# US 11,419,932 B2 · Nucleic acid nanostructure platform for antigen presentation and vaccine formulations formed therefrom > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 11,419,932 B2 - Document ID: US11419932B2 - Status: Granted - Kind: B2 - Application number: 16/752,394 - Filed: 2020-01-24 - Published: 2020-07-30 - Granted: 2022-08-23 - Earliest claimed: 2019-01-24 - Assignees: Massachusetts Institute of Technology - Applicants: Massachusetts Institute of Technology - Inventors: Mark Bathe; Remi Veneziano; Eike-Christian Wamhoff; Tyson Moyer; Benjamin Joseph Read; Darrell Irvine - Web page: https://patentgrep.com/patent/US11419932B2 ## CPC - A61K 39/12: Viral antigens - A61K 39/385: Haptens or antigens, bound to carriers - A61K 9/0019: {Injectable compositions; Intramuscular, intravenous, arterial, subcutaneous administration; Compositions to be administered through the skin in an invasive manner (non-active ingredients are additionally classified in A61K47/00)} - A61K 9/513: {Organic macromolecular compounds; Dendrimers} - A61K 39/21: Retroviridae, e.g. equine infectious anemia virus - A61P 31/18: for HIV - C07K 14/162: {env, e.g. gp160, gp110/120, gp41, V3, peptid T, CD4-Binding site} - C12N 15/11: DNA or RNA fragments; Modified forms thereof (DNA or RNA not used in recombinant technology, C07H21/00); {Non-coding nucleic acids having a biological activity} - A61K 2039/55588: {Adjuvants of undefined constitution} - A61K 2039/6025: {Nucleotides} - A61K 2039/6093: {Synthetic polymers, e.g. polyethyleneglycol [PEG], Polymers or copolymers of (D) glutamate and (D) lysine} - A61K 2039/64: {characterised by the architecture of the carrier-antigen complex, e.g. repetition of carrier-antigen units} - B82Y 5/00: Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery - C12N 2310/51: in polymeric form, e.g. multimers, concatemers - G16B 15/10: Nucleic acid folding - G16B 40/10: Signal processing, e.g. from mass spectrometry [MS] or from PCR - A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D) - A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS - C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00) - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) - B82Y: SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY ## Abstract Compositions containing a nucleic acid nanostructure having a desired geometric shape and antigens bound to its surface are provided. The nanostructures can be, for example, in the form of a 6-helix bundle or icosahedron. The nanostructure design allows for control of the relative position and/or stoichiometry of the antigen bound to its surface. The antigens displayed on the nanostructure surface are arranged with the preferred number, spacing, and 3D organization to elicit a robust immune response. The displayed antigen can be an HIV immunogen such as eOD-GT6, eOD-GT8, or variants thereof. The compositions may thus be useful as immunogens, vaccines, immunostimulators, adjuvants, and the like. Methods of inducing immune responses, inducing protective immunity, inducing the production of neutralizing antibodies or inhibitory antibodies, inducing tolerance, and treating cancer, infectious or autoimmune diseases are also provided. ## Claims ### Claim 1 An immunogenic composition comprising (i) a nucleic acid nanostructure comprising nucleic acids folded into a a defined three-dimensional geometric shape, and (ii) from two up to 1,000 copies of an antigen, wherein the antigen is selected from the group consisting of peptides, proteins, nucleic acids, lipids, and polysaccharides; wherein the antigen is bound to the surface of the nucleic acid nanostructure, wherein the distance between adjacent copies of the antigen is from 1 nm to 500 nm, inclusive, wherein the number of copies of the antigen, the distance between adjacent copies of the antigen, the location of the antigen on the nanostructure, the rigidity/flexibility of the antigen, the dimensionality of the antigen, the topology of the nanostructure, the ultra-structural organization of the nanostructure, the geometric shape of the nanostructure, or a combination thereof improves an immune response induced by the antigen relative to a control having an equal amount of the same antigen, wherein the control comprises the same nucleic acid nanostructure having a single copy of the antigen bound thereto. ### Claim 2 (depends on 1) The composition of claim 1, wherein the number of copies of the antigen is 2 to 100, or 3 to 75, or 4 to 60, or 5 to 50, or 10 to 50, or 5 to 25, or 5 to 10 inclusive. ### Claim 3 (depends on 2) The composition of claim 2, wherein the number of copies of the antigen is 5, 6, 7, 8, 9, or 10. ### Claim 4 (depends on 1) The composition of claim 1, wherein the distance between adjacent copies of the antigen is 1 nm to 150 nm, or 10 nm to 80 nm, or 15 nm to 50 nm, or 25 nm to 30 nm inclusive. ### Claim 5 (depends on 1) The composition of claim 1, wherein the geometric shape is selected from the group consisting of a helix bundle, cuboidal structure, icosahedral structure, tetrahedral structure, cuboctahedral structure, octahedral structure, and hexahedral structure. ### Claim 6 (depends on 1) The composition of claim 1, wherein the geometric shape is a polyhedron or a 6-helix bundle. ### Claim 7 (depends on 1) The composition of claim 1, wherein the geometric shape is a polyhedron, and wherein the polyhedron is an icosahedron. ### Claim 8 (depends on 1) The composition of claim 1, wherein the copies of the antigen are covalently or non-covalently bound to the nanostructure. ### Claim 9 (depends on 1) The composition of claim 1, wherein the antigen is indirectly or directly bound to the nanostructure via outwardly facing nucleic acid overhangs extending from the 3′ or 5′ ends of selected staple strands of the nanostructure. ### Claim 10 (depends on 1) The composition of claim 1, wherein the nucleic acid is DNA. ### Claim 11 (depends on 10) The composition of claim 10, wherein the nucleic acid overhangs hybridize to the complementary target RNA, DNA or PNA covalently linked to the antigen. ### Claim 12 (depends on 11) The composition of claim 11, wherein the covalent linkage is formed by maleimide-thiol coupling. ### Claim 13 (depends on 1) The composition of claim 1, comprising two or more structurally different antigens. ### Claim 14 (depends on 1) The composition of claim 1, wherein the antigen(s) is associated with one or more diseases or conditions selected from infectious diseases, autoimmune diseases, and cancer. ### Claim 15 (depends on 14) The composition of claim 14, wherein the antigen is an HIV immunogen. ### Claim 16 (depends on 15) The composition of claim 15, wherein the antigen binds to a broadly neutralizing antibody. ### Claim 17 (depends on 16) The composition of claim 16, wherein the antigen is an HIV gp120 epitope. ### Claim 18 (depends on 17) The composition of claim 17, wherein the epitope encompasses the CD4 binding site of gp120. ### Claim 19 (depends on 15) The composition of claim 15, wherein the antigen is selected from eOD-GT6, eOD-GT8, or variants thereof. ### Claim 20 (depends on 1) The composition of claim 1, further comprising one or more moieties incorporated in and/or linked to the nanostructure. ### Claim 21 (depends on 20) The composition of claim 20, wherein one or more of the moieties is an adjuvant. ### Claim 22 (depends on 20) The composition of claim 20, wherein one or more of the moieties is a targeting molecule. ### Claim 23 (depends on 20) The composition of claim 20, wherein one or more of the moieties is a therapeutic agent. ### Claim 24 (depends on 1) The composition of claim 1, wherein the composition is coated with a coating agent. ### Claim 25 (depends on 24) The composition of claim 24, wherein the coating agent is a naturally occurring or synthetic cationic oligomer or polymer or cooligomer, optionally comprising or consisting of PEG moieties. ### Claim 26 (depends on 24) The composition of claim 24 wherein the coating agent comprises or consists of (a) 10 lysine units optionally conjugated terminally to a linear PEG moiety, optionally wherein the PEG has a molecular weight of approximately 5000 Da; (b) poly(2-dimethylaminoethyl methacrylate (PDMAEMA) or a PEG copolymer thereof optionally having a molecular weight range between 5000 Da to 20000 Da; (c) linear polyethyleneimine (PEI), optionally, in a molecular weight range between 5000 Da and 10000 Da; (iv) chitosan optionally a molecular weight range between 4000 Da and 6000 Da optionally with deacetylation of more than 90%. ### Claim 27 (depends on 24) The composition of claim 24, wherein the coating agent comprises or consists of a minor groove binder. ### Claim 28 (depends on 27) The composition of claim 27, wherein the minor groove binder increases stabilization, optionally wherein the stabilization comprises protecting the protection for endonuclease. ### Claim 29 (depends on 27) The composition of claim 27, wherein the minor groove binder is selected from bisamidines, polyamides, bisbenzimidazoles and combinations thereof. ### Claim 30 (depends on 1) The composition of claim 1, wherein the nanostructure is an a icosahedron comprising 5 to 50 copies of the antigen, and wherein the copies of the antigen are spaced 10 nm to 40 nm inclusive apart. ### Claim 31 (depends on 1) The composition nanostructure of claim 1, wherein the nanostructure is an a pentagonal bipyramidal structure comprising 10 to 40 copies of the antigen, and wherein the copies of the antigen are spaced 10 nm to 40 nm inclusive apart. ### Claim 32 (depends on 1) A pharmaceutical composition comprising the immunogenic composition of claim 1 in an effective amount to induce an immune response in a subject in need thereof, with or without the aid of an adjuvant, and a pharmaceutically acceptable carrier, diluent, preservative, excipient, or combination thereof. ### Claim 33 (depends on 32) The pharmaceutical composition of claim 32, further comprising an adjuvant. ### Claim 34 (depends on 32) A method of inducing an immune response in a subject comprising administering to the subject an effective amount of the pharmaceutical composition of claim 32. ### Claim 35 (depends on 34) The method of claim 34, further comprising administering the subject an adjuvant. ### Claim 36 (depends on 1) The immunogenic composition of claim 1, wherein the geometric shape of nanostructure is an icosahedron. ### Claim 37 (depends on 1) The immunogenic composition of claim 1, wherein the number of copies of antigen is 10 to 40, and the inter-antigen distance between adjacent antigens is 15 nm or more and is linear, planar, or a combination thereof, or 14 nm or less and is linear. ### Claim 38 An immunogenic composition comprising (i) nucleic acid nanostructure consisting of nucleic acids folded into a a defined three-dimensional icosohedral shape, and (ii) from five up to fifty copies of a peptide antigen, wherein the peptide antigen is selected from the group consisting of eOD-GT6, eOD-GT8, p31 and p5; wherein the antigen is bound to the surface of the nucleic acid nanostructure, wherein the distance between adjacent copies of the antigen is from 10 nm to 40 nm, inclusive, wherein the nanostructure improves an immune response induced by the antigen relative to control comprising the same nucleic acid nanostructure having a single copy of the antigen bound thereto.