WO2000077031A2 - Muc1 ligands - Google Patents

Abstract

Novel ligands that bind to MUC1 are disclosed. The ligands were isolated using an improved phage display technique using MUC1 tandem repeat as a target. Uses of the ligand to detect, monitor or treat cancer as well as to prepare antibodies is also described.

Description

Title: MUCl Ligands FIELD OF THE INVENTION

The present invention relates to ligands that bind to MUCl and uses of the ligands to diagnose, monitor and treat cancer. BACKGROUND OF THE INVENTION

Mucins are high molecular weight glycoproteins which are expressed on the surface of normal and cancer tissues. The epithelial cell mucin encoded by the MUCl gene, is commonly expressed by adenocarcinomas of the pancreas, breast, ovary as well as by several other tumors of ductal epithelial cell origin. The protein core of mucins contains a variable number of tandem repeats (VNTRs) rich in O- glycosylation sites. The aberrant glycosylation of mucin tandem repeats by malignant cells results in the display of unique tumor-associated structures on their surface (1-4). In particular, mammary epithelial cells express mucins harbouring 40 to 80 copies of the MUCl tandem repeat, a 20-amino acid long domain with the sequence Pro-Asp-Thr-Arg-Pro-Ala- Pro-Gly-Ser-Thr-Ala-Pro-Pro-Ala-His-Gly-Val-Thr-Ser-Ala (5-8). All threonines and serines present in the MUCl tandem repeat are normally O-glycosylated in the context of milk-derived mucin (9), a process initiated by at least four distinct human UDP-GalNAc:polypeptide N- acetylgalactosaminyltransferases (10,11). A comprehensive analysis of 56 monoclonal antibodies that bind to the tumor-associated MUCl mucin has revealed that a majority of them recognize peptide epitopes within the sequence Ala-Pro-Asp-Thr-Arg-Pro-Ala-Pro (ref.12 and references thereafter) suggesting that the threonine residue within this sequence is underglycosylated in malignant cells exposing this segment of the tandem repeat. In addition, mucin-specific IgMs have been detected in sera from patients with breast and ovarian cancers and have been shown to recognize this epitope (13-15). MUCl has clinical relevance as it is found on the surface of many tumors and is a useful diagnostic and therapeutic tool. In addition, MUC1 is shed from the surface of many cancers and serum concentrations may be useful for detecting certain cancers and monitoring the response to cancer therapy. Expression of MUCl is also used for micrometastatic tumor cell detection in patients with solid tumors such as breast cancer. MUCl is also a potential target for tumor immunotherapy.

To date, clinical strategies aimed at targeting MUCl-expressing tumor cells have been limited to the use of monoclonal antibodies and related fragments in guided immunotherapies (16-19) and at developing vaccination approaches based on the MUCl tandem repeat (20-22). Small MUCl-binding peptides would offer clear advantages over antibodies (12) and their single chain variants (23), in terms of structural simplicity, penetration into solid tumors (24-26) and their lack of immunogenicity.

In view of the foregoing, there is a need in the art to develop small ligands that bind MUCl which would be useful diagnostic and therapeutic tools.

SUMMARY OF THE INVENTION

The present inventors have isolated several novel peptide ligands that bind to MUCl. The ligands were isolated using an improved phage display technique using MUCl tandem repeats as a target. Accordingly, the present invention provides isolated and purified ligands that bind to MUCl.

In one embodiment, the ligand comprises the sequence X_J-X₂- X₃ wherein:

X_j is Pro, Thr or Ser; X₂ is any amino acid; and

X₃ is Pro, Ala, Lys, His, Thr, Asn, Tyr or Phe.

The present invention further provides a method of isolating a ligand that binds to MUCl comprising:

(a) providing a MUCl target molecule wherein the MUCl target molecule comprises at least 3 tandem repeats of the sequence PDTRPAPGSTAPPAHGVTSA; (b) contacting the MUCl target molecule with a peptide or small molecule library, under conditions to allow the MUCl target molecule to bind to any MUCl ligands in the library, to prepare a test sample; (c) panning the test sample under high stringency conditions; and

(d) isolating the MUCl ligands bound to the MUCl in the test sample.

The present invention also provides the use of the ligands that bind MUCl to detect, monitor or treat cancer as well as to prepare antibodies.

Other features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples while indicating preferred embodiments of the invention are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description. BRIEF DESCRIPTION OF THE DRAWINGS The invention will now be described in relation to the drawings in which:

Figure 1A-C are graphs showing the binding of biotinylated

MUCl-Lpl, MUCl-Lp2 and MUCl-Lp3 to MUCl octapeptides synthesized on plastic pins was measured at 450 nm using a streptavidin-HRP conjugate. Each bar represents the average absorbance readings calculated for assays performed on six copies of each MUCl octapeptide.

Figure 2A-C are graphs showing the inhibition by MUCl ligand peptides of anti-MUCl mAb BC2 binding to the MUCl tandem repeat. The mAb BC2 was dispensed into MUCl/3TR-coated wells in the presence or absence of MUCl peptide ligands. The term mAb BC2 % relative binding represents the ratio, expressed as a percentage, of absorbance values between wells treated or not with increasing concentrations of a MUCl ligand. Figure 2A, TMGFTAPRFPHY (MUCl-Lpl), ♦ ; TMGFTA, □; FTAPRF, Δ; PRFPHY, 0; Figure 2B, SWWPFPPQPDPA (MUCl-Lp2), ♦; SWWPFP, Q; PFPPQP, Δ; PQPDPA, 0; Figure 2C, YTKSDPLKLLES (MUC1- Lp3), ♦ ; YTKSDP, Q ; SDPLKL, Δ ; LKLLES, 0. The peptide YTVTNSWTWWSPLQQA (■) does not bind to the MUCl repeat and was used as a negative control.

Figure 3A-C are graphs showing the binding of radiolabelled MUCl ligand peptides to cells. Curves depict the total (■, □) and nonspecific (A, Δ) binding of ¹²⁵I-labelled MUCl ligands to either MUC1⁺ T47D (B,A) and MUCl^" Daudi cells (d,A). Figure 3A, binding curves for ¹²⁵I- labelled MUCl-Lpl; Figure 3B, binding curves for ¹²⁵I-labelled MUCl-Lp2; Figure 3C, binding curves for ¹²⁵I-labelled MUCl-Lp3.

Figure 4A and B are graphs showing competitive displacement of radiolabelled peptide ligands from T47D cells with unlabelled MUCl ligands. Figure 4A, Displacement curves for ¹²⁵I-labelled MUCl-Lpl (Q),

MUCl-Lp2 (Δ) and MUCl-Lp3 (A ) in the presence of increasing concentrations of their respective unlabelled ligand. Figure 4B, Displacement curves for ^{1 5}I-labelled MUCl-Lpl with either unlabelled

MUCl-Lpl (□), MUCl-Lp2 (Δ) or MUCl-Lp3 (A). DETAILED DESCRIPTION OF THE INVENTION

The following standard one letter and three letter abbreviations for the amino acid residues may be used throughout the specification: A, Ala - alanine; R, Arg - Arginine; N, Asn - Asparagine; D, Asp - Aspartic acid; C, Cys - Cysteine; Q, Gin - Glutamine; E, Glu - Glutamic acid; G, Gly - Glycine; H, His - Histidine; I, He - Isoleucine; L, Leu - Leucine; K, Lys - Lysine; M, Met - Methionine; F, Phe - Phenyalanine; P, Pro - Proline; S, Ser - Serine; T, Thr - Threonine; W, Trp - Tryptophan; Y, Tyr - Tyrosine; and V, Val - Valine; 1. Ligands of the Invention As hereinbefore mentioned, the present inventors have isolated several novel peptide ligands that bind to MUCl. Accordingly, the present invention provides isolated and purified ligands that bind to MUCl.

In order to isolate MUCl ligands with high specificity for MUCl, an improved screening assay was developed by the inventors which is discussed in greater detail below. In summary, a 100-amino acid long peptide sequence corresponding to 5 consecutive 20 amino acid long tandem repeats of the MUCl mucin was chemically synthesized and used as a target in a solid-phase screening assay to probe a phage display library. The 20 amino acid long tandem repeat had the following sequence PDTRPAPGSTAPPAHGVTSA (SEQ.ID.NO.rl). The MUCl target was directly applied to plates and contacted with a phage display library expressing random 12 amino acid sequences. The phage that bound to the MUCl using high stringency conditions (i.e. high salt) were selected. Fifteen distinct, 12-residue long peptide sequences were identified after several rounds of phage planning which are shown in Table 1.

Using the improved screening assay, the following ligands were isolated: TMGFTAPRFPHY (SEQ.ID.NO.:2), SWWPFPPQPDPA (SEQ.ID.NO.:3), YTKSDPLKLLES (SEQ.ID.NO.:4), VVPVHWSRGVVL (SEQ.ID.NO.:5), HIPVAALAPRMT (SEQ.ID.NO.:6), LGLQPPTSALDP (SEQ.ID.NO.:7), TPAFSPLPTDLL (SEQ.ID.NO.:8), ELNTHLATNVFT (SEQ.ID.NO.:9), IDVHSINFLATL (SEQ.ID.NO.:10), THPWSLKSTSFF (SEQ.ID.NO.:ll), YITPYAHLAGGN (SEQ.ID.NO.:12), SLPIPSHARLQN (SEQ.ID.NO.:13), YLPYATLSQNSH (SEQ.ID.NO.:14), WHIPPNIGRTFS (SEQ.ID.NO.:15) and TSNPHTRHYYPI (SEQ.ID.NO.:16). The above MUCl ligands isolated by the inventors' improved method share a common motif, X₁-X₂-X^ wherein: Xi is Pro, Thr or Ser; X₂ is any amino acid; and X₃ is Pro, Ala, Lys, His, Thr, Asn, Tyr or Phe. Preferably, X₁ is Pro or Ser; X₂ is Leu, lie, Tyr, Ala, Val, Phe, Pro,

Met, His, Arg, Gin, Asp or Glu and X₃ is Pro or Phe. In one embodiment, the MUCl ligand has the sequence TMGFTAPRFPHY (SEQ.ID.NO.:2) which is also referred to as MUCl-Lpl herein. In order to determine the MUCl binding site of MUCl-Lpl, the inventors synthesized hexapeptides covering the MUCl-Lpl sequence and found that the sequence FTAPRF (SEQ.ID.NO.:17) and PRFPHY (SEQ.ID.NO.:18) were also able to bind MUCl. Both of these sequences share the common tripeptide PRF (SEQ.ID.NO.:19) consistent with the common motif X₁-X₂-X₃ described above. Accordingly, the present invention includes a MUCl ligand comprising the sequence PRF, which includes the sequences FTAPRF and PRFPHY.

In another embodiment, the MUCl ligand has the sequence SWWPFPPQPDPA (SEQ.ID.NO.:3) which is also referred to as MUCl-Lp2 herein. By synthesizing peptides spanning MUCl-Lp2, the inventors determined that the peptide SWWPFP (SEQ.ID.NO.:20) was a useful MUCl ligand. The inventors further determined that peptides containing the motif P-X-P (SEQ.ID.NO.:21) such as Pro-Gin-Pro (SEQ.ID.NO.:22); Pro- Asp- Pro (SEQ.ID.NO.:23); and Pro-Phe-Pro (SEQ.ID.NO.:24) could also bind MUCl which is consistent with the formula X₁-X₂-X₃ above. Accordingly, the present invention includes MUCl ligand comprising the sequence P- X-P, wherein X can be any amino acid.

In a further embodiment, the MUCl ligand has the sequence YTKSDPLKLLES (SEQ.ID.NO.:4) which is referred to as MUCl-Lp3 herein. By synthesizing peptides spanning MUCl-Lp3, the inventors determined that the sequences SDPLKL (SEQ.ID.NO.:25) and YTKSDP (SEQ.ID.NO.:26) could also bind MUCl. These sequences share the motif Ser- Asp-Pro (SEQ.ID.NO.:27) which is consistent with the formula X X₂-X₃ above. Accordingly, the present invention includes a MUCl ligand comprising the sequence SDP, which includes the sequences SDPLKL and YTKSDP.

The term "MUCl ligand" as used herein means a peptide that can bind MLJCl. The term includes peptides that are of a formula or sequence as defined above and fragments, analogs and derivatives of the peptides which maintain the ability to bind MUCl. The term also includes peptides isolated according to the method of the invention.

The term "analog" includes any peptide having an amino acid residue sequence substantially identical to the sequence of the MUCl ligands described herein in which one or more residues have been conservatively substituted with a functionally similar residue and which displays the ability to mimic a MUCl ligand. Examples of conservative substitutions include the substitution of one non-polar (hydrophobic) residue such as alanine, isoleucine, valine, leucine or methionine for another, the substitution of one polar (hydrophilic) residue for another such as between arginine and lysine, between glutamine and asparagine, between glutamine and glutamic acid, between asparagine and aspartic acid, between glycine and serine, the substitution of one basic residue such as lysine, arginine or histidine for another, or the substitution of one acidic residue, such as aspartic acid or glutamic acid for another. The phrase "conservative substitution" also includes the use of a chemically derivatized residue in place of a non-derivatized residue provided that such polypeptide displays the requisite activity.

The term "derivative" refers to a peptide having one or more residues chemically derivatized by reaction of a functional side group. Such derivatized molecules include for example, those molecules in which free amino groups have been derivatized to form amine hydrochlorides, p-toluene sulfonyl groups, carbobenzoxy groups, t- butyloxycarbonyl groups, chloroacetyl groups or formyl groups. Free carboxyl groups may be derivatized to form salts, methyl and ethyl esters or other types of esters or hydrazides. Free hydroxyl groups may be derivatized to form O-acyl or O-alkyl derivatives. The imidazole nitrogen of histidine may be derivatized to form N-im-benzylhistidine. Also included as derivatives are those peptides which contain one or more naturally occurring amino acid derivatives of the twenty standard amino acids. For examples: 4-hydroxyproline may be substituted for proline; 5- hydroxylysine may be substituted for lysine; 3-methylhistidine may be substituted for histidine; homoserine may be substituted for serine; and ornithine may be substituted for lysine.

MUCl ligands of the present invention also include any peptide having one or more additions and /or deletions or residues relative to the sequence of a peptide whose sequence is shown herein, so long as the requisite activity is maintained or increased.

The term "fragment" refers to any subject peptide having an amino acid residue sequence shorter than that of a peptide whose amino acid residue sequence is shown herein. By studying the binding sites recognized by the MUCl ligands of the invention, the inventors determined that the ligands likely bind dipeptide motifs Ala-Pro (SEQ.ID.NO.: 28) and/or Pro-Ala (SEQ.ID.NO.:29) within the MUCl tandem repeat. Specifically, MUCl-Lpl binds the motif Pro-Ala-X-Gly-X-Thr (SEQ.ID.NO.:30) wherein X can be any amino acid. Accordingly, the present invention provides a MUCl ligand which binds to the sequence Ala-Pro or Pro-Ala. In a preferred embodiment, the MUCl ligand binds to the sequence Pro-Ala-X-Gly-X-Thr, wherein X can be any amino acid. 2. Method of Isolating Ligands As mentioned previously, the present inventors have isolated several MUCl ligands using an improved screening assay. Importantly, using a traditional phage display technique wherein the MUCl target is biotinylated and applied to streptavidin coated plates and then probed with a phage display library, no peptides were isolated. The improvement in the present method is due to the target used and the assay conditions employed.

As a target, the inventors used several repeats of the MUC tandem repeat, PDTRPAPGSTAPPAHGVTSA (SEQ.ID.NO.:l), coated directly on plates. Such a target is improved over traditional biotinylated MUCl bound to streptavidin as it allows MUCl to adopt a proper secondary structure. In particular, a MUCl peptide comprising three consecutive MUCl repeats adopts a secondary structure composed of repeating knob-like structures (type II β turns) connected by extended spacers. The knobs protrude away from the long axis of the mucin with the most predominant antigenic site, APDTR (SEQ.ID.NO.:31), forming the accessible tip of the knob. As a result, such a target represents a constrained, well defined and attractive target to search for ligands. The MUCl tandem repeat target may be glycosylated, partially glycosylated or ungly cosy lated .

The constrained target was used to probe a phage display peptide library. Several rounds of phage panning were done, each at higher salt concentrations. The phage that bound the MUCl target at 400mM salt concentration were isolated. As a result the method isolated ligands that bind to the MUCl target under high stringency conditions.

Accordingly, the present invention provides a method of isolating a ligand that binds to MUCl comprising: (a) providing a MUCl target molecule wherein the MUCl target molecule comprises at least 3 tandem repeats of the sequence PDTRPAPGSTAPPAHGVTSA (SEQ.ID.NO.:l);

(b) contacting the MUCl target molecule with a peptide or small molecule library, under conditions to allow the MUCl target to bind to any MUCl ligands in the library, to prepare a test sample;

(c) panning the test sample under high stringency conditions; and

(d) isolating the MUCl ligands bound to the MUCl in the test sample. The library is preferably a phage display peptide library but may also be a combinatorial peptide library or a combinatorial small molecule library.

The high stringency conditions preferably consist of a round of panning at high salt concentrations, for example about 200-400mM NaCl, preferably at least 300 mM NaCl. It will be appreciated by one of skill in the art that high stringency conditions can consist of any condition that can destabilize protein interactions such as altering pH or using detergents, organic solvents or reducing agents.

Generally in step (c) the sample is panned in several rounds of panning, with the stringency conditions for phage binding increased at each round. Preferably there are 3 rounds of panning, each of reduced incubation time. In the first round of panning, phage binding is preferably performed at 75 mM NaCl; in the second round, the phage binding is preferably performed at 150 mM NaCl; and in the third round, the phage binding is preferably performed at least 300 mM NaCl. More preferably there are 4 rounds of phage panning wherein a second round is conducted at the same biochemical conditions as the first round although at a decreased incubation time. A preferred method of the phage panning strategy of the present invention is shown in Table 3.

The present invention also includes any ligand isolated according to the method including, and in addition to, the ligands described under 1. Ligands of the Invention.

Once potential ligands have been isolated, screening methods may be designed in order to determine if the molecules that bind to the MUCl and are useful in the methods of the present invention. For example, the ligands can be tested to see if they bind MUCl or MUCl expressing cells as described in the Examples herein. 3. Uses of the Ligands

The present invention includes all uses of the ligands that bind to MUCl as described herein. Some of the uses include the diagnosis, prognosis and treatment of cancer as well as the preparation of antibodies, (a) Diagnosis or Monitoring of Cancer

In one embodiment, the present invention provides a use of a ligand to MUCl to diagnose a cancer that is associated with MUCl.

The term "a cancer that is associated with MUCl" means any type of cancer wherein the cancer or tumour cells have underglycosylated

MUCl on their surface and/or they secrete or shed MUCl from their surface. Such cancers include breast, lung, colorectal, gastric, liver and pancreatic carcinomas.

In another embodiment, the present invention provides a use of a ligand to MUCl as a prognostic tool or to monitor the efficacy of treatment of a cancer that is associated with MUCl.

The present invention also provides a method of diagnosing or monitoring a cancer that is associated with MUCl comprising contacting a sample from a patient with a MUCl ligand of the invention and assaying for binding between the MUCl ligand and MUCl in the sample, if present, wherein the presence of MUCl indicates the presence of a cancer that is associated with MUCl. Samples which may be tested include blood, urine, serum, tears, saliva, feces, tissues and the like. For solid tumors a tissue biopsy may be used.

The method used to detect the cancer can be any method known in the art. For example, the binding of the ligands with MUCl may be used in known immunoassays which rely on the binding interaction between a ligand of the invention and MUCl. Examples of such assays are radioimmunoassays, enzyme immunoassays (e.g. ELISA), immunofluorescence, immunoprecipitation, latex agglutination, hemagglutination, and histochemical tests. The resulting MUCl bound to the ligand may be isolated by conventional isolation techniques, for example, salting out, chromatography, electrophoresis, gel filtration, fractionation, absorption, polyacrylamide gel electrophoresis, agglutination, or combinations thereof. Thus, the ligands may be used to identify or quantify the amount of a MUCl in a sample in order to diagnose the presence of a tumor.

For use in diagnostic assays, the ligand may be labelled with a detectable marker including various enzymes, fluorescent materials, luminescent materials and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, biotin, alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; and examples of suitable radioactive material include S-35, Cu-64, Ga-67, Zr-89, Ru-97, Tc-99m, Rh-105, Pd-109, In-Ill, 1-123, 1-125, 1131, Re-186, Au-198, Au-199, Pb-203, At-211, Pb-212 and Bi-212. The ligands may also be labelled or conjugated to one partner of a ligand binding pair. Representative examples include avidin-biotin and riboflavin-riboflavin binding protein. Methods for conjugating or labelling the ligands discussed above with the representative labels set forth above may be readily accomplished using conventional techniques.

The ligands of the invention may be used in immuno- histochemical analyses, for example, at the cellular and sub-subcellular level, to detect MUCl, to localise it to particular cells and tissues, and to specific subcellular locations, and to quantitate the level of expression. The ligands of the invention may also be used in flow cytometry.

Cytochemical techniques known in the art for localizing antigens using light and electron microscopy may be used to detect MUCl. Generally, a ligand of the invention may be labelled with a detectable substance and MUCl may be localised in tissues and cells based upon the presence of the detectable substance. Examples of detectable substances include various enzymes such as biotin, alkaline phosphatase, β- galactosidase, or acetylcholinesterase; fluorescent materials such as fluorescein; luminescent materials such as luminol; and, radioactive materials such as radioactive iodine I¹²⁵, 1¹³¹ or tritium. Ligands may also be coupled to electron dense substances, such as ferritin or colloidal gold, which are readily visualised by electron microscopy.

The ligand may be immobilized on a carrier or solid support such as nitrocellulose, glass, polyacrylamides, gabbros, and magnetite. The support material may have any possible configuration including spherical (e.g. bead), cylindrical (e.g. inside surface of a test tube or well, or the external surface of a rod), or flat (e.g. sheet, test strip). When an insolubilized ligand is used protein bound to the ligand is isolated by washing. For example, when the sample is blotted onto a nitrocellulose membrane, the ligand bound to MUCl is separated from the unreacted ligand by washing with a buffer, for example, phosphate buffered saline (PBS) with bovine serum albumin (BSA). Indirect methods may also be employed in which the ligand -

MUCl reaction is amplified by the introduction of an antibody, having specificity for the ligand.

When labelled ligand is used, the presence of a tumor can be determined by measuring the amount of labelled ligand bound to MUCl in the sample or of the unreacted labelled ligand. The appropriate method of measuring the labelled material is dependent upon the labelling agent.

Where a radioactive label is used as a detectable substance, a MUCl may be localized by radioautography. The results of radioautography may be quantitated by determining the density of particles in the radioautographs by various optical methods, or by counting the grains.

When unlabelled ligand is used in the method of the invention, the presence of MUCl can be determined by measuring the amount of ligand bound to MUCl using substances that interact specifically with the ligand to cause agglutination or precipitation. In particular, labelled antibody against a ligand of the invention, can be added to the reaction mixture. The presence of MUCl can be determined by a suitable method from among the already described techniques depending on the type of labelling agent. The reagents suitable for carrying out the diagnostic methods of the invention may be packaged into convenient kits providing the necessary materials, packaged into suitable containers. Such kits may include all the reagents required to detect MUCl in a sample by means of the methods described herein, and optionally suitable supports useful in performing the methods of the invention. (b) Therapeutic Uses

In a further embodiment, the present invention provides a use of a ligand to MUCl to treat or prevent a cancer that has increased MUCl levels. In such an embodiment the ligand may be coupled to an anticancer agent and used to target the agent to the cancer.

Accordingly, the present invention provides a use of a MUCl ligand to prepare a medicament to treat or prevent a cancer that is associated with MUCl. The present invention also provides a use of a MUCl ligand to treat or prevent a cancer that is associated with MUCl. The invention further includes a method of treating or preventing a cancer associated with MUCl comprising administering an effective amount of a MUCl ligand coupled to an anticancer agent to an animal in need thereof.

The term "animal" as used herein includes all members of the animal kingdom. Preferably, the animal is a mammal, more preferably a human.

The ligands coupled to anticancer agents may be formulated into pharmaceutical compositions for adminstration to subjects in a biologically compatible form suitable for administration in vivo. By "biologically compatible form suitable for administration in vivo" is meant a form of the substance to be administered in which any toxic effects are outweighed by the therapeutic effects. The substances may be administered to living organisms including humans, and animals. Administration of an effective amount of the pharmaceutical compositions of the present invention is defined as an amount effective, at dosages and for periods of time necessary to achieve the desired result. For example, a therapeutically active amount of a substance may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of antibody to elicit a desired response in the individual. Dosage regima may be adjusted to provide the optimum therapeutic response. For example, several divided doses may be administered daily or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation.

The active substance may be administered in a convenient manner such as by injection (subcutaneous, intravenous, etc.), oral administration, inhalation, transdermal application, or rectal administration. Depending on the route of administration, the active substance may be coated in a material to protect the compound from the action of enzymes, acids and other natural conditions which may inactivate the compound. The compositions described herein can be prepared by per se known methods for the preparation of pharmaceutically acceptable compositions which can be administered to subjects, such that an effective quantity of the active substance is combined in a mixture with a pharmaceutically acceptable vehicle. Suitable vehicles are described, for example, in Remington's Pharmaceutical Sciences (Remington's Pharmaceutical Sciences, Mack Publishing Company, Easton, Pa., USA 1985). On this basis, the compositions include, albeit not exclusively, solutions of the substances in association with one or more pharmaceutically acceptable vehicles or diluents, and contained in buffered solutions with a suitable pH and iso-osmotic with the physiological fluids. (c) Antibodies

The ligands of the invention may also be used to prepare antibodies to the ligands. Conventional methods can be used to prepare the antibodies including polyclonal antisera or monoclonal antibodies. To produce polyclonal antibodies, a mammal, (e.g., a mouse, hamster, or rabbit) can be immunized with an immunogenic form of the ligand which elicits an antibody response in the mammal. Techniques for conferring immunogenicity on a peptide include conjugation to carriers or other techniques well known in the art. For example, the peptide can be administered in the presence of adjuvant. The progress of immunization can be monitored by detection of antibody titers in plasma or serum. Standard ELISA or other immunoassay procedures can be used with the immunogen as antigen to assess the levels of antibodies. Following immunization, antisera can be obtained and, if desired, polyclonal antibodies isolated from the sera. To produce monoclonal antibodies, antibody producing cells

(lymphocytes) can be harvested from an immunized animal and fused with myeloma cells by standard somatic cell fusion procedures thus immortalizing these cells and yielding hybridoma cells. Such techniques are well known in the art, (e.g., the hybridoma technique originally developed by Kohler and Milstein (Nature 256, 495-497 (1975)) as well as other techniques such as the human B-cell hybridoma technique (Kozbor et al., Immunol. Today 4, 72 (1983)), the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al., Monoclonal Antibodies in Cancer Therapy (1985) Allen R. Bliss, Inc., pages 77-96), and screening of combinatorial antibody libraries (Huse et al., Science 246, 1275 (1989)). Hybridoma cells can be screened immunochemically for production of antibodies specifically reactive with the peptide and the monoclonal antibodies can be isolated. Therefore, the invention also contemplates hybridoma cells secreting monoclonal antibodies with specificity for a protein of the invention.

The term "antibody" as used herein is intended to include fragments thereof which also specifically react with a protein, of the invention, or peptide thereof. Antibodies can be fragmented using conventional techniques and the fragments screened for utility in the same manner as described above. For example, F(ab') fragments can be generated by treating antibody with pepsin. The resulting F(ab')₂ fragment can be treated to reduce disulfide bridges to produce Fab' fragments.

Chimeric antibody derivatives, i.e., antibody molecules that combine a non-human animal variable region and a human constant region are also contemplated within the scope of the invention. Chimeric antibody molecules can include, for example, the antigen binding domain from an antibody of a mouse, rat, or other species, with human constant regions. Conventional methods may be used to make chimeric antibodies containing the immunoglobulin variable region which recognizes a protein of the invention (See, for example, Morrison et al., Proc. Natl Acad. Sci. U.S.A. 81,6851 (1985); Takeda et al, Nature 314, 452 (1985), Cabilly et al., U.S. Patent No. 4,816,567; Boss et al., U.S. Patent No. 4,816,397; Tanaguchi et al., European Patent Publication EP171496; European Patent Publication 0173494, United Kingdom patent GB 2177096B).

Monoclonal or chimeric antibodies specifically reactive with a ligand of the invention as described herein can be further humanized by producing human constant region chimeras, in which parts of the variable regions, particularly the conserved framework regions of the antigen- binding domain, are of human origin and only the hypervariable regions are of non-human origin. Such immunoglobulin molecules may be made by techniques known in the art, (e.g., Teng et al., Proc. Natl. Acad. Sci. U.S.A., 80, 7308-7312 (1983); Kozbor et al, Immunology Today, 4, 7279 (1983); Olsson et al, Meth. Enzymol., 92, 3-16 (1982)), and PCT Publication WO92/06193 or EP 0239400). Humanized antibodies can also be commercially produced (Scotgen Limited, 2 Holly Road, Twickenham, Middlesex, Great Britain). Specific antibodies, or antibody fragments, reactive against a ligand of the invention may also be generated by screening expression libraries encoding immunoglobulin genes, or portions thereof, expressed in bacteria with the ligands of the invention. For example, complete Fab fragments, VH regions and FV regions can be expressed in bacteria using phage expression libraries (See for example Ward et al., Nature 341, 544- 546: (1989); Huse et al, Science 246, 1275-1281 (1989); and McCafferty et al. Nature 348, 552-554 (1990)).

The following non-limiting examples are illustrative of the present invention: EXAMPLES Example 1

Preparation of MUCl Ligands Cell Lines The human breast cancer cell line T47D (American Type

Culture Collection; Rockville, MD) was cultured at 37°C in α-MEM, Iscove's modification of DMEM (IMDM), or RPMI 1640 in the presence of 5% C0₂ with 10% FCS (Cansera International Inc., Rexdale, Ontario). The expression of the MUCl epitope on these cell lines was confirmed by flow cytometry using a series of anti-MUCl mAb BC-2 (28,29). Peptide Synthesis

All peptides were assembled by solid-phase peptide synthesis on an Applied Biosystems 341A Peptide Synthesizer using Wang resin supports (4-hydroxymethylphenoxymethyl copolystyrene -1% divinylbenzene; Applied Biosystems) and 9-fluorenyloxycarbonyl protected (Fmoc) amino acids (NovaBiochem, San Diego, CA). Two MUCl peptides were constructed, namely a 60-amino acid (MUCl-60mer) and a 100-amino acid long peptide (MUCl-lOOmer) corresponding to three and five consecutive tandem repeats of the MUCl mucin. Each repeat was composed of the sequence Pro-Asp-Thr-Arg-Pro-Ala-Pro-Gly-Ser-Thr-Ala- Pro-Pro-Ala-His-Gly-Val-Thr-Ser-Ala. The peptides SWWPFPPQPDPA (SEQ.ID.NO.:3) and YSWWPFPPQPDPA (SEQ.ID.NO.:41) corresponding to sequences derived from our phage display searches were synthesized by Fmoc chemistry using 2-chloro-trityl chloride resin (200-400 mesh; NovaBiochem).

Some peptides were biotinylated at their N-terminus by adding two N-terminal glycines to the sequence of these peptides and by subsequently treating the deprotected peptide resins (0.125 mmoles) with 3 molar equivalents of biotin (92 mg) and HATU/HOBt (1:1 ratio; 200 mg) dissolved in 5 mL N-methylpyrrolidone. After 5 minutes, 6 molar equivalents of diisopropylethylamine were added and the reaction left to occur overnight with constant stirring. Peptides were released from their supports by suspending and mildly agitating each peptide resin in 82.5% (v/v) TFA: 5% (v/v) phenol: 5% (v/v) thioanisole: 5% (v/v) water:2.5% (v/v) EDT for 2 hours at room temperature. Each treated resin was filtered and the cleaved peptide was extracted from the resin with 1 mL TFA. The subsequent filtrate was recovered and the peptide precipitated with diethylether. Crude peptides were redissolved in water and lyophilized. The MUCl peptides were purified to homogeneity by reverse phase HPLC (Waters HPLC 510 System). Analytical separations were performed on a Rapid Resolution Zorbax SB-C₁₈ column (4.6 x 75mm; 3.5 μ particles) at a flow rate of 1 mL/min while semi-preparative separations were carried out on a Zorbax SB-C₁₈ column (9.4 x 250mm; 5μ particles) operating at a flow rate of 2 mL/min. In the case of MUCl-lOOmer, the columns were equilibrated in solvent A (0.1% TFA/AcN) and the peptide was eluted using a 30-minute gradient going from 10% to 35 % mobile phase B (0.1%TFA/60%AcN). For the MUCl-60mer, the columns were equilibrated in 0.1% TFA/20%AcN (eluent A) and the peptide was resolved using a 28-minute gradient going from 0% to 28 % eluent B (0.1% TFA/AcN). For all other peptides, the same columns were equilibrated in 95% eluent A: 5% eluent B and the peptides were eluted using a 40-minute gradient going from 5% to 60% eluent B. The mass and composition of MUCl peptides were confirmed by mass spectrometry and amino acid analysis. MUCl-60mer, MH+ observed 5625.1 (calc. 5625.1), biotinylated homolog, MH+ observed 5851.9 (calc. 5851.4); MUCl-lOOmer, MH+ observed 9362 (calc.9363). Amino acid composition: MUCl-60mer; Asp, found 0.8 (exp. 1); Ser, found 2.1 (exp. 2); Gly, found 2.1 (exp. 2); Arg, found 1.0 (exp.l); Thr, found 2.6 (exρ.3); Ala, found 4.2 (exp. 4); Pro, found 4.8 (exp. 5); Val, found 1.0 (exp. 1); His, N.D; MUCl-lOOmer; Asp, found 1.1 (exp. 1); Ser, found 2.4 (exp. 2); Gly, found 2.4 (exp. 2); Arg/Thr, found 4.0 (exp.4); Ala, found 3.7 (exp. 4); Pro, found 4.4 (exp. 5); Val, found 1.1 (exp. 1); His, N.D. The mass of other peptides were also confirmed by mass spectrometry: TMGFTAPRFPHY, MH+ observed 1424.2 (calc.1424.6); biotinylated homolog, MH+ observed 1765.5 (calc. 1765.7); YTKSDPLKLLES, MH+ observed 1393.4 (calc.1393.5); biotinylated homolog, MH+ observed 1733.4 (calc. 1734.6); SWWPFPPQPDPA, MH+ observed 1424.2 (calc. 1424.6); biotinylated homolog, MH+ observed 1765.7 (calc. 1765.7); YSWWPFPPQPDPA, MH+ observed 1586.8 (calc.1587.7). Pin Synthesis

Overlapping octapeptides spanning the entire sequence of the 20-amino acid long MUCl tandem repeat were synthesized by Fmoc chemistry on derivatized high density polyethylene pins (Epitope Scanning kit; Cambridge Research Biochemicals, Wilmington, DE) following methods described previously (13-15). Six copies of each peptide were prepared for statistical reasons (see section on ELISA results). Pins harboring the peptide sequences PLAQ (positive control using an antipeptide antibody provided by the supplier) and GLAQ (negative control) were synthesized as control sequences to monitor the quality of the synthesis.

Panning strategy of phage display library

Phage library searches were performed using the Ph.D-12 Peptide Library (New England Biolabs, Beverly, MA), a M13 bacteriophage library displaying random 12-amino acid long linear peptides fused to each phage coat protein. The protocols used in phage panning followed guidelines suggested by the manufacturer. Briefly, polyvinyl chloride 96- well plates were coated with the 100-amino acid long synthetic MUCl (5 repeats of the core sequence) in 0.1 M carbonate buffer, pH 9.6, at 37°C for 30 minutes or 4°C overnight. Wells were subsequently treated for 30 minutes at 37°C with PBS containing 0.5% (w/v) bovine serum albumin (BSA) and 0.05% (v/v) Tween-20. Plates were then washed with PBS and 100 μL aliquot of the phage library-containing solution were dispensed in each well (2xl0ⁿ pfu/ml binding buffer). The stringency condition used for phage binding was altered at each round of panning. During the first round of panning, phage binding was performed overnight at room temperature in 10 mM PBS, pH 7.4 containing 75 mM sodium chloride, 0.5% (w/v) bovine serum albumin (BSA) and 0.05% Tween-20. The second round of phage binding was shortened to 2 hours using the same conditions. The third round of panning binding was performed at RT for 30 minutes in PBS, pH 7.4, containing 0.5% (w/v) BSA, 0.05% (V/V) Tween-20. The last round of panning was done at room temperature for 30 minutes in lOmM PB pH7.4 containing different concentrations of NaCl (200mM, 250mM, 300mM, 350mM, 400mM). Between each panning round, the plates were washed 10 times at room temperature in the same binding buffer as used in the panning assay. The bound phages were eluted by dispensing 100 μl of 0.2M Glycine-HCl,pH 2.2, containing 1% BSA in each well. One microliter of the phage eluate was used to titer the phage and the remaining eluate was amplified. After the last round of panning, clones recovered from the highest binding stringency conditions were picked and amplified. Phage DNA were prepared and sequenced. Mapping of peptides and phage binding sites on the MUCl tandem repeat MUCl peptides covalently attached to polyethylene pins by their C-terminus were incubated in blocking buffer (1% [wt/vol] bovine serum albumin, 1% [wt/vol] ovalbumin, 0.1% [vol/vol] Tween 20 in 10 mM phosphate-buffered saline [PBS, pH 7.4]) for 1 hour to prevent the non specific absorption of phages, peptides or secondary antibodies. The pins were subsequently incubated overnight at 4°C in wells containing 150 μL aliquots of solutions of either purified phages or related biotinylated synthetic peptides (μg/mL) prepared in blocking buffer. After 4 washes in PBS containing 0.05% (vol/vol) Tween 20, the pins were incubated for 1 hour in wells containing 100 μL of either rabbit anti-phage antibody (for detecting phages, 1:1000 dilution) or streptavidin-HRP conjugate (for detecting peptides, 1:1000 dilution). In the case of phage detection, the pins were further washed and incubated for 1 hour with a goat anti-rabbit immunoglobulin-peroxidase construct (100 μL of a 1:1000 dilution) diluted in blocking buffer. All pins were finally washed and the binding of phages or peptides was detected by incubating the pins in microtiter plates containing 100 μL of 0.05% (wt/vol) 2,2'-azino-bis(3-ethylbenzthiazoline-6- sulfonate) (ABTS) dissolved in 0.1 M sodium phosphate-0.08 M citric acid (pH 4.0) - 0.003% (vol/vol) hydrogen peroxide per well. Absorbance readings at 405 nm of solutions in each well were recorded with a Titertek plate reader. Each point represents the average absorbance reading calculated for assays performed on six copies of each overlapping MUCl octapeptide. Flow Cytometry

Breast cancer cells (1-2 x 10⁵ cells; T47D) were suspended in 50 μl of PBS (pH 7.4; supplemented with ImM CaCl₂, ImM MgCl₂, 1% (w/v) BSA, 0.05% sodium azide) containing either 200 μM of a biotinylated peptide or the monoclonal antibody BC-2 (IgGl, 1:100 dilution; Serotec, Oxford, England). The cells were incubated at 37°C for 60 minutes, subsequently washed three times with PBS, resuspended in 50 μl of the same buffer containing 1 μL of 1 mg/mL phycoerythrin (PE)-streptavidin conjugate (Molecular Probes; Eugene, OR) or 1 μL of a 0.2 mg/mL PE- antimouse Ig kappa light chain conjugate (PharMingen, Lajolla, CA) and finally incubated at 4°C for 30 minutes. The cells were washed three times with PBS and resuspended in 200 μl of PBS containing 5 μl of 7- aminoactinomycin D (7-AAD, 0.1 mg/mL in PBS, pH 7.4). Flow cytometry was performed on a Becton Dickinson FACScan and the data analysed using CellQuest software. Radioligand Binding Assays

Synthetic, tyrosine-containing MUCl peptide ligands were iodinated using the chloramine T method (32). Briefly, 100 μg of peptide dissolved in 20 μL of water was dispensed into polypropylene tube. A 10 μL aliquot of Na¹²⁵I (ImCi; Dupont) as well as 10 μL of chloramine T (BDH; 2mg/mL in water) were added to the tube and the iodination reaction was allowed to proceed for 1 minute at room temperature in a fumehood. The reaction was stopped with 10 μL of sodium metabisulfite (4 mg/mL in water) and the mixture diluted to 1 mL with 0.1% (v/v) TFA /water. The radiolabeled peptides were loaded and desalted on disposable C18 cartridges (MiUipore) in the same eluent. The labeled peptides were then eluted from the cartridges with 100% methanol and concentrated by evaporating the organic phase under a stream of nitrogen gas. The purity of labeled peptides was > 95% as verified by thin layer chromatography and their specific activity range in value from 15-20 μCi/μmol. The breast cancer cell line T47D expresses MUCl on its surface and was used for ligand binding assays and competition assays. For binding assays, increasing concentrations of each radiolabeled peptide in the presence or absence of an excess unlabeled peptide (200 fold excess) were incubated with 10⁵ cells in 0.2 ml of binding buffer (PBS, pH7.4, ImM CaCl_2/ ImM MgCl₂, 1% (w/v) BSA, 0.05% sodium azide) at room temperature for 60 minutes. The reaction mixture were spun through an oil column (84 % [v/v] silicon oil and 16% paraffin oil). After freezing the column on dry ice for 20 minutes, the tip of the column containing the cell pellet was cut off. The radioactivity of both the tip and the remaining column (supernatant) were counted using a Gamma counter. Peptide binding constants were derived from titration curves using GRAPHPAD software. For competition assays, radioiodinated peptides were incubated with different concentrations of unlabeled peptides (MUCl peptide ligands or the lOOmer synthetic MUCl peptide) and dispensed into tubes containing 5 x 10⁴ T47D cells suspended in 150 μL of binding buffer. Displacement curves were constructed from experiment performed in duplicate. Plate Binding Assays

Wells of 96-well polystyrene plates (NUNC) were coated with 100 μL of streptavidin (SIGMA; 10 μg/ml solution in 0.1 M carbonate buffer [pH 9.6]), at either 37°C for 30 minutes or overnight at 4°C. The plates were washed three times with PBS, and the biotinylated 60-mer MUCl peptide (0.5 μg/mL; 100 μL) prepared in binding buffer, was added to the wells and incubated at 37°C for 30 minutes. The mAb BC-2 (100 μL; 1:5000 dilution) pre-mixed with increasing concentrations of a MUCl peptide ligand (1 μM - lOOOμM) were dispensed in MUCl-coated wells and the binding event left to proceed at 37°C for 60 minutes. The plates were subsequently washed with PBS. Aliquots of anti-mouse IgG-HRP conjugate (100 μL; 1:500 dilution; SIGMA) were placed in each well and incubated for 30 minutes at room temperature. Following a final washing step in PBS, 100 μL aliquot of the color substrate 3, 3', 5,5'- tetramethylbenzidine (TMB, 100 μg/ml in 0.1M sodium acetate buffer, pH5.5, 1.3mM H₂0 ) was placed in each well to reveal the presence of the peroxidase enzyme. The reaction was stopped after a 30-minute incubation period at room temperature by adding 100 μL of a 2M H₂S0₄ solution. Absorbance readings were recorded at 450 nm using a plate reader (Titertek Multiskan MCC/340). Results of the Screening Strategy

The inventors have synthesized by solid phase peptide synthesis and purified a 100 amino acid-long analog of MUCl which c ontains five consecutive tandem repe ats ([PDTRPAPGSTAPPAHGVTSA]₅). The objective of this study was to identify one or more peptide ligands able to recognize and bind specifically to the mucin MUCl tandem repeat. One solution was to perform searches within phage display library for potential peptide ligands. The success in finding such ligands depends in part on the structure and nature of the target itself. The 100-amino acid long peptide representing 5 consecutive MUCl tandem repeats (MUCl lOOmer) was thus synthesized in order to ensure the presence of secondary structure observed in the MUCl mucin. A phage library was selected where random 12-amino acid sequences are presented as fused domains onto the M13 coat protein. Panning procedures were devised where reduced incubation times and increasing salt concentrations were used during phage binding steps prior to the elution of bound phages.

The screening of a phage display peptide library for sequences for possible ligands to the MUCl peptide tandem repeat identifies several distinct 12-amino acid long peptide sequences which are shown in Table 1. Three distinct peptide sequences derived from screening a phage display peptide library were shown to bind to the MUCl peptide tandem repeat. These are identified as MUCl-Lpl; MUCl-Lp2 and MUCl-Lp3 in Table 1. The binding of these peptides to MUCl expressed on the breast cancer cell line T47D was shown to be specific (displaced with the corresponding unlabeled analogs) with affinity constants in the micromolar range.

Based on the sequence of the ligands isolated, the inventors identified a motif that was common to the ligands. The motif in each ligand is shown in Table 2. Generally, the motif comprises the sequence X₁-X -X₃ wherein X₁ is Pro, Thr or Ser; X₂ is any amino acid; and X₃ is Pro, Ala, Lys, His, Thr, Asn, Tyr or Phe. Preferably, X_x is Pro; X₂ is a hydrophobic amino acid (i.e. Ala, Val, Leu, He, Pro, Met, Phe or Try) and X₃ is Pro.

Discussion

The underglycosylated or deglycosylated forms of the MUCl tandem repeat represent targets for immunotherapy or for designing cancer vaccines. The value of the MUCl repeat as an immunogen for the generation of useful B- or T-cell responses is presently being evaluated in the context of clinical trials. More than fifty monoclonal antibodies have also been raised against surface determinants on epithelial cell cancers including breast, colorectal and ovarian cancers, and been shown to recognize a common short peptide region of the MUCl tandem repeat. From practical reasons, the use of these antibodies as therapeutic agents is hampered by their size, affinity and structure leading to issues such as their immunogenicity and their reduced ability to penetrate into tumors. Small ligands able to bind specifically to tumor-associated forms of the MUCl epitope would be advantageous in these respects. The challenge was to identify small peptides able to bind to the

20-amino acid tandem repeat of MUCl, a sequence that is predicted to adopt a minimal but potentially unique secondary structure. Using a phage display strategy, the inventors identified many peptides able to bind specifically to the determinant found on the MUCl tandem repeat. These peptides offer the potential for developing diagnostic /therapeutic low molecular-weight ligands directed at MUCl sites present on cancer cells. The MUCl tandem repeat represents one of the best defined target in terms of developing guided cancer therapies. Recent studies have suggested the need to identify low molecular agents that can target cells expressing underglycosylated forms of the MUCl mucin. Mucins serve a range of functions associated with the physical protection of mucosal surfaces (lubrication), in coping with rapid changes in pH and osmolarity, or in binding via its carbohydrate side chains to pathogenic strains of bacteria or viruses or in blocking the activity of neutrophils, cytotoxic T cells and NK cells. Example 2

Defining the binding sites of three MUCl ligands on the MUCl tandem repeat

The binding of MUCl-Lpl (SEQ.ID.NO.:2), MUCl-Lp2 (SEQ.ID.NO.:3), and MUCl-Lp3 (SEQ.ID.NO.:4) to the MUCl tandem repeat was confirmed and further delineated using overlapping octapeptides assembled on plastic pins, covering the entire sequence of the 20-amino acid long MUCl tandem repeat. Biotinylated analogs of these MUCl ligands were synthesized and shown to bind to more than one region of the tandem repeat (Figure 1). Their binding patterns suggest that they associate with short, duplicated motifs present within the MUCl sequence (Figure 1). More precisely, the two dominant epitopes recognized by MUCl-Lpl were Thr-Arg-Pro-Ala-Pro-Gly-Ser-Thr (SEQ.ID.NO.:32) and Ala-Pro-Pro-Ala-His-Gly-Val-Thr (SEQ.ID.NO.:33), sequences which harbour the common motif Pro-Ala-X-Gly-X-Thr (SEQ.ID.NO.:30). In the case of MUCl-Lp2, the MUCl peptides recognized were Thr-Arg-Pro-Ala- Pro-Gly-Ser-Thr (SEQ.ID.NO.:32), Arg-Pro-Ala-Pro-Gly-Ser-Thr-Ala (SEQ.ID.NO.:34), Pro-Ala-Pro-Gly-Ser-Thr-Ala-Pro (SEQ.ID.NO.:35) and Ala-His-Gly-Val-Thr-Ser-Ala-Pro (SEQ.ID.NO.:36) suggesting single or combinations of two possible binding units namely Ala-Pro (SEQ.ID.NO.:28) and Gly-X-Thr (SEQ.ID.NO.:37). MUCl-Lp3, unlike the previous two ligands, appears to bind to a broad array of MUCl sequences containing Ala-Pro (SEQ.ID.NO.:28) or Pro-Ala (SEQ.ID.NO.:29) dipeptides. In summary, epitope mapping studies indicate that all three synthetic ligands may recognize at least in part the dipeptides Ala-Pro and/or Pro- Ala. MUCl-Lp3 requires the presence of only these dipeptide motifs within the MUCl repeat. Interestingly, most monoclonal antibodies that bind to the tumor-associated MUCl repeat recognize parts or all of the sequence Ala-Pro-Asp-Thr-Arg-Pro-Ala-Pro (SEQ.ID.NO.:38) where Ala- Pro- Asp-Thr-Arg (SEQ.ID.NO.:39) represents an accessible bulge displayed on the surface of the underglycosylated MUCl repeats (12). This region includes two Ala-Pro and one Pro- Ala sequences. The two MUCl Gly-X- Thr regions defined in the MUCl-Lpl and -Lp2 binding sites are located on both sides of the protruding knob-like structure of each repeat (27). Their location would suggest that searches for small MUCl ligands may led to peptides associated with distinct and potentially less accessible regions of the MUCl repeat. Defining structural motifs explaining the association of MUCl binders to the MUCl tandem repeat

The specificity of our MUCl-ligand peptides (MUCl-Lp) for the MUCl tandem repeat was also confirmed in a displacement assay where unlabelled MUCl-Lps were shown to inhibit the binding of a well known anti-MUCl antibody to the synthetic MUC1/3TR peptide (Figure 2). Briefly, the mAb BC2 (28) recognizes the sequence Ala-Pro-Asp-Thr-Arg (SEQ.ID.NO.:39) within the MUCl repeat, reacts with MUCl components in the sera of patients with breast cancer, and binds avidly to synthetic analogs of the MUCl tandem repeat with a reported affinity constant of 2.5 x 10⁹ M"¹ (29). Peptide mapping analyses (Figure 1) suggest that MUCl-Lp2 and MUCl-Lp3 peptides bind to the Ala-Pro dipeptide sequence present in the Ala-Pro-Asp-Thr-Arg epitope recognized by mAb BC2 (Figure 1) and as such these ligands should competitively inhibit the binding of mAb BC2 to MUC1 /3TR. MUCl-Lpl binds to sites in proximity to the mAb BC2 epitope and could also sterically interfere with this interaction. The relative inhibitory potential of individual MUCl ligand peptides was measured in a displacement assay involving the binding of mAb BC2 to MUC1/3TR. As expected, MUCl-Lp2 and Lp3 were better able to displace mAb BC2 bound to MUC1/3TR than MUCl-Lpl while an irrelevant peptide (YTVTNSWTWWSPLQQA (SEQ.ID.NO.:40)) was unable to inhibit this interaction (Figure 2). Sets of three overlapping hexapeptides covering each of the MUCl-Lp sequences were synthesized to further define relevant residues present in MUCl-binding peptides. For MUCl- Lpl, the sequences Phe-Thr-Ala-Pro-Arg-Phe (SEQ.ID.NO.:17) and Pro-Arg- Phe-Pro-His-Tyr (SEQ.ID.NO.:18) were equal to MUCl-Lpl as competitive inhibitors, suggesting that the common tripeptide Pro-Arg-Phe (SEQ.ID.NO.:19) may represent part of its putative MUCl-binding motif (Figure 2A). In the case of MUCl-Lp2, the peptide Ser-Trp-Trp-Pro-Phe-Pro (SEQ.ID.NO.:20) was comparable to the 12-amino acid ligand itself in competing with mAb BC2 for binding to the MUCl repeat. The other two hexapeptides were weaker inhibitors and contained one or more tripeptides with the motif Pro-X-Pro (SEQ.ID.NO.:21) (Pro-Gln-Pro (SEQ.ID.NO.:22), Pro-Asp-Pro (SEQ.ID.NO.:23), Pro-Phe-Pro (SEQ.ID.NO.:24); Figure 2B). Finally, MUCl-Lp3 and to a lesser extent, Ser- Asp-Pro-Leu-Lys-Leu (SEQ.ID.NO.:25) and Tyr-Thr-Lys-Ser-Asp-Pro (SEQ.ID.NO.:26) were inhibitors of mAb BC2 association with MUCl (Figure 2C). The recurrent tripeptide present in these MUCl-Lp3 analogs is the sequence Ser- Asp-Pro (SEQ.ID.NO.:27).

In summary, the recognition of Ala-Pro elements within the MUCl repeat by all three peptide ligands would suggest the occurrence of a common structural motif within the sequences of MUCl-Lpl, -Lp2 and- Lp3 (Table 1) accounting for at least part of their MUCl-binding character. An analysis of antibody displacement curves by all three MUCl binders and their respective hexapeptide analogs (Figure 2) revealed a tripeptide motif within MUCl-Lpl, -Lp2, and -Lp3 defined by either Pro or Ser at the first position followed by a charged /polar amino acid and ending with either a Pro or a Phe residue. All deduced insert sequences of MUCl- binding phages (Table 1) were then aligned to further defined the putative MUCl-ligand pattern. Several other sequences harboured motifs similar to the ones initially deduced from the three most common sequences (Table 2). This analysis only led to a broadening of possible residues within these motifs, particularly at the second and third positions of the tripeptide segment. Nevertheless, the motif typically contains one or more proline residues preferentially located at the N- and /or C-terminus of the segment.

A search for proteins harboring the tripeptide motif interestingly identified the MUCl tandem repeat itself as containing the related but not identical tripeptide motifs Pro-Asp-Thr, Pro- Ala-Pro, Thr- Ala-Pro, and Pro-Pro-Ala. This finding would suggest a possible homophilic aggregation of MUCl molecules via their tandem repeats. MUC1/5TR however remains monomeric in solution as monitored by high performance gel filtration chromatography (results not shown). Other proline-rich sequences present in WW (Pro-X-Tyr) or SH3 (Pro-X-X- Pro) domain ligands partly resemble the MUCl ligand motif (38,39). The motifs Pro-Pro-Gin and Pro-Gln-Pro are found in the tandem repeats of rhodopsin and gliadin respectively (40). The latter motifs are preceded by a Tyr or Phe residues and are part of an ensemble of proteins presenting a repetitive structural pattern defined as polyproline, β turn helices (40). The interesting feature of this structural element appears to be its ability to exist as a series of local interconverting structures (β-turn) centered at the Tyr/Phe-Pro bond and causing no major change in the overall polyproline helical character of the peptide chain. This built-in local flexibility may potentially represent a molecular switch associated with the recognition and posttranslational modification of tyrosine (phosphorylation), serine or threonine (glycosylation in mucin, phosphorylation) residues often found in such repeats. The tandem repeats located at the C- terminal of the RNA polymerase II as well as those of WW and SH3 domain ligands may adopt related structures in solution (41). In summary, the identified MUCl ligand peptide motifs may possess an inherent potential to locally adapt to the conformation adopted by distinct peptide regions of the MUCl tandem repeat. Example 3

MUCl ligands bind specifically to MUCl-expressing cells

MUCl-Lpl, -Lp2 and Lp3 were radio-iodinated to determine if these peptides could bind specifically to the MUCl repeat presented on tumor cells. Labelling was facilitated by the presence of unique, naturally occurring C- or N-terminal tyrosine residues in the sequence of MUCl- Lpl and -Lp3 respectively. A tyrosine was added to the N-terminus of the MUCl-Lp2 sequence to complete the analysis. Two cell lines were used to construct binding curves for all three labelled ligands: T47D, an established MUCl-expressing breast cancer cell line and Daudi, a human B-lymphoma cell line that does not express MUCl mucin. Binding curves presented in Figure 3 highlight the fact that all three MUCl ligands associated specifically with T47D cells while MUCl-negative Daudi cells did not express significant or detectable levels of ligand receptors. The specific binding of radiolabeled MUCl-Lps to T47D cells was saturable, as determined from the difference in counts (cpm) between total and nonspecific binding. The dissociation constant and number of binding sites of each MUCl ligands on T47D cells are presented in Table 4. The peptide ligands bind to T47D cells with K_d values in the micromolar range. MUCl-Lpl represents the most avid MUCl ligand with the fewest number of binding sites on T47D cells while MUCl-Lp2 and -Lp3 bind to significantly more sites on these cells suggesting that the motifs that they recognize on the MUCl tandem repeat are less complex than the binding site for MUCl-Lpl. The association of MUCl ligand peptides to T47D cells was reversible as defined by the concentration-dependent displacement of radiolabeled MUCl-Lpl, -Lp2 and -Lp3 from these cells with their respective unlabelled MUCl-Lps (Figure 4A). The distinct selectivity of MUCl-Lpl for the MUCl repeat was further confirmed by the fact that unlabelled MUCl-Lpl was significantly better than MUCl-Lp2 and -Lp3 in competing with radio-iodinated MUCl-Lpl for binding to T47D cells (Figure 4B). The results presented in Table 4 provide a strong rationale for the sequence motifs deduced from our epitope mapping studies. More precisely, the dipeptide motifs Ala-Pro and Pro-Ala occur frequently within the MUCl tandem repeat (2 Ala-Pro, 2 Pro-Ala, one additional Ala- Pro linking two repeats). MUCl-Lp3 was thus expected to bind to a higher number of sites on MUCl than MUCl-Lpl and MUCl-Lp2 which recognize additional residues. The association of MUCl-Lp3 to simple dipeptide motifs also implied that its affinity for the tandem repeat would be comparatively lower than MUCl-Lpl and MUCl-Lp2. The tabulation of binding constants and number of binding sites for each ligand on MUCl- expressing breast cancer cells (T47D) support these predictions. MUCl-Lp3 was the weakest MUCl binder and bound to 40 times more sites on MUCl- expressing cells than MUCl-Lpl and to 3 fold more sites than MUCl-Lp2 confirming that it recognizes a more promiscuous target on the tandem repeat than the other two MUCl ligands. As expected, MUCl-Lpl which bound to a relatively defined site, has the fewest number of binding sites on T47D cells and displays a higher affinity and selectivity (Figure 4B) for MUCl sites on cells than MUCl-Lp2 and -Lp3. Prospects for deriving small ligands displaying high affinity and selectivity for the MUCl tandem repeat

The frequent exposure of peptide domains in the MUCl tandem repeat defines an important class of related tumor-associated epitopes on the surface of epithelial cancer cells. More importantly, the pattern of internalization and recycling of membranous MUCl suggests that ligands targeting such sites will be routed inside MUCl-expressing cells and could serve as delivery vehicles (42). Single-chain Fv antibodies directed at the MUCl core peptide tandem repeat have recently been identified (23). However, the mass of such structures remains high (> 10 kD). Issues relating to their ability to penetrate into solid tumors or to recognize sterically hindered peptide epitopes in the context of underglycosylated forms of MUCl-expressing tumor cells will need to be addressed. The design of peptide "mimics" of MUCl-directed antibodies has recently been suggested to alleviate some of these issues (43). The MUCl ligands identified in this study have affinity constants in the micromolar range suggesting that their MUCl recognition motifs could be improved by constructing and probing phage display or synthetic peptides sub-libraries using MUCl-Lp sequences as starting templates. The selectivity of MUCl-Lpl for the MUCl tandem repeat appears to be based on a relatively complex discontinuous motif, namely Pro-Ala-X-Gly-X- Thr. This finding would suggest that an increase in affinity constant may also be gained by constraining the structure of MUCl ligands through the use of peptide mimetics rather than through library searches involving a limited spectrum of amino acid building blocks.

In conclusion, short peptides that bind to the tumor-associated MUCl tandem repeat were identified by screening a phage display peptide library Three synthetic peptides were shown to bind specifically to MUC1- expressing breast cancer cells but not to MUCl-negative cells. More importantly, the alignment of peptides derived from sequencing inserts of MUCl-binding phages as well as antibody inhibition assays suggest the existence of short proline-containing peptide motifs in the identified MUCl binders. These peptides can now be used as lead templates in developing small ligands directed at MUCl sites present on cancer cells.

While the present invention has been described with reference to what are presently considered to be the preferred examples, it is to be understood that the invention is not limited to the disclosed examples. To the contrary, the invention is intended to cover various modifications and equivalent arrangements included within the spirit and scope of the appended claims.

All publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety. TABLE 1

Duodecapeptide sequences deduced from sequencing phage DNA inserts of MUCl-binding phages

Peptide Sequence i Frequency SEQ.ID.NO.

TMGFTAPRFPHY (MUCl-Lpl) 12/34 2 SWWPFPPQPDPA (MUCl-Lp2 2/34 3 YTKSDPLKLLES (MUCl-Lp3) 8/34 4 VVPVHWSRGVVL 1/34 5

HIPVAALAPRMT 1/34 6

LGLQPPTSALDP 1/34 7 TPAFSPLPTDLL 1/34 8

ELNTHLATNVFT 1/34 9

IDVHSINFLATL 1/34 10

THPWSLKSTSFF 1/34 11

YITPYAHLAGGN 1/34 12

SLPIPSHARLQN 1/34 13

YLPYATLSQNSH 1/34 14

WHIPPNIGRTFS 1/34 15

TSNPHTRHYYPI 1/34 16

¹ One-letter amino acid code

TABLE 2

Possible tripeptide motifs that bind to the peptide core of the MUCl tandem repeat

TPAFS PLP TDLL

SL PIP SHARLQN

SWW PFP PQPDPA

SWWPFPPQ PDP A

SWWPFP PQP DPA

SWWPF PPQ PDPA

LGLQ PPT SALDP

WHI PPN IGRTFS

YTKSD PLK LLES

V V PVH WSRGVVL

HI PVA ALAPRMT

YIT PYA HLAGGN

YL PYA TLSQNSH

TMGFTA PRF PHY

TSN PHT RHYYPI

TMGFTAPRF PHY

TMGF TAP RFPHY

THP WSLKSTSFF

YTK SDP LKLLES

TABLE 3

Phage panning strategy used to identify phages that bind specifically to the peptide core of the MUCl tandem repeat

S/NS stands for the ratio of phages specifically bound to the target (S) versus non-specifically bound phages (NS). TABLE 4

Binding parameters of peptide ligands to MUCl-expressing T47D cells

Peptide K_d Binding sites per cell

(μM) (x 10⁵)

MUCl-Lpl 1.9 (± 2.2) 1.5 (± 1.1) MUCl-Lp2 2.4 (± 1.6) 22 (± 10) MUCl-Lp3 8.3 (± 1.4) 60 (± 8.6)

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Claims

We Claim:

1. An isolated and purified ligand that binds to MUCl and which comprises the sequence X_J-X₂-X_S wherein X_! is Pro, Thr or Ser; X₂ is any amino acid; and X₃ is Pro, Ala, Lys, His, Thr, Asn, Tyr or Phe or an analog or derivative thereof.

2. A ligand according to claim 1 which comprises the sequence Xj- X -X₃ wherein X₁ is Pro, Thr or Ser; X₂ is Leu, He, Tyr, Ala, Val, Phe, Pro, Met, His, Arg, Asp, Gin or Glu; and X₃ is Pro, Ala, Lys, His, Thr, Asn, Tyr or Phe.

3. A ligand according to claim 2 wherein X_τ is Pro or Ser, X₂ is

Arg, Asp, Gin or Phe and X₃ is Pro or Phe.

4. A ligand according to claim 1 wherein X_l is Pro; X is Arg and X₃ is Phe.

5. A ligand according to claim 4 comprising the sequence FTAPRF (SEQ.ID.NO.:17).

6. A ligand according to claim 4 comprising the sequence PRFPHY (SEQ.ID.NO.:18).

7. A ligand according to claim 4 comprising the sequence TMGFTAPRFPHY (SEQ.ID.NO.:2).

8. A ligand according to claim 1 wherein X₁ is Pro; X₂ is any amino acid and X₃ is Pro.

9. A ligand according to claim 8 comprising the sequence

SWWPFP (SEQ.ID.NO.:20).

10. A ligand according to claim 8 comprising the sequence SWWPFPPQPDPA (SEQ.ID.NO.:3).

11. A ligand according to claim 1 wherein X- is Ser; X₂ is Asp and X₃ is Pro.

12. A ligand according to claim 11 comprising the sequence

SDPLKL (SEQ.ID.NO.:25).

13. A ligand according to claim 11 comprising the sequence YTKSDP (SEQ.ID.NO.:26).

14. A ligand according to claim 11 comprising the sequence YTKSDPLKLLES (SEQ.ID.NO.:4).

15. A ligand according to claim 1 wherein the ligand is selected from the group consisting of TMGFTAPRFPHY (SEQ.ID.NO.:2), SWWPFPPQPDPA (SEQ.ID.NO.:3), YTKSDPLKLLES (SEQ.ID.NO.:4), VVPVHWSRGVVL (SEQ.ID.NO.:5), HIPVAALAPRMT (SEQ.ID.NO.:6), LGLQPPTSALDP (SEQ.ID.NO.:7), TPAFSPLPTDLL (SEQ.ID.NO.:8), ELNTHLATNVFT (SEQ.ID.NO.:9), IDVHSINFLATL (SEQ.ID.NO.:10), THPWSLKSTSFF (SEQ.ID.NO.:ll), YITPYAHLAGGN (SEQ.ID.NO.:12), SLPIPSHARLQN (SEQ.ID.NO.:13), YLPYATLSQNSH (SEQ.ID.NO.:14), WHIPPNIGRTFS (SEQ.ID.NO.:15) and TSNPHTRHYYPI (SEQ.ID.NO.:16) or an analog, derivative or fragment of the ligand.

16. An isolated and purified ligand which binds to the sequence PDTRPAPGSTAPPAHGVTSA (SEQ.ID.NO.:l) of MUCl or a portion thereof.

17. A ligand according to claim 16 which binds to the sequence TRPAPGST (SEQ.ID.NO.:32).

18. A ligand according to claim 16 which binds to the sequence Ala-Pro (SEQ.ID.NO.:28) and /or Pro- Ala (SEQ.ID.NO.:29).

19. A ligand according to claim 16 which binds to the sequence Pro- Ala-X-Gly-X-Thr (SEQ.ID.NO.-.30) wherein X is any amino acid.

20. A method of isolating a ligand that binds to MUCl comprising:

(a) providing a MUCl target molecule wherein the MUCl target molecule comprises at least 3 tandem repeats of the sequence PDTRPAPGSTAPPAHGVTSA (SEQ.ID.NO.:l);

(b) contacting the MUCl target molecule with a peptide or small molecule library, under conditions to allow the MUCl target to bind to any MUCl ligands in the library, to prepare a test sample;

(c) panning the test sample under high stringency conditions; and

(d) isolating the MUCl ligands bound to the MUCl in the test sample.

21. A method according to claim 20 wherein the library is a peptide phage display library or a synthetic peptide library.

22. A method according to claim 20 wherein the high stringency conditions consist of high salt concentrations.

23. A method according to claim 22 wherein the high salt concentration is about 200-400mM NaCl.

24. A method according to claim 22 wherein the high salt concentration is at least 300 mM NaCl.

25. A method according to claim 20 wherein step (c) comprises of three rounds of panning, the first round at a salt concentration of 75 mM, the second round at a salt concentration of 150 mM and the third round at a salt concentration of at least 300 mM.

26. A method according to claim 21 wherein step (c) comprises four rounds of panning, the first and second rounds at a salt concentration of 75 mM, the third round at a salt concentration of 150 mM and the fourth round at a salt concentration of at least 300 mM.

27. A ligand isolated according to the method as claimed in any one of claims 20 to 26.

28. A use of the ligand according to any one of claims 1 to 19 to detect the presence of MUCl in a sample.

29. A use of a ligand according to any one of claims 1 to 19 to treat or prevent a cancer associated with MUCl.

30. A use of a ligand according to any one of claims 1 to 19 to prepare a medicament to treat or prevent a cancer associated with MUCl.

31. A use of a ligand according to any one of claims 1 to 19 to prepare a diagnostic agent to detect a cancer associated with MUCl.

32. A method of diagnosing or monitoring a cancer that is associated with MUCl comprising contacting a sample from a patient with a MUCl ligand according to any one of claims 1 to 19 and assaying for binding between the MUCl ligand and MUCl in the sample, if present, wherein the presence of MUCl indicates the presence of a cancer that is associated with MUCl.

33. An antibody that binds to a ligand according to any one of claims 1 to 19.