Small molecule inhibitors of caspases

1. A compound having the structure (I):

and pharmaceutically acceptable derivatives thereof,

wherein R 1 is H, an aliphatic, heteroaliphatic, aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl moiety;

n is 0 or 1;

A is CR A , C(R A ) 2 , C═O, S, NR A , N(R A ) 2 , or O;

B is CR B , C(R B ) 2 , C═O, S, NR B , N(R B ) 2 , or O;

D is CR D , C(R D ) 2 , C═O, S, NR D , N(R D ) 2 , or O;

E is CR E , C(R E ) 2 , C═O, S, NR E , N(R E ) 2 , or O;

G is CR G , C(R G ) 2 , C═O, S, NR G , N(R G ) 2 , or O;

J is CR J ;

each of A—B, B—D, D—E, E—G, G—J and A—J are connected by a single or double bond as valency and stability permits;

each occurrence of R A , R B , R D , R E , R G and R J is independently hydrogen, halogen, —OR 2 , —N(R 2 ) 2 , —SR 2 , —CN, —COOR 2 , —COR 2 , —CON(R 2 ) 2 , —SOR 2 , —SO 2 R 2 , —SO 2 N(R 2 ) 2 , —NR 2 SO 2 R 2 , —O(C═O)N(R 2 ) 2 , —NR 2 (C═O)N(R 2 ) 2 , —NR 2 (C═S)N(R 2 ) 2 , —NR 2 SO 2 N(R 2 ) 2 , or an aliphatic, heteroaliphatic, aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl moiety optionally independently substituted with one or more occurrences of R 2 , wherein each occurrence of R 2 is independently hydrogen, halogen, —OR 3 , —N(R 3 ) 2 , —SR 3 , —CN, —COOR 3 , —COR 3 , —CON(R 3 ) 2 , —SOR 3 , —SO 2 R 3 , —SO 2 N(R 3 ) 2 , —NR 3 SO 2 R 3 , —O(C═O)N(R 3 ) 2 , —NR 3 (C═O)N(R 3 ) 2 , —NR 3 (C═S)N(R 3 ) 2 , —NR 3 SO 2 N(R 3 ) 2 , or an aliphatic, heteroaliphatic, aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl moiety;

wherein each occurrence of R 3 is independently hydrogen, or an aliphatic, heteroaliphatic, aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl moiety,

and wherein at least one of R B or R D comprises —SR 2 , —SOR 2 , —SO 2 R 2 , —SO 2 N(R 2 ) 2 , —NR 2 SO 2 R 2 , —N(R 2 ) 2 , —(C═O)N(R 2 ) 2 , —NR 2 (C═O)R 2 , —O(C═O)N(R 2 ) 2 , —NR 2 (C═O)N(R 2 ) 2 , —NR 2 (C═S)N(R 2 ) 2 , —NR 2 SO 2 N(R 2 ) 2 , or is an alkyl or heteroalkyl group substituted with one or more occurrences of R 2 , wherein R 2 is —SR 3 , —SOR 3 , —SO 2 R 3 , —SO 2 N(R 3 ) 2 , —NR 3 SO 2 R 3 , —N(R 3 ) 2 , —(C═O)N(R 3 ) 2 , —NR 3 (C═O)R 3 , —O(C═O)N(R 3 ) 2 , —NR 3 (C═O)N(R 3 ) 2 , —NR 3 (C═S)N(R 3 ) 2 , —NR 3 SO 2 N(R 3 ) 2 , wherein R 3 is an aliphatic, heteroaliphatic, aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl moiety,

whereby each of the foregoing aliphatic, heteroaliphatic, alkyl and heteroalkyl moieties may be independently substituted or unsubstituted, cyclic or acyclic, linear or branched, and each of the foregoing aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl and heteroalkylheteroaryl moieties may be independently substituted or unsubstituted.

2. The compound of claim 1 , having one or more of the following limitations:

a) R 1 is not CH 2 X, if X is F or Cl;

b) if

 represents pyridyl, then R D is —SR 2 , —SOR 2 , —SO 2 R 2 , —SO 2 N(R 2 ) 2 , —NR 2 SO 2 R 2 , —NR 2 SO 2 N(R 2 ) 2 ; or R D is an alkyl or heteroalkyl group substituted with one or more occurrences of R 2 , wherein R 2 is —SR 3 , —SOR 3 , —SO 2 R 3 , —SO 2 N(R 3 ) 2 , —NR 3 SO 2 R 3 , —N(R 3 ) 2 , —(C═O)N(R 3 ) 2 , —NR 3 (C═O)R 3 , —O(C═O)N(R 3 ) 2 , —NR 3 (C═O)N(R 3 ) 2 , —NR 3 (C═S)N(R 3 ) 2 , —NR 3 SO 2 N(R 3 ) 2 , wherein each occurrence of R 3 is independently an aliphatic, heteroaliphatic, aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl moiety; or

c) if

 represents isoxazole, then R B or R D is not a group —CR X R Y NHR 3 , wherein at least one of R X or R Y is a group other than hydrogen.

3. The compound of claim 1 , wherein

is an aryl or heteroaryl moiety.

4. The compound of claim 1 , wherein

is an aryl or heteroaryl moiety having one of the structures:

wherein R A —R G are as defined in claim 1 .

5. The compound of claim 1 , wherein the compound has the structure:

wherein R 1 and R A —R G are as defined in claim 1 .

6. The compound of claim 1 , wherein the compound has the structure:

wherein R 1 , R A , R B and R D are as defined in claim 1 .

7. The compound of any one of claims 4 - 6 , wherein one of R B or R D is

—(C 0-3 alkyl)NR 3 —SO 2 —(C 0-3 alkyl)R 4 ;

—(C 0-3 alkyl)SO 2 —NR 3 —(C 0-3 alkyl)R 4 ;

—(C 0-3 alkyl)NR 3 (C 0-3 alkyl)R 4 ;

—(C 0-3 alkyl)CONR 3 (C 0-3 alkyl)R 4 ;

—(C 0-3 alkyl)OCONR 3 (C 0-3 alkyl)R 4 ;

—(C 0-3 alkyl)NR 3 CONR 3 (C 0-3 alkyl)R 4 ;

—(C 0-3 alkyl)NR 3 (C═S)NR 3 (C 0-3 alkyl)R 4 ;

—(C 0-3 alkyl)NR 3 SO 2 NR 3 (C 0-3 alkyl)R 4 ,

wherein each of the alkyl groups is independently substituted or unsubstituted, cyclic or acyclic, linear or branched, and wherein each occurrence of R 3 and R 4 is independently hydrogen or a substituted or unsubstituted alkyl, heteroalkyl, aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl moiety.

8. The compound of any one of claims 4 - 6 , wherein one of R B or R D is

wherein each occurrence of R X and R Y is independently hydrogen or lower alkyl; each occurrence of R 3a is independently hydrogen, lower alkyl or lower acyl; and each occurrence of R 3b and R 4 is independently a substituted or unsubstituted aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl moiety.

9. The compound of any one of claims 4 - 6 , wherein one of R B or R D is one of the structures:

wherein each occurrence of R X and R Y i s independently hydrogen or lower alkyl; and each occurrence of R 3 and R 4 is independently a substituted or unsubstituted aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl moiety.

10. The compound of any one of claims 4 - 6 , wherein R 1 is hydrogen or a substituted or unsubstituted aryl, heteroaryl, alkylaryl, heteroalkylaryl, alkylheteroaryl, or heteroalkylheteroaryl moiety.

11. The compound of any one of claims 4 - 6 , wherein R 1 is hydrogen or

wherein R 5 is substituted or unsubstituted aryl, heteroaryl, alkyl or heteroalkyl; and m, p and q are each independently an integer from 0-6.

12. The compound of any one of claims 4 - 6 , wherein R 1 is hydrogen or

wherein R 5 is substituted or unsubstituted aryl, heteroaryl, alkyl or heteroalkyl; wherein the aryl, heteroaryl, alkyl or heteroalkyl group may be substituted with one or more occurrences of hydrogen, halogen, hydroxyl, lower alkoxy and/or lower alkyl; and m, p and q are each independently an integer from 0-6.

13. The compound of any one of claims 4 - 6 , wherein R 1 is hydrogen or

wherein R 6a and R 6b are each independently hydrogen, halogen, hydroxyl, lower alkoxy, or lower alkyl.

14. The compound of any one of claims 4 - 6 , wherein R 1 is hydrogen or

wherein R 6a is hydrogen and R 6b is halogen.

15. The compound of any one of claims 4 - 6 , wherein R 1 is hydrogen or

wherein R 6a is hydrogen and R 6b is Cl.

16. The compound of any one of claims 4 - 6 , wherein each occurrence of R 3 and R 4 is independently a substituted or unsubstituted aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl moiety.

17. The compound of any one of claims 4 - 6 , wherein each occurrence of R 3 and R 4 independently comprises an aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl moiety substituted with at least —COOH.

18. The compound of any one of claims 4 - 6 , wherein each occurrence of R 3 and R 4 is independently phenyl or —(CH 2 )phenyl substituted with —COOH (or an ester or bioisostere thereof) and optionally further substituted with one or more of hydroxyl, alkoxy, thio, thioalkyl, —COOH, —COO(alkyl), —CONH 2 , —NH(CO)alkyl, —SO 2 R 4a , lower alkyl, lower heteroalkyl, aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl, or heteroalkylheteroaryl, or wherein two adjacent groups taken together form an aryl, heteroaryl, cycloaliphatic, or heterocycloaliphatic group, wherein R 4a is acyl, or substituted or unsubstituted alkyl or aryl.

19. The compound of any one of claims 4 - 6 , wherein each occurrence of R 3 and R 4 is independently phenyl or —(CH 2 )phenyl substituted with COOH or an ester or bioisostere of COOH.

20. The compound of any one of claims 4 - 6 , wherein each occurrence of R 3 and R 4 is independently phenyl or —(CH 2 )phenyl substituted with any one of COOH, acylsulfonamide, —CONH 2 , tetrazole, or 5-oxo-1,2,4-oxadiazole.

21. The compound of any one of claims 4 - 6 , wherein one of R B or R D is —(C 0-3 alkyl)NR 3 —SO 2 —(C 0-3 alkyl)R 4 ; —(C 0-3 alkyl)SO 2 —NR 3 —(C 0-3 alkyl)R 4 ; —(C 0-3 alkyl)NR 3 (C 0-3 alkyl)R 4 ; —(C 0-3 alkyl)CONR 3 (C 0-3 alkyl)R 4 ; —(C 0-3 alkyl)OCONR 3 (C 0-3 alkyl)R 4 ; —(C 0-3 alkyl)NR 3 CONR 3 (C 0-3 alkyl)R 4 ; —(C 0-3 alkyl)NR 3 (C═S)NR 3 (C 0-3 alkyl)R 4 ; —(C 0-3 alkyl)NR 3 SO 2 NR 3 (C 0-3 alkyl)R 4 ; or subgroups defined generally above and herein, and the remaining groups R A , R E , R G , and one of R B or R D are each independently hydrogen, alkyl, alkoxy, halogen, hydroxyl, thio or thioalkyl.

22. A compound having the structure:

wherein Q is an aryl or heteroaryl moiety substituted with

 wherein R 3a is hydrogen, a nitrogen protecting group, lower alkyl or lower acyl; R 7a is hydrogen, a protecting group, lower alkyl or lower acyl; R 7b is hydrogen, a protecting group or lower alkyl; R X and R Y are independently hydrogen or lower alkyl; and R 1 is hydrogen or

 wherein R 5 is substituted or unsubstituted aryl, heteroaryl, alkyl or heteroalkyl; wherein the aryl, heteroaryl, alkyl or heteroalkyl group may be substituted with one or more occurrences of hydrogen, halogen, hydroxyl, lower alkoxy and/or lower alkyl; and m, p and q are each independently an integer from 0-6.

23. The compound of claim 22 , wherein Q is an aryl or heteroaryl moiety having one of the structures:

wherein R A —R G are as defined in claim 1 , and one of R A —R G is

 wherein R 3a is hydrogen, a nitrogen protecting group, lower alkyl or lower acyl; R 7a is hydrogen, a protecting group, lower alkyl or lower acyl; R 7b is hydrogen, a protecting group or lower alkyl.

24. The compound of claim 22 having the structure:

wherein Q is an aryl or heteroaryl moiety; R 3a is hydrogen, a nitrogen protecting group, lower alkyl or lower acyl; R 7a is hydrogen, a protecting group, lower alkyl or lower acyl; R 7b is hydrogen, a protecting group or lower alkyl; R X and R Y are independently hydrogen or lower alkyl; and R 1 is hydrogen or

 wherein R 5 is substituted or unsubstituted aryl, heteroaryl, alkyl or heteroalkyl; wherein the aryl, heteroaryl, alkyl or heteroalkyl group may be substituted with one or more occurrences of hydrogen, halogen, hydroxyl, lower alkoxy and/or lower alkyl; and m, p and q are each independently an integer from 0-6.

25. The compound of claim 24 having the structure:

26. The compound of claim 22 having the structure:

wherein R 3a is hydrogen, a nitrogen protecting group, lower alkyl or lower acyl; and R 7a is hydrogen, a protecting group, lower alkyl or lower acyl; R 7b is hydrogen, a protecting group or lower alkyl; R A and R B are each independently hydrogen, lower alkyl, hydroxyl, lower alkoxy, or halogen; R X and R Y are independently hydrogen or lower alkyl; and R 1 is hydrogen or

 wherein R 5 is substituted or unsubstituted aryl, heteroaryl, alkyl or heteroalkyl; wherein the aryl, heteroaryl, alkyl or heteroalkyl group may be substituted with one or more occurrences of hydrogen, halogen, hydroxyl, lower alkoxy and/or lower alkyl; and m, p and q are each independently an integer from 0-6.

27. The compound of claim 26 having the structure:

28. The compound of claim 22 having the structure:

wherein R 3a is hydrogen, a nitrogen protecting group, lower alkyl or lower acyl; and R 7a is hydrogen, a protecting group, lower alkyl or lower acyl; R 7b is hydrogen, a protecting group or lower alkyl; R A , R B , R E and R G are each independently hydrogen, lower alkyl, hydroxyl, lower alkoxy, or halogen; R X and R Y are independently hydrogen or lower alkyl; and R 1 is hydrogen or

 wherein R 5 is substituted or unsubstituted aryl, heteroaryl, alkyl or heteroalkyl; wherein the aryl, heteroaryl, alkyl or heteroalkyl group may be substituted with one or more occurrences of hydrogen, halogen, hydroxyl, lower alkoxy and/or lower alkyl; and m, p and q are each independently an integer from 0-6.

29. The compound of claim 28 having the structure:

30. The compound of any one of claims 22 - 29 wherein R 1 is hydrogen or

and R 3a is hydrogen, Me or Ac.

31. A pharmaceutical composition comprising:

a compound of any one of claims 1 - 6 , 22 , 24 , 26 or 28 ; and

a pharmaceutically acceptable carrier or diluent.

32. The pharmaceutical composition of claim 31 , wherein the compound is present in an amount effective to inhibit a caspase.

33. The pharmaceutical composition of claim 32 , wherein the caspase is caspase-3 or caspase-7.

34. The pharmaceutical composition of claim 31 , optionally further comprising an additional therapeutic agent.

35. A method for treating a caspase-mediated disorder comprising:

administering to a subject in need thereof a therapeutically effective amount of a compound of any one of claims 1 - 6 , 22 , 24 , 26 or 28 .

36. The method of claim 35 , optionally comprising further administering an additional therapeutic agent.

37. A method for treating a disorder caused by excessive apoptosis comprising:

administering to a subject in need thereof a therapeutically effective amount of a compound of any one of claims 1 - 6 , 22 , 24 , 26 or 28 .

38. The method of claim 37 , optionally comprising further administering an additional therapeutic agent.

39. The method of claim 35 , wherein the disorder is any one of: stroke, traumatic, brain injury, spinal cord injury, meningitis, Alzheimer's disease, Parkinson's disease, Huntington's disease, Kennedy's disease, prion disease, multiple sclerosis, spinal muscular atrophy, myocardial infarction, congestive heart failure and various other forms of acute and chronic heart disease, atherosclerosis, aging, bums, organ transplant rejection, graft versus host disease, hepatitis-B, -C, -G, various forms of liver disease including acute alcoholic hepatitis, yellow fever, dengue fever, Japanese encephalitis, glomerulonephritis, renal disease, H pylori -associated gastric and duodenal ulcer disease, HIV infection, tuberculosis, alopecia, diabetes, sepsis, Shigellosis, uveitis, inflammatory peritonitis, pancreatitis, erythematosus, scleroderma, chronic thyroiditis, Graves' disease, autoimmune gastritis, autoimmune hemolytic anemia, autoimmune neutropenia, thrombocytopenia, HIV-related encephalitis, myasthenia gravis, small bowel isehemia in disease or post-surgery, psoriasis, atopic dermatitis, myelodysplatic syndrome, acute and chronic myelogenous leukemia, metastatic melanoma, Kaposi's sarcoma, or Wiscott-Aldrich syndrome.

40. The method of claim 37 , wherein the disorder is any one of: stroke, traumatic, brain injury, spinal cord injury, meningitis, Alzheimer's disease, Parkinson's disease, Huntington's disease, Kennedy's disease, prion disease, multiple sclerosis, spinal muscular atrophy, myocardial infarction, congestive heart failure and various other forms of acute and chronic hear disease, atherosclerosis, aging, bums, organ transplant rejection, graft versus host disease, hepatitis-B, -C, -G, various forms of liver disease including acute alcoholic hepatitis, yellow fever, dengue fever, Japanese encephalitis, glomerulonephritis, renal disease, H. pylori -associated gastric and duodenal ulcer disease, HIV infection, tuberculosis, alopecia, diabetes, sepsis, Shigellosis, uveitis, inflammatory peritonitis, pancreatitis, erythematosus, scleroderma, chronic thyroiditis, Graves' disease, autoimmune gastritis, autoimmune hemolytic anemia, autoimmune neutropenia, thrombocytopenia, HIV-related encephalitis, myasthenia gravis, small bowel isehemia in disease or post-surgery, psoriasis, atopic dermatitis, myelodysplatic syndrome acute and chronic myelogenous leukemia, metastatic melanoma, Kaposi's sarcoma, or Wiscott-Aldrich syndrome.

41. A method for inhibiting an apoptotic caspase comprising:

contacting cells with an effective amount of any one of any one of the compounds of claims 1 - 6 , 22 , 24 , 26 or 28 .

42. A method for inhibiting caspase-3 or caspase-7 comprising:

contacting cells with an effective amount of any one of the compounds of claims 1 - 6 , 22 , 24 , 26 or 28 .

43. The method of claim 42 , wherein the method of inhibiting comprises inhibiting caspase-3.