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US-12617822-B2 - Arc-based capsids and uses thereof

US12617822B2US 12617822 B2US12617822 B2US 12617822B2US-12617822-B2

Abstract

Disclosed herein, in certain embodiments, are recombinant Arc and endogenous Gag polypeptides, and methods of using recombinant Arc and endogenous Gag polypeptides.

Inventors

  • Colin Malone
  • Ian Peikon
  • Zachary Gilbert
  • Andrey PISAREV
  • Adam FRAITES
  • Jessica Crisp

Assignees

  • VNV NEWCO INC.

Dates

Publication Date
20260505
Application Date
20221013

Claims (11)

  1. 1 . A capsid comprising a recombinant endogenous Gag polypeptide and a heterologous cargo, wherein (a) the endogenous Gag polypeptide comprises (i) at least one capsid forming subunit from an endogenous Gag polypeptide that is not an Arc polypeptide and (ii) an RNA binding domain modified to bind to a heterologous cargo, and (b) the RNA binding domain is fused to the at least one capsid forming subunit through a linker.
  2. 2 . The capsid of claim 1 , wherein the cargo is an RNA and is bound to the RNA binding domain.
  3. 3 . The capsid of claim 1 , wherein the at least one capsid forming subunit is from an endogenous Gag polypeptide that is not an Arc polypeptide.
  4. 4 . The capsid of claim 1 , wherein the endogenous Gag polypeptide is a Paraneoplastic Ma antigen family polypeptide, a retrotransposon Gag-like (RTL) family polypeptide, or a SCAN domain family polypeptide.
  5. 5 . The capsid of claim 1 , wherein the linker is non-cleavable.
  6. 6 . The capsid of claim 5 , wherein the linker is selected from (EAAAK) n (SEQ ID NO: 70), or (EAAAR) n (SEQ ID NO: 71), where n is from 1 to 5, and up to 30 residues of glutamic acid-proline or lysine-proline repeats.
  7. 7 . The capsid of claim 5 , wherein the linker comprises (a) (GGGGS) n (SEQ ID NO: 72) or (GGGS) n (SEQ ID NO: 73), wherein n is 1 to 10, (b) KESGSVSSEQLAQFRSLD (SEQ ID NO: 74), or (c) EGKSSGSGSESKST (SEQ ID NO: 75).
  8. 8 . The capsid of claim 1 , wherein the linker is cleavable.
  9. 9 . The capsid of claim 8 , wherein the linker is cleaved by endogenous enzymes.
  10. 10 . The capsid of claim 1 , wherein the linker is fused to the C-terminus of the at least one capsid forming subunit.
  11. 11 . The capsid of claim 1 , wherein the linker is fused to the N-terminus of the at least one capsid forming subunit.

Description

CROSS REFERENCE This application is a continuation of U.S. application Ser. No. 17/382,102, filed Jul. 21, 2021, which is a continuation of U.S. application Ser. No. 17/277,119, filed Mar. 17, 2021, which is a U.S. national phase entry of International Application No. PCT/US2019/051786, filed Sep. 18, 2019, which claims the benefit of U.S. Provisional Patent Application No. 62/733,015, filed Sep. 18, 2018, each of which is incorporated herein by reference in its entirety. SEQUENCE LISTING The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on Oct. 25, 2022, is named 54838-702-306_SL.xml and is 131,736 bytes in size. SUMMARY OF THE DISCLOSURE Disclosed herein, in certain embodiments, are recombinant and engineered Arc polypeptides and recombinant and engineered endogenous Gag (endo-Gag) polypeptides. In some embodiments, also included are Arc-based capsids and endo-Gag based capsids, either loaded or empty, and methods of preparing the capsids. Additionally included are methods of delivery of the Arc-based capsids and endo-Gag-based capsids to a site of interest. Disclosed herein, in certain embodiments, is a capsid comprising a recombinant Arc polypeptide or a recombinant endogenous Gag polypeptide and a therapeutic agent. In some embodiments, the therapeutic agent is a nucleic acid. In some embodiments, the nucleic acid is an RNA. In some embodiments, the recombinant Arc polypeptide is a human Arc polypeptide comprising an amino acid sequence that is SEQ ID NO: 1 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 1. In some embodiments, the recombinant Arc polypeptide is an Arc polypeptide comprising: a) an amino acid sequence that is SEQ ID NO: 2 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 2; b) an amino acid sequence that is SEQ ID NO: 3 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 3; c) an amino acid sequence that is SEQ ID NO: 4 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 4; d) an amino acid sequence that is SEQ ID NO: 5 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 5; e) an amino acid sequence that is SEQ ID NO: 6 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 6; f) an amino acid sequence that is SEQ ID NO: 7 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 7; g) an amino acid sequence that is SEQ ID NO: 8 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 8; h) an amino acid sequence that is SEQ ID NO: 9 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 9; i) an amino acid sequence that is SEQ ID NO: 10 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 10; or j) an amino acid sequence that is SEQ ID NO: 11 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 11; or k) an amino acid sequence that is SEQ ID NO: 12 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 12; or 1) an amino acid sequence that is SEQ ID NO: 13 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 13; or m) an amino acid sequence that is SEQ ID NO: 14 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 14; or n) an amino acid sequence that is SEQ ID NO: 15 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 15. In some embodiments, the recombinant endogenous Gag polypeptide is a human endogenous Gag polypeptide. In some embodiments, the recombinant endogenous Gag polypeptide is an endogenous Gag polypeptide comprising: a) an amino acid sequence that is SEQ ID NO: 16 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 16; b) an amino acid sequence that is SEQ ID NO: 17 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 17; c) an amino acid sequence that is SEQ ID NO: 18 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 18; d) an amino acid sequence that is SEQ ID NO: 19 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 19; e) an amino acid sequence that is SEQ ID NO: 20 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 20; f) an amino acid sequence that is SEQ ID NO: 21 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 21; or g) an amino acid sequence that is SEQ ID NO: 22 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 22; or h) an amino acid sequence that is SEQ ID NO: 23 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 23; or i) an amino acid sequence that is SEQ ID NO: 24 or an amino acid sequence that is at least 90% identical to the SEQ ID NO: 24; or j) an amino acid sequence that is SEQ ID NO: 25 or an amino acid seq