Claims
- 1. A method of designing specific inhibitors of a Pin1 polypeptide, comprising the steps of:
(a) determining the three-dimensional structures of crystallized Pin1 polypeptides in complex with small molecules; (b) employing the three-dimensional structures from step (a) to form an interaction template; (c) employing sequence and structural alignments to identify conserved amino acids among proline isomerases and distinguishing those amino acids that are specific to Pin1 to define a specificity template; (d) using the interaction template and the specificity template in conjunction with molecular modeling to design inhibitors specific to Pin1 or Pin1-like proline isomerases; and (e) determining the affinity and specificity of the inhibitors to Pin1.
- 2. A method for designing or selecting an inhibitor of a Pin1 polypeptide, comprising the steps of:
a) using a three dimensional structure of a crystallized Pin1 polypeptide having a substitution, deletion or insertion of one or more amino acids of the sequence set forth in SEQ ID NO:1 to form a Pin1 interaction template; and b) employing the Pin1 interaction template to design or select the Pin1 inhibitor.
- 3. The method of claim 2, wherein the crystallized Pin1 polypeptide has a substitution, insertion or deletion of one or more amino acids within the WW-domain of the Pin-1 polypeptide.
- 4. The method of claim 3, wherein the crystallized Pin1 polypeptide has one amino acid substitution.
- 5. The method of claim 4, wherein the amino acid substitution of the crystallized Pin1 polypeptide is at position 14 of the amino acid sequence set forth in SEQ ID NO:1.
- 6. The method of claim 5, wherein the amino acid substitution at position 14 of the crystallized Pin1 polypeptide is a nonpolar amino acid.
- 7. The method of claim 6, wherein the nonpolar amino acid at position 14 is alanine.
- 8. The method of claim 2, wherein the crystallized Pin1 polypeptide further comprises a small molecule within the active site of the Pin1 polypeptide.
- 9. The method of claim 2, wherein the three dimensional structure of more than one crystallized Pin1 polypeptide is used to form the Pin1 interaction template.
- 10. The method of claim 2, wherein the three dimensional structure of more than one crystallized Pin1 polypeptide comprising a small molecule within the active site of the Pin1 polypeptide is used to form the Pin1 interaction template.
- 11. The method of claim 2, further comprising the step of using a Pin1 specificity template.
- 12. The method of claim 2, further comprising the step of contacting the inhibitor with a Pin1 polypeptide in the presence of a substrate to determine the ability of the inhibitor to inhibit the Pin1 polypeptide.
- 13. The method of claim 2, 7 or 8, further comprising the step of determining the affinity and specificity of the inhibitor.
- 14. The method according to claims 1 or 2, wherein said inhibitor is designed or selected de novo.
- 15. The method according to claims 1 or 2, wherein said inhibitor is designed or selected from a known inhibitor.
- 16. The method according to claims 1 or 2, wherein said three-dimensional structure is used to design or select chemical entities or fragments that bind to at least one of the following portions of the Pin1 active site: the hydrophobic pocket, the cysteine/scrine valley, the phosphate binding pocket, the substrate grove and the lip regions.
- 17. The method of claim 16, wherein the identified chemical entities or fragments are covalently linked.
- 18. The method according to anyone of claims 1 or 2 wherein said inhibitor is a competitive inhibitor of Pin1.
- 19. The method according to anyone of claims 1 or 2 wherein said inhibitor is a non-competitive or uncompetitive inhibitor of Pin1.
- 20. A Pin1 polypeptide in the crystallized form having a substitution, insertion or deletion of one or more amino acids of the amino acid sequence set forth in SEQ ID NO:1, wherein the active site of the Pin1 polypeptide is accessible to solvent and available for interaction with an inhibitor in a crystallized form.
- 21. The crystallized Pin1 polypeptide of claim 20 wherein the substitution, insertion or deletion of one or more amino acids is within the WW-domain of the Pin-i polypeptide.
- 22. The crystallized Pin1 polypeptide of claim 21 having one amino acid substitution.
- 23. The crystallized Pin1 polypeptide of claim 21, having an amino acid substitution at position 14 of the amino acid sequence set forth in SEQ ID NO:1.
- 24. The crystallized Pin1 polypeptide of claim 23, wherein the amino acid substitution at position 14 is a nonpolar amino acid.
- 25. The crystallized Pin1 polypeptide of claim 24, wherein the nonpolar amino acid at position 14 is alanine (SEQ ID NO:2).
- 26. The crystallized Pin1 polypeptide of any one of claims 20-25, wherein the polypeptide crystallizes within 7 days.
- 27. The crystallized Pin1 polypeptide of claim 26, wherein the polypeptide crystallizes within 3 days.
- 28. The crystallized Pin1 polypeptide of claim 26, wherein the polypeptide crystallizes within 2 days.
- 29. The crystallized Pin1 polypeptide of claim 26, wherein the polypeptide crystallizes within 24 hours.
- 30. The crystallized Pin 1 polypeptide of any of claims 20-25, having a resolution of about 3 Å or less.
- 31. The crystallized Pin1 polypeptide of claim 30, having a resolution of 2 Å or less.
- 32. The crystallized Pin1 polypeptide of claim 25, wherein the three dimensional structure of the polypeptide has the space group P3121.
- 33. The crystallized Pin1 polypeptide of claim 32 defined by the atomic coordinates set forth in FIG. 1.
- 34. A crystallized fragment of the Pin1 polypeptide of any of claims 20-25.
- 35. The crystallized fragment of claim 34, wherein the fragment comprises the active site of the Pin1 polypeptide.
- 36. The crystallized Pin1 polypeptide of claim 20, further comprising a Pin1 polypeptide inhibitor in the active site.
- 37. The Pin1 polypeptide inhibitor of claim 36, wherein the inhibitor is a small molecule.
- 38. A method for designing an inhibitor of a second peptidyl/prolyl isomerase comprising the steps of:
(a) providing a first peptidyl/prolyl isomerase having a known three-dimensional structure; (b) identifying amino acids in the active site of said first peptidyl/prolyl isomerase that form close contacts with a compound know to bind to said active site; (c) employing protein alignment means to identify in a second peptidyl/prolyl isomerase one or more amino acids that align with, but differ in identity from, said close contact amino acids in said first peptidyl/prolyl isomerase; (d) altering an amino acid in the active site of said second peptidyl/prolyl isomerase identified in step (c) to produce a mutant second peptidyl/prolyl isomerase; (e) determining that said compound binds with at least 10-fold greater affinity to said mutant second peptidyl/prolyl isomerase than to said second peptidyl/prolyl isomerase, and (f) using molecular modeling means to determine how to modify said compound to design an inhibitor of said second peptidyl/prolyl isomerase, wherein said inhibitor binds to said second peptidyl/prolyl isomerase with at least 10-fold greater affinity than said compound binds to said peptidyl/prolyl isomerase, respectively.
- 39. The method according to claim 38, wherein said first peptidyl/prolyl isomerase is Pin1 having the amino acid sequence set forth in SEQ ID NO:1.
- 40. The method according to claim 38, wherein said second peptidyl/prolyl isomerase is selected from the group consisting of hCyP-A, hCyP-B, hCyP-C, NKCA, hFKBP-12, hFKBP-13, Par14 and hFKBP-25.
RELATED APPLICATIONS
[0001] This application is claims priority to U.S. Provisional Application No. 60/361,227 filed Mar. 1, 2002. This application is related to U.S. Application No. 60/257,412, filed Dec. 22, 2000; U.S. application Ser. No. 09/726,464, filed Nov. 29, 2000; U.S. application Ser. No. 08/988,842, filed Dec. 11, 1997; U.S. application Ser. No. 10/027,864, filed Dec. 21, 2001; and WO 99/12962, published Mar. 8, 1999; PTZ-034, entitled “Pin1-Modulating Compounds and Methods of Use Thereof”, filed Mar. 3, 2003; PTZ-035, entitled “Pin1-Modulating Compounds and Methods of Use Thereof”, filed Mar. 3, 2003; PTZ-036, entitled “Pin1-Modulating Compounds and Methods of Use Thereof”, filed Mar. 3, 2003; U.S. Provisional Application Serial No. 60/361,246, filed Mar. 1, 2002; U.S. Provisional Application Serial No. 60/361,206, filed Mar. 1, 2002; and U.S. Provisional Application Serial No. 60/361,231, filed Mar. 1, 2002 the entire contents of which are expressly incorporated by reference.
Provisional Applications (1)
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60361227 |
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US |