Substituted pyridines as irreversible inhibitors of menin-MLL interaction

1. A compound according to formula (I):

or a pharmaceutically acceptable salt or stereoisomer thereof,

wherein:

A is N;

Cy is:

wherein:

Q is =N—, —NH—, —O—, or —S—; and

Z is —CR 5a = or —N=;

wherein Cy is optionally substituted with one or more independently selected R 7 substituents;

X is —C(R 3b ) 2 —, —NR 3 a-, or —O—;

W is —C(O)—, —S(O)—, or —S(O) 2 —;

Y is a single bond, —C(R 3b ) 2 —, —NR 3a —, or —O—;

(i) R 1 is H, halo, CN, C 1 - 6 alkyl, or C 1 - 6 haloalkyl; and

R 2 is CH 2 —Cy 2 -NHC(O)—C(R 6a )═C(R 6b )(R 6c ) or Cy 2 -NHC(O)—C(R 6a )═C(R 6b )(R 6c ); or

(ii) R 1 is CH 2 —Cy 2 -NHC(O)—C(R 6a )═C(R 6b )(R 6c ) or Cy 2 -NHC(O)—C(R 6a )═C(R 6b )(R 6c ); and

R 2 is H, halo, CN, C 1-6 alkyl, or C 1-6 haloalkyl;

each R 3a is independently H or C 1-6 alkyl;

each R 3b is independently H or C 1-6 alkyl;

each R 4a is independently H, halo, CN, C 1 - 6 alkyl, C(O)R, C(O)N(R) 2 , C(O)OR, N(R) 2 , NRC(O)R, OR, S(O) 2 R, C 3 - 7 cycloalkyl, a 4- to 7-membered heterocycloalkyl ring, phenyl, an 8- to 10-membered bicyclic aryl ring, or a 5- or 6-membered heteroaryl ring, wherein the 4- to 7-membered heterocycloalkyl ring has 1 or 2 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, and the 5- or 6-membered heteroaryl ring has 1, 2, 3, or 4 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur;

each R 4b is independently H, halo, CN, C 1 - 6 alkyl, C(O)R, C(O)N(R) 2 , C(O)OR, N(R) 2 , NRC(O)R, OR, S(O) 2 R, C 3 - 7 cycloalkyl, a 4- to 7-membered heterocycloalkyl ring, phenyl, an 8- to 10-membered bicyclic aryl ring, or a 5- or 6-membered heteroaryl ring, wherein the 4- to 7-membered heterocycloalkyl ring has 1 or 2 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, and the 5- or 6-membered heteroaryl ring has 1, 2, 3, or 4 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur;

each R 7 is independently a 4- to 7-membered heterocycloalkyl ring, phenyl, an 8- to 10-membered bicyclic aryl ring, or a 5- or 6-membered heteroaryl ring, wherein each 4- to 7-membered heterocycloalkyl ring independently has 1 or 2 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, and each 5- or 6-membered heteroaryl ring independently has 1, 2, 3, or 4 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, and further wherein each 4- to 7-membered heterocycloalkyl ring, phenyl, 8- to 10-membered bicyclic aryl ring, and 5- or 6-membered heteroaryl ring is optionally and independently substituted with one or more substituents independently selected from the group consisting of halo, CN, C 1 - 6 alkyl, C 1 - 6 haloalkyl, NH 2 , NH(C 1 - 6 alkyl), N(C 1 - 6 alkyl) 2 , OH, and O(C 1 - 6 alkyl);

each R is independently H, C 1 - 6 aliphatic, a saturated or partially unsaturated 4- to 7-membered heterocyclic ring, phenyl, an 8- to 10-membered bicyclic aryl ring, or a 5- or 6-membered heteroaryl ring, wherein the saturated or partially unsaturated 4- to 7-membered heterocyclic ring has 1 or 2 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, and the 5- or 6-membered heteroaryl ring has 1, 2, 3, or 4 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur; or

two geminal R groups, together with the nitrogen atom to which they are attached, form a saturated or partially unsaturated 4- to 7-membered heterocyclic ring or a 5- or 6-membered heteroaryl ring, wherein the 4- to 7-membered heterocyclic ring or the 5- or 6-membered heteroaryl ring has 0, 1, 2, or 3 additional heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur;

R 5a is H, halo, CN, C 1-6 alkyl, or C 1-6 haloalkyl;

R 6a is H or C 1-6 alkyl;

R 6b is H or C 1-6 alkyl; or

R 6a and R 6b , joined together, form a single bond;

R 6c is H or C 1-6 alkyl, wherein the C 1-6 alkyl is optionally substituted with N(CH 3 ) 2 ;

Cy 2 is a 4- to 7-membered heterocycloalkyl ring, phenyl, or pyridyl, wherein the 4- to 7-membered heterocycloalkyl ring has 1 or 2 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur;

m is 1, 2, or 3; and

n is 1, 2, 3, or 4.

2. The compound according to claim 1 , or a pharmaceutically acceptable salt or stereoisomer thereof, wherein —XWY— is —CH 2 C(O)NH—, —CH 2 S(O)NH—, —CH 2 S(O) 2 NH—, —NHC(O)—, —NHC(O)CH 2 , —NHC(O)NH—, —NHS(O)CH 2 —, —NHS(O)NH—, —NHS(O) 2 CH 2 —, or —NHS(O) 2 NH—.

3. The compound according to claim 1 , or a pharmaceutically acceptable salt or stereoisomer thereof, wherein:

R 7 is pyrrolidinyl, piperidinyl, piperazinyl, morpholinyl, imidazolyl, or pyridyl;

wherein the imidazolyl is optionally substituted with one or more substituents independently selected from the group consisting of F, Cl, CN, CH 3 , CH 2 CH 3 , CH(CH 3 ) 2 , and CF 3 ; and

wherein the pyridyl is optionally substituted with one or more substituents independently selected from the group consisting of F, Cl, CN, CH 3 , CH 2 CH 3 , CH(CH 3 ) 2 , CF 3 , NH 2 , and OH.

4. The compound according to claim 1 , or a pharmaceutically acceptable salt or stereoisomer thereof, wherein Cy 2 is azetidinyl, pyrrolidinyl, piperidinyl, azepinyl, phenyl, or pyridyl.

5. The compound according to claim 1 , wherein the compound is according to formula (XXI):

or a pharmaceutically acceptable salt or stereoisomer thereof,

wherein:

R 8 is H; and

R 9 is H.

6. The compound according to claim 1 , wherein the compound is according to formula (IIc) or formula (IId):

or a pharmaceutically acceptable salt or stereoisomer thereof,

wherein:

R 2 is H, F, Cl, CN, CH 3 , CH 2 CH 3 , CH(CH 3 ) 2 , or CF 3 .

7. The compound according to claim 1 , wherein the compound is according to formula (IIIc) or formula (IIId):

or a pharmaceutically acceptable salt or stereoisomer thereof,

wherein:

R 1 is H, F, Cl, CN, CH 3 , CH 2 CH 3 , CH(CH 3 ) 2 , or CF 3 .

8. The compound according to claim 1 , wherein the compound is according to formula (XXIIa) or formula (XXIIb):

or a pharmaceutically acceptable salt or stereoisomer thereof.

9. The compound according to claim 1 , wherein the compound is according to formula (IVa), formula (IVb), formula (XXIIIa), or formula (XXIIIb):

or a pharmaceutically acceptable salt or stereoisomer thereof,

wherein:

p is 0, 1, 2, or 3.

10. The compound according to claim 1 , wherein the compound is according to formula (Va), formula (Vb), formula (XXIVa), or formula (XXIVb):

or a pharmaceutically acceptable salt or stereoisomer thereof,

wherein:

p is 0, 1, 2, or 3.

11. The compound according to claim 1 , wherein the compound is according to formula (VIa), formula (VIb), formula (XXVa), or formula (XXVb):

or a pharmaceutically acceptable salt or stereoisomer thereof,

wherein:

p is 0, 1, 2, or 3.

12. The compound according to claim 1 , wherein the compound is according to formula (VIIa), formula (VIIb), formula (VIIc), formula (VIIIa), formula (VIIIb), formula (VIIIc), formula (XXVIa), formula (XXVIb), or formula (XXVIc):

or a pharmaceutically acceptable salt or stereoisomer thereof.

13. The compound according to claim 12 , or a pharmaceutically acceptable salt or stereoisomer thereof, wherein:

(i)R 6a is H;

R 6b is H; and

R 6c is H; or

(ii) R 6a is H;

R 6b is H; and

R 6c is CH 3 or CH 2 CH 3 ; or

(iii) R 6a is H;

R 6b is H; and

R 6c is CH 2 N(CH 3 ) 2 ; or

(iv) R 6a and R 6b , joined together, form a single bond; and

R 6c is CH 3 .

14. The compound according to claim 1 , wherein the compound is according to formula (IXa), formula (IXb), formula (IXc), formula (Xa), formula (Xb), formula (Xc), formula (XIa), formula (XIb), formula (XIc), formula (XIIa), formula (XIIb), or formula (XIIc):

or a pharmaceutically acceptable salt or stereoisomer thereof.

15. The compound according to claim 1 , wherein the compound is according to formula (XIIIa), formula (XIIIb), formula (XIIIc), formula (XIVa), formula (XIVb), or formula (XIVc):

or a pharmaceutically acceptable salt or stereoisomer thereof.

16. The compound according to claim 1 , wherein the compound is according to formula (XVI), formula (XVII), formula (XXVIIa), formula (XXVIIb), formula (XXVIIc), formula (XXVIIIa), formula (XXVIIIb), or formula (XXVIIIc):

or a pharmaceutically acceptable salt or stereoisomer thereof.

17. The compound according to claim 1 , wherein the compound is according to formula (XXIXa), formula (XXIXb), or formula (XXIXc):

or a pharmaceutically acceptable salt or stereoisomer thereof.

18. The compound according to claim 1 , wherein the compound is:

or a pharmaceutically acceptable salt or stereoisomer thereof.

19. The compound according to claim 1 , wherein the compound is:

or a pharmaceutically acceptable salt or stereoisomer thereof.

20. The compound according to claim 1 , wherein the compound is:

or a pharmaceutically acceptable salt or stereoisomer thereof.

21. The compound according to claim 1 , wherein the compound is:

or a pharmaceutically acceptable salt or stereoisomer thereof.

22. The compound according to claim 1 , wherein the compound is:

or a pharmaceutically acceptable salt or stereoisomer thereof.

23. A pharmaceutical composition comprising a pharmaceutically acceptable carrier and a therapeutically effective amount of a compound according to claim 1 , or a pharmaceutically acceptable salt or stereoisomer thereof.

24. The pharmaceutical composition according to claim 23 , wherein the pharmaceutical composition is formulated for a route of administration selected from the group consisting of buccal administration, nasal administration, oral administration, parenteral administration, rectal administration, and topical administration.

25. A method for inhibiting menin-MLL activity in a patient, comprising administering to the patient in need thereof a therapeutically effective amount of the pharmaceutical composition according to claim 23 .

26. The method according to claim 25 , wherein the patient has an autoimmune disease or an autoimmune condition.