Claims for Patent: 7,491,704

Summary for Patent: 7,491,704

Title:	Compounds for enzyme inhibition
Abstract:	Peptide-based compounds including heteroatom-containing, three-membered rings efficiently and selectively inhibit specific activities of N-terminal nucleophile (Ntn) hydrolases. The activities of those Ntn having multiple activities can be differentially inhibited by the compounds described. For example, the chymotrypsin-like activity of the 20S proteasome may be selectively inhibited with the inventive compounds. The peptide-based compounds include at least three peptide units, an epoxide or aziridine, and functionalization at the N-terminus. Among other therapeutic utilities, the peptide-based compounds are expected to display anti-inflammatory properties and inhibition of cell proliferation.
Inventor(s):	Smyth; Mark S. (San Mateo, CA), Laidig; Guy J. (Menlo Park, CA), Borchardt; Ronald T. (Lawrence, KS), Bunin; Barry A. (San Mateo, CA), Crews; Craig M. (New Haven, CT), Musser; John H. (San Carlos, CA)
Assignee:	Proteolix, Inc. (South San Francisco, CA)
Application Number:	11/786,217
Patent Litigation and PTAB cases:	See patent lawsuits and PTAB cases for patent 7,491,704
Patent Claims:	1. A method of treating cancer, comprising administering a compound having a structure of formula (I) or a pharmaceutically acceptable salt thereof, ##STR00029## wherein each A is independently selected from C.dbd.O, C.dbd.S, and SO.sub.2; or A is optionally a covalent bond when adjacent to an occurrence of Z; L is absent or is selected from C.dbd.O, C.dbd.S, and SO.sub.2; M is absent or is C.sub.1-12alkyl; Q is absent or is selected from O, NH, and N--C.sub.1-6alkyl; X is selected from O, NH, and N--C.sub.1-6alkyl; Y is absent or is selected from O, NH, N--C.sub.1-6alkyl, S, SO, SO.sub.2, CHOR.sup.10, and CHCO.sub.2R.sup.10; each Z is independently selected from O, S, NH, and N--C.sub.1-6alkyl; or Z is optionally a covalent bond when adjacent to an occurrence of A; R.sup.1 and R.sup.3 are independently optionally substituted C.sub.1-6aralkyl; R.sup.2 and R.sup.4 are independently selected from optionally substituted C.sub.1-6alkyl, C.sub.1-6hydroxyalkyl, and C.sub.1-6alkoxyalkyl; R.sup.5 is N(R.sup.6)LQR.sup.7; R.sup.6 is selected from hydrogen, OH, and C.sub.1-6alkyl; R.sup.7 is selected from hydrogen, C.sub.1-6alkyl, C.sub.1-6alkenyl, C.sub.1-6alkynyl, aryl, C.sub.1-6aralkyl, heteroaryl, C.sub.1-6heteroaralkyl, R.sup.8ZAZ-C.sub.1-8alkyl-, R.sup.11Z-C.sub.1-8alkyl-, (R.sup.8O)(R.sup.9O)P(.dbd.O)O--C.sub.1-8alkyl-ZAZ-C.sub.1-8alkyl-, R.sup.8ZAZ-C.sub.1-8alkyl-ZAZ-C.sub.1-8alkyl-, heterocyclylMZAZ-C.sub.1-8alkyl-, (R.sup.8O)(R.sup.9O)P(.dbd.O)O--C.sub.1-8alkyl-, (R.sup.10).sub.2N--C.sub.1-12alkyl-, (R.sup.10).sub.3N.sup.+--C.sub.1-12alkyl-, heterocyclylM-, carbocyclylM-, R.sup.11SO.sub.2C.sub.1-8alkyl-, and R.sup.11SO.sub.2NH; or R.sup.6 and R.sup.7 together are C.sub.1-6alkyl-Y--C.sub.1-6alkyl, C.sub.1-6alkyl-ZAZ-C.sub.1-6alkyl, ZAZ-C.sub.1-6alkyl-ZAZ-C.sub.1-6alkyl, ZAZ-C.sub.1-6alkyl-ZAZ, or C.sub.1-6alkyl-A, thereby forming a ring; R.sup.8 and R.sup.9 are independently selected from hydrogen, metal cation, C.sub.1-6alkyl, C.sub.1-6alkenyl, C.sub.1-6alkynyl, aryl, heteroaryl, C.sub.1-6aralkyl, and C.sub.1-6heteroaralkyl, or R.sup.8 and R.sup.9 together are C.sub.1-6alkyl, thereby forming a ring; each R.sup.10 is independently selected from hydrogen and C.sub.1-6alkyl; and R.sup.11 is independently selected from hydrogen, C.sub.1-6alkyl, C.sub.1-6alkenyl, C.sub.1-6alkynyl, carbocyclyl, heterocyclyl, aryl, heteroaryl, C.sub.1-6aralkyl, and C.sub.1-6heteroaralkyl, provided that when R.sup.6 is H or CH.sub.3 and Q is absent, LR.sup.7 is not hydrogen, unsubstituted C.sub.1-6alkylC.dbd.O, a further chain of amino acids, t-butoxycarbonyl (Boc), benzoyl (Bz), fluoren-9-ylmethoxycarbonyl (Fmoc), triphenylmethyl(trityl), benzyloxycarbonyl (Cbz), trichloroethoxycarbonyl (Troc); or substituted or unsubstituted aryl or heteroaryl; and in any occurrence of the sequence ZAZ, at least one member of the sequence must be other than a covalent bond. 2. A method of claim 1, wherein R.sup.2 and R.sup.4 are C.sub.1-6aralkyl. 3. A method of claim 2, wherein X is O, R.sup.1is 2-phenylethyl, R.sup.2 is isobutyl, R.sup.3 is phenylmethyl, and R.sup.4 is isobutyl. 4. A method of claim 3, wherein L and Q are absent and R.sup.6 is C.sub.1-6alkyl. 5. A method of claim 4, wherein R.sup.7 is selected from C.sub.1-6alkyl, C.sub.1-6alkenyl, C.sub.1-6alkynyl, C.sub.1-6aralkyl, and C.sub.1-6heteroaralkyl. 6. A method of claim 5, wherein R.sup.7 is C.sub.1-6alkyl. 7. A method of claim 6, wherein R.sup.7 is butyl. 8. A method of claim 5, wherein R.sup.7 is C.sub.1-6alkenyl. 9. A method of claim 8, wherein R.sup.7 is allyl. 10. A method of claim 5, wherein R.sup.7 is C.sub.1-6alkynyl. 11. A method of claim 10, wherein R.sup.7 is propargyl. 12. A method of claim 5, wherein R.sup.7 is C.sub.1-6aralkyl. 13. A method of claim 12, wherein R.sup.7 is phenylmethyl. 14. A method of claim 5, wherein R.sup.7 is C.sub.1-6heteroaralkyl. 15. A method of claim 14, wherein R.sup.7 is selected from 2-pyridyl, 3-pyridyl, and 4-pyridyl. 16. A method of claim 3, wherein Q is absent and L is SO.sub.2. 17. A method of claim 16, wherein R.sup.7 is selected from C.sub.1-6alkyl and aryl. 18. A method of claim 17, wherein R.sup.7 is C.sub.1-6alkyl. 19. A method of claim 18, wherein R.sup.7 is methyl. 20. A method of claim 17, wherein R.sup.7 is aryl. 21. A method of claim 20, wherein R.sup.7 is phenyl. 22. A method of claim 3, wherein L is C.dbd.O. 23. A method of claim 22, wherein R.sup.7 is selected from hydrogen, C.sub.1-6alkyl, C.sub.1-6alkenyl, C.sub.1-6alkynyl, aryl, C.sub.1-6aralkyl, heteroaryl, C.sub.1-6heteroaralkyl, R.sup.8ZA-C.sub.1-8alkyl-, R.sup.11Z-C.sub.1-8alkyl-, (R.sup.8O)(R.sup.9O)P(.dbd.O)O--C.sub.1-8-alkyl-ZAZ-C.sub.1-8alkyl-, (R.sup.8O)(R.sup.9O)P(.dbd.O)O--C.sub.1-8alkyl-Z-C.sub.1-8alkyl-, R.sup.8ZA-C.sub.1-8alkyl-ZAZ-C.sub.1-8alkyl-, heterocyclylMZAZ-C.sub.1-8alkyl-, (R.sup.8O)(R.sup.9O)P(.dbd.O)O--C.sub.1-8alkyl-, (R.sup.10).sub.2N--C.sub.1-8alkyl-, (R.sup.10).sub.3N.sup.+--C.sub.1-8alkyl-, heterocyclylM-, carbocyclylM-, R.sup.11SO.sub.2C.sub.1-8alkyl-, and R.sup.11SO.sub.2NH; or R.sup.6 and R.sup.7 together are C.sub.1-6alkyl-Y--C.sub.1-6alkyl, C.sub.1-6alkyl-ZA-C.sub.1-6alkyl, A-C.sub.1-6alkyl-ZA-C.sub.1-6alkyl, A-C.sub.1-6alkyl-A or C.sub.1-6alkyl-A, thereby forming a ring; and each occurrence of Z and A is independently other than a covalent bond. 24. A method of claim 23, wherein Q is absent. 25. A method of claim 24, wherein R.sup.6 and R.sup.7 are C.sub.1-6alkyl. 26. A method compound of claim 25, wherein R.sup.7 is selected from ethyl, isopropyl, 2,2,2-trifluoroethyl, and 2-(methylsulfonyl)ethyl. 27. A method of claim 24, wherein R.sup.7 is C.sub.1-6aralkyl. 28. A method of claim 27, wherein R.sup.7 is selected from 2-phenylethyl, phenylmethyl, (4-methoxyphenyl)methyl, (4-chlorophenyl)methyl, and (4-fluorophenyl)methyl. 29. A method of claim 24, wherein R.sup.6 is C.sub.1-6alkyl and R.sup.7 is aryl. 30. A method of claim 29, wherein R.sup.7 is substituted or unsubstituted phenyl. 31. A method of claim 23, wherein Q is absent or O and R.sup.7 is carbocyclylM-. 32. A method of claim 31, wherein carbocyclyl is cyclopropyl or cyclohexyl. 33. A method of claim 24, wherein R.sup.7 is selected from R.sup.8ZA-C.sub.1-8alkyl-, R.sup.11Z-C.sub.1-8alkyl-, (R.sup.8O)(R.sup.9O)P(.dbd.O)O--C.sub.1-8alkyl-ZAZ-C.sub.1-8alkyl-, (R.sup.8O)(R.sup.9O)P(.dbd.O)O--C.sub.1-8alkyl-Z-C.sub.1-8alkyl-, R.sup.8ZA-C.sub.1-8alkyl-ZAZ-C.sub.1-8alkyl-, heterocyclylMZAZ-C.sub.1-8alkyl-, (R.sup.8O)(R.sup.9O)P(.dbd.O)O--C.sub.1-8alkyl-, A is C.dbd.O, and Z is O or NH. 34. A method of claim 33, wherein Z is O. 35. A method of claim 34, wherein R.sup.7 is heterocyclylMZAZ-C.sub.1-8alkyl- and heterocyclyl is oxodioxolenyl or N(R.sup.12)(R.sup.13), wherein R.sup.12 and R.sup.13 together are C.sub.1-6alkyl-Y--C.sub.1-6alkyl, thereby forming a ring. 36. A method of claim 35, wherein R.sup.7 is selected from (R.sup.10).sub.2N--C.sub.1-8alkyl- and (R.sup.10).sub.3N.sup.+(CH.sub.2).sub.n--, and R.sup.10 is C.sub.1-6alkyl. 37. A method of claim 24, wherein R7 is heterocyclyiM- and heterocyclyl is selected from morpholino, piperidino, piperazino, and pyrrolidino. 38. A method of claim 23, wherein Q is O or NH. 39. A method of claim 38, wherein R.sup.6 is C.sub.1-6alkyl and R.sup.7 is selected from C.sub.1-6alkyl, C.sub.1-6aralkyl, and C.sub.1-6heteroaralkyl. 40. A method of claim 39, wherein R.sup.7 is selected from methyl, ethyl, isopropyl, phenylmethyl, and (4-pyridyl)methyl. 41. A method of claim 23, wherein R.sup.6 and R.sup.7 together are C.sub.1-6alkyl-Y--C.sub.1-6alkyl, C.sub.1-6alkyl-ZA-C.sub.1-6alkyl, or C.sub.1-6alkyl-A, thereby forming a ring. 42. A method e of claim 41, wherein L is C.dbd.O, Q and Y are absent, and R.sup.6 and R.sup.7 together are C.sub.1-3alkyl-Y--C.sub.1-3alkyl. 43. A method of claim 1, wherein L and Q are absent, and R.sup.6 and R.sup.7 together are C.sub.1-3alkyl-Y--C.sub.1-3alkyl. 44. A method of claim 41, wherein L is C.dbd.O, Q is absent, Y is selected from NH and N--C.sub.1-6alkyl, and R.sup.6 and R.sup.7 together are C.sub.1-3alkyl-Y--C.sub.1-3alkyl. 45. A method of claim 41, wherein L is C.dbd.O, Y is absent and R.sup.6 and R.sup.7 together are C.sub.1-3alkyl-Y--C.sub.1-3alkyl. 46. A method of claim 41, wherein L and A are C.dbd.O and R.sup.6 and R.sup.7 together are C.sub.1-2alkyl-ZA-C.sub.1-2alkyl. 47. A method of claim 41, wherein L and A are C.dbd.O and R.sup.6 and R.sup.7 together are C.sub.2-3alkyl-A. 48. A method of treating cancer, comprising administering a compound having a structure of formula II or a pharmaceutically acceptable salt thereof, ##STR00030## wherein each A is independently selected from C.dbd.O, C.dbd.S, and SO.sub.2; or A is optionally a covalent bond when adjacent to an occurrence of Z; L is absent or is selected from C.dbd.O, C.dbd.S, and SO.sub.2; M is absent or is C.sub.1-12alkyl; Q is absent or is selected from O, NH, and N--C.sub.1-6alkyl; X is selected from O, NH, and N--C.sub.1-6alkyl; Y is absent or is selected from O, NH, N--C.sub.1-6alkyl, S, SO, SO.sub.2, CHOR.sup.10, and CHCO.sub.2R.sup.10; each Z is independently selected from O, S, NH, and N--C.sub.1-6alkyl; or Z is optionally a covalent bond when adjacent to an occurrence of A; R.sup.2 and R.sup.4 are independently selected from optionally substituted C.sub.1-6alkyl, C.sub.1-6hydroxyalkyl, and C.sub.1-6alkoxyalkyl; R.sup.5 is N(R.sup.6)LQR.sup.7; R.sup.6 is selected from hydrogen, OH, and C.sub.1-6alkyl; R.sup.7 is selected from hydrogen, C.sub.1-6alkyl, C.sub.1-6alkenyl, C.sub.1-6alkynyl, aryl, C.sub.1-6aralkyl, heteroaryl, C.sub.1-6heteroaralkyl, R.sup.8ZAZ-C.sub.1-8alkyl-, R.sup.11Z-C.sub.1-8alkyl-, (R.sup.8O)(R.sup.9O)P(.dbd.O)O--C.sub.1-8alkyl-ZAZ-C.sub.1-8alkyl-, R.sup.8ZAZ-C.sub.1-8alkyl-ZAZ-C.sub.1-8alkyl-, heterocyclylMZAZ-C.sub.1-8alkyl-, (R.sup.8O)(R.sup.9O)P(.dbd.O)O--C.sub.1-8alkyl-, (R.sup.10).sub.2N-C.sub.1-12alkyl-, (R.sup.10).sub.3N+--C.sub.1-12alkyl-, heterocyclylM-, carbocyclylM-, R.sup.11SO.sub.2C.sub.1-8alkyl-, and R.sup.11SO.sub.2NH; or R.sup.6 and R.sup.7 together are C.sub.1-6alkyl-Y--C.sub.1-6alkyl, C.sub.1-6alkyl-ZAZ-C.sub.1-6alkyl, ZAZ-C.sub.1-6alkyl-ZAZ-C.sub.1-6alkyl, ZAZ-C.sub.1 6alkyl-ZAZ, or C.sub.1-6alkyl-A; R.sup.8 and R.sup.9 are independently selected from hydrogen, metal cation, C.sub.1-6alkyl, C.sub.1-6alkenyl, C.sub.1-6alkynyl, aryl, heteroaryl, C.sub.1-6aralkyl, and C.sub.1-6heteroaralkyl, or R.sup.8 and R.sup.9 together are C.sub.1-6alkyl, thereby forming a ring; each R.sup.10 is independently selected from hydrogen and C.sub.1-6alkyl; and R.sup.11 is independently selected from hydrogen, C.sub.1-6alkyl, C.sub.1-6alkenyl, C.sub.1-6alkynyl, carbocyclyl, heterocyclyl, aryl, heteroaryl, C.sub.1-6aralkyl, and C.sub.1-6heteroaralkyl, provided that when R.sup.6 is H or CH.sub.3 and Q is absent, LR.sup.7 is not hydrogen, unsubstituted C.sub.1-6alkylC.dbd.O, a further chain of amino acids, t-butoxycarbonyl (Boc), benzoyl (Bz), fluoren-9-ylmethoxycarbonyl (Fmoc), triphenylmethyl(trityl), benzyloxycarbonyl (Cbz), trichloroethoxycarbonyl (Troc); or substituted or unsubstituted aryl or heteroaryl; and in any occurrence of the sequence ZAZ, at least one member of the sequence must be other than a covalent bond.