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 mRNA produces a therapeutic result, e.g., in a subject in need thereof.
1. A method for deamination of an adenosine in an mRNA, the method comprising contacting a cell with an oligonucleotide comprising the structure:
[A m ]-X 1 -X 2 -X 3 —[B n ]
wherein each of A and B is a nucleotide;
m and n are each, independently, an integer from 1 to 50, and A and B combined consist of 18 to 80 nucleotides;
X 1 , X 2 , and X 3 are each, independently, a nucleotide, wherein at least one of X 1 , X 2 , and X 3 has the structure of any one of Formula I-IV:
wherein N 1 is hydrogen or a nucleobase;
R 6 is hydrogen, hydroxy, or halogen;
R 7 is hydrogen, hydroxy, halogen, or C 1 -C 6 alkoxy;
R 8 is hydrogen or halogen;
R 9 is hydrogen or hydroxy, halogen, or C 1 -C 6 alkoxy;
R 10 is hydrogen or halogen; and
R 11 is hydrogen or hydroxy, halogen, or C 1 -C 6 alkoxy,
wherein when X 1 has the structure of any one of Formulas I to IV, each of X 2 and X 3 is a ribonucleotide; when X 2 has the structure of any one of Formulas I to IV, each of X 1 and X 3 is a ribonucleotide; when X 3 has the structure of any one of Formulas I to IV, each of X 1 and X 2 is a ribonucleotide; when X 1 and X 2 each have the structure of any one of Formulas I to IV, X 3 is a ribonucleotide; when X 1 and X 3 each have the structure of any one of Formulas I to IV, X 2 is a ribonucleotide; and when X 1 and X 3 each have the structure of any one of Formulas I to IV, X 1 is a ribonucleotide.
2. The method of claim 1 , wherein at least 80% of the nucleotides of [A m ] and/or [B n ] include a nucleobase, a sugar, and an internucleoside linkage.
3. The method of claim 1 , wherein halogen is fluoro.
4. The method of claim 1 , wherein C 1 -C 6 alkoxy is OCH 3 .
5. The method of claim 1 , wherein at least one of X 1 , X 2 and X 3 has the structure of Formula II, in which each of R 8 and R 9 is hydrogen.
6. The method of claim 1 , wherein at least 20% of the nucleotides of [A m ] and [B n ] combined are 2′-O-methyl-nucleotides.
7. The method of claim 1 , wherein m and n are each, independently, an integer from 5 to 40; at least one of X 1 , X 2 , and X 3 has the structure of Formula II, wherein R 8 and R 9 are each hydrogen, and each of X 1 , X 2 and X 3 that does not have the structure of Formula II is a ribonucleotide; [A m ] and [B n ] each include at least five terminal 2′-O-methyl-nucleotides and at least four terminal phosphorothioate linkages; and at least 20% of the nucleotides of [A m ] and [B n ] combined are 2′-O-methyl-nucleotides.
8. The method of claim 1 , wherein the oligonucleotide further comprises one or more adenosine deaminase acting on RNA (ADAR)-recruiting domains.
9. The method of claim 1 , wherein the oligonucleotide is conjugated to a targeting moiety.
10. A method of treating a disorder in a subject in need thereof, the method comprising administering to the subject an effective amount of an oligonucleotide comprising the structure:
[A m ]-X 1 -X 2 -X 3 —[B n ]
wherein each of A and B is a nucleotide;
m and n are each, independently, an integer from 1 to 50, and A and B combined consist of 18 to 80 nucleotides;
X 1 , X 2 , and X 3 are each, independently, a nucleotide, wherein at least one of X 1 , X 2 , and X 3 has the structure of any one of Formula I-IV:
wherein N 1 is hydrogen or a nucleobase;
R 6 is hydrogen, hydroxy, or halogen;
R 7 is hydrogen, hydroxy, halogen, or C 1 -C 6 alkoxy;
R 8 is hydrogen or halogen;
R 9 is hydrogen or hydroxy, halogen, or C 1 -C 6 alkoxy;
R 10 Is hydrogen or halogen; and
R 11 is hydrogen or hydroxy, halogen, or C 1 -C 6 alkoxy,
wherein when X 1 has the structure of any one of Formulas I to IV, each of X 2 and X 3 is a ribonucleotide; when X 2 has the structure of any one of Formulas I to IV, each of X 1 and X 3 is a ribonucleotide; when X 3 has the structure of any one of Formulas I to IV, each of X 1 and X 2 is a ribonucleotide; when X 1 and X 2 each have the structure of any one of Formulas I to IV, X 3 is a ribonucleotide; when X 1 and X 3 each have the structure of any one of Formulas I to IV, X 2 is a ribonucleotide; and when X 2 and X 3 each have the structure of any one of Formulas I to IV, X 1 is a ribonucleotide.
11. The method of claim 10 , wherein at least 80% of the nucleotides of [A m ] and/or [B n ] include a nucleobase, a sugar, and an internucleoside linkage.
12. The method of claim 10 , wherein halogen is fluoro.
13. The method of claim 10 , wherein C 1 -C 6 alkoxy is OCH 3 .
14. The method of claim 10 , wherein at least one of X 1 , X 2 , and X 3 has the structure of Formula II, in which each of R 8 and R 9 is hydrogen.
15. The method of claim 10 , wherein at least 20% of the nucleotides of [A m ] and [B n ] combined are 2′-O-methyl-nucleotides.
16. The method of claim 10 , wherein m and n are each, independently, an integer from 5 to 40; at least of X 1 , X 2 , and X 3 has the structure of Formula II, wherein R 8 and R 9 are each hydrogen, and each of X 1 , X 2 and X 3 that does not have the structure of Formula II is a ribonucleotide; [A m ] and [B n ] each include at least five terminal 2′-O-methyl-nucleotides and at least four terminal phosphorothioate linkages; and at least 20% of the nucleotides of [A m ] and [B n ] combined are 2′-O-methyl-nucleotides.
17. The method of claim 10 , wherein the oligonucleotide further comprises one or more adenosine deaminase acting on RNA (ADAR)-recruiting domains.
18. The method of claim 10 , wherein the oligonucleotide is conjugated to a targeting moiety.