Arginine methyltransferase inhibitors and uses thereof

1. A compound of Formula (VI):

or a pharmaceutically acceptable salt thereof,

wherein X is N, Z is NR 4 , and Y is CR 5 ; or

X is NR 4 , Z is N, and Y is CR 5 ; or

X is CR 5 , Z is NR 4 , and Y is N; or

X is CR 5 , Z is N, and Y is NR 4 ;

R x is optionally substituted C 1-4 alkyl or optionally substituted C 3-4 cycloalkyl;

L 1 is a bond, —O—, —N(R B )—, —S—, —C(O)—, —C(O)O—, —C(O)S—, —C(O)N(R B )—, —C(O)N(R B )N(R B )—, —OC(O)—, —OC(O)N(R B )—, —NR B C(O)—, —NR B C(O)N(R B )—, —NR B C(O)N(R B )N(R B )—, —NR B C(O)O—, —SC(O)—, —C(═NR B )—, —C(═NNR B )—, —C(═NOR A )—, —C(═NR B )N(R B )—, —NR B C(═NR B )—, —C(S)—, —C(S)N(R B )—, —NR B C(S)—, —S(O)—, —OS(O) 2 —, —S(O) 2 O—, —SO 2 —, —N(R B )SO 2 —, —SO 2 N(R B )—, or an optionally substituted C 1-6 saturated or unsaturated hydrocarbon chain, wherein one or more methylene units of the hydrocarbon chain is optionally and independently replaced with —O—, —N(R B )—, —S—, —C(O)—, —C(O)O—, —C(O)S—, —C(O)N(R B )—, —C(O)N(R B )N(R B )—, —OC(O)—, —OC(O)N(R B )—, —NR B C(O)—, —NR B C(O)N(R B )—, —NR B C(O)N(R B )N(R B )—, —NR B C(O)O—, —SC(O)—, —C(═NR B )—, —C(═NNR B )—, —C(═NOR A )—, —C(═NR B )N(R B )—, —NR B C(═NR B )—, —C(S)—, —C(S)N(R B )—, —NR B C(S)—, —S(O)—, —OS(O) 2 —, —S(O) 2 O—, —SO 2 —, —N(R B )SO 2 —, or —SO 2 N(R B )—;

each R A is independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen protecting group when attached to an oxygen atom, and a sulfur protecting group when attached to a sulfur atom;

each R B is independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, and a nitrogen protecting group, or an R B and R W on the same nitrogen atom may be taken together with the intervening nitrogen to form an optionally substituted heterocyclic ring;

Ring A is optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl;

R 3 is hydrogen, C 1-4 alkyl, or C 3-4 cycloalkyl;

R 4 is hydrogen, optionally substituted C 1-6 alkyl, optionally substituted C 2-6 alkenyl, optionally substituted C 2-6 alkynyl, optionally substituted C 3-7 cycloalkyl, optionally substituted 4- to 7-membered heterocyclyl; or optionally substituted C 1-4 alkyl-Cy;

Cy is optionally substituted C 3-7 cycloalkyl, optionally substituted 4- to 7-membered heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl; and

R 5 is hydrogen, halo, —CN, optionally substituted C 1-4 alkyl, or optionally substituted C 3-4 cycloalkyl;

wherein, and unless otherwise specified,

heterocyclyl or heterocyclic refers to a radical of a 3-10 membered nonaromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur;

carbocyclyl or carbocyclic refers to a radical of a nonaromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms and zero heteroatoms in the non-aromatic ring system; aryl refers to a radical of a monocyclic or polycyclic aromatic ring system having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system; and

heteroaryl refers to a radical of a 5-10 membered monocyclic or bicyclic 4n+2 aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur.

2. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein the compound is of Formula (VI-a), Formula (VI-b), Formula (VI-c), Formula VI-d), Formula (VI-e), Formula (VI-f), Formula (VI-g), Formula (VI-h), Formula (VI-i), Formula (VI-j), Formula (VI-k), or Formula (VI-l):

or a pharmaceutically acceptable salt thereof;

wherein p is 1, 2, 3, 4, 5, or 6.

3. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein R 4 is hydrogen or optionally substituted C 1-6 alkyl.

4. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein R 5 is hydrogen or optionally substituted C 1-4 alkyl.

5. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein Ring A is of Formula (q-7)-(q-17):

wherein:

V 21 , V 22 , V 23 , and V 24 are each independently O, S, NR N , C═O, or C(R C ) 2 as valency permits, provided no more than two of V 21 , V 22 , V 23 , and V 24 is O, S, or NR N , or

wherein one of V 21 , V 22 , V 23 , and V 24 and another of V 21 , V 22 , V 23 , and V 24 adjacent to each other are joined to form an N═C(R C ) or C(R C )═C(R C ) group provided the ring thus formed is not an aromatic ring;

each instance of R C is independently hydrogen, halo, —CN, —NO 2 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, —OR A , —N(R B ) 2 , —SR A , —C(═O)R A , —C(O)OR A , —C(O)SR A , —C(O)N(R B ) 2 , —C(O)N(R B )N(R B ) 2 , —OC(O)R A , —OC(O)N(R B ) 2 , —NR B C(O)R A , —NR B C(O)N(R B ) 2 , —

6. The compound of claim 5 , or a pharmaceutically acceptable salt thereof, wherein Formula (q-7)-(q-17) is of Formula (q-46)-(q-49):

7. The compound of claim 5 , or a pharmaceutically acceptable salt thereof, wherein Formula (q-7)-(q-17) is of Formula (q-46a)-(q-49a):

8. The compound of claim 5 , or a pharmaceutically acceptable salt thereof, wherein Formula (q-7)-(q-17) is of Formula (q-50a)-(q-57a):

NR B C(O)N(R B )N(R B ) 2 , —NR B C(O)OR A , —SC(O)R A , —C(═NR B )R A , —C(═NNR B )R A , —C(═NOR A )R A , —C(═NR B )N(R B ) 2 , —NR B C(═NR B )R B , —C(═S)R A , —C(═S)N(R B ) 2 , —NR B C(═S)R A , —S(O)R A , —OS(O) 2 R A , —SO 2 R A , —NR B SO 2 R A , or —SO 2 N(R B ) 2 ;

each instance of R N is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —C(═O)R A , —C(═O)OR A , —C(═O)SR A , —C(═O)N(R B ) 2 , —C(═NR B )R A , —C(═NNR B )R A , —C(═NOR A )R A , —C(═NR B )N(R B ) 2 , —C(═S)R A , —C(═S)N(R B ) 2 , —S(═O)R A , —SO 2 R A , —SO 2 N(R B ) 2 , or a nitrogen protecting group, or two R N groups are joined to form an optionally substituted heterocyclic ring, or one R N group and one R D group are joined to form an optionally substituted heterocyclic ring;

each instance of R F is independently hydrogen or halo; and

each instance of R D is independently hydrogen, halo, —CN, —NO 2 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, —OR A , —N(R B ) 2 , —SR A , —C(═O)R A , —C(O)OR A , —C(O)SR A , —C(O)N(R B ) 2 , —C(O)N(R B )N(R B ) 2 , —OC(O)R A , —OC(O)N(R B ) 2 , —NR B C(O)R A , —NR B C(O)N(R B ) 2 , —NR B C(O)N(R B )N(R B ) 2 , —NR B C(O)OR A , —SC(O)R A , —C(═NR B )R A , —C(═NNR B )R A , —C(═NOR A )R A , —C(═NR B )N(R B ) 2 , —NR B C(═NR B )R B , —C(═S)R A , —C(═S)N(R B ) 2 , —NR B C(═S)R A , —S(O)R A , —OS(O) 2 R A , —SO 2 R A , —NR B SO 2 R A , or —SO 2 N(R B ) 2 ; or two R D groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring.

9. The compound of claim 5 , or a pharmaceutically acceptable salt thereof, wherein Formula (q-7)-(q-17) is of Formula (r-1) to (r-4):

wherein V 26 , V 27 , V 28 , V 29 , and V 30 are each independently O, S, NR Na , C═O, or C(R E ) 2 as valency permits, provided no more than two of V 26 , V 27 , V 28 , V 29 , and V 30 is O, S, or NR Na ; or

wherein one of V 26 , V 27 , V 28 , V 29 , and V 30 and another of V 26 , V 27 , V 28 , V 29 , and V 30 adjacent to each other are joined to form an N═C(R E ) or C(R E )═C(R E ) group;

each instance of R E is independently hydrogen, halo, —CN, —NO 2 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, —OR A , —N(R B ) 2 , —SR A , —C(═O)R A , —C(O)OR A , —C(O)SR A , —C(O)N(R B ) 2 , —C(O)N(R B )N(R B ) 2 , —OC(O)R A , —OC(O)N(R B ) 2 , —NR B C(O)R A , —NR B C(O)N(R B ) 2 , —NR B C(O)N(R B )N(R B ) 2 , —NR B C(O)OR A , —SC(O)R A , —C(═NR B )R A , —C(═NNR B )R A , —C(═NOR A )R A , —C(═NR B )N(R B ) 2 , —NR B C(═NR B )R B , —C(═S)R A , —C(═S)N(R B ) 2 , —NR B C(═S)R A , —S(O)R A , —OS(O) 2 R A , —SO 2 R A , —NR B SO 2 R A , or —SO 2 N(R B ) 2 ; or two R E groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring; and

each instance of R Na is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —C(═O)R A , —C(═O)OR A , —C(═O)SR A , —C(═O)N(R B ) 2 , —C(═NR B )R A , —C(═NNR B )R A , —C(═NOR A )R A , —C(═NR B )N(R B ) 2 , —C(═S)R A , —C(═S)N(R B ) 2 , —S(═O)R A , —SO 2 R A , —SO 2 N(R B ) 2 , or a nitrogen protecting group.

10. The compound of claim 5 , or a pharmaceutically acceptable salt thereof, wherein Formula (q-7)-(q-17) is of Formula (r-5) to (r-24):

wherein V 26 , V 27 , V 28 , V 29 , and V 30 are each independently O, S, NR Na , C═O, or C(R E ) 2 as valency permits, provided no more than two of V 26 , V 27 , V 28 , V 29 , and V 30 is O, S, or NR Na ; or

wherein one of V 26 , V 27 , V 28 , V 29 , and V 30 and another of V 26 , V 27 , V 28 , V 29 , and V 30 adjacent to each other are joined to form an N═C(R E ) or C(R E )═C(R E ) group;

each instance of R E is independently hydrogen, halo, —CN, —NO 2 , optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, —OR A , —N(R B ) 2 , —SR A , —C(═O)R A , —C(O)OR A , —C(O)SR A , —C(O)N(R B ) 2 , —C(O)N(R B )N(R B ) 2 , —OC(O)R A , —OC(O)N(R B ) 2 , —NR B C(O)R A , —NR B C(O)N(R B ) 2 , —NR B C(O)N(R B )N(R B ) 2 , —NR B C(O)OR A , —SC(O)R A , —C(═NR B )R A , —C(═NNR B )R A , —C(═NOR A )R A , —C(═NR B )N(R B ) 2 , —NR B C(═NR B )R B , —C(═S)R A , —C(═S)N(R B ) 2 , —NR B C(═S)R A , —S(O)R A , —OS(O) 2 R A , —SO 2 R A , —NR B SO 2 R A , or —SO 2 N(R B ) 2 ; or two R E groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring; and

each instance of R Na is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —C(═O)R A , —C(═O)OR A , —C(═O)SR A , —C(═O)N(R B ) 2 , —C(═NR B )R A , —C(═NNR B )R A , —C(═NOR A )R A , —C(═NR B )N(R B ) 2 , —C(═S)R A , —C(═S)N(R B ) 2 , —S(═O)R A , —SO 2 R A , —SO 2 N(R B ) 2 , or a nitrogen protecting group.

11. The compound of claim 10 , or a pharmaceutically acceptable salt thereof, wherein Formula (r-5) to (r-24) is of Formula (r-148) to (r-161):

12. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, selected from:

and pharmaceutically acceptable salts thereof.

13. A pharmaceutical composition comprising a compound of claim 1 , or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.

14. A kit or packaged pharmaceutical comprising a compound of claim 1 , or a pharmaceutically acceptable salt thereof, and instructions for use thereof.

15. A method of inhibiting an arginine methyl-tranfserase (RMT) comprising contacting a cell with an effective amount of a compound of claim 1 , or a pharmaceutically acceptable salt thereof.

16. A method of modulating gene expression comprising contacting a cell with an effective amount of a compound of claim 1 , or a pharmaceutically acceptable salt thereof.

17. A method of modulating transcription comprising contacting a cell with an effective amount of a compound of claim 1 , or a pharmaceutically acceptable salt thereof.

18. A method of treating a RMT-mediated disorder, comprising administering to a subject in need thereof a therapeutically effective amount of a compound of claim 1 , or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition of claim 13 .

19. The method of claim 18 , wherein the disorder is a proliferative disorder, a neurological disorder, a muscular dystrophy, an autoimmune disorder, a vascular disorder, or a metabolic disorder.

20. The method of claim 19 , wherein the disorder is cancer or amyotrophic lateral sclerosis.