Translation enhancing nucleic acid compounds: aso coupled translation - upregulation 1 (act-up1) and uses thereof

Abstract

Disclosed herein are methods and compounds for enhancing gene expression by ACT-UP1 compounds. Such methods and compounds are useful for increasing expression of certain genes, many of which are associated, with a variety of diseases and disorders.

Description

Abstract This paper discloses methods and compounds for enhancing gene expression using ACT-UP1 compounds. These methods and compounds can be used to increase the expression of certain genes, many of which are associated with a variety of diseases and conditions.

Claims

What is claimed is:

1. An antisense oligonucleotide (ASO) Coupled Translation - Upregulation 1 (ACT-UP 1) compound, wherein the ACT-UP 1 compound comprises an ASO component joined to a protein recruiting sequence (PRS) component, wherein the ASO component is capable of hybridizing to a target mRNA, wherein the PRS is capable of recruiting translation related proteins, and wherein the ACT-UP1 compound is capable of enhancing protein expression.

2. The ACT-UP 1 compound of claim 1, wherein the PRS is 5 to 20, 5 to 19, 5 to 18, 5 to 17, 5 to 16, 5 io 15, 5 to 14, 5 to 13, 5 to 12, 5 to 11, 5 to 10, 5 to 9, 5 to 8, 5 to 7, or 5 to 6 linked nucleosides in length.

3. The ACT-UP 1 compound of claim 1, wherein the PRS is a derivative of a DRACH consensus sequence or a sequence comprising (a) a DRACH consensus sequence and (b) additional sequence comprising one or more repeats or partial repeats of a DRACH consensus sequence.

4. The ACT-UP1 compound of claim 3, wherein the DRACH consensus sequence is GGACU (SEQ ID NO: 8) or a derivative thereof.

5. The ACT-UP1 compound of claim 1. wherein the PRS is a derivative of a GGACU sequence (SEQ ID NO: 8).

6. The ACT-UP 1 compound of claim 4 or 5, wherein the GGACU or its derivative is selected from one of GGACU (SEQ ID NO: 8), GGACUGGAC (SEQ ID NO: 10), GGACUGGACU (SEQ ID NO: 11) and ACGGACUUGGACU (SEQ ID NO: 12).

7. The ACT-UP1 compound of claim 1, wherein the PRS is a derivative of a poly(A), poly(C), poly(T), or poly(U) sequence in the 3’UTR of a mRNA.

8. The ACT-UP 1 compound of claim 7, wherein the derivative of the poly(A) tail is AAACUAAACU (SEQ ID NO: 13).(SEQ ID NO: 15),(SEQ ID NO:99),(SEQ ID NO: 102); the poly(C) sequence is(SEQ ID NO: 93); the poly(U) sequence is UUUUUUUUUU (SEQ ID NO: 94).

9. The ACT-UP 1 compound of claim 1, wherein the compound comprises 17 to 45, 17 to 44, 17 to 43, 17 to 42, 17 to 41, 17 to 40, 17 to 39, 17 to 38, 17 to 37, 17 to 36, 17 to 35, 17 to 34, 17 to 33, 17 to 32, 17 to 31, 17 to 30, 17 to 29, 17 to 28, 17 to 27, 17 to 26, 17 to 25, 19 to 45, 19 to 40,19 to 35, 19 to 34, 19 to 33, 19 to 32, 19 to 31, 19 to 30, 19 to 29, 19 to 28, 19 to 27, 19 to 26, 19 to 25, 22 to 45, 22 to 40, 22 to 35, 22 to 34, 22 to 33, 22 to 32, 22 to 31 , 22 to 30, 22 to 29, 22 to 28, 22 to 27, 22 to 26, 22 to 25, 25 to 45, 25 to 40, 25 to 35, 25 to 34, 25 to 33, 25 to 32, 25 to 31, 25 to 30, 25 to 29, 25 to 28, or 25 to 27 linked subunits.

10. The ACT-UPl compound of claim 1, wherein the ASO is 12 to 25, 12 to 24, 12 to 23, 12 to 22, 12 to 21 , 12 to 20, 12 to 19, 12 to 18 , 12 to 17, 12 to 16, 12 to 15 , or 12 to 14 linked nucleosides in length.

11. The ACT-UPl compound of claim 1, wherein the ACT-UPl compound is a trans-acting protein enhancer.

12. The ACT-UP 1 compound of claim 1, wherein the target mRNA is a mammalian mRNA, a plant mRNA, a yeast mRNA, or a bacteria mRNA.

13. The ACT-UP1 compound of claim 12, wherein the ACT-UP 1 compound targets a region about20 to 50, 40 to 70, 60 to 90, 80 to 110, 100 to 130, 120 to 150, 140 to 170, 160 to 190, 180 to 210, 200 to 230, 220 to 250, 240 to 300, or 280 to 500 nucleotides downstream of a stop codon on the mRNA.

14. The ACT-UP1 compound of claim 12, wherein the target mRNA is JAG1, RAB9, PBGD, RNase Hl, HNF4A or FGF21.

15. The ACT-UPl compound of claim 1, further comprising a conjugate.

16. The ACT-UP 1 compound of claim 15, wherein the conjugate can be selected from cholesterols, lipids, carbohydrates, phospholipids, biotin, phenazine, folate, phenanthridine, anthraquinone, acridine, fluoresceins, rhodamines, coumarins, peptides, antibodies, dyes, and tocopherol.

17. The ACT-UPl compound of claim 15, wherein the conjugate is an N-Acetylgalactosamine (GalNAc)-containing compound.

18. The ACT-UP 1 compound of claim 1, wherein the compound comprises at least one chemical modification.

19. The ACT-UP1 compound of claim 18, wherein the compound is fully chemically modified.

20. The ACT-UP1 compound of claim 18, wherein the ASO and PRS comprise the same chemical modification.

21. The ACT-UP 1 compound of claim 18, wherein the ASO and PRS comprise different chemical modifications.

22. The ACT-UP 1 compound of claim 21, wherein the PRS chemical modification is 2’-O-methyl (2’-OMe).

23. The ACT-UP 1 compound of any of claims 18 to 21 , wherein the chemical modification can be selected from 2’-O-methyl (2’-OMe), 2’-O-(2-methoxyethyl) (2’-MOE), 2’-fluoro (2’~F), constrained ethyl (cEt), unlocked nucleic acid (UNA), locked nucleic acid (LNA), 2’-MOE modified T, and / or 5 -methylcytosine base.

24. The ACT-UP i compound of claim 1, wherein the compound comprises at least one modified internucleoside linkage.

25. The ACT-UP 1 compound of claim 24, wherein the at least one modified intcrnuclcosidc linkage is a phosphorothioate internucleotide (PS) linkage.

26. The ACT-UP1) compound according to any of claims 1 to 25, comprising 17 to 45 linked nucleosides in length, wherein the ACT-UP 1 compound comprises an ASO component comprising 12 to 25 linked nucleosides in length joined to a protein recruiting sequence (PRS) component comprising 5 to 20 linked nucleosides in length.

27. The ACT-UP1 compound according to any of claims 1 to 26, comprising 22 to 35 linked nucleosides in length, wherein the ACT-UP 1 compound comprises an ASO component comprising 12 to 25 linked nucleosides in length joined to a protein recruiting sequence (PRS) component comprising the sequence GGACUGGACU (SEQ ID NO: 11) or the sequence AAACUAAACU (SEQ ID .NO: 13).

28. l^he ACT-UP 1 of any of claims 1 to 27, wherein the compound increases expression of a protein by at least about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 250%, or 300%.

29. A pharmaceutical composition comprising the ACT-UP 1 compound of any preceding claim, alone or in combination with a pharmaceutically acceptable carrier and / or excipient.

30. A method for increasing translation of a target mRNA in a cell comprising administering the ACT-UP1 compound of any of claims 1 to 28 or the pharmaceutical composition of claim 29 to the cell, in an amount sufficient to increase translation of the target mRNA.

31. A method for treating a haploinsufficiency disorder in a subject comprising administering the ACT-UP1 compound of any of claims 1 to 28 or the pharmaceutical composition of claim 29 to the subject, in an amount sufficient to treat the haploinsufficiency disorder in the subject.

32. The method of claim 30 or 31, where the ACT-UP1 compound or the pharmaceutical composition can be administered subcutaneously, intravenously, or intrathecally to the subject.

33. A process for preparing compound of any one of claims 1-9, wherein the process comprises the steps of: a. preparing the compound by sequential coupling of modified and / or unmodified nucleotides and / or linkers via the phosphoramidite oligonucleotide synthesis on a conjugate modified or unmodified solid support; b. optionally, coupling a conjugate moiety to the compound on the solid support via the phosphoramidite oligonucleotide synthesis: c. detaching the compound from the solid support and removing the solid support; and d. optionally, adding a conjugate post cleavage. e. optionally, further purifying the compound, optionally using chromatography.

34. The ACT-UP 1 compound of claim 1, wherein the ASO component is joined to the PRS directly or indirectly.

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