MODIFIED POLYNUCLEOTIDES ENCODING SIAH E3 UBIQUITIN PROTEIN LIGASE 1

• US 20140141068A1
• Filed: 12/16/2013
• Published: 05/22/2014
• Est. Priority Date: 04/02/2012
• Status: Active Grant

• Current Assignee: Moderna TX, Inc. (Moderna, Inc.)
• Original Assignee: Moderna Therapeutics, Inc. (Moderna, Inc.)
• Inventors: Bancel, Stephane, Chakraborty, Tirtha, de Fougerolles, Antonin, Whoriskey, Susan, Weiss, Ron
• Granted Patent: US 9,255,129 B2
• Time in Patent Office: Days
• US Class Current: 424/450
• CPC Class Codes: A61K 31/7088 Compounds having three or more nucleosides or nucleotides
• CPC Class Codes: A61K 31/7115 Nucleic acids or oligonucleotides having modified bases, i.e. other than adenine, guanine, cytosine, uracil or thymine
• 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 38/17 from animals; from humans enzyme inhibitors A61K38/005
• CPC Class Codes: A61K 38/1767 from invertebrates
• CPC Class Codes: A61K 38/177 Receptors; Cell surface antigens; Cell surface determinants
• CPC Class Codes: A61K 38/1816 Erythropoietin [EPO]
• CPC Class Codes: A61K 38/1866 Vascular endothelial growth factor [VEGF]
• CPC Class Codes: A61K 38/1891 Angiogenesic factors; Angiogenin
• CPC Class Codes: A61K 38/191 Tumor necrosis factors [TNF], e.g. lymphotoxin [LT], i.e. TNF-beta
• CPC Class Codes: A61K 38/193 Colony stimulating factors [CSF]
• CPC Class Codes: A61K 38/212 IFN-alpha
• CPC Class Codes: A61K 38/215 IFN-beta
• CPC Class Codes: A61K 38/36 Blood coagulation or fibrinolysis factors
• CPC Class Codes: A61K 38/363 Fibrinogen
• CPC Class Codes: A61K 38/44 Oxidoreductases (1)
• CPC Class Codes: A61K 38/45 Transferases (2)
• CPC Class Codes: A61K 38/4833 Thrombin (3.4.21.5)
• CPC Class Codes: A61K 38/4846 Factor VII (3.4.21.21); Factor IX (3.4.21.22); Factor Xa (3.4.21.6); Factor XI (3.4.21.27); Factor XII (3.4.21.38)
• CPC Class Codes: A61K 39/3955 against proteinaceous materials, e.g. enzymes, hormones, lymphokines
• CPC Class Codes: A61K 47/10 : Alcohols; Phenols; Salts thereof, e.g. glycerol; Polyethylene glycols [PEG]; Poloxamers; PEG/POE alkyl ethers
• CPC Class Codes: A61K 47/34 : Macromolecular compounds obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyesters, polyamino acids, polysiloxanes, polyphosphazines, copolymers of polyalkylene glycol or poloxamers A61K47/10 takes precedence
• CPC Class Codes: A61K 47/54 : the modifying agent being an organic compound
• CPC Class Codes: A61K 47/542 : Carboxylic acids, e.g. a fatty acid or an amino acid
• CPC Class Codes: A61K 47/543 : Lipids, e.g. triglycerides; Polyamines, e.g. spermine or spermidine
• CPC Class Codes: A61K 48/00 : Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
• CPC Class Codes: A61K 48/0033 : the non-active part being non-polymeric
• 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: A61K 48/0066 : Manipulation of the nucleic acid to modify its expression pattern, e.g. enhance its duration of expression, achieved by the presence of particular introns in the delivered nucleic acid
• CPC Class Codes: A61K 48/0075 : characterised by an aspect of the delivery route, e.g. oral, subcutaneous
• CPC Class Codes: 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
• CPC Class Codes: A61K 9/1271 : Non-conventional liposomes, e.g. PEGylated liposomes, liposomes coated with polymers liposome as conjugate A61K47/6911
• CPC Class Codes: A61K 9/1272 : with substantial amounts of non-phosphatidyl, i.e. non-acylglycerophosphate, surfactants as bilayer-forming substances, e.g. cationic lipids with cholesterol as the only non-phosphatidyl surfactant A61K9/127; lipids as modifying agent A61K47/543
• CPC Class Codes: A61K 9/1277 : Processes for preparing; Proliposomes
• CPC Class Codes: A61K 9/14 : Particulate form, e.g. powders, Processes for size reducing of pure drugs or the resulting products, Pure drug nanoparticles microspheres A61K9/16; microcapsules A61K9/50; nanocapsules, nanoparticles of the matrix type A61K9/51
• CPC Class Codes: A61K 9/145 : with organic compounds
• CPC Class Codes: A61K 9/5031 : obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyethylene glycol, poly(lactide-co-glycolide)
• CPC Class Codes: A61K 9/5123 : Organic compounds, e.g. fats, sugars
• CPC Class Codes: A61K 9/5146 : obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyethylene glycol, polyamines, polyanhydrides
• CPC Class Codes: A61K 9/5153 : Polyesters, e.g. poly(lactide-co-glycolide)
• CPC Class Codes: C07K 14/005 : from viruses
• CPC Class Codes: C07K 14/435 : from animals; from humans
• CPC Class Codes: C07K 14/47 : from mammals
• CPC Class Codes: C07K 14/4705 : stimulating, promoting or activating activity
• CPC Class Codes: C07K 14/4713 : Autoimmune diseases, e.g. Insulin-dependent diabetes mellitus, multiple sclerosis, rheumathoid arthritis, systemic lupus erythematosus; Autoantigens
• CPC Class Codes: C07K 14/475 : Growth factors; Growth regulators
• CPC Class Codes: C07K 14/485 : Epidermal growth factor [EGF], i.e. urogastrone
• CPC Class Codes: C07K 14/505 : Erythropoietin [EPO]
• CPC Class Codes: C07K 14/515 : Angiogenesic factors; Angiogenin
• CPC Class Codes: C07K 14/525 : Tumour necrosis factor [TNF]
• CPC Class Codes: C07K 14/535 : Granulocyte CSF; Granulocyte-macrophage CSF
• CPC Class Codes: C07K 14/56 : IFN-alpha
• CPC Class Codes: C07K 14/565 : IFN-beta
• CPC Class Codes: C07K 14/62 : Insulins
• CPC Class Codes: C07K 14/705 : Receptors; Cell surface antigens; Cell surface determinants tumour specific antigens C07K14/4748
• CPC Class Codes: C07K 14/745 : Blood coagulation or fibrinolysis factors
• CPC Class Codes: C07K 14/75 : Fibrinogen
• CPC Class Codes: C07K 16/00 : Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies antibodies with enzymatic activity, e.g. abzymes C12N9/0002
• CPC Class Codes: C07K 16/2887 : against CD20
• CPC Class Codes: C07K 16/32 : against translation products of oncogenes
• CPC Class Codes: C07K 19/00 : Hybrid peptides , i.e. peptides covalently bound to nucleic acids, or non-covalently bound protein-protein complexes
• CPC Class Codes: 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
• CPC Class Codes: C12N 15/52 : Genes encoding for enzymes or proenzymes
• CPC Class Codes: C12N 15/67 : General methods for enhancing the expression
• CPC Class Codes: C12N 15/85 : for animal cells
• CPC Class Codes: C12N 15/87 : Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
• CPC Class Codes: C12N 15/88 : using microencapsulation, e.g. using amphiphile liposome vesicle
• CPC Class Codes: C12N 2840/00 : Vectors comprising a special translation-regulating system
• CPC Class Codes: C12N 2840/85 : mammalian
• CPC Class Codes: C12N 9/0069 : acting on single donors with incorporation of molecular oxygen, i.e. oxygenases (1.13)
• CPC Class Codes: C12N 9/1051 : Hexosyltransferases (2.4.1)
• CPC Class Codes: C12N 9/16 : acting on ester bonds (3.1)
• CPC Class Codes: C12N 9/2402 : hydrolysing O- and S- glycosyl compounds (3.2.1)
• CPC Class Codes: C12N 9/2445 : Beta-glucosidase (3.2.1.21)
• CPC Class Codes: C12N 9/644 : Coagulation factor IXa (3.4.21.22)
• CPC Class Codes: C12N 9/6451 : Coagulation factor XIIa (3.4.21.38)
• CPC Class Codes: C12N 9/88 : Lyases (4.)
• CPC Class Codes: C12N 9/93 : Ligases (6)
• CPC Class Codes: C12P 13/04 : Alpha- or beta- amino acids other amino acids C12P13/005
• CPC Class Codes: C12P 21/00 : Preparation of peptides or proteins single cell protein C12N1/00
• CPC Class Codes: C12P 21/005 : Glycopeptides, glycoproteins
• CPC Class Codes: C12Y 113/12007 : Photinus-luciferin 4-monooxygenase (ATP-hydrolysing) (1.13.12.7), i.e. firefly-luciferase
• CPC Class Codes: C12Y 304/21005 : Thrombin (3.4.21.5)
• CPC Class Codes: C12Y 304/21022 : Coagulation factor IXa (3.4.21.22)
• CPC Class Codes: C12Y 603/02019 : Ubiquitin-protein ligase (6.3.2.19), i.e. ubiquitin-conjugating enzyme

Abstract

The invention relates to compositions and methods for the preparation, manufacture and therapeutic use of oncology-related polynucleotides, oncology-related primary transcripts and oncology-related mmRNA molecules.

Claims

1. A method of producing a protein of interest in a cell, tissue or organism comprising contacting said cell, tissue or organism with a nucleic acid encoding SEQ ID NO:

8363, wherein said nucleic acid comprises a coding region, said coding region having an altered G/C content as compared to the G/C content of the coding region comprising nucleotides 1455-2303 of SEQ ID NO;

3826.

2. The method of claim 1, wherein the coding region which has an altered G/C content is selected from the group of nucleic acid sequences consisting of SEQ ID NO:

12851, 17339, 21827, 26315, 30803 and 33622-33708.

3. The method of claim 2, wherein the G/C content in the coding region is decreased as compared to the G/C content in the coding region of SEQ ID NO:

3826.

4. The method of claim 3, wherein the coding region with a decreased G/C content is selected from the group consisting of SEQ ID NO:

33633, 33655 and 33695.

5. The method of claim 2, wherein the G/C content in the coding region is increased as compared to the G/C content in the coding region of SEQ ID NO:

3826.

6. The method of claim 5, wherein the coding region with an increased G/C content is selected from the group consisting of SEQ ID NO:

12851, 17339, 21827, 26315, 30803, 33622-33632, 33634-33654, 33656-33694 and 33696-33708.

7. The method of claim 2, wherein the nucleic acid comprises at least one untranslated region 5′

relative to the coding region and at least one untranslated region 3′

relative to the coding region.

8. The method of claim 7, wherein the 5′

untranslated region is heterologous to the coding region of the nucleic acid.

9. The method of claim 7, wherein the 3′

untranslated region is heterologous to the coding region of the nucleic acid.

10. The method of claim 7, wherein the 5′

untranslated region and the 3′

untranslated region are heterologous to the coding region of the nucleic acid.

11. The method of claim 7, wherein the nucleic acid comprises at least two stop codons.

12. A nucleic acid encoding SEQ ID NO:

8363, wherein said nucleic acid comprises a coding region, said coding region having an altered G/C content as compared to the G/C content of the coding region comprising nucleotides 1455-2303 of SEQ ID NO;

3826.

13. The nucleic acid of claim 12, wherein the coding region which has an altered G/C content is selected from the group of nucleic acid sequences consisting of SEQ ID NO:

12851, 17339, 21827, 26315, 30803 and 33622-33708.

14. The nucleic acid of claim 12, wherein the G/C content in the coding region is decreased as compared to the G/C content in the coding region of SEQ ID NO:

3826.

15. The nucleic acid of claim 14, wherein the coding region with a decreased G/C content is selected from the group consisting of SEQ ID NO:

33633, 33655 and 33695.

16. The nucleic acid of claim 12, wherein the G/C content in the coding region is increased as compared to the G/C content in the coding region of SEQ ID NO:

3826.

17. The nucleic acid of claim 16, wherein the coding region with an increased G/C content is selected from the group consisting of SEQ ID NO:

12851, 17339, 21827, 26315, 30803, 33622-33632, 33634-33654, 33656-33694 and 33696-33708.

18. The nucleic acid of claim 12, wherein the nucleic acid comprises at least one untranslated region 5′

relative to the coding region and at least one untranslated region 3′

relative to the coding region.

19. The nucleic acid of claim 18, wherein the 5′

untranslated region is heterologous to the coding region of the nucleic acid.

20. The nucleic acid of claim 18, wherein the 3′

untranslated region is heterologous to the coding region of the nucleic acid.

21. The nucleic acid of claim 18, wherein the 5′

untranslated region and the 3′

untranslated region are heterologous to the coding region of the nucleic acid.

22. The nucleic acid of claim 18, wherein the nucleic acid comprises at least two stop codons.

23. A pharmaceutical composition comprising the codon optimized nucleic acid of claim 12 and a pharmaceutically acceptable excipient.

24. The pharmaceutical composition of claim 23 wherein the pharmaceutically acceptable excipient is selected from a solvent, aqueous solvent, non-aqueous solvent, dispersion media, diluent, dispersion, suspension aid, surface active agent, isotonic agent, thickening or emulsifying agent, preservative, lipid, lipidoids liposome, lipid nanoparticle, core-shell nanoparticles, polymer, lipoplex, peptide, protein, cell, hyaluronidase, and mixtures thereof.