IP Library › Patent Application 19335913
Patent Application
App. No. 19/335,913

CARBAMATE NUCLEOTIDE ANALOGUES

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Quick Facts
Patent No.
US None
App. No.
19/335,913
Abstract

Disclosed herein, inter alia, are compounds and methods of making and using thereof.

Claims (63)

1 . A compound, or a salt thereof, having the formula:

B 1 is a nucleobase;

R 1 is a polyphosphate moiety, monophosphate moiety, 5′-nucleoside protecting group, or —OH;

R 2 is hydrogen, halogen, —CCl 3 , —CBr 3 , —CF 3 , —CI 3 , —CHCl 2 , —CHBr 2 , —CHF 2 ,

—CHI 2 , —CH 3 Cl, —CH 2 Br, —CH 2 F, —CH 2 I, —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH,

—SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC(O)NHNH 2 , —NHC(O)NH 2 , —NHSO 2 H,

—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl 3 , —OCF 3 , —OCBr 3 , —OCI 3 , —OCHCl 2 , —OCHBr 2 ,

—OCHI 2 , —OCHF 2 , —OCH 3 Cl, —OCH 2 Br, —OCH 2 I, —OCH 2 F, —N 3 , —SF 5 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, or a polymerase-compatible cleavable moiety;

L 1 is a bond or a covalent linker; and

R 3 is hydrogen, halogen, —CCl 3 , —CBr 3 , —CF 3 , —CI 3 , —CHCl 2 , —CHBr 2 , —CHF 2 ,

—CHI 2 , —CH 3 Cl, —CH 2 Br, —CH 2 F, —CH 2 I, —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH,

—SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC(O)NHNH 2 , —NHC(O)NH 2 , —NHSO 2 H,

—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl 3 , —OCF 3 , —OCBr 3 , —OCI 3 , —OCHCl 2 , —OCHBr 2 ,

—OCHI 2 , —OCHF 2 , —OCH 3 Cl, —OCH 2 Br, —OCH 2 I, —OCH 2 F, —N 3 , —SF 5 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl.

2 . A compound, or a salt thereof, having the formula:

wherein,

B 2 is a divalent nucleobase;

R 1 is a polyphosphate moiety, monophosphate moiety, 5′-nucleoside protecting group, or —OH;

R 2 is hydrogen, halogen, —CCl 3 , —CBr 3 , —CF 3 , —CI 3 , —CHCl 2 , —CHBr 2 , —CHF 2 ,

—CHI 2 , —CH 3 Cl, —CH 2 Br, —CH 2 F, —CH 2 I, —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH,

—SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC(O)NHNH 2 , —NHC(O)NH 2 , —NHSO 2 H,

—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl 3 , —OCF 3 , —OCBr 3 , —OCI 3 , —OCHCl 2 , —OCHBr 2 ,

—OCHI 2 , —OCHF 2 , —OCH 3C 1, —OCH 2 Br, —OCH 2 I, —OCH 2 F, —N 3 , —SF 5 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, or a polymerase-compatible cleavable moiety;

L 1 is a bond or a covalent linker; and

R 3 is hydrogen, halogen, —CCl 3 , —CBr 3 , —CF 3 , —CI 3 , —CHCl 2 , —CHBr 2 , —CHF 2 ,

—CHI 2 , —CH 3 Cl, —CH 2 Br, —CH 2 F, —CH 2 I, —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH,

—SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC(O)NHNH 2 , —NHC(O)NH 2 , —NHSO 2 H,

—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl 3 , —OCF 3 , —OCBr 3 , —OCI 3 , —OCHCl 2 , —OCHBr 2 ,

—OCHI 2 , —OCHF 2 , —OCH 3 Cl, —OCH 2 Br, —OCH 2 I, —OCH 2 F, —N 3 , —SF 5 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl;

R 4 is a detectable moiety; and L 100 is a divalent linker.

3 . The compound of claim 1 , wherein L 1 -R 3 is:

4 . The compound of claim 1 , wherein L 1 -R 3 is:

5 . The compound of claim 1 , wherein R 2 is hydrogen.

6 . The compound of claim 1 , wherein R 1 is a monophosphate moiety or polyphosphate moiety.

7 . The compound of claim 1 , wherein B 1 is a cytosine or a derivative thereof, guanine or a derivative thereof, adenine or a derivative thereof, thymine or a derivative thereof, uracil or a derivative thereof, hypoxanthine or a derivative thereof, xanthine or a derivative thereof, 7-methylguanine or a derivative thereof, 5,6-dihydrouracil or a derivative thereof, 5-methylcytosine or a derivative thereof, or 5-hydroxymethylcytosine or a derivative thereof.

8 . The compound of claim 1 wherein B 1 is

9 . The compound of claim 2 , wherein L 100 is a divalent linker comprising

wherein R 9 is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.

10 . The compound of claim 2 , wherein L 100 is a divalent linker comprising

wherein R 102 is unsubstituted C 1 -C 4 alkyl.

11 . The compound of claim 2 , wherein L 100 is

-L 101 -L 102 -L 103 -L 104 -L 105 -;

wherein L 101 , L 102 , L 103 , L 104 , and L 105 are independently a bond, —NH—, —O—,

—C(O)—, —C(O)NH—, —NHC(O)—, —NHC(O)NH—, —C(O)O—, —OC(O)—, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.

12 . The compound of claim 2 , wherein L 100 is a divalent linker comprising:

13 . The compound of claim 2 , wherein L 100 is a divalent linker comprising:

14 . The compound of claim 2 , wherein L 100 is a divalent linker comprising:

15 . The compound of claim 2 , wherein L 100 is a divalent linker comprising

16 . The compound of claim 2 , wherein L 100 is a divalent linker comprising

wherein L 2 is a bond or a divalent linker; and

R 6 is hydrogen, halogen, —CCl 3 , —CBr 3 , —CF 3 , —CI 3 , —CHCl 2 , —CHBr 2 , —CHF 2 ,

—CHI 2 , —CH 3 Cl, —CH 2 Br, —CH 2 F, —CH 2 I, —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH,

—SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC(O)NHNH 2 , —NHC(O)NH 2 , —NHSO 2 H,

—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl 3 , —OCF 3 , —OCBr 3 , —OCI 3 , —OCHCl 2 , —OCHBr 2 ,

—OCHI 2 , —OCHF 2 , —OCH 3 Cl, —OCH 2 Br, —OCH 2 I, —OCH 2 F, —N 3 , —SF 5 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl.

17 . The compound of claim 2 , having the formula:

wherein L 100 has the formula:

18 . The compound of claim 2 , having the formula:

wherein L 100 has the formula:

19 . The compound of claim 2 , having the formula:

wherein L 100 has the formula:

20 . The compound of claim 2 , having the formula:

wherein L 100 has the formula: