Compositions and methods to treat latent viral infections

• US 9,487,802 B2
• Filed: 07/02/2015
• Issued: 11/08/2016
• Est. Priority Date: 05/30/2014
• Status: Expired due to Fees

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Inventors: Quake, Stephen R., Wang, Jianbin
• Primary Examiner(s): Zou, Nick
• Application Number:
  US14/790,748
• Publication Number:
  US 20150376583A1
• Time in Patent Office: 495 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: A61K 48/005 characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 31/14 for RNA viruses
• CPC Class Codes: A61P 31/18 for HIV
• CPC Class Codes: A61P 31/20 for DNA viruses
• CPC Class Codes: A61P 31/22 for herpes viruses
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C12N 15/1133 against herpetoviridae, e.g. HSV
• CPC Class Codes: C12N 15/86 Viral vectors
• CPC Class Codes: C12N 15/907 in mammalian cells
• CPC Class Codes: C12N 2310/20 involving clustered regularly interspaced short palindromic repeats [CRISPRs]
• CPC Class Codes: C12N 2330/51 Specially adapted vectors
• CPC Class Codes: C12N 2810/60 from viruses
• CPC Class Codes: C12N 2820/60 from viruses
• CPC Class Codes: C12N 9/16 acting on ester bonds (3.1)
• CPC Class Codes: C12N 9/22 Ribonucleases RNAses, DNAses catalytic nucleic acids C12N15/113
• CPC Class Codes: C12Y 301/00 Hydrolases acting on ester bonds (3.1)
• CPC Class Codes: Y02A 50/30 Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Abstract

Viral infection is a persistent cause of human disease. Guided nuclease systems target the genomes of viral infections, rendering the viruses incapacitated.

Claims

1. A method for treating an infection by a virus, the method comprising:

introducing into a cell a vector comprising an origin of replication of the virus, said origin of replication is not transcribed to generate a sequence-specific targeting moiety, a sequence encoding a nuclease, and a sequence encoding a sequence-specific targeting moiety that targets the nuclease to a genome of the virus;

targeting the nuclease to a viral nucleic acid within the genome of the virus by means of the sequence-specific targeting moiety; and

cleaving the viral nucleic acid with the nuclease without interfering with the host genome.

2. The method of claim 1, wherein the nuclease is selected from the group consisting of a zinc-finger nuclease, a transcription activator-like effector nuclease, and a meganuclease.

3. The method of claim 1, wherein the nuclease is a Cas9 nuclease and the sequence-specific targeting moiety comprises a guide RNA.

4. The method of claim 1, wherein the viral nucleic acid is latent in a host cell.

5. The method of claim 1, wherein said cleaving step comprises creating a double-strand break in said viral nucleic acid.

6. The method of claim 1, further comprising the step of inserting a polynucleotide into the viral nucleic acid.

7. The method of claim 1, wherein the viral nucleic acid is from a virus selected from the group consisting of adenovirus, herpes simplex virus, varicella-zoster virus, Epstein-Barr virus, human cytomegalovirus, human herpesvirus type 8, human papillomavirus, BK virus JC virus, and smallpox.

8. The method of claim 1, wherein the vector is a viral vector selected from the group consisting of retrovirus, lentivirus, adenovirus, herpesvirus, poxvirus, alphavirus, vaccinia virus, and adeno-associated viruses.

9. The method of claim 1, wherein the vector is introduced into the cell via a non-viral vector.

10. The method of claim 9, wherein said non-viral vector is selected from the group consisting of a nanoparticle, a cationic lipid, a cationic polymer, a metallic nanoparticle, a nanorod, a liposome, microbubbles, a cell-penetrating peptide, and a liposphere.

11. The method of claim 9, wherein the non-viral vector comprises polyethyleneglycol.

12. The method of claim 1, wherein the vector is a plasmid.

13. The method of claim 12, wherein the nuclease is a Cas9 nuclease and the sequence-specific targeting moiety comprises a guide RNA.

14. The method of claim 13, wherein the viral nucleic acid is latent in a host cell.

15. The method of claim 14, wherein the viral nucleic acid is from Epstein-Barr virus.

16. The method of claim 15, wherein the cleaving step comprises creating a double-strand break in the viral nucleic acid.

17. A method for treating an infection by a virus, the method-comprising:

introducing into a cell a plasmid that comprises an origin of replication of the virus, said origin of replication is not transcribed to generate a guide RNA, a sequence encoding a Cas9 nuclease, and a sequence encoding a guide RNA that targets a portion of a genome of the virus;

targeting the Cas9 nuclease to the portion of the genome of the virus by means of the guide RNA; and

cleaving the genome of the virus with the Cas9 nuclease without interfering with the host genome.

18. The method of claim 17, further comprising increasing copy number of the plasmid preferentially in cells infected by the virus by means of the viral origin of replication of the virus.

19. The method of claim 18, wherein the portion of the genome of the virus comprises a 20 nucleotide segment 5′

to a protospacer adjacent motif within the genome of the virus, and wherein a portion of the guide RNA is at least 60% complementary to the portion of the genome of the virus, and wherein the portion of the guide RNA has no match in a human genome.

20. The method of claim 18, wherein the guide RNA binds to the genome of the virus within a latency-related target.