Modified oligonucleotides and methods of use
Modified oligonucleotides comprising modifications at the 2′ and/or 3′ position(s) along with methods of making and use, e.g., against HBV are disclosed.
1. A chimeric antisense oligonucleotide represented by Formula (A):
5′-X-Y-Z3′ (A),
wherein
X-Y-Z is a chimeric oligonucleotide comprising a sequence of 18 to 22 nucleosides, optionally conjugated at the 5′ and/or 3′ end to a ligand targeting group;
X is a domain comprising a sequence of modified nucleosides that is 3 to 10 nucleosides in length;
Z is a domain comprising a sequence of modified nucleosides that is 3 to 10 nucleosides in length; and
Y is a domain comprising a sequence of 2 to 10 2′-deoxy-nucleosides linked through thiophosphate intersubunit linkages,
each modified nucleoside in the X domain and each modified nucleoside in the Z domain are nucleosides of Formula (1)
wherein
R is H or a positively charged counter ion,
B is a nucleobase independently selected from the group consisting of adenine, guanine, thymine, cytosine, uracil, 5-methylcytosine, 2,6-diaminopurine, and 5-methyluracil,
R 1 is —CR′ 3 , —CR′ 2 OCR′ 3 , —(CR′ 2 ) 3 OCR′ 3 , —(CR′ 2 ) 1-2 CR′ 3 , —(CR′ 2 ) 2 OCR′ 3 , or —Et, and
R′ is independently in each instance H or F, and
wherein the oligonucleotide comprises a nucleobase sequence that is complementary or hybridizes to a target RNA.
2. The oligonucleotide of claim 1 ,
wherein R is H,
R is —(CR′ 2 ) 2 OCR′ 3 , and
each R′ is H.
3. The oligonucleotide of claim 1 , wherein the X domain and the Z domain each comprise a sequence of modified nucleosides that is 4-6 nucleosides in length.
4. The oligonucleotide of claim 1 , wherein R 1 is —Et.
5. The oligonucleotide of claim 1 , wherein R 1 is —(CH 2 ) 2 OCH 3 .
6. The oligonucleotide of claim 1 , wherein the Y domain comprises 10 2′-deoxy-nucleosides.
7. The oligonucleotide of claim 6 , wherein the X domain and the Z domain each comprise a sequence of modified nucleosides that is 5 nucleosides in length.
8. The oligonucleotide of claim 1 , wherein the ligand targeting group comprises a GalNAc moiety.
9. The oligonucleotide of claim 1 , wherein each B is independently selected from the group consisting of adenine, guanine, thymine, cytosine, uracil, 5-methylcytosine, 2,6-diaminopurine, and 5-methyluracil.
10. The oligonucleotide of claim 1 , wherein each 2′-deoxy-nucleoside of the Y domain has a nucleobase independently selected from the group consisting of adenine, guanine, thymine, cytosine, uracil, 5-methylcytosine, 2,6-diaminopurine, and 5-methyluracil.
11. The oligonucleotide of claim 1 , wherein the target RNA is viral RNA.
12. The oligonucleotide of claim 1 , wherein the oligonucleotide comprises a nucleobase sequence that is complementary or hybridizes to the target RNA at a higher affinity than an unmodified oligonucleotide of the same sequence.
13. The oligonucleotide of claim 1 , wherein the oligonucleotide complexed with the target RNA under physiological conditions has a melting temperature of >37° C.
14. A pharmaceutical composition comprising the oligonucleotide of claim 1 and a pharmaceutically acceptable excipient.
15. The pharmaceutical composition of claim 14 , wherein the pharmaceutical composition is formulated for parenteral delivery.