CA2250067A1 - In vitro fluorescence polarization assay - Google Patents

Abstract

An in vitro assay method permits the identification of a test substance which inhibits the mutual association of a pair of proteins. The method includes the steps of providing a pair of proteins capable of mutual association, one of said proteins bearing a covalently linked fluorophore; preparing a mixture containing the two proteins and at least one test substance; irradiating the mixture with polarized light of a suitable wavelength permitting excitation of the fluorophore as indicated by emission of polarized light; measuring the degree of polarization of the emission, and determining the effect of the presence or concentration of the test substance in decreasing the observed emission polarization of a mixture of the two proteins alone. Inhibitory activity of in the test substance correlates with decreased depolarization values.

Description

CA 022~0067 1998-09-21 W O 97/39326 rCT~US97/06746 IN VITl~O FLUORESCENCE POLARIZATION ASSAY

Technical Field of the Invention The invention relates to materials and methods for the identification of inhibitors of protein:protein interactions, especially those involved in cellular signal transduction.

Back~round of the Invention Cellular signal transduction, i.e., the series of events leading from extracellular events to intracellular sequelae, is an aspect of cellular function in both normal and disease states. Numerous proteins that function as signal transducing molecules have been identified, including receptors, docking or recruiting proteins and enzymes such as receptor and non-receptor tyrosine kinases, phosphatases and other molecules with enzymatic or regulatory activities. These molecules generally demonstrate the capacity to associate specifically with other proteins to form a si~n~ling complex that can alter cell activity.
Signaling proteins often contain domain(s) of conserved sequence, which serve as non-catalytic modules that direct protein-protein interactions during signal transduction. Such domains include among others, SH2, phosphotyrosine interaction ("PI"), WW and SH3 domains. SH2 and PI domains recognize, i.e., bind to, proteins containing characteristic peptide sequences which include one or more phosphorylated tyrosine residues. WW and SH3 domains recognize proteins cont:lining characteristic peptide sequences which need not contain phosphotyrosine residues. Significant information related to such domains, proteins cont~ining them, the production ofproteins cont~ining such domains (including protein fragments and fusion proteins), the characteristic peptide sequences which they recognize and the biological and/or clinical role played by the interactions of such proteins has been described in the scientific literature.
In cases in which the interaction of particular protein molecules is associated with the cause or symptoms of a disease or pathological condition, compounds capable of interfering with that protein:protein interaction may be useful in preventing or treating the disease or condition in m~mm~ , including human patients.
Critical tools for the discovery of such inhibitors of protein:protein interactions are binding assays. the well-known two-hybrid interaction/binding assay described by Song and Fields, Nature, 340:245-247 (1989) has been used to study the interactions of protein-protein interacting partners [See, Fields et al, US Patent No. 5,283,173 (I Feb CA 022~0067 1998-09-21 W 097/39326 PCTrUS97/06746 1994)~. Such approaches have also been used to identify presumed SH2 dependent interactions using yeast [Xing, Z. et al., Mol. Biol. Cell, 5:413-421 (1994); and Osborne, M.A. et al., Biotechnol., 13: 1474 1478 (1995)] or to detect the inhibition of two-hybrid formation in yeast [Chaudhuri, B. et al., FEBS Lett., 357: 221-226 (1995)]. See, also, International patent application No. PCT/US95/03208, incorporated herein by reference for background information on SH3 domains and their ligands including information on the design and preparation of proteins containing various SH3 domains, preparation of peptide ligands for an SH3 domain of interest, and biological/clinical roles of SH3 mediated interactions. See, PCT/US97/02635, incorporated herein by reference, for information on receptor domains (e.g., SH2 and PI domains) for phosphotyrosine-cont~ining lig~n(l~ including the design and ple~aldlion of proteins containing various SH2 domains, plel)alalion of peptide ligands for an SH2 domain of interest, and biological/clinical roles of SH2-mediated interactions.
Competitive binding assays have been described for detecting test substances which interfere with the association of proteins cont~ining an SH2 domain with their phosphotyrosine cont~inin~; ligands. See, e.g., Pawson, US Patent No. 5,352,660. More recently reported binding assays have utili~ed surface plasmon resonance (Biacore) [see, e.g., Panayotou et al, Mol. Cell. Biol., 13: 3567-3576 (1993)] or radioactive ligand based assays. The former has a relatively low throughput, while the latter requires cumbersome filtration manipulations and generates radioactive waste, an increasingly difficult disposal issue.
The availability of materials and methods designed for the rapid and effective identification of inhibitors of protein:protein interactions would be a boon for drug discovery efforts aimed at a wide variety of target protein mediators. It would permit higher-throughput and more efficient identification and development of new ph~ eutical compositions cont~ining inhibitors of protein:protein interactions linked to undesirable or pathological conditions.

Summary of the Invention The present invention addresses this need by providing novel materials and methods for in vilro competitive binding assays for identifying substances which inhibit or interfere with the binding together of pairs of proteins capable of mutual association, i.e., binding. to forrn binding complexes. Of particular interest are assays for identifying compounds capable of inhibiting the binding of intracellular proteins or protein domains, especially those involved in cellular signal transduction with their binding partners.

CA 022~0067 1998-09-21 W 097/39326 PCTrUS9i/06746 Such proteins include, for instance, proteins which contain one or more SH2 domains, PI
domains, SH3 domains, or WW domains, each with its respective protein ligand.
In one aspect, the invention provides an in vitro assay method for identifying atest substance which inhibits the mutual association of a first protein to a second protein.
The method includes the steps of preparing a mixture containing the first protein, the second protein bearing a covalently linked fluorophore, and at least one test substance.
The mixture is irradiated with polarized light of a suitable wavelength permitting excitation of the fluorophore as indicated by emission of polarized light. The degree of polarization of the emission is measured and the effect of the presence or concentration of the test substance is determined. Inhibitory activity of the test substance is shown by a decrease in the observed emission polarization values of the mixture of the first and second proteins in the presence of the text substance as compared with the same protein mixture in the absence of the test substance.
Inhibition of protein:protein association can result from binding a test substance to the first protein or to the labeled ligand protein or peptide. Thus, the assay method can be viewed as a method for identifying a test substance which competitively binds to either member of the binding pair. As above, the degree of polarization of the emission is measured, and the effect of the presence or concentration of the test substance in decreasing the observed emission polarization is observed and compared with a mixture in the absence of the test substance. Competitive binding of the test substance correlates with decreased depolarization values.
In still another aspect, the invention provides an inhibitor of the association of a first protein with a second protein, first identified by the methods above.
In yet another aspect, the invention provides components or reagents, e.g.,a protein bearing a covalently linked fluorophore, useful in the methods of the invention.
The components or reagents can further be packaged in a kit with instructions for use in the described methods.
Other aspects and advantages of the present invention are described further in the following detailed description of the preferred embodiments thereof.

Brief Description of the Drawin~s Fig. 1 depicts the structure of a fluorescent probe FMT 1, described in Example 2.
Fig. 2A is the saturation curve of FMTl binding to Src SH2, which plots bound Src/total tracer vs. total Src concentration. Non-linear least squares fit for a saturation experiment between probe FMTI and the Src-SH2 domain. Calculated Kd is 0.24 withan error of 0.008 ~M, (Chi)~ of 0.0027, R of 0.9987.

CA 022~0067 1998-09-21 W O 97/39326 PCTrUS97106746 Fig. 2B is the Scatchard analysis (transformation) of the data in Fig. 2A, plotting Rb/Rf vs. Bound. Calculated Kd is 0.26 ~lM, with an R value of 0.992 for the linear fit.
Fig. 3 is an Src competition curve (2% DMSO) plotting % probe binding vs.
inhibitor concentration for the following tetrapeptides: Ac-pYEEI (open circle); Ac-pYpYEEI (closed square); Ac-pYGGL (plus sign); Ac-pYEDL (open triangle); Ac-DGVpYTGL (closed triangle).
Fig. 4A is a depiction of a 96 well plate of the experiment of Example 5, long format, with an arrow illustrating the direction of dilution. Clear circles are sample wells, gray circles are wells containing probe alone and dark circles are wells cont~ining probe and protein Fig. 4B is a depiction of a 96 well plate of the experiment of Example 5, short format, with an arrow illustrating the direction of dilution per 4 rows of wells. Circles are defined as in Fig. 4A.
Fig. 5 depicts the structure of an alternative fluorescent probe for use in the Src-SH2 assay, described in Exarnple 2.
Fig. 6A is a depiction of performance of the FP assay with no inhibitor present.In this figure, the fluorescein-labeled second protein (or probe) binds IO its binding partner (first protein having an SH2 domain). Light from the vertical polarized light source remains polarized due to the slow rotation of the bound complex.
Fig. 6B is a depiction of performance of the FP assay with inhibitor present. Inthis figure, the inhibitor binds to the SH2 domain-containing first protein, thereby preventing binding of the fluorescein-labeled second protein (or probe). The small unbound probe rotates more quickly than does the complex of Fig. 6A. Light from the vertical polarized light source becomes depolarized due to the quick rotation of the unbound probe.

Detailed Description of the Invention The present invention addresses the needs of the art by providing a fluorescencepolarization (FP)-based assay, for identifying and measuring the capacity of a test substance to disrupt or inhibit the association between a pair of proteins. The novel assay methods and materials disclosed herein have the advantages of being robust, non-radioactive, and amenable to varying degrees of automation.

I. Components of the Assay To facilitate underst~n(ling of this invention, the following descriptions of the components of the assay are provided:

CA 022~0067 1998-09-21 ~I The protein protein interaction The assay of the present invention is designed to enable one to detect an inhibitor of any protein:protein interaction. By the term "protein:protein interaction" or "mutual association" of proteins is meant any complex or binding, covalent or non-covalent, which naturally forms between two different proteins. One example of a protein:protein association involves the complex formed between a receptor and its naturally-occurring ligand. Interactions between fragments of proteins, i.e., peptides, with another protein or peptide are also encompassed by the term protein:protein interaction. Examples of protein:protein binding abound in the art, e.g., the binding between an antibody and a protein antigen or epitope, the binding between a cell-surface receptor and its protein ligand, the binding of various sign~lling proteins with their protein binding pairs, etc.
Specific examples of a protein:protein interaction, which are used herein to demonstrate the method of this invention involve, as a first protein, a protein cont~ining one or more SH2 domains, and/or SH3 domains (Syk, Zap, Src and Lck) and, as a second protein, a ligand for that first protein. For additional background information on Zap and Syk proteins and their SH2 domains, and peptide ligands, see, International Patent Application Nos. PCT/US96/13918, incorporated herein by reference.

B The first protein~pep~ide molecule of the binding pair For the purposes of the present invention, and for using currently conventional detection e~uipment, it is preferred to use a first protein/peptide that has a significantly greater molecular weight than the second protein or peptide, which naturally interacts with it. For purposes of this invention, the larger protein which participates in the protein:protein interaction is referred to as the first protein. It is the second protein or peptide which is labelled with the fluorophore according to the assay method.
Generally, the first protein of the binding pair has a molecular weight of at least 2 to about 100 times greater than the molecular weight of the labeled second protein/peptide of the binding pair. Often, the first protein of the binding pair has a molecular weight of at least 25 to about 50 times greater than the molecular weight of the labeled second protein/peptide of the binding pair.
The first protein need not necessarily be rigorously purified in production, as described below, but it is important to know the concentration of the first protein for certain quantitative purposes, e.g., for the construction of a saturation curve or to determine Kd values for the affinity of the two protein components.

CA 022~0067 1998-09-21 One specifically exemplified "first protein" of the examples contains an SH2 domain which serves as a receptor for a tyrosine phosphorylated peptide. Such a receptor may be a protein, a fusion protein, polypeptide, peptide or fragment thereof which contains a "phosphopeptide binding domain" (PBD). A PBD is a receptor domain present, e.g., in certain sign~ling proteins, which is capable of binding to a phosphorylated protein or phosphopeptide and thereby of directing protein-protein or protein-peptide association. For example, an "SH2 domain" is one such receptor domain. The receptor can be a polypeptide cont~ining one or more SH2, or other phosphopeptide binding domains. The receptor may be located within a larger protein, or may be a peptide fragment thereof. The receptor is preferably of human or other anlmal orlgm.
Numerous proteins containing such receptors (e.g., SH2 domains, PI domains, etc.) are known. See, e.g., US Patent No. 5,352,660.
Another specifically exemplified "first protein" contains an SH3 domain which serves as a receptor for a corresponding peptide sequence or motif. Such a receptor may be a protein, a fusion protein, polypeptide, peptide or fragment thereof which contains an SH3 or SH3-like domain.
Another specifically exemplified "first protein" contains both an SH2 and an SH3 domain.

C. The second protein/peptide of the binding pair The second protein is a ligand (naturally-occurring or otherwise) of the first protein or receptor. The second protein is generally the smaller of the two proteins in the binding pair and is preferably the protein of the pair which is labeled with a fluorescent moiety, thereby forming the "probe" component useful in the methods described herein.
In one example, the second protein or "ligand" is a protein, fusion protein, peptide or fragment thereof which contains one or more tyrosine residues, which is capable of binding selectively and with specificity to a phosphopeptide binding domain when at least one of the peptide ligand's tyrosine residues is phosphorylated. An "SH2 ligand" is an example of such a ligand.
A considerable wealth of information on the sequence specificity of peptide ligands for receptors, e.g., SH2, SH3, PI, and WW domains, etc. is also known. When it is used as a probe in the assay of this invention, this ligand is labeled with a suitable fluorophore as discussed in more detail below. Typically, the probe peptide or protein binds to its (usually) larger binding partner with a Kd in the range of about 0.1 to about 1000 nM. More desirably, the two binding partners bind to each other with a Kd better CA 022~0067 1998-09-21 Wo 97l39326 PcT/uss7lo6746 than (i.e., numerically smaller than) about 300 nM, more preferably with a Kd in the range of about 5 to about 50 nM.

D. Methods of producing the first and second proteins/peptides of the binding pair DNA sequence information and expression technology is available which permits recombinant production of any desired protein(s)/peptide(s) using a variety of expression systems. To produce the proteins used in these assays, one may express DNAs encoding the whole protein or a portion of the protein containing at least a domain of interest. The protein or portion of the protein may be expressed as a fusion protein, also by conventional techniques, especially in the case of the larger of the two binding proteins.
Any materials and methods conventional for producing a protein may be used including both prokaryotic and eukaryotic systems. For example, such proteins/peptides may be expressed by baculovirus, bacterial, yeast or m~mm~ n expression systems,whether as full-length proteins, fragments containing the receptor domain(s) or as fusion proteins. Such expression systems are conventional in the art. See, for examples, the descriptions in Sambrook et al, Molecular Cloning A Laboratory Manual., 2d edit., Cold Spring Harbor Laboratory, NY (1989).
The use of conventional protein/peptide expression technology permits the production of any interacting protein pair of any size. The expression systems and the conventional components thereof used to express the protein components of this invention are well within the skill of the art and do not limit the scope of this invention.
By way of illustration, expression vectors for a protein or domain of interest can be constructed by ligating into a conventional expression vector the DNA sequence encoding the desired protein, protein domain or, if known, a consensus homology domain for the domain of interest, alone or preferably with additional flanking sequence.
With routine experimentation, one can determine, if desired, whether such additional fl~nking amino acids enhance stability, improve expression levels, improve its ability to interact with ligands or other proteins or be necessary or desirable for linking to a fusion protein for reasons discussed below. For example, for human Src the SH3 consensus homology domain includes amino acids 91-140. We have prepared SH3 domain proteinfrom E. coli expression vectors using amino acids 84-145, which contain an additional 7 amino acids on the N-terminal side of the homology domain and S amino acids on the C-terminal side.
The desired protein or protein domain may be expressed within all or part of itsnatural context, as an isolated domain, in a tandem array containing two or more of the same or different domains, or as a fusion protein with other unrelated domains including CA 022F,0067 1998-09-21 but not limited to SH2-like domains, protein kinase domains, glutathinone S-transferase (GST), epitope tags, kinase recognition sequences, maltose binding protein, signal sequences, biotin-modification sequences, etc.
The proteins or protein domains may be modified to:
~ facilitate purification e.g. by expression as a fusion to glutathione-S-transferase, maltose binding protein, metal-chelation sequences (poly-histidine), protein A or others;
~ facilitate identification or quantitation, e.g by covalent modification using biotin, fluorophores, chromophores, scintillons, spin labels, radioactive or non-radioactive isotope tags, magnetic particles, metal coloids, etc;
~ adhere to defined solid supports, e.g. by expression as a fusion to an epitope tag or other antigenic domain; engineered to provide unique or uniquely accessible protein features e.g. N-terminal serine, cysteine, Iysine or others, etc.
~ remove undesirable features that pose experimental complications, e.g by mutation of cysteines that participate in unnatural domain dimerization ~ improve stability under conditions of binding assays (e.g. by altering the natural coding sequence to encode cysteines that form stabilizing disulfides).

E. The "test substance"
A "test substance or inhibitor" is defined herein as a compound or composition which binds selectively to either the first protein or the second protein which participate in the protein:protein interaction. Alternatively, the test substance selectively blocks or otherwise inhibits the interaction between these two proteins. For example, this inhibitor can bind to the first protein with competitive avidity vis-a-vis its naturally occurring binding protein, or it can bind the second protein. Where the two proteins are exemplified as a tyrosine phosphorylated receptor and its naturally occurring ligand, the inhibitor can bind to the receptor competitively with the ligand, or it can selectively block or otherwise inhibit the interaction between the receptor and ligand normally mediated by one or more tyrosine phosphorylated peptides or domains.
Test substances or compositions to be assessed for their ability to bind selectively to the first or second protein of interest can be obtained from a variety of sources, including, for exarnple, microbial broths, cellular extracts, conditioned media from cells, synthetic compounds and combinatorial libraries. The assay method of this invention may be used to screen natural product and test compound libraries or structurally-biased diversity libraries to identify desired inhibitors. The test substance may be selected from a mixture of one or more test peptides, wherein said mixture is provided in the form of a CA 022~0067 1998-09-21 W O 97/39326 PCTrUS97/06746 g library of synthetic peptides or in the form of a phage library displaying the various peptides.

F. ~1 "fluorescentmoiety"
A "fluorophore" or "fluorescent moiety" is a fluorescent molecule which, in solution and upon excitation with polarized light, emits light back into a fixed plane (i.e., the light remains polarized). Numerous known fluorescent labeling moieties of a wide variety of structures and characteristics are suitable for use in the practice of this invention. Similarly, methods and materials are known for covalently linking them to other molecules [see, e.~., Richard P. ~ugl~nd, Molecular Probes: Handbook of Fluorescent Probes and Research Chemicals 1992-1994 (Sth edit, 1994, Molecular Probes, Inc.)]. In choosing a fluorophore, it is preferred that the lifetime of the fluorophore's exited state be long enough, relative to the rate of motion of the labeled probe or peptide, to permit measurable loss of polarization following emission. Suitable fluorophores include fluorescein, fluorescein isothiocyanate, rho~mine, dichlorotriazinylamine fluorescein, dansyl chloride, phycoerythrin, and umbelliferone.
It is typically preferred to use a fluorophore having an excitation wavelength and emission wavelength in the visible rather than ultraviolet range of the spectrum to avoid possible interference from test compound fluorescence. Preferably the fluorophore is covalently linked to the smaller protein, i.e., the second protein, to be labeled, e.g., a peptide ligand, using a sufficiently short linker to avoid introducing undue motion to the fluorophore, i.e., motion not correlated to the motion of the labelled peptide.
More specifically, the examples below provide a description of the method used by these inventors in which a fluorescent moiety is chemically attached by covalent bonds onto a second protein molecule (a peptide ligand). In Example 2, the phospho-Tyr cont~ining peptide is labelled with fluorescein in vitro. One of skill in the art will understand that any method of production of such phosphopeptides is applicable.

G. "Fluorescence polarization"
FP, first described by Perrin, J. Phys. Rad., I :390-401 (1926), is based upon the finding that the emission of light by a fluorophore can be depolarized by a number of factors, the most predominant being rotational diffusion, or, in other words, the rate at which a molecule tumbles in solution. "Polarization" is the measurement of the average angular displacement of the fluorophore which occurs between the absorption and subsequent emission of a photon. This angular displacement of the fluorophore is, in turn, dependent upon the rate and extent of rotational diffusion during the lifetime of the CA 022~0067 1998-09-21 WO 97/39326 PCT~U~97/06746 excited state, which is influenced by the viscosity of the solution and the size and shape of the diffusing fluorescent species. If viscosity and temperature are held constant, the polarization is directly related to the molecular volume or size of the fluorophore. In addition, the polarization value is a dimensionless number (being a ratio of vertical and horizontal fluorescent intensities) and is not affected by the intensity of the fluorophore.

F. Additional Information Relating to Illustrative Signal Transducing Domains of Particular Interest (i) SH2 or SH2-like Domains The term "SH2 domain" refers to a sequence which is substantially homologous to a Src homology region 2 (SH2 region). The Src homology region 2 is a noncatalytic domain of~l00 amino acids which was originally identified in the viral Fps and viral Src cytoplasmic tyrosine kinases by virtue of its effects on both catalytic activity and substrate phosphorylation (T. Pawson, Oncogene 3, 491 (1988) and I. Sadowski et al., Mol. Cell. Biol. 6, 4396 (1986)). SH2 domains have been found in a variety of eukaryotic proteins, some of which function in intracellu}ar signal transduction. Many are known in the art. Examples (including counterparts from various species) of SH2 domain-cont~ining proteins include (1) members of the src-family protein tyrosine kinases (Src, Lyn, Fyn, Lck, Hck, Fgr, Yes), (2) Shc (3) Tsk, (4) Btk, (5) VAV, (6) Grb2, (7) Crk, and (8) signal transducer and transcription (STAT) proteins. In addition, a number of proteins, such as ZAP-70, p85 phosphatidylinositol 3' kinase (PI3K), Syk, GTPase Activating Protein (GAP), and Phospholipase C g~mm~, have two SH2 domains. SH2 domain-contzlining proteins have been identified in human, rodent, sheep, bovine, C. elegans, Drosophila, Xenopus, flatworm, freshwater sponge, and hydra.One way to identify new SH2 or SH2-like domains from unknown DNA, RNA
or protein sequence is by using one of many available computer alignment programs.
One example is pfscan, which can be run via the World Wide Web (WWW) site at http://ulrec3.unil.ch/software/profilesc~n.html. To use the program, a protein sequence is tested against a "profile" describing the SH2 domain motif. According to the program inforrnation, the particular strength of profiles is that they can be used to describe very divergent protein motifs. These profiles are normally derived from multiple alignments of the initial sequence set. In addition to the sequences themselves, a profile identifies which types of residues are allowed at what position within the domain, which amino acids are conserved, which ones are not, which positions or regions can allow insertions, and which regions may be dispensable. Additional information on Pfscan and PROSITE

CA 022~0067 l998-09-2l wo 97139326 PCT/US97/06746 can be obtained at the web page http://ulrec3.unil.ch/index.html operated by theBioinformatics Group at the ISREC (Swiss Institute for Experimental Cancer Research).
As an example we analyzed the peptide sequence of human Src with the pfscan program. The results are shown below. The program clearly identified the SH2 domain of Src as encompassing the region from amino acids 150-247 of the Src peptide sequence. In addition, the SH3 and kinase domains were identified by pfscan.

NScore raw from-to Profile ¦ Description 26.9695 1792 pos. 150-247 PS50001 ¦ SH2 Src homology 2 (SH2) domain 20.2947 1182 pos. 83-144 PS50002 ¦ SH3 Src homology 3 ~SH3) domain 43.4246 2912 pos. 269-522 PS50011 ¦ PROTEIN_KINASE_DOM Protein kinase The NScore of a match is the negative decadic logarithm of the expected number of matches of the given quality (or better) in a random database of the given size. For NScores ~1 this converges to the probability of finding the match in the database.
Since the number of expected matches depends on the size of the database, the decadic logarithm of the ~l~t~b~ce size must be subtracted before the calculation:
-log(NExp) = NScore - log (DBsize) where (NExp=Expected number of chance matches) and (DBsize=size of the database in characters).
The following table gives somes examples on how to convert the NScores into probabilities for the SwissProt database and the nonredundant (nr) protein database. The calculation is based on a database size of 18,531,385 residues for SwissProt (log=7.27) 58,154,119 residues for the nr database (log=7.76) CA 022~0067 l998-09-2l W 097/39326 PCTrUS97/06746 Expected chance matches in:
NScore SwissProt nonredundant 7.0 1.8 5.8 7.5 0.58 1.82 8.0 0.18 0.58 8.5 0.058 0.182 9.0 0.018 0.058 9.5 0.006 0.0182 10.0 0.0018 0.0058 10.5 0.0006 0.0018 ...and so on...

The segment of a test sequence contains an SH2 domain with an SH2 profile NScorevalue > 7.5, preferably > 8, more preferably > 9, more preferably > 10.
As a second example, the N-terminal 160 amino acid sequence from human ZAP-70 was applied to pfscan. The result indicated an SH2 domain bounded by amino acids 10-102.

NScore raw from-to Profile ¦ Description 16.4402 1082 pos. 10-102 PS50001 ¦ SH2 Src homology 2 (SH2) domain SH2 domains can be identified using other computer alignment programs, such as MegAlign within the DNAstar computer package (Madison, WI). To do this, one or more known SH2 domains and a test sequence are aligned by the clustal method. A
sequence having 3 25%, in some cases 30 - 50 %. in other cases > 50%, amino acids identical to a known SH2 domain is identified as an SH2 homology domain. The positions of identical amino acids between the test sequence and different known SH2 domains can vary, except for one position. All SH2 domains identified to date have a conserved arginine residue approximately 25-40 residues from the start of the SH2 homology domain. In human src this arginine is found within the sequence FLVRES,where abbreviations for the amino acid residues are: F, Phe; L, Leu; V, Val; R, Arg; E, Glu; S, Ser.
Another way to identify SH2 or SH2-like domains is by running a query in the federated nucleotide or protein databases for the SH2 domain feature. In the SWISS-PROT database, this is listed under the FT or "feature" heading. SWISS-PROT database can be accessed over the WWW at EBI http://www.ebi.ac.uk. For example, in the file listed for human Src (P 1293 1 )? the region containing the SH2 domain is shown to be 1 50-247.

CA 022~0067 l998-09-2l SWISS-PROT: P12931 ID SRC_HUMANSTANDARD; PRT; 535 AA.
AC P12931;
DR MIM; 190090; -.
DR PROSITE; PS00107; PROTEIN_KINASE_ATP.
DR PROSITE; PS00109; PROTEIN_KINASE_TYR.
DR PROSITE; PS50001; SH2.
DR PROSITE; PS50002; SH3.
DR PROSITE; PS50011; PROTEIN_KINASE_DOM.
DR PRODOM [Domain structure / List of seq. sharing at least 1 domain]
DR SWISS-2DPAGE; GET REGION ON 2D PAGE.
KW TRANSFERASE; TYROSINE-PROTEIN KINASE; PROTO-ONCOGENE;
PHOSPHORYLATION;
KW ATP-BINDING; MYRISTYLATION; SH3 DOMAIN; SH2 DOMAIN.
FT INIT_MET O 0 BY SIMILARITY.
FT LIPID 1 1 MYRISTATE (BY SIMILARITY).
FT DOMAIN83 144 SH3.
FT DOMAIN150 247 SH2.
FT DOMAIN269 522 PROTEIN KINASE.
FT NP_BIND275283 ATP (BY SIMILARITY).
FT BINDING297297 ATP (BY SIMILARITY).
FT ACT_SITE 388 388 BY SIMILARITY.
FT MOD_RES419419 PHOSPHORYLATION (AUTO-) (BY
SIMILARITY).
FT MOD_RES529529 PHOSPHORYLATION (BY SIMILARITY).

Yet another way to identify SH2 or SH2-like domains may be accomplished by screening a cDNA expression library with a phosphorylated peptide ligand for a known SH2 domain to isolate cDNAs for SH2 proteins. One could use PCR or low stringency screening with an SH2-specific probe. The SH2 domain or protein cont~ining the SH2 domain may be isolated from naturally occuring sources (e.g. cells, tissues, organs, etc);
produced recombinantly in bacteria, yeast or eukaryotic cells; produced in vitro using cell free translation systems; or produced synthetically (e.g. peptide synthesis).
Certain SH2 or SH2-like domains may not be identified via the pfscan program nor exhibit significant homology with known SH2 domain sequences to be detected by computer alignment programs. These sequences may, nevertheless, exhibit the same or CA 022~0067 l998-09-2l similar three-dimensional structure as known SH2 domains and function as an SH2-like domain and function to bind phosphotyrosine-cont~inin~ peptides or proteins. The three-dimensional structure of several known SH2 domains have been determined. S~I2 domains are characterized as two anti-parallel beta sheets composed of 5 or 6 beta strands. Regions forming an alpha helix may or may not be present within the domain.
SH2 or SH2-like domains may be recognized as having an SH2-like domain structurewhen solved by x-ray crystallography or NMR spectroscopy. Alternatively, a predicted structure by homology modeling may be used to identify a particular protein sequence as an SH2-like domain.
The alignment of SH2 domains used to generate the SH2 profile for pfscan, as taken from http://ulrec3.unil.ch/prf_details/alignments/SH2.msf (profile matrix can be obtained from http://ulrec3.unil.ch/cgi-bin/get_pstpr~?SH2) is based on alignment o3~
approximately 390 SH2 domains from proteins of various species. The list of proteins cont~inin~; SH2 domains used in the alignments in the Swiss-Prot Database includes the following (P # is the Swiss-Prot Database Accession number):

P00519, A}3Ll_HUMAN P00520, ABL_MOUSE P00521, F~3L_MLVA}3 P00522, A~3L_DROME P00523, SRC_CHICK P00524, SRC_RSVSR

P00525, SRC_AVISR P00526, SRC_RSVP P00527, YES AVISY

P00528, SRCl_DROME P00530, FPS_FU~SV P00541, FPS_AVISP

P00542, FES_FSVGA P00543, FES_FSVST P00544, FGR_FSVGR

P03949, ABLl_CAEEL P05433, GAGC_AVISC P05480, SRCN_MOUSE

P06239, LCK_HUMAN P06240, LCK_MOUSE P06241, FYN_HUMAN

P07332, FES_HUMAN P07947, YES_HUMAN P07948, LYN_HUMAN

P08103, HCK_MOUSE P08487, PIP4_BOVIN P08630, SRC2_DROME

P08631, HCK_HUMAN P09324, YES_CHICK P09769, FGR_HUMAN

P09851, GTPA_BOVIN P10447, A}3L_FSVHY P10686, PIP4_RAT

P10936, YES_XENLA P12931, SRC_HUMAN P13115, SRCl_XENLA

P13116, SRC2_XENLA P13406, FYN_XENLA P14084, SRC_AVISS

P14085, SRC_AVIST P14234, FGR_MOUSE P14238, FES_FELCA

P15054, SRC_AVIS2 P15498, VAV_HUMAN P16277, BLK_MOUSE

P16333, NCK_HUMAN P16591, FER_HUMAN P16879, FES_MOUSE

P16885, PIP5_HUMAN P17713, STK_HYDAT P18106, FPS_DROME

P19174, PIP4_HUMAN P20936, GTPA_HUMAN P23615, SPT6_YEAST

P23726, P85B_BOVIN P23727, P85A_BOVIN P24135, PIP5_RAT

P24604, TEC_MOUSE P25020, SRC_RSVHl P25911, LYN MOUSE

CA 022~0067 l998-09-2l P26450, P85A_MOUSE P27446, FYN_XIPHE P27447, YES_XIPHE
P27870, VAV_MOUSE P27986, P85A_HUMAN P29349, CSW_DROME
P29350, PTN6_HUMAN P29351, PTN6_MOUSE P29353, SHC_HUMAN
P29354, GRB2_HUMAN P29355, SEM5_CAEEL P31693, SRC_RSVPA
P32577, CSK_RAT P34265, YKFl_CAEEL P35235, PTNB_MOUSE
P35991, BTK_MOUSE P39688, FYN_MOUSE P40763, STA3_HUMAN
P41239, CSK_CHICK P41240, CSK_HUMAN P41241, CSK_MOUSE
P41242, CTK_MOUSE P41243, CTK_RAT P41499, PTNB_RAT
P42224, STAl_HUMAN P42225, STAl_MOUSE P42226, STA2_HUMAN
P42227, STA3_MOUSE P42228, STA4_MOUSE P42229, STA5_HUMAN
P42230, STA5_MOUSE P42231, STA5_SHEEP P42232, STAB_MOUSE
P42679, CTK_HUMAN P42680, TEC_HUMAN P42681, TXK_HUMAN
P42682, TXK_MOUSE P42683, LCK CHICK P42684, ABL2_HUMAN
P42685, FRK_HUMAN P42686, SRKl_SPOLA P42687, SPKl_DUGTI
P42688, SRK2_SPOLA P42689, SRK3_SPOLA P42690, SRK4_SPOLA
P43403, ZA70_HUMAN P43404, ZA70_MOUSE P43405, SYK_HUMAN
P46108, CRK_HUMAN P46109, CRKL_HUMAN Q00655, SYK_PIG
Q02977, YRK_CHICK Q03526, ITK_MOUSE Q04205, TENS_CHICK
Q04736, YES_MOUSE Q04929, CRK CHICK Q05876, FYN_CHICK
Q06124, PTNB_HUMAN Q06187, BTK_HUMAN Q07014, LYN_RAT
Q07883, GRB2_CHICK Q08012, DRK_DROME Q08881, ITK_HUMAN

A general method to identify an SH2 domain within a test peptide or nucleotide sequence follows:

I . Translate the cDNA or RNA into single letter code protein sequence. This could be accomplished using a computer program such as DNA strider or EditSeq in the DNAstar package.

2. Go to the WWW site at http://ulrec3.unil.ch/software/profilescan.html 3. Copy the test sequence into the appropriate box in the pfscan forrn 4. Submit the form to the pfscan server 5. The results are sent back through the web browser or via e-mail.

CA 022~0067 1998-09-21 SH2 and SH2-like domains as described in the foregoing paragraphs may be used in the practice of this invention. Using information provided herein, and by analogy to the examples provided below, one may carry out this invention with any SH2 domain, SH2-like domain, PID or PID-like domain and a peptide ligand therefor, e.g. in place of ZAP, Syk, Src or Fyn SH2 domains.

(ii) PID or PID-like Domains An alternative phosphotyrosine binding domain to SH2 domains is the so-called phosphotyrosine interaction domain (PID). This domain, con~ining on average about 160 amino acid residues, was originally identified in the Shc protein. In contrast to SH2 domains, which recognize sequences having a consensus pTyr-Xaa-Xaa-Xaa-Xaa (a phosphotyrosine followed by three or more amino acids), PID domains recognize se~uences with the consensus Asn-Xaa-Pro-pTyr (also called NPXY in single lettercode). The invention described in this application is also relevant to PID and PID-like domains. In this case, the coding sequence for a PID domain is substituted in the appropriate vector for the SH2 domain coding sequence and a ligand that recognizes the PID domain replaces the SH2 domain ligand. Phosphorylation of the PID ligand could be accomplished using v-Src, as described herein. Alternative protein kinases could be used to phosphorylate the PID ligand. In addition, a protein kinase endogenous within the cell could catalyze phosphorylation of the PID ligand.
Significant information concerning these domains is known in the art. A detaileddescription of the PID domains can also be found on the WWW at the site http://w~,vw.bork.embl-heidelberg.de/Modules/pid-gif.html. The following information is taken from that site:

Documentation - PROSITE description Beside SH2,the phosphotyrosine interaction domain (PI domain or PID)[3] is the second phosphotyrosine-binding domain found inthetransformingproteinShc[1,2]. Shc couples activated growth factor receptors to a sign~lling pathway that regulates the proliferation of m~mm~ n cells and it might participate in the transforming activity of oncogenic tyrosine kinases. The PI domain specifically binds to the Asn-Pro-Xaa-Tyr(p) motif found in many tyrosine-phosphorylated proteins including growth factor receptors. PID has also been found in the Shc related protein Sck [I] and several otherwise unrelated regulatory proteins [3] which are listed below.

CA 022~0067 1998-09-21 ~ M~mm~ n Shc (46 kD and 52 kD isoforms) contains one N-terminal PID, a collagen-like domain and a C-terminal SH2 domain.
~ Human Shc related protein Sck contains one PI domain and a SH2 domain.
~mm~ n X11 is expressed prominently in the nervous system. It contains 2 disc homologous regions (DHR) of about 100 AA downstream of the PID.
~ Drosophila nuclear Numb protein is required in deterrnination of cell fate during sensory organ formation in drosophila embryos. It has one PID.
~ Caenorhabditis hypothetical protein F56D2.1 contains an N-terminal metalloproteinase domain followed by one PID.
~ Rat FE65. The WW domain as well as the 2 PIDs found in the sequence of FE65 indicate that this protein is probably involved in signal transduction.
~ Drosophila protein disabled is a cytoplasmic, tyrosine phosphorylated protein found in CNS axons and body wall muscles. Itis involvedinembryonic neural development. It contains one N-terminal PI domain.
~ Mouse mitogen responsive phosphoprotein isoforms P96, P93 and P67 which are produced by alternative splicing, contain one N-terminal PID. This is also true for the differentially expressed human ortholog Doc-2.
Human EST05045 protein fragment has one PID.

References:
[ 1] Kavanaugh W.M., Williams L.T. Science 266:1862-1865(1994) [ 2] Blaiki, P. et al., J.Biol.Chem. 269, 32031-32034 (1994) [ 3] Bork P., Margolis B. Cell 80, 693 (1995) A PI domain alignment based on a number of PI domains from various species is illustrated in the WWW site at http://ulrec3.unil.ch/prf_details/alignments/PID.msf.
Another such alignment is shown at the web site at http://www.bork.embl-heidelberg.de/Modules/pi-~li html (iii) SH3 and SH3-like domains The term "SH3-like domain" refers to a sequence which is substantially homologous to a Src homology region 3 (SH3 region). The Src homology 3 region is a noncatalytic domain of ~60 amino acids which was originally identified in the viral Fps and viral Src cytoplasmic tyrosine kinases by virtue of its effects on both catalytic activity and substrate phosphorylation (T. Pawson, Oncogene 3, 491 (1988) and I.

CA 022~0067 1998-09-21 Wo 97/39326 PCT/US97/06746 Sadowski et al., Mol. Cell. Biol. 6, 4396 (1986)). SH3 domains have been found in a variety of eukaryotic proteins, some of which function in intracellular signal transduction. Examples (including counterparts from various species) of SH3 domain-containing proteins include ( 1 ) members of the src-family protein tyrosine kinases (Src, Lyn, Fyn, Lck, Hck, Fgr, Yes), (2) Grb-2, which has two SH3 domains, (3) Sprk, a-threonine/serine protein kinase, (4) Tsk, (5) Btk, (6) Vav, (7) GTPase Activating Protein (GAP), (8) p40, p47, and p67 proteins of the neutrophil oxidase complex, and (9)phosphatidylinositol 3' kinase, (10) Crk, (11) phospholipase C g~mrn~, (12) Abl. SH3 domain-cont~ining proteins have been identified in human, rodent, bovine, C. elegans, and yeast. Other SH3 domains may be selected from the scientific literature or identified by sequence analysis or cloning by the methods described above. See e.g.
PCT/US95/03208 for a wealth of background information relating to SH3 domains and their ligands.
Certain SH3 or SH3-like domains may not match any of the 18 conserved amino acids nor exhibit significant homology with known SH3 domain sequences to be detected by computer alignment programs. These sequences may, nevertheless, exhibit the same or similar three-dimensional structure as known SH3 domains and function as an SH3-like domain. The three-dimensional structure of several known SH3 domainshave been determined. SH3 domains are characterized as two anti-parallel beta sheets composed of 5 or 6 beta strands. Regions forming an alpha helix may or may not be present within the domain. SH3 or SH3-like domains may be recognized as having an SH3-like domain structure when solved by x-ray crystallography or NMR spectroscopy.
Alternatively, a predicted structure by homology modeling may be used to identify a particular protein sequence as an SH3-like domain.

Il. The Assay Protocol The in vitro assay method of this invention utilizes FP for identifying a test substance which competitively binds to, or inhibits the mutual association of, a first protein molecule to a second protein molecule. Fluorescence polarization is an extremely useful method for studying ligand-protein and protein-protein interaction.
The present invention is based upon the observation that changes in polarization will occur if a fluorescent molecule undergoes a molecular weight change due to cleavage or binding to another molecule. Fluorophores that are of a low-molecular weight, and/or are very flexible, have low polarization values, while those that have a high molecular weight, and/or are rigid, have higher polarization values.

CA 022~0067 1998-09-21 W O 97/39326 PCT~US97/06746 This intrinsic property of the fluorescent moiety is utilized in the assay of this invention. According to this method, a mixture is made which contains the following components:
(a) a selected amount of a first protein molecule, e.g., a tyrosine phosphorylated receptor, which is capable of binding or otherwise mutually associating with a smaller second protein molecule;
(b) a selected amount of a smaller, second protein molecule, which is covalently linked to, or labeled with, a fluorophore. In the examples below, it is the peptide ligand that is labelled with a fluorophore by covalent linkage, thereby forming fluorophore-labeled probes of low molecular weight; and (c) a selected, potentially competitively-inhibiting test substance.
This mixture is accomplished under conditions suitable to permit complex formation between the first and second proteins, if they were admixed in the absence of test substance. Thus, according to this method, in the event that the test substance is, in fact, an inhibitor of the protein:protein complex formation, the conditions are also suitable to permit its competitive binding to the first or second proteins.
This mixture of (a), (b) and (c) is irradiated with plane polarized light of a wavelength which is sufficient to excite the fluorophore. The light subsequently emitted by the fluorescent second protein is polarized to varying degrees depending on the molecular volume of the fluorescent second protein. In the unbound state in solution, low molecular weight peptides rotate rapidly, and give low polarization readings.
When in the presence of its binding/interacting first protein partner, e.g., a receptor, the lower-molecular weight fluorescent second protein binds to the higher molecular weight first protein, e.g., a tyrosine phosphorylated protein or peptide receptor. When the labeled second protein binds to its target first protein and is min~ted by plane polarized light, the large first protein:second protein complextumbles more slowly, and the polarization readings increase. The method of this invention thus follows changes in the ratio of polarization in the horizontal and vertical planes of the emission wavelength range. This is in distinct contrast to following changes in the intensity of absorbance within a particular wavelength range, which is the way conventional fluorescent labels are used. The change measured by the presentinvention is a direct measure of the binding of the labeled second protein to the first protein.
This difference in polarization values of free labeled second protein vs. bound second protein:first protein complex is used to measure the bound and free ratios of the second protein and analyze its binding to the first protein when in the presence of a test CA 022~0067 1998-09-21 substance. Such measurement may occur in either saturation or competition experiments. The FP assay of this invention can thus be used in many solutions, including in the cytoplasm of the cell.
The degree of polarization of the emission is measured without the necessity to separate the components in the mixture. Finally, the effect of the presence or concentration of the test substance is determined by comparing the ratio of the polarization levels of the mixture with the polarization levels of the same amounts of the first and second proteins/peptides in the absence of test compound.
If competitive binding occurs between the first or second protein and the test substance instead of between the two proteins, so that the protein:protein complex is not formed, the second protein will remain free in solution and low polarization will be measured. If the test substance is not an inhibitor or a good inhibitor, the complex will be formed and the polarization of the mixture will increase. Thus a decrease in the observed emission polarization depolarization values from known polarization levels of the first protein:second protein complex in the absence of test compound is noted in the presence of an inhibitor test substance.
Since the method of this invention follows changes in the ratio of polarization in the horizontal and vertical planes of the emission wavelength range, rather than changes in the intensity of absorbance within a particular wavelength range, the method is less vulnerable to interference from high absorbance of test compounds in solution.
The methods of this invention are susceptible to automation. For example, all orseveral of the steps outlined above may be performed by an apparatus programmed to conduct automatically two or more steps for a given test substance or one or more steps for a plurality of test substances or test substance concentrations. As one example, any standard fluorometer equipped for polarization experiments or measurements may be used in practicing this invention to both irradiate the mixture and measure the polarization. Wavelengths suitable to excite the fluorophore depend on the nature of the fluorophore, as described above. Typically, one uses cut off filters to define awavelength range which is determined by the excitation and emission wavelengths of the fluorophore. For fluorescein carboxyamide peptides, one would typically use an excitation cutoff filter of 485nM. Also, non-polarizing material should be used for any component of the ap~aldLus, including the test chambers in which samples are evaluated, which will be in the light path. Plastics and fiber optics are generally avoided in such uses in favor of optical glasses, quartz, etc.
In addition to using standard fluorometers, one can also use specialty fluorometers such as the Jolley FPM1 (for individual samples) or the Jolley FPM2 (for CA 022~0067 1998-09-21 high-throughput assays in 96-well format). Such fluorometers have been optimized for polarization measurements and have much higher sensitivity than standard fluorometers.
Other automated equipment may provide both the admixing step combined with the other steps, and/or the comparison of the polarization of the control mixture without the test substance and the test mixture with the test substance. One of skill in the area of automation may use various apparatus to substantially automate the assays of this invention.
In yet another aspect, the invention provides components or reagents, e.g.,a protein bearing a covalently linked fluorophore, useful in the methods of the invention.
The components or reagents can further be packaged in a kit with instructions for use in the described methods.

III. The Inhibitors Once a compound has been identified as an inhibitor, it can be produced using known methods, such as by recombinant methods of protein production or chemical synthesis. It can also be obtained from the source in which it was initially identified.

A. Counterscreens Having identified an inhibitor of a protein:ligand association by means of the assay of this invention, one may use counterscreens against one or more other protein:
ligand pairs to identify nonspecific inhibitors, or confirm inhibitor specificity. Test compounds identified as inhibitors by the method of this invention may be further evaluated for binding activity with respect to one or more additional proteins of interest, or with respect to additional proteins containing the domain(s), using various approaches, a number of which are well known in the art. The counterscreen may be carried out using the methods and materials of the subject invention, or may be conducted using alternative approaches for the detection of direct or competitive binding, including, e.g., cell-based assays or surface plasmon resonance (BIAcore~) technology [see, e.g., Panayotou et al, Mol. Cell. Biol.. I3: 3567-3576 (1993)].The inhibitors identified in the assay system of this invention can be further evaluated by conventional methods for assessing toxicological and pharmacological activity. For example, test compounds identified as inhibitors may further be evaluated for activity in inhibiting cellular or other biological events mediated by a pathway involving the protein:ligand interaction of interest using a suitable cell-based assay or an animal model. Cell-based assays and animal models suitable for evaluating inhibitory CA 022~0067 1998-09-21 Wo 97139326 PCT/US97/06746 activity of a test compound with respect to a wide variety of cellular and other biological events are known in the art. New assays and models are regularly developed and reported in the scientific literature.
By way of nonlimiting example, compounds which bind to an SH2 domain involved in the transduction of a signal leading to asthma or allergic episodes may be evaluated in a mast cell or basophil degranulation assay. The inhibitory activity of a test compound identified as an SH2 inhibitor by the method of this invention with respect to cellular release of specific mediators such as hi~t~mine, leukotrienes, hormonalmediators and/or cytokines, as well as its biological activity with respect to the levels of phosphatidylinositol hydrolysis or tyrosine phosphorylation can be characterized with conventional in vitro assays as an indication of biological activity. [See, e.g., Edward L.
Barsumian et al, Eur. J. Immunol.. 11:317 323 (1981); M. J. Forrest, Biochem.
Pharmacol., 42:1221-1228 (1991) (measuring N-acetyl-betagluco.s~min~ e from activated neutrophils); and V. M. Stephan et al., J. Biol. Chem., 267:5434-5441 (1992)].
For example, histamine release can be measured by a radioimmllnf)assay using a kit available from AMAC Inc. (Westbrook, ME). One can thus evaluate the biological activity of inhibitors identified by the method of this invention and compare them to one another and to known active compounds or clinically relevant compounds which can be used as positive controls.
Generally speaking, in such assays IC50 scores of 150-300 uM are considered of interest, scores of 50-150 uM are considered good, and scores below about 50 uM are of high interest. Prior to or in addition to in vil~o models, inhibitors identified by this invention may also be tested in an ex vivo assay for their ability to block antigen-stimulated contraction of sensitized guinea pig tracheal strip tissue. Activity in this assay has been shown to be useful in predicting the efficacy of potential anti-asthrna drugs.
Numerous animal models of asthma have been developed and can be used [for reviews, see Larson, "Experimental Models of Reversible Airway Obstruction", in THE
LUNG, Scientific Foundations, Crystal, West et al. (eds.), Raven Press, New York, pp.
953-965 (1991); Warner et al., Am. Rev. Respir. Dis., 141:253 257 (1990)]. Species used in animal models of asthma include mice, rats, guinea pigs, rabbits, dogs, sheep and - primates. Other in vivo models available are described in Cross et al., Lab Invest., 63:162-170 (1990); and Koh, et al., Science, 256:1210-1213 (1992).
By way of further example, inhibitors identified by the method of this inventionwhich bind to a protein involved in the transduction of a signal involved in the initiation, maintenance or spread of cancerous growth may be evaluated in relevant conventional in CA 022~0067 1998-09-21 W 097t39326 . PCT~US97/06746 vitro and in vivo assays. See e.g., Ishii et al., J. Antibiot., XLII:1877-1878 (1989); and US Patent 5,206,249 (issued 27 April 1993).

B. Uses of Inhibitors Identified by This Invention Inhibitors identified by this invention may be used as biological reagents in assays as described herein for functional classification of a particular protein, particularly a newly discovered protein. Families or classes of proteins may thus be defined functionally, with respect to ligand specificity. Moreover, inhibitors identified by this invention can be used to inhibit the occurrence of biological events resulting from molecular interactions mediated by a the protein or protein:ligand pair of interest.
Inhibiting such interactions can be useful in research aimed at better understanding the regulation and biological significance of such events.
Such inhibitory agents would be useful, for example, in the diagnosis, prevention or treatment of conditions or diseases resulting from a cellular process(es) mediated by a targeted interaction. For example, a patient can be treated to prevent the occurrence or progression of osteoporosis or to reverse its course by ~(1mini~tering to the patient in need thereof an SH2 binding or blocking agent which selectively binds Src SH2.
There are many other conditions for which phosphopeptide binding or blocking agents may be useful therapeutically, including, e.g., breast cancer where the SH2 domain-cont~inin~ proteins Src, PLCgamma and Grb7 have been implicated. Other relevant conditions include prostate cancer, in which case targeting Grb2, PLCg, and PI3K, all of which contain SH2 domains, may be useful in treatment or prevention of the disease. Inhibition of the interaction of Grb2 or Abl SH2 domains with Bcr-abl may be useful to treat chronic myelogenous leukemia (CML) or acute myelogenous leukemia(AML).
Still other relevant applications of an PBP inhibitor would be to prevent interferon-, growth factor-, or cytokine-mediated diseases (e.g. infl~mm~tory diseases) by targeting the PBDs of STAT proteins. Agents that block the SH2 domains of ZAP-70, which is involved in activation of T-cells, would be useful in the treatment of autoimmune diseases. An inhibitor that blocks one or both SH2 domains of ZAP-70 would also be useful as an immunosuppressant to prevent rejection of skin and organ transplants.
Likewise, by further way of example, SH3 inhibtors would be useful in the diagnosis, prevention or treatment of conditions or diseases resulting from a cellular processes mediated by an SH3-based interaction. For example, a patient can be treated to prevent the occurence or progression of osteoporosis or to reverse its course by CA 022~0067 1998-09-21 ~rlmini~tering to the patient in need thereof an SH3 inhibitor which selectively binds to or inhibits interactions with src SH3. There are many other conditions for which SH3 inhibitors can be used therapeutically, including restenosis, rheumatoid arthritis, gout, asthma, emphysema, immune vasculitis, ulcerative colitis, psoriasis and acute respiratory distress syndrome, in which an SH3 of neutrophil oxidase p47 and p67complex has been implicated. Other relevant conditions include chronic myelogenous leukemia, in which case SH3 domains of Grb-2 are targeted. It has recently been shown that the BCR-abl oncogene in CML participates in the ras pathway for growth stimulation through its interaction with Grb-2. In these cells, inhibition of the interaction of Grb-2 SH3 domains with the SOS oncogene will block its ability to stimulate cell proliferation. Still other relevant conditions include cancers such as breast cancer, glioblastomas, head and neck tumors and ovarian tumors, for which the SH3 domain of Grb-2 would be targeted. For example, tumors with associated amplification of receptors for EG~ and PDGF could be inhibited by blocking activation of the Ras pathway through inhibition of the interaction between Grb-2 (SH3)and Ras. Furthermore, since the SH3 domain of Src family kinases are believed to be involved in activation of T-cells, B-cells, mast cells, and NK cells and since the SH3 domains of the tyrosine kinases Tsk and Btk are believed to be involved in T-cell (Tsk SH3) and B-cell (Btk SH3) function an SH3 inhibitor identified by the subject invention could be ~(lmini~tered to a patient in need thereof to suppress immune function.
An inhibitor of a protein:ligand interaction identified by the method of this invention can be formulated into a ph~rm~reutical composition containing a pharmaceutically acceptable carrier and/or other excipient(s) using conventionalmaterials and means. Such a composition can be a~mini~tered to an animal, eitherhuman or non-human, for therapy of a disease or condition resulting from cellular events involving the targeted protein-ligand interaction. Administration of such composition may be by any conventional route (parenteral, oral, inhalation, and the like) using apl)lo~,iate formulations as are well known in this art. The inhibitor can be employed in admixture with conventional excipients, ie, pharmaceutically acceptable organic or inorganic carrier substances suitable for parenteral ~-lmini~tration.

C. Pharmaceutical Compositions and Methods i. Compositions CA 022~0067 1998-09-21 W O 97/39326 PCTrUS97/06746 Inhibitors identified by this invention can be formulated into pharmaceutical compositions cont~ining a therapeutically (or prophylactically) effective amount of the inhibitor in admixture with a pharmaceutically acceptable carrier and/or other excipients (i.e., pharrnaceutically acceptable organic or inorganic carrier substances suitable for parenteral ~Aminictration) using conventional materials and means. Such a carrier includes but is not limited to saline, buffered saline, dextrose, water, glycerol, ethanol, and combinations thereof. The carrier and composition can be sterile. The formulation should suit the mode of a-lmini.~tration.
The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. The composition can be a liquid solution, suspension, emulsion, tablet, pill, capsule, sustained release formulation, or powder. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, e~c.
In a specific embodiment, the composition is formulated in accordance with routine procedures as a pharmaceutical composition adapted for intravenous a-lmini~tration to human beings. Typically, compositions for intravenous ~llmini.~tration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic to ease pain at the side of the injection.
Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a Iyophilized powder or water free concentrate in a herrnetically sealed container such as an ampoule or sachette indicating the quantity of active agent.
Where the composition is to be a~1ministered by infusion, it can be dispensed with an infusion bottle cont~ining sterile pharmaceutical grade water or saline. Where the composition is ;l(lmini~tered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to ~-imini~tratjon.
Topical compositions include a ph~rmaçologically acceptable topical carrier~ such as a gel, an ointment, a lotion, or a cream, which includes, without limitation, such carriers as water, glycerol, alcohol, propylene glycol, fatty alcohols, triglycerides, fatty acid esters, or mineral oils. Other topical carriers include liquid petroleum, isopropyl palmitate, polyethylene glycol, ethanol (95%), polyoxyethylene monolaurate (5%) in water, or sodium lauryl sulfate (5%) in water. Other materials such as anti-oxidants, humectants, viscosity stabilizers, and similar agents may be added as necessary.Materials and methods for producing the various formulations are well known in the art [see e.g US Patent Nos. 5,182,293 and 4,837,311 1.

CA 022~0067 1998-09-21 Wo 97/39326 PCT/US97/06746 ii. Methods The invention provides methods of treating, preventing and/or alleviating the symptoms and/or severity of a disease or disorder referred to above by a(lmini.~tration to a subject of the inhibitor in an amount effective therefor. The subject will be an animal, including but not limited to anim~l~ such as cows, pigs, chickens, etc., and is preferably a m~mm~l, and most preferably human. By "m~mm~l~" is meant rodents such as mice,rats and guinea pigs as well as dogs, cats, horses, cattle, sheep, nonhuman primates and humans. Such effective amounts can be readily determined by evaluating the inhibitors identified by this invention in conventional assays well-known in the art, including assays described herein.
Administration of such composition may be by any conventional route using appl()p"ate formulations as are well known in this art. Various delivery systems are known and can be used to ~1mini.~ter the inhibitor, e.g., encapsulation in liposomes, microparticles, microcapsules. One mode of delivery of interest is via pulmonarya-lmini.stration. Other methods of introduction include but are not limited to intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, nasal and oral routes. The inhibitor may be ~lmini~tered by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g, oral mucosa, rectal and intestinal mucosa, etc.) and may be ~flmini.~tered together with other biologically active agents.
Administration can be systemic or local. For treatment or prophylaxis of nasal, bronchial or pulmonary conditions, preferred routes of atlmini~tration are oral, nasal or via a bronchial aerosol or nebulizer. In specific embodiments, it may thus be desirable to aflminicter the inhibitor locally to the area in need of treatment; this may be achieved by, for example, and not by way of limitation, local infusion during surgery, topical application, by injection, by means of a catheter, by means of a suppository, or by means of a skin patch or implant, said implant being of a porous, nonporous, or gelatinous material, including membranes, such as sialastic membranes, or fibers.
Administration to an individual of an effective amount of the inhibitor can also be accomplished topically by a(lmini~tering the compound(s) directly to the affected area of the skin of the individual. In certain instances, it is expected that the inhibitor may be disposed within devices placed upon, in, or under the skin. Such devices include patches, implants, and injections which release the compound into the skin, by either passive or active release mech~ni~m~

CA 022~0067 1998-09-21 W 097/39326 PCTrUS97/06746 The amount of the inhibitor which will be effective in the treatment or prevention of a particular disorder or condition will depend on the nature of the disorder or condition, and can be deterrnined by standard clinical techni~ues. In addition, in vitro or in vivo assays may optionally be employed to help identify optimal dosage ranges.
Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems. For example, a typical effective dose of the inhibitor is in the range of about 0.01 to about 50 mg/kgs, preferably about 0.1 to about 10 mg/kg of m~mm~ n body weight, a(lministered in single or multiple doses. Generally, the inhibitor may be a~mini.stered to patients in need of such treatment in a daily dose range of about 1 to about 2000 mg per patient.
The precise dosage level of the inhibitor, as the active component(s), should bedetermined by the attending physician or other health care provider and will depend upon well known factors, including the phosphopeptide binding interaction under consideration, the route of atlmini.stration, and the age, body weight, sex and general health of the individual; the nature, severity and clinical stage of the disease, and the use (or not) of concomitant therapies.

C. Kits The invention also provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention. Optionally associated with such container(s) can be a notice in the form prescribed by a governrnental agency regulating the manufacture, use or sale of pharmaceutical or biological products, which notice reflects approval by the agency of manufacture, use or sale for human ~mini.stration.
Other components such as physiologically acceptable surfactants (e.g., glycerides), excipients (e.g., lactose), carriers, and diluents may also be included.
The following examples illustrate various aspects of this invention. These examples do not limit the scope of this invention which is defined by the appended claims. The contents of all references, pending patent applications, published patent applications, issued patents and information contained in web sites, cited throughout this application (including the "Back~round" Section) are hereby expressly incorporated by reference.

IV. Examples CA 022~0067 1998-09-21 W O g7/39326 PCTrUS97/06746 The following examples illustrate various aspects of this invention. These examples do not limit the scope of this invention which is defined by the appended claims.
The introduction of a 96-well plate reader (FPM2, Jolley Instruments) with a high sensitivity towards fluorescein and fluorescein conjugates (in the low nanomolar probe concentration range) has allowed the development of 96-well based FP assays.
These examples describe an FP assay and the necessary components for measuring the binding of compounds to the Src-SH2 domain.

ExamPle 1 - PEPTIDE SYNTHESIS
Peptide synthesis was performed manually using Fmoc-Rink amide resin [4-(2',4'-dimethoxyphenyl-Fmoc-aminomethyl) phenoxy resin; (Advanced Chemtech)] with substitution levels of 0.3-0.6 mmole/g. Standard FMOC synthesis methods were used.
The wash and deprotection solvent used was dimethyl acetamide (DMA); the coupling solvent used was N-methylpyrrolidone (NMP). For amino acid couplings, four equivalents of amino acid, four equivalents of coupling reagent, 2-(1 H-benzotriazole- 1-yl)-1,1,3,3-tetramethyluronium tetrafluoroborate (TBTU), and eight equivalents of N-methylmorpholine (NMM) were used per equivalent of amine on the resin. Amino acids used were Fmoc-Gly, Fmoc-Glu(Tbu), Fmoc-lle, Fmoc-Thr(Tbu), and Fmoc-Tyr(Tbu).
Fmoc deprotection was done using 20% piperidine in DMA.
Peptides were phosphorylated on the solid-phase using standard methodology [see, e.g., Merrifield, J. Am. Chem. Soc., 85:2149-2154 (1963)]. Resins and l-l,H-tetrazole were dried under vacuum over P2O5 overnight. To a portion of resin (0.1-0.5 g) mixed with 50 equivalents of 1-1 ,H-tetrazole was added I ml/0. I g of dry DMA. The resin was stirred and swelled for 20 minutes. 10 equivalents of dibenzyl N,N-diethylphosphoramidite (Toronto Research Chemicals, Inc.) was then added, the resin mixture was stirred for 15 minutes, sonicated for 30 minutes, and stirred for 15 minutes.
Resin was washed 5x with DMA. Oxidization was performed by adding 3 equivalents of chlorobenzylperoxide in DMA, with stirring for 30 minutes, and sonication for 30 minutes. Finally, peptides were washed 5X DMA, 3X CH2CI2, and 3X MeOH, followed by vacuum drying overnight.
Final cleavage from the resin and side chain deprotection was done using 90:10:10:5 ratios oftrifluoroacetic acid (TFA):H2O:ethane dithiol (EDT):tri-isopropyl silane (TIPS). Scavengers were added to resin, followed by addition of TFA with stirring for 2.5 hours. Resin was filtered off. TFA was removed by blowing under N2 for several hours. Crude peptide slurry was resuspended in water, and extracted three CA 022~0067 1998-09-21 W 097139326 PCTrUS97/06746 -30-times with an equal portion of ice-cold diethyl ether. Excess ether was removed by blowing under N2. The crude peptide mix was Iyophilized overnight.
All peptides were purified in the following manner. Crude Iyophilized peptides were dissolved in DMSO at a concentration of 100-300 mgs per ml. Peptides were purified on a Semi-Preparative reverse phase HPLC column (Vydac). A series of 15-30 ul injections of crude peptides in 100% DMSO were used. Purity was checked using an analytical reverse phase HPLC column, with a diode-array spectrophotometer. One pass was adequate to give greater than 90% purity.

Example 2 - PROBE SYNTHESIS
An exemplary fluorescent probe (Fig. 1 or Fig. 5) was designed to consist of thefluorescent moiety, 5-carboxyfluorescein, coupled to a pentapeptide ligand based on the known Src-SH2 high affinity tetrapeptide sequence derived from the core middle-Tantigen. The peptide ligand sequence is GpYEEI, cont~ining the core middle-T antigen high-affinity Src-SH2 sequence (pYEEI), with an N-terminal glycine for ease of coupling.
5-Carboxyfluorescein was chosen for several reasons. It is one of the few defined isomer fluoresceins available. It yields a conjugate with less flexibility than many available fluoresceins, which is important for minimi7.ing the "propeller effect"
that can interfere with FP based measurements and an activated version is commercially available (Molecular Probes, Inc.).
The probe sequence was prepared as follows: The peptide GpYEEI was coupled to the fluorescein moiety directly on the resin. The peptide sequence was assembled on Rink amide resin~ and phosphorylated as described above. The resultant sequence was Fmoc-GpYEEI-RlNK. The peptide/resin was deprotected with 20% piperidine in DMA, removing the FMOC protecting group, and leaving the free-amino terrninus available for coupling. After thorough washing with DMA, 1.1 equivalent of 5-carboxyfluorescein succinimidyl ester (Molecular Probes) was added with 6 equivalents of diisopropylethylamine. Coupling was carried out for 1.5 hours, followed by I NMP and 3 DMA washes, and by a repeat coupling as above. The completed probe was cleavedand worked up as described above, yielding a probe termed FMTI.
Two exemplary labeled probes for Src SH2 domain, prepared as described above are:
fluorescein-G-pYEEI-NH2 and fluorescein-pYpYpYIE-NH2 CA 022~0067 1998-09-21 Wo 97/39326 PCT/US97/06746 Example 3 - PROTEIN PRODUCTION - Src Human Src encoding residues 145-251 [Tanaka, A. and Fujita, D.J., Mol. Cell.
Bioh 6:3900-3909 (1986)] was cloned into the pT7 expression vector and transformed into ~ coli BL21 (DE3). Protein was produced ~rom the growth and induction of 27liters of culture in minim~l medium. In a typical preparation, the culture was grown at 37~C to an optical density (OD) of 1.0 at 595 nm. The culture was induced with 1 mM
isopropyl-~-D-thiogalactopyranoside (IPTG) and the temperature was dropped to 25~C.
The culture was harvested 21 hours later.
The cells were Iysed in 50 mM potassium phosphate, 250 mM NaCI, 5 mM DTT, 2 mM E;DTA, 1 mm PMSF, pH 7.0 using a French pressure cell at 16,000 psi. The protein was purified over carboxy-sulfon (J. T. Baker), a weak-strong cation exchanger.
The column was equilibrated with 50 mM potassium phosphate, 5 mM DTT, 0.02%
NaN3, pH 7.0 and loaded with filtered bacterial lysate at 2 ml/minute. The Src protein was eluted with a 1 M NaCl gradient. The eluate was concentrated using a Centriprep 10 concentrator (Amicon, 10,000 MW cutoff) and centrifuged at 3000 x g. The protein was then purified by gel filtration on a Sephacryl S-100 (Pharmacia) column equilibrated with 20 mM potassium phosphate,50 mM NaCl,5 mM DTT, 1 mM EDTA, 0.02%
NaN3, pH 7.4. Purity, as measured by SDS gel electrophoresis and RP-HPLC, is >95%.
The purified protein is stored frozen in 50 mM potassium phosphate,500 mM NaCI, 10% glycerol, 5 mM DTT, 5 mM EDTA, 0.02% NaN3, pH 7.4.

Example 4 - A FLUORESCENCE-POLARIZATION BASED SRC-SH2 BINDING
ASSAY
A. FP - General All polarization methods were performed on an FPM2 96-well plate reader (Jolley), with standard cutoff filters (excitation = 485 nm; emission = 530 nm).Saturation experiments were used to explore various conditions for the assay, with the aim of maximi7in~ the protein and assay stability, and of determining Kds of theprotein/probe interaction.
B. Saturation Experiments For saturation experiments, fixed concentrations of probe were used, and increasing concentrations of Src-SH2 were added. This is the reverse of the way such assays are commonly done with radioactive ligands.
A saturation experiment was conducted in which the Src-SH2 domain is varied in concentration from a high of 40 uM to a low of 39 nM. The fluorescent probe FMT1(Fig. I ) was kept at a fixed concentration of 20 nM. Amino acid analysis was used to CA 022~0067 1998-09-21 quantitate both the protein and probe concentrations. The results are illustrated in the saturation curve and Scatchard analysis of Figs. 2A and 2B, respectively from this experiment.
The data shown in Figs. 2A and 2B show that the affinity of the probe for the receptor domain is applo~l,ate for conducting competitive binding assays and that saturable binding to a single site is observed, consistent with the assay of this invention and with competitive, reversible binding to a single site.

C. Competition Experiments For competition experiments, fixed concentrations of probe and protein were used, and increasing concentrations of peptides were added.
The designed probe FMT- 1 has a Kd of ~0.3 uM towards Src-SH2 in the standard buffer conditions. Some variation in observed Kd values will occur withchanges in buffer conditions.
As illustrated in Fig. 3, a Src competition assay (2% DMSO buffer) was conducted for the following tetrapeptides: Ac-pYEEI (open circle); Ac-pYpYEEI
(closed square); Ac-pYGGL (plus sign); Ac-pYEDL (open triangle); Ac-DGVpYTGL
(closed triangle). Fig. 3 shows the competition curve plotting % probe binding vs.
inhibitor concentration obtained in one set of experiments.

Table I
Representative Peptide competitive IC50s Sequences Number IC50 Ac-pYEEI I 8 Ac-pYpYEEI 2 1.5 Ac-pYpYpYIE 3 0.5 Ac-pYTGL 4 100 Ac-pYGGL 5 700 Data of this sort demonstrates that the materials and methods of this invention can be used to conduct a competitive binding assay with inhibitory substances having a range of IC50 values.
Illustrative protocols according to this invention are both manual and automatedand are performed as follows:

D. Manual Assays CA 022~0067 1998-09-21 W O 97/39326 PCT~US97/06746 Two different plates can be run for each experiment - a 2% DMSO and 20%
DMSO plate.
Buffers All buffer components were low-fluorescence grade (Panvera Corporation).
Standard (STD) buffer contains 20 mM phosphate (pH 7.4), 100 mM NaCl, 2 mM DTT, 1 mM EDTA, and 100 ug/ml BGG. Standard buffer is prepared by ple~ g NaCI, EDTA and phosphate stocks in Millipore water or the cleanest available water supply.
The buffer is brought to volume in the same clean water.
The five buffers needed for these experiments are standard (STD) buffer, STD
Buffer + 4% DMSO, 100% DMSO, STD buffer with labelled probe alone and STD
buffer with Src protein and labelled probe.
One liter is made up of 100 ml of I M NaCI, 20 ml of I M phosphate (pH 7.4), 2 ml of 500 mM EDTA, 20 ml of 5 mg/ml BGG, and 858 ml of Clean Water.
The standard buffer is made up and stored at 4~C. Before each use, the DTT is added at 2 mM. This standard buffer is employed to make up the Standard Buffer + 4%
DMSO stock also. This can be stored at 4~C as well and DTT can be added before use.

Protein and Control Peptide The SRC protein is used at a concentration of 0.75 uM final. An example of SRC stock solution is 416.6 uM in STD buffer. The peptide Ac-pYEEI is used at 100 uM final. It is desirable to make a 2X stock of this.
Probe Fluor-GpYEEI is used as the probe at a concentration of 20 nM final. The probe stock sent is 10 uM in STD buffer.
As one exarnple, to prepare 25 mls of protein and only 2 mls of probe alone, thefollowing steps are followed:
(a) 27 mls Standard buffer (add 2 mM DTT) (b) Add Probe-1515 at 2X or 40 nM = 108uL
(c) Remove 2 mls for Probe Alone (d) To the rem~inin~ 25 mls add SRC at 2X or 1.50 uM = 90 uL
This is now the Protein and Probe solution.

Secondary Stocks Each compound/peptide and the control peptide is in separate tubes. They are at 2X stocks.

CA 022~0067 1998-09-21 W O 97/39326 PCTrUS97/06746 It is desirable to make primary stock at 50 mM in 100% DMSO, then make the secondary stocks in STD Buffer + 4% DMSO at the appropriate concentration for the desired experiment.
One example of a secondary stock is made by combining 2 mM stock in STD
Buffer + 4% DMSO for one embodiment of an assay (Long Format, 2% DMSO).
Another is 5 mM stock in 100% DMSO for Lon~ Format assay with 20% DMSO.
Another secondary stock solution is 400 uM stock in STD buffer + 4% DMSO for Short Format assay #1 and #2 -2% DMSO. 1 mM stock in 100% DMSO for Short Format #1 and #2 -20% DMSO

Lon~ Format Assay A 1:2 dilution is used with first well at 1 mM final. For Plate 1 - 2% DMSO, theassay protocol is as follows:
(a) 50 ul Standard Buffer + 4% DMSO in column 2-12.
(b) 100 ul of 8 different compounds (2 mM stock/SB+4% DMSO) in each well in column 1 row A-H.
(c) Serially dilute 50 ul (1:2) horizontally down plate to column 10.
(d) Add 50 ul probe alone to column 12.
(e) Add 50 ul protein and probe to column 1-11.
(fl 1 oo ul final volume per well.
(g) Read plate on FPM2.
For Plate 1 - 20% DMSO, the assay protocol is as follows:
(a) 20 ul 100% DMSO in columns 2-12.
(b) 40 ul of 8 different compounds (5 mM stock/100% DMSO) in each well in column 1 row A-H.
(c) Serially dilute 20 ul (1:2) horizontally down plate to column 10.
(d) Add 50 ul probe alone to column 12.
(e) Add 50 ul protein and probe to column 1-11.
(fl Add 50 ul STD buffer to entire plate.
(g) 100 ul final volume per well.
(h) Read plate on FPM2.

Short Format #l Assay A 1:3 dilution with first well at 200 uM final. Compounds/peptides are used in duplicate. These examples are for a 1:3 dilution but volumes may be changed to accommodate any desired dilution.

CA 022~0067 1998-09-21 W O 97/39326 PCTrUS97/06746 For Plate I - 2% DMSO, the assay protocol is as follows:
(a) 50 ul Standard Buffèr + 4% DMSO in row B-D and F-G.
(b) 75 ul of 11 different compounds (400 uM/SB+4% DMSO) in duplicate each well in column 1-10, row A and column 1-12, row E.
(c) Serially dilute 25 ul (1:3) vertically down plate from A-D then from E-H.
(d) Add 50 ul probe alone to column 12.
(e) Add 50 ul protein and probe to column 1-11 A-D and 1-12 E-H.
(f) 100 ul final volume per well.
(g) Read plate on FPM2.
For Plate 2 - 20% DMSO, the assay protocol is as follows:
(a) 20 ul 100% DMSO in row B-D and F-G.
(b) 30 ul of 11 different compounds (1 mM/100% DMSO) in duplicate each well in column 1-10, row A and column 1-12, row E.
(c) Serially dilute 10 ul (1 :3) vertically down plate from A-D then from E-H.
(d) Add 50 ul probe alone to column 12.
(e) Add 50 ul protein and probe to column 1-11 A-D and 1-12 E-H.
(f) 100 ul final volume per well.
(g) Add 30 ul STD buffer to entire plate.
(h) Read plate on FPM2.

Short Format #2 AssaY
A 1 :3 dilution with first well at 200 uM final. Compounds/peptides are used in singly. These examples are for a 1 :3 dilution but volumes may be changed to accommodate whatever dilution you wish.
For Plate I - 2% DMSO, the assay protocol is as follows:
(a) 50 ul Standard Buffer + 4% DMSO in column 2-4 and 6-8 in 10-12.
(b) 75 ul of 16 different compounds in (400 uM/SB+4% DMSO) each well in column 1 and 5.
(c) 75 ul of 6 different (400 uM/SB+4% DMSO) compounds to column 9, A-F only. Total of 22 compounds.
(d) Serially dilute 25 ul (1 :3) horizontally down plate from 1 -4 then from 5-8, then from 9-12.
(e) Add 50 ul probe alone to row H, columns 9-12.
(f) Add 50 ul protein and probe row A-H, columns 1-8 and A-G, columns 9-12.
(g) There should be 100 ul final volume per well.

CA 022~0067 1998-09-21 W 097/39326 PCTrUS97/06746 (h) Read plate on FPM2.
For Plate 2 - 20% DMSO assay, the following protocol is followed:
(a) 20 ul 100% DMSO in column 2-4 and 6-8 and 10-12.
(b) 30 ul of 16 different compounds (1 mM/100% DMSO) in each well in column 1 and 5.
(c) 30 ul of 6 different compounds (1 mM/100% DMSO) to column 9, A-F
only. Total of 22 compounds.
(d) Serially dilute 10 ul (1:3) horizontally down plate from 1-4 then from 5-8, then from 9-12.
(e) Add 50 ul probe alone to row H, column 9-12.
(f) Add 50 ul protein and probe row A-H, columns 1-8 and A-G, columns 9-12.
(h) Add 50 ul STD buffer to entire plate.
(i) There should be 100 ul final volume per well.
(j) Read plate on FPM2.

E. Automated Assays ( 1 ) Short dilution This assay is run with l/3 dilution steps with first well at 200 uM, 4 wells down, 22 cpds/plate, "landscape" orientation of plate with respect to Genesis deck.
(i) 20% DMSO
(ii) 2% DMSO
(2) Lon~ dilution This assay is run with 1/2 dilution steps with first well at 1 mM, 10 wells down, 8 cpds/plate, "landscape" orientation of plate with respect to Genesis deck.
(i) 20% DMSO
(ii) 2% DMSO
Dilution 5 Buffers:
- Buffer + 4% DMSO
- 100% DMSO
- Buffer with probe alone - Buffer with protein and probe - Buffer (3) Short Format Each compound is in a separate well of a 96 well plate.

CA 022~0067 1998-09-21 Plate 1 - 2% DMSO
- 50 ul 4~/0 DMSO in columns 2? 3. 4, 6, 7, 8, 10, 11 and 12.
- 75 ul of 22 different compounds (400 uM stock, 4% DMSO) each well in all rows of columns I and 5 and rows A through F of column 9.
- 75 ul of Buffer ~ 4% DMSO to wells G9 and H9.
- Serially dilute 25 ul (1 :3) across plate from I to 4, throwing away last 25 ul, then from 5 to 8, and 9 to 12. This leaves 50 ul of liquid/well.
- Add 50 ul protein and probe to the entire plate except wells H9, 10, 11 and 12.
- Add 50 ul probe alone to wells H9, 10, 11 and 12.
- 100 ul final volume per well.
- Read plate.
Plate 2 - 20-% DMSO
- 20 ul 100% DMSO in columns 2, 3, 4, 6, 7, 8, 10, 11 and 12.
- 30 ul of 22 different compounds (1 mM stock, 100% DMSO) each well in all rows of columns I and 5 and rows A through F of column 9.
-30uloflO0%DMSOtowellsG9andH9.
- Serially dilute 10 ul (1 :3) across plate from 1 to 4, throwing away last 25 ul, then from 5 to 8, and 9 to 12. This leaves 50 ul of liquid/well.
- Add 50 ul protein and probe to the entire plate except wells H9, 10, 11 and 12.
- Add 50 ul probe alone to wells H9, 10, 11 and 12.
- Add 30 ul STD buffer to entire plate.
- 100 ul final volume per well.
- Read plate.
(4) Lon~ Format Each compound is located in a separate well of a 96 well plate.
Plate I - 2% DMSO
- 50 ul 4% DMSO in columns 2-12.
- 100 ul of 8 different compounds in each well in column I, row A-H.
- Add 50 ul of std. 3 to well A11.
- Serially dilute 50 ul (1 :2) across plate to column 10, throwing away last 50 ul (all rows).
- Serially dilute 50 ul from well Al l down to Hl l, throwing away last 50 ul.

CA 022~0067 1998-09-21 W O 97/39326 PCT~US97/06746 - Add 50 ul protein and probe to the entire plate except A12, B12, C12 and D12.
- Add 50 ul probe alone to A12, B12, C12 and D12.
- 100 ul final volume per well.
- Read plate.
Plate 2 - 20-% DMSO
- 20 ul 100% DMSO in rows 2-12.
- 40 ul of 8 different compounds in each well in column 1, row A-H.
- Add 20 ul of std. 4 to well Al l .
- Serially dilute 20 ul (1 :2) across plate to column 10 throwing away last 20 ul (all rows).
- Serially dilute 20 ul from well A11 down to H11, throwing away last 20 ul.
- Add 50 ul protein and probe to the entire plate except A 12, B 12, C 12 and D12.
- Add 50 ul probe alone to A12, B12, C12 and D12.
- Add 30 ul STD buffer to entire plate.
- 100 ul final volume per well.
- Read plate.
* Once diluted, the plate can be read between S and 30 minutes.
* Assay plate is transferred to FPM2 machine for 3 minute read.

Example 5 - FP-BASED ZAP, SYK, and LCK ASSAYS
In addition to the example of the Src SH2 domain and its phosphoTyr-containing peptide ligand which is linked to the fluorophore which are exemplified in Examples 1-4 above, the assay has also been used for the proteins Zap, Syk and Lck. Those three proteins are produced analogously to the production of Src in E. coli, as described above with slight variations in production parameters such as salt concentration, DTT
concentration, protein concentration, temperature and the like.
While Src has a single SH2 domain, ZAP and Syk comprise two SH2 domains and the Lck protein comprises one SH2 domain and one SH3 domain.
The "first proteins" produced for these assays are produced generally as described for Src aal45-251 in Example 3. The proteins are represented in the table below. The term "NC" means that the first protein contains both the N terminal and C
terminal SH2 domains. The sequences of Zap, Syk and Lck are known in the art. See also PCT/US96/13918 CA 022~0067 1998-09-21 W O 97/39326 PCTrUS97106746 Table I
First Amino Acid Residues of the Protein Naturally Occurrin~ Protein - NC-ZAP aal-259 NC-Syk aal-260 Lck aa 109-266 The probes for each assay are designed and used as described above. For example, an exemplary probe for N,C-ZAP proteins7 i.e., proteins cont~inin~ the two SH2 domains of human ZAP in series, is fluorescein-GpYNELNLGRRGEEpYEVL-NH,. As another example, an exemplary probe for N,C-Syk proteins, i.e., proteinscont~ining the two SH2 domains of human Syk in series, is fluorescein-ApYTGLSTRNQETpYETL-NH2. The SRC probe was also used with Lck.
The Lck protein has been assayed against fluorophore-labeled phosphopeptide ligand for the SH2 domain, fluorophore-labeled peptide ligand for the SH3 domain and fluorophore-labeled phosphopeptide double ligand for the SH2 and SH3 domains.
The assay format described in Example 4 is reproduced for these binding pairs and results obtained.

The data shown in Figs. 2A and 2B show that the affinity of the probe for the receptor domain is appropriate for conducting competitive binding assays and that saturable binding to a single site is observed, consistent with the assay of this invention and with competitive, reversible binding to a single site. The data obtained from the saturation assay can, within the methods of the present invention, be used to assess whether a particular probe would be useful. For example, if a probe performs at a particular level in a saturation assay (e.g." Kd <I 0uM and mP difference values >50 (difference in observed polarization in the presence and absence of protein)), it is indicative of its suitability for use in a competition assay of this invention.

Example 6 - A FLUORESCENCE-POLARIZATION BASED HUMAN

CA 022~0067 1998-09-21 W O 97139326 PCT~US97/06746 A. Assay- General All assay methods, including buffers and instrumental usage, were perforrned generally as in the case of Src SH2 assay described in the previous examples, but substituting a human GRB2 protein (for Src SH2) and a probe specific for the GRB2 Sl I2 domain (in place of the Src-specific probe). The human GRB2 protein tested in the assay comprised amino acid residues 55 - 152 of huGRB2 [see Cell 70: 431-442 (1992)], although longer sequences encompassing the SH2 domain may also be used. Production and purification of the protein domain was similar to methods described above, especially the use of a phosphotyrosine column to purify the GRE~2 SH2domain.

B. Saturation Experiments As in previous examples, saturation experiments were perforrned with fixed concentrations of probe and increasing concentrations of Grb-2-SH2.
The following Grb-2-specific SH2 probe (" FPgb2") was synthesized using the techniques described in Example 1 (~H O

J~ I OH ~p-P-OH

f ~ b~NJ~N~ NJ~NHz FPgb2, Fluor-GpYVNV-NH2 in which "Fluor" represents 5-carboxyfluorescein conjugated through an amide bond to the peptide containing the sequence GpYVNV. That tetrapeptide sequence is specific for Grb-2 SH2 domain binding. This probe had applop-iate characteristics and an appropriate saturation curve with the GRB2 SH2 protein to (e.g., appropriate Kd and total mP difference on protein binding) to serve as a probe for a competition assay.

Example 7- A FLUORESCENCE-POLARIZATION BASED Src SH3 BINDING
ASSAY

CA 022~0067 1998-09-21 WO 97139326 PCTrUS97/06746 A. Assay- General All assay methods, including buffers and instrumental usage, were performed generally as in the case of Src SH2 assay described in a previous example(s), but substituting a protein cont~ining peptide sequence spanning the Src SH2 and SH3 domains (amino acid residues 84-251) [see Mol. Cell. Biol. 7(5): 1978-1983 (1987)], and a probe specific for the Src SH3 domain (in place of the Src-specific SH2 probe). Note that larger or smaller Src proteins may be used, so long as they include the Src SH3 domain (with or without the Src SH2 domain). Production and purification of the protein were essentially as described above, e.g., see Example 3. The following details are provided:

Src-SH2-SH3 Domain Purification:
I) French press Iysis, 50mM Potassium phosphate, SmM DTT, 2mM EDTA, ImM
PMSF, pH 7.0 2) 40um WP Carboxy-sulfon column --~633mgs 3) Phosphotyrosine Agarose column-->512mgs 4) Dialysis against 50mM Potassium phosphate, 10% Glycerol, 500mM NaCl, 5mM EDTA, 0.02% NaN3, pH 7.0 B. Saturation Experiments As in a previous example(s), saturation experiments were performed with fixed concentrations of probe and increasing concentrations of Src-SH2-SH3 protein.
The following Src SH3 specific probe ("FPSI 13 ") was synthesized using the techniques described in Exarnple 1:

Fluor-PLARRPLPPLP-NH2 in which "Fluor" represents 5-carboxyfluorescein conjugated through an arnide bond to the peptide containing the sequence PLARRPLPPLP, which is specific for Src SH3 domain binding. This probe had appropriate characteristics and an appropriate saturation curve with the Src protein to (e.g., appropriate Kd and total mP difference on protein binding) to serve as a probe for a competition assay.

~ Exarnple 8- A FLUORESCENCE-POLARIZATION BASED Src SH2-SH3 DOUBLE
BINDING ASSAY
A. Assay- General CA 022~0067 1998-09-21 W O 97139326 PCT~US97/06746 Proteins such as Src contain both an SH2 and an SH3 domain. Certain proteins can bind to such SH2-SH3 proteins not through SH2 or SH3 domains alone, but through both domains at once. One example is the protein, pl30CAS, which is thought to bind Src via both SH2 and SH3 domains. The SH3 and SH2 binding sequences of p 130CAS
have been identified by deletional and site-specific mutagenesis (Nakamoto et. al.. JBC
271, 8959-8965, 1996). Residues 733-738 (RPLPSP) have been shown to be involved in binding (presumably to the SH3 domain), as has residue Tyr-762 (presumably phosphorylated and responsible for binding Src SH2). Fluorescent probes for FP assays were designed based on these sequences. Such probes can be used in assays that allow simultaneous screening for both SH2-specific and SH3-specific inhibitors. One such probe ("FPC130 ") is the following:

Fluor-RPLPSPPKFTSQDSPDGQYENSEGGWMEDpYDWHL

This is the native sequence from pl30CAS (733-767). Derivative probes based on the foregoing but using different component SH2 and/or SH3 sequences may be used to vary the affinity or protein specificity, and especially to increase the overall affinity of probe for the desired target protein.
All assay methods, including buffers and instrumental usage, were performed generally as in the case of Src SH2 assay described in Example 4, but substituting a protein containing peptide sequence spanning the Src SH2 and SH3 domains (for Src SH2) and the SH2-SH3 probe described above (in place of the Src-specific SH2 probe).

B. Saturation Experiments As in a previous example(s), saturation experiments were performed with fixed concentrations of probe and increasing concentrations of protein (Src-SH2-SH3 in this case).

The Src SH2-SH3 specific probe, FPC130, was synthesized using the techniques described in Example 1:

Fluor-RPLPSPPKFTSQDSPDGQYENSEGGWMEDpYDYVHL

in which "Fluor" represents S-carboxyfluorescein conjugated through an amide bond to the peptide containing the sequence PLARRPLPPLP, which is specific for Src Sh3 domain binding (any other fluorescent probe might be substituted). This probe had CA 022~0067 1998-09-21 W O 97/39326 PCT~US97/06746 appropriate characteristics and an appropriate saturation curve with the Src protein to (e.g., ~p,opl,ate Kd and total mP difference on protein binding) to serve as a probe for a competition assay.

Example 9 - A FL UORESCENCE-POLA~IZATION BASED HUMAN
Src-SH2 BINDING ASSAYUSING AN ALTERNATE PROBE:

A. Assay- General A competition assay was developed for Src-SH2 (applicable to any fragment of Srccontaining the SH2 domain) with a non-fluorescein fluorophore. The fluorophore is one of a family of fluorescent molecules cont~ining the core fluorophore, 4,4-difluoro-4 bora-3a,4a-diaza-s-indacene (commercially available from Molecular Probes Inc.). The structure of the fluorophore-peptide probe is:

OH O

~N ~I'HN~ JlH ~ NHZ

~3~

The fluorophore is BODIPY-TRX, and has spectral characteristics very similar to the Texas Red family of fluorophores. The use of a red fluorophore widens the utility of the assay, and permits one to screen test compounds that might have fluorescence characteristics similar to fluorescein itself.
All assay methods, including buffers and instrumental usage, were performed generally as in the case of Src SH2 assay described in Example 4, but substituting the new probe, shown above, and using different filters on the fluorimeter, to match the CA 022~0067 1998-09-21 W 097/39326 PCTrUS97/06746 -44-spectral characteristics of this alternate probe. Specifically, the excitation/emission filters used with the above are 591/635, compared to 485/530 for fluorescein.
Synthesis of the peptide portion of the probe was as described in Example 1, with production of the peptide NH2-pYEEI. The probe was further synthesized by coupling the free amine peptide, NH2-pYEEI, with the succinimidyl ester of the BODIPY-TRXprobe in a 66% DMSO buffer (34% O.lM NaBicarbonate). Completion of reaction was monitored by silica gel TLC (4:1:1, butanol, H20, Acetic Acid solvent system), and was done by 24 hrs. The resultant peptide was quite hydrophobic, and was purified by the same TLC system as just described.

CA 022~0067 1998-09-21 W O 97/39326 PCT~US97106746 B. Saturation Experiments As in a previous example(s), saturation experiments were performed with fixed concentrations of probe and increasing concentrations of Src-SH2 protein. The only difference was the use of an alternate set of filters for the red probe, as described in A
above.
This probe showed an adequate Kd and total mP difference on protein binding to be a probe for a competition assay.

This invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein wil} become apparent to those skilled in the art from the foregoing description. Such modifications are intended to fall within the scope of the appended claims.

The disclosures of the patents, patent applications and publications cited herein are incorporated by reference in their entireties.

CA 022~0067 l998-09-2l SEQUENCE LISTING

(1) GENERAL INFORMATION:
(i) APPLICANT: Ariad Pharmaceuticals, Inc.
(ii) TITLE OF INVENTION: In Vitro Fluorescence Polarization Assay (iii) NUM8ER OF SEQUENCES: 20 (iv) CORRESPONDENCE ADDRESS:
(A) ADDRESSEE: LAHIVE & COCKFIELD
(B) STREET: 28 State Street, 24th Floor (C) CITY: Boston (D) STATE: Massachusetts (E) COUNTRY: USA
(F) ZIP: 02109-1875 (v) COMPUTER READA8LE FORM:
(A) MEDIUM TYPE: Floppy disk (B) COMPUTER: IBM PC compatible (C) OPERATING SYSTEM: PC-DOS/MS-DOS
(D) SOFTWARE: PatentIn Release #1.0, Version #1.25 (vi) CURRENT APPLICATION DATA:
(A) APPLICATION NUMBER: PCT/US97/06746 (8) FILING DATE: April 18, 1997 (C) CLASSIFICATION:
(vii) PRIOR APPLICATION DATA:
(A) APPLICATION NUMBER: US 60/029,870 (B) FILING DATE: 06-NOV-1996 (viii) ATTORNEY/AGENT INFORMATION:
(A) NAME: Elizabeth A. Hanley (B) REGISTRATION NUMBER: 33,505 (C) REFERENCE/DOCKET NUMBER: AFI-006PC
(ix) TELECOMMUNICATION INFORMATION:
(A) TELEPHONE: (617)227-7400 (B) TELEFAX: (617)742-4214 (2) INFORMATION FOR SEQ ID NO:1:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 4 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site ~ CA 022~0067 1998-09-21 (B) LOCATION: 1 (D) OTHER INFORMATION: /note= Tyr is Phosphorylated Tyrosine (xi) S~Uu~N~ DESCRIPTION: SEQ ID NO:l:
Tyr Glu Glu Ile (2) INFORMATION FOR SEQ ID NO:2:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 5 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 1,2 (D) OTHER INFORMATION: /note= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:
Tyr Tyr Glu Glu Ile (2) INFORMATION FOR SEQ ID NO:3:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 4 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 1 (D) OTHER INFORMATION: /note= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:
Tyr Gly Gly Leu (2) INFORMATION FOR SEQ ID NO:4:
(i) SEQUENCE CHARACTERISTICS:

CA 022~0067 1998-09-21 , (A) LENGTH: 4 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 1 (D) OTHER INFORMATION: /note= Tyr is Phosphorylated Tyrosine (xi) S~u~ DESCRIPTION: SEQ ID NO:4:
Tyr Glu Asp Leu (2) INFORMATION FOR SEQ ID NO:5:

(i) S~Qu~N~ CHARACTERISTICS:
(A) LENGTH: 7 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v~ FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Mofified-site (B) LOCATION: 4 (D~ OTHER INFORMATION: /note= Tyr is Phosphorylated Tyrosine (xi~ SEQUENCE DESCRIPTION: SEQ ID NO:5:

Asp Gly Val Tyr Thr Gly Leu (2) INFORMATION FOR SEQ ID NO:6:

(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 6 amino acids (B) TYPE: amino acid (D~ TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:

CA 022~0067 1998-09-21 -Phe Leu Val Arg Glu Ser (2) INFORMATION FOR SEQ ID NO:7:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 5 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 1 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7:
Tyr Xaa Xaa Xaa Xaa (2) INFORMATION FOR SEQ ID NO:8:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 4 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 4 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8:
Asn Xaa Pro Tyr (2) INFORMATION FOR SEQ ID NO:9:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 4 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide CA 022~0067 1998-09-21 (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 4 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:9:
Asn Pro Xaa Tyr (2) INFORMATION FOR SEQ ID NO:10:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 5 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 2 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:10:
Gly Tyr Glu Glu Ile (2) INFORMATION FOR SEQ ID NO:ll:

(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 5 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 1-3 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:ll:
Tyr Tyr Tyr Ile Glu CA 022~0067 l998-09-2l (2) INFORMATION FOR SEQ ID NO:12:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 4 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 1 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12:
Tyr Thr Gly Leu (2) INFORMATION FOR SEQ ID NO:13:
( i ) ~QU~N~ CHARACTERISTICS:
(A) LENGTH: 17 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 2,14 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13:
Gly Tyr Asn Glu Leu Asn Leu Gly Arg Arg Gly Glu Glu Tyr Glu Val Leu (2) INFORMATION FOR SEQ ID NO:14:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 16 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear CA 022~0067 1998-09-21 (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 2,13 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:14:
Ala Tyr Thr Gly Leu Ser Thr Arg Asn Gln Glu Thr Tyr Glu Thr Leu (2) INFORMATION FOR SEQ ID NO:15:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 5 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 2 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:15:
Gly Tyr Val Asn Val (2) INFORMATION FOR SEQ ID NO:16:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 5 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 2 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine CA 022~0067 l998-09-2l (xi) S~Qu~N~ DESCRIPTION: SEQ ID NO:16:
Gly Tyr Val Asn Val (2) INFORMATION FOR SEQ ID NO:17:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 11 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (xi) SEQUENCE DESCRIPTION: SEQ ID NO:17:
Pro Leu Ala Arg Arg Pro Leu Pro Pro Leu Pro (2) INFORMATION FOR SEQ ID NO:18:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 11 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (xi) SEQUENCE DESCRIPTION: SEQ ID NO:18:
Pro Leu Ala Arg Arg Pro Leu Pro Pro Leu Pro (2) INFORMATION FOR SEQ ID NO:19:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 35 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 30 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine CA 022~0067 l998-09-2l .
t (xi) SEQUENCE DESCRIPTION: SEQ ID NO:19:
Arg Pro Leu Pro Ser Pro Pro Lys Phe Thr Ser Gln Asp Ser Pro Asp Gly Gln Tyr Glu Asn Ser Glu Gly Gly Trp Met Glu Asp Tyr Asp Tyr Val His Leu (2) INFORMATION FOR SEQ ID NO:20:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 5 amino acids (B) TYPE: amino acid ~D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (v) FRAGMENT TYPE: internal (ix) FEATURE:
(A) NAME/KEY: Modified-site (B) LOCATION: 2-4 (D) OTHER INFORMATION: note/= Tyr is Phosphorylated Tyrosine (xi) SEQUENCE DESCRIPTION: SEQ ID NO:20:
Gly Tyr Tyr Tyr Ile AFI\006PC\SEQLIST DOC

Claims (12)

WHAT IS CLAIMED IS:

1. An in vitro assay method for identifying a test substance which inhibits the mutual association of two protein molecules, said method comprising:
(a) providing a first protein molecule and a second protein molecule capable of mutual association, said second protein molecule bearing a covalently linked fluorophore, (b) preparing a mixture containing said first and second protein molecules and at least one test substance, (c) irradiating said mixture with polarized light of a suitable wavelength permitting excitation of the fluorophore as indicated by emission of polarized light, (d) measuring the degree of polarization of the emission, and (e) determining the effect of the presence or concentration of the test substance in decreasing the observed emission polarization of a mixture of said first and second protein molecules in the absence of said test substance, wherein inhibitory activity of said test substance correlates with decreased depolarization values.

2. The method according to claim I wherein one of said protein molecules contains at least one domain selected from the group consisting of SH2 domains. PI domains, SH3 domains and WW domains, and the other said protein molecule is a ligand therefor.

3. The method according to claim 2 wherein one of said protein molecules contains at least one domain selected from the group consisting of SH2 domains and PI domains, and the other said protein molecule comprises a phosphotyrosine-containing peptide sequence.

4. The method according to claim 1 wherein said one or more steps are performed by an apparatus programmed to conduct automatically two or more steps for a given test substance or one or more steps for a plurality of test substances or test substance concentrations.

5. The method according to claim I where said fluorophore is fluorescein.

6. In a method for identifying a substance which inhibits the mutual association of a pair of proteins, said method comprising admixing said pair of proteins with one or more test substances which comprise candidate inhibitors, and determining whether the association of the pair of proteins has been inhibited by the presence of the candidate inhibitors, the improvement comprising:
(a) using a pair of proteins, wherein one of said proteins is covalently linked to a fluorophore, (b) irradiating said mixture of proteins and test substance with polarized lightof a suitable wavelength permitting excitation of the said fluorophore as indicated by emission of polarized light, (c) measuring the degree of polarization of the emission, and (d) determining the effect of the presence or concentration of the test substance in decreasing the observed emission polarization from that of a mixture of said proteins in the absence of said test substance, wherein competitive binding of said test substance correlates with observed depolarization values.

7. The method according to claim 6 wherein one of said proteins contains at least one domain selected from the group consisting of SH2 domains, PI domains, SH3 domains and WW domains, and the other said protein is a ligand therefor.

8. The method according to claim 7 wherein one of said proteins contains at least one domain selected from the group consisting of SH2 domains and PI domains, and the other said protein comprises a phosphotyrosine-containing peptide sequence.

9. The method according to claim 6 wherein said one or more steps are performed by an apparatus programmed to conduct automatically two or more steps for a given test substance or one or more steps for a plurality of test substances or test substance concentrations .

10. The method according to claim 6 where said fluorophore is fluorescein.

11. An inhibitor of the association of a pair of proteins, identified by the method of claim 1 or claim 6.

12. An in vitro assay method for identifying a test substance which competitively binds to either a receptor tyrosine-phosphorylated peptide and/or its ligand, said method comprising:
(a) providing a receptor for a tyrosine-phosphorylated peptide, (b) providing said ligand for said receptor, said ligand bearing a covalently linked fluorescent moiety, (c) irradiating a mixture containing (a), (b) and said test substance with polarized light of a suitable wavelength permitting excitation of the fluorophore as indicated by emission of polarized light, (d) measuring the degree of polarization of the emission, and (e) determining the effect of the presence or concentration of the test substance in decreasing the observed emission polarization of a mixture of (a) and (b) alone, wherein competitive binding of said test substance correlates with decreased depolarization values.