Protein kinase conjugates and inhibitors

• US 9,556,426 B2
• Filed: 09/15/2010
• Issued: 01/31/2017
• Est. Priority Date: 09/16/2009
• Status: Active Grant

• Current Assignee: Celgene Car LLC (Bristol-Myers Squibb Company)
• Original Assignee: Celgene Avilomics Research Inc. (Bristol-Myers Squibb Company)
• Inventors: Singh, Juswinder, Petter, Russell Colyn, Niu, Deqiang, Qiao, Lixin, Kluge, Arthur, Lobb, Roy, Ghosh, Shomir, Zhu, Zhendong
• Primary Examiner(s): Steele, Amber D
• Application Number:
  US12/882,484
• Publication Number:
  US 20110117073A1
• Time in Patent Office: 2,330 Days
• US Class Current: 1/1
• CPC Class Codes: A61K 47/545 Heterocyclic compounds A61K47/558 takes precedence
• CPC Class Codes: A61K 47/62 the modifying agent being a protein, peptide or polyamino acid
• CPC Class Codes: A61P 11/06 Antiasthmatics
• CPC Class Codes: A61P 17/06 Antipsoriatics
• CPC Class Codes: A61P 19/00 Drugs for skeletal disorders
• CPC Class Codes: A61P 25/28 for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• CPC Class Codes: A61P 27/02 Ophthalmic agents
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/02 Immunomodulators
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: A61P 9/00 Drugs for disorders of the cardiovascular system
• CPC Class Codes: C07D 213/72 Nitrogen atoms nitro radicals C07D213/61
• CPC Class Codes: C07D 213/74 Amino or imino radicals substituted by hydrocarbon or substituted hydrocarbon radicals
• CPC Class Codes: C07D 213/81 Amides; Imides
• CPC Class Codes: C07D 213/82 in position 3
• CPC Class Codes: C07D 215/22 attached in position 2 or 4
• CPC Class Codes: C07D 231/12 with only hydrogen atoms, hydrocarbon or substituted hydrocarbon radicals, directly attached to ring carbon atoms
• CPC Class Codes: C07D 239/42 One nitrogen atom nitro radicals C07D239/30
• CPC Class Codes: C07D 239/48 Two nitrogen atoms
• CPC Class Codes: C07D 333/68 Carbon atoms having three bonds to hetero atoms with at the most one bond to halogen
• CPC Class Codes: C07D 401/12 : linked by a chain containing hetero atoms as chain links
• CPC Class Codes: C07D 401/14 : containing three or more hetero rings
• CPC Class Codes: C07D 403/04 : directly linked by a ring-member-to-ring-member bond
• CPC Class Codes: C07D 403/06 : linked by a carbon chain containing only aliphatic carbon atoms
• CPC Class Codes: C07D 403/12 : linked by a chain containing hetero atoms as chain links
• CPC Class Codes: C07D 403/14 : containing three or more hetero rings
• CPC Class Codes: C07D 409/04 : directly linked by a ring-member-to-ring-member bond
• CPC Class Codes: C07D 409/12 : linked by a chain containing hetero atoms as chain links
• CPC Class Codes: C07D 409/14 : containing three or more hetero rings
• CPC Class Codes: C07D 413/12 : linked by a chain containing hetero atoms as chain links
• CPC Class Codes: C07D 413/14 : containing three or more hetero rings
• CPC Class Codes: C07D 417/12 : linked by a chain containing hetero atoms as chain links
• CPC Class Codes: C07D 417/14 : containing three or more hetero rings
• CPC Class Codes: C07D 471/04 : Ortho-condensed systems
• CPC Class Codes: C07D 471/10 : Spiro-condensed systems
• CPC Class Codes: C07D 487/04 : Ortho-condensed systems
• CPC Class Codes: C07D 495/04 : Ortho-condensed systems
• CPC Class Codes: C07D 498/04 : Ortho-condensed systems
• CPC Class Codes: C12N 9/1205 : Phosphotransferases with an alcohol group as acceptor (2.7.1), e.g. protein kinases
• CPC Class Codes: C12N 9/96 : Stabilising an enzyme by forming an adduct or a composition; Forming enzyme conjugates

Abstract

The invention relates to protein conjugates that contain a protein kinase containing a cysteine residue in the ATP binding site and an inhibitor that is covalently and irreversibly bonded to said cysteine residue, such that the activity of the protein kinase is irreversibly inhibited. The invention also relates to compounds that irreversibly inhibit protein kinases.

Claims

1. A protein kinase conjugate that has the formula,

X—

M—

S—

CH₂-Prot

wherein, Prot is a human protein kinase or portion thereof comprising a cysteine residue containing amino acid sequence selected from the group consisting of SEQ ID NOs;

1, 6, 7, 8, 9, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, and 45;

S—

CH₂ is the sulfur atom and methylene group from the side chain of said cysteine residue;

M is a modifier moiety that is formed by the covalent bonding of a warhead group with the side chain of said cysteine residue;

X is a chemical moiety that binds in or near the ATP binding site of the protein kinase; and

wherein the protein kinase conjugate is formed in association with a cell.

2. The conjugate of claim 1, wherein the warhead group is -L-Y, wherein

L is a covalent bond or a bivalent C_1-8 saturated or unsaturated, straight or branched, hydrocarbon chain, wherein one, two, or three methylene units of L are optionally and independently replaced by cyclopropylene, —

NR—

, —

N(R)C(O)—

, —

C(O)N(R)—

, —

N(R)SO₂—

, —

SO₂N(R)—

, —

O—

, —

C(O)—

, —

OC(O)—

, —

CH(OH)—

, —

C(O)O—

, —

S—

, —

SO—

, —

SO₂—

, —

C(═

S)—

, —

C(═

NR)—

, —

N═

N—

, or —

C(═

N₂)—

;

Y is hydrogen, nitrile, C_1-6 aliphatic optionally substituted with one or more OH, NRxRy, oxo, halogen, NO₂, or CN, or a 3-10 membered monocyclic or bicyclic, saturated, partially unsaturated, or aryl ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and wherein said ring is substituted with 1-4 R^e groups; and

R, Rx and Ry are independently hydrogen, lower alkyl, lower haloalkyl, or lower cycloalkyl;

each R^e is independently selected from -Q-Z, OH, oxo, NO₂, halogen, CN, a suitable leaving group, or a C_1-6 aliphatic optionally substituted with oxo, halogen, NO₂, or CN, wherein;

Q is a covalent bond or a bivalent C_1-6 saturated or unsaturated, straight or branched, hydrocarbon chain, wherein one or two methylene units of Q are optionally and independently replaced by —

N(R)—

, —

S—

, —

O—

, —

C(O)—

, —

OC(O)—

, —

C(O)O—

, —

SO—

, or —

SO₂—

, —

N(R)C(O)—

, —

C(O)N(R)—

, —

N(R)SO₂—

, or —

SO₂N(R)—

; and

Z is hydrogen or C_1-6 aliphatic optionally substituted with oxo, halogen, NO₂, or CN.

3. The conjugate of claim 1, wherein the warhead group is

4. The conjugate of claim 1, wherein the modifier moiety taken together with the side chain Sulfur and methylene of the cysteine residue have a formula selected from the group consisting of

5. The conjugate of claim 1, wherein Prot is a kinase or portion of a kinase comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:

1, 6, 7, 8, and 9.

6. The conjugate of claim 1, wherein Prot is a kinase selected from the group consisting of JAK3, C-KIT, FAK2, FLT3, FES, CDKL4, or wherein Prot is a portion of JAK3 wherein the portion of JAK3 comprises the amino acid sequence of SEQ ID NO:

1, a portion of C-KIT wherein the portion of C-KIT comprises the amino acid sequence of SEQ ID NO;

41, a portion of FAK2 wherein the portion of FAK2 comprises the amino acid sequence of SEQ ID NO;

6, a portion of FLT3 wherein the portion of FLT3 comprises the amino acid sequence of SEQ ID NO;

7 or 41, a portion of FES wherein the portion of FES comprises the amino acid sequence of SEQ ID NO;

8, or a portion of CDKL4 wherein the portion of CDLK4 comprises the amino acid sequence of SEQ ID NO;

9.

7. The conjugate of claim 1, wherein Prot is a kinase or portion of a kinase comprising a cysteine residue containing amino acid sequence selected from the group consisting of SEQ ID NOs:

26, 27, 28 and 29.

8. The conjugate of claim 1, wherein Prot is a kinase selected from the group consisting of PFTAIRE1, JNK1, JNK2, JNK3, BMPR2, or wherein Prot is a portion of PFTAIRE1 wherein the portion of PFTAIRE1 comprises the amino acid sequence of SEQ ID NO:

26, a portion of JNK1 wherein the portion of JNK1 comprises the amino acid sequence of SEQ ID NO;

28, a portion of JNK2 wherein the portion of JNK2 comprises the amino acid sequence of SEQ ID NO;

27, a portion of JNK3 wherein the portion of JNK3 comprises the amino acid sequence of SEQ ID NO;

28, or a portion of BMPR2 wherein the portion of BMPR2 comprises the amino acid sequence of SEQ ID NO;

29.

9. The conjugate of claim 1, wherein Prot is a kinase or portion of a kinase comprising a cysteine residue containing amino acid sequence selected from the group consisting of SEQ ID NOs:

30, 31, 32 and 33.

10. The conjugate of claim 1, wherein Prot is a kinase selected from the group consisting of TNK1, YES, FGR, SRC, LIMK1, or wherein Prot is a portion of TNK1 wherein the portion of TNK1 comprises the amino acid sequence of SEQ ID NO:

30, a portion of YES wherein the portion of YES comprises the amino acid sequence of SEQ ID NO;

31, a portion of FOR wherein the portion of FOR comprises the amino acid sequence of SEQ ID NO;

32, a portion of SRC wherein the portion of SRC comprises the amino acid sequence of SEQ ID NO;

31, or a portion of LIMK1 wherein the portion of LIMK1 comprises the amino acid sequence of SEQ ID NO;

33.

11. The conjugate of claim 1, wherein Prot is a kinase or portion of a kinase comprising a cysteine residue containing amino acid sequence selected from the group consisting of SEQ ID NOs:

35, 36 and 37.

12. The conjugate of claim 1, wherein Prot is a kinase selected from the group consisting of FAK, ALK1, ALK2, or wherein Prot is a portion of FAK wherein the portion of FAK comprises the amino acid sequence of SEQ ID NO:

35, a portion of ALK1 wherein the portion of ALK1 comprises the amino acid sequence of SEQ ID NO;

36, a portion of ALK2 wherein the portion of ALK2 comprises the amino acid sequence of SEQ ID NO;

37.

13. The conjugate of claim 1, wherein Prot is a kinase or portion of a kinase comprising a cysteine residue containing amino acid sequence selected from the group consisting of SEQ ID NOs:

38, 39 and 40.

14. The conjugate of claim 1, wherein Prot is a kinase selected from the group consisting of ZAP70, CRIK, ERK3, CK1g1, CK1g2, CK1g3, or wherein Prot is a portion of ZAP70 wherein the portion of ZAP70 comprises the amino acid sequence of SEQ ID NO:

38, a portion of CRIK wherein the portion of CRIK comprises the amino acid sequence of SEQ ID NO;

39, a portion of ERK3 wherein the portion of ERK3 comprises the amino acid sequence of SEQ ID NO;

40, a portion of CK1g1 wherein the portion of CK1g1 comprises the amino acid sequence of SEQ ID NO;

38, or a portion of CK1g2 wherein the portion of CK1g2 comprises the amino acid sequence of SEQ ID NO;

38, or a portion of CK1g3 wherein the portion of CK1g3 comprises the amino acid sequence of SEQ ID NO;

38.

15. The conjugate of claim 1, wherein Prot is a kinase or portion of a kinase comprising a cysteine residue containing amino acid sequence selected from the group consisting of SEQ ID NOs:

41, 42, and 43.

16. The conjugate of claim 1, wherein Prot is a kinase selected from the group consisting of FMS, RON, FGR, or wherein Prot is a portion of FMS wherein the portion of FMS comprises the amino acid sequence of SEQ ID NO:

41, a portion of RON wherein the portion of RON comprises the amino acid sequence of SEQ ID NO;

42, or a portion of FGR wherein the portion of FGR comprises the amino acid sequence of SEQ ID NO;

43.

17. The conjugate of claim 1, wherein Prot is a kinase or portion of a kinase comprising a cysteine residue containing amino acid sequence of SEQ ID NO:

44.

18. The conjugate of claim 1, wherein Prot is ALK or a portion thereof that comprises a cystein residue containing amino acid sequence of SEQ ID NO:

44.

19. The conjugate of claim 1, wherein Prot is a kinase or portion of a kinase comprising a cysteine residue containing amino acid sequence of SEQ ID NO:

45.

20. The conjugate of claim 1, wherein Prot is B-RAF or a portion thereof that comprises a cysteine residue containing amino acid sequence of SEQ ID NO:

45.

21. The conjugate of claim 1, wherein, if the protein kinase is JAK3, the cysteine residue is Cys945.

22. The conjugate of claim 1, wherein Prot is C-KIT or a portion thereof, wherein the C-KIT or a portion thereof comprises the amino acid sequence SEQ ID NO:

41.

23. The conjugate of claim 6, wherein Prot is C-KIT or a portion thereof, wherein the C-KIT or a portion thereof comprises the amino acid sequence SEQ ID NO:

41.

24. The conjugate of claim 6, wherein Prot comprises the amino acid sequence SEQ ID NO:

41.

25. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

1.

26. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

6.

27. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

7.

28. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

8.

29. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

9.

30. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

26.

31. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

27.

32. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

28.

33. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

29.

34. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

30.

35. The conjugate of claim 1. wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

31.

36. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

32.

37. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

33.

38. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

35.

39. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

36.

40. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

37.

41. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

38.

42. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

39.

43. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

40.

44. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

41.

45. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

42.

46. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

43.

47. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

44.

48. The conjugate of claim 1, wherein the cysteine residue containing amino acid sequence is SEQ ID NO:

45.