Selective serine/threonine kinase inhibitors

• US 20070082884A1
• Filed: 04/12/2004
• Published: 04/12/2007
• Est. Priority Date: 04/11/2003
• Status: Active Grant

• Current Assignee: Regents of the University of California (University of California)
• Original Assignee: Regents of the University of California (University of California)
• Inventors: Zhang, Chao, Taunton, Jack, Shokat, Kevan, Cohen, Michael
• Granted Patent: US 7,687,506 B2
• Time in Patent Office: Days
• US Class Current: 514/212.70
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07D 487/04 Ortho-condensed systems

Abstract

Inhibition of protein kinases having one or more cysteine residues within the ATP binding site is effected by contacting the kinase, per se or in a cell or subject, with an inhibitory-effective amount of a compound having a heterocyclic core structure comprised of two or more fused rings containing at least one nitrogen ring atom, and an electrophilic substituent that is capable of reacting with a cysteine residue within the ATP binding site of a kinase. Preferred compounds include certain pyrrolopyrimidines and oxindoles having such an electrophilic substituent and optionally an aromatic or heteroaromatic substituent that is capable of interacting with a threonine or smaller residue located in the gatekeeper position of the kinase. Kinases lacking such cysteine residues may be engineered or modified so that they are capable of being inhibited by such compounds by replacing a valine or other amino acid residue within the ATP binding site by a cysteine residue.

Claims

1. A pyrrolopyrimidine compound having an electrophilic substituent that is capable of forming a covalent bond with a cysteine residue within the ATP binding site of a kinase, exclusive of the compound 5-(4-phenoxyphenyl)-6-cyano-7-cyclopentyl-4-aminopyrrolo[2,3-d]pyrimidine.

61. A therapeutic composition comprising (a) a kinase inhibitory-effective amount of a composition according to any of claims 1-46 and a pharmaceutically acceptable carrier.

62. A composition for inhibiting kinase activity comprising an effective inhibitory amount of a compound according to any of claims 1-46.

63. A composition according to claim 62 for inhibiting activity of a kinase selected from the group consisting of Rsk1,2,3,4, Msk1-2, Plk1-3, MEKK1, and Nek2.

2. A compound having the formula (I):

4. A compound according to claim 2 or 3 in which E is an electrophilic group that comprises a carbonyl, an epoxide, or an olefin conjugated to an electron withdrawing group.

5. A compound according to claim 2 or 3 in which R² is hydrogen.

6. A compound according to claim 2 or 3 in which R² is a group having the formula (CH₂)_bR^b.

7. A compound according to claim 6 in which b is 0.

8. A compound according to claim 7 in which R² is an optionally substituted phenyl group.

9. A compound according to claims 2 or 3 in which E comprises a carbonyl, an epoxide, or an olefin conjugated to an electron withdrawing group.

10. A compound according to claim 9 in which E comprises an olefin conjugated to a carbonyl, nitro, cyano, carboxyl, carboxamide, sulfoxide, sulfonyl, sulfonamide, or sulfonate group.

11. A compound according to claims 2 or 3 in which E comprises a carbonyl group.

12. A compound according to claim 11 in which the carbonyl group has the formula —

C(O)(CH₂)_nR in which R is a halogen and n is 0 or an integer from 1 to 6.

13. A compound according to claim 12 in which n is 0.

14. A compound according to claim 12 in which n is 1.

15. A compound according to claim 11 in which the carbonyl group has the formula —

(CH₂)_mC(O)R in which m is 0 or an integer from 1 to 6 and R is a halogen.

16. A compound according to claim 15 in which m is 0.

17. A compound according to claim 15 in which m is 1.

18. A compound according to any of claims 12-17 in which R is chloro.

19. A compound according to any of claims 12-17 in which R is fluoro.

20. A compound according to claim 11 in which the carbonyl group comprises an olefinically unsaturated ketone.

21. A compound according to claim 20 in which the carbonyl group is —

C(O)CH═

CH₂.

22. A compound according to claims 2 or 3 in which E is an olefin carboxylate having the formula CH═

CHC(O)OR′

where R′

is an optionally substituted aliphatic, aromatic, or heterocyclic moiety.

23. A compound according to claim 22 in which R′

is methyl.

24. A compound according to claims 2 or 3 in which E is an olefin carboxamide having the formula —

CH═

C(O)NR″

R′

″

where R″ and

R′

″

are optionally substituted aliphatic, aromatic, or heterocyclic moieties.

25. A compound according to claims 2 or 3 in which E comprises an epoxide.

48. A method of inhibiting a protein kinase that has one or more cysteine residues within its ATP binding site, comprising contacting the kinase with an inhibitory-effective amount of a compound according to claim 2.

56. A method according to claim 54 in which the compound is a compound according to claim 2.

3. A compound having the formula (IA):

49. A method of inhibiting a protein kinase that has one or more cysteine residues within its ATP binding site, comprising contacting the kinase with an inhibitory-effective amount of a compound according to claim 3.

57. A method according to claim 54 in which the compound is a compound according to claim 3.

26. A compound having the formula (II):

30. A compound according to any of claims 26-29 in which E comprises a carbonyl, an epoxide, or an olefin conjugated to an electron withdrawing group.

31. A compound according to any of claims 26-29 in which E comprises an olefin conjugated to a carbonyl, nitro, cyano, carboxyl, carboxamide, sulfoxide, sulfonyl, sulfonamide, or sulfonate group.

32. A compound according to any of claims 26-29 in which E comprises a carbonyl group.

33. A compound according to claim 32 in which the carbonyl group has the formula —

C(O)(CH₂)_nR in which R is a halogen and n is 0 or an integer from 1 to 6.

34. A compound according to claim 33 in which n is 0.

35. A compound according to claim 33 in which n is 1.

36. A compound according to claim 32 in which the carbonyl group has the formula —

(CH₂)_mC(O)R in which m is 0 or an integer from 1 to 6 and R is a halogen.

37. A compound according to claim 36 in which m is 0.

38. A compound according to claim 36 in which m is 1.

39. A compound according to any of claims 33-38 in which R is chloro.

40. A compound according to any of claims 33-38 in which R is fluoro.

41. A compound according to claim 32 in which the carbonyl group comprises an olefinically unsaturated ketone.

42. A compound according to claim 41 in which the carbonyl group is —

C(O)CH═

CH₂.

43. A compound according to any of claims 26-29 in which E is an olefin carboxylate having the formula CH═

CHC(O)OR′

where R′

is an optionally substituted aliphatic, aromatic, or heterocyclic moiety.

44. A compound according to claim 43 in which R′

is methyl.

45. A compound according to any of claims 26-29 in which E is an olefin carboxamide having the formula —

CH═

C(O)NR″

R′

″

where R″ and

R′

″

are optionally substituted aliphatic, aromatic, or heterocyclic moieties.

46. A compound according to any of claims 26-29 in which E comprises an epoxide.

58. A method according to claim 54 in which the compound is a compound according to any of claims 26-29.

27. A compound having the formula (III):

28. A compound having the formula (IV):

29. A compound having the formula (V):

47. A method of inhibiting a protein kinase that has one or more cysteine residues within its ATP binding site, comprising contacting the kinase with an inhibitory-effective amount of a compound having a heterocyclic core structure comprised of two or more fused rings containing at least one nitrogen ring atom, and an electrophilic substituent that is capable of forming a covalent bond with a cysteine residue within the ATP binding site of a kinase.

50. A method of inhibiting a protein kinase that has one or more cysteine residues within its ATP binding site, comprising contacting the kinase with an inhibitory-effective amount of a compound having the formula (II), (III), (IV) or (V):

51. A method of imparting to a protein kinase the capability of being inhibited by a compound having a heterocyclic core structure comprised of two or more fused rings containing at least one nitrogen ring atom, and an electrophilic substituent that is capable of reacting with a cysteine residue within the ATP binding site of a kinase, comprising replacing an amino acid residue other than a cysteine residue within the ATP binding site of the protein kinase with a cysteine residue.

52. A method of imparting to a protein kinase the capability of being inhibited by a compound having a heterocyclic core structure comprised of two or more fused rings containing at least one nitrogen ring atom, and an electrophilic substituent that is capable of forming a covalent bond with a cysteine residue within the ATP binding site of a kinase, comprising replacing a methionine, leucine, isoleucine, lysine, arginine, tryptophan, glutamine, asparagine, proline, tyrosine, histidine, glutamic acid, aspartic acid, valine, or phenylalanine residue in the gatekeeper position of the ATP binding site with a smaller residue.

53. A method for inhibiting the morphological transformation of a cell in which such a kinase is expressed comprising contacting the cell or the kinase with an inhibitory-effective amount of a compound having a heterocyclic core structure comprised of two or more fused rings containing at least one nitrogen ring atom, and an electrophilic substituent that is capable of forming a covalent bond with a cysteine residue within the ATP binding site of a kinase.

54. A method for inhibiting the proliferation of a tumor cell comprising contacting the cell with an inhibitory-effective amount of a compound having a heterocyclic core structure comprised of two or more fused rings containing at least one nitrogen ring atom, and an electrophilic substituent that is capable of forming a covalent bond with a cysteine residue within the ATP binding site of a kinase.

55. A method according to claim 54 in which the compound is a pyrrolopyrimidine.

59. A method according to claim 54 in which the cell is contacted with an inhibitory-effective amount of a plurality of such compounds.

60. An array for testing for inhibition of protein kinase activity comprising one or a plurality of compounds having a heterocyclic core structure comprised of two or more fused rings containing at least one nitrogen ring atom, and an electrophilic substituent that is capable of forming a covalent bond with a cysteine residue within the ATP binding site of a kinase.