Modified gapmer oligonucleotides and methods of use

Patent metadata

Field	Value
Publication number	US-11466274-B2
Application number	US-202016887063-A
Country	US
Kind code	B2
Filing date	May 29, 2020
Priority date	May 31, 2019
Publication date	Oct 11, 2022
Grant date	Oct 11, 2022

Abstract

The disclosure includes antisense oligonucleotides, including gapmer antisense oligonucleotides, along with methods of making and use, e.g., against HBV.

First claim

What is claimed is:

1. An antisense oligonucleotide (ASO) comprising 14-22 nucleotide units, wherein the ASO comprises:
(a) a central region (B′) comprising 6 or more contiguous DNA nucleosides, wherein at least the nucleotide at position 3 from the 5′ end of the central region is a modified nucleotide, and wherein at least 5 of the DNA nucleosides in the central region are connected by phosphorothioate linkages,
(b) a 5′-wing region (A′) comprising 2 to 6 locked nucleosides and at least one 2′ substituted nucleoside, and
(c) a 3′-wing region (C′) comprising 3 to 6 locked nucleosides, wherein at least 3 of the locked nucleosides in the 3′-wing region are connected by phosphorothioate linkages,
wherein the central region of the ASO is complementary or hybridizes to a viral target RNA sequence in an X region or an S region of HBV; and
wherein at least one of the 5′ wing region and the 3′ wing region contains at least one locked nucleoside independently selected from scpBNA, AmNA (N—H), AmNA (N-Me), GuNA, GuNA (N—R) where R is selected from Me, Et, i-Pr, t-Bu and combinations thereof,
wherein the modified nucleotide in a central region is selected from

wherein:
R is a halogen or R′—C═C—; and
R′ is C 6-12 aryl, 5- to 12-membered heteroaryl, hydroxy-C 1-6 alkyl, or C1-7 alkanoyloxy.

2. A pharmaceutical composition comprising an ASO according to claim 1 .

3. The ASO of claim 1 , wherein the 5′-wing region comprises 2 to 6 phosphorothioate-linked locked nucleosides.

4. The ASO of claim 1 , wherein the 5′ or 3′ wing region further comprises at least one locked nucleoside independently selected from locked nucleic acid A (lnA), locked nucleic acid-5methyl C (ln(5m)C); locked nucleic acid G (lnG); locked nucleic acid T (lnT), and combinations thereof.

5. An antisense oligonucleotide (ASO) selected from:
(i) 5′-mA-lnGpslnApslnTpslnApslnApsApsAps(5oh)CpsGps(5m)Cps(5m)CpsGps(5m)CpslnApslnGpslnA pscp(5m)C-3′ (SEQ ID NO: 420),
(ii) 5′-GalNac4-ps2-p-mA-lnGpslnApslnTpslnApslnApsApsAps(5oh)CpsGps(5m)Cps(5m)CpsGps(5m)CpslnApslnGpslnA pscp(5m)C-3′ (SEQ ID NO: 400),
(iii) 5′-lnGpslnApslnTpslnApslnApsApsAps(5oh)CpsGps(5m)Cps(5m)CpsGps(5m)CpslnApslnGpslnA pscp(5m)C-3′ (SEQ ID NO: 421),
(iv) 5′-mU-lnGpslnApscpTpsTps(5m)Cps(8nh)ApsGps(5m)CpsGps(5m)Cps(5m)CpsGpsApsln(5m)CpslnG pslnGpslnG-3′ (SEQ ID NO: 422),
(v) 5′-GalNac4-ps2-p-mU-po-lnGpslnApscpTpsTps(5m)Cps(8nh)ApsGps(5m)CpsGps(5m)Cps(5m)CpsGpsApsln(5m)CpslnG pslnGpslnG-3′ (SEQ ID NO: 156), and
(vi) 5′-lnGpslnApscpTpsTps(5m)Cps(8nh)ApsGps(5m)CpsGps(5m)Cps(5m)CpsGpsApsln(5m)CpslnG pslnGpslnG-3′ (SEQ ID NO: 404).

6. The ASO of claim 5 , wherein the ASO is 5′-mA-lnGpslnApslnTpslnApslnApsApsAps(5oh)CpsGps(5m)Cps(5m)CpsGps(5m)CpslnApslnGpslnA pscp(5m)C-3′ (SEQ ID NO: 420).

7. The ASO of claim 5 , wherein the ASO is 5′-GalNac4-ps2-p-mA-lnGpslnApslnTpslnApslnApsApsAps(5oh)CpsGps(5m)Cps(5m)CpsGps(5m)CpslnApslnGpslnA pscp(5m)C-3′ (SEQ ID NO: 400).

8. The ASO of claim 5 , wherein the ASO is 5′-lnGpslnApslnTpslnApslnApsApsAps(5oh)CpsGps(5m)Cps(5m)CpsGps(5m)CpslnApslnGpslnA pscp(5m)C-3′ (SEQ ID NO: 421).

9. The ASO of claim 5 , wherein the ASO is 5′-mU-lnGpslnApscpTpsTps(5m)Cps(8nh)ApsGps(5m)CpsGps(5m)Cps(5m)CpsGpsApsln(5m)CpslnG pslnGpslnG-3′ (SEQ ID NO: 422).

10. The ASO of claim 5 , wherein the ASO is 5′-GalNac4-ps2-p-mU-po-lnGpslnApscpTpsTps(5m)Cps(8nh)ApsGps(5m)CpsGps(5m)Cps(5m)CpsGpsApsln(5m)CpslnG pslnGpslnG-3′ (SEQ ID NO: 156).

11. The ASO of claim 5 , wherein the ASO is 5′ lnGpslnApscpTpsTps(5m)Cps(8nh)ApsGps(5m)CpsGps(5m)Cps(5m)CpsGpsApsln(5m)CpslnG pslnGpslnG-3′ (SEQ ID NO: 404).

12. The ASO of claim 1 further comprising a targeting group.

13. The ASO of claim 12 , wherein the targeting group comprises a GalNAc moiety.

14. The ASO of claim 5 further comprising a targeting group.

15. The ASO of claim 14 , wherein the targeting group comprises a GalNAc moiety.

16. A method of treating a subject having a Hepatitis B virus (HBV) infection, comprising administering to the subject a therapeutically effective amount of the ASO of claim 1 .

Assignees

• Aligos Therapeutics Inc

Inventors

• Beigelman Leonid
• Pandey Rajendra K
• Rajwanshi Vivek Kumar
• Smith David Bernard
• Hong Jin

Classifications

• A61P31/20 Primary

  for DNA viruses · CPC title

• C12N2310/315

  Phosphorothioates · CPC title

• C12N2310/3521

  Methyl · CPC title

• C12N2310/333

  Modified A · CPC title

• A61K31/7125

  Nucleic acids or oligonucleotides having modified internucleoside linkage, i.e. other than 3'-5' phosphodiesters · CPC title