Methods and compositions for inhibiting the interaction of menin with MLL proteins

1. A compound of Formula II-A:

or a pharmaceutically acceptable salt thereof, wherein:

X 2 is CR 2 or N;

X 5 is S;

X 6 is CR 3 or N;

L 3 is a carbonyl, O, S, —NR 5 —, —NR 6 CH 2 —, —NR 6 C(═O)—, —NR 6 SO 2 —, alkylene, alkenylene, heteroalkylene, alkylenecarbonyl, alkenylenecarbonyl, or heteroalkylenecarbonyl;

L 2 is a bond, carbonyl, O, S, —NR 5 —, —NR 6 CH 2 —, —NR 6 C(═O)—, —NR 6 SO 2 —, alkylene, alkenylene, heteroalkylene, alkylenecarbonyl, alkenylenecarbonyl, or heteroalkylenecarbonyl;

m is an integer from 0 to 12;

B is selected from B-I, B-II, B-III, and B-IV;

wherein B is connected at any ring atom to L 2 ;

B-I is

B-II is

B-III is

B-IV is

each of Z 1 , Z 2 , Z 3 , and Z 4 is independently CR 7 , N, or NR 9 ;

Z 5 is C or N;

each of Z 6 , Z 7 , and Z 8 is independently CR 8 , N, NR 9 , O, or S;

each of Z 9 , Z 10 , and Z 11 is independently CR 10 , CR 11 R 12 , NR 13 , O, or S;

n is an integer from 0 to 6;

each of R 1 , R 2 , R 3 , R 5 , R 6 , R 7 , R 8 , R 9 , R 10 , R 11 , R 12 , and R 13 is at each occurrence, independently selected from H, halo, hydroxyl, amino, cyano, dialkylphosphine oxide, oxo, carboxyl, amido, acyl, alkyl, cycloalkyl, heteroalkyl, haloalkyl, aminoalkyl, hydroxyalkyl, alkoxy, alkylamino, cycloalkyl alkyl, cycloalkyloxy, cycloalkylalkyloxy, cycloalkylamino, cycloalkylalkylamino, heterocyclyl, heterocyclyl alkyl, heterocyclyloxy, heterocyclylalkyloxy, heterocyclyl amino, heterocyclylalkylamino, aryl, aralkyl, aryloxy, aralkyloxy, arylamino, aralkyl amino, heteroaryl, heteroarylalkyl, heteroaryloxy, heteroarylalkyloxy, heteroarylamino, and heteroarylalkylamino;

each of R A and R B is, at each occurrence, independently selected from halo, hydroxyl, amino, cyano, dialkylphosphine oxide, oxo, carboxyl, amido, acyl, alkyl, cycloalkyl, heteroalkyl, haloalkyl, aminoalkyl, hydroxyalkyl, alkoxy, alkylamino, cycloalkylalkyl, cycloalkyloxy, cycloalkylalkyloxy, cycloalkylamino, cycloalkylalkylamino, heterocyclyl, heterocyclylalkyl, heterocyclyloxy, heterocyclylalkyloxy, heterocyclylamino, heterocyclylalkylamino, aryl, aralkyl, aryloxy, aralkyloxy, arylamino, aralkylamino, heteroaryl, heteroarylalkyl, heteroaryloxy, heteroarylalkyloxy, heteroarylamino, and heteroarylalkylamino,

wherein two R A groups or two R B groups attached to the same atom or different atoms can together optionally form a bridge or ring; and

R 14 is halo, hydroxyl, amino, cyano, dialkylphosphine oxide, oxo, carboxyl, amido, acyl, alkyl, cycloalkyl, heteroalkyl, haloalkyl, aminoalkyl, hydroxyalkyl, alkoxy, alkylamino, cycloalkylalkyl, cycloalkyloxy, cycloalkylalkyloxy, cycloalkyl amino, cycloalkylalkylamino, heterocyclyl, heterocyclylalkyl, heterocyclyloxy, heterocyclylalkyloxy, heterocyclylamino, heterocyclylalkylamino, aryl, aralkyl, aryloxy, aralkyloxy, arylamino, aralkylamino, heteroaryl, heteroarylalkyl, heteroaryloxy, heteroarylalkyloxy, heteroarylamino, or heteroarylalkylamino.

2. The compound of claim 1 , wherein R 14 is halo, hydroxyl, alkoxy, alkylamino, amino, cyano, amido, alkyl, heteroalkyl, or haloalkyl.

3. The compound of claim 1 , wherein X 6 is CR 3 and R 3 in X 6 is selected from H, halo, amino, carboxyl, and alkyl.

4. The compound of claim 1 , wherein L 3 is carbonyl, O, S, or —NR 5 —.

5. The compound of claim 1 , wherein L 2 is C 1 -C 4 alkylene.

6. The compound of claim 1 , wherein X 2 is N.

7. The compound of claim 1 , wherein R 1 is a haloalkyl.

8. The compound of claim 1 , wherein m is 0 and n is 1 or 2.

9. The compound of claim 1 , wherein R 5 is H or alkyl.

10. The compound of claim 1 , wherein B is B-II.

11. The compound of claim 10 , wherein B-II is

12. The compound of claim 1 , comprising B-II, wherein:

Z 1 and Z 2 are CR 7 ;

Z 5 is C;

Z 6 is NR B ; and

Z 7 and Z 8 are CR 8 .

13. The compound of claim 1 , comprising B-II, wherein:

Z 1 is CCH 3 ;

Z 2 and Z 8 are CH;

Z 5 is C;

Z 6 is NR B ; and

Z 7 is CCN.

14. The compound of claim 1 , comprising an R B selected from:

wherein:

G is selected from a bond, alkylene, heteroalkylene, C 3-12 carbocycle, 3- to 12-membered heterocycle, and combinations thereof, wherein G is optionally substituted with one or more R 32 groups;

V is absent or selected from a C 3-12 carbocycle, and 3- to 12-membered heterocycle;

wherein V is optionally substituted with one or more R 32 groups;

each of R 21 and R 32 is, at each occurrence, independently selected from:

H, halogen, —OR 20 , —SR 20 , —N(R 20 ) 2 , —N(R 20 )C(O)R 20 , —C(O)R 20 , —C(O)OR 20 , —C(O)N(R 20 ) 2 , —OC(O)R 20 , —S(O) 2 R 20 , —S(O) 2 N(R 20 ) 2 , —N(R 20 )S(O) 2 R 20 , —NO 2 , ═O, ═S, ═N(R 20 ), —P(O)(OR 20 ) 2 , —P(O)(R 20 ) 2 , —OP(O)(OR 20 ) 2 , and —CN;

C 1-6 alkyl, C 2-6 alkenyl, and C 2-6 alkynyl, each of which is independently optionally substituted at each occurrence with one or more substituents selected from halogen, —OR 20 , —SR 20 , —N(R 20 ) 2 , —N(R 20 )C(O)R 20 , —C(O)R 20 , —C(O)OR 20 , —C(O)N(R 20 ) 2 , —OC(O)R 20 , —S(O) 2 R 20 , —S(O) 2 N(R 20 ) 2 , —N(R 20 )S(O) 2 R 20 , —NO 2 , ═O, ═S, ═N(R 20 ), —P(O)(OR 20 ) 2 , —P(O)(R 20 ) 2 , —OP(O)(OR 20 ) 2 , —CN, C 3-10 carbocycle, and 3- to 10-membered heterocycle; and

C 3-10 carbocycle and 3- to 10-membered heterocycle;

wherein two R 32 on the same carbon atom can come together to form a C 3-10 carbocycle or 3- to 10-membered heterocycle;

wherein each C 3-10 carbocycle and 3- to 10-membered heterocycle of R 32 is independently optionally substituted with one or more substituents selected from halogen, —OR 20 , —SR 20 , —N(R 20 ) 2 , —N(R 20 )C(O)R 20 , —C(O)R 20 , —C(O)OR 20 , —C(O)N(R 20 ) 2 , —OC(O)R 20 , —S(O) 2 R 20 ), —S(O) 2 N(R 20 ) 2 , —N(R 20 )S(O) 2 R 20 , —NO 2 , ═O, ═S, ═N(R 20 ), —P(O)(OR 20 ) 2 , —P(O)(R 20 ) 2 , —OP(O)(OR 20 ) 2 , —CN, C 1-6 alkyl, C 2-6 alkenyl, and C 2-6 alkynyl;

R 20 is, at each occurrence, independently selected from:

hydrogen;

C 1-6 alkyl, C 2-6 alkenyl, and C 2-6 alkynyl, each of which is independently optionally substituted at each occurrence with one or more substituents selected from halogen, —OR 30 , —SR 30 , —N(R 30 ) 2 , —N(R 30 )C(O)R 30 , —C(O)R 30 , —C(O)OR 30 , —C(O)N(R 30 ) 2 , —OC(O)R 30 , —S(O) 2 R 30 , —S(O) 2 N(R 30 ) 2 , —N(R 30 )S(O) 2 R 30 , —NO 2 , —P(O)(OR 30 ) 2 , —P(O)(R 30 ) 2 , —OP(O)(OR 30 ) 2 , and CN; and

3- to 10-membered heterocycle and C 3-10 carbocycle; and

R 30 is, at each occurrence, independently selected from hydrogen, C 1-6 alkyl, C 2-6 alkenyl, and C 2-6 alkynyl.

15. The compound of claim 14 , wherein V is selected from:

any one of which is optionally substituted with one or more R 32 groups.

16. The compound of claim 14 , wherein G is alkylene optionally substituted with one or more R 32 groups.

17. A pharmaceutical composition comprising a compound of claim 1 and a pharmaceutically acceptable carrier.

18. The compound of claim 14 , wherein:

X 5 is S;

X 6 is CR 3 , wherein R 3 in X 6 is selected from H, halo, amino, carboxyl, and alkyl;

L 2 is C 1 -C 4 alkylene;

L 3 is carbonyl, O, S, or —NR 5 —;

B is

Z 1 and Z 2 are CR 7 ;

Z 5 is C;

Z 6 is NR B ;

Z 7 and Z 8 are CR 8 ;

R 1 is a haloalkyl;

R 14 is halo, hydroxyl, alkoxy, alkylamino, amino, cyano, amido, alkyl, heteroalkyl, or haloalkyl; and

V is selected from C 3-12 carbocycle and 3- to 12-membered heterocycle, each of which optionally substituted with one or more R 32 groups.