Oligonucleotide compounds comprising non-nucleotide overhangs

• US 8,859,751 B2
• Filed: 01/06/2011
• Issued: 10/14/2014
• Est. Priority Date: 01/07/2010
• Status: Active Grant

• Current Assignee: Quark Pharmaceuticals, Inc
• Original Assignee: Quark Pharmaceuticals, Inc
• Inventors: Avkin-Nachum, Sharon, Feinstein, Elena
• Primary Examiner(s): ZARA, JANE J
• Application Number:
  US13/521,033
• Publication Number:
  US 20130035368A1
• Time in Patent Office: 1,377 Days
• Field of Search: 435/6.1, 435/91.1, 435/91.31, 435/6, 435/455, 536/23.1, 536/24.5, 536/24.31, 514/44
• US Class Current: 536/24.5
• CPC Class Codes: A61K 31/713 Double-stranded nucleic acids or oligonucleotides
• CPC Class Codes: A61P 1/02 Stomatological preparations, e.g. drugs for caries, aphtae, periodontitis
• CPC Class Codes: A61P 1/16 for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
• CPC Class Codes: A61P 11/00 Drugs for disorders of the respiratory system
• CPC Class Codes: A61P 13/12 of the kidneys
• CPC Class Codes: A61P 17/02 for treating wounds, ulcers, burns, scars, keloids, or the like
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 27/02 Ophthalmic agents
• CPC Class Codes: A61P 27/06 Antiglaucoma agents or miotics
• CPC Class Codes: A61P 27/16 Otologicals
• CPC Class Codes: A61P 37/06 Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: A61P 9/00 Drugs for disorders of the cardiovascular system
• CPC Class Codes: A61P 9/10 for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/317 with an inverted bond, e.g. a cap structure
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/332 Abasic residue
• CPC Class Codes: C12N 2310/344 Position-specific modifications, e.g. on every purine, at the 3'-end
• CPC Class Codes: C12N 2310/351 : Conjugate
• CPC Class Codes: C12N 2310/3527 : Other alkyl chain

Abstract

The invention relates to siRNA compounds comprising one non-nucleotide moiety covalently attached to at least one of the sense or antisense strands to down-regulate the expression of human genes. The invention also relates to pharmaceutical compositions comprising such compounds and a pharmaceutically acceptable carrier and to methods of treating and/or preventing the incidence or severity of various diseases or conditions associated with the target genes and/or symptoms associated with such diseases or conditions.

Claims

1. A double-stranded nucleic acid molecule comprising a sense strand and an antisense strand, wherein the antisense strand comprises a non-nucleotide overhang covalently attached via a phosphodiester or a phosphorothioate linkage to the 3′

or to the 2′

position of the sugar residue of the 3′

terminal nucleotide,

wherein the non-nucleotide overhang is selected from the group consisting of C3Pi, C3Ps, C3Pi-C3OH, C3Pi-C3Pi, C3Pi-C3Ps, C3Ps-C3OH, C3Ps-C3Pi, C3Ps-C3Ps, C3Pi-C3Pi-C3OH, C3Ps-C3Ps-C3OH, C3Pi-C3Ps-C3OH, C3Ps-C3Pi-C3OH, C3Pi-C3Pi-C3Pi, C3Ps-C3Ps-C3Ps, C3Pi-C3Ps-C3Ps, C3Ps-C3Pi-C3Ps, C3Ps-C3Ps-C3Pi, C3Pi-C3Pi-C3Ps, C3Ps-C3Pi-C3Pi, C3Pi-C3Ps-C3Pi, C3Pi-rAb, C3Pi-dAb, C3Ps-rAb, C3Ps-dAb, rAbPi-C3OH, rAbPi-C3Pi, rAbPs-C3OH, rAbPs-C3Pi, dAbPi-C3OH, dAbPi-C3Pi, dAbPs-C3OH and dAbPs-C3Pi; and

wherein each Pi is a phosphodiester linkage and each Ps is a phosphorothioate linkage;

or a pharmaceutically acceptable salt of such molecule.

2. The double-stranded nucleic acid molecule of claim 1 having structure (A1)

3. The molecule of claim 2, wherein x=y=19.

4. The molecule of claim 2, wherein Z′

is present.

5. The molecule of claim 2, wherein Z comprises a non-nucleotide overhang selected from the group consisting of C3Pi-C3OH, C3Pi-C3Pi, C3Pi-C3Ps, C3Ps-C3Pi, C3Ps-C3OH and C3Ps-C3Ps.

6. The molecule of claim 4, wherein Z′

is a non-nucleotide overhang selected from the group consisting of C3OH, C3Pi and C3Ps, wherein Pi is a phosphodiester linkage and Ps is a phosphorothioate linkage.

7. A composition comprising the molecule of claim 1 or a pharmaceutically acceptable salt of such molecule, and a pharmaceutically acceptable carrier.

8. A method for treating a subject suffering from a disease or disorder associated with expression of a target gene comprising administering to the subject the molecule of claim 1 or a pharmaceutically acceptable salt of such molecule, in an amount effective to down-regulate expression of the target gene, thereby treating the subject.

9. The molecule of claim 1, wherein the non-nucleotide overhang is covalently attached to the 3′

position of the sugar residue of the 3′

terminal nucleotide such that the 3′

terminal nucleotide has one of the following structures;

10. The molecule of claim 1, wherein the non-nucleotide overhang is selected from the group consisting of C3Pi-C3OH, C3Pi-C3Pi, C3Pi-C3Ps, C3Ps-C3OH, C3Ps-C3Pi and C3Ps-C3Ps.

11. The molecule of claim 1, wherein the non-nucleotide overhang is selected from the group consisting of —

C3Pi-C3Pi-C3OH, —

C3Ps-C3Ps-C3OH, —

C3Pi-C3Ps-C3OH, —

C3Ps-C3Pi-C3OH, —

C3Pi-C3Pi-C3Pi, —

C3Ps-C3Ps-C3Ps, —

C3Pi-C3Ps-C3Ps, —

C3Ps-C3Pi-C3Ps, —

C3Ps-C3Ps-C3Pi, —

C3Pi-C3Pi-C3Ps, —

C3Ps-C3Pi-C3Pi and —

C3Pi-C3Ps-C3Pi.

12. The molecule of claim 1, wherein the non-nucleotide overhang is selected from the group consisting of —

C3Pi-rAb, —

C3Pi-dAb, —

C3Ps-rAb and —

C3Ps-dAb.

13. The molecule of claim 1, further comprising a non-nucleotide overhang covalently attached to the 3′

terminal nucleotide in the sense strand, wherein the non-nucleotide overhang covalently attached to the 3′

terminal nucleotide in the sense strand is selected from the group consisting of propanol, a C3 alkyl moiety linked to a phosphodiester and a C3 alkyl moiety linked to a phosphorothioate.

14. The molecule of claim 13, wherein the non-nucleotide overhang covalently attached to the 3′

terminal nucleotide in the sense strand is propanol; and

wherein the 3′

terminal sugar residue has the following structure;

15. The molecule of claim 13, wherein the non-nucleotide overhang covalently attached to the 3′

terminal nucleotide in the sense strand is C3 alkyl moiety linked to a phosphodiester; and

wherein the 3′

terminal sugar residue has the following structure;

16. The molecule of claim 13, wherein the non-nucleotide overhang covalently attached to the 3′

terminal nucleotide in the antisense strand is selected from the group consisting of C3Pi-C3OH, C3Pi-C3Pi, C3Pi-C3Ps, C3Ps-C3OH, C3Ps-C3Pi and C3Ps-C3Ps; and

wherein each Pi is a phosphodiester linkage and each Ps is a phosphorothioate linkage.

17. The molecule of claim 16, wherein the non-nucleotide overhang covalently attached to the 3′

terminal nucleotide in the antisense strand is C3Pi-C3OH; and

wherein the 3′

terminal sugar residue has the following structure;

18. The molecule of claim 16, wherein the non-nucleotide overhang covalently attached to the 3′

terminal nucleotide in the antisense strand is C3Pi-C3Pi; and

wherein the 3′

terminal sugar residue has the following structure;

19. The double stranded nucleic acid molecule of claim 2, wherein each of x and y is independently an integer between 18 and 27.

20. The double stranded nucleic acid molecule of claim 19, wherein x=y.

21. The double stranded nucleic acid molecule of claim 4, wherein Z′

is a non-nucleotide overhang is selected from the group consisting of C3OH, C3Pi, C3Pi-C3OH, C3Pi-C3Pi, C3Pi-C3Ps, C3Ps, C3Ps-C3OH, C3Ps-C3Pi, C3Ps-C3Ps, C3Pi-C3Pi-C3OH, C3Ps-C3Ps-C3OH, C3Pi-C3Ps-C3OH, C3Ps-C3Pi-C3OH, C3Pi-C3Pi-C3Pi, C3Ps-C3Ps-C3Ps, C3Pi-C3Ps-C3Ps, C3Ps-C3Pi-C3Ps, C3Ps-C3Ps-C3Pi, C3Pi-C3Pi-C3Ps, C3Ps-C3Pi-C3Pi, C3Pi-C3Ps-C3Pi, C3Pi-rAb, C3Pi-dAb, C3Ps-rAb, C3Ps-dAb, rAbPi-C3OH, rAbPi-C3Pi, rAbPs-C3OH, rAbPs-C3Pi, dAbPi-C3OH, dAbPi-C3Pi, dAbPs-C3OH and dAbPs-C3Pi.

22. The double stranded nucleic acid molecule of claim 4, wherein Z′

is an inorganic phosphate.