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US20110082186A1 - Compositions for inhibiting gene expression and uses thereof - Google Patents

Compositions for inhibiting gene expression and uses thereof Download PDF

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US20110082186A1
US20110082186A1 US12/869,185 US86918510A US2011082186A1 US 20110082186 A1 US20110082186 A1 US 20110082186A1 US 86918510 A US86918510 A US 86918510A US 2011082186 A1 US2011082186 A1 US 2011082186A1
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oligonucleotide
seq
based compound
oligonucleotides
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Sudhir Agrawal
Ekambar Kandimalla
Mallikarjuna Putta
Tao Lan
Lakshmi Bhagat
Daqing Wang
Dong Yu
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Aceragen Inc
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Idera Pharmaceuticals Inc
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Assigned to IDERA PHARMACEUTICALS, INC. reassignment IDERA PHARMACEUTICALS, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: AGRAWAL, SUDHIR, BHAGAT, LAKSHMI, KANDIMALLA, EKAMBAR, LAN, TAO, PUTTA, MALLIKARJUNA, WANG, DAQING, YU, DONG
Priority to US13/038,924 priority patent/US20120016004A1/en
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    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1138—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against receptors or cell surface proteins
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    • C12N2310/51—Physical structure in polymeric form, e.g. multimers, concatemers

Definitions

  • the present invention relates to compounds, compositions, and methods of use for the inhibition of gene expression and/or activity or for diagnosing, treating and/or preventing diseases and/or conditions that respond to the inhibition of gene expression and/or activity.
  • RNAi RNA inhibition
  • Zamecnik & Stephenson published the first demonstration of using antisense oligonucleotides as a means to inhibit translation of viral proteins (Zemecnik and Stephenson (1978) Proc. Natl. Acad. Sci. 75: 285-288), there has been great interest in utilizing oligonucleotide-based compounds to inhibit expression of genes. These initial efforts utilized single-stranded, unmodified oligodeoxyribonucleotides or oligoribonucleotides (Agrawal et al. (1992) Ann. NY Acad. Sci.
  • oligodoexyribonucleotides that incorporated nuclease-resistant phosphorothioate and/or methylphosphonate linkages (Agrawal et. al (1988) Proc. Natl. Acad. Sci. 85:7079-7083; Metelev & Agrawal U.S. Pat. No. 5,652,355; Metelev & Agrawal U.S. Pat. No. 6,143,881; Matsukura et al. (1987) Proc. Natl. Acad. Sci. 84:7706).
  • Ribozymes form stem loop structures and bind to an RNA target to mediate its cleavage directly (Cech, T. (1990) Ann. Rev. Biochem. 59:543). Ribozymes selectively bind to target-RNA and catalyze a transesterification or a hydrolysis reaction to cleave specific phosphodiester linkages in single-stranded RNA. If introduced into cells, ribozymes have the potential to bind to target-mRNA and inhibit translation of such mRNA.
  • RNA-interfering technologies (e.g. short interfering-RNA (siRNA), microRNA (miRNA), DNA-directed-RNAi (ddRNAi), and single-stranded RNAi (ssRNAi)) in mammalian systems.
  • RNAi refers to the process of post-transcriptional inhibition of gene expression using short oligonucleotides that are designed to hybridize to specific mRNA targets (Fire et al. (1998) Nature 391:806-811; Zamore et al. (2000) Cell, 101:25-33).
  • RNA-induced silencing complex RISC is thought to be present in cells to catalytically break down specific mRNA molecules.
  • ssRNAi single-stranded RNAi
  • RNAi technologies are able to selectively bind to target mRNA, such molecules have also been recognized to induce non-specific immune stimulation through interaction with TLR3 (Kleinman et al., (2008) Nature 452:591-597; De Veer et. al. (2005) Immun. Cell Bio. 83:224-228; Kariko et al. (2004) J. Immunol. 172:6545-6549).
  • This non-specific immune activation has raised questions as to the utility of RNAi technologies as pharmaceutical agents.
  • each of the antisense-based technologies has been used with some success, as a result of being based on oligonucleotides, each of these technologies has the inherent problem of being unstable in vivo and having the potential to produce off-target effects, for example unintended immune stimulation (Agrawal & Kandimalla (2004) Nature Biotech. 22:1533-1537).
  • these oligonucleotides appear to have the additional issue of inefficient, in vivo delivery to cells (Medarova et. al (2007) Nature Med. 13:372-377).
  • antisense oligonucleotide drug candidates only one such compound has been approved as a drug by the FDA. This antisense compound was approved for treating CMV, but has never been marketed as a product. Additionally, no ribozyme or siRNA drug candidate has yet been approved by the FDA.
  • RNA/DNA hybrid molecule (Metelev at al. (1994) Bioorg. Med. Chem. Lett. 4:2929-2934; Metelev U.S. Pat. No. 5,652,355; Metelev & Agrawal U.S. Pat. No. 6,143,881; Metelev& Agrawal U.S. Pat. No. 6,346,614; Metelev & Agrawal U.S. Pat. No. 6,683,167, Metelev & Agrawal U.S. Pat. No. 7,045,609).
  • polypyrimidine oligonucleotides that bind to double-stranded DNA or RNA targets.
  • Polypyrimidine oligonucleotides can bind to duplex DNA in the major groove through Hoogsteen hydrogen bonding and form triplex structures containing one polypurine and two polypyrimidine strands with T:A-T and C:G-C + base triplets (Moser, H. E. and Dervan, P. B. (1987) Science 238, 645-650; Cooney, et al (1988) Science 241, 456-459).
  • Intramolecular triplexes are also formed when the DNA homopurine and homopryrimidine strands melt and refold (Vasqueza, K. M. and Wilson, J. H. (1998) Trends Bioche. Sci. 23, 4-9).
  • the presence of a third strand introduces severe restrictions in the flexibility of the DNA, changing its ability to recognize specific proteins along the major groove (Shields, G. C., et al. (1997) Am. Chem. Soc., 119, 7463-7469; Jimenez-Garcia, E., et al. (1998) J. Biol. Chem. 273, 24640-24648, resulting in an inhibiton of transcription and ultimately reduced gene expression.
  • Oligonucleotides that can sequence-specifically bind to double-stranded DNA or RNA can act as transcriptional/translational regulators and offered a promising antigen/antisense strategy to control the regulation of gene expression (Giovannangeli, C. and Helene, C. (1997) Antisense Nucleic Acid Drug Dev., 413; Giovannangeli, C., et al. (1996) Biochemistry 35, 10539; Maher, L. J., et al. (1992) Biochemistry 31, 70).
  • the conditions for forming stable triplexes are problematic because of limited base recognition and the non-physiologic acidic pH conditions required for protonation of cytosines in the triplex-forming oligonucleotides.
  • polypyrimidine oligonucleotides with inverted polarity linked via a linker i.e. one sequence having polarity followed by another sequence with 3′ ⁇ 5′ polarity, or vice versa
  • linker i.e. one sequence having polarity followed by another sequence with 3′ ⁇ 5′ polarity, or vice versa
  • the sequence on one side of the inversion binds to polypurine strand of a duplex according to the triple helix code and the sequence on the other side will bind to the adjacently located polypurine site in the opposite strand of the duplex ( FIG. 14 ).
  • triple helix recognition can be extended by switching recognition from one strand of the duplex to the other and then back again, if desired and such target sequence stretch is available.
  • these oligonucleotides may also form D-loops with the duplex as shown in Diagram 1B.
  • the region of the first polarity may form triplex, while the inverted portion displaces a section of one strand of the duplex to result in a substitute duplex in the relevant region.
  • the switchback oligonucleotides are capable of significant duplex binding activity, these oligonucleotides may be useful to inactivate the disease causing and undesirable DNA or RNA that are in duplex form.
  • the composition of the molecules is limited to polypyrimidine sequences targeting polypurine sites of double-stranded RNA or DNA.
  • Such oligonucleotides containing complementary sequences attached through 3′-3′ or 5′-5′ linkages form parallel-stranded duplexes through Hoogsteen or reverse Hoogsteen base pairing.
  • a complementary polypyrimidine strand When a complementary polypyrimidine strand is available, they form triple helical structures ( FIG. 15 ).
  • the present invention is directed to compounds, compositions, and methods useful for modulating gene expression using oligonucleotide-based compounds comprising two or more single stranded antisense oligonucleotides that are linked through their 5′-ends to allow the presence of two or more accessible 3′-ends, which effectively inhibit or decrease gene expression.
  • oligonucleotide-based compounds comprising two or more single stranded antisense oligonucleotides that are linked through their 5′-ends to allow the presence of two or more accessible 3′-ends, which effectively inhibit or decrease gene expression.
  • the present inventors have discovered that such oligonucleotide compounds are more effective than non-linked antisense oligonucleotides.
  • the invention provides novel synthetic oligonucleotide-based compounds comprising two or more oligonucleotides that are complementary to one or more mRNA sequence, wherein the oligonucleotides are linked through their 5′ ends to allow the presence of two or more accessible 3′-ends, and specifically hybridize to and inhibit the expression of the one or more mRNA sequence.
  • compositions may comprise any synthetic oligonucleotide-based compounds according to the first aspect in a pharmaceutically or physiologically acceptable carrier.
  • the invention provides a method for inhibiting gene expression, the method comprising contacting a cell with a synthetic oligonucleotide-based compound according to the first aspect of the invention.
  • the invention provides a method for inhibiting gene expression in a mammal, the method comprising administering to the mammal a synthetic oligonucleotide-based compound according to the first aspect of the invention.
  • the invention provides a method for inhibiting a TLR-mediated, Bcl-2-mediated, EGFR-mediated, mdm2-mediated, MyD88-mediated, PCSK9-mediated, survivin-mediated or VEGF-mediated response in a mammal through administration of a synthetic oligonucleotide-based compound according to the first aspect of the invention wherein the oligonucleotides are complementary to one or more TLR, Bcl-2, EGFR, mdm2, MyD88, PCSK9, survivin or VEGF mRNA sequence.
  • the invention provides a method for inhibiting a TLR-mediated, Bcl-2-mediated, EGFR-mediated, mdm2-mediated, MyD88-mediated, PCSK9-mediated, survivin-mediated or VEGF-mediated response in a mammal though administration of a synthetic oligonucleotide-based compound according to the first aspect of the invention wherein the oligonucleotides are complementary to one or more TLR, Bcl-2, EGFR, mdm2, MyD88, PCSK9, survivin or VEGF mRNA sequence in combination with an antagonist of TLR, EGFR, mdm2, MyD88, PCSK9, survivin or VEGF protein activity.
  • the invention provides methods for inhibiting gene expression in a mammal, such methods comprising administering to the mammal an oligonucleotide-based compound according to the invention.
  • the mammal is a human.
  • the oligonucleotide-based compound according to the invention is administered to a mammal in need of inhibiting its immune response.
  • the invention provides methods for therapeutically treating a patient having a disease or disorder, such methods comprising administering to the patient an oligonucleotide-based compound according to the invention in a therapeutically effective amount.
  • the disease or disorder to be treated is cancer, an autoimmune disorder, infectious disease, airway inflammation, inflammatory disorders, skin disorder, allergy, asthma or a disease caused by a pathogen.
  • Pathogens include, without limitation, bacteria, parasites, fungi, viruses, viroids, and prions.
  • the invention provides methods for preventing a disease or disorder, such methods comprising administering to a subject at risk for developing the disease or disorder an oligonucleotide-based compound according to the invention in a pharmaceutically effective amount.
  • the disease or disorder to be prevented is cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, allergy, asthma or a disease caused by a pathogen.
  • Pathogens include, without limitation, bacteria, parasites, fungi, viruses, viroids, and prions.
  • the invention provides a method of preventing or treating a disorder, such methods comprises isolating cells capable of producing cytokines or chemokines including, but not limited to, immune cells, T-regulatory cells, B-cells, PBMCs, pDCs, and lymphoid cells; culturing such cells under standard cell culture conditions, treating such cells ex vivo with an oligonucleotide-based compound according to the first aspect of the invention such that the isolated cells produce or secrete decreased levels of cytokines or chemokines, and administering or re-administering the treated cells to a patient in need of therapy to inhibit cytokines and/or chemokines for the prevention and/or treatment of disease.
  • This aspect of the invention would be in accordance with standard adoptive cellular immunotherapy techniques to produce activated immune cells.
  • the invention provides a composition comprising a compound according to the first aspect of the invention and one or more vaccines, antigens, antibodies, cytotoxic agents, chemotherapeutic agents (both traditional chemotherapy and modern targeted therapies), kinase inhibitors, allergens, antibiotics, agonist, antagonist, antisense oligonucleotides, ribozymes, RNAi molecules, siRNA molecules, miRNA molecules, aptamers, proteins, gene therapy vectors, DNA vaccines, adjuvants, co-stimulatory molecules or combinations thereof.
  • FIG. 1A is a synthetic scheme for the linear synthesis of antisense oligonucleotides of the invention.
  • FIG. 1B is synthetic scheme for the parallel synthesis of antisense oligonucleotides of the invention.
  • FIGS. 2A and 2B depict the antisense activity of exemplary antisense oligonucleotides according to the invention in HEK293 cells expressing murine TLR9.
  • the data demonstrate the ability of antisense oligonucleotides according to the invention to inhibit TLR9 agonist activity in cells cultured and treated according to Example 2.
  • FIG. 2C depicts the antisense activity of exemplary antisense oligonucleotides according to the invention in HEK293 cells expressing murine TLR7.
  • the data demonstrate the ability of antisense oligonucleotides according to the invention to inhibit TLR7 agonist activity in cells cultured and treated according to Example 2.
  • FIG. 2D depicts the antisense activity of exemplary antisense oligonucleotides according to the invention in HEK293 cells expressing murine MyD88.
  • the data demonstrate the ability of antisense oligonucleotides according to the invention to inhibit MyD88 agonist activity in cells cultured and treated according to Example 2.
  • FIG. 3 depicts the antisense activity of exemplary antisense oligonucleotides according to the invention in mouse splenocytes.
  • the data demonstrate the ability of antisense oligonucleotides according to the invention to inhibit TLR9 mRNA translation, or protein synthesis, in splenocytes treated according to Example 2.
  • FIG. 4 depicts the antisense activity of exemplary antisense oligonucleotides according to the invention in human PBMCs.
  • the data demonstrate the ability of antisense oligonucleotides according to the invention to inhibit TLR9 mRNA translation, or protein synthesis, in human PBMCs treated according to Example 2.
  • FIGS. 5A and 5B depict the activity of exemplary antisense oligonucleotides according to the invention to inhibit TLR9-induced IL-12 following in vivo administration according to Example 3.
  • the data demonstrate that administration of an exemplary TLR9 antisense oligonucleotide according to the invention can cause down-regulation of TLR9 expression in vivo and prevent the induction of IL-12 by a TLR9 agonist. More generally, the data demonstrate the ability of a TLR9 antisense oligonucleotide according to the invention to inhibit the induction of pro-inflammatory cytokines by a TLR9 agonist.
  • FIG. 5C depicts the duration of in vivo activity of exemplary antisense oligonucleotides according to the invention to inhibit MyD88-induced IL-12 following in vivo administration according to Example 3.
  • the data demonstrate that administration of an exemplary MyD88 antisense oligonucleotide according to the invention can cause down-regulation of MyD88 expression in vivo and prevent the induction of IL-12 by a TLR9 agonist for a longer duration than either linear antisense oligonucleotides or 3′-3′ linked antisense oligonucleotides.
  • the data demonstrate the ability of a MyD88 antisense oligonucleotide according to the invention to inhibit the induction of pro-inflammatory cytokines by a TLR agonist.
  • FIG. 6 depicts the activity of exemplary antisense oligonucleotides according to the invention to inhibit TLR9-induced IL-12 in a dose dependent manner following in vivo administration according to Example 3.
  • the data demonstrate that in vivo administration of a TLR9 antisense oligonucleotide according to the invention can cause down-regulation of TLR9 expression in vivo in a dose dependent manner and prevent the induction of IL-12 by a TLR9 agonist. More generally, the data demonstrate the ability of a TLR9 antisense oligonucleotide according to the invention to selectively inhibit the induction of pro-inflammatory cytokines by a TLR9 agonist.
  • FIG. 7 depicts the activity of exemplary antisense oligonucleotides according to the invention to inhibit TLR9-induced IL-12 in a time dependent manner following in vivo administration according to Example 3.
  • the data demonstrate that in vivo administration of a TLR9 antisense oligonucleotide according to the invention can cause down-regulation of TLR9 expression in vivo in a time dependent manner and prevent the induction of IL-12 by a TLR9 agonist for an extended period of time. More generally, the data demonstrate the ability of a TLR9 antisense oligonucleotide according to the invention to inhibit the induction of pro-inflammatory cytokines by a TLR9 agonist in a time dependent manner.
  • FIGS. 8A , 8 B, 8 C depict the antisense activity of exemplary antisense oligonucleotides according to the invention in murine J774 cells.
  • the data demonstrate the ability of antisense oligonucleotides according to the invention to inhibit TLR9 mRNA, transcription, translation, or protein synthesis, in murine J774 cells treated according to Example 2.
  • FIG. 8D depicts the antisense activity of exemplary antisense oligonucleotides according to the invention in human HeLa cells.
  • the data demonstrate the ability of antisense oligonucleotides according to the invention to inhibit VEGF mRNA transcription in human HeLa cells treated according to Example 2.
  • FIG. 9 depicts the antisense activity of exemplary antisense oligonucleotides according to the invention in human B cells.
  • the data demonstrate the ability of antisense oligonucleotides according to the invention to inhibit TLR9 mRNA translation, or protein synthesis, in human B cells treated according to Example 2.
  • FIG. 10 depicts the antisense activity of exemplary antisense oligonucleotides according to the invention in human pDCs.
  • the data demonstrate the ability of antisense oligonucleotides according to the invention to inhibit TLR9 mRNA translation, or protein synthesis, in human pDCs treated according to Example 2.
  • FIG. 11 depicts the activity of exemplary antisense oligonucleotides according to the invention to inhibit TLR9-induced IL-12 following in vivo administration according to Example 3.
  • the data demonstrate that in vivo administration of an exemplar TLR9 antisense oligonucleotide according to the invention can cause down-regulation of TLR9 expression in vivo and prevent the induction of IL-12 by a TLR9 agonist. More generally, the data demonstrate the ability of a TLR9 antisense oligonucleotide according to the invention to inhibit the induction of pro-inflammatory cytokines by a TLR9 agonist.
  • FIG. 12 depicts the antisense activity of exemplary antisense oligonucleotides according to the invention in HEK293 cells expressing mouse TLR7.
  • the data demonstrate the ability of antisense oligonucleotides according to the invention to inhibit TLR7 agonist activity in cells cultured and treated according to Example 2.
  • FIG. 13 depicts the selective binding and cleavage of exemplary antisense oligonucleotides according to the invention treated according to Example 4.
  • Lane 1 is substrate alone;
  • Lane 2 is T1 nuclease;
  • Lane 3 is 5′-AAUGCUUGUCUGUGCAGUCC-3′ (SEQ ID NO.
  • Lane 8 is dsRNA; and Lane 9 is 20-mer DNA antisense; wherein all sequences have phosphorothioate backbone except where indicated with an “o” (phosphodiester linkage); underlined nucleotides indicate 2′-O-methylribonucleotides.
  • oligonucleotides according to the invention provide an optimal structure for binding and cleavage by proteins and enzymes associated with RNAi-mediated inhibition of gene expression.
  • FIG. 14 shows switchback triplex-forming (A) and D-loop (B) modes of binding oligonucleotides with inverted polarity.
  • FIG. 15 shows parallel-stranded hairpin modes of oligonucleotides containing purine-pyrimidine strands attached covalently at either 3′-3′ or 5′-5′ ends.
  • FIG. 16 shows antisense mode of binding of the oligonucleotide-based compounds according to the invention.
  • the invention relates to the therapeutic and prophylactic use of novel antisense oligonucleotides to down-regulate gene expression.
  • novel antisense oligonucleotides to down-regulate gene expression.
  • Such molecules are useful, for example, in providing compositions for modulation of gene expression or for treating and/or preventing diseases and/or conditions that are capable of responding to modulation of gene expression in patients, subjects, animals or organisms.
  • 2′-O-substituted means substitution of the 2′ position of the pentose moiety with an —O— lower alkyl group containing 1-6 saturated or unsaturated carbon atoms (for example, but not limited to, 2′-O-methyl), or with an —O-aryl or allyl group having 2-6 carbon atoms, wherein such alkyl, aryl or allyl group may be unsubstituted or may be substituted, (for example, with 2′-O-methoxyethyl, ethoxy, methoxy, halo, hydroxyl, trifluoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxyl, carbalkoxyl, or amino groups); or with a hydroxyl, an amino or a halo group, but not with a 2′-H group.
  • the oligonucleotides of the invention include four or five 2′-O-alky nucleotides at their 5′ terminus, and/or four or five 2′-O-alky nucleotides at their 3′ terminus.
  • 3′ when used directionally, generally refers to a region or position in a polynucleotide or oligonucleotide 3′ (toward the 3′ end of the nucleotide) from another region or position in the same polynucleotide or oligonucleotide.
  • 3′ end generally refers to the 3′ terminal nucleotide of the component oligonucleotides.
  • “Two or more oligonucleotides linked at their 3′ ends” generally refers to a linkage between the 3′ terminal nucleotides of the oligonucleotides which may be directly via 5′, 3′ or 2′ hydroxyl groups, or indirectly, via a non-nucleotide linker. Such linkages may also be via a nucleoside, utilizing both 2′ and 3′ hydroxyl positions of the nucleoside. Such linkages may also utilize a functionalized sugar or nucleobase of a 3′ terminal nucleotide.
  • 5′ when used directionally, generally refers to a region or position in a polynucleotide or oligonucleotide 5′ (toward the 5′ end of the nucleotide) from another region or position in the same polynucleotide or oligonucleotide.
  • 5′ end generally refers to the 5′ terminal nucleotide of the component oligonucleotides.
  • “Two or more single-stranded antisense oligonucleotides linked at their 5′ ends” generally refers to a linkage between the 5′ terminal nucleotides of the oligonucleotides which may be directly via 5′, 3′ or 2′ hydroxyl groups, or indirectly, via a non-nucleotide linker. Such linkages may also be via a nucleoside, utilizing both 2′ and 3′ hydroxyl positions of the nucleoside. Such linkages may also utilize a functionalized sugar or nucleobase of a 5′ terminal nucleotide.
  • oligonucleotides having one or two fewer nucleoside residues, or from one to several additional nucleoside residues are contemplated as equivalents of each of the embodiments described above.
  • accessible generally means when related to a compound according to the invention, that the relevant portion of the molecule is able to be recognized by the cellular components necessary to elicit an intended response to the compound.
  • agonist generally refers to a substance that binds to a receptor of a cell and induces a response.
  • An agonist often mimics the action of a naturally occurring substance such as a ligand.
  • antagonist generally refers to a substance that attenuates the effects of an agonist or ligand.
  • airway inflammation generally includes, without limitation, inflammation in the respiratory tract caused by allergens, including asthma.
  • allergen generally refers to an antigen or antigenic portion of a molecule, usually a protein, which elicits an allergic response upon exposure to a subject.
  • a subject is allergic to the allergen as indicated, for instance, by the wheal and flare test or any method known in the art.
  • a molecule is said to be an allergen even if only a small subset of subjects exhibit an allergic (e.g., IgE) immune response upon exposure to the molecule.
  • allergy generally includes, without limitation, food allergies, respiratory allergies and skin allergies.
  • antigen generally refers to a substance that is recognized and selectively bound by an antibody or by a T cell antigen receptor.
  • Antigens may include but are not limited to peptides, proteins, lipids, carbohydrates, nucleosides, nucleotides, nucleic acids, and combinations thereof. Antigens may be natural or synthetic and generally induce an immune response that is specific for that antigen.
  • autoimmune disorder generally refers to disorders in which “self” antigen undergo attack by the immune system. Such term includes, without limitation, lupus erythematosus, multiple sclerosis, type I diabetes mellitus, irritable bowel syndrome, Chron's disease, rheumatoid arthritis, septic shock, alopecia universalis, acute disseminated encephalomyelitis, Addison's disease, ankylosing spondylitis, antiphospholipid antibody syndrome, autoimmune hemolytic anemia, autoimmune hepatitis, Bullous pemphigoid, chagas disease, chronic obstructive pulmonary disease, hydrox disease, dermatomyositis, endometriosis, Goodpasture's syndrome, Graves' disease, Guillain-Barré syndrome, Hashimoto's disease, hidradenitis suppurativa, idiopathic thrombocytopenic purpura, interstitial cystitis, morphe
  • biological instability generally refers to a molecule's ability to be degraded and subsequently inactivated in vivo.
  • degradation results from exonuclease activity and/or endonuclease activity, wherein exonuclease activity refers to cleaving nucleotides from the 3′ or 5′ end of an oligonucleotide, and endonuclease activity refers to cleaving phosphodiester bonds at positions other than at the ends of the oligonucleotide.
  • cancer generally refers to, without limitation, any malignant growth or tumor caused by abnormal or uncontrolled cell proliferation and/or division. Cancers may occur in humans and/or mammals and may arise in any and all tissues. Treating a patient having cancer may include administration of a compound, pharmaceutical formulation or vaccine according to the invention such that the abnormal or uncontrolled cell proliferation and/or division, or metastasis is affected.
  • carrier generally encompasses any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, oil, lipid, lipid containing vesicle, microspheres, liposomal encapsulation, or other material for use in pharmaceutical formulations. It will be understood that the characteristics of the carrier, excipient or diluent will depend on the route of administration for a particular application. The preparation of pharmaceutically acceptable formulations containing these materials is described in, for example, Remington's Pharmaceutical Sciences, 18 th Edition, ed. A. Gennaro, Mack Publishing Co., Easton, Pa., 1990.
  • co-administration generally refers to the administration of at least two different substances sufficiently close in time to modulate an immune response.
  • Co-administration refers to simultaneous administration, as well as temporally spaced order of up to several days apart, of at least two different substances in any order, either in a single dose or separate doses.
  • combination with generally means administering an oligonucleotide-based compound according to the invention and another agent useful for treating the disease or condition that does not abolish the activity of the compound in the course of treating a patient.
  • administration may be done in any order, including simultaneous administration, as well as temporally spaced order from a few seconds up to several days apart.
  • Such combination treatment may also include more than a single administration of the compound according to the invention and/or independently the other agent.
  • the administration of the compound according to the invention and the other agent may be by the same or different routes.
  • subject or “subject” or “patient” generally refers to a mammal, such as a human.
  • kinase inhibitor generally refers to molecules that antagonize or inhibit phosphorylation-dependent cell signaling and/or growth pathways in a cell.
  • Kinase inhibitors may be naturally occurring or synthetic and include small molecules that have the potential to be administered as oral therapeutics.
  • Kinase inhibitors have the ability to rapidly and specifically inhibit the activation of the target kinase molecules.
  • Protein kinases are attractive drug targets, in part because they regulate a wide variety of signaling and growth pathways and include many different proteins. As such, they have great potential in the treatment of diseases involving kinase signaling, including cancer, cardiovascular disease, inflammatory disorders, diabetes, macular degeneration and neurological disorders.
  • a non-limiting example of a kinase inhibitor is sorafenib.
  • linear synthesis generally refers to a synthesis that starts at one end of an oligonucleotide and progresses linearly to the other end. Linear synthesis permits incorporation of either identical or non-identical (in terms of length, base composition and/or chemical modifications incorporated) monomeric units into an oligonucleotide.
  • mammal is expressly intended to include warm blooded, vertebrate animals, including, without limitation, humans, non-human primates, rats, mice, cats, dogs, horses, cattle, cows, pigs, sheep and rabbits.
  • nucleoside generally refers to compounds consisting of a sugar, usually ribose, deoxyribose, pentose, arabinose or hexose, and a purine or pyrimidine base.
  • nucleotide generally refers to a nucleoside comprising a phosphorous-containing group attached to the sugar.
  • modified nucleoside or “nucleotide derivative” generally is a nucleoside that includes a modified heterocyclic base, a modified sugar moiety, or any combination thereof.
  • the modified nucleoside or nucleotide derivative is a non-natural pyrimidine or purine nucleoside, as herein described.
  • a modified nucleoside or nucleotide derivative, a pyrimidine or purine analog or non-naturally occurring pyrimidine or purine can be used interchangeably and refers to a nucleoside that includes a non-naturally occurring base and/or non-naturally occurring sugar moiety.
  • a base is considered to be non-natural if it is not guanine, cytosine, adenine, thymine or uracil and a sugar is considered to be non-natural if it is not 13-ribo-furanoside or 2′-deoxyribo-furanoside.
  • modified oligonucleotide as used herein describes an oligonucleotide in which at least two of its nucleotides are covalently linked via a synthetic linkage, i.e., a linkage other than a phosphodiester linkage between the 5′ end of one nucleotide and the 3′ end of another nucleotide in which the 5′ nucleotide phosphate has been replaced with any number of chemical groups.
  • modified oligonucleotide also encompasses 2′-O,4′-C-methylene-b-D-ribofuranosyl nucleic acids, arabinose nucleic acids, substituted arabinose nucleic acids, hexose nucleic acids, peptide nucleic acids, morpholino, and oligonucleotides having at least one nucleotide with a modified base and/or sugar, such as a 2′-O-substituted, a 5-methylcytosine and/or a 3′-O-substituted ribonucleotide.
  • nucleic acid encompasses a genomic region or an RNA molecule transcribed therefrom. In some embodiments, the nucleic acid is mRNA.
  • linker generally refers to any moiety that can be attached to an oligonucleotide by way of covalent or non-covalent bonding through a sugar, a base, or the backbone.
  • the non-covalent linkage may be, without limitation, electrostatic interactions, hydrophobic interactions, ⁇ -stacking interactions, hydrogen bonding and combinations thereof.
  • Non-limiting examples of such non-covalent linkage includes Watson-Crick base pairing, Hoogsteen base pairing, and base stacking.
  • the linker can be used to attach two or more nucleosides or can be attached to the 5′ and/or 3′ terminal nucleotide in the oligonucleotide.
  • Such linker can be either a non-nucleotide linker or a nucleoside linker.
  • non-nucleotide linker generally refers to a chemical moiety, other than a linkage directly between two nucleotides that can be attached to an oligonucleotide by way of covalent or non-covalent bonding.
  • non-nucleotide linker is from about 2 angstroms to about 200 angstroms in length, and may be either in a cis or trans orientation.
  • nucleotide linkage generally refer to a chemical linkage to join two nucleosides through their sugars (e.g. 3′-3′, 2′-3′,2′-5′, 3′-5′,5′-5′) consisting of a phosphorous atom and a charged, or neutral group (e.g., phosphodiester, phosphorothioate, phosphorodithioate or methylphosphonate) between adjacent nucleosides.
  • sugars e.g. 3′-3′, 2′-3′,2′-5′, 3′-5′,5′-5′
  • neutral group e.g., phosphodiester, phosphorothioate, phosphorodithioate or methylphosphonate
  • oligonucleotide refers to a polynucleoside formed from a plurality of linked nucleoside units, which may include, for example, deoxyribonucleotides or ribonucleotides, synthetic or natural nucleotides, phosphodiester or modified linkages, natural bases or modified bases natural sugars or modified sugars, or combinations of these components.
  • the nucleoside units may be part of viruses, bacteria, cell debris or oligonucleotide-based compositions (for example, siRNA and microRNA).
  • Such oligonucleotides can also be obtained from existing nucleic acid sources, including genomic or cDNA, but are preferably produced by synthetic methods.
  • each nucleoside unit includes a heterocyclic base and a pentofuranosyl, trehalose, arabinose, 2′-deoxy-2′-substituted nucleoside, 2′-deoxy-2′-substituted arabinose, 2′-O-substitutedarabinose or hexose sugar group.
  • the nucleoside residues can be coupled to each other by any of the numerous known internucleoside linkages.
  • internucleoside linkages include, without limitation, phosphodiester, phosphorothioate, phosphorodithioate, methylphosphonate, alkylphosphonate, alkylphosphonothioate, phosphotriester, phosphoramidate, siloxane, carbonate, carboalkoxy, acetamidate, carbamate, morpholino, borano, thioether, bridged phosphoramidate, bridged methylene phosphonate, bridged phosphorothioate, and sulfone internucleoside linkages.
  • oligonucleotide also encompasses polynucleosides having one or more stereospecific internucleoside linkage (e.g., (R P )- or (S P )-phosphorothioate, alkylphosphonate, or phosphotriester linkages).
  • R P stereospecific internucleoside linkage
  • S P phosphorothioate
  • alkylphosphonate alkylphosphonate
  • phosphotriester linkages e.g., oligonucleotide and “dinucleotide” are expressly intended to include polynucleosides and dinucleosides having any such internucleoside linkage, whether or not the linkage comprises a phosphate group.
  • these internucleoside linkages may be phosphodiester, phosphorothioate or phosphorodithioate linkages, or combinations thereof.
  • the nucleotides of the synthetic oligonucleotides are linked by at least one phosphorothioate internucleotide linkage.
  • the phosphorothioate linkages may be mixed Rp and Sp enantiomers, or they may be stereoregular or substantially stereoregular in either Rp or Sp form (see Iyer et al. (1995) Tetrahedron Asymmetry 6:1051-1054).
  • one or more of the oligonucleotides within the antisense compositions of the invention contain one or more 2′-O,4′-C-methylene-b-D-ribofuranosyl nucleic acids, wherein the ribose is modified with a bond between the 2′ and 4′ carbons, which fixes the ribose in the 3′-endo structural conformation.
  • an oligonucleotide that is complementary to a single-stranded RNA sequence means that the oligonucleotide forms a sufficient number of hydrogen bonds through Watson-Crick interactions of its nucleobases with nucelobases of the single-stranded RNA sequence to form a double helix with the single-stranded RNA sequence under physiological conditions. This is in contrast to oligonucleotides that form a triple helix with a double-stranded DNA or RNA through Hoogsteen hydrogen bonding.
  • complementary is intended to mean an oligonucleotide that binds to the nucleic acid sequence under physiological conditions, for example, by Watson-Crick base pairing (interaction between oligonucleotide and single-stranded nucleic acid) or by Hoogsteen base pairing (interaction between oligonucleotide and double-stranded nucleic acid) or by any other means, including in the case of an oligonucleotide, binding to RNA and causing pseudoknot formation. Binding by Watson-Crick or Hoogsteen base pairing under physiological conditions is measured as a practical matter by observing interference with the function of the nucleic acid sequence.
  • peptide generally refers to oligomers or polymers of amino acids that are of sufficient length and composition to affect a biological response, for example, antibody production or cytokine activity whether or not the peptide is a hapten.
  • peptide may include modified amino acids (whether or not naturally or non-naturally occurring), where such modifications include, but are not limited to, phosphorylation, glycosylation, pegylation, lipidization, and methylation.
  • pharmaceutically acceptable means a non-toxic material that does not interfere with the effectiveness of a compound according to the invention or the biological activity of a compound according to the invention.
  • physiologically acceptable refers to a non-toxic material that is compatible with a biological system such as a cell, cell culture, tissue, or organism.
  • a biological system such as a cell, cell culture, tissue, or organism.
  • the biological system is a living organism, such as a mammal, particularly a human.
  • prophylactically effective amount generally refers to an amount sufficient to prevent or reduce the development of an undesired biological effect.
  • terapéuticaally effective amount generally refers to an amount sufficient to affect a desired biological effect, such as a beneficial result, including, without limitation, prevention, diminution, amelioration or elimination of signs or symptoms of a disease or disorder.
  • a desired biological effect such as a beneficial result, including, without limitation, prevention, diminution, amelioration or elimination of signs or symptoms of a disease or disorder.
  • the total amount of each active component of the pharmaceutical composition or method is sufficient to show a meaningful patient benefit, for example, but not limited to, healing of chronic conditions characterized by immune stimulation.
  • a “pharmaceutically effective amount” will depend upon the context in which it is being administered.
  • a pharmaceutically effective amount may be administered in one or more prophylactic or therapeutic administrations.
  • the term refers to that ingredient alone.
  • the term refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.
  • treatment generally refers to an approach intended to obtain a beneficial or desired result, which may include alleviation of symptoms, or delaying or ameliorating a disease progression.
  • gene expression generally refers to process by which information from a gene is used in the synthesis of a functional gene product, which may be a protein.
  • the process may involve transcription, RNA splicing, translation, and post-translational modification of a protein, and may include mRNA, preRNA, ribosomal RNA, and other templates for protein synthesis.
  • the invention provides novel oligonucleotide-based compounds comprising two or more single-stranded antisense oligonucleotides linked at their 5′ ends, wherein the compounds have two or more accessible 3′ ends.
  • the linkage at the 5′ ends of the component oligonucleotides is independent of the other oligonucleotide linkages and may be directly via 5′, 3′ or 2′ hydroxyl groups, or indirectly, via a non-nucleotide linker or a nucleoside, utilizing either the 2′ or 3′ hydroxyl positions of the nucleoside.
  • Linkages may also utilize a functionalized sugar or nucleobase of a 5′ terminal nucleotide.
  • Oligonucleotide-based compounds according to the invention comprise two identical or different sequences conjugated at their 5′-5′ ends via a phosphodiester, phosphorothioate or non-nucleoside linker (Diagram 3). Such compounds comprise 15 to 27 nucleotides that are complementary to specific portions of mRNA targets of interest for antisense down regulation of gene product. Oligonucleotide-based compounds according to the invention that comprise identical sequences are able to bind to a specific mRNA via Watson-Crick hydrogen bonding interactions and inhibit protein expression ( FIG. 16 ). Oligonucleotide-based compounds according to the invention that comprise different sequences are able to bind to two or more different regions of one or more mRNA target and inhibit protein expression.
  • Such compounds are comprised of heteronucleotide sequences complementary to target mRNA and form stable duplex structures through Watson-Crick hydrogen bonding. Surprisingly, such sequences containing two free 3′-ends (5′-5′-attached antisense) are more potent inhibitors of gene expression than those containing a single free 3′-end or no free 3′-end.
  • Oligonucleotide-based compounds according to the invention are useful in treating and/or preventing diseases wherein inhibiting a gene expression would be beneficial.
  • Oligonucleotide-based compounds according to the invention include, but are not limited to, antisense oligonucleotides comprising naturally occurring nucleotides, modified nucleotides, modified oligonucleotides and/or backbone modified oligonucleotides.
  • antisense oligonucleotides that inhibit the translation of mRNA encoded proteins may produce undesired biological effects, including but not limited to insufficient antisense activity, inadequate bioavailability, suboptimal pharmacokinetics or pharmacodynamics, unintended immune stimulation, off target activity, and biologic instability.
  • an antisense oligonucleotide according to the invention requires many considerations beyond simple design of a molecule that is complementary to the target RNA sequence.
  • preparation of antisense oligonucleotides according to the invention is intended to incorporate changes necessary to limit secondary structure interference with antisense activity, enhance the oligonucleotide's target specificity, minimize interaction with binding or competing factors (for example, proteins), optimize cellular uptake, bioavailability, pharmacokinetics, and pharmacodynamics, and/or inhibit, prevent or suppress immune cell activation.
  • oligonucleotide-based compounds of the invention may be described by the following formula.
  • L is a nucleotide linker or non-nucleotide linker; N1-N8, at each occurrence, is independently a nucleotide or nucleotide derivative; Nm and Nn, at each occurrence, are independently a nucleotide or nucleotide derivative; and wherein m and n are independently numbers from 0 to about 40.
  • Representative non-nucleotide linkers are set forth in Table 1.
  • the small molecule linker is glycerol or a glycerol homolog of the formula HO—(CH 2 ) o —CH(OH)—(CH 2 ) p —OH, wherein o and p independently are integers from 1 to about 6, from 1 to about 4 or from 1 to about 3.
  • the small molecule linker is a derivative of 1,3-diamino-2-hydroxypropane.
  • Some such derivatives have the formula HO—(CH 2 ) m —C(O)NH—CH 2 —CH(OH)—CH 2 —NHC(O)—(CH 2 ) m —OH, wherein m is an integer from 0 to about 10, from 0 to about 6, from 2 to about 6 or from 2 to about 4.
  • Some non-nucleotide linkers according to the invention permit attachment of more than two oligonucleotide-based compounds of the invention.
  • the small molecule linker glycerol has three hydroxyl groups to which such oligonucleotides may be covalently attached.
  • Some oligonucleotide-based compounds of the invention therefore, comprise two or more oligonucleotides linked to a nucleotide or a non-nucleotide linker. Such oligonucleotides according to the invention are referred to as being “branched”.
  • Oligonucleotide-based compounds according to the invention may comprise at least two linked antisense oligonucleotides with two or more free 3′ ends. Some of the ways in which two or more oligonucleotides can be linked are shown in Table 2.
  • L is a linker or a nucleotide linkage and Domain A and/or Domain B are antisense oligonucleotides that are designed to selectively hybridize to the same, target RNA sequence or different target RNA sequences.
  • L is a linker and Domain A and/or Domain B and/or Domain C are antisense oligonucleotides that are designed to selectively hybridize to the same target RNA sequence or different target RNA sequences.
  • Domain A and/or Domain B and/or Domain C of Formulas II and/or III are antisense oligonucleotides that are designed to selectively hybridize to the same target RNA sequence.
  • Domain A and/or Domain B and/or Domain C can be designed to hybridize to the same region on the target RNA sequence or to different regions of the same target RNA sequence.
  • Domain A, Domain B, and Domain C are independently RNA or DNA-based oligonucleotides.
  • the oligonucleotides comprise mixed backbone oligonucleotides.
  • one or more of Domain A and/or Domain B and/or Domain C of Formula IV is an antisense oligonucleotide that is designed to selectively hybridize to one target RNA sequence and one or more of the remaining Domain A and/or Domain B and/or Domain C is an antisense oligonucleotide that is designed to selectively hybridized to a different target RNA sequence.
  • one or more of Domain A, Domain B or Domain C of Formula IV is an antagonist of a cell-surface or intracellular receptor.
  • the antagonist is a TLR antagonist.
  • one or more of Domain A and/or Domain B and/or Domain C of Formula II, III, IV and/or V is an RNA-based oligonucleotide hybridized to a complimentary RNA-based oligonucleotide such that the domain comprises an siRNA molecule.
  • the component oligonucleotides of oligonucleotide-based compounds of the invention are at least 14 nucleotides in length, but are preferably 15 to 40 nucleotides long, preferably 20 to 30 nucleotides in length.
  • the component oligonucleotides of the oligonucleotide-based compounds of the invention can independently be 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 nucleotides in length.
  • These oligonucleotides can be prepared by the art recognized methods such as phosphoramidate or H-phosphonate chemistry which can be carried out manually or by an automated synthesizer.
  • the synthetic antisense oligonucleotides of the invention may also be modified in a number of ways without compromising their ability to hybridize to mRNA. Such modifications may include at least one internucleotide linkage of the oligonucleotide being an alkylphosphonate, phosphorothioate, phosphorodithioate, methylphosphonate, phosphate ester, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate hydroxyl, acetamidate or carboxymethyl ester or a combination of these and other internucleotide linkages between the 5′ end of one nucleotide and the 3′ end of another nucleotide in which the 5′ nucleotide phosphodiester linkage has been replaced with any number of chemical groups.
  • the synthetic antisense oligonucleotides of the invention may comprise combinations of internucleotide linkages.
  • U.S. Pat. No. 5,149,797 describes traditional chimeric oligonucleotides having a phosphorothioate core region interposed between methylphosphonate or phosphoramidate flanking regions.
  • U.S. Pat. No. 5,652,356 discloses “inverted” chimeric oligonucleotides comprising one or more nonionic oligonucleotide region (e.g.
  • oligonucleotide phosphorothioate alkylphosphonate and/or phosphoramidate and/or phosphotriester internucleoside linkage flanked by one or more region of oligonucleotide phosphorothioate.
  • Various synthetic antisense oligonucleotides with modified internucleotide linkages can be prepared according to standard methods.
  • the phosphorothioate linkages may be mixed Rp and Sp enantiomers, or they may be made stereoregular or substantially stereoregular in either Rp or Sp form.
  • oligonucleotide-based compounds of the invention include those that are internal or at the end(s) of the oligonucleotide molecule and include additions to the molecule of the internucleoside phosphate linkages, such as cholesterol, cholesteryl, or diamine compounds with varying numbers of carbon residues between the amino groups and terminal ribose, deoxyribose and phosphate modifications which cleave, or crosslink to the opposite chains or to associated enzymes or other proteins which bind to the genome.
  • the internucleoside phosphate linkages such as cholesterol, cholesteryl, or diamine compounds with varying numbers of carbon residues between the amino groups and terminal ribose, deoxyribose and phosphate modifications which cleave, or crosslink to the opposite chains or to associated enzymes or other proteins which bind to the genome.
  • modified oligonucleotides include oligonucleotides with a modified base and/or sugar such as 2′-O,4′-C-methylene-b-D-ribofuranosyl, or arabinose instead of ribose, or a 3′,5′-substituted oligonucleotide having a sugar which, at both its 3′ and 5′ positions, is attached to a chemical group other than a hydroxyl group (at its 3′ position) and other than a phosphate group (at its 5′ position).
  • a modified base and/or sugar such as 2′-O,4′-C-methylene-b-D-ribofuranosyl, or arabinose instead of ribose
  • modifications to sugars of the oligonucleotide-based compounds of the invention include modifications to the 2′ position of the ribose moiety which include but are not limited to 2′-O-substituted with an —O-alkyl group containing 1-6 saturated or unsaturated carbon atoms, or with an —O-aryl, or —O-allyl group having 2-6 carbon atoms wherein such —O-alkyl, —O-aryl or —O-allyl group may be unsubstituted or may be substituted, for example with halo, hydroxyl, trifluoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxy, carbalkoxyl or amino groups. None of these substitutions are intended to exclude the presence of other residues having native 2′-hydroxyl group in the case of ribose or 2′ H— in the case of deoxyribose.
  • the oligonucleotides-based compounds according to the invention can comprise one or more ribonucleotides.
  • U.S. Pat. No. 5,652,355 discloses traditional hybrid oligonucleotides having regions of 2′-O-substituted ribonucleotides flanking a DNA core region.
  • 5,652,356 discloses an “inverted” hybrid oligonucleotide that includes an oligonucleotide comprising a 2′-O-substituted (or 2′ OH, unsubstituted) RNA region which is in between two oligodeoxyribonucleotide regions, a structure that “inverted relative to the “traditional” hybrid oligonucleotides.
  • Non-limiting examples of particularly useful oligonucleotides of the invention have 2′-O-alkylated ribonucleotides at their 3′, 5′, or 3′ and 5′ termini, with at least four, and in some exemplary embodiments five, contiguous nucleotides being so modified.
  • Non-limiting examples of 2′-O-alkylated groups include 2′-O-methyl, 2′-O-ethyl, 2′-O-propyl, 2′-O-butyls and 2′-O-methoxy-ethyl.
  • the oligonucleotide-based compounds of the invention may conveniently be synthesized using an automated synthesizer and phosphoramidite approach as schematically depicted in FIG. 1B , and further described in Example 1.
  • the oligonucleotide-based compounds of the invention are synthesized by a linear synthesis approach (see FIG. 1A ).
  • An alternative mode of synthesis is “parallel synthesis”, in which synthesis proceeds outward from a central linker moiety (see FIG. 1 ).
  • a solid support attached linker can be used for parallel synthesis, as is described in U.S. Pat. No. 5,912,332.
  • a universal solid support such as phosphate attached controlled pore glass support can be used.
  • Parallel synthesis of the oligonucleotide-based compounds of the invention has several advantages over linear synthesis: (1) parallel synthesis permits the incorporation of identical monomeric units; (2) unlike in linear synthesis, both (or all) the monomeric units are synthesized at the same time, thereby the number of synthetic steps and the time required for the synthesis is the same as that of a monomeric unit; and (3) the reduction in synthetic steps improves purity and yield of the final immune modulatory oligoribonucleotide product.
  • the oligonucleotide-based compounds of the invention may conveniently be deprotected with concentrated ammonia solution or as recommended by the phosphoramidite supplier, if a modified nucleoside is incorporated.
  • the product oligonucleotide-based compounds is preferably purified by reversed phase HPLC, detritylated, desalted and dialyzed.
  • oligonucleotide-based compounds of the invention are shown in SEQ ID NO. 1 through SEQ ID NO. 175 in Table 3 below.
  • the oligonucleotide-based compounds have phosphorothioate (PS) linkages, but may also include phosphodiester (o) linkages.
  • PS phosphorothioate
  • o phosphodiester
  • the composition lacks immune stimulatory activity of certain oligonucleotide compositions. It is known that certain oligonucleotide-based compositions can possess immune stimulatory motifs. This immune stimulatory activity requires the oligonucleotides to be non-linked or linked at their 3′ ends.
  • oligonucleotide-based compositions according to the invention utilizing a linkage at the 5′ ends, as set forth in Formulas I, II, III or IV, that any inherent immune stimulatory activity is suppressed, as compared to the immune stimulatory activity that would be present in non-linked or oligonucleotide-based compositions linked at their 3′ ends or in a 2′-5′ fashion.
  • the structure of the oligonucleotide-based compound according to the invention provides an optimal compound for binding by enzymes and other proteins that are involved in RNaseH-mediated and/or RNAi-mediated inhibition of gene expression.
  • the oligonucleotide-based compounds according to the invention can be selectively bound by RNaseH, Dicer, Argonaut, RISC or other proteins that are involved in RNAi-mediated inhibition of gene expression. This selective binding provides optimal oligonucleotide-based compounds for utilizing RNaseH-mediated and/or RNAi-mediated inhibition of gene expression in vitro and in vivo.
  • the invention provides pharmaceutical formulations comprising an oligonucleotide-based compound according to the invention and a physiologically acceptable carrier.
  • the invention provides a method for inhibiting gene expression, the method comprising contacting a cell with a synthetic oligonucleotide-based compound according to the first aspect of the invention.
  • the invention provides a method for inhibiting gene expression in a mammal, the method comprising administering to the mammal a synthetic oligonucleotide-based compound according to the first aspect of the invention.
  • the synthetic oligonucleotide-based compounds according to the first aspect of the invention can inhibit the expression and activity of certain genes related to cellular proliferation, including but not limited to oncogenes.
  • the invention provides a method of inhibiting a TLR-mediated, Bcl-2-mediated, EGFR-mediated, mdm2-mediated, MyD88-mediated, PCSK9-mediated, survivin-mediated or VEGF-mediated response in a mammal though administration of a synthetic oligonucleotide-based compound according to the first aspect of the invention wherein the oligonucleotides are complementary to one or more mRNA sequence encoding a molecule involved in TLR signaling or Bcl-2, EGFR, mdm2, MyD88, PCSK9, survivin or VEGF activity.
  • the invention provides a method of inhibiting a TLR-mediated, Bcl-2-mediated, EGFR-mediated, mdm2-mediated, MyD88-mediated, PCSK9-mediated, survivin-mediated or VEGF-mediated response in a mammal through administration of a synthetic oligonucleotide-based compound according to the first aspect of the invention wherein the oligonucleotides are complementary to one or more TLR, Bcl-2, EGFR, mdm2, MyD88, PCSK9, survivin or VEGF mRNA sequence in combination with an antagonist of TLR, Bcl-2, EGFR, mdm2, MyD88, PCSK9, survivin or VEGF protein activity.
  • the invention provides methods for inhibiting gene expression in a mammal, such methods comprising administering to the mammal an oligonucleotide-based compound according to the invention.
  • the mammal is a human.
  • the oligonucleotide-based compound according to the invention is administered to a mammal in need of inhibiting its immune response.
  • the invention provides methods for therapeutically treating a patient having a disease or disorder, such methods comprising administering to the patient an oligonucleotide-based compound according to the invention in a therapeutically effective amount.
  • the disease or disorder to be treated is cancer, an autoimmune disorder, infectious disease, airway inflammation, inflammatory disorders, allergy, asthma, or a disease caused by a pathogen.
  • Pathogens include bacteria, parasites, fungi, viruses, viroids, and prions.
  • the invention provides methods for preventing a disease or disorder, such methods comprising administering to a subject at risk for developing the disease or disorder an oligonucleotide-based compound according to the invention in a pharmaceutically effective amount.
  • a subject is considered at risk for developing a disease or disorder if the subject has been or may be or will be exposed to an etiologic agent of the disease or disorder or is genetically predispositioned to contract the disease or disorder.
  • the disease or disorder to be prevented is cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, allergy, asthma, or a disease caused by a pathogen.
  • Pathogens include bacteria, parasites, fungi, viruses, viroids, and prions.
  • the invention provides a method of preventing or treating a disorder, such methods comprises isolating cells capable of producing cytokines or chemokines including, but not limited to, immune cells, T-regulatory cells, B-cells, PBMCs, pDCs, and lymphoid cells; culturing such cells under standard cell culture conditions, treating such cells ex vivo with an oligonucleotide-based compound according to the first aspect of the invention such that the isolated cells produce or secrete decreased levels of cytokines or chemokines, and administering or re-administering the treated cells to a patient in need of therapy to inhibit cytokines and/or chemokine for the prevention and/or treatment of disease.
  • This aspect of the invention would be in accordance with standard adoptive cellular immunotherapy techniques to produce activated immune cells.
  • the cells capable of producing cytokines or chemokines may be isolated from subjects with or without a disease or disorder. Such isolation may include identification and selection and could be performed using standard cell isolation procedures, including those set forth in the specific examples below. Such isolated cells would be cultured according to standard cell culturing procedures and using standard cell culture conditions, which may include the culturing procedures and conditions set forth in the specific examples below.
  • the isolated cells would be cultured in the presence of at least one oligonucleotide-based compound according to the invention, in an amount and for a time period sufficient to suppress or inhibit the production and/or secretion of cytokines and/or chemokines as compared to the isolated cells cultured in the absence of such one or more oligonucleotide-based compound according to the invention.
  • Such time may be from minutes, to hours, to days.
  • Such isolated and treated cells may find use following re-administration to the donor or administration to a second patient, wherein such donor or second patient are in need of suppressed or inhibited production and/or secretion of cytokines and/or chemokines.
  • re-administration to a donor or administration to a second patient having cancer an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, allergy, asthma, or a disease caused by a pathogen.
  • Such re-administration or administration may be accomplished using various modes, including catheter or injection administration or any other effective route.
  • This aspect of the invention may also find use in patients who may have a limited or incomplete ability to mount an immune response or are immune compromised (e.g. patient infected with HIV and bone marrow transplant patients).
  • the invention provides a composition comprising a compound according to the first aspect of the invention and one or more vaccines, antigens, antibodies, cytotoxic agents, chemotherapeutic agents (both traditional chemotherapy and modern targeted therapies), kinase inhibitors, allergens, antibiotics, agonist, antagonist, antisense oligonucleotides, ribozymes, RNAi molecules, siRNA molecules, miRNA molecules, aptamers, proteins, gene therapy vectors, DNA vaccines, adjuvants, co-stimulatory molecules or combinations thereof.
  • the oligonucleotide-based compound according to the invention can variously act by producing direct gene expression modulation effects alone and/or in combination with any other agent useful for treating or preventing the disease or condition that does not diminish the gene expression modulation effect of the oligonucleotide-based compound according to the invention.
  • the agent(s) useful for treating or preventing the disease or condition includes, but is not limited to, vaccines, antigens, antibodies, preferably monoclonal antibodies, cytotoxic agents, kinase inhibitors, allergens, antibiotics, siRNA molecules, antisense oligonucleotides, TLR antagonist (e.g.
  • TLR3 and/or TLR7 and/or antagonists of TLR8 and/or antagonists of TLR9 include chemotherapeutic agents (both traditional chemotherapy and modern targeted therapies), targeted therapeutic agents, activated cells, peptides, proteins, gene therapy vectors, peptide vaccines, protein vaccines, DNA vaccines, adjuvants, and co-stimulatory molecules (e.g. cytokines, chemokines, protein ligands, trans-activating factors, peptides or peptides comprising modified amino acids), or combinations thereof.
  • the oligonucleotide-based compound according to the invention may be administered in combination with one or more chemotherapeutic compound, targeted therapeutic agent and/or monoclonal antibody.
  • the agent can include DNA vectors encoding for antigen or allergen.
  • the oligonucleotide-based compound according to the invention can be administered in combination with other compounds (for example lipids or liposomes) to enhance the specificity or magnitude of the gene expression modulation of the oligonucleotide-based compound according to the invention.
  • administration of oligonucleotide-based compounds according to the invention can be by any suitable route, including, without limitation, parenteral, mucosal delivery, oral, sublingual, transdermal, topical, inhalation, intranasal, aerosol, intraocular, intratracheal, intrarectal, vaginal, by gene gun, dermal patch or in eye drop or mouthwash form.
  • Administration of the therapeutic compositions of oligonucleotide-based compounds according to the invention can be carried out using known procedures using an effective amount and for periods of time effective to reduce symptoms or surrogate markers of the disease.
  • an effective amount of an oligonucleotide-based compound according to the invention for treating a disease and/or disorder could be that amount necessary to alleviate or reduce the symptoms, or delay or ameliorate a tumor, cancer, or bacterial, viral or fungal infection.
  • an effective amount of an oligonucleotide-based compound according to the invention is an amount sufficient to achieve the desired modulation as compared to the gene expression in the absence of the oligonucleotide-based compound according to the invention.
  • the effective amount for any particular application can vary depending on such factors as the disease or condition being treated, the particular oligonucleotide being administered, the size of the subject, or the severity of the disease or condition.
  • One of ordinary skill in the art can empirically determine the effective amount of a particular oligonucleotide without necessitating undue experimentation.
  • the therapeutic composition When administered systemically, the therapeutic composition is preferably administered at a sufficient dosage to attain a blood level of oligonucleotide-based compound according to the invention from about 0.0001 micromolar to about 10 micromolar. For localized administration, much lower concentrations than this may be effective, and much higher concentrations may be tolerated.
  • a total dosage of oligonucleotide-based compound according to the invention ranges from about 0.001 mg per patient per day to about 200 mg per kg body weight per day. In certain embodiments, the total dosage may be 0.08, 0.16, 0.32, 0.48, 0.32, 0.64, 1, 10 or 30 mg/kg body weight administered daily, twice weekly or weekly. It may be desirable to administer simultaneously, or sequentially a therapeutically effective amount of one or more of the therapeutic compositions of the invention to an individual as a single treatment episode.
  • the methods according to this aspect of the invention are useful for model studies of gene expression.
  • the methods are also useful for the prophylactic or therapeutic treatment of human or animal disease.
  • the methods are useful for pediatric and veterinary inhibition of gene expression applications.
  • oligonucleotide-based compounds of the invention were chemically synthesized using phosphoramidite chemistry on automated DNA/RNA synthesizer.
  • TAC protected (Except U) 2′-O-TBDMS RNA monomers, A, G, C and U, were purchased from Sigma-Aldrich. 7-deaza-G, inosine and loxoribine monomers were purchased from ChemGenes Corporation. 0.25M 5-ethylthio-1H-tetrazole, PAC— anhydride Cap A and Cap B were purchased from Glen Research.
  • Oligonucleotide-based compounds of the invention were synthesized at 1-2 ⁇ M scale using a standard RNA synthesis protocol.
  • Oligonucleotide-based compounds of the invention were cleaved from solid support and the solution was further heated at 65° C. to removing protecting groups of exo cyclic-amines. The resulting solution was dried completely in a SpeedVac.
  • Oligonucleotide-based compounds of the invention were purified by ion exchange HPLC.
  • Buffer A 20 mM Tris-HCl, pH 7.0, 20% acetinitrile
  • Buffer B 3.0 M NaCl, 20 mM Tris-HCl, pH 7.0, 20% acetonitrile
  • CC-18 Sep-Pak cartridge purchased from Waters was first conditioned with 10 ml of acetonitrile followed by 10 ml of 0.5 M sodium acetate. 10 ml of the solution of oligonucleotide-based compounds of the invention was loaded. 15 ml of water was then used to wash out the salt. The oligonucleotide-based compounds of the invention was eluted out by 1 ml of 50% acetonitrile in water.
  • the solution is placed in SpeedVac for 30 minutes. The remaining solution was filter through a 0.2 micro filter and then was lyophilized to dryness. The solid was then re-dissolved in water to make the desired concentration.
  • the final solution was stored below 0° C.
  • Oligonucleotide-based compounds of the invention were analyzed by capillary electrophoresis according to the following conditions.
  • Capillary 62 cm ssDNA capillary
  • Sample preparation 0.2 OD of oligonucleotide-based composition according to the invention was dissolved in 200 ul of RNAse-free water.
  • Oligonucleotide-based compounds of the invention were analyzed by ion exchange HPLC according to the following conditions
  • Buffer A 100 mM Tris-HCl, pH 8.0, 20% acetinitrile.
  • Buffer B 2.0 M LiCl, 100 mM Tris-HCl, pH 8.0, 20% acetonitrile
  • oligonucleotide-based compounds of the invention was loaded on 20% polyacrylamide gel and was running at constant power of 4 watts for approximately 5 hours. The gel was viewed under short wavelength UV light.
  • PBMCs Peripheral blood mononuclear cells
  • pDCs Human plasmacytoid dendritic cells
  • Human PBMCs were plated in 48-well plates using 5 ⁇ 10 6 cells/ml.
  • Human pDCs were plated in 96-well dishes using 1 ⁇ 10 6 cells/ml.
  • the exemplary oligonucleotide-based compounds of the invention dissolved in DPBS (pH 7.4; Mediatech), were added to the cell cultures at doses of 0, 0.01, 1.0 or 10.0 ⁇ g/ml.
  • the cells were then incubated at 37° C. for 24 hours and subsequently stimulated with 10 ⁇ g/ml TLR9 agonist for 24 h. After treatment and stimulation, the supernatants were collected for luminex multiplex or ELISA assays.
  • the levels of IFN- ⁇ , IL-6, and/or IL-12 were measured by sandwich ELISA.
  • the required reagents including cytokine antibodies and standards, were purchased from PharMingen.
  • Human B cells were isolated from PBMCs by positive selection using the CD19 Cell Isolation Kit (Miltenyi Biotec, Auburn, Calif.) according to the manufacturer's instructions.
  • the culture medium used for the assay consisted of RPMI 1640 medium supplemented with 1.5 mM glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 50 ⁇ M 2-mercaptoethanol, 100 IU/ml penicillin-streptomycin mix and 10% heat-inactivated fetal bovine serum.
  • a total of 0.5 ⁇ 10 6 B cells per ml (i.e.1 ⁇ 10 5 /200 ⁇ l/well) were incubated in 96 well flat bottom plates with 50 ⁇ g/ml of exemplary oligonucleotide-based compounds of the invention for 24 hours. After 24 hours, cells were stimulated with 10 ⁇ g/ml TLR9 agonist for 24 h. Following treatment and stimulation, cell extracts were prepared and analyzed for the amount of TLR9 mRNA.
  • HEK293 cells stably expressing mouse TLR9 or TLR7 were plated in 48-well plates in 250 ⁇ L/well DMEM supplemented with 10% heat-inactivated FBS in a 5% CO2 incubator. At 80% confluence, cultures were transiently transfected with 400 ng/mL of the secreted form of human embryonic alkaline phosphatase (SEAP) reporter plasmid (pNifty2-Seap) (Invivogen) in the presence of 4 ⁇ L/mL of lipofectamine (Invivogen, Carlsbad, Calif.) in culture medium.
  • SEAP human embryonic alkaline phosphatase
  • Plasmid DNA and lipofectamine were diluted separately in serum-free medium and incubated at room emperature for 5 min. After incubation, the diluted DNA and lipofectamine were mixed and the mixtures were incubated further at room temperature for 20 min. Aliquots of 25 ⁇ L of the DNA/lipofectamine mixture containing 100 ng of plasmid DNA and 1 ⁇ L of lipofectamine were added to each well of the cell culture plate, and the cells were transfected for 6 h.
  • TLR9 or TLR7 specific oligonucleotide-based compounds of the invention were added to the wells, and incubation continued for 24 h.
  • cells were then stimulated with the 10 ⁇ g/ml TLR9 or TLR7 agonist for 24 h.
  • HEK293 cells stably expressing mouse TLR7 or TLR8 or another specific RNA target would be plated in 48-well plates in 250 ⁇ L/well DMEM supplemented with 10% heat-inactivated FBS in a 5% CO2 incubator.
  • cultures would be transiently transfected with 400 ng/mL of the secreted form of human embryonic alkaline phosphatase (SEAP) reporter plasmid (pNifty2-Seap) (Invivogen) in the presence of 4 ⁇ L/mL of lipofectamine (Invivogen, Carlsbad, Calif.) in culture medium. Plasmid DNA and lipofectamine would be diluted separately in serum-free medium and incubated at room temperature for 5 min. After incubation, the diluted DNA and lipofectamine would be mixed and the mixtures would be incubated further at room temperature for 20 min.
  • SEAP human embryonic alkaline phosphatase
  • Murine J774 macrophage cells (American Type Culture Collection, Rockville, Md.) were cultured in Dulbecco's modified Eagle's medium supplemented with 10% (v/v) fetal bovine serum (FBS) and antibiotics (100 IU/ml penicillin G/100 ⁇ g/ml streptomycin). J774 cells were plated at a density of 5 ⁇ 10 6 cells/well in six-well plates. For dose dependent experiments, the J774 cells were then treated with 0, 1, 10, 50 or 100 ⁇ g/ml of TLR9 specific oligonucleotide-based compounds of the invention and incubation continued for 24 h.
  • FBS fetal bovine serum
  • antibiotics 100 IU/ml penicillin G/100 ⁇ g/ml streptomycin
  • the J774 cells were then treated with 0, 1 or 3 ⁇ g/ml of TLR9 specific oligonucleotide-based compounds of the invention or control oligonucleotides and incubation continued for 48 h.
  • the J774 cells were then treated with 0, or 50 ⁇ g/ml of TLR9 specific oligonucleotide-based compounds of the invention or control oligonucleotides and incubation continued for 48 h.
  • cellular extracts were prepared and analyzed for the amount of TLR9 mRNA or TLR9 protein.
  • HeLa cells 5 ⁇ 10 6 HeLa cells (ATCC, Manassas, Va.) were plated in a 12-well culture plate in Dulbecco's Modified Eagle Medium (DMEM, Mediatech, Manassas, Va.) supplemented with 10% fetal bovine serum (FBS, Mediatch, Manassas, Va.).
  • DMEM Dulbecco's Modified Eagle Medium
  • FBS fetal bovine serum
  • 5 ⁇ l Lipofectamine® 2000 Invitrogen, Carlsbad, Calif.
  • 5 ⁇ g antisense oligonucleotides were mixed in 100 ⁇ l DMEM without serum and incubated at room temperature for 15 minutes.
  • RNA was used to reverse transcribe to cDNA using a High Capacity cDNA Reverse Transcription kit (Appliedbiosystems, Carlsbad, Calif.) according to manufacturer's recommendation.
  • a High Capacity cDNA Reverse Transcription kit (Appliedbiosystems, Carlsbad, Calif.) according to manufacturer's recommendation.
  • primers and probes for VEGF catalog no. Hs00900057_m 1
  • GAPDH Hs99999905_m1
  • 50 ng cDNA was used in the qPCR with Taqman® Fast Universal PCR Master Mix (Applied Biosystems) and reactions were run on an Applied Biosystems StepOnePlusTM Real-Time PCR System according to manufacturer's instructions. Data is depicted in FIG.
  • Spleen cells from 4- to 8-week old C57BL/6 mice were cultured in RPMI complete medium.
  • Mouse spleen cells were plated in 24-well dishes using 5 ⁇ 10 6 cells/ml, treated with TLR9 specific oligonucleotide-based compounds of the invention dissolved in TE buffer (10 mM Tris-HCl, pH 7.5, 1 mM EDTA), and incubated at 37° C. for 24 hrs. Following antisense treatment, cells were then stimulated with 10 ⁇ g/ml TLR9 agonist for 24 hrs. After treatment and stimulation, the supernatants were collected and the secretion of IL-12 and IL-6 in cell culture supernatants was measured by sandwich ELISA.
  • oligonucleotide-based compounds according to the invention or control oligonucleotides were treated as follows:
  • the 5′-end [ ⁇ -32P] labeled target mRNA e.g. SED ID NO. 21; 10 nM human/mouse TLR7
  • complementary RNA or DNA 10 nM; human/mouse TLR7
  • Buffer (10 ⁇ buffer, Invitrogen) were heated at 85° C. for 5 min, and then cooled down to room temperature for 20 min to allow annealing of the two strands.
  • the human dicer enzyme (0.025U, Invitrogen) was added to reaction solution, and then incubated at 37° C. for 1 hr. 1 ml of stop solution (Invitrogen) and 10 ml of gel loading dye were added to sample solution and mixed well. The sample was frozen immediately at ⁇ 80° C. RNA digestion products were analyzed on 16% denaturing PAGE and the gel was exposed to x-ray film and the autoradiogram was developed. Results are shown in FIG. 13 .

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