Substituted pyrimidines for treating bacterial infections

1. A compound of Formula II:

or a pharmaceutically acceptable salt thereof,

wherein:

R 1 is H, C 1-6 alkyl, or C 1-6 alkoxy;

R 2 is H, C 1-6 alkyl, —N(R a ) 2 , —OH, or C 1-6 alkoxy;

R 3 is —NH 2 , —OH, or —SH;

Z is O or S;

L 1 is a bond, —C 1-4 alkylene-NR b —, —C 1-4 alkylene-O—, —C 1-4 alkylene-S—, —C 1-4 alkylene-S(O) 2 —, —C(O)—, —C(O)NR b —, —C(O)O—, or —NR b C(O)—;

L 2 is —(CR 4 R 5 ) n —C 0-3 alkylene-, —(CR 4 R 5 ) n —C 0-3 alkylene-CHOR c —, —(CR 4 R 5 ) n —C 0-3 alkylene-C(NOH)—, —(CR 4 R 5 ) n —C 0-3 alkylene-C(O)—, —(CR 4 R 5 ) n —C 0-3 alkylene-C(O)NR 5 —, —(CR 4 R 5 ) n —C 0-3 alkylene-NR 5 —, —(CR 4 R 5 ) n —C 0-3 alkylene-NR 5 C(O)—, —(CR 4 R 5 ) n —C 0-3 alkylene-NR 5 S(O) 2 —, —(CR 4 R 5 ) n —C 0-3 alkylene-O—, —(CR 4 R 5 ) n —C 0-3 alkylene-S(O) 2 —, or —(CR 4 R 5 ) n —C 0-3 alkylene-S(O) 2 NR 5 —;

each R 4 is independently H or C 1-6 alkyl, wherein the C 1-6 alkyl is optionally substituted with one or more substituents independently selected from the group consisting of halogen, —CN, —NO 2 , C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, —C(NR a )NR b R c , —C(O)R a , —C(O)NR b R c , —C(O)OR a , —NR b R c , —NR a C(NR d )NR b R c , —NR a C(O)R d , —NR a C(O)NR b R c , —NR a C(O)OR d , —NR a S(O)R d , —NR a S(O)NR b R c , —NR a S(O) 2 R d , —NR a S(O) 2 NR b R c , —OR a , —OC(NR a )NR b R c , —OC(O)R a , —OC(O)NR b R c , —OC(O)OR a , —OS(O)R a , —OS(O)NR b R c , —OS(O) 2 R a , —OS(O) 2 NR b R c , —P(O)R a R d , —P(O)(OR a )R d , —P(O)(OR a )(OR d ), —SR a , —S(O)R a , —S(O)NR b R c , —S(O) 2 R a , —S(O) 2 NR b R c , C 3-10 cycloalkyl, C 6-14 aryl, heteroaryl, and heterocyclyl, wherein the C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-10 cycloalkyl, C 6-14 aryl, heteroaryl, or heterocyclyl substituent is optionally further substituted with one or more substituents independently selected from the group consisting of halogen, —CN, —NO 2 , —C(O)R a , —C(O)NR b R c , —C(O)OR a , —NR b R c , —NR a C(O)R d , —NR a C(O)NR b R c , —NR a C(O)OR d , —NR a S(O) 2 R d , —NR a S(O) 2 NR b R c , —OR a , —OC(O)R a , —OC(O)NR b R c , —OC(O)OR a , —OS(O) 2 R a , —OS(O)NR b R c , —SR a , —S(O)R a , —S(O) 2 R a , and —S(O) 2 NR b R c ;

each R 5 is independently H, C 1-6 alkyl, —C 0-4 alkylene-halogen, —C 0-4 alkylene-CN, —C 0-4 alkylene-NO 2 , —C 0-4 alkylene-C 2-4 alkenyl, —C 0-4 alkylene-C 2-4 alkynyl, —C 0-4 alkylene-C(O)H, —C 0-4 alkylene-C(O)—C 1-6 alkyl, —C 0-4 alkylene-C(O)NR b R f , —C 0-4 alkylene-C(O)OR f , —C 0-4 alkylene-N(R f ) 2 , —C 0-4 alkylene-NR b C(O)R f , —C 0-4 alkylene-OR f , —C 0-4 alkylene-S(O) 2 R f , —C 0-4 alkylene-C 6-14 aryl, —C 1-4 alkylene-5- to 14-membered heteroaryl, C 2-6 alkenyl, C 2-6 alkynyl, C 3 -C 8 cycloalkyl, C 2 -C 7 heterocyclyl, C 6-14 aryl, or 5- to 14-membered heteroaryl, wherein the C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3 -C 8 cycloalkyl, C 6-14 aryl, or 5- to 14-membered heteroaryl is optionally substituted with one or more substituents independently selected from the group consisting of halogen, —CN, —NO 2 , C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, —C(NR a )NR b R c , —C(O)R a , —C(O)NR b R c , —C(O)OR a , —NR b R c , —NR a C(NR d )NR b R c , —NR a C(O)R d , —NR a C(O)NR b R c , —NR a C(O)OR d , —NR a S(O)R d , —NR a S(O)NR b R c , —NR a S(O) 2 R d , —NR a S(O) 2 NR b R c , —OR a , —OC(NR a )NR b R c , —OC(O)R a , —OC(O)NR b R c , —OC(O)OR a , —OS(O)R a , —OS(O)NR b R c , —OS(O) 2 R a , —OS(O) 2 NR b R c , —P(O)R a R d , —P(O)(OR a )R d , —P(O)(OR a )(OR d ), —SR a , —S(O)R a , —S(O)NR b R c , —S(O) 2 R a , —S(O) 2 NR b R c , C 3-10 cycloalkyl, heterocyclyl, C 6-14 aryl, and heteroaryl, wherein the C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-10 cycloalkyl, heterocyclyl, C 6-14 aryl, or heteroaryl is optionally further substituted with one or more substituents independently selected from the group consisting of halogen, —CN, —NO 2 , —C(O)R a , —C(O)NR b R c , —C(O)OR a , —NR b R c , —NR a C(O)R d , —NR a C(O)NR b R c , —NR a C(O)OR d , —NR a S(O) 2 R d , —NR a S(O) 2 NR b R c , —OR a , —OC(O)R a , —OC(O)NR b R c , —OC(O)OR a , —OS(O)NR b R c , —OS(O) 2 R a , —SR a , —S(O)R a , —S(O) 2 R a , and —S(O) 2 NR b R c ;

each R f is independently H, alkyl, alkenyl, alkynyl, alkoxy, cycloalkyl, heterocyclyl, aryl, or heteroaryl, wherein the alkyl, alkenyl, alkynyl, alkoxy, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more substituents independently selected from the group consisting of halogen, —CN, —NO 2 , C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, —C(NR a )NR b R c , —C(O)R a , —C(O)NR b R c , —C(O)OR a , —NR b R c , —NR a C(NR d )NR b R c , —NR a C(O)R d , —NR a C(O)NR b R c , —NR a C(O)OR d , —NR a S(O)R d , —NR a S(O)NR b R c , —NR a S(O) 2 R d , —NR a S(O) 2 NR b R c , —OR a , —OC(NR a )NR b R c , —OC(O)R a , —OC(O)NR b R c , —OC(O)OR a , —OS(O)R a , —OS(O)NR b R c , —OS(O) 2 R a , —OS(O) 2 NR b R c , —P(O)R a R d , —P(O)(OR a )R d , —P(O)(OR a )(OR d ), —SR a , —S(O)R a , —S(O)NR b R c , —S(O) 2 R a , —S(O) 2 NR b R c , C 3-10 cycloalkyl, heterocyclyl, C 6-14 aryl, and heteroaryl, wherein the C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-10 cycloalkyl, heterocyclyl, C 6-14 aryl, or heteroaryl is optionally further substituted with one or more substituents independently selected from the group consisting of halogen, —CN, —NO 2 , —C(O)R a , —C(O)NR b R c , —C(O)OR a , —NR b R c , —NR a C(O)R d , —NR a C(O)NR b R c , —NR a C(O)OR d , —NR a S(O) 2 R d , —NR a S(O) 2 NR b R c , —OR a , —OC(O)R a , —OC(O)NR b R c , —OC(O)OR a , —OS(O) 2 R a , —OS(O)NR b R c , —SR a , —S(O)R a , —S(O) 2 R a , and —S(O) 2 NR b R c ;

L 3 is —C 2-6 alkenylene- or —C 2-6 alkynylene-;

L 4 is —C 1-4 alkylene-, —C(O)—, —C(O)NR e —, —C(O)O—, or —NR e C(O)—;

G 1 is —C 6-14 arylene- or -5- to 14-membered heteroarylene-;

G 2 is —C 6-14 arylene- or -5- to 14-membered heteroarylene-;

G 3 is H, alkyl, alkenyl, alkynyl, alkoxy, C 3-7 cycloalkyl, C 3-10 heterocycloalkyl, C 3-10 heterocycloalkylene-C 1-4 alkyl, aryl, or heteroaryl, wherein the alkyl, alkenyl, alkynyl, alkoxy, C 3-7 cycloalkyl, C 3-10 heterocycloalkyl, aryl, or heteroaryl is optionally substituted with one or more substituents independently selected from the group consisting of halogen, —CN, —NO 2 , C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, —C(NR a )NR b R c , —C(O)R a , —C(O)NR b R c , —C(O)OR a , —NR b R c , —NR a C(NR d )NR b R c , —NR a C(O)R d , —NR a C(O)NR b R c , —NR a C(O)OR d , —NR a S(O)R d , —NR a S(O)NR b R c , —NR a S(O) 2 R d , —NR a S(O) 2 NR b R c , —OR a , —OC(NR a )NR b R c , —OC(O)R a , —OC(O)NR b R c , —OC(O)OR a , —OS(O)R a , —OS(O)NR b R c , —OS(O) 2 R a , —OS(O) 2 NR b R c , —P(O)R a R d , —P(O)(OR a )R d , —P(O)(OR a )(OR d ), —SR a , —S(O)R a , —S(O)NR b R c , —S(O) 2 R a , —S(O) 2 NR b R c , C 3-10 cycloalkyl, heterocyclyl, C 6-14 aryl, and heteroaryl, wherein the C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-10 cycloalkyl, heterocyclyl, C 6-14 aryl, or heteroaryl is optionally further substituted with one or more substituents independently selected from the group consisting of halogen, —CN, —NO 2 , —C(O)R a , —C(O)NR b R c , —C(O)OR a , —NR b R c , —NR a C(O)R d , —NR a C(O)NR b R c , —NR a C(O)OR d , —NR a S(O) 2 R d , —NR a S(O) 2 NR b R c , —OR a , —OC(O)R a , —OC(O)NR b R c , —OC(O)OR a , —OS(O)NR b R c , —OS(O) 2 R a , —SR a , —S(O)R a , —S(O) 2 R a , and —S(O) 2 NR b R c ;

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

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

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

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

R e is H or C 1-6 alkyl; and

n is 1 or 2.

2. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein L 1 is a bond, —C 1-4 alkylene-NR b —, —C 1-4 alkylene-O—, —C 1-4 alkylene-S—, or —C 1-4 alkylene-S(O) 2 —.

3. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein L 2 is —(CR 4 R 5 ) n —C 0-3 alkylene-, —(CR 4 R 5 ) n —C 0-3 alkylene-CHOR c —, —(CR 4 R 5 ) n —C 0-3 alkylene-C(O)—, —(CR 4 R 5 ) n —C 0-3 alkylene-C(O)NR 5 —, —(CR 4 R 5 ) n —C 0-3 alkylene-NR 5 —, —(CR 4 R 5 ) n —C 0-3 alkylene-NR 5 C(O)—, —(CR 4 R 5 ) n —C 0-3 alkylene-O—, or —(CR 4 R 5 ) n —C 0-3 alkylene-S(O) 2 —.

4. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein L 2 is —(CR 4 R 5 ) n —C 0-3 alkylene- or —(CR 4 R 5 ) n —C 0-3 alkylene CHOR c .

5. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein L 3 is —C 2-6 alkynylene-.

6. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein each R 5 is independently —C 1-4 alkylene-N(R f ) 2 , —C 1-4 alkylene-OR f , —C 1-4 alkylene-S(O) 2 R f , —C 1-4 alkylene-C 6-14 aryl, or —C 1-4 alkylene-5- to 14-membered heteroaryl.

7. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein:

each R 4 is independently H; and

each R 5 is independently H, —C 1-6 alkyl, or —C 0-4 alkylene-OR f .

8. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein:

each R 4 is independently H; and

each R 5 is independently H, —C 0-4 alkylene-CN, —C 0-4 alkylene-C(O)—C 1-6 alkyl, or —C 0-4 alkylene-OR f .

9. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein:

each R 4 is independently H; and

each R 5 is independently H, —C 1-4 alkylene-C(O)NR′R f , —C 1-4 alkylene-N(R f ) 2 , —C 1-4 alkylene-NR b C(O)R f , or —C 1-4 alkylene-OR f .

10. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein:

R 1 is H or C 1-6 alkyl;

R 2 is H, C 1-6 alkyl, —OH, or C 1-6 alkoxy;

R 3 is —OH;

Z is O;

L 1 is a bond, —C 1-4 alkylene-NR b —, —C 1-4 alkylene-S(O) 2 —, —C(O)—, —C(O)NR b —, —C(O)O—, or —NR b C(O)—;

L 2 is —(CR 4 R 5 ) n —C 0-3 alkylene-, —(CR 4 R 5 ) n —C 0-3 alkylene-CHOR c —, —(CR 4 R 5 ) n —C 0-3 alkylene-C(NOH)—, —(CR 4 R 5 ) n —C 0-3 alkylene-C(O)—, —(CR 4 R 5 ) n —C 0-3 alkylene-C(O)NR 5 —, —(CR 4 R 5 ) n —C 0-3 alkylene-NR 5 —, —(CR 4 R 5 ) n —C 0-3 alkylene-NR 5 C(O)—, or —(CR 4 R 5 ) n —C 0-3 alkylene-O—;

each R 5 is independently H, C 1-6 alkyl, —C 1-4 alkylene-N(R f ) 2 , —C 1-4 alkylene-OR f , or —C 1-4 alkylene-S(O) 2 R f ;

L 3 is —C 2-6 alkynylene-;

G 1 is —C 6 arylene- or -5- to 6-membered heteroarylene-;

G 2 is —C 6 arylene- or -5- to 6-membered heteroarylene-; and

G 3 is H, C 1-4 alkylene-O—C 1-4 alkyl, alkoxy, C 3-7 cycloalkyl, C 3-10 heterocycloalkyl, C 3-10 heterocycloalkylene-C 1-4 alkyl, C 3-10 heterocycloalkylene-O—C 1-4 alkyl, C 6-14 aryl, or 5- to 14-membered heteroaryl, wherein the C 1-4 alkyl, alkoxy, C 3-7 cycloalkyl, C 3-10 heterocycloalkyl, C 6-14 aryl, or heteroaryl is optionally substituted.

11. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein:

R 1 is H or C 1-6 alkyl;

R 2 is H or C 1-6 alkyl;

R 3 is —OH;

Z is O;

L 1 is a bond, —C(O)—, —C(O)NR b —, —C(O)O—, or —NR b C(O)—;

L 2 is —[C(R 4 )(R 5 )] n —C 0-3 alkylene-;

each R 5 is independently H or C 1-6 alkyl;

L 3 is —C 2-6 alkynylene-;

L 4 is —C 1-4 alkylene- or —C(O)—;

G 1 is —C 6 arylene- or -5- to 6-membered heteroarylene-;

G 2 is —C 6 arylene- or -5- to 6-membered heteroarylene-; and

G 3 is H, C 1-4 alkylene-O—C 1-4 alkyl, alkoxy, C 3-7 cycloalkyl, C 3-10 heterocycloalkyl, C 3-10 heterocycloalkylene-C 1-4 alkyl, C 3-10 heterocycloalkylene-O—C 1-4 alkyl, C 6-14 aryl, or 5- to 14-membered heteroaryl, wherein the C 1-4 alkyl, alkoxy, C 3-7 cycloalkyl, C 3-10 heterocycloalkyl, C 6-14 aryl, or heteroaryl is optionally substituted; and

n is 1.

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

or a pharmaceutically acceptable salt thereof.

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

14. A method for modulating the activity of UDP-{3-O—[(R)-3-hydroxymyristoyl]}-N-acetylglucosamine deacetylase in a subject, comprising administering to the subject in need thereof a therapeutically effective amount of a compound of claim 1 , or a pharmaceutically acceptable salt thereof.

15. A method for treating a gram-negative bacterial infection in a subject, comprising administering to the subject in need thereof a therapeutically effective amount of a compound of claim 1 , or a pharmaceutically acceptable salt thereof.

16. A compound selected from the group consisting of:

or a pharmaceutically acceptable salt thereof.