in which the atoms of two isomers are arranged differently in space. Atropic isomers owe their existence to a restricted rotation caused by hindrance of rotation of large groups about a central bond. Such atropic isomers typically exist as a mixture, however as a result of recent advances in chromatography techniques, it has been possible to separate mixtures of two atropic isomers in select cases.
  • Tautomer is one of two or more structural isomers that exist in equilibrium and is readily converted from one isomeric form to another. This conversion results in the formal migration of a hydrogen atom accompanied by a switch of adjacent conjugated double bonds. Tautomers exist as a mixture of a tautomeric set in solution. In solutions where tautomerization is possible, a chemical equilibrium of the tautomers will be reached. The exact ratio of the tautomers depends on several factors, including temperature, solvent and pH. The concept of tautomers that are interconvertable by tautomerizations is called tautomerism.
  • keto-enol tautomerism a simultaneous shift of electrons and a hydrogen atom occurs.
  • Ring-chain tautomerism arises as a result of the aldehyde group (—CHO) in a sugar chain molecule reacting with one of the hydroxy groups (—OH) in the same molecule to give it a cyclic (ring-shaped) form as exhibited by glucose.
  • tautomeric pairs are: ketone-enol, amide-nitrile, lactam-lactim, amide-imidic acid tautomerism in heterocyclic rings (e.g., in nucleobases such as guanine, thymine and cytosine), amine-enamine and enamine-enamine.
  • Benzimidazoles also exhibit tautomerism, when the benzimidazole contains one or more substituents in the 4, 5, 6 or 7 positions, the possibility of different isomers arises.
  • 2,5-dimethyl-1H-benzo[d]imidazole can exist in equilibrium with its isomer 2,6-dimethyl-1H-benzo[d]imidazole via tautomerization.
  • crystal polymorphs means crystal structures in which a compound (or a salt or solvate thereof) can crystallize in different crystal packing arrangements, all of which have the same elemental composition. Different crystal forms usually have different X-ray diffraction patterns, infrared spectral, melting points, density hardness, crystal shape, optical and electrical properties, stability and solubility. Recrystallization solvent, rate of crystallization, storage temperature, and other factors may cause one crystal form to dominate. Crystal polymorphs of the compounds can be prepared by crystallization under different conditions.
  • Compounds of the invention may be crystalline, semi-crystalline, non-crystalline, amorphous, mesomorphous, etc.
  • the compounds of any of the Formulae disclosed herein or the DOT1L inhibitors identified by the methods of the invention include the compounds themselves, as well as their N-oxides, salts, their solvates, and their prodrugs, if applicable.
  • a salt for example, can be formed between an anion and a positively charged group (e.g., amino) on the compound or inhibitor (e.g., a substituted nucleoside compound such as a substituted purine or 7-deazapurine compound).
  • Suitable anions include chloride, bromide, iodide, sulfate, bisulfate, sulfamate, nitrate, phosphate, citrate, methanesulfonate, trifluoroacetate, glutamate, glucuronate, glutarate, malate, maleate, succinate, fumarate, tartrate, tosylate, salicylate, lactate, naphthalenesulfonate, and acetate.
  • a salt can also be formed between a cation and a negatively charged group (e.g., carboxylate) on the compound or inhibitor (e.g., a substituted nucleoside compound such as a substituted purine or 7-deazapurine compound).
  • Suitable cations include sodium ion, potassium ion, magnesium ion, calcium ion, and an ammonium cation such as tetramethylammonium ion.
  • the compound or inhibitor e.g., a substituted nucleoside compound such as a substituted purine or 7-deazapurine compound
  • examples of prodrugs include esters and other pharmaceutically acceptable derivatives, which, upon administration to a subject, are capable of providing active substituted nucleoside compound such as a substituted purine or 7-deazapurine.
  • the compounds of the present invention can exist in either hydrated or unhydrated (the anhydrous) form or as solvates with other solvent molecules.
  • hydrates include hemihydrates, monohydrates, dihydrates, trihydrates, etc.
  • solvates include ethanol solvates, acetone solvates, etc.
  • Solvate means solvent addition forms that contain either stoichiometric or non stoichiometric amounts of solvent. Some compounds have a tendency to trap a fixed molar ratio of solvent molecules in the crystalline solid state, thus forming a solvate. If the solvent is water the solvate formed is a hydrate; and if the solvent is alcohol, the solvate formed is an alcoholate. Hydrates are formed by the combination of one or more molecules of water with one molecule of the substance in which the water retains its molecular state as H 2 O. A hemihydrate is formed by the combination of one molecule of water with more than one molecule of the substance in which the water retains its molecular state as H 2 O.
  • analog refers to a chemical compound that is structurally similar to another but differs slightly in composition (as in the replacement of one atom by an atom of a different element or in the presence of a particular functional group, or the replacement of one functional group by another functional group).
  • an analog is a compound that is similar or comparable in function and appearance, but not in structure or origin to the reference compound.
  • the term “derivative” refers to compounds that have a common core structure, and are substituted with various groups as described herein. For example, all of the compounds represented by Formula (I) are substituted purine compounds or substituted 7-deazapurine compounds, and have Formula (I) as a common core.
  • bioisostere refers to a compound resulting from the exchange of an atom or of a group of atoms with another, broadly similar, atom or group of atoms.
  • the objective of a bioisosteric replacement is to create a new compound with similar biological properties to the parent compound.
  • the bioisosteric replacement may be physicochemically or topologically based.
  • Examples of carboxylic acid bioisosteres include, but are not limited to, acyl sulfonimides, tetrazoles, sulfonates and phosphonates. See, e.g., Patani and LaVoie, Chem. Rev . 96, 3147-3176, 1996.
  • the present invention is intended to include all isotopes of atoms occurring in the present compounds.
  • Isotopes include those atoms having the same atomic number but different mass numbers.
  • isotopes of hydrogen include tritium and deuterium
  • isotopes of carbon include C-13 and C-14.
  • the present invention provides methods for the synthesis of the compounds of any of the Formulae disclosed herein.
  • the present invention also provides detailed methods for the synthesis of various disclosed compounds of the present invention according to the schemes and the Examples described in WO2012/075381, WO2012/075492, WO2012/082436, and WO2012/75500, the contents of which are hereby incorporated by reference in their entireties.
  • compositions are described as having, including, or comprising specific components, it is contemplated that compositions also consist essentially of, or consist of, the recited components.
  • methods or processes are described as having, including, or comprising specific process steps, the processes also consist essentially of, or consist of, the recited processing steps.
  • steps or order for performing certain actions is immaterial so long as the invention remains operable.
  • two or more steps or actions can be conducted simultaneously.
  • assays of DOT1L enzymatic activity were performed under balanced conditions (all substrates present at concentrations equal to their respective K M values) using a radiometric assay of S-[methyl- 3 H]adenosyl-L-methionine transfer from SAM to chicken erythrocyte nucleosomes as previously described. Reactions were initiated by addition of S-[methyl- 3 H]adenosyl-L-methionine and allowed to run at room temperature for 120 minutes before being quenched by the addition of 800 ⁇ M cold SAM.
  • Compound IC 50 values were determined from assays of enzymatic activity in which compound was titrated into reaction mixtures by 3-fold serial dilution from DMSO stocks. For each titration, 10 concentrations of inhibitor were used along with 100% inhibition (2.5 ⁇ M SAH) and 0% inhibition (1 ⁇ L of neat DMSO per well) controls. Plots of residual enzyme velocity as a function of inhibitor concentration were fit to a standard Langmuir isotherm equation (12) to derive estimates of the IC 50 value of the compound. As described herein, the inhibition modality of key compounds within the aminonucleoside series were tested and always found to be competitive with SAM and noncompetitive with respect to nucleosome substrate. For most compounds, the K i value was calculated from the IC 50 value using the appropriate equation for competitive inhibition with respect to SAM.
  • the inhibition modality with respect to the two substrates were determined by dual titration of compound and varied substrate concentration while holding the other substrate fixed at its K M value. Plots of velocity as a function of varied substrate at multiple inhibitor concentrations were globally fit to a general equation for enzyme inhibition using Graphpad Prism. Selection of the modality for each data set was done by evaluating the value of ⁇ , a term related to the degree of cooperative or anticooperative interaction between substrate and inhibitor binding, as previously described. A value of ⁇ 10 was taken as consistent with competitive inhibition, while a value of ⁇ 0.1 was taken as consistent with uncompetitive inhibition. Values of ⁇ between 10 and 0.1 were considered to be consistent with noncompetitive inhibition.
  • K i value was determined by measuring the IC 50 value of the compound (vide supra) at varying concentrations of enzyme from 5 nM to 0.25 nM.
  • a plot of IC 50 as a function of enzyme concentration was fit to a linear equation and the y-intercept value was equivalent to K i (1+[S]/K M ) where [S] and K M refer to SAM, the substrate with which these inhibitors compete. Knowing the values of [S] and K M used in the assay, the K i value was then calculated from the y-intercept value.
  • Ligand association and dissociation rate constants were determined by surface plasmon resonance (SPR).
  • DOT1L was stored in 20 mM Tris-HCl, 200 mM NaCl, 1 mM EDTA, 1 mM DTT, pH 7.8 and immobilized by direct amine coupling, diluting enzyme into coupling buffer containing 10 mM Hepes pH 7.4, 1 mM TCEP.
  • Immobilization run buffer contained 10 mM Hepes pH 7.4, 150 mM NaCl, 500 ⁇ M TCEP, and approximately 10,000 RUs (response units) of DOT1L was captured.
  • a reference channel of a surface that was activated in parallel and blocked was created in a second flow cell was also created. Data was captured on either a Biacore 4000 (chip CM5) or a Biorad ProteOn (chip GLM).
  • K d determinations were determined using run buffer containing 20 mM Tris pH 8.0, 10 mM NaCl, 100 mM KCl, 0.002% Tween-20, 500 ⁇ M TCEP, 2% DMSO, with the following injection parameters: 30 ⁇ l/min flow rate, with a 30 second association phase followed by monitoring dissociation for 30 seconds. Experiments were carried out at 25° C.
  • the human leukemia cell line MV4-11 harboring the MLL-AF4 translocation was obtained from ATCC (CRL-9591). Cells were grown in Iscove's Modified Dulbecco's Medium (IMDM) with 10% Fetal Bovine Serum (FBS). All cell culture reagents were purchased from Invitrogen Life Technologies and cells were maintained in a humidified incubator set to 37° C., 5% CO 2 .
  • IMDM Iscove's Modified Dulbecco's Medium
  • FBS Fetal Bovine Serum
  • Cell proliferation was assessed by plating, in triplicate, exponentially growing MV4-11 cells in a 96 well plate at a density of 3 ⁇ 10 4 cells/well in a final volume of 150 ⁇ L. Cells were incubated in the presence of compound at increasing concentrations up to 50 ⁇ M. Viable cell numbers were determined every 3-4 days for a total of 14 days using the Guava Viacount assay (Millipore #4000-0040). Analysis was performed on a Guava EasyCyte Plus instrument (Millipore) according to the manufacturer's protocol. On days of cell counts, growth media and compound were replaced and cells split back to a density of 5 ⁇ 10 4 cells/well. Total cell number is expressed as split-adjusted viable cells per well. IC 50 values were determined from concentration dependent curves at day 14 using the Graphpad Prism software.
  • MV4-11 cells Exponentially growing MV4-11 cells were seeded in a 12-well plate at 2 ⁇ 10 5 cells/well in a final volume of 2 mls. Cells were incubated in the presence of increasing concentrations of Compound C94, C118, or D16 up to 50 ⁇ M. Control cells were treated with 0.2% DMSO control. Cells (1-2 ⁇ 10 6 ) were harvested after 96 hours of compound incubation and histones were extracted. An indirect enzyme-linked immunosorbent assay (ELISA) using acid extracted histones was run using matching microtiter plates (Immulon 4HBX #3855, Thermo Labsystems).
  • ELISA enzyme-linked immunosorbent assay
  • Plates were coated for total H3 and H3K79me2 detection with either 75 ng or 1500 ng/well of histones respectively.
  • the coating antigen was diluted in coating buffer (PBS+0.05% BSA) for a final volume of 100 ⁇ l and allowed to incubate overnight.
  • the plates were blocked with 300 ⁇ l blocking buffer (PBST+2% BSA) for 2 hours at RT, followed by a 2 hour incubation with 100 ⁇ l primary antibody (1:750 H3K79me2, CST 5472; or 1:5000 total H3, Abcam ab1791) diluted in blocking buffer at RT.
  • MV4-11 cells Exponentially growing MV4-11 cells were plated in a 12 well plate at 2 ⁇ 10 5 cells/well in a final volume of 2 mL. Cells were incubated with increasing concentration of test compounds (e.g., Compounds C94, C118, and D16 up to 50 ⁇ M for 6 days. Compound and media were refreshed on day 4 and cells split back to 5 ⁇ 10 5 cells/well. Cells were pelleted and processed as previously described.
  • test compounds e.g., Compounds C94, C118, and D16 up to 50 ⁇ M for 6 days. Compound and media were refreshed on day 4 and cells split back to 5 ⁇ 10 5 cells/well. Cells were pelleted and processed as previously described.
  • DOT1L bound structures were obtained by the soaking method.
  • the DOT1L-SAM crystals were cross-linked by exposing the crystal containing hanging drop over the vapor of 1 ⁇ l of 25% glutaraldehyde, pH 3.0, for 1 hr (13, 14) and then soaked with mother liquor containing 1 mM compound overnight.
  • the crystals were cryo-protected with 35% glucose in mother liquor and flash-frozen in liquid nitrogen.
  • the diffraction data sets were collected at beamline 17U at the Shanghai Synchrotron Radiation Facility. All data were processed by HKL2000.
  • DOT1L methyl transfer from the thiomethyl moiety of SAM to the ⁇ -N of the bound side chain of lysine 79 of histone H3 (H3K79) proceeds through a simple S N 2 mechanism, requiring stringent alignment of the molecular orbitals of the methyl donor and acceptor atoms.
  • the crystal structures of DOT1L bound to SAM and to the reaction product SAH illustrate a highly ordered active site with superimposable SAM and SAH configurations in the bound structure.
  • the thiomethyl group of SAM is directed into a contiguous channel that forms the lysine binding pocket of the enzyme, thus facilitating facile group transfer once the ternary enzyme-SAM-histone complex has formed.
  • DOT1L functions by a distributive mechanism, requiring dissociation of the enzyme from the histone substrate after each round of lysine 79 methylation.
  • the above biochemical data provided a starting point for inhibitor design.
  • the drug design started based on the structure of the reaction product SAH, with the following key objectives.
  • First objective was to reduce the polar surface area of the ligand by replacement of charged and/or polar functionalities.
  • Second objective was to engage recognition elements within both the SAM/SAH binding pocket and the adjacent lysine binding pocket to gain the affinity advantages of bisubstrate inhibitors.
  • these two goals should be accomplished while reasonable ligand efficiency is maintained and/or the pharmacological tractability of the compound series is improved.
  • the isopropyl group of Compound C2 was speculated to reach into the lysine binding pocket. Based on this assumption, this functionality was further developed to further engage elements within this channel and simultaneously engage recognition elements within the amino acid binding pocket by varying the substituent.
  • key intermediate species along the synthetic route were tested.
  • the FMoc-protected intermediate Compound C64 displayed potency for inhibition of DOT1L, with a K i of 20 ⁇ M. The instability of this compound precluded detailed structural characterization by crystallography. This finding did, however, lead to replacing the functionality with a short tether, linked to a large hydrophobic group.
  • tolerance of DOT1L inhibitors for substitutions within the nucleoside portion of the pharmacophore was determined.
  • substitutions on the nucleoside were not well tolerated.
  • the ring nitrogen at position 7 could be substituted by carbon; the resulting deazapurine compounds demonstrated potent inhibition of DOT1L as exemplified by compound D8, an inhibitor displaying a K i of 4 nM.
  • Conformational adaptation appears to play a critical role in driving inhibitor potency among the aminonucleoside inhibitors of DOT1L.
  • Table 5 summarizes the kinetics of inhibitor association and dissociation with DOT1L for the enzymatic product SAH and for three key compounds (Compounds C94, C118 and D16), as measured by surface plasmon resonance.
  • the enhancement in target potency seen across this series appears to be driven by a reduction in the dissociation rate of the inhibitors from the binary enzyme-inhibitor complex (k off ) which results in a dramatic change in the residence time ( ⁇ ) of the binary complex from 5 seconds to 1 hour in going from C94 to D16; while the dissociation rate constants and residence times change by over three orders of magnitude among these compounds, the association rate constant (k on ) is virtually invariant across the pharmacophore series and is several orders of magnitude slower than the calculated diffusion limit. More advanced inhibitors within the aminonucleoside series continue this trend, displaying residence times greater than 24 hours with no attendant change in association rate constant (such as Compound A2).
  • the relatively slow association rate constants seen for SAH and the aminonucleosides also suggest a conformational gating of compound access to the SAM/SAH binding site.
  • the upper limit of the association rate constant for diffusion-limited small molecule binding to a protein has been estimated to be on the order of 10 9 M ⁇ 1 s ⁇ 1 . More typically values of the association rate constant for small molecule substrates binding to enzymes are about 10 7 M ⁇ 1 s ⁇ 1 and typical values for the residence time of enzyme substrates and products are in the millisecond to second range ( 23 ).
  • the rates of association and dissociation are slow relative to other natural ligands of enzymes.
  • crystal structures of SAM and SAH bound to DOT1L revealed an occluded active site with no clear, unobstructed pathway from bulk solvent to the active site for compound association or dissociation; thus some conformational adaptation must attend enzyme turnover in order for substrate to access the binding pocket and for product to be released.
  • the first is referred to as a conformational selection mechanism in which the free enzyme exists in two conformational states that are in (slow) equilibrium with one another: a state that binds inhibitor and one that does not. Binding of the inhibitor shifts the equilibrium in favor of the inhibitor-binding conformation.
  • the second mechanism is referred to as the induced-fit mechanism.
  • the inhibitor binds to the enzyme in a non-optimal conformational state and then induces a conformational adjustment of the enzyme to create a more complementary, tighter binding state of the binary enzyme-inhibitor complex.
  • a third mechanism of slow association and slow dissociation results from situations in which the conformation of the enzyme does not change, but other factors limit the rate of ligand binding and dissociation. In this third situation, binding is often gated by the need for slow displacement of structured water molecules within the active site, displacement of metal binding ligands, and similar slow processes that are distinct from conformational adjustments of the protein per se.
  • the induced-fit mechanism is predominant among enzyme-inhibitor interactions.
  • the current data do not allow one to definitively distinguish between the two conformational adaptation models described above.
  • the low-affinity conformational state appears to be kinetically (and thermodynamically) insignificant in terms of inhibitor interactions. This is evident from the excellent agreement between the K i values for the inhibitor series, determined from the concentration dependent effects of compounds on enzyme activity, and the K d values determined from the SPR binding experiments (Table 5).
  • the K d values in Table 5 are calculated simply as the ratio of k off over k on , thus assuming a single step binding and dissociation mechanism.
  • the DOT1L-Compound C118 structure reveals that the inhibitor reaches into a heretofore-unrecognized pocket immediately adjacent to the amino acid binding subsite of the SAM/SAH binding pocket of the enzyme ( FIG. 4 ).
  • This pocket which does not exist in the structures of the enzyme with SAM, SAH or Compound C1—is opened up by the tert-butyl phenyl urea functionality of Compound C118.
  • the crystal structure of C118 reveals a number of novel interactions with DOT1L.
  • the charged 5′-amino group of the compound forms a hydrogen bond with the carbonyl oxygen of Gly163.
  • the urea region occupies the binding site of the amino acid region of SAM.
  • the terminal propyl nitrogen of the urea interacts with the side chain oxygen atom of Asp161 in the same binding mode as the carboxylate nitrogen atom in SAM.
  • the urea carbonyl oxygen interacts with the nitrogen atom of Asn241, similar to the interaction of one of the carboxylate oxygen atoms of SAM.
  • the proximal nitrogen atom of the urea (attached to the aromatic ring) coordinates with Asp161 ( FIG. 4A ).
  • the steric bulk of the tert-butyl phenyl opens up the novel hydrophobic pocket by changing the side chain conformation of Phe239, Tyr312, Met147 and Leu143, inducing a significant conformational change in the 130s' loop to flip Thr139 (a residue that otherwise interacts with the carboxylate terminus of SAM) away from the SAM binding pocket ( FIG. 4B ).
  • the movement of Tyr312 causes a change in a loop consisting of residues 302-312 (300s' loop). These changes result in both the 130s' and 300s' loops of DOT1L becoming disordered ( FIG. 4C ).
  • the crystal structure of the DOT1L-D16 complex reveals D16 binds to DOT1L in a similar manner as C118, with the 5′-amino isopropyl group occupying a region near that occupied by the methyl group of the thiomethyl on SAM ( FIG. 5 ).
  • the high potency, longer residence time compounds C118 and D16 are associated with a novel conformation of the enzyme that expands the contiguous active site cavity to include a new pocket; the crystal structures of these compounds suggest that these inhibitors “punch through” a protein wall to create this new pocket and to thus engage recognition elements both within the SAM/SAH binding pocket and the newly formed hydrophobic pocket. Because this conformational change is unique to DOT1L, these compounds show excellent selectivity against other PMTs (9).
  • inhibitor-induced displacement of key structural water molecules within enzyme active sites is a critical component of high-affinity ligand interactions. This may be a contributing factor in the tight-binding interactions between DOT1L and the aminonucleoside inhibitors presented here.
  • the resolution of the various enzyme-inhibitor co-crystal structures is not sufficient for us to make any definitive statements with regard to the role of structural water molecule displacement in the binding of these compounds to DOT1L.
  • Inhibition of DOT1L is expected to lead to a concentration-dependent diminution of H3K79 methylation levels in treated cells.
  • the diminution of H3K79 methylation is expected to translated into reduced transcription of leukemogenic genes such as HOXA9(27) and thus to a concomitant inhibition of cell proliferation.
  • the potent, selective DOT1L inhibitor D16 indeed leads to concentration-dependent inhibition of intracellular H3K79 dimethylation (H3K79me2), of HOXA9 gene transcription and antiproliferative effects selectively for MLL-rearranged leukemia cells.
  • Compounds C94, C118 and D16 provide a structurally related series of DOT1L inhibitors, spanning almost 4 orders of magnitude in target affinity, with which to test the relationship between enzyme inhibition and cellular efficacy.
  • Various concentrations of each of these compounds were applied to MV4-11 cells bearing a chromosomal rearrangement of the MLL gene and the impact on H3K79me2 level, HOXA9 message and cell proliferation were assessed at appropriate time points, taking into account the distinct kinetics of compound impact on each of these cellular parameters. Table 6 below summarizes the results of these studies.
  • the potent and selective inhibition of DOT1L by the aminonucleoside series translates into potent and selective inhibition of intracellular H3K79 methylation and to selective cell killing for leukemic cells bearing the MLL chromosomal translocation.
  • the quantitative correlation between target engagement, intracellular inhibition of H3K79 methylation, and antiproliferative effects is striking, and leaves little doubt that the selective phenotypic effects of these compounds are driven directly by ablation of DOT1L enzymatic activity.
  • These data provide a solid foundation upon which further optimization of DOT1L inhibitors may be conducted.
  • the data provide compelling proof of concept for the application of DOT1L inhibitors for selective killing of MLL-rearranged leukemias and thus portent the utility of DOT1L inhibitors for therapeutic intervention in this disease.
  • the enzymatic activity of the protein methyltransferase (PMT) DOT1L has been shown to be a driver of cell proliferation in MLL-rearranged leukemia. Structure-guided design, together with robust biochemical and biological assays, was used to optimize the potency, selectivity and pharmacological features of the aminonucleosides, resulting in the Compound A2.
  • Compound A2 is a S-adenosyl methionine (SAM) competitive inhibitor of DOT11L that displays a K i value of 80 ⁇ M and a drug-target residence time of >24 hours.
  • SAM S-adenosyl methionine
  • the compound is highly selective for DOT1L, demonstrating >37,000-fold selectivity against all other PMTs tested. Crystallographic studies reveal that the high affinity, durable inhibition of DOT1L by Compound A2 has its origin in a conformational adaptation of the protein that attends inhibitor binding, extending the compound binding pocket to include novel recognition elements beyond the SAM binding active site, as illustrated in FIG. 6 .
  • Compound A2 Treatment of leukemia cells with Compound A2 results in concentration- and time-dependent diminution of H3K79 methylation without effect on the methylation status of other histone sites. The diminution of H3K79 methylation leads to inhibition of key MLL target genes and selective, apoptotic cell killing in MLL-rearranged leukemia cells, but has minimal impact on non-rearranged cells.
  • Compound A2 is highly soluble in aqueous solution and can thus be formulated for intravenous administration. The effective pharmacokinetic half-life of Compound A2 in systemic circulation has been measured to be 0.25 and 1.5 h in rats and dogs, respectively. A nude rat subcutaneous xenograft model of MLL-rearranged leukemia has been established.
  • Groups 1, 2, 3, and 4 female RH nu/nu rats (7 weeks old, weighing 120-160 g) bearing MV4-11 xenograft tumors of sizes ranging from 300-600 mm 3 were implanted with a catheter in the femoral vein).
  • the infusion flow rate was set at 1,500 ⁇ L/hour/kg and was adjusted to the most recent mean body weight of each treatment group (as an example, the infusion flow rate was 300 ⁇ L/hour for a group of rats having a mean body weight of 200 g).
  • Group 1 received vehicle via a 21-day continuous IV infusion.
  • Group 2 received 21-day continuous IV infusion of the test substance at 35 mg/kg/day.
  • Group 3 received a daily 8-hour continuous IV infusion of the test substance at 67 mg/kg/day for 21 consecutive days. Between two IV infusions of the test substance, the rats were kept under IV infusion with NaCl 0.9% solution. Group 4 received a 21-day continuous IV infusion of the test substance at 70 mg/kg/day. Syringes used for the IV infusion were replaced every day.
  • Blood samples were taken from all animals in Groups 1, 2, and 4 on designated days and assayed for plasma levels of Compound A2. Tumor size was measured on the designated days as shown in FIG. 1 . The rats were terminated when the subcutaneous tumor reached a maximum volume of 9,000 mm 3 or at a maximum of 55 days after tumor cells injection.
  • Compound A2 is thus a potent, selective inhibitor of DOT1L that demonstrates strong efficacy in a rat xenograft model of MLL-rearranged leukemia.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Evolutionary Biology (AREA)
  • Genetics & Genomics (AREA)
  • Computing Systems (AREA)
  • Library & Information Science (AREA)
  • Pharmacology & Pharmacy (AREA)
  • General Chemical & Material Sciences (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Animal Behavior & Ethology (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
US14/420,877 2012-08-10 2013-08-12 Inhibitors of protein methyltransferase dot1l and methods of use thereof Abandoned US20150284422A1 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
US14/420,877 US20150284422A1 (en) 2012-08-10 2013-08-12 Inhibitors of protein methyltransferase dot1l and methods of use thereof

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201261682090P 2012-08-10 2012-08-10
PCT/US2013/054580 WO2014026198A1 (fr) 2012-08-10 2013-08-12 Inhibiteurs de protéine méthyltransférase de dot1l et leurs procédés d'utilisation
US14/420,877 US20150284422A1 (en) 2012-08-10 2013-08-12 Inhibitors of protein methyltransferase dot1l and methods of use thereof

Related Parent Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2013/054580 A-371-Of-International WO2014026198A1 (fr) 2012-08-10 2013-08-12 Inhibiteurs de protéine méthyltransférase de dot1l et leurs procédés d'utilisation

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US15/176,052 Continuation US10112968B2 (en) 2012-08-10 2016-06-07 Inhibitors of protein methyltransferase DOT1L and methods of use thereof

Publications (1)

Publication Number Publication Date
US20150284422A1 true US20150284422A1 (en) 2015-10-08

Family

ID=50068625

Family Applications (3)

Application Number Title Priority Date Filing Date
US14/420,877 Abandoned US20150284422A1 (en) 2012-08-10 2013-08-12 Inhibitors of protein methyltransferase dot1l and methods of use thereof
US15/176,052 Active US10112968B2 (en) 2012-08-10 2016-06-07 Inhibitors of protein methyltransferase DOT1L and methods of use thereof
US16/134,520 Abandoned US20190100552A1 (en) 2012-08-10 2018-09-18 Inhibitors of protein methyltransferase dot1l and methods of use thereof

Family Applications After (2)

Application Number Title Priority Date Filing Date
US15/176,052 Active US10112968B2 (en) 2012-08-10 2016-06-07 Inhibitors of protein methyltransferase DOT1L and methods of use thereof
US16/134,520 Abandoned US20190100552A1 (en) 2012-08-10 2018-09-18 Inhibitors of protein methyltransferase dot1l and methods of use thereof

Country Status (3)

Country Link
US (3) US20150284422A1 (fr)
EP (1) EP2882750A4 (fr)
WO (1) WO2014026198A1 (fr)

Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9446064B2 (en) 2013-03-14 2016-09-20 Epizyme, Inc. Combination therapy for treating cancer
US9597348B2 (en) 2012-09-06 2017-03-21 Epizyme, Inc. Method of treating leukemia
US10112968B2 (en) 2012-08-10 2018-10-30 Epizyme, Inc. Inhibitors of protein methyltransferase DOT1L and methods of use thereof
CN110092804A (zh) * 2019-03-29 2019-08-06 广州盈升生物科技有限公司 一种含双环基团的嘌呤化合物及其制备方法
US10968247B2 (en) 2013-03-15 2021-04-06 Epizyme, Inc. Methods of synthesizing substituted purine compounds
WO2022271540A1 (fr) * 2021-06-21 2022-12-29 Mayo Foundation For Medical Education And Research Inhibiteurs de dot1l

Families Citing this family (19)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
SI2794627T1 (sl) 2011-12-22 2019-02-28 Alios Biopharma, Inc. Substituirani nukleozidi, nukleotidi in njihovi analogi
US9441007B2 (en) 2012-03-21 2016-09-13 Alios Biopharma, Inc. Substituted nucleosides, nucleotides and analogs thereof
USRE48171E1 (en) 2012-03-21 2020-08-25 Janssen Biopharma, Inc. Substituted nucleosides, nucleotides and analogs thereof
CA2960287A1 (fr) * 2014-09-17 2016-03-24 Epizyme, Inc. Formulations injectables permettant de traiter le cancer
WO2016090271A1 (fr) * 2014-12-05 2016-06-09 Epizyme, Inc. Traitement de la leucémie par administration de l'inhibiteur de dot1l pinometostat
US9694084B2 (en) 2014-12-23 2017-07-04 Dana-Farber Cancer Institute, Inc. Methods to induce targeted protein degradation through bifunctional molecules
WO2016105518A1 (fr) 2014-12-23 2016-06-30 Dana-Farber Cancer Institute, Inc. Procédés pour induire la dégradation ciblée de protéines par des molécules bifonctionnelles
GB201519573D0 (en) 2015-11-05 2015-12-23 King S College London Combination
ES3044036T3 (en) 2016-01-26 2025-11-26 Memorial Sloan Kettering Cancer Center Targeting chromatin regulators for inhibiting leukemogenic gene expression in npm1
US11944627B2 (en) 2017-03-24 2024-04-02 Kura Oncology, Inc. Methods for treating hematological malignancies and Ewing's sarcoma
JP7555938B2 (ja) 2019-01-30 2024-09-25 モンテリノ・セラピューティクス・インコーポレイテッド アンドロゲン受容体を標的とするユビキチン化のための二官能性化合物および方法
KR20210145787A (ko) 2019-04-02 2021-12-02 알리고스 테라퓨틱스 인코포레이티드 Prmt5를 표적으로 하는 화합물
SI4106876T1 (sl) 2020-02-18 2025-11-28 Gilead Sciences, Inc. Protivirusne spojine
TWI775313B (zh) 2020-02-18 2022-08-21 美商基利科學股份有限公司 抗病毒化合物
TWI883391B (zh) 2020-02-18 2025-05-11 美商基利科學股份有限公司 抗病毒化合物
EP4153587A4 (fr) * 2020-05-18 2024-06-12 Montelino Therapeutics, Inc. Composés bi-fonctionnels et procédés d'ubiquitination ciblée du récepteur des androgènes
JP7688152B2 (ja) 2021-04-16 2025-06-03 ギリアード サイエンシーズ， インコーポレイテッド アミドを使用してカルバヌクレオシドを調製する方法
EP4387977A1 (fr) 2021-08-18 2024-06-26 Gilead Sciences, Inc. Composés phospholipidiques et leurs procédés de production et d'utilisation
US11981672B2 (en) 2021-09-13 2024-05-14 Montelino Therapeutics Inc. Bi-functional compounds and methods for targeted ubiquitination of androgen receptor

Family Cites Families (38)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020127598A1 (en) 2000-03-27 2002-09-12 Wenqiang Zhou Solution-phase combinatorial library synthesis and pharmaceutically active compounds produced thereby
EP1138689A1 (fr) 2000-03-28 2001-10-04 Roche Diagnostics GmbH Bases puriniques liées en position N8- ou C8- comme nucléosides universelles utilisées pour hybridization avec oligonucléotides
EP1138688A1 (fr) 2000-03-28 2001-10-04 Roche Diagnostics GmbH Bases puriniques liées en position N8- ou C8- comme nucléosides universelles utilisées pour hybridization avec oligonucléotides
US6534651B2 (en) 2000-04-06 2003-03-18 Inotek Pharmaceuticals Corp. 7-Substituted isoindolinone inhibitors of inflammation and reperfusion injury and methods of use thereof
US20040043959A1 (en) 2002-03-04 2004-03-04 Bloom Laura A. Combination therapies for treating methylthioadenosine phosphorylase deficient cells
JP2005533108A (ja) 2002-07-16 2005-11-04 メルク　エンド　カムパニー　インコーポレーテッド Ｒｎａ依存性ｒｎａウイルスポリメラーゼの阻害剤としてのヌクレオシド誘導体
AU2002951247A0 (en) 2002-09-06 2002-09-19 Alchemia Limited Compounds that interact with kinases
EP1572097A4 (fr) 2002-09-30 2010-02-17 Smithkline Beecham Corp Derives nucleosidiques servant au traitement d'une infection par le virus de l'hepatite c
WO2006015357A2 (fr) 2004-08-02 2006-02-09 University Of Virginia Patent Foundation Analogues de 2-propynyle adenosine comprenant des groupes 5'-ribose modifies presentant une activite agoniste a2a
US7576069B2 (en) 2004-08-02 2009-08-18 University Of Virginia Patent Foundation 2-polycyclic propynyl adenosine analogs having A2A agonist activity
US20100035945A1 (en) * 2004-12-06 2010-02-11 Xiaodong Cheng Small molecule inhibitors of bacterial dam dna methyltransferases
WO2006078752A2 (fr) 2005-01-21 2006-07-27 Methylgene, Inc. Inhibiteurs d'adn-methyltransferase
CA2596424C (fr) 2005-02-04 2016-03-29 Millennium Pharmaceuticals, Inc. Inhibiteurs d'enzymes d'activation e1
WO2006113458A1 (fr) 2005-04-15 2006-10-26 Bristol-Myers Squibb Company Inhibiteurs heterocycliques des proteines arginine methyle transferases
WO2006113615A2 (fr) 2005-04-15 2006-10-26 Sloan-Kettering Institute For Cancer Research Agents antimicrobiens et utilisations de ceux-ci
CN110003216A (zh) 2006-02-02 2019-07-12 千禧药品公司 E1活化酶抑制剂
JP5468782B2 (ja) 2006-03-02 2014-04-09 エージェンシー フォー サイエンス，テクノロジー アンド リサーチ 癌治療と幹細胞調節のための方法
GB0607953D0 (en) 2006-04-21 2006-05-31 Novartis Ag Organic compounds
US8188063B2 (en) 2006-06-19 2012-05-29 University Of Virginia Patent Foundation Use of adenosine A2A modulators to treat spinal cord injury
US20080132525A1 (en) 2006-12-04 2008-06-05 Methylgene Inc. Inhibitors of DNA Methyltransferase
WO2008124150A1 (fr) 2007-04-09 2008-10-16 University Of Virginia Patent Foundation Méthode de traitement de l'entérite, d'une lésion intestinale et de la diarrhée provoquées par des bactéries c. difficile au moyen d'un agoniste du récepteur a2a de l'adénosine
CN101417967A (zh) 2007-10-26 2009-04-29 浙江海正药业股份有限公司 组蛋白去乙酰酶抑制剂、其组合物及其应用
US20090181920A1 (en) 2008-01-09 2009-07-16 Pgxhealth, Llc Intrathecal treatment of neuropathic pain with a2ar agonists
AR072906A1 (es) 2008-08-06 2010-09-29 Novartis Ag Nucleosidos modificados utiles como antivirales
EP2332953A1 (fr) 2008-09-05 2011-06-15 Kotobuki Pharmaceutical Co., Ltd. Dérivé d'amine substituée et composition médicamenteuse contenant ledit dérivé en tant que principe actif
WO2010048149A2 (fr) 2008-10-20 2010-04-29 Kalypsys, Inc. Modulateurs hétérocycliques de gpr119 pour le traitement d'une maladie
CN102066372B (zh) 2009-08-24 2014-09-17 苏州爱斯鹏药物研发有限责任公司 含脲基的5，6元杂芳双环化合物作为激酶抑制剂
JP5794659B2 (ja) * 2010-04-19 2015-10-14 国立大学法人九州工業大学 ヒストンメチル化酵素活性の測定方法
AU2011336264A1 (en) 2010-12-03 2013-06-20 Epizyme, Inc. Carbocycle-substituted purine and 7-deazapurine compounds
AU2011336272A1 (en) 2010-12-03 2013-06-20 Epizyme, Inc. 7-deazapurine modulators of histone methyltransferase, and methods of use thereof
WO2012082436A2 (fr) 2010-12-03 2012-06-21 Epizyme, Inc. Modulateurs d'histone méthyltransférase et leurs procédés d'utilisation
WO2012075381A1 (fr) 2010-12-03 2012-06-07 Epizyme, Inc. Composés purines et 7-déazapurines substituées en tant que modulateurs d'enzymes épigéniques
WO2014026198A1 (fr) 2012-08-10 2014-02-13 Epizyme, Inc. Inhibiteurs de protéine méthyltransférase de dot1l et leurs procédés d'utilisation
CA2883781A1 (fr) 2012-09-06 2014-03-13 Epizyme, Inc. Methode de traitement de la leucemie
AU2013361076B2 (en) 2012-12-21 2018-08-30 Epizyme, Inc. DOT1 L inhibitors for use in the treatment of leukemia
AU2014236348B2 (en) 2013-03-14 2018-05-10 Epizyme, Inc. Combination therapy for treating cancer
US9446064B2 (en) 2013-03-14 2016-09-20 Epizyme, Inc. Combination therapy for treating cancer
EP2968387A4 (fr) 2013-03-15 2017-04-05 Epizyme, Inc. Procédés de synthèse de composés de purine substitués

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
Daigle et al. Cancer Cell (2011), Vol. 20, pages 53-65. *
Marrone et al. Annu. Rev. Pharmacol. Toxicol (1997), Vol. 37, pages 71-90. *

Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10112968B2 (en) 2012-08-10 2018-10-30 Epizyme, Inc. Inhibitors of protein methyltransferase DOT1L and methods of use thereof
US9597348B2 (en) 2012-09-06 2017-03-21 Epizyme, Inc. Method of treating leukemia
US10881680B2 (en) 2012-09-06 2021-01-05 Epizyme, Inc. Method of treating leukemia
US11633420B2 (en) 2012-09-06 2023-04-25 Epizyme, Inc. Method of treating leukemia
US9446064B2 (en) 2013-03-14 2016-09-20 Epizyme, Inc. Combination therapy for treating cancer
US10525074B2 (en) 2013-03-14 2020-01-07 Epizyme, Inc. Combination therapy for treating cancer
US10968247B2 (en) 2013-03-15 2021-04-06 Epizyme, Inc. Methods of synthesizing substituted purine compounds
US11572383B2 (en) 2013-03-15 2023-02-07 Epizyme, Inc. Methods of synthesizing substituted purine compounds
US11753433B2 (en) 2013-03-15 2023-09-12 Epizyme, Inc. Methods of synthesizing substituted purine compounds
CN110092804A (zh) * 2019-03-29 2019-08-06 广州盈升生物科技有限公司 一种含双环基团的嘌呤化合物及其制备方法
WO2022271540A1 (fr) * 2021-06-21 2022-12-29 Mayo Foundation For Medical Education And Research Inhibiteurs de dot1l

Also Published As

Publication number Publication date
WO2014026198A1 (fr) 2014-02-13
US10112968B2 (en) 2018-10-30
US20190100552A1 (en) 2019-04-04
EP2882750A1 (fr) 2015-06-17
US20170137455A1 (en) 2017-05-18
EP2882750A4 (fr) 2016-08-17

Similar Documents

Publication Publication Date Title
US10112968B2 (en) Inhibitors of protein methyltransferase DOT1L and methods of use thereof
US20230087806A1 (en) Methods of using ehmt2 inhibitors
US20220175789A1 (en) Ezh2 inhibitors for treating lymphoma
JP6592071B2 (ja) ヒトｅｚｈ２の阻害剤およびその使用方法
US20200113923A1 (en) Dot1l inhibitors for use in the treatment of leukemia
US10695347B2 (en) Pyrimidine derivative and use thereof
US9334527B2 (en) Inhibitors of human EZH2, and methods of use thereof
US20210213014A1 (en) Methods of using ehmt2 inhibitors in immunotherapies
KR20220097455A (ko) Btk 억제제로서의 피롤로피리미딘 화합물 및 이의 용도
US11267806B2 (en) Indazole compound for use in inhibiting kinase activity, composition and application thereof
US11718611B2 (en) Benzenesulfonylbenazamide compound for inhibiting BCL-2 protein and composition and use thereof
WO2009039321A1 (fr) Inhibiteurs de la prolyl hydroxylase
US10280165B2 (en) Pyridopyrimidinones and methods of use thereof
US8343977B2 (en) Substituted triazolo-pyrimidine compounds
WO2025054190A1 (fr) Formulations pharmaceutiques et programmes de dosage d'un inhibiteur de yap/taz-tead
CN116472046B (zh) 作为Cdc7抑制剂的盐型及其晶型
Esan Discovery of Acetyl CoA Synthetase and SARS-CoV-2 Protease Inhibitors
HK1262367A1 (en) Pyrimidine derivative and use thereof
HK1262367B (en) Pyrimidine derivatives and their use for the treatment of cancer

Legal Events

Date Code Title Description
AS Assignment

Owner name: EPIZYME, INC., MASSACHUSETTS

Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNORS:OLHAVA, EDWARD J.;CHESWORTH, RICHARD;POLLOCK, ROY M.;AND OTHERS;SIGNING DATES FROM 20150421 TO 20150630;REEL/FRAME:036197/0480

STCB Information on status: application discontinuation

Free format text: ABANDONED -- FAILURE TO RESPOND TO AN OFFICE ACTION

AS Assignment

Owner name: BIOPHARMA CREDIT PLC, UNITED KINGDOM

Free format text: SECURITY INTEREST;ASSIGNOR:EPIZYME, INC.;REEL/FRAME:051057/0848

Effective date: 20191118

AS Assignment

Owner name: EPIZYME, INC., MASSACHUSETTS

Free format text: TERMINATION AND RELEASE OF SECURITY INTEREST IN PATENTS AT REEL/FRAME: 051057/0848;ASSIGNOR:BIOPHARMA CREDIT PLC;REEL/FRAME:061165/0501

Effective date: 20220812