MicroRNA compounds and methods for modulating miR-122
Described herein are compositions and methods for the inhibition of miR-122 activity. The compositions have certain nucleoside modifications that yield potent inhibitors of miR-122 activity. The compounds may comprise conjugates to facilitate delivery to the liver. The compositions may be administered to subjects infected with hepatitis C virus, as a treatment for hepatitis C virus and related conditions.
1. A compound comprising a modified oligonucleotide consisting of 16 to 22 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide is complementary to miR-122 (SEQ ID NO: 1) and wherein the modified oligonucleotide comprises at least 16 contiguous nucleosides of the following nucleoside pattern I in the 5′ to 3′ orientation:
(R) X -N Q -N Q -N B -N B -N Q -N B -N Q -N B -N Q -N B -N B -(NZ) Y
wherein each R is, independently, a non-bicyclic nucleoside or a bicyclic nucleoside;
X is from 4 to 10;
each N B is, independently, a bicyclic nucleoside;
each N Q is, independently, a non-bicyclic nucleoside;
Y is 0 or 1; and
N Z is a modified nucleoside or an unmodified nucleoside.
2. The compound of claim 1 , wherein the modified oligonucleotide comprises at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, or 22 contiguous nucleosides of nucleoside pattern I.
3. The compound of claim 1 wherein each bicyclic nucleoside is independently selected from an LNA nucleoside, a cEt nucleoside, and an ENA nucleoside.
4. The compound of claim 1 , wherein each bicyclic nucleoside is a cEt nucleoside.
5. The compound of claim 1 wherein each non-bicyclic nucleoside is independently selected from a β-D-deoxyribonucleoside, a β-D-ribonucleoside, 2′-O-methyl nucleoside, a 2′-O-methoxyethyl nucleoside, and a 2′-fluoronucleoside.
6. The compound of claim 1 wherein each non-bicyclic nucleoside is independently selected from a β-D-deoxyribonucleoside, and a 2′-O-methoxyethyl nucleoside.
7. The compound of claim 1 , wherein X is 4, 7, or 10.
8. The compound of claim 1 , wherein Y is 0.
9. The compound of claim 1 wherein:
a. X is 7;
each R is a 2′-O-methoxyethyl nucleoside;
each N B is an S-cEt nucleoside;
each N Q is a β-D-deoxyribonucleoside; and Y is 0;
b. X is 4; (R) x is N R1 —N R2 —N R3 —N R4 , wherein each of N R1 and N R3 is a S-cEt nucleoside and each of N R2 and N R4 is a β-D-deoxyribonucleoside;
each N B is an S-cEt nucleoside;
each N Q is a β-D-deoxyribonucleoside;
Y is 1; and N Z is a β-D-deoxyribonucleoside
c. X is 4; (R) x is N R1 —N R2 —N R3 —N R4 , wherein each of N R1 and N R4 is a S-cEt nucleoside and each of N R2 and N R3 is a β-D-deoxyribonucleoside;
each N B is an S-cEt nucleoside;
each N Q is a β-D-deoxyribonucleoside;
Y is 1; and N Z is a 2′-O-methoxyethyl nucleoside
d. X is 7; (R) x is N R1 —N R2 —N R3 —N R4 —N R5 —N R6 —N R7 , wherein each of N R1 , N R2 , N R3 , and N R4 and is a 2′-O-methoxyethyl nucleoside, each of N R5 and N R7 is a β-D-deoxyribonucleoside, and N R6 is S-cEt nucleoside;
each N B is an S-cEt nucleoside;
each N Q is a β-D-deoxyribonucleoside; and Y is 0;
e. X is 7; (R) x is N R1 —N R2 —N R3 —N R4 —N R5 —N R6 —N R7 , wherein each of N R1 , N R2 , N R3 , N R4 , and N R5 is a 2′-O-methoxyethyl nucleoside, N R6 is S-cEt nucleoside, and N R7 is a β-D-deoxyribonucleoside;
each N B is an S-cEt nucleoside;
each N Q is a β-D-deoxyribonucleoside; and Y is 0;
f. X is 7; (R) x is N R1 —N R2 —N R3 —N R4 —N R5 —N R6 —N R7 , wherein each of N R1 , N R2 , N R3 , N R4 , N R5 , and N R6 is 2′-O-methoxyethyl nucleoside, and N R7 is a β-D-deoxyribonucleoside;
each N B is an S-cEt nucleoside;
each N Q is a β-D-deoxyribonucleoside; and Y is 0;
g. X is 10; (R) x is N R1 —N R2 —N R3 —N R4 —N R5 —N R6 —N R7 —N R8 —N R9 —N R10 , wherein each of N R1 , N R2 , N R3 , N R4 , N R5 , and N R6 is 2′-O-methoxyethyl nucleoside, each of N R7 and N R9 is a an S-cEt nucleoside; each of N R8 and N R10 is a β-D-deoxyribonucleoside;
each N B is an S-cEt nucleoside;
each N Q is a β-D-deoxyribonucleoside; and Y is 0;
h. X is 10; (R) x is N R1 —N R2 —N R3 —N R4 —N R5 —N R6 —N R7 —N R8 —N R9 —N R10 , wherein each of N R1 , N R2 , N R3 , N R4 , N R5 , and N R6 is 2′-O-methoxyethyl nucleoside, each of N R7 and N R9 is a an S-cEt nucleoside; and each of N R8 and N R10 is a β-D-deoxyribonucleoside;
each N B is an S-cEt nucleoside;
each N Q is a β-D-deoxyribonucleoside;
Y is 1 and Nz is a 2′-O-methoxyethyl nucleoside;
i. X is 4; (R) x is N R1 —N R2 —N R3 —N R4 wherein each of N R1 and N R4 is an S-cEt nucleoside, and each of N R1 and N R3 is a β-D-deoxyribonucleoside;
each N B is an S-cEt nucleoside;
each N Q is a β-D-deoxyribonucleoside;
Y is 1 and N Z is a β-D-deoxyribonucleoside;
j. X is 4; (R) x is N R1 —N R2 —N R3 —N R4 , wherein N R1 is a 2′-O-methoxyethyl nucleoside, each of N R2 and N R4 is an S-cEt nucleoside, and N R3 is a β-D-deoxyribonucleoside;
each N B is an S-cEt nucleoside;
each N Q is a β-D-deoxyribonucleoside;
Y is 1 and N Z is a 2′-O-methoxyethyl nucleoside.
10. The compound of claim 1 , wherein the nucleobase sequence of the modified oligonucleotide is at least 90% complementary to the nucleobase sequence of miR-122 (SEQ ID NO: 1).
11. The compound of claim 1 , wherein at least one internucleoside linkage is a modified internucleoside linkage.
12. The compound of claim 1 , wherein the nucleobase sequence of the modified oligonucleotide is selected from SEQ ID NOs: 3 to 6, wherein each T is independently selected from T and U.
13. The compound of claim 1 , wherein the compound comprises a conjugate moiety linked to the 5′ terminus or the 3′ terminus of the modified oligonucleotide.
14. The compound of claim 13 , wherein the conjugate moiety comprises at least one ligand selected from a carbohydrate, cholesterol, a lipid, a phospholipid, an antibody, a lipoprotein, a hormone, a peptide, a vitamin, a steroid, and a cationic lipid.
15. The compound of claim 13 , wherein the compound has the structure:
L n -linker-MO
wherein each L is, independently, a ligand and n is from 1 to 10; and MO is a modified oligonucleotide.
16. The compound of claim 13 , wherein the compound has the structure:
L n -linker-X-MO
wherein each L is, independently, a ligand and n is from 1 to 10; X is a phosphodiester linkage or a phosphorothioate linkage; and MO is a modified oligonucleotide.
17. The compound of claim 13 , wherein the compound has the structure:
L n -linker-X 1 —N m —X 2 -MO
wherein each L is, independently, a ligand and n is from 1 to 10; each N of N m is, independently, a modified or unmodified nucleoside and m is from 1 to 5; X 1 and X 2 are each, independently, a phosphodiester linkage or a phosphorothioate linkage; and MO is a modified oligonucleotide.
18. The compound of claim 17 , wherein if n is greater than 1, La-linker has the structure:
(L-Q′ n S-Q″—
wherein each L is, independently, a ligand; n is from 1 to 10; S is a scaffold; and Q′ and Q″ are, independently, linking groups.
19. The compound of claim 18 , wherein Q′ and Q″ are each independently selected from a peptide, an ether, polyethylene glycol, an alkyl, a C 1 -C 20 alkyl, a substituted C 1 -C 20 alkyl, a C 2 -C 20 alkenyl, a substituted C 2 -C 20 alkenyl, a C 2 -C 20 alkynyl, a substituted C 2 -C 20 alkynyl, a C 1 -C 20 alkoxy, a substituted C 1 -C 20 alkoxy, amino, amido, a pyrrolidine, 8-amino-3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate, and 6-aminohexanoic acid.
20. The compound of claim 18 , wherein the scaffold links 2, 3, 4, or 5 ligands to a modified oligonucleotide.
21. The compound of claim 17 , wherein the compound has the structure:
wherein:
B is selected from —O—, —S—, —Z—P(Z′)(Z″)O—, —Z—P(Z′)(Z″)O—N m —X—, and —Z—P(Z′)(Z″)O—N m —Y—;
MO is a modified oligonucleotide;
R N is selected from H, methyl, ethyl, propyl, isopropyl, butyl, and benzyl;
Z, Z′, and Z″ are each independently selected from O and S;
each N is, independently, a modified or unmodified nucleoside;
m is from 1 to 5;
X is selected from a phosphodiester linkage and a phosphorothioate linkage;
Y is a phosphodiester linkage; and
the wavy line indicates the connection to the rest of the linker and ligand(s).
22. The compound of claim 17 , wherein n is from 1 to 5.
23. The compound of claim 17 , wherein at least one ligand is a carbohydrate.
24. The compound of claim 17 , wherein at least one ligand is selected from mannose, glucose, galactose, ribose, arabinose, fructose, fucose, xylose, D-mannose, L-mannose, D-galactose, L-galactose, D-glucose, L-glucose, D-ribose, L-ribose, D-arabinose, L-arabinose, D-fructose, L-fructose, D-fucose, L-fucose, D-xylose, L-xylose, alpha-D-mannofuranose, beta-D-mannofuranose, alpha-D-mannopyranose, beta-D-mannopyranose, alpha-D-glucofuranose, Beta-D-glucofuranose, alpha-D-glucopyranose, beta-D-glucopyranose, alpha-D-galactofuranose, beta-D-galactofuranose, alpha-D-galactopyranose, beta-D-galactopyranose, alpha-D-ribofuranose, beta-D-ribofuranose, alpha-D-ribopyranose, beta-D-ribopyranose, alpha-D-fructofuranose, alpha-D-fructopyranose, glucosamine, galactosamine, sialic acid, N-acetylgalactosamine.
25. The compound of claim 17 , wherein each ligand is N-acetylgalactosamine.
26. The compound of claim 17 , wherein the compound has the structure:
wherein each N of N m is, independently, a modified or unmodified nucleoside and m is from 1 to 5; X 1 and X 2 are each, independently, a phosphodiester linkage or a phosphorothioate linkage; and MO is a modified oligonucleotide.
27. The compound of claim 26 , wherein at least one of X 1 and X 2 is a phosphodiester linkage.
28. The compound of claim 26 , wherein each of X 1 and X 2 is a phosphodiester linkage.
29. The compound of claim 17 , wherein m is 1, 2, or 3.
30. The compound of claim 17 , wherein N m is N′ p N″, wherein each N′ is, independently, a modified or unmodified nucleoside and p is from 0 to 4; and N″ is a nucleoside comprising an unmodified sugar moiety.
31. The compound of claim 30 , wherein p is 0, 1, or 2.
32. The compound of claim 30 , wherein each N′ comprises an unmodified sugar moiety.
33. The compound of claim 30 , wherein N″ is a β-D-deoxyriboadenosine or a β-D-deoxyriboguanosine.
34. The compound of claim 17 , wherein the sugar moiety of each N is independently selected from a β-D-ribose, a β-D-deoxyribose, a 2′-O-methoxy sugar, a 2′-O-methyl sugar, a 2′-fluoro sugar, and a bicyclic sugar moiety.