Compositions comprising thienopyrimidine and thienopyridine compounds and methods of use thereof

1. A compound of Formula 4b:

or a pharmaceutically acceptable salt thereof, wherein

each of R 1 , R7, R 3 , R 4 , R 5 , R 6 , R 7 , and R is independently H, alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkene, alkyne, heteroalkyl, alcohol, diol, substituted diol, ether, amine, alkylamine, thiol, thioalkyl, halogen, carbocyclic ring, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycloalkyl, substituted heterocycloalkyl, aldehyde; ketone, CO—(CH 2 ) 1-6 —H, CO-ethenyl, CO-propenyl, CO-ethynyl, CO-propynyl, CO—(CH 2 ) 1-6 -aryl, CO—(CH 2 ) 1-6 -heteroaryl, CO—(CH 2 ) 1-3 -trifluoromethane, CO—(CH 2 ) 1-6 -cycloalkane, carboxylic acid, alkylcarboxylic acid, ester, alkylester, amide, CO-amino-dialkyl, alkylamide; sulfoxide, sulfone, SO 2 —(CH 2 ) 1-6 —H, SO 2 -alkenyl, SO 2 -alkynyl, SO 2 NH 2 , SO 2 —NH-alkyl, SO 2 -amino-dialkyl, sulfinic acid, cyano, alkylcyano, methylcarbonitrile, cyanate, thiocyanate, azide, or phosphate;

wherein R 6 is present at one or more positions of the indole;

Y is N, C—H, or

R a is alkyl, substituted alkyl, Amy, cycloalkyl, heteroalkyl, alkyl-substituted aryl, substituted aryl, aromatic heterocycle, non-aromatic heterocycle, alcohol, ether, amine, cyano, sulfonyl, aldehyde, or aromatic group;

L is alkylene, oxalkylene, or absent; wherein when L is absent the bonds attached to L do not exist; and

each of E and G is independently N or C, wherein each of E and G is independently optionally substituted with R 6 .

2. The compound or pharmaceutically acceptable salt of claim 1 , represented by the structure of Formula 4:

3. The compound or pharmaceutically acceptable salt of claim 1 , represented by the structure of Formula 4c:

wherein X is a bond, alkylene, substituted alkylene, heteroalkylene, or substituted heteroalkylene;

J is N, C—H, or C—R 12 ;

M is N—R 9 , O, S, SO 2 , or C—(R 9 ) 2 ;

each R 9 is independently H, alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkene, alkyne, heteroalkyl, alcohol, diol, substituted diol, ether, amine, alkylamine, thiol, thioalkyl, halogen, carbocyclic ring, aryl, substituted aryl, heteroaryl, substituted heteroalkyl, heterocycloalkyl, substituted heterocycloalkyl, aldehyde, ketone, CO-alkyl, CO-alkenyl, CO-alkynyl, CO—(CH 2 ) 1-6 -aryl, CO—(CH 2 ) 1-6 -heteroaryl, CO—(CH 2 ) 1-3 -trifluoromethane, CO—(CH 2 ) 1-6 -cycloalkane, carboxylic acid, alkylcarboxylic acid, ester, alkylester, amide, CO-amino-dialkyl, alkylamide, sulfoxide, sulfone, SO 2 —(CH 2 ) 1-6 —H, SO 2 -alkenyl, SO 2 -alkynyl, SO 2 NH 2 , SO 2 —NH— alkyl, SO 2 -amino-dialkyl, sulfinic acid, cyano, alkylcyano, methylcarbonitrile, cyanate, thiocyanate, azide, or phosphate;

R 10 is H, alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkene, alkyne, heteroalkyl, alcohol, diol, substituted diol, ether, amine, alkylamine, thiol, thioalkyl, halogen, carbocyclic ring, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycloalkyl, substituted heterocycloalkyl, aldehyde, ketone, CO—(CH 2 ) 1-6 —H, CO-ethenyl, CO-propenyl, CO-ethynyl, CO-propynyl, CO—(CH 2 ) 1-6 -aryl, CO—(CH 2 ) 1-6 -heteroaryl, CO—(CH 2 ) 1-3 -trifluoromethane, CO—(CH 2 ) 1-6 -cycloalkane, carboxylic acid, alkylcarboxylic acid, ester, alkylester, amide, CO-amino-dialkyl, alkylamide, sulfoxide, sulfone, SO 2 —(CH 2 ) 1-6 —H, SO 2 -alkenyl, SO 2 -alkynyl, SO 2 NH 2 , SO 2 —NH-alkyl, SO 2 -amino-dialkyl, sulfinic acid, ═O, cyano, alkylcyano, methylcarbonitrile, cyanate, thiocyanate, azide, or phosphate; and

R 12 is alkyl, substituted alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, hydroxyl, alcohol, amino, alkoxy, alkylamine, halogen, ketone, CO-alkyl, CO-alkenyl, CO-alkynyl, CO—(CH 2 ) 1-6 -aryl, CO—(CH 2 ) 1-6 -heteroaryl, CO—(CH 2 ) 1-3 -trifluoromethane, CO—(CH 2 ) 1-6 -cycloalkane, carboxylic acid, alkylcarboxylic acid, ester, alkylester, amide, alkylamide, cyano, alkylcyano, CONH 2 , SO 2 NH 2 , SO 2 -amino-dialkyl, SO 2 —NH-alkyl, CO-amino-dialkyl, SO 2 —(CH 2 ) 1-6 —H, SO 2 -alkenyl, SO 2 -alkynyl, carbocyclic ring, aryl, substituted aryl, heteroaryl, or heterocycloalkyl.

4. The compound or pharmaceutically acceptable salt of claim 3 , wherein X is (CH 2 ) 0-6 .

5. The compound or pharmaceutically acceptable salt of claim 3 , wherein X is alkylene or substituted alkylene.

6. The compound or pharmaceutically acceptable salt of claim 3 , wherein X is heteroalkylene or substituted heteroalkylene.

7. The compound or pharmaceutically acceptable salt of claim 3 , wherein J is N.

8. The compound or pharmaceutically acceptable salt of claim 3 , wherein M is N—R 9 .

9. The compound or pharmaceutically acceptable salt of claim 3 , wherein R 9 is H, alkyl, substituted alkyl, alcohol, formyl, CO-alkyl, CO-alkenyl, CO-alkynyl, CO—(CH 2 ) 1-6 -aryl, CO—(CH 2 ) 1-6 -heteroaryl, CO—(CH 2 ) 1-3 -trifluoromethane, CO—(CH 2 ) 1-6 -cycloalkane, CONH 2 , SO 2 NH 2 , SO 2 -amino-dialkyl, SO 2 —NH-alkyl, CO-amino-dialkyl, SO 2 —(CH 2 ) 1-6 —H, SO 2 -alkenyl, or SO 2 -alkynyl.

10. The compound or pharmaceutically acceptable salt of claim 3 , wherein R 10 is H, alkyl, ═O, trifluoromethane, or alcohol.

11. The compound or pharmaceutically acceptable salt of claim 1 , represented by the structure of Formula 4d:

wherein T is heteroaryl, cycloalkane, 5-membered ring comprising carbon atoms and one or more of N, S, and/or O; or 6-membered ring comprising carbon atoms and one or more of N, S, and/or O; wherein T is optionally substituted with R 11 at any position; and

R 11 is H, alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkene, alkyne, heteroalkyl, alcohol, diol, substituted diol, ether, amine, alkylarnine, thiol, thioalkyl, halogen, carbocyclic ring, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycloalkyl, substituted heterocycloalkyl, aldehyde, ketone, CO—(CH 2 ) 1-6 —H, CO-ethenyl, CO-propenyl, CO-ethynyl, CO-propynyl, CO—(CH 2 ) 1-6 -aryl, CO—(CH 2 ) 1-6 -heteroaryl, CO—(CH 2 ) 1-3 -trifluoromethane, CO—(CH 2 ) 1-6 -cycloalkane, carboxylic add, alkylcarboxylic add, ester, alkylester, amide, CO-amino-dialkyl, alkylamide, sulfoxide, sulfone, SO 2 —(CH 2 ) 1-6 —H, SO 2 -alkenyl, SO 2 -alkynyl, SO 2 NH 2 , SO 2 —NH-alkyl, SO 2 -amino-dialkyl, sulfinic acid, cyano, alkylcyano, methylcarbonitrile, cyanate, thiocyanate, azide, or phosphate.

12. The compound or pharmaceutically acceptable salt of claim 11 , wherein T is cycloalkane.

13. The compound or pharmaceutically acceptable salt of claim 12 , wherein T comprises two or more rings that are fused, bridged, or spiro-connected.

14. The compound or pharmaceutically acceptable salt of claim 11 , wherein T is 5-membered ring comprising carbon atoms and one or more of N, S, and/or O or 6-membered ring comprising carbon atoms and one or more of N, S, and/or 0.

15. The compound or pharmaceutically acceptable salt of claim 11 , wherein R 11 is H, alkyl, substituted alkyl, alcohol, ether, amine, halogen, ketone, or amide.

16. The compound or pharmaceutically acceptable salt of claim 11 , wherein R 11 is H, alkyl, alcohol, O-alkyl, O—(CH 2 ) 1-3 -cycloalkane, (CH 2 ) 1-3 —O—(CH 2 ) 1-3 —O-alkyl, (CH 2 ) 1-3 —O—(CH 2 ) 1-3 -cycloalkane, or (CH 2 ) 1-3 -heteroaryl.

17. The compound or pharmaceutically acceptable salt of claim 1 , represented by the structure of Formula 7b:

18. The compound or pharmaceutically acceptable salt of claim 1 , wherein Y is N.

19. The compound or pharmaceutically acceptable salt of claim 18 , wherein L is absent.

20. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 1 is alkyl or substituted alkyl.

21. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 1 is a halogen-substituted alkyl group.

22. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 2 is H, alkyl, substituted alkyl, halogen, alcohol, ether, or amine.

23. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 2 is H.

24. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 3 is H, alkyl, amine, alcohol, heterocycloalkyl, or substituted alkyl.

25. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 3 is H.

26. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 4 is H, alkyl, substituted alkyl, alcohol, or amine.

27. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 5 is H, alkyl, substituted alkyl, or alcohol.

28. The compound or pharmaceutically acceptable salt of claim 1 , wherein each R 6 is independently alkyl, substituted alkyl, alcohol, ether, halogen, amine, or cyano.

29. The compound or pharmaceutically acceptable salt of claim 28 , wherein each R 6 is independently alkyl, haloalkane, alcohol, ether, halogen, or amine.

30. The compound or pharmaceutically acceptable salt of claim 28 , comprising an R 6 connected to position 3, 4, or 6 of the indole.

31. The compound or pharmaceutically acceptable salt of claim 28 , comprising more than one R 6 .

32. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 7 is H, alkyl, substituted alkyl, alcohol, ether, heteroaryl, substituted heteroaryl, amide, or amine.

33. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 7 is H, alkyl or substituted alkyl.

34. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 7 is H, alkyl, haloalkane, alcohol, alkyl-SO 2 -alkyl, alkyl-heterocycloalkyl, alkyl-heteroaryl, substituted alkyl-heteroaryl, (CH 2 ) n —OR 13 , (CH 2 ) n R 13 , (CH 2 ) n —O—(CH 2 ) m —R 13 , (CH 2 ) 1-6 —CO—NH 2 , (CH 2 ) 1-6 —CO-halogen, diol-substituted alkyl-R 14 , diol-substituted heteroalkyl-R 14 , heterocycloalkyl, substituted heterocycloalkyl, heteroaryl, or substituted heteroaryl, wherein n is 1-10; m is 1-10; R 13 is aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocycloalkyl, or substituted heterocycloalkyl; and R 14 is amide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocycloalkyl, or substituted heterocycloalkyl.

35. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 7 is alkyl-heterocycloalkyl, alkyl-heteroaryl, or substituted alkyl-heteroaryl.

36. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 7 is (CH 2 ) n —OR 13 , (CH 2 ) n R 13 , or (CH 2 ) n —O—(CH 2 ) m —R 13 , wherein n is 1-10, m is 1-10, and R 13 is aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocycloalkyl, or substituted heterocycloalkyl.

37. The compound or pharmaceutically acceptable salt of claim 36 , wherein the cycloalkyl or substituted cycloalkyl comprises two or more rings that are fused, bridged, or spiro-connected.

38. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 8 is H, alkyl, substituted alkyl, alcohol, heteroaryl, substituted heteroaryl, cyano, amine, amide, sulfonylmethane, or ketone.

39. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 8 is cyano.

40. The compound or pharmaceutically acceptable salt of claim 1 , wherein R 6 , R 7 , or R 8 is cyano, halo, alkyl, substituted alkyl, alcohol, heteroaryl, substituted heteroaryl, amine, amide, heterocycle, ether, or ketone.

41. The compound or pharmaceutically acceptable salt of claim 1 , wherein R a is halo-substituted alkyl, (CH 2 )—OH, (CH 2 ) n —OR 15 , amine, cyano, or aldehyde, wherein n is 0-10 and R 15 is alkyl, (CH 2 ) n -aryl, (CH 2 ) n -heterocycle, aryl, substituted aryl, heteroaryl, or heterocycle.

42. The compound or pharmaceutically acceptable salt of claim 1 , wherein L is absent.

43. The compound or pharmaceutically acceptable salt of claim 1 , wherein the compound is selected from:

44. A pharmaceutical composition comprising the compound or pharmaceutically acceptable salt of claim 1 and a pharmaceutically acceptable carrier.

45. The pharmaceutical composition of claim 44 , further comprising a second pharmaceutical agent.

46. A method for the treatment of leukemia comprising administering the compound or pharmaceutically acceptable salt of claim 1 to a subject suffering from leukemia.

47. The method of claim 46 , wherein said leukemia comprises AML, ALL, or Mixed Lineage Leukemia.

48. A method of inhibiting the interaction of menin and one or more of a MLL protein, a MLL fusion protein, and a MLL Partial Tandem Duplication comprising administering the compound or pharmaceutically acceptable salt of claim 1 to a sample comprising menin and one or more of the MLL protein, the MLL fusion protein, and the MLL Partial Tandem Duplication.

49. The method of claim 48 , wherein the MLL protein is MLL1 or MLL2.

50. A method of treating a disorder mediated by menin interaction with another protein or by chromosomal rearrangement on chromosome 11q23, comprising administering to a subject in need thereof a therapeutically effective amount of the compound or pharmaceutically acceptable salt of claim 1 .