IP Library › Granted Patent US 11,673,898

Granted Patent B2

US 11,673,898 · App. 16/944,040 · Granted Jun 13, 2023

Substituted inhibitors of menin-MLL and methods of use

Inventors: Tao Wu (Carlsbad, CA); Liansheng Li (San Diego, CA); Yi Wang (San Diego, CA); Pingda Ren (San Diego, CA); Jolanta Grembecka (Ann Arbor, MI); Tomasz Cierpicki (Ann Arbor, MI); Szymon Klossowski (Ann Arbor, MI); Jonathan Pollock (Ann Arbor, MI); Dmitry Borkin (Ann Arbor, MI)

Assignees: KURA ONCOLOGY, INC.; THE REGENTS OF THE UNIVERSITY OF MICHIGAN

C07D495/04 A61P35/00

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Quick Facts

Patent No.: US 11,673,898
App. No.: 16/944,040
Granted: Jun 13, 2023
Kind: B2

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Abstract

The present disclosure provides methods of inhibiting the interaction of menin with MLL1, MLL2 and MLL-fusion oncoproteins with compositions of Formula (II-A). The methods are useful for the treatment of leukemia, solid cancers, diabetes and other diseases dependent on activity of MLL1, MLL2, MLL fusion proteins, and/or menin. Compositions of Formula (II-A) for use in these methods are also provided.

Claims (102)

1. A method of treating a disease or condition in a subject, comprising administering to the subject a therapeutically effective amount of a compound of Formula (II-A):

or a pharmaceutically acceptable salt thereof, wherein:

C is selected from C 3-12 carbocycle and 3- to 12-membered heterocycle;

L 2 is selected from bond, —C(O)—, —C(O)O—, —C(O)N(R 51 )—, —C(O)N(R 51 )C(O)—, —C(O)N(R 51 )C(O)N(R 51 )—, —C(NR 51 )—, —S(O) 2— , —S(O)O—, —S(O)—, —S(O) 2 O—, —S(O) 2 N(R 51 )—, —S(O)N(R 51 )—, alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, and heteroalkynylene, wherein each of the alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, and heteroalkynylene is optionally substituted with one or more R 50 ;

L 3 is selected from alkylene, alkenylene, and alkynylene, each of which is substituted with one or more R 56 and optionally further substituted with one or more R 50 ;

R 1 and R 3 are each independently selected from hydrogen and R 50 ;

R 2 is R 50 ;

R A , R B , and R C are each independently selected at each occurrence from R 50 , or two R A groups, two R B groups, or two R C groups attached to the same atom or different atoms can together optionally form a bridge or ring;

m, n, and p are each independently an integer from 0 to 6;

R 50 is independently selected at each occurrence from:

halogen, —NO 2 , —CN, —OR 52 , —SR 52 , —N(R 52 ) 2 , —NR 53 R 54 , —S(═O)R 52 , —S(—O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , —NR 52 S(═O) 2 N(R 52 ) 2 , —NR 52 S(═O) 2 NR 53 R 54 , —C(O)R 52 , —C(O)OR 52 , —OC(O)R 52 , —OC(O)OR 52 , —OC(O)N(R 52 ) 2 , —OC(O)NR 53 R 54 , —NR 52 C(O)R 52 , —NR 52 C(O)OR 52 , —NR 52 C(O)N(R 52 ) 2 , —NR 52 C(O)NR 53 R 54 , —C(O)N(R 52 ) 2 , —C(O)NR 53 R 54 , —P(O)(OR 52 ) 2 , and —P(O)(R 52 ) 2 , or two R 50 groups attached to the same carbon are taken together to form ═O, =S, or =N(R 52 );

C 1-10 alkyl, C 2-10 alkenyl, and C 2-10 alkynyl, each of which is optionally substituted at each occurrence with one or more substituents selected from halogen, —NO 2 , —CN, —OR 52 , —SR 52 , —N(R 52 ) 2 , —NR 53 R 54 , —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , —NR 52 S(═O) 2 N(R 52 ) 2 , —NR 52 S(═O) 2 NR 53 R 54 , —C(O)R 52 , —C(O)OR 52 , —OC(O)R 52 , —OC(O)OR 52 , —OC(O)N(R 52 ) 2 , —OC(O)NR 53 R 54 , —NR 52 C(O)R 52 , —NR 52 C(O)OR 52 , —NR 52 C(O)N(R 52 ) 2 , —NR 52 C(O)NR 53 R 54 , —C(O)N(R 52 ) 2 , —C(O)NR 53 R 54 , —P(O)(OR 52 ) 2 , —P(O)(R 52 ) 2 , ═O, ═S, ═N(R 52 ), C 3-12 carbocycle, and 3- to 12-membered heterocycle; and

C 3-12 carbocycle and 3- to 12-membered heterocycle;

wherein each C 3-12 carbocycle and 3- to 12-membered heterocycle in R 50 is optionally substituted with one or more substituents independently selected from halogen, —NO 2 , —CN, —OR 52 , —SR 52 , —N(R 52 ) 2 , —NR 53 R 54 , —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , —NR 52 S(═O) 2 N(R 52 ) 2 , —NR 52 S(═O) 2 NR 53 R 54 , —C(O)R 52 , —C(O)OR 52 , —OC(O)R 52 , —OC(O)OR 52 , —OC(O)N(R 52 ) 2 , —OC(O)NR 53 R 54 , —NR 52 C(O)R 52 , —NR 52 C(O)OR 52 , —NR 52 C(O)N(R 52 ) 2 , —NR 52 C(O)NR 53 R 54 , —C(O)N(R 52 ) 2 , —C(O)NR 53 R 54 , —P(O)(OR 52 ) 2 , —P(O)(R 52 ) 2 , ═O, ═S, ═N(R 52 ), C 1-6 alkyl, C 1-6 haloalkyl, C 2-6 alkenyl, and C 2-6 alkynyl;

R 51 is independently selected at each occurrence from:

hydrogen, —C(O)R 52 , —C(O)OR 52 , —C(O)N(R 52 ) 2 , and —C(O)NR 53 R 54 ; and

C 1-6 alkyl, C 2-6 alkenyl, and C 2-6 alkynyl, each of which is optionally substituted at each occurrence with one or more substituents independently selected from halogen, —NO 2 , —CN, —OR 52 , —SR 52 , —N(R 52 ) 2 , —NR 53 R 54 , —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , —NR 52 S(═O) 2 N(R 52 ) 2 , —NR 52 S(═O) 2 NR 53 R 54 , —C(O)R 52 , —C(O)OR 52 , —OC(O)R 52 , —OC(O)OR 52 , —OC(O)N(R 52 ) 2 , —OC(O)NR 53 R 54 , —NR 52 C(O)R 52 , —NR 52 C(O)OR 52 , —NR 52 C(O)N(R 52 ) 2 , —NR 52 C(O)NR 53 R 54 , —C(O)N(R 52 ) 2 , —C(O)NR 53 R 54 , —P(O)(OR 52 ) 2 , —P(O)(R 52 ) 2 , ═O, ═S, ═N(R 52 ), C 3-12 carbocycle, and 3- to 12-membered heterocycle; and

C 3-12 carbocycle and 3- to 12-membered heterocycle;

wherein each C 3-12 carbocycle and 3- to 12-membered heterocycle in R 51 is optionally substituted with one or more substituents independently selected from halogen, —NO 2 , —CN, —OR 52 , —SR 52 , —N(R 52 ) 2 , —NR 53 R 54 , —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , —NR 52 S(═O) 2 N(R 52 ) 2 , —NR 52 S(═O) 2 NR 53 R 54 , —C(O)R 52 , —C(O)OR 52 , —OC(O)R 52 , —OC(O)OR 52 , —OC(O)N(R 52 ) 2 , —OC(O)NR 53 R 54 , —NR 52 C(O)R 52 , —NR 52 C(O)OR 52 , —NR 52 C(O)N(R 52 ) 2 , —NR 52 C(O)NR 53 R 54 , —C(O)N(R 52 ) 2 , —C(O)NR 53 R 54 , —P(O)(OR 52 ) 2 , —P(O)(R 52 ) 2 , ═O, ═S, ═N(R 52 ), C 1-6 alkyl, C 1-6 haloalkyl, C 2-6 alkenyl, and C 2-6 alkynyl;

R 52 is independently selected at each occurrence from hydrogen; and C 1-20 alkyl, C 2-20 alkenyl, C 2-20 alkynyl, C 1-6 heteroalkyl, C 3-12 carbocycle, and 3- to 12-membered heterocycle, each of which is optionally substituted by halogen, —CN, —NO 2 , —NH 2 , —NHCH 3 , —NHCH 2 CH 3 , ═O, —OH, —OCH 3 , —OCH 2 CH 3 , C 3-12 carbocycle, or 3- to 6-membered heterocycle;

R 53 and R 54 are taken together with the nitrogen atom to which they are attached to form a heterocycle;

R 56 is independently selected at each occurrence from:

—NO 2 , —OR 59 , —SR 52 , —NR 53 R 54 , —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , —NR 52 S(═O) 2 N(R 52 ) 2 , —NR 52 S(═O) 2 NR 53 R 54 , —C(O)R 52 , —C(O)OR 52 , —OC(O)R 52 , —OC(O)OR 52 , —OC(O)N(R 52 ) 2 , —OC(O)NR 53 R 54 , —NR 52 C(O)R 52 , —NR 52 C(O)OR 52 , —NR 52 C(O)N(R 52 ) 2 , —NR 52 C(O)NR 53 R 54 , —C(O)N(R 52 ) 2 , —C(O)NR 53 R 54 , —P(O)(OR 52 ) 2 , —P(O)(R 52 ) 2 , C 1-10 alkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-12 carbocycle, and 3- to 12-membered heterocycle, or two R 56 groups attached to the same carbon are taken together to form ═O, ═S, or ═N(R 52 );

wherein each C 1-10 alkyl, C 2-10 alkenyl, and C 2-10 alkynyl in R 56 is optionally substituted at each occurrence with one or more substituents independently selected from halogen, —NO 2 , —CN, —OR 59 , —SR 52 , —N(R 52 ) 2 , —NR 53 R 54 , —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , —NR 52 S(═O) 2 N(R 52 ) 2 , —NR 52 S(═O) 2 NR 53 R 54 , —C(O)R 52 , —C(O)OR 52 , —OC(O)R 52 , —OC(O)OR 52 , —OC(O)N(R 52 ) 2 , —OC(O)NR 53 R 54 , —NR 52 C(O)R 52 , —NR 52 C(O)OR 52 , —NR 52 C(O)N(R 52 ) 2 , —NR 52 C(O)NR 53 R 54 , —C(O)N(R 52 ) 2 , —C(O)NR 53 R 54 , —P(O)(OR 52 ) 2 , —P(O)(R 52 ) 2 , ═O, ═S, ═N(R 52 ), C 3-12 carbocycle, and 3- to 12-membered heterocycle;

wherein each C 3-12 carbocycle and 3- to 12-membered heterocycle in R 56 is optionally substituted with one or more substituents independently selected from halogen, —NO 2 , —CN, —OR 52 , —SR 52 , —N(R 52 ) 2 , —NR 53 R 54 , —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , —NR 52 S(═O) 2 N(R 52 ) 2 , —NR 52 S(═O) 2 NR 53 R 54 , —C(O)R 52 , —C(O)OR 52 , —OC(O)R 52 , —OC(O)OR 52 , —OC(O)N(R 52 ) 2 , —OC(O)NR 53 R 54 , —NR 52 C(O)R 52 , —NR 52 C(O)OR 52 , —NR 52 C(O)N(R 52 ) 2 , —NR 52 C(O)NR 53 R 54 , —C(O)N(R 52 ) 2 , —C(O)NR 53 R 54 , —P(O)(OR 52 ) 2 , —P(O)(R 52 ) 2 , ═O, ═S, ═N(R 52 ), C 1-6 alkyl, C 1-6 haloalkyl, C 2-6 alkenyl, and C 2-6 alkynyl; and

further wherein R 56 optionally forms a bond to ring C; and

R 59 is independently selected at each occurrence from C 1-20 alkyl, C 2-20 alkenyl, C 2-20 alkynyl, C 1-6 heteroalkyl, C 3-12 carbocycle, and 3- to 12-membered heterocycle, each of which is optionally substituted by halogen, —CN, —NO 2 , —NH 2 , —NHCH 3 , —NHCH 2 CH 3 , ═O, —OH, —OCH 3 , —OCH 2 CH 3 , C 3-12 carbocycle, or 3- to 6-membered heterocycle,

wherein when R 56 is —CH 3 , L 3 is not further substituted with —OH, —NH 2 , or —CN; and

wherein the disease or condition comprises leukemia, hematologic malignancy, myelodysplastic syndrome, myelodysplastic/myeloproliferative neoplasm, solid tumor cancer, prostate cancer, breast cancer, liver cancer, brain tumor, or diabetes.

2. The method of claim 1 , wherein R C is selected from —C(O)R 52 , —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , C 1-3 alkyl, and C 1-3 haloalkyl, or two R C groups attached to the same carbon are taken together to form ═O, or two R C groups attached to different atoms can together form a C 1-3 bridge.

3. The method of claim 1 , wherein C is 5- to 12-membered saturated heterocycle, wherein the heterocycle comprises at least one nitrogen atom.

4. The method of claim 1 , wherein C—(R C ) p is selected from:

wherein R 57 is selected from —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , and C 1-10 alkyl, wherein the C 1-10 alkyl is substituted with one or more substituents selected from —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , and —NR 52 S(═O) 2 R 52 .

5. The method of claim 1 , wherein:

R 2 is selected from halogen, —OR 52 , —N(R 52 ) 2 , —CN, C 1-3 alkyl, C 1-3 alkyl-N(R 52 ) 2 , C 1-3 haloalkyl, C 2-3 alkenyl, and C 2-3 alkynyl; and

R 3 is selected from hydrogen, halogen, —OH, —N(R 52 ) 2 , —CN, —C(O)OR 52 , C 1-3 alkyl, and C 1 3 haloalkyl.

6. The method of claim 1 , wherein R 1 is C 1-3 haloalkyl.

7. The method of claim 1 , wherein m is 0.

8. The method of claim 1 , wherein n is an integer from 1 to 3.

9. The method of claim 1 , wherein L 2 is C 1-4 alkylene, optionally substituted with one or more R 50 .

10. The method of claim 1 , wherein L 3 is substituted with ═O, C 1-6 alkyl C 1-6 haloalkyl, C 1-3 alkyl(cyclopropyl), C 1-3 alkyl(NR 52 C(O)R 52 ), or —O(C 1-6 alkyl).

11. The method of claim 1 , wherein L 3 is selected from

12. The method of claim 11 , wherein R 56 is methyl.

13. The method of claim 1 , wherein:

L 2 is —CH 2 —;

L 3 is selected from C 1-6 alkylene, C 2-6 alkenylene, and C 2-6 alkynylene, each of which is substituted with one or more R 56 and optionally further substituted with one or more R 50 ;

m is an integer from 0 to 3;

n is an integer from 1 to 3; and

R 56 is independently selected at each occurrence from:

—OR 59 , C 1-10 alkyl, C 2-10 alkenyl, and C 2-10 alkynyl, or two R 56 groups attached to the same carbon are taken together to form ═O,

further wherein R 56 optionally forms a bond to ring C.

14. The method of claim 13 , wherein p is 1 and R C is —S(═O) 2 R 52 , S( 50 O) 2 N(R 52 ) 2 , or —S(═O) 2 —NR 53 R 54 .

15. The method of claim 13 , wherein the stereoisomer is provided in at least 90% enantiomeric excess.

16. The method of claim 1 , wherein the disease or condition is associated with MLL fusion proteins.

17. The method of claim 1 , wherein the disease or condition is mediated by chromosomal rearrangement on chromosome 11q23.

18. The method of claim 1 , wherein the disease or condition is mediated by an interaction between menin and another protein.

19. The method of claim 1 , wherein the compound has the structure of Formula (II-C):

or a pharmaceutically acceptable salt thereof;

wherein R 2 , C, L 3 , R B , R C , and p are each defined as in claim 2 .

20. The method of claim 1 , wherein the compound has the structure of Formula (II-F) or Formula (II-H):

or a pharmaceutically acceptable salt thereof;

wherein R 2 , R C , and R 56 are each defined as in claim 2 .

21. The method of claim 1 , wherein the compound is selected from the group consisting of:

and pharmaceutically acceptable salts thereof.

22. The method of claim 1 , wherein the compound is:

or a pharmaceutically acceptable salt thereof.

23. A method of inhibiting an interaction of menin with one or more of MLL1, MLL2, an MLL fusion protein, and an MLL Partial Tandem Duplication, comprising contacting menin with an effective amount of a compound of Formula (II-A):

or a pharmaceutically acceptable salt thereof, wherein:

C is selected from C 3-12 carbocycle and 3- to 12-membered heterocycle;

L 2 is selected from bond, —C(O)—, —C(O)O—, —C(O)N(R 51 )—, —C(O)N(R 51 )C(O)—, —C(O)N(R 51 )C(O)N(R 51 )—, —C(NR 51 )—, —S(O) 2 —, —S(O)O—, —S(O)—, —S(O) 2 O—, —S(O) 2 N(R 51 )—, —S(O)N(R 51 )—, alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, and heteroalkynylene, wherein each of the alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, and heteroalkynylene is optionally substituted with one or more R 50 ;

L 3 is selected from alkylene, alkenylene, and alkynylene, each of which is substituted with one or more R 56 and optionally further substituted with one or more R 50 ;

R 1 and R 3 are each independently selected from hydrogen and R 50 ;

R 2 is R 50 ;

m, n, and p are each independently an integer from 0 to 6;

R 50 is independently selected at each occurrence from:

halogen, —NO 2 , —CN, —OR 52 , —SR 52 , —N(R 52 ) 2 , —NR 53 R 54 , —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , —NR 52 S(═O) 2 N(R 52 ) 2 , —NR 52 S(═O) 2 NR 53 R 54 , —C(O)R 52 , —C(O)OR 52 , —OC(O)R 52 , —OC(O)OR 52 , —OC(O)N(R 52 ) 2 , —OC(O)NR 53 R 54 , —NR 52 C(O)R 52 , —NR 52 C(O)OR 52 , —NR 52 C(O)N(R 52 ) 2 , —NR 52 C(O)NR 53 R 54 , —C(O)N(R 52 ) 2 , —C(O)NR 53 R 54 , —P(O)(OR 52 ) 2 , and —P(O)(R 52 ) 2 , or two R 50 groups attached to the same carbon are taken together to form ═O, ═S, or =N(R 52 );

C 1-10 alkyl, C 2-10 alkenyl, and C 2-10 alkynyl, each of which is optionally substituted at each occurrence with one or more substituents independently selected from halogen, —NO 2 , —CN, —OR 52 , —SR 52 , —N(R 52 ) 2 , —NR 53 R 54 , —S(═O)R 52 , —S(═O) 2 R 52 , —S(═O) 2 N(R 52 ) 2 , —S(═O) 2 NR 53 R 54 , —NR 52 S(═O) 2 R 52 , —NR 52 S(═O) 2 N(R 52 ) 2 , —NR 52 S(═O) 2 NR 53 R 54 , —C(O)R 52 , —C(O)OR 52 , —OC(O)R 52 , —OC(O)OR 52 , —OC(O)N(R 52 ) 2 , —OC(O)NR 53 R 54 , —NR 52 C(O)R 52 , —NR 52 C(O)OR 52 , —NR 52 C(O)N(R 52 ) 2 , —NR 52 C(O)NR 53 R 54 , —C(O)N(R 52 ) 2 , —C(O)NR 53 R 54 , —P(O)(OR 52 ) 2 , —P(O)(R 52 ) 2 , ═O, ═S, ═N(R 52 ), C 3-12 carbocycle, and 3- to 12-membered heterocycle; and

C 3-12 carbocycle and 3- to 12-membered heterocycle;

R 51 is independently selected at each occurrence from:

hydrogen, —C(O)R 52 , —C(O)OR 52 , —C(O)N(R 52 ) 2 , and —C(O)NR 53 R 54 ; and

C 3-12 carbocycle and 3- to 12-membered heterocycle;

R 53 and R 54 are taken together with the nitrogen atom to which they are attached to form a heterocycle;

R 56 is independently selected at each occurrence from:

further wherein R 56 optionally forms a bond to ring C; and

wherein when R 5 6 is —CH 3 , L 3 is not further substituted with —OH, —NH 2 , or —CN.

24. The method of claim 23 , wherein the compound is:

or a pharmaceutically acceptable salt thereof.

25. The method of claim 23 , wherein the compound is selected from the group consisting of:

and pharmaceutically acceptable salts thereof.

26. The method of claim 1 , wherein the compound is

27. The method of claim 23 , wherein the compound is

Assignments (7)