RNA-editing oligonucleotides and uses thereof
The present disclosure features useful compositions and methods to treat disorders for which deamination of an adenosine in an RNA produces a therapeutic result in a subject in need thereof.
1 . An oligonucleotide capable of binding and recruiting an ADAR enzyme to perform editing on a target adenosine of a target RNA, the oligonucleotide comprising the structure:
wherein
m+n is 24 to 50, n is at least 4, and m is at least 20;
-X 1 -X 2 -X 3 - is a Central Triplet of the oligonucleotide;
X 1 is position −1 of the oligonucleotide, X 2 is position 0 of the oligonucleotide, and X 3 is position +1 of the oligonucleotide;
[A] m is a first domain at positions −(m+1) to −2 of the oligonucleotide;
[B] n is a second domain at positions +2 to +(n+1) of the oligonucleotide;
each A and B is a nucleotide comprising a nucleobase, a sugar (“an A/B sugar”), and an internucleotide linkage;
each X 1 , X 2 , and X 3 comprises a nucleobase, a sugar (“an X sugar”), and an internucleotide linkage;
the A/B sugars and the X 3 sugar are selected from 2′-methoxy-ribose, 2′-MOE-ribose, 2′-deoxy-2′-fluororibose, 2′-fluoro-arabinose, 2-methoxy-arabinose, 2′deoxyribose and a locked nucleic acid (LNA);
the X 1 sugar is 2′-deoxy-2′-fluororibose or 2′deoxyribose;
the X 2 sugar is a beta-homo-DNA sugar;
the A/B sugars and the X sugars, collectively, are 10-70% 2′-deoxy-2′-fluororibose;
the internucleotide linkages of the oligonucleotide are 30-100% phosphorothioate and mesyl phosphoramidate linkages, and 3, 4, 5, 6, 7, 8, 9, or 10 internucleotide linkages are mesyl phosphoramidate linkages;
the internucleotide linkage (i) between the nucleotide at position −(m+1) and the nucleotide at position −(m) (the 5′end), (ii) between the nucleotide at position +(n) and the nucleotide at position +(n+1) (the 3′-end), or (iii) at each the 5′-end and 3′-end of the oligonucleotide is a mesyl phosphoramidate linkage; and
the internucleotide linkage between the nucleotide at position −(m) and the nucleotide at position −(m−1) and the internucleotide linkage between the nucleotide at position +(n−1) and the nucleotide at position +(n) are independently a phosphorothioate or a mesyl phosphoramidate linkage.
2 . The oligonucleotide of claim 1 , wherein the X 3 nucleobase is hypoxanthine.
3 . The oligonucleotide of claim 1 , wherein no more than four sequential A/B sugars are 2′-deoxy-2′-fluororibose.
4 . The oligonucleotide of claim 1 , wherein the A/B sugars and X sugars, collectively, are 20-50% 2′-deoxy-2′-fluororibose.
5 . The oligonucleotide of claim 1 , wherein the A/B sugars are selected from 2′-methoxy-ribose, 2′-deoxy-2′-fluororibose, and 2′deoxyribose.
6 . The oligonucleotide of claim 1 , wherein the X 2 nucleobase is cytosine.
7 . The oligonucleotide of claim 1 , wherein the X 1 sugar is 2-deoxyribose.
8 . The oligonucleotide of claim 1 , wherein the internucleotide linkage between X 1 and X 2 is a phosphorothioate.
9 . The oligonucleotide of claim 1 , wherein the internucleotide linkage between X 2 and X 3 is a phosphorothioate.
10 . The oligonucleotide of claim 1 , wherein the internucleotide linkage between the nucleotide at position −2 and X 1 is a phosphorothioate.
11 . The oligonucleotide of claim 1 , wherein the internucleotide linkage between the nucleotide at position −9 and the nucleotide at position −8 is a mesyl phosphoramidate.
12 . The oligonucleotide of claim 1 , wherein the internucleotide linkage between the nucleotide at position −11 and the nucleotide at position −10 is a mesyl phosphoramidate.
13 . The oligonucleotide of claim 1 , wherein the internucleotide linkage between the nucleotide at position +1 and the nucleotide at position +2 is a mesyl phosphoramidate.
14 . The oligonucleotide of claim 1 , wherein the internucleotide linkage between the nucleotide at position +9 and the nucleotide at position +10 is a mesyl phosphoramidate.
15 . The oligonucleotide of claim 1 , wherein the internucleotide linkage between the nucleotide at position +1 and the nucleotide at position +2 and the internucleotide linkage between the nucleotide at position +9 and the nucleotide at position +10 are a mesyl phosphoramidate.
16 . The oligonucleotide of claim 1 , having 30-70% phosphorothioate and phosphoramidate linkages.
17 . The oligonucleotide of claim 1 , having 40-60% phosphorothioate and mesyl phosphoramidate linkages.
18 . The oligonucleotide of claim 1 , wherein n+m is 39.
19 . The oligonucleotide of claim 1 , wherein the A/B sugar at position +3 is a 2′-deoxy-2′-fluororibose.
20 . The oligonucleotide of claim 1 , wherein the A/B sugar at position −5 is a 2′-deoxy-2′-fluororibose.
21 . The oligonucleotide of claim 1 , wherein the A/B sugar at position −16 is a 2′-deoxy-2′-fluororibose.
22 . The oligonucleotide of claim 1 , wherein the A/B sugar at position −20 is a 2′-deoxy-2′-fluororibose.
23 . The oligonucleotide of claim 1 , wherein the A/B sugar at each of positions +3, −5, −16, and −20 is a 2′-deoxy-2′-fluororibose.
24 . A pharmaceutical composition comprising the oligonucleotide of claim 1 and a pharmaceutically acceptable excipient.
25 . The pharmaceutical composition of claim 24 , wherein the oligonucleotide is encapsulated in a lipid nanoparticle (LNP).
26 . An oligonucleotide capable of binding and recruiting an ADAR enzyme to perform editing on a target adenosine of a target RNA comprising the structure:
wherein
m+n is 29 to 50, n is at least 9, and m is at least 20;
-X 1 -X 2 -X 3 - is a Central Triplet of the oligonucleotide;
X 1 is position −1 of the oligonucleotide, X 2 is position 0 of the oligonucleotide, and X 3 is position +1 of the oligonucleotide;
[A] m is a first domain at positions −(m+1) to −2 of the oligonucleotide;
[B] n is a second domain at positions +2 to +(n+1) of the oligonucleotide;
each A and B is a nucleotide comprising a nucleobase, a sugar (“an A/B sugar”), and an internucleotide linkage;
each X 1 , X 2 , and X 3 comprises a nucleobase, a sugar (“an X sugar”), and an internucleotide linkage;
the A/B sugars and the X 3 sugar are selected from 2′-methoxy-ribose, 2′-MOE-ribose, 2′-deoxy-2′-fluororibose, 2′-fluoro-arabinose, 2-methoxy-arabinose, 2′deoxyribose and a locked nucleic acid (LNA);
the X 1 and X 3 sugars are 2′deoxyribose;
the X 2 sugar is a beta-homo-DNA sugar;
the A/B sugars and the X sugars, collectively, are 10-70% 2′-deoxy-2′-fluororibose;
the internucleotide linkages of the oligonucleotide are 30-100% phosphorothioate and mesyl phosphoramidate linkages, and 5 internucleotide linkages are mesyl phosphoramidate linkages;
the internucleotide linkage between the nucleotide at position −(m+1) and the nucleotide at position −(m) (the 5′end) is a mesyl phosphoramidate linkage,
the internucleotide linkage between the nucleotide at position +(n) and the nucleotide at position +(n+1) (the 3′-end) is a mesyl phosphoramidate linkage;
the internucleotide linkage between the nucleotide at position +1 and the nucleotide at position +2 is a mesyl phosphoramidate;
the internucleotide linkage between the nucleotide at position −9 and the nucleotide at position −8 is a mesyl phosphoramidate; and
the internucleotide linkage between the nucleotide at position −11 and the nucleotide at position −10 is a mesyl phosphoramidate.
27 . The oligonucleotide of claim 26 , wherein said oligonucleotide is complementary to a SERPINA1 mRNA transcript.
28 . A pharmaceutical composition comprising the oligonucleotide of claim 27 and a pharmaceutically acceptable excipient.
29 . The pharmaceutical composition of claim 28 , wherein the oligonucleotide is encapsulated in a lipid nanoparticle (LNP).