WO2013151665A2 - Modified polynucleotides for the production of proteins associated with human disease - Google Patents

Modified polynucleotides for the production of proteins associated with human disease Download PDF

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Publication number
WO2013151665A2
WO2013151665A2 PCT/US2013/030061 US2013030061W WO2013151665A2 WO 2013151665 A2 WO2013151665 A2 WO 2013151665A2 US 2013030061 W US2013030061 W US 2013030061W WO 2013151665 A2 WO2013151665 A2 WO 2013151665A2
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WO
WIPO (PCT)
Prior art keywords
optionally substituted
independently
alkyl
polynucleotide
attorney docket
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2013/030061
Other languages
English (en)
French (fr)
Other versions
WO2013151665A3 (en
Inventor
Stephane Bancel
Tirtha Chakraborty
Antonin De Fougerolles
Sayda M. ELBASHIR
Matthias John
Atanu Roy
Susan Whoriskey
Kristy M. WOOD
Paul Hatala
Jason P. SCHRUM
Kenechi Ejebe
Jeff Lynn ELLSWORTH
Justin Guild
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Moderna Inc
Original Assignee
Moderna Therapeutics Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=49235350&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2013151665(A2) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Application filed by Moderna Therapeutics Inc filed Critical Moderna Therapeutics Inc
Priority to HK15108015.7A priority Critical patent/HK1207306A1/xx
Priority to EP21196458.0A priority patent/EP3978030A1/en
Priority to JP2015504564A priority patent/JP2015516143A/ja
Priority to EP18200782.3A priority patent/EP3501550A1/en
Priority to CA2869005A priority patent/CA2869005A1/en
Priority to AU2013243948A priority patent/AU2013243948A1/en
Priority to EP13722158.6A priority patent/EP2849799A2/en
Priority to AU2013243834A priority patent/AU2013243834A1/en
Priority to JP2015504587A priority patent/JP6348482B2/ja
Priority to PCT/US2013/031821 priority patent/WO2013151736A2/en
Priority to US14/390,106 priority patent/US9221891B2/en
Priority to HK15107400.2A priority patent/HK1206639B/en
Priority to EP13713306.2A priority patent/EP2833922B1/en
Priority to CN201380028186.5A priority patent/CN104870022B/zh
Priority to CA2868418A priority patent/CA2868418A1/en
Priority to CN202010645626.3A priority patent/CN112390871A/zh
Priority to EP18204317.4A priority patent/EP3520820A1/en
Publication of WO2013151665A2 publication Critical patent/WO2013151665A2/en
Publication of WO2013151665A3 publication Critical patent/WO2013151665A3/en
Anticipated expiration legal-status Critical
Priority to US14/824,247 priority patent/US9572896B2/en
Priority to US15/403,517 priority patent/US10493167B2/en
Priority to JP2017012947A priority patent/JP6953135B6/ja
Priority to AU2017232121A priority patent/AU2017232121B2/en
Priority to AU2018200375A priority patent/AU2018200375B2/en
Priority to AU2019202835A priority patent/AU2019202835A1/en
Priority to US16/442,168 priority patent/US10583203B2/en
Priority to JP2019225097A priority patent/JP2020072670A/ja
Priority to US16/811,648 priority patent/US20210077634A1/en
Priority to AU2020257150A priority patent/AU2020257150A1/en
Priority to JP2022020499A priority patent/JP2022078081A/ja
Priority to AU2023263451A priority patent/AU2023263451A1/en
Priority to JP2024018721A priority patent/JP2024063025A/ja
Ceased legal-status Critical Current

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Definitions

  • introduced DNA can integrate into host cell genomic DNA at some frequency, resulting in alterations and/or damage to the host cell genomic DNA.
  • the heterologous deoxyribonucleic acid (DNA) introduced into a cell can be inherited by daughter cells (whether or not the heterologous DNA has integrated into the chromosome) or by offspring.
  • nucleic acid based compounds or polynucleotides which encode a polypeptide of interest (e.g., modified mRNA or mmRNA) and which have structural and/or chemical features that avoid one or more of the problems in the art, for example, features which are useful for optimizing formulation and delivery of nucleic acid-based therapeutics while retaining structural and functional integrity, overcoming the threshold of expression, improving expression rates, half life and/or protein concentrations, optimizing protein localization, and avoiding deleterious bio-responses such as the immune response and/or degradation pathways.
  • a polypeptide of interest e.g., modified mRNA or mmRNA
  • compositions, methods, processes, kits and devices for the design, preparation, manufacture and/or formulation of modified mRNA (mmRNA) molecules are described herein.
  • FIG. 1 is a schematic of a primary construct of the present invention.
  • either the 5 '-or 3 '-end of the cDNA template encodes a ligase ribozyme sequence such that during in vitro transcription, the resultant nucleic acid molecule can contain an active ribozyme sequence capable of ligating the 5 '-end of a nucleic acid molecule to the 3 '-end of a nucleic acid molecule.
  • the ligase ribozyme may be derived from the Group I Intron, Group I Intron, Hepatitis Delta Virus, Hairpin ribozyme or may be selected by SELEX (systematic evolution of ligands by exponential enrichment).
  • the ribozyme ligase reaction may take 1 to 24 hours at temperatures between 0 and 37°C.
  • multiple distinct polynucleotides, primary constructs or mmRNA may be linked together through the 3 '-end using nucleotides which are modified at the 3 '-terminus.
  • Chemical conjugation may be used to control the stoichiometry of delivery into cells.
  • the glyoxylate cycle enzymes, isocitrate lyase and malate synthase may be supplied into HepG2 cells at a 1 : 1 ratio to alter cellular fatty acid metabolism.
  • more than two polynucleotides may be linked together using a functionalized linker molecule.
  • a functionalized saccharide molecule may be chemically modified to contain multiple chemical reactive groups (SH-, NH 2 -, N 3 , etc%) to react with the cognate moiety on a 3 '-functionalized mRNA molecule (i.e., a 3'-maleimide ester, 3'-NHS-ester, alkynyl).
  • primary constructs or mmRNA of the present invention can be designed to be conjugated to other polynucleotides, dyes, intercalating agents ⁇ e.g. acridines), cross-linkers ⁇ e.g. psoralene, mitomycin C), porphyrins (TPPC4, texaphyrin, Sapphyrin), polycyclic aromatic hydrocarbons ⁇ e.g., phenazine, dihydrophenazine), artificial endonucleases ⁇ e.g.
  • transport/absorption facilitators ⁇ e.g., aspirin, vitamin E, folic acid), synthetic
  • ribonucleases proteins, e.g., glycoproteins, or peptides, e.g., molecules having a specific affinity for a co-ligand, or antibodies e.g., an antibody, that binds to a specified cell type such as a cancer cell, endothelial cell, or bone cell, hormones and hormone receptors, non-peptidic species, such as lipids, lectins, carbohydrates, vitamins, cofactors, or a drug.
  • proteins e.g., glycoproteins, or peptides, e.g., molecules having a specific affinity for a co-ligand
  • antibodies e.g., an antibody, that binds to a specified cell type such as a cancer cell, endothelial cell, or bone cell
  • hormones and hormone receptors non-peptidic species, such as lipids, lectins, carbohydrates, vitamins, cofactors, or a drug.
  • Conjugation may result in increased stability and/or half life and may be particularly useful in targeting the polynucleotides, primary constructs or mmRNA to specific sites in the cell, tissue or organism.
  • the mmRNA or primary constructs may be administered with, or further encode one or more of RNAi agents, siRNAs, shRNAs, miRNAs, miRNA binding sites, antisense RNAs, ribozymes, catalytic DNA, tRNA, RNAs that induce triple helix formation, aptamers or vectors, and the like.
  • RNAi agents siRNAs, shRNAs, miRNAs, miRNA binding sites, antisense RNAs, ribozymes, catalytic DNA, tRNA, RNAs that induce triple helix formation, aptamers or vectors, and the like.
  • the multiple functionalities of bifunctional polynucleotides may be encoded by the RNA (the function may not manifest until the encoded product is translated) or may be a property of the polynucleotide itself. It may be structural or chemical.
  • polynucleotides and primary constructs having sequences that are partially or substantially not translatable e.g., having a noncoding region.
  • Such noncoding region may be the "first region" of the primary construct.
  • the noncoding region may be a region other than the first region.
  • Such molecules are generally not translated, but can exert an effect on protein production by one or more of binding to and sequestering one or more translational machinery components such as a ribosomal protein or a transfer R A (tRNA), thereby effectively reducing protein expression in the cell or modulating one or more pathways or cascades in a cell which in turn alters protein levels.
  • translational machinery components such as a ribosomal protein or a transfer R A (tRNA)
  • polypeptides include gene products, naturally occurring polypeptides, synthetic polypeptides, homologs, orthologs, paralogs, fragments and other equivalents, variants, and analogs of the foregoing.
  • a polypeptide may be a single molecule or may be a multi-molecular complex such as a dimer, trimer or tetramer. They may also comprise single chain or multichain
  • polypeptides such as antibodies or insulin and may be associated or linked. Most commonly disulfide linkages are found in multichain polypeptides.
  • polypeptide may also apply to amino acid polymers in which one or more amino acid residues are an artificial chemical analogue of a corresponding naturally occurring amino acid.
  • compositions which are polypeptide based including variants and derivatives. These include substitutional, insertional, deletion and covalent variants and derivatives.
  • derivative is used synonymously with the term “variant” but generally refers to a molecule that has been modified and/or changed in any way relative to a reference molecule or starting molecule.
  • mmR A encoding polypeptides containing substitutions, insertions and/or additions, deletions and covalent modifications with respect to reference sequences, in particular the polypeptide sequences disclosed herein, are included within the scope of this invention.
  • sequence tags or amino acids such as one or more lysines
  • Sequence tags can be used for peptide purification or localization.
  • Lysines can be used to increase peptide solubility or to allow for
  • “Insertional variants” when referring to polypeptides are those with one or more amino acids inserted immediately adjacent to an amino acid at a particular position in a native or starting sequence. "Immediately adjacent" to an amino acid means connected to either the alpha-carboxy or alpha-amino functional group of the amino acid.
  • Covalent derivatives when referring to polypeptides include modifications of a native or starting protein with an organic proteinaceous or non-proteinaceous derivatizing agent, and/or post-translational modifications. Covalent modifications are traditionally introduced by reacting targeted amino acid residues of the protein with an organic derivatizing agent that is capable of reacting with selected side-chains or terminal residues, or by harnessing mechanisms of post-translational modifications that function in selected recombinant host cells.
  • polypeptides when referring to polypeptides are defined as distinct amino acid sequence-based components of a molecule.
  • Features of the polypeptides encoded by the mmRNA of the present invention include surface manifestations, local conformational shape, folds, loops, half-loops, domains, half-domains, sites, termini or any combination thereof.
  • fold refers to the resultant conformation of an amino acid sequence upon energy minimization.
  • a fold may occur at the secondary or tertiary level of the folding process.
  • secondary level folds include beta sheets and alpha helices.
  • tertiary folds include Attorney Docket No.: 2030.1310PCT/M310.20 domains and regions formed due to aggregation or separation of energetic forces.
  • Regions formed in this way include hydrophobic and hydrophilic pockets, and the like.
  • Such bridging moieties may comprise a cysteine-cysteine bridge (Cys-Cys) typical in polypeptides having disulfide bridges or alternatively bridging moieties may be non-protein based such as the dibromozylyl agents used herein.
  • Cys-Cys cysteine-cysteine bridge
  • bridging moieties may be non-protein based such as the dibromozylyl agents used herein.
  • domain refers to a motif of a polypeptide having one or more identifiable structural or functional characteristics or properties (e.g., binding capacity, serving as a site for protein-protein interactions).
  • sub- domains may be identified within domains or half-domains, these subdomains possessing less than all of the structural or functional properties identified in the domains or half domains from which they were derived.
  • amino acids that comprise any of the domain types herein need not be contiguous along the backbone of the polypeptide (i.e., nonadjacent amino acids may fold structurally to produce a domain, half-domain or subdomain).
  • site As used herein when referring to polypeptides the terms "site” as it pertains to amino acid based embodiments is used synonymously with "amino acid residue” and "amino acid side chain.”
  • a site represents a position within a peptide or polypeptide that may be modified, manipulated, altered, derivatized or varied within the polypeptide based molecules of the present invention.
  • any of the features have been identified or defined as a desired component of a polypeptide to be encoded by the primary construct or mmR A of the Attorney Docket No.: 2030.1310PCT/M310.20 invention, any of several manipulations and/or modifications of these features may be performed by moving, swapping, inverting, deleting, randomizing or duplicating.
  • manipulation of features may result in the same outcome as a modification to the molecules of the invention.
  • a manipulation which involved deleting a domain would result in the alteration of the length of a molecule just as modification of a nucleic acid to encode less than a full length molecule would.
  • Modifications and manipulations can be accomplished by methods known in the art such as, but not limited to, site directed mutagenesis.
  • the resulting modified molecules may then be tested for activity using in vitro or in vivo assays such as those described herein or any other suitable screening assay known in the art.
  • the polypeptides may comprise a consensus sequence which is discovered through rounds of experimentation.
  • a "consensus" sequence is a single sequence which represents a collective population of sequences allowing for variability at one or more sites.
  • protein fragments, functional protein domains, and homologous proteins are also considered to be within the scope of polypeptides of interest of this invention.
  • any protein fragment meaning a polypeptide sequence at least one amino acid residue shorter than a reference polypeptide sequence but otherwise identical
  • a reference protein 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 or greater than 100 amino acids in length.
  • the primary constructs or mmRNA of the present invention may be designed to encode polypeptides of interest selected from any of several target categories including, but not limited to, biologies, antibodies, vaccines, therapeutic proteins or Attorney Docket No.: 2030.1310PCT/M310.20 peptides, cell penetrating peptides, secreted proteins, plasma membrane proteins, cytoplasmic or cytoskeletal proteins, intracellular membrane bound proteins, nuclear proteins, proteins associated with human disease, targeting moieties or those proteins encoded by the human genome for which no therapeutic indication has been identified but which nonetheless have utility in areas of research and discovery.
  • target categories including, but not limited to, biologies, antibodies, vaccines, therapeutic proteins or Attorney Docket No.: 2030.1310PCT/M310.20 peptides, cell penetrating peptides, secreted proteins, plasma membrane proteins, cytoplasmic or cytoskeletal proteins, intracellular membrane bound proteins, nuclear proteins, proteins associated with human disease, targeting moieties or those proteins encoded by the human genome
  • primary constructs or mrnRNA may encode variant polypeptides which have a certain identity with a reference polypeptide sequence.
  • a "reference polypeptide sequence” refers to a starting polypeptide sequence. Reference sequences may be wild type sequences or any sequence to which reference is made in the design of another sequence.
  • a "reference polypeptide sequence” may, e.g., be any one of SEQ ID NOs: 35608-71005 as disclosed herein, e.g., any of SEQ ID NOs
  • 36052, 36053, 36054 36055, 36056, 36057 36058, 36059, 36060 36061, 36062, 36063

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HK15108015.7A HK1207306A1 (en) 2012-04-02 2013-03-09 Modified polynucleotides for the production of proteins associated with human disease
EP21196458.0A EP3978030A1 (en) 2012-04-02 2013-03-09 Modified polynucleotides for the production of proteins associated with human disease
JP2015504564A JP2015516143A (ja) 2012-04-02 2013-03-09 ヒト疾患に関連するタンパク質の産生のための修飾ポリヌクレオチド
EP18200782.3A EP3501550A1 (en) 2012-04-02 2013-03-09 Modified polynucleotides for the production of proteins associated with human disease
CA2869005A CA2869005A1 (en) 2012-04-02 2013-03-09 Lipid nanoparticle compositions including polynucleotides encoding proteins
AU2013243948A AU2013243948A1 (en) 2012-04-02 2013-03-09 Modified polynucleotides for the production of proteins associated with human disease
EP13722158.6A EP2849799A2 (en) 2012-04-02 2013-03-09 Modified polynucleotides for the production of proteins associated with human disease
EP18204317.4A EP3520820A1 (en) 2012-04-02 2013-03-15 In vivo production of proteins
CN202010645626.3A CN112390871A (zh) 2012-04-02 2013-03-15 蛋白质的体内产生
AU2013243834A AU2013243834A1 (en) 2012-04-02 2013-03-15 In vivo production of proteins
JP2015504587A JP6348482B2 (ja) 2012-04-02 2013-03-15 タンパク質のインビボ産生
PCT/US2013/031821 WO2013151736A2 (en) 2012-04-02 2013-03-15 In vivo production of proteins
US14/390,106 US9221891B2 (en) 2012-04-02 2013-03-15 In vivo production of proteins
HK15107400.2A HK1206639B (en) 2012-04-02 2013-03-15 In vivo production of proteins
EP13713306.2A EP2833922B1 (en) 2012-04-02 2013-03-15 In vivo production of proteins
CN201380028186.5A CN104870022B (zh) 2012-04-02 2013-03-15 蛋白质的体内产生
CA2868418A CA2868418A1 (en) 2012-04-02 2013-03-15 In vivo production of proteins
US14/824,247 US9572896B2 (en) 2012-04-02 2015-08-12 In vivo production of proteins
US15/403,517 US10493167B2 (en) 2012-04-02 2017-01-11 In vivo production of proteins
JP2017012947A JP6953135B6 (ja) 2012-04-02 2017-01-27 タンパク質のインビボ産生
AU2017232121A AU2017232121B2 (en) 2012-04-02 2017-09-21 In vivo production of proteins
AU2018200375A AU2018200375B2 (en) 2012-04-02 2018-01-19 Modified polynucleotides for the production of proteins associated with human disease
AU2019202835A AU2019202835A1 (en) 2012-04-02 2019-04-23 In vivo production of proteins
US16/442,168 US10583203B2 (en) 2012-04-02 2019-06-14 In vivo production of proteins
JP2019225097A JP2020072670A (ja) 2012-04-02 2019-12-13 タンパク質のインビボ産生
US16/811,648 US20210077634A1 (en) 2012-04-02 2020-03-06 In vivo production of proteins
AU2020257150A AU2020257150A1 (en) 2012-04-02 2020-10-23 In vivo production of proteins
JP2022020499A JP2022078081A (ja) 2012-04-02 2022-02-14 タンパク質のインビボ産生
AU2023263451A AU2023263451A1 (en) 2012-04-02 2023-11-07 In vivo production of proteins
JP2024018721A JP2024063025A (ja) 2012-04-02 2024-02-09 タンパク質のインビボ産生

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