US20150025231A1 - Compositions and methods for modulation of ikbkap splicing - Google Patents

Compositions and methods for modulation of ikbkap splicing Download PDF

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US20150025231A1
US20150025231A1 US14/371,941 US201314371941A US2015025231A1 US 20150025231 A1 US20150025231 A1 US 20150025231A1 US 201314371941 A US201314371941 A US 201314371941A US 2015025231 A1 US2015025231 A1 US 2015025231A1
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certain embodiments
compound
modified
oligonucleotide
nucleosides
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C. Frank Bennett
Frank Rigo
Adrian R. Krainer
Rahul Sinha
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Cold Spring Harbor Laboratory
Ionis Pharmaceuticals Inc
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Cold Spring Harbor Laboratory
Isis Pharmaceuticals Inc
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Definitions

  • Newly synthesized eukaryotic mRNA molecules also known as primary transcripts or pre-mRNA, made in the nucleus, are processed before or during transport to the cytoplasm for translation. Processing of the pre-mRNAs includes addition of a 5′ methylated cap and an approximately 200-250 base poly(A) tail to the 3′ end of the transcript.
  • Another step in mRNA processing is splicing of the pre-mRNA, which occurs in the maturation of 90-95% of mammalian mRNAs.
  • Introns or intervening sequences
  • Exons are regions of a primary transcript that remain in the mature mRNA when it reaches the cytoplasm. The exons are spliced together to form the mature mRNA sequence.
  • Splice junctions are also referred to as splice sites with the junction at the 5′ side of the intron often called the “5′ splice site,” or “splice donor site” and the junction at the 3′ side of the intron called the “3′ splice site” or “splice acceptor site.”
  • the 3′ end of an upstream exon is joined to the 5′ end of the downstream exon.
  • the unspliced RNA (or pre-mRNA) has an exon/intron junction at the 5′ end of an intron and an intron/exon junction at the 3′ end of an intron.
  • Cryptic splice sites are those that are not used in wild-type pre-mRNA, but may be used when the natural splice site is inactivated or weakened by mutation, or in conjunction with a mutation that creates a new splice site elsewhere on the pre-mRNA.
  • Alternative splicing defined as the splicing together of different combinations of exons or exon segments, often results in multiple mature mRNA transcripts expressed from a single gene.
  • Point mutations can either disrupt a current splice site or create a new splice site, resulting in mRNA transcripts comprised of a different combination of exons or with deletions in exons.
  • Point mutations also can result in activation of a cryptic splice site(s), disrupt a branch site (which functions during an intermediate step in splicing catalysis) or disrupt regulatory cis elements (i.e., splicing enhancers or silencers, which can be created, destroyed, strengthened or weakened by mutation) (Cartegni et al., Nat. Rev. Genet., 2002, 3, 285-298; Crawczak et al., Hum. Genet., 1992, 90, 41-54).
  • Antisense oligonucleotides have been used to target mutations that lead to aberrant splicing in several genetic diseases in order to redirect splicing to give a desired splice product (Kole, Acta Biochimica Polonica, 1997, 44, 231-238).
  • diseases include ⁇ -thalassemia (Dominski and Kole, Proc. Natl. Acad. Sci. USA, 1993, 90, 8673-8677; Sierakowska et al., Nucleosides & Nucleotides, 1997, 16, 1173-1182; Sierakowska et al., Proc. Natl. Acad. Sci. USA, 1996, 93, 12840-44; Lacerra et al., Proc. Natl.
  • dystrophy Kobe Takeshima et al., J. Clin. Invest., 1995, 95, 515-520
  • Duchenne muscular dystrophy (Dunckley et al. Nucleosides & Nucleotides, 1997, 16, 1665-1668; Dunckley et al. Human Mol. Genetics, 1998, 5, 1083-90); osteogenesis imperfecta (Wang and Marini, J. Clin Invest., 1996, 97, 448-454); and cystic fibrosis (Friedman et al., J. Biol. Chem., 1999, 274, 36193-36199).
  • Antisense compounds have also been used to alter the ratio of the long and short forms of Bcl-x pre-mRNA (U.S. Pat. No. 6,172,216; U.S. Pat. No. 6,214,986; Taylor et al., Nat. Biotechnol. 1999, 17, 1097-1100) or to force skipping of specific exons containing premature termination codons (Wilton et al., Neuromuscul. Disord., 1999, 9, 330-338).
  • 5,627,274 and WO 94/26887 disclose compositions and methods for combating aberrant splicing in a pre-mRNA molecule containing a mutation using antisense oligonucleotides which do not activate RNAse H.
  • Antisense compounds targeting splicing-inhibitory elements in exons or their flanking introns have also been used to increase the use of such exons during splicing, e.g., in the context of spinal muscular atrophy (Cartegni Nat Struct Biol; Imaizumi; Hua PLoS Biol; Singh; other Hua et al papers, etc.).
  • Familial dysautonomia a rare genetic disorder found almost exclusively in the Ashkenazi Jewish population, is an autosomal recessive condition that is caused by a single intronic point mutation in intron 20 (IVS20+6T ⁇ C) of the IKBKAP gene (Maayan, C., Kaplan, E., Shachar, S., Peleg, O., and Godfrey, S. 1987, “Incidence of familial dysautonomia in Israel 1977-1981 ,” Clin Genet. 32:106-108; Slaugenhaupt, S. A., and Gusella, J. F. 2002, “Familial dysautonomia,” Curr Opin Genet Dev 12:307-311; Anderson, S.
  • FD also known as Riley-Day syndrome and hereditary sensory autonomic neuropathy type-III (HSAN-III), is characterized by poor development and progressive degeneration of sensory and autonomic neurons.
  • Notable symptoms include anhidrosis, decreased taste, depressed deep tendon reflexes, postural hypotension, loss of pain and temperature perception, alacrima, gastroesophageal reflux, and scoliosis (Axelrod, F. B., and Simson, G. G. V. 2007 “Hereditary sensory and autonomic neuropathies: types II, III, and IV,” Orphanet Journal of Rare Diseases 2:).
  • the extent and severity of the symptoms vary among patients, but even with advanced management, the disease leads to premature death, with only half of the patients surviving to 40 years of age.
  • Antisense technology is an effective means for modulating the expression of one or more specific gene products, including alternative splice products, and is uniquely useful in a number of therapeutic, diagnostic, and research applications.
  • the principle behind antisense technology is that an antisense compound, which hybridizes to a target nucleic acid, modulates gene expression activities, such as transcription, splicing or translation, through one of a number of antisense mechanisms.
  • the sequence specificity of antisense compounds makes them extremely attractive as tools for target validation and gene functionalization, as well as therapeutics to selectively modulate the expression of genes involved in disease.
  • the present disclosure provides compounds comprising oligonucleotides.
  • such oligonucleotides are complementary to an IKBKAP transcript.
  • the oligonucleotide is complementary to a target region of the IKBKAP transcript comprising exon 20, intron 19, and intron 20.
  • the IKBKAP transcript comprises a mutation that results in an aberrant splice site.
  • the IKBKAP transcript comprises a mutation that results in the exclusion of exon 20 from the mature IKBKAP mRNA.
  • oligonucleotides inhibit aberrant splicing of a mutant IKBKAP transcript.
  • normal splicing of the IKBKAP transcript is increased.
  • functional IKAP protein having exon 20 is increased.
  • functional IKAP protein having exons 20-37 is increased.
  • a compound comprising a modified oligonucleotide consisting of 8 to 30 linked nucleosides and having a nucleobase sequence comprising at least 8 contiguous nucleobases complementary to a target region of equal length of an IKBKAP transcript.
  • nucleobase sequence comprises at least 8 contiguous nucleobases complementary to intron 19, intron 20, or exon 20 of an IKBKAP transcript.
  • the compound of any of embodiments 1 to 10 having a nucleobase sequence comprising at least 9 contiguous nucleobases complementary to a target region of equal length of an IKBKAP transcript.
  • the compound of any of embodiments 1 to 10 having a nucleobase sequence comprising at least 11 contiguous nucleobases complementary to a target region of equal length of an IKBKAP transcript.
  • the compound of embodiment 22, wherein the 2′-substitutent of at least one 2′-substituted sugar moiety is selected from the group consisting of 2′-OMe, 2′-F, and 2′-MOE.
  • each nucleoside of the modified oligonucleotide is a modified nucleoside, each independently comprising a modified sugar moiety.
  • modified oligonucleotide comprises at least two modified nucleosides comprising modified sugar moieties that are the same as one another.
  • modified oligonucleotide comprises at least two modified nucleosides comprising modified sugar moieties that are different from one another.
  • each nucleoside of the modified oligonucleotide is a modified nucleoside.
  • each nucleoside of the modified oligonucleotide is a modified nucleoside, and each modified nucleoside comprises the same modification.
  • the compound of embodiment 35, wherein the 2′-substituted sugar moiety is selected from 2′-F, 2′-OMe, and 2′-MOE.
  • each internucleoside linkage is a modified internucleoside linkage.
  • nucleobase sequence comprises at least 8 contiguous nucleobases complementary to intron 19, intron 20, or exon 20 of a nucleic acid molecule encoding IKAP.
  • oligonucleotide comprises a nucleobase sequence comprising a portion of at least 8 contiguous nucleobases complementary to an equal length portion of nucleobases 34622 to 34895 of SEQ ID NO: 1.
  • oligonucleotide comprises a nucleobase sequence comprising a portion of at least 8 contiguous nucleobases complementary to an equal length portion of nucleobases 34622 to 34721 of SEQ ID NO: 1.
  • oligonucleotide comprises a nucleobase sequence comprising a portion of at least 8 contiguous nucleobases complementary to an equal length portion of nucleobases 34722 to 34795 of SEQ ID NO: 1.
  • oligonucleotide comprises a nucleobase sequence comprising a portion of at least 8 contiguous nucleobases complementary to an equal length portion of nucleobases 34796 to 34881 of SEQ ID NO: 1.
  • oligonucleotide comprises a nucleobase sequence comprising a portion of at least 8 contiguous nucleobases complementary to an equal length portion of nucleobases 34722 to 34795 of SEQ ID NO: 1.
  • oligonucleotide comprises a nucleobase sequence comprising a portion of at least 8 contiguous nucleobases complementary to an equal length portion of nucleobases 34801 to 34828 of SEQ ID NO: 1.
  • oligonucleotide comprises a nucleobase sequence comprising a portion of at least 8 contiguous nucleobases complementary to an equal length portion of nucleobases 34801 to 34826 of SEQ ID NO: 1.
  • oligonucleotide comprises a nucleobase sequence comprising a portion of at least 8 contiguous nucleobases complementary to an equal length portion of nucleobases 34802 to 34821 of SEQ ID NO: 1.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 60, 61, 62, 63, 64, 65, 66, 67, or 68.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 60.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 61.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 62.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 63.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 64.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 65.
  • the compound of any of embodiments 1 to 46, wherein the oligonucleotide comprises a nucleobase sequence comprises an at least 8 nucleobase portion of SEQ ID NO: 66.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 67.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 68.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 40, 41, 42, 43, or 44.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 40.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 41.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 42.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 43.
  • oligonucleotide comprises a nucleobase sequence comprising an at least 8 nucleobase portion of SEQ ID NO: 44.
  • a pharmaceutical composition comprising the compound of any of embodiments 1 to 70, and a pharmaceutically acceptable carrier or diluent.
  • a method of modulating splicing in an IKBKAP transcript in a cell comprising contacting the cell with a compound according to any of embodiments 1 to 70.
  • a method of increasing inclusion of exon 20 in an IKBKAP transcript comprising contacting a cell with the compound of any of embodiments 1 to 70.
  • a method of increasing functional IKAP protein in a cell comprising contacting the cell with a compound according to any of embodiments 1 to 70.
  • a method of increasing IKAP protein having amino acids encoded by exons 20-37 in a cell comprising contacting the cell with a compound according to any of embodiments 1 to 70.
  • a method for treating a condition characterized at least in part by defective splicing of an IKBKAP transcript comprising administering a therapeutically effective amount of the compound of any of embodiments 1 to 70, to a subject in need thereof.
  • a compound of any of embodiments 1 to 70 for use in treating Familial Dysautonomia is provided.
  • FIGS. 1A-D These figures illustrate inclusion levels of exon 20.
  • FIGS. 2A-F illustrate the inclusion percentages of IKBKAP exon 20 in response to different doses of antisense oligonucleotide compounds.
  • FIGS. 2C and 2F illustrate inclusion percentages of IKBKAP exon 20 in different tissues from ICV or subcutaneous injections.
  • FIGS. 3A-B These figures illustrate minigene constructs.
  • FIGS. 4A-D These figures illustrate microwalks of antisense oligonucleotide compounds on different regions of an IKBKAP gene.
  • FIG. 5 This figure illustrates the stability of skipped mRNAs with or without the premature termination codon using RT-PCR.
  • IKBKAP Transcript means a transcript transcribed from an IKBKAP Gene.
  • IKBKAP Gene means GENBANK Accession No NT 008470.16 truncated from nucleotides 13290828 to 13358424, designated herein as SEQ ID NO: 1.
  • aberrant splice site means a splice site that results from a mutation in the native DNA and mRNA. In certain embodiments, aberrant splice sites result in mRNA transcripts comprised of a different combination of exons. In certain embodiments, aberrant splice sites result in mRNA transcripts with deletions of exons. In certain embodiments, aberrant splice sites result in mRNA transcripts with deletions of portions of exons, or with extensions of exons, or with new exons. In certain embodiments, aberrant splice sites result in mRNA transcripts comprising premature stop codons.
  • nucleoside means a compound comprising a nucleobase moiety and a sugar moiety. Nucleosides include, but are not limited to, naturally occurring nucleosides (as found in DNA and RNA) and modified nucleosides. Nucleosides may be linked to a phosphate moiety.
  • chemical modification means a chemical difference in a compound when compared to a naturally occurring counterpart.
  • chemical modification does not include differences only in nucleobase sequence.
  • Chemical modifications of oligonucleotides include nucleoside modifications (including sugar moiety modifications and nucleobase modifications) and internucleoside linkage modifications.
  • furanosyl means a structure comprising a 5-membered ring comprising four carbon atoms and one oxygen atom.
  • naturally occurring sugar moiety means a ribofuranosyl as found in naturally occurring RNA or a deoxyribofuranosyl as found in naturally occurring DNA.
  • sugar moiety means a naturally occurring sugar moiety or a modified sugar moiety of a nucleoside.
  • modified sugar moiety means a substituted sugar moiety, a bicyclic or tricyclic sugar moiety, or a sugar surrogate.
  • substituted sugar moiety means a furanosyl comprising at least one substituent group that differs from that of a naturally occurring sugar moiety.
  • Substituted sugar moieties include, but are not limited to furanosyls comprising substituents at the 2′-position, the 3′-position, the 5′-position and/or the 4′-position.
  • 2′-substituted sugar moiety means a furanosyl comprising a substituent at the 2′-position other than H or OH. Unless otherwise indicated, a 2′-substituted sugar moiety is not a bicyclic sugar moiety (i.e., the 2′-substituent of a 2′-substituted sugar moiety does not form a bridge to another atom of the furanosyl ring.
  • MOE means —OCH 2 CH 2 OCH 3 .
  • bicyclic sugar moiety means a modified sugar moiety comprising a 4 to 7 membered ring (including but not limited to a furanosyl) comprising a bridge connecting two atoms of the 4 to 7 membered ring to form a second ring, resulting in a bicyclic structure.
  • the 4 to 7 membered ring is a sugar ring.
  • the 4 to 7 membered ring is a furanosyl.
  • the bridge connects the 2′-carbon and the 4′-carbon of the furanosyl.
  • sugar surrogate means a structure that does not comprise a furanosyl and that is capable of replacing the naturally occurring sugar moiety of a nucleoside, such that the resulting nucleoside is capable of (1) incorporation into an oligonucleotide and (2) hybridization to a complementary nucleoside.
  • Such structures include rings comprising a different number of atoms than furanosyl (e.g., 4, 6, or 7-membered rings); replacement of the oxygen of a furanosyl with a non-oxygen atom (e.g., carbon, sulfur, or nitrogen); or both a change in the number of atoms and a replacement of the oxygen.
  • Such structures may also comprise substitutions corresponding to those described for substituted sugar moieties (e.g., 6-membered carbocyclic bicyclic sugar surrogates optionally comprising additional substituents).
  • Sugar surrogates also include more complex sugar replacements (e.g., the non-ring systems of peptide nucleic acid).
  • Sugar surrogates include without limitation morpholino, modified morpholinos, cyclohexenyls and cyclohexitols.
  • nucleotide means a nucleoside further comprising a phosphate linking group.
  • linked nucleosides may or may not be linked by phosphate linkages and thus includes, but is not limited to “linked nucleotides.”
  • linked nucleosides are nucleosides that are connected in a continuous sequence (i.e., no additional nucleosides are present between those that are linked).
  • nucleobase means a group of atoms that can be linked to a sugar moiety to create a nucleoside that is capable of incorporation into an oligonucleotide, and wherein the group of atoms is capable of bonding with a complementary naturally occurring nucleobase of another oligonucleotide or nucleic acid. Nucleobases may be naturally occurring or may be modified.
  • heterocyclic base or “heterocyclic nucleobase” means a nucleobase comprising a heterocyclic structure.
  • unmodified nucleobase or “naturally occurring nucleobase” means the naturally occurring heterocyclic nucleobases of RNA or DNA: the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) (including 5-methyl C), and uracil (U).
  • modified nucleobase means any nucleobase that is not a naturally occurring nucleobase.
  • modified nucleoside means a nucleoside comprising at least one chemical modification compared to naturally occurring RNA or DNA nucleosides. Modified nucleosides comprise a modified sugar moiety and/or a modified nucleobase.
  • bicyclic nucleoside or “BNA” means a nucleoside comprising a bicyclic sugar moiety.
  • constrained ethyl nucleoside or “cEt” means a nucleoside comprising a bicyclic sugar moiety comprising a 4′-CH(CH 3 )—O-2′ bridge.
  • locked nucleic acid nucleoside or “LNA” means a nucleoside comprising a bicyclic sugar moiety comprising a 4′-CH 2 —O-2′ bridge.
  • 2′-substituted nucleoside means a nucleoside comprising a substituent at the 2′-position other than H or OH. Unless otherwise indicated, a 2′-substituted nucleoside is not a bicyclic nucleoside.
  • 2′-deoxynucleoside means a nucleoside comprising 2′-H furanosyl sugar moiety, as found in naturally occurring deoxyribonucleosides (DNA).
  • a 2′-deoxynucleoside may comprise a modified nucleobase or may comprise an RNA nucleobase (e.g., uracil).
  • oligonucleotide means a compound comprising a plurality of linked nucleosides.
  • an oligonucleotide comprises one or more unmodified ribonucleosides (RNA) and/or unmodified deoxyribonucleosides (DNA) and/or one or more modified nucleosides.
  • oligonucleoside means an oligonucleotide in which none of the internucleoside linkages contains a phosphorus atom.
  • oligonucleotides include oligonucleosides.
  • modified oligonucleotide means an oligonucleotide comprising at least one modified nucleoside and/or at least one modified internucleoside linkage.
  • nucleoside linkage means a covalent linkage between adjacent nucleosides in an oligonucleotide.
  • naturally occurring internucleoside linkage means a 3′ to 5′ phosphodiester linkage.
  • modified internucleoside linkage means any internucleoside linkage other than a naturally occurring internucleoside linkage.
  • oligomeric compound means a polymeric structure comprising two or more sub-structures.
  • an oligomeric compound comprises an oligonucleotide.
  • an oligomeric compound comprises one or more conjugate groups and/or terminal groups.
  • an oligomeric compound consists of an oligonucleotide.
  • terminal group means one or more atoms attached to either, or both, the 3′ end or the 5′ end of an oligonucleotide. In certain embodiments a terminal group is a conjugate group. In certain embodiments, a terminal group comprises one or more terminal group nucleosides.
  • conjugate means an atom or group of atoms bound to an oligonucleotide or oligomeric compound.
  • conjugate groups modify one or more properties of the compound to which they are attached, including, but not limited to pharmacodynamic, pharmacokinetic, binding, absorption, cellular distribution, cellular uptake, charge and/or clearance properties.
  • conjugate linking group means any atom or group of atoms used to attach a conjugate to an oligonucleotide or oligomeric compound.
  • antisense compound means a compound comprising or consisting of an oligonucleotide at least a portion of which is complementary to a target nucleic acid to which it is capable of hybridizing, resulting in at least one antisense activity.
  • antisense activity means any detectable and/or measurable change attributable to the hybridization of an antisense compound to its target nucleic acid.
  • detecting or “measuring” means that a test or assay for detecting or measuring is performed. Such detection and/or measuring may result in a value of zero. Thus, if a test for detection or measuring results in a finding of no activity (activity of zero), the step of detecting or measuring the activity has nevertheless been performed.
  • detecttable and/or measureable activity means a statistically significant activity that is not zero.
  • essentially unchanged means little or no change in a particular parameter, particularly relative to another parameter which changes much more.
  • a parameter is essentially unchanged when it changes less than 5%.
  • a parameter is essentially unchanged if it changes less than two-fold while another parameter changes at least ten-fold.
  • an antisense activity is a change in the amount of a target nucleic acid.
  • the amount of a non-target nucleic acid is essentially unchanged if it changes much less than the target nucleic acid does, but the change need not be zero.
  • expression means the process by which a gene ultimately results in a protein.
  • Expression includes, but is not limited to, transcription, post-transcriptional modification (e.g., splicing, polyadenylation, addition of 5′-cap, mRNA turnover), and translation and post-translational modification.
  • target nucleic acid means a nucleic acid molecule to which an antisense compound hybridizes.
  • mRNA means an RNA molecule that encodes a protein.
  • pre-mRNA means an RNA transcript that has not been fully processed into mRNA. Pre-RNA includes one or more introns.
  • transcript means an RNA molecule transcribed from DNA.
  • Transcripts include, but are not limited to mRNA, pre-mRNA, and partially processed RNA.
  • targeting means the association of an antisense compound to a particular target nucleic acid molecule or a particular region of a target nucleic acid molecule.
  • An antisense compound targets a target nucleic acid if it is sufficiently complementary to the target nucleic acid to allow hybridization under physiological conditions.
  • nucleobase complementarity or “complementarity” when in reference to nucleobases means a nucleobase that is capable of base pairing with another nucleobase.
  • adenine (A) is complementary to thymine (T).
  • adenine (A) is complementary to uracil (U).
  • complementary nucleobase means a nucleobase of an antisense compound that is capable of base pairing with a nucleobase of its target nucleic acid.
  • nucleobases at a certain position of an antisense compound are capable of hydrogen bonding with a nucleobase at a certain position of a target nucleic acid
  • the position of hydrogen bonding between the oligonucleotide and the target nucleic acid is considered to be complementary at that nucleobase pair.
  • Nucleobases comprising certain modifications may maintain the ability to pair with a counterpart nucleobase and thus, are still capable of nucleobase complementarity.
  • non-complementary in reference to nucleobases means a pair of nucleobases that do not form hydrogen bonds with one another.
  • complementary in reference to oligomeric compounds (e.g., linked nucleosides, oligonucleotides, or nucleic acids) means the capacity of such oligomeric compounds or regions thereof to hybridize to another oligomeric compound or region thereof through nucleobase complementarity under stringent conditions.
  • Complementary oligomeric compounds need not have nucleobase complementarity at each nucleoside. Rather, some mismatches are tolerated.
  • complementary oligomeric compounds or regions are complementary at 70% of the nucleobases (70% complementary).
  • complementary oligomeric compounds or regions are 80% complementary.
  • complementary oligomeric compounds or regions are 90% complementary.
  • complementary oligomeric compounds or regions are 95% complementary.
  • complementary oligomeric compounds or regions are 100% complementary.
  • hybridization means the pairing of complementary oligomeric compounds (e.g., an antisense compound and its target nucleic acid). While not limited to a particular mechanism, the most common mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases.
  • “specifically hybridizes” means the ability of an oligomeric compound to hybridize to one nucleic acid site with greater affinity than it hybridizes to another nucleic acid site.
  • an antisense oligonucleotide specifically hybridizes to more than one target site.
  • percent complementarity means the percentage of nucleobases of an oligomeric compound that are complementary to an equal-length portion of a target nucleic acid. Percent complementarity is calculated by dividing the number of nucleobases of the oligomeric compound that are complementary to nucleobases at corresponding positions in the target nucleic acid by the total length of the oligomeric compound.
  • percent identity means the number of nucleobases in a first nucleic acid that are the same type (independent of chemical modification) as nucleobases at corresponding positions in a second nucleic acid, divided by the total number of nucleobases in the first nucleic acid.
  • modulation means a change of amount or quality of a molecule, function, or activity when compared to the amount or quality of a molecule, function, or activity prior to modulation.
  • modulation includes the change, either an increase (stimulation or induction) or a decrease (inhibition or reduction) in gene expression.
  • modulation of expression can include a change in splice site selection of pre-mRNA processing, resulting in a change in the absolute or relative amount of a particular splice-variant compared to the amount in the absence of modulation.
  • motif means a pattern of chemical modifications in an oligomeric compound or a region thereof. Motifs may be defined by modifications at certain nucleosides and/or at certain linking groups of an oligomeric compound.
  • nucleoside motif means a pattern of nucleoside modifications in an oligomeric compound or a region thereof.
  • the linkages of such an oligomeric compound may be modified or unmodified.
  • motifs herein describing only nucleosides are intended to be nucleoside motifs. Thus, in such instances, the linkages are not limited.
  • sugar motif means a pattern of sugar modifications in an oligomeric compound or a region thereof.
  • linkage motif means a pattern of linkage modifications in an oligomeric compound or region thereof.
  • the nucleosides of such an oligomeric compound may be modified or unmodified.
  • motifs herein describing only linkages are intended to be linkage motifs. Thus, in such instances, the nucleosides are not limited.
  • nucleobase modification motif means a pattern of modifications to nucleobases along an oligonucleotide. Unless otherwise indicated, a nucleobase modification motif is independent of the nucleobase sequence.
  • sequence motif means a pattern of nucleobases arranged along an oligonucleotide or portion thereof. Unless otherwise indicated, a sequence motif is independent of chemical modifications and thus may have any combination of chemical modifications, including no chemical modifications.
  • nucleoside having a modification of a first type may be an unmodified nucleoside.
  • “differently modified” mean chemical modifications or chemical substituents that are different from one another, including absence of modifications.
  • a MOE nucleoside and an unmodified DNA nucleoside are “differently modified,” even though the DNA nucleoside is unmodified.
  • DNA and RNA are “differently modified,” even though both are naturally-occurring unmodified nucleosides. Nucleosides that are the same but for comprising different nucleobases are not differently modified.
  • nucleoside comprising a 2′-OMe modified sugar and an unmodified adenine nucleobase and a nucleoside comprising a 2′-OMe modified sugar and an unmodified thymine nucleobase are not differently modified.
  • the same type of modifications refers to modifications that are the same as one another, including absence of modifications.
  • two unmodified DNA nucleosides have “the same type of modification,” even though the DNA nucleoside is unmodified.
  • Such nucleosides having the same type modification may comprise different nucleobases.
  • pharmaceutically acceptable carrier or diluent means any substance suitable for use in administering to an animal.
  • a pharmaceutically acceptable carrier or diluent is sterile saline.
  • such sterile saline is pharmaceutical grade saline.
  • substituted nucleoside and “substituent group,” means an atom or group that replaces the atom or group of a named parent compound.
  • a substituent of a modified nucleoside is any atom or group that differs from the atom or group found in a naturally occurring nucleoside (e.g., a modified 2′-substituent is any atom or group at the 2′-position of a nucleoside other than H or OH).
  • Substituent groups can be protected or unprotected.
  • compounds of the present invention have substituents at one or at more than one position of the parent compound. Substituents may also be further substituted with other substituent groups and may be attached directly or via a linking group, such as an alkyl or hydrocarbyl group, to a parent compound.
  • substituted in reference to a chemical functional group means an atom or group of atoms differs from the atom or group of atoms normally present in the named functional group.
  • a substituent replaces a hydrogen atom of the functional group (e.g., in certain embodiments, the substituent of a substituted methyl group is an atom or group other than hydrogen which replaces one of the hydrogen atoms of an unsubstituted methyl group).
  • groups amenable for use as substituents include without limitation, halogen, hydroxyl, alkyl, alkenyl, alkynyl, acyl (—C(O)R aa ), carboxyl (—C(O)O—R aa ), aliphatic groups, alicyclic groups, alkoxy, substituted oxy (—O—R aa ), aryl, aralkyl, heterocyclic radical, heteroaryl, heteroarylalkyl, amino (—N(R bb )—(R cc )), imino( ⁇ NR bb ), amido (—C(O)N(R bb )(R cc ) or —N(R bb )C(O)R aa ), azido (—N 3 ), nitro (—NO 2 ), cyano (—CN), carbamido (—OC(O)N(R bb )(R cc ) or
  • each R aa , R bb and R cc is, independently, H, an optionally linked chemical functional group or a further substituent group with a preferred list including without limitation, alkyl, alkenyl, alkynyl, aliphatic, alkoxy, acyl, aryl, aralkyl, heteroaryl, alicyclic, heterocyclic and heteroarylalkyl. Selected substituents within the compounds described herein are present to a recursive degree.
  • alkyl means a saturated straight or branched hydrocarbon radical containing up to twenty four carbon atoms.
  • alkyl groups include without limitation, methyl, ethyl, propyl, butyl, isopropyl, n-hexyl, octyl, decyl, dodecyl and the like.
  • Alkyl groups typically include from 1 to about 24 carbon atoms, more typically from 1 to about 12 carbon atoms (C 1 -C 12 alkyl) with from 1 to about 6 carbon atoms being more preferred.
  • alkenyl means a straight or branched hydrocarbon chain radical containing up to twenty four carbon atoms and having at least one carbon-carbon double bond.
  • alkenyl groups include without limitation, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, dienes such as 1,3-butadiene and the like.
  • Alkenyl groups typically include from 2 to about 24 carbon atoms, more typically from 2 to about 12 carbon atoms with from 2 to about 6 carbon atoms being more preferred.
  • Alkenyl groups as used herein may optionally include one or more further substituent groups.
  • alkynyl means a straight or branched hydrocarbon radical containing up to twenty four carbon atoms and having at least one carbon-carbon triple bond.
  • alkynyl groups include, without limitation, ethynyl, 1-propynyl, 1-butynyl, and the like.
  • Alkynyl groups typically include from 2 to about 24 carbon atoms, more typically from 2 to about 12 carbon atoms with from 2 to about 6 carbon atoms being more preferred.
  • Alkynyl groups as used herein may optionally include one or more further substituent groups.
  • acyl means a radical formed by removal of a hydroxyl group from an organic acid and has the general Formula —C(O)—X where X is typically aliphatic, alicyclic or aromatic. Examples include aliphatic carbonyls, aromatic carbonyls, aliphatic sulfonyls, aromatic sulfinyls, aliphatic sulfinyls, aromatic phosphates, aliphatic phosphates and the like. Acyl groups as used herein may optionally include further substituent groups.
  • alicyclic means a cyclic ring system wherein the ring is aliphatic.
  • the ring system can comprise one or more rings wherein at least one ring is aliphatic.
  • Preferred alicyclics include rings having from about 5 to about 9 carbon atoms in the ring.
  • Alicyclic as used herein may optionally include further substituent groups.
  • aliphatic means a straight or branched hydrocarbon radical containing up to twenty four carbon atoms wherein the saturation between any two carbon atoms is a single, double or triple bond.
  • An aliphatic group preferably contains from 1 to about 24 carbon atoms, more typically from 1 to about 12 carbon atoms with from 1 to about 6 carbon atoms being more preferred.
  • the straight or branched chain of an aliphatic group may be interrupted with one or more heteroatoms that include nitrogen, oxygen, sulfur and phosphorus.
  • Such aliphatic groups interrupted by heteroatoms include without limitation, polyalkoxys, such as polyalkylene glycols, polyamines, and polyimines. Aliphatic groups as used herein may optionally include further substituent groups.
  • alkoxy means a radical formed between an alkyl group and an oxygen atom wherein the oxygen atom is used to attach the alkoxy group to a parent molecule.
  • alkoxy groups include without limitation, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, sec-butoxy, ten-butoxy, n-pentoxy, neopentoxy, n-hexoxy and the like.
  • Alkoxy groups as used herein may optionally include further substituent groups.
  • aminoalkyl means an amino substituted C 1 -C 12 alkyl radical.
  • the alkyl portion of the radical forms a covalent bond with a parent molecule.
  • the amino group can be located at any position and the aminoalkyl group can be substituted with a further substituent group at the alkyl and/or amino portions.
  • aralkyl and arylalkyl mean an aromatic group that is covalently linked to a C 1 -C 12 alkyl radical.
  • the alkyl radical portion of the resulting aralkyl (or arylalkyl) group forms a covalent bond with a parent molecule. Examples include without limitation, benzyl, phenethyl and the like.
  • Aralkyl groups as used herein may optionally include further substituent groups attached to the alkyl, the aryl or both groups that form the radical group.
  • aryl and “aromatic” mean a mono- or polycyclic carbocyclic ring system radicals having one or more aromatic rings.
  • aryl groups include without limitation, phenyl, naphthyl, tetrahydronaphthyl, indanyl, idenyl and the like.
  • Preferred aryl ring systems have from about 5 to about 20 carbon atoms in one or more rings.
  • Aryl groups as used herein may optionally include further substituent groups.
  • halo and “halogen,” mean an atom selected from fluorine, chlorine, bromine and iodine.
  • heteroaryl and “heteroaromatic,” mean a radical comprising a mono- or polycyclic aromatic ring, ring system or fused ring system wherein at least one of the rings is aromatic and includes one or more heteroatoms. Heteroaryl is also meant to include fused ring systems including systems where one or more of the fused rings contain no heteroatoms. Heteroaryl groups typically include one ring atom selected from sulfur, nitrogen or oxygen.
  • heteroaryl groups include without limitation, pyridinyl, pyrazinyl, pyrimidinyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl, quinolinyl, isoquinolinyl, benzimidazolyl, benzooxazolyl, quinoxalinyl and the like.
  • Heteroaryl radicals can be attached to a parent molecule directly or through a linking moiety such as an aliphatic group or hetero atom.
  • Heteroaryl groups as used herein may optionally include further substituent groups.
  • the present invention provides oligomeric compounds.
  • such oligomeric compounds comprise oligonucleotides optionally comprising one or more conjugate and/or terminal groups.
  • an oligomeric compound consists of an oligonucleotide.
  • oligonucleotides comprise one or more chemical modifications. Such chemical modifications include modifications to one or more nucleoside (including modifications to the sugar moiety and/or the nucleobase) and/or modifications to one or more internucleoside linkage.
  • oligomeric compounds of the invention comprise one or more modified nucleosides comprising a modified sugar moiety.
  • Such oligomeric compounds comprising one or more sugar-modified nucleosides may have desirable properties, such as enhanced nuclease stability or increased binding affinity with a target nucleic acid relative to oligomeric compounds comprising only nucleosides comprising naturally occurring sugar moieties.
  • modified sugar moieties are substitued sugar moieties.
  • modified sugar moieties are bicyclic or tricyclic sugar moieties.
  • modified sugar moieties are sugar surrogates. Such sugar surogates may comprise one or more substitutions corresponding to those of substituted sugar moieties.
  • modified sugar moieties are substituted sugar moieties comprising one or more substituent, including but not limited to substituents at the 2′ and/or 5′ positions.
  • sugar substituents suitable for the 2′-position include, but are not limited to: 2′-F, 2′-OCH 3 (“OMe” or “O-methyl”), and 2′-O(CH 2 ) 2 OCH 3 (“MOE”).
  • sugar substituents at the 2′ position is selected from allyl, amino, azido, thio, O-allyl, O—C 1 -C 10 alkyl, O—C 1 -C 10 substituted alkyl; O—C 1 -C 10 alkoxy; O—C 1 -C 10 substituted alkoxy, OCF 3 , O(CH 2 ) 2 SCH 3 , O(CH 2 ) 2 —O—N(Rm)(Rn), and O—CH 2 —C( ⁇ O)—N(Rm)(Rn), where each Rm and Rn is, independently, H or substituted or unsubstituted C 1 -C 10 alkyl.
  • sugar substituents at the 5′-position include, but are not limited to:, 5′-methyl (R or S); 5′-vinyl, and 5′-methoxy.
  • substituted sugars comprise more than one non-bridging sugar substituent, for example, 2′-F-5′-methyl sugar moieties (see, e.g., PCT International Application WO 2008/101157, for additional 5′,2′-bis substituted sugar moieties and nucleosides).
  • Nucleosides comprising 2′-substituted sugar moieties are referred to as 2′-substituted nucleosides.
  • a 2′-substituted nucleoside comprises a 2′-substituent group selected from halo, allyl, amino, azido, O—C 1 -C 10 alkoxy; O—C 1 -C 10 substituted alkoxy, SH, CN, OCN, CF 3 , OCF 3 , O-alkyl, S-alkyl, N(R m )-alkyl; O— alkenyl, S— alkenyl, or N(R m )-alkenyl; O— alkynyl, 5-alkynyl, N(R m )-alkynyl; O-alkylenyl-O-alkyl, alkynyl, alkaryl, aralkyl, O-alkaryl, O-aralkyl, O-al
  • These 2′-substituent groups can be further substituted with one or more substituent groups independently selected from hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO 2 ), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.
  • a 2′-substituted nucleoside comprises a 2′-substituent group selected from F, NH 2 , N 3 , OCF 3 , O—CH 3 , O(CH 2 ) 3 NH 2 , CH 2 —CH—CH 2 , O—CH 2 —CH—CH 2 , OCH 2 CH 2 OCH 3 , O(CH 2 ) 2 SCH 3 , O—(CH 2 ) 2 —O—N(R m )(R n ), O(CH 2 ) 2 O(CH 2 ) 2 N(CH 3 ) 2 , and N-substituted acetamide (O—CH 2 —C( ⁇ O)—N(R m )(R n ) where each R m and R n is, independently, H, an amino protecting group or substituted or unsubstituted C 1 -C 10 alkyl.
  • a 2′-substituted nucleoside comprises a sugar moiety comprising a 2′-substituent group selected from F, OCF 3 , O—CH 3 , OCH 2 CH 2 OCH 3 , O(CH 2 ) 2 SCH 3 , O—(CH 2 ) 2 —O—N(CH 3 ) 2 , —O(CH 2 ) 2 —O—(CH 2 ) 2 N(CH 3 ) 2 , and O—CH 2 —C( ⁇ O)—N(H)CH 3 .
  • a 2′-substituted nucleoside comprises a sugar moiety comprising a 2′-substituent group selected from F, OCF 3 , O—CH 3 , OCH 2 CH 2 OCH 3 , O(CH 2 ) 2 SCH 3 , O—(CH 2 ) 2 —O—N(CH 3 ) 2 , —O(CH 2 ) 2 —O—(CH 2 ) 2 N(
  • a 2′-substituted nucleoside comprises a sugar moiety comprising a 2′-substituent group selected from F, O—CH 3 , and OCH 2 CH 2 OCH 3 .
  • modified sugar moieties comprise a bridging sugar substituent that forms a second ring resulting in a bicyclic sugar moiety.
  • the bicyclic sugar moiety comprises a bridge between the 4′ and the 2′ furanose ring atoms.
  • 4′ to 2′ sugar substituents include, but are not limited to: —[C(R a )(R b )] n —, —[C(R a )(R b )] n —O—, —C(R a R b )—N(R)—O— or, —C(R a R b )—O—N(R)—; 4′-CH 2 -2′,4′-(CH 2 ) 2 -2′,4′-(CH 2 ) 3 -2′,4′-(CH 2 )—O-2′ (LNA); 4′-(CH 2 )—S-2; 4′-(CH 2 ) 2 —O-2′ (ENA); 4′-CH(CH 3 )—O-2′ (cEt) and 4′-CH(CH 2 OCH 3 )—O-2′, and analogs thereof (see, e.g., U.S.
  • such 4′ to 2′ bridges independently comprise from 1 to 4 linked groups independently selected from —[C(R a )(R b )] n , —C(R a ) ⁇ C(R b )—, —C(R a ) ⁇ N—, —C( ⁇ NR a )—, —C( ⁇ O)—, —C( ⁇ S)—, —O—, —Si(R a ) 2 —, —S( ⁇ O) x —, and —N(R a )—;
  • x 0, 1, or 2;
  • n 1, 2, 3, or 4;
  • each R a and R b is, independently, H, a protecting group, hydroxyl, C 1 -C 12 alkyl, substituted C 1 -C 12 alkyl, C 2 -C 12 alkenyl, substituted C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, substituted C 2 -C 12 alkynyl, C 5 -C 20 aryl, substituted C 5 -C 20 aryl, heterocycle radical, substituted heterocycle radical, heteroaryl, substituted heteroaryl, C 5 -C 7 alicyclic radical, substituted C 5 -C 7 alicyclic radical, halogen, OJ 1 , NJ 1 J 2 , SJ 1 , N 3 , COOJ 1 , acyl (C( ⁇ O)—H), substituted acyl, CN, sulfonyl (S( ⁇ O) 2 -J 1 ), or sulfoxyl (S( ⁇ O)-J 1 ); and
  • each J 1 and J 2 is, independently, H, C 1 -C 12 alkyl, substituted C 1 -C 12 alkyl, C 2 -C 12 alkenyl, substituted C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, substituted C 2 -C 12 alkynyl, C 5 -C 20 aryl, substituted C 5 -C 20 aryl, acyl (C( ⁇ O)—H), substituted acyl, a heterocycle radical, a substituted heterocycle radical, C 1 -C 12 aminoalkyl, substituted C 1 -C 12 aminoalkyl, or a protecting group.
  • Bicyclic nucleosides include, but are not limited to, (A) ⁇ -L-Methyleneoxy (4′-CH 2 —O-2′) BNA, (B) ⁇ -D-Methyleneoxy (4′-CH 2 —O-2′) BNA (also referred to as locked nucleic acid or LNA), (C) Ethyleneoxy (4′-(CH 2 ) 2 —O-2′) BNA, (D) Aminooxy (4′-CH 2 —O—N(R)-2′) BNA, (E) Oxyamino (4′-CH 2 —N(R)—O-2′) BNA, (F) Methyl(methyleneoxy) (4′-CH(CH 3 )—O-2′) BNA (also referred to as constrained ethyl or cEt), (G) methylene-thio (4′-CH 2 —S
  • Bx is a nucleobase moiety and R is, independently, H, a protecting group, or C 1 -C 12 alkyl.
  • bicyclic sugar moieties and nucleosides incorporating such bicyclic sugar moieties are further defined by isomeric configuration.
  • a nucleoside comprising a 4′-2′ methylene-oxy bridge may be in the ⁇ -L configuration or in the ⁇ -D configuration.
  • ⁇ -L-methyleneoxy (4′-CH 2 —O-2′) bicyclic nucleosides have been incorporated into antisense oligonucleotides that showed antisense activity (Frieden et al., Nucleic Acids Research, 2003, 21, 6365-6372).
  • substituted sugar moieties comprise one or more non-bridging sugar substituent and one or more bridging sugar substituent (e.g., 5′-substituted and 4′-2′ bridged sugars).
  • bridging sugar substituent e.g., 5′-substituted and 4′-2′ bridged sugars.
  • modified sugar moieties are sugar surrogates.
  • the oxygen atom of the naturally occurring sugar is substituted, e.g., with a sulfur, carbon or nitrogen atom.
  • such modified sugar moiety also comprises bridging and/or non-bridging substituents as described above.
  • certain sugar surogates comprise a 4′-sulfur atom and a substitution at the 2′-position (see, e.g., published U.S. Patent Application US2005/0130923, published on Jun. 16, 2005) and/or the 5′ position.
  • carbocyclic bicyclic nucleosides having a 4′-2′ bridge have been described (see, e.g., Freier et al., Nucleic Acids Research, 1997, 25(22), 4429-4443 and Albaek et al., J. Org. Chem., 2006, 71, 7731-7740).
  • sugar surrogates comprise rings having other than 5-atoms.
  • a sugar surrogate comprises a six-membered tetrahydropyran.
  • Such tetrahydropyrans may be further modified or substituted.
  • Nucleosides comprising such modified tetrahydropyrans include, but are not limited to, hexitol nucleic acid (HNA), anitol nucleic acid (ANA), manitol nucleic acid (MNA) (see Leumann, C J. Bioorg . & Med. Chem . (2002) 10:841-854), fluoro HNA (F-HNA), and those compounds having Formula VII:
  • Bx is a nucleobase moiety
  • T 3 and T 4 are each, independently, an internucleoside linking group linking the tetrahydropyran nucleoside analog to the antisense compound or one of T 3 and T 4 is an internucleoside linking group linking the tetrahydropyran nucleoside analog to the antisense compound and the other of T 3 and T 4 is H, a hydroxyl protecting group, a linked conjugate group, or a 5′ or 3′-terminal group;
  • q1, q2, q3, q4, qs, q6 and q 7 are each, independently, H, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, or substituted C 2 -C 6 alkynyl; and
  • each of R 1 and R 2 is independently selected from among: hydrogen, halogen, substituted or unsubstituted alkoxy, NJ 1 J 2 , SJ 1 , N 3 , OC( ⁇ X)J 1 , OC( ⁇ X)NJ 1 J 2 , NJ 3 C( ⁇ X)NJ 1 J 2 , and CN, wherein X is O, S or NJ 1 , and each J 1 , J 2 , and J 3 is, independently, H or C 1 -C 6 alkyl.
  • the modified THP nucleosides of Formula VII are provided wherein q 1 , q 2 , q 3 , q 4 , q 5 , q 6 and q 7 are each H. In certain embodiments, at least one of q 1 , q 2 , q 3 , q 4 , q 5 , q 6 and q 7 is other than H. In certain embodiments, at least one of q b q 2 , q 3 , q 4 , q 5 , q 6 and q 7 is methyl. In certain embodiments, THP nucleosides of Formula VII are provided wherein one of R 1 and R 2 is F. In certain embodiments, R 1 is fluoro and R 2 is H, R 1 is methoxy and R 2 is H, and R 1 is methoxyethoxy and R 2 is H.
  • sugar surrogates comprise rings having more than 5 atoms and more than one heteroatom.
  • nucleosides comprising morpholino sugar moieties and their use in oligomeric compounds has been reported (see for example: Braasch et al., Biochemistry, 2002, 41, 4503-4510; and U.S. Pat. Nos. 5,698,685; 5,166,315; 5,185,444; and 5,034,506).
  • morpholino means a sugar surrogate having the following structure:
  • morpholinos may be modified, for example by adding or altering various substituent groups from the above morpholino structure.
  • sugar surrogates are referred to herein as “modified morpholinos.”
  • nucleosides of the present invention comprise one or more unmodified nucleobases. In certain embodiments, nucleosides of the present invention comprise one or more modified nucleobases.
  • modified nucleobases are selected from: universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases as defined herein.
  • nucleobases include tricyclic pyrimidines such as phenoxazine cytidine([5,4-b][1,4]benzoxazin-2(3H)-one), phenothiazine cytidine (1H-pyrimido[5,4-b][1,4]benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g., 9-(2-aminoethoxy)-H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one), carbazole cytidine (2H-pyrimido[4,5-b]indol-2-one), pyridoindole cytidine (H-pyrido[3′,2′:4,5]pyrrolo[2,3-d]pyrimidin-2-one).
  • tricyclic pyrimidines such as phenoxazin
  • Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone.
  • Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering , Kroschwitz, J. I., Ed., John Wiley & Sons, 1990, 858-859; those disclosed by Englisch et al., Angewandte Chemie , International Edition, 1991, 30, 613; and those disclosed by Sanghvi, Y. S., Chapter 15 , Antisense Research and Applications , Crooke, S. T. and Lebleu, B., Eds., CRC Press, 1993, 273-288.
  • the present invention provides oligomeric compounds comprising linked nucleosides.
  • nucleosides may be linked together using any internucleoside linkage.
  • the two main classes of internucleoside linking groups are defined by the presence or absence of a phosphorus atom.
  • Representative phosphorus containing internucleoside linkages include, but are not limited to, phosphodiesters (P ⁇ O), phosphotriesters, methylphosphonates, phosphoramidate, and phosphorothioates (P ⁇ S).
  • Non-phosphorus containing internucleoside linking groups include, but are not limited to, methylenemethylimino (—CH 2 —N(CH 3 )—O—CH 2 —), thiodiester (—O—C(O)—S—), thionocarbamate (—O—C(O)(NH)—S—); siloxane (—O—Si(H) 2 —O—); and N,N′-dimethylhydrazine (—CH 2 —N(CH 3 )—N(CH 3 )—).
  • Modified linkages, compared to natural phosphodiester linkages, can be used to alter, typically increase, nuclease resistance of the oligomeric compound.
  • internucleoside linkages having a chiral atom can be prepared as a racemic mixture, or as separate enantiomers.
  • Representative chiral linkages include, but are not limited to, alkylphosphonates and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing internucleoside linkages are well known to those skilled in the art.
  • oligonucleotides described herein contain one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric configurations that may be defined, in terms of absolute stereochemistry, as (R) or (S), ⁇ or ⁇ such as for sugar anomers, or as (D) or (L) such as for amino acids etc. Included in the antisense compounds provided herein are all such possible isomers, as well as their racemic and optically pure forms.
  • Neutral internucleoside linkages include without limitation, phosphotriesters, methylphosphonates, MMI (3′-CH 2 —N(CH 3 )—O-5′), amide-3 (3′-CH 2 —C( ⁇ O)—N(H)-5′), amide-4 (3′-CH 2 —N(H)—C( ⁇ O)-5′), formacetal (3′-O—CH 2 —O-5′), and thioformacetal (3′-S—CH 2 —O-5′).
  • Further neutral internucleoside linkages include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides (See for example: Carbohydrate Modifications in Antisense Research ; Y. S. Sanghvi and P. D. Cook, Eds., ACS Symposium Series 580; Chapters 3 and 4, 40-65). Further neutral internucleoside linkages include nonionic linkages comprising mixed N, O, S and CH 2 component parts.
  • the present invention provides oligomeric compounds comprising oligonucleotides.
  • such oligonucleotides comprise one or more chemical modification.
  • chemically modified oligonucleotides comprise one or more modified nucleosides.
  • chemically modified oligonucleotides comprise one or more modified nucleosides comprising modified sugars.
  • chemically modified oligonucleotides comprise one or more modified nucleosides comprising one or more modified nucleobases.
  • chemically modified oligonucleotides comprise one or more modified internucleoside linkages.
  • the chemical modifications define a pattern or motif.
  • the patterns of chemical modifications of sugar moieties, internucleoside linkages, and nucleobases are each independent of one another.
  • an oligonucleotide may be described by its sugar modification motif, internucleoside linkage motif and/or nucleobase modification motif (as used herein, nucleobase modification motif describes the chemical modifications to the nucleobases independent of the sequence of nucleobases).
  • oligonucleotides comprise one or more type of modified sugar moieties and/or naturally occurring sugar moieties arranged along an oligonucleotide or region thereof in a defined pattern or sugar modification motif.
  • Such motifs may include any of the sugar modifications discussed herein and/or other known sugar modifications.
  • the oligonucleotides comprise or consist of a region having a gapmer sugar modification motif, which comprises two external regions or “wings” and an internal region or “gap.”
  • the three regions of a gapmer motif (the 5′-wing, the gap, and the 3′-wing) form a contiguous sequence of nucleosides wherein at least some of the sugar moieties of the nucleosides of each of the wings differ from at least some of the sugar moieties of the nucleosides of the gap.
  • the sugar moieties of the nucleosides of each wing that are closest to the gap differ from the sugar moiety of the neighboring gap nucleosides, thus defining the boundary between the wings and the gap.
  • the sugar moieties within the gap are the same as one another.
  • the gap includes one or more nucleoside having a sugar moiety that differs from the sugar moiety of one or more other nucleosides of the gap.
  • the sugar modification motifs of the two wings are the same as one another (symmetric gapmer).
  • the sugar modification motifs of the 5′-wing differs from the sugar modification motif of the 3′-wing (asymmetric gapmer).
  • oligonucleotides comprise 2′-MOE modified nucleosides in the wings and 2′-F modified nucleosides in the gap.
  • oligonucleotides are fully modified. In certain such embodiments, oligonucleotides are uniformly modified. In certain embodiments, oligonucleotides are uniform 2′-MOE. In certain embodiments, oligonucleotides are uniform 2′-F. In certain embodiments, oligonucleotides are uniform morpholino. In certain embodiments, oligonucleotides are uniform BNA. In certain embodiments, oligonucleotides are uniform LNA. In certain embodiments, oligonucleotides are uniform cEt.
  • oligonucleotides comprise a uniformly modified region and additional nucleosides that are unmodified or differently modified.
  • the uniformly modified region is at least 5, 10, 15, or 20 nucleosides in length.
  • the uniform region is a 2′-MOE region.
  • the uniform region is a 2′-F region.
  • the uniform region is a morpholino region.
  • the uniform region is a BNA region.
  • the uniform region is a LNA region.
  • the uniform region is a cEt region.
  • the oligonucleotide does not comprise more than 4 contiguous unmodified 2′-deoxynucleosides.
  • antisense oligonucleotides comprising more than 4 contiguous 2′-deoxynucleosides activate RNase H, resulting in cleavage of the target RNA.
  • such cleavage is avoided by not having more than 4 contiguous 2′-deoxynucleosides, for example, where alteration of splicing and not cleavage of a target RNA is desired.
  • oligonucleotides comprise modified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or modified internucleoside linkage motif.
  • internucleoside linkages are arranged in a gapped motif, as described above for sugar modification motif.
  • the internucleoside linkages in each of two wing regions are different from the internucleoside linkages in the gap region.
  • the internucleoside linkages in the wings are phosphodiester and the internucleoside linkages in the gap are phosphorothioate.
  • the sugar modification motif is independently selected, so such oligonucleotides having a gapped internucleoside linkage motif may or may not have a gapped sugar modification motif and if it does have a gapped sugar motif, the wing and gap lengths may or may not be the same.
  • oligonucleotides comprise a region having an alternating internucleoside linkage motif. In certain embodiments, oligonucleotides of the present invention comprise a region of uniformly modified internucleoside linkages. In certain such embodiments, the oligonucleotide comprises a region that is uniformly linked by phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide is uniformly linked by phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate and at least one internucleoside linkage is phosphorothioate.
  • the oligonucleotide comprises at least 6 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 8 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 10 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 6 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 8 consecutive phosphorothioate internucleoside linkages.
  • the oligonucleotide comprises at least one block of at least 10 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least block of at least one 12 consecutive phosphorothioate internucleoside linkages. In certain such embodiments, at least one such block is located at the 3′ end of the oligonucleotide. In certain such embodiments, at least one such block is located within 3 nucleosides of the 3′ end of the oligonucleotide.
  • oligonucleotides comprise chemical modifications to nucleobases arranged along the oligonucleotide or region thereof in a defined pattern or nucleobases modification motif.
  • nucleobase modifications are arranged in a gapped motif.
  • nucleobase modifications are arranged in an alternating motif.
  • each nucleobase is modified.
  • none of the nucleobases is chemically modified.
  • oligonucleotides comprise a block of modified nucleobases.
  • the block is at the 3′-end of the oligonucleotide.
  • the block is within 3 nucleotides of the 3′-end of the oligonucleotide.
  • the block is at the 5′-end of the oligonucleotide.
  • the block is within 3 nucleotides of the 5′-end of the oligonucleotide.
  • nucleobase modifications are a function of the natural base at a particular position of an oligonucleotide.
  • each purine or each pyrimidine in an oligonucleotide is modified.
  • each adenine is modified.
  • each guanine is modified.
  • each thymine is modified.
  • each cytosine is modified.
  • each uracil is modified.
  • cytosine moieties in an oligonucleotide are 5-methyl cytosine moieties.
  • 5-methyl cytosine is not a “modified nucleobase.” Accordingly, unless otherwise indicated, unmodified nucleobases include both cytosine residues having a 5-methyl and those lacking a 5 methyl. In certain embodiments, the methylation state of all or some cytosine nucleobases is specified.
  • the present invention provides oligomeric compounds including oligonucleotides of any of a variety of ranges of lengths.
  • the invention provides oligomeric compounds or oligonucleotides consisting of X to Y linked nucleosides, where X represents the fewest number of nucleosides in the range and Y represents the largest number of nucleosides in the range.
  • X and Y are each independently selected from 8, 9, 10, 11, 12, 13, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, and 50; provided that X ⁇ Y.
  • the invention provides oligomeric compounds which comprise oligonucleotides consisting of 8 to 9, 8 to 10, 8 to 11, 8 to 12, 8 to 13, 8 to 14, 8 to 15, 8 to 16, 8 to 17, 8 to 18, 8 to 19, 8 to 20, 8 to 21, 8 to 22, 8 to 23, 8 to 24, 8 to 25, 8 to 26, 8 to 27, 8 to 28, 8 to 29, 8 to 30, 9 to 10, 9 to 11, 9 to 12, 9 to 13, 9 to 14, 9 to 15, 9 to 16, 9 to 17, 9 to 18, 9 to 19, 9 to 20, 9 to 21, 9 to 22, 9 to 23, 9 to 24, 9 to 25, 9 to 26, 9 to 27, 9 to 28, 9 to 29, 9 to 30, 10 to 11, 10 to 12, 10 to 13, 10 to 14, 10 to 15, 10 to 16, 10 to 17, 10 to 18, 10 to 19, 10 to 20, 10 to 21, 10 to 22, 10 to 23, 10 to 24, 10 to 25, 10 to 26, 10 to 27, 10 to 28, 10 to 29, 10 to 30, 11 to 12, 11 to 13, 11 to 14, 11 to 15, 11 to 16, 11 to 17, 11 to 18, 11 to 19, 11 to 20, 11 to 21, 11 to 22, 11 to 23, 11 to 15, 11 to 16, 11 to
  • the oligomeric compound or oligonucleotide may, nonetheless further comprise additional other substituents.
  • an oligonucleotide comprising 8-30 nucleosides excludes oligonucleotides having 31 nucleosides, but, unless otherwise indicated, such an oligonucleotide may further comprise, for example one or more conjugates, terminal groups, or other substituents.
  • a gapmer oligonucleotide has any of the above lengths.
  • a gapmer having a 5′-wing region consisting of four nucleotides, a gap consisting of at least six nucleotides, and a 3′-wing region consisting of three nucleotides cannot have an overall length less than 13 nucleotides.
  • the lower length limit is 13 and that the limit of 10 in “10-20” has no effect in that embodiment.
  • an oligonucleotide is described by an overall length range and by regions having specified lengths, and where the sum of specified lengths of the regions is less than the upper limit of the overall length range, the oligonucleotide may have additional nucleosides, beyond those of the specified regions, provided that the total number of nucleosides does not exceed the upper limit of the overall length range.
  • Such additional nucleosides may be 5′ of the 5′-wing and/or 3′ of the 3′ wing.
  • oligonucleotides of the present invention are characterized by their sugar motif, internucleoside linkage motif, nucleobase modification motif and overall length. In certain embodiments, such parameters are each independent of one another. Thus, each internucleoside linkage of an oligonucleotide having a gapmer sugar motif may be modified or unmodified and may or may not follow the gapmer modification pattern of the sugar modifications. Thus, the internucleoside linkages within the wing regions of a sugar-gapmer may be the same or different from one another and may be the same or different from the internucleoside linkages of the gap region.
  • sugar-gapmer oligonucleotides may comprise one or more modified nucleobase independent of the gapmer pattern of the sugar modifications.
  • modified nucleobase independent of the gapmer pattern of the sugar modifications.
  • a description of an oligonucleotide or oligomeric compound is silent with respect to one or more parameter, such parameter is not limited.
  • an oligomeric compound described only as having a gapmer sugar motif without further description may have any length, internucleoside linkage motif, and nucleobase modification motif. Unless otherwise indicated, all chemical modifications are independent of nucleobase sequence.
  • oligomeric compounds are modified by attachment of one or more conjugate groups.
  • conjugate groups modify one or more properties of the attached oligomeric compound including but not limited to pharmacodynamics, pharmacokinetics, stability, binding, absorption, cellular distribution, cellular uptake, charge and clearance.
  • Conjugate groups are routinely used in the chemical arts and are linked directly or via an optional conjugate linking moiety or conjugate linking group to a parent compound such as an oligomeric compound, such as an oligonucleotide.
  • Conjugate groups includes without limitation, intercalators, reporter molecules, polyamines, polyamides, polyethylene glycols, thioethers, polyethers, cholesterols, thiocholesterols, cholic acid moieties, folate, lipids, phospholipids, biotin, phenazine, phenanthridine, anthraquinone, adamantane, acridine, fluoresceins, rhodamines, coumarins and dyes.
  • Certain conjugate groups have been described previously, for example: cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci.
  • a conjugate group comprises an active drug substance, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fen-bufen, ketoprofen, (S)-(+)-pranoprofen, carprofen, dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indo-methicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic.
  • active drug substance for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fen-bufen, ketoprofen, (S)-(+)-pranoprofen, carprofen, dansyls
  • conjugate groups are directly attached to oligonucleotides in oligomeric compounds.
  • conjugate groups are attached to oligonucleotides by a conjugate linking group.
  • conjugate linking groups including, but not limited to, bifunctional linking moieties such as those known in the art are amenable to the compounds provided herein.
  • Conjugate linking groups are useful for attachment of conjugate groups, such as chemical stabilizing groups, functional groups, reporter groups and other groups to selective sites in a parent compound such as for example an oligomeric compound.
  • a bifunctional linking moiety comprises a hydrocarbyl moiety having two functional groups.
  • One of the functional groups is selected to bind to a parent molecule or compound of interest and the other is selected to bind essentially any selected group such as a chemical functional group or a conjugate group.
  • the conjugate linker comprises a chain structure or an oligomer of repeating units such as ethylene glycol or amino acid units.
  • functional groups that are routinely used in a bifunctional linking moiety include, but are not limited to, electrophiles for reacting with nucleophilic groups and nucleophiles for reacting with electrophilic groups.
  • bifunctional linking moieties include amino, hydroxyl, carboxylic acid, thiol, unsaturations (e.g., double or triple bonds), and the like.
  • conjugate linking moieties include pyrrolidine, 8-amino-3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) and 6-aminohexanoic acid (AHEX or AHA).
  • ADO 8-amino-3,6-dioxaoctanoic acid
  • SMCC succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate
  • AHEX or AHA 6-aminohexanoic acid
  • linking groups include, but are not limited to, substituted C 1 -C 10 alkyl, substituted or unsubstituted C 2 -C 10 alkenyl or substituted or unsubstituted C 2 -C 10 alkynyl, wherein a nonlimiting list of preferred substituent groups includes hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl and alkynyl.
  • Conjugate groups may be attached to either or both ends of an oligonucleotide (terminal conjugate groups) and/or at any internal position.
  • conjugate groups are at the 3′-end of an oligonucleotide of an oligomeric compound. In certain embodiments, conjugate groups are near the 3′-end. In certain embodiments, conjugates are attached at the 3′ end of an oligomeric compound, but before one or more terminal group nucleosides. In certain embodiments, conjugate groups are placed within a terminal group.
  • oligomeric compounds comprise an oligonucleotide.
  • an oligomeric compound comprises an oligonucleotide and one or more conjugate and/or terminal groups.
  • conjugate and/or terminal groups may be added to oligonucleotides having any of the chemical motifs discussed above.
  • an oligomeric compound comprising an oligonucleotide having region of alternating nucleosides may comprise a terminal group.
  • oligomeric compounds of the present invention are antisense compounds. Such antisense compounds are capable of hybridizing to a target nucleic acid, resulting in at least one antisense activity. In certain embodiments, antisense compounds specifically hybridize to one or more target nucleic acid.
  • a specifically hybridizing antisense compound has a nucleobase sequence comprising a region having sufficient complementarity to a target nucleic acid to allow hybridization and result in antisense activity and insufficient complementarity to any non-target so as to avoid non-specific hybridization to any non-target nucleic acid sequences under conditions in which specific hybridization is desired (e.g., under physiological conditions for in vivo or therapeutic uses, and under conditions in which assays are performed in the case of in vitro assays).
  • the present invention provides antisense compounds comprising oligonucleotides that are fully complementary to the target nucleic acid over the entire length of the oligonucleotide. In certain embodiments, oligonucleotides are 99% complementary to the target nucleic acid. In certain embodiments, oligonucleotides are 95% complementary to the target nucleic acid. In certain embodiments, such oligonucleotides are 90% complementary to the target nucleic acid.
  • such oligonucleotides are 85% complementary to the target nucleic acid. In certain embodiments, such oligonucleotides are 80% complementary to the target nucleic acid. In certain embodiments, an antisense compound comprises a region that is fully complementary to a target nucleic acid and is at least 80% complementary to the target nucleic acid over the entire length of the oligonucleotide. In certain such embodiments, the region of full complementarity is from 6 to 14 nucleobases in length.
  • antisense compounds comprise or consist of an oligonucleotide comprising a region that is complementary to a target nucleic acid.
  • the target nucleic acid is an endogenous RNA molecule.
  • the target nucleic acid is a pre-mRNA.
  • the target nucleic acid is an IKBKAP transcript.
  • the target RNA is an IKBKAP pre-mRNA.
  • an antisense compound is complementary to a region of an IKBKAP pre-mRNA. In certain embodiments, an antisense compound is complementary within a region of an IKBKAP pre-mRNA comprising intron 19, intron 20, or exon 20. In certain embodiments, an antisense compound is complementary to a region of an IKBKAP pre-mRNA consisting of intron 19, intron 20, or exon 20. In certain embodiments, an antisense compound is complementary to a region of an IKBKAP pre-mRNA consisting of exon 20 or intron 20. In certain embodiments, an antisense compound is complementary to a region of an IKBKAP pre-mRNA within intron 19. In certain embodiments, an antisense compound is complementary to a region of an IKBKAP pre-mRNA within intron 20. In certain embodiments, an antisense compound is complementary to a region of an IKBKAP pre-mRNA within exon 20.
  • an antisense oligonucleotide modulates splicing of a pre-mRNA. In certain embodiments, an antisense oligonucleotide modulates splicing an IKBKAP pre-mRNA. In certain such embodiments, the IKBKAP pre-mRNA is transcribed from a mutant variant of IKBKAP. In certain embodiments, the mutant variant comprises an aberrant splice site. In certain embodiments, the aberrant splice site of the mutant variant comprises a mutation that weakens the 5′-splice site of exon 20. In certain embodiments, an antisense oligonucleotide reduces aberrant splicing of an IKBKAP pre-mRNA.
  • an antisense oligonucleotide increases the amount of exon 20 included in normally spliced IKBKAP mRNA. In certain embodiments, an antisense oligonucleotide increases the amount of exon 20 skipped IKBKAP mRNA.
  • the present invention provides pharmaceutical compositions comprising one or more antisense compound.
  • such pharmaceutical composition comprises a suitable pharmaceutically acceptable diluent or carrier.
  • a pharmaceutical composition comprises a sterile saline solution and one or more antisense compound.
  • such pharmaceutical composition consists of a sterile saline solution and one or more antisense compound.
  • the sterile saline is pharmaceutical grade saline.
  • a pharmaceutical composition comprises one or more antisense compound and sterile water.
  • a pharmaceutical composition consists of one or more antisense compound and sterile water.
  • the sterile saline is pharmaceutical grade water.
  • a pharmaceutical composition comprises one or more antisense compound and phosphate-buffered saline (PBS). In certain embodiments, a pharmaceutical composition consists of one or more antisense compound and sterile phosphate-buffered saline (PBS). In certain embodiments, the sterile saline is pharmaceutical grade PBS.
  • antisense compounds may be admixed with pharmaceutically acceptable active and/or inert substances for the preparation of pharmaceutical compositions or formulations.
  • Compositions and methods for the formulation of pharmaceutical compositions depend on a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.
  • compositions comprising antisense compounds encompass any pharmaceutically acceptable salts, esters, or salts of such esters.
  • pharmaceutical compositions comprising antisense compounds comprise one or more oligonucleotide which, upon administration to an animal, including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof.
  • the disclosure is also drawn to pharmaceutically acceptable salts of antisense compounds, prodrugs, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents.
  • Suitable pharmaceutically acceptable salts include, but are not limited to, sodium and potassium salts.
  • a prodrug can include the incorporation of additional nucleosides at one or both ends of an oligomeric compound which are cleaved by endogenous nucleases within the body, to form the active antisense oligomeric compound.
  • Lipid moieties have been used in nucleic acid therapies in a variety of methods.
  • the nucleic acid is introduced into preformed liposomes or lipoplexes made of mixtures of cationic lipids and neutral lipids.
  • DNA complexes with mono- or poly-cationic lipids are formed without the presence of a neutral lipid.
  • a lipid moiety is selected to increase distribution of a pharmaceutical agent to a particular cell or tissue.
  • a lipid moiety is selected to increase distribution of a pharmaceutical agent to fat tissue.
  • a lipid moiety is selected to increase distribution of a pharmaceutical agent to muscle tissue.
  • compositions provided herein comprise one or more modified oligonucleotides and one or more excipients.
  • excipients are selected from water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylase, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose and polyvinylpyrrolidone.
  • a pharmaceutical composition provided herein comprises a delivery system.
  • delivery systems include, but are not limited to, liposomes and emulsions. Certain delivery systems are useful for preparing certain pharmaceutical compositions including those comprising hydrophobic compounds. In certain embodiments, certain organic solvents such as dimethylsulfoxide are used.
  • a pharmaceutical composition provided herein comprises one or more tissue-specific delivery molecules designed to deliver the one or more pharmaceutical agents of the present invention to specific tissues or cell types.
  • pharmaceutical compositions include liposomes coated with a tissue-specific antibody.
  • a pharmaceutical composition provided herein comprises a co-solvent system.
  • co-solvent systems comprise, for example, benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase.
  • co-solvent systems are used for hydrophobic compounds.
  • a non-limiting example of such a co-solvent system is the VPD co-solvent system, which is a solution of absolute ethanol comprising 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant Polysorbate 80TM and 65% w/v polyethylene glycol 300.
  • the proportions of such co-solvent systems may be varied considerably without significantly altering their solubility and toxicity characteristics.
  • co-solvent components may be varied: for example, other surfactants may be used instead of Polysorbate 80TM; the fraction size of polyethylene glycol may be varied; other biocompatible polymers may replace polyethylene glycol, e.g., polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose.
  • a pharmaceutical composition provided herein is prepared for oral administration. In certain embodiments, pharmaceutical compositions are prepared for buccal administration.
  • a pharmaceutical composition is prepared for administration by injection (e.g., intravenous, subcutaneous, intramuscular, etc.).
  • a pharmaceutical composition comprises a carrier and is formulated in aqueous solution, such as water or physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer.
  • other ingredients are included (e.g., ingredients that aid in solubility or serve as preservatives).
  • injectable suspensions are prepared using appropriate liquid carriers, suspending agents and the like.
  • compositions for injection are suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
  • Certain solvents suitable for use in pharmaceutical compositions for injection include, but are not limited to, lipophilic solvents and fatty oils, such as sesame oil, synthetic fatty acid esters, such as ethyl oleate or triglycerides, and liposomes.
  • Aqueous injection suspensions may contain substances that increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran.
  • such suspensions may also contain suitable stabilizers or agents that increase the solubility of the pharmaceutical agents to allow for the preparation of highly concentrated solutions.
  • a pharmaceutical composition is prepared for transmucosal administration.
  • penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
  • a pharmaceutical composition provided herein comprises an oligonucleotide in a therapeutically effective amount.
  • the therapeutically effective amount is sufficient to prevent, alleviate or ameliorate symptoms of a disease or to prolong the survival of the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art.
  • one or more modified oligonucleotide provided herein is formulated as a prodrug.
  • a prodrug upon in vivo administration, is chemically converted to the biologically, pharmaceutically or therapeutically more active form of an oligonucleotide.
  • prodrugs are useful because they are easier to administer than the corresponding active form.
  • a prodrug may be more bioavailable (e.g., through oral administration) than is the corresponding active form.
  • a prodrug may have improved solubility compared to the corresponding active form.
  • prodrugs are less water soluble than the corresponding active form.
  • a prodrug is an ester.
  • the ester is metabolically hydrolyzed to carboxylic acid upon administration.
  • the carboxylic acid containing compound is the corresponding active form.
  • a prodrug comprises a short peptide (polyaminoacid) bound to an acid group.
  • the peptide is cleaved upon administration to form the corresponding active form.
  • the present invention provides compositions and methods for reducing the amount or activity of a target nucleic acid in a cell.
  • the cell is in an animal.
  • the animal is a mammal.
  • the animal is a rodent.
  • the animal is a primate.
  • the animal is a non-human primate.
  • the animal is a human.
  • the present invention provides methods of administering a pharmaceutical composition comprising an oligomeric compound of the present invention to an animal.
  • Suitable administration routes include, but are not limited to, oral, rectal, transmucosal, intestinal, enteral, topical, suppository, through inhalation, intrathecal, intracerebroventricular, intraperitoneal, intranasal, intraocular, intratumoral, and parenteral (e.g., intravenous, intramuscular, intramedullary, and subcutaneous).
  • pharmaceutical intrathecals are administered to achieve local rather than systemic exposures.
  • pharmaceutical compositions may be injected directly in the area of desired effect (e.g., into the eyes, ears).
  • a pharmaceutical composition is administered to an animal having at least one symptom associated with Familial Dysautonomia. In certain embodiments, such administration results in amelioration of at least one symptom. In certain embodiments, administration of a pharmaceutical composition to an animal results in a decrease of aberrantly spliced IKBKAP mRNA in a cell of the animal. In certain embodiments, such administration results in an increase in normally spliced IKBKAP mRNA and/or an increase in mRNA containing exon 20. In certain embodiments, such administration results in an increase in normally spliced IKBKAP mRNA and/or an increase in mRNA containing exons 20-37.
  • such administration results in an increase in normally spliced IKBKAP mRNA and/or a decrease in exon 20 skipped mRNA. In certain embodiments, such administration results in a decrease in truncated IKAP protein and an increase in normal IKAP protein.
  • administration of a pharmacueutical composition results in amelioration of: anhidrosis, decreased taste, depressed deep tendon reflexes, postural hypertension, loss of pain and temperature perception, alacrima, gastroesophageal reflux, and scoliosis. In certain embodiments, such amelioration is the reduction in severity of such defects. In certain embodiments, amelioration is the delayed onset of such defects.
  • amelioration is the slowed progression of such defects. In certain embodiments, amelioration is the prevention of such defects. In certain embodiments, amelioration is the slowed progression of such defects. In certain embodiments, amelioration is the reversal of such defects.
  • one tests for defects in a human IKBKAP transgene In certain embodiments, one identifies an animal having one or more splicing defects in a human IKBKAP transgene. In certain embodiments, a pharmaceutical composition is administered to an animal identified as having a defect in a human IKBKAP transgene. In certain embodiments, the animal is tested following administration.
  • the disclosure also provides an antisense compound as described herein, for use in any of the methods as described herein.
  • the invention provides an antisense compound comprising an antisense oligonucleotide for use in treating a disease or condition associated FD by administering the antisense compound directly into the central nervous system (CNS) or cerebrospinal fluid (CSF).
  • CNS central nervous system
  • CSF cerebrospinal fluid
  • the antisense compound is administered systemically.
  • the systemic administration is by intravenous or intraperitoneal injection.
  • systemic administration and the administration into the central nervous system are performed at the same time. In certain embodiments, systemic administration and the administration into the central nervous system are performed at different times.
  • the invention provides systemic administration of antisense compounds, either alone or in combination with delivery into the CSF.
  • pharmaceutical compositions are administered systemically.
  • pharmaceutical compositions are administered subcutaneously.
  • pharmaceutical compositions are administered intravenously.
  • pharmaceutical compositions are administered by intramuscular injection.
  • compositions are administered both directly to the CSF (e.g., IT and/or ICV injection and/or infusion) and systemically.
  • RNA nucleoside comprising a 2′-OH sugar moiety and a thymine base
  • RNA methylated uracil
  • nucleic acid sequences provided herein are intended to encompass nucleic acids containing any combination of natural or modified RNA and/or DNA, including, but not limited to such nucleic acids having modified nucleobases.
  • an oligomeric compound having the nucleobase sequence “ATCGATCG” encompasses any oligomeric compounds having such nucleobase sequence, whether modified or unmodified, including, but not limited to, such compounds comprising RNA bases, such as those having sequence “AUCGAUCG” and those having some DNA bases and some RNA bases such as “AUCGATCG” and oligomeric compounds having other modified or naturally occurring bases, such as “AT me CGAUCG,” wherein me C indicates a cytosine base comprising a methyl group at the 5-position.
  • IKBKAP minigenes were constructed by cloning the genomic fragments comprising either exon 19 to exon 21 (designated herein as wt19-21) or exon 19 to exon 22 (designated herein as wt19-22).
  • the IKBKAP genomic fragments spanning exons 19-21 and 19-22 were amplified using specific primers.
  • the genomic fragment for wt19-21 was amplified using the forward primer sequence IKAP19F6 (GGGGAAGGATCCGCCATGGAGTTAATGGTGTGTTTAGCATTACAGG, designated herein as SEQ ID NO: 2) and reverse primer sequence IKAP21R3 (GGGGAATCTAGACTTAGGGTTATG ATCATAAATCAGATTGAG, designated herein as SEQ ID NO: 3).
  • the genomic fragment for wt19-22 was amplified using the forward primer sequence IKAP19F6 and reverse primer sequence IKAP22R (GGGGAATCTAGATTACTTCAATTCTGTAAAAAACAAGTTAATATG, designated herein as SEQ ID NO: 4).
  • the IKBKAP gene in human genomic DNA was used as a template.
  • the major mutation found in FD (IVS20+6T ⁇ C) (Dong, J. et al., 2002. Am. J. Med. Genet. 110: 253-257) was introduced into both the wt19-21 and wtl 9-22 minigenes by site-directed mutagenesis to create the minigenes mt19-21 and mtl 9-22.
  • Each minigene vector construct was transfected individually into HEK-293 cells cultured in Dulbecco's modified Eagle's medium (Invitrogen) supplemented with 10% (v/v) fetal bovine serum.
  • the transfection was conducted by electroporation (Gene Pulsar II apparatus, Bio-Rad) to co-transfect 3 ⁇ g of the construct into 7 ⁇ 10 5 HEK-293 cells resuspended in 70 ⁇ L volume of Optimem (Invitrogen) and plated in 6-well plates, as described previously (Hua, Y., et al., 2007. PLoS Biol 5:e73).
  • cDNA synthesized from total RNA extracted from HEK-293 cells was amplified, as described previously (Hua, Y., et al., 2007. PLoS Biol 5:e73).
  • wt19-21 and mt19-21 were amplified with forward primer pcDNAF (TAATACGACTCACTATAGGG, designated herein as SEQ ID NO: 5) and reverse primer IKAP21R4 (CTTAGGGTTATGATCATAAATCAG, designated herein as SEQ ID NO: 6).
  • wt19-22 and mt-19-22 were amplified with forward primer pcDNAF and reverse primer IKAP22R2 (TTCAATTCTGTAAAAAACAAG, designated herein as SEQ ID NO: 7). Consistent predominant skipping of exon 20 was observed in the mutant versions of the minigenes, thus recapitulating the aberrant splicing observed in FD patients.
  • Antisense oligonucleotides were designed targeting a human IKBKAP nucleic acid and were tested for their effects on IKBKAP pre-mRNA in vitro. Together, the overlapping antisense oligonucleotides spanned the entire 74-nucleotide region of the IKBKAP exon 20 sequence, as well as the 100-nucleotide intronic regions immediately upstream and downstream of exon 20.
  • the antisense oligonucleotides are presented in Table 1, and were designed as uniform 2′-O-methoxyethyl ribose (MOE) oligonucleotides with phosphate backbones. Each oligonucleotide is 15 nucleosides in length.
  • cytosine residues throughout the oligonucleotide are 5-methylcytosines.
  • ‘Start Site’ indicates the 5′-most nucleoside to which the oligonucleotide is targeted in the human gene sequence.
  • “Stop site” indicates the 3′-most nucleoside to which the oligonucleotide is targeted in the human gene sequence.
  • Each oligonucleotide listed in Table 1 is targeted to the human IKBKAP genomic sequence (the complement of GENBANK Accession No NT 008470.16 truncated from nucleotides 13290828 to 13358424, designated herein as SEQ ID NO: 1).
  • ISIS 414161 has one mismatch with SEQ ID NO: 1.
  • HEK-293 cells harboring the mtl 9-21 minigene vector construct at a density of 7 ⁇ 10 5 cells per well were transfected using electroporation (Gene Pulsar II apparatus, Bio-Rad) with 0.007 nmol antisense oligonucleotide, as previously described (Hua, Y., et al., 2007. PLoS Biol 5:e73).
  • ISIS 383548, ISIS 383553, and ISIS 383874 which were used as control oligonucleotides that do not cause any exon skipping, were similarly transfected. These oligonucleotides served as controls for non-specific effects of uniform MOE oligonucleotides with phosphate backbones.
  • RNAs harboring the wt19-21 minigene and the mt19-21 minigene alone were also cultured and were used as controls for exon 20 inclusion levels.
  • cDNA synthesized from total RNA extracted from HEK-293 cells was amplified using the forward primer pcDNAF and reverse primer sequence IKAP21R4 to assay the splicing pattern of expressed RNAs by RT-PCR.
  • the PCR amplicons were labeled with a 32 P-dCTP.
  • the PCR products were then separated by native PAGE, followed by phosphorimage analysis on a FUJIFILM FLA-5100 instrument (Fuji Medical Systems USA Inc.).
  • the band intensities were quantified using Multi Gauge software Version 2.3 (FUJIFILM), and values were normalized for the G+C content according to the DNA sequence.
  • results are presented in Table 1 and FIG. 4 .
  • the results indicate that 6 consecutive antisense oligonucleotides, ISIS 414161, ISIS 414162, ISIS 414163, ISIS 414164, ISIS 414165, and ISIS 414166, targeting a 40-nucleotide intronic region immediately downstream of the 5′ splice site of exon 20 markedly increased inclusion of exon 20. This suggests the presence of multiple splicing silencer elements or inhibitory secondary structures within this region, designated herein as ISS-40.
  • antisense oligonucleotides which target a 20-nucleotide region in the upstream intron 19 (designated herein as ISS-20) also had a positive effect on exon 20 inclusion (Table 1 and FIG. 4 ).
  • Antisense oligonucleotides targeting exon 20 resulted in near-complete exon skipping. Treatment with antisense oligonucleotides targeting the 3′ and 5′ splice sites caused increased skipping of exon 20.
  • Certain other antisense oligonucleotides targeting intronic regions also caused increased skipping because they targeted important cis-acting splicing elements, the polypyrimidine tract, or the 5′ splice site of intron 20.
  • ISIS 414167 and ISIS 414168 which target an intronic splicing enhancer (designated herein as ISE-20), also significantly decreased the levels of the included RNA isoform compared to the untreated control.
  • the results from the three sets of control oligonucleotide-treated cells were combined and the average is presented in Table 1, designated as ‘control oligonucleotide’. ‘n/a’ indicates ‘not applicable. ‘n.d.’ indicates that there is no data for that particular oligonucleotide.
  • Skipping of exon 20 causes a frameshift that introduces a premature termination codon (PTC) in exon 21, thereby making the mRNA potentially susceptible to degradation according to the characterized rules of the nonsense-mediated mRNA decay (NMD) pathway (Nagy, E., and Maquat, L. E. 1998 . Trends Biochem Sci 23:198-199).
  • NMD nonsense-mediated mRNA decay
  • a similar experiment to the one described above was conducted utilizing the wt19-22 and the mt19-22 minigenes to determine if the NMD pathway controls the stability of the skipped mRNA isoform.
  • the same pattern of inclusion or skipping of exon 20 was observed with the wt19-22 and mtl 9-22 minigenes as observed with the corresponding 19-21 minigenes. Therefore, there is no evidence that the skipped mRNA isoform resulting from mt19-22 minigene was subject to NMD.
  • mt19-22FC minigene a single nucleotide in exon 21 of the mt19-22 minigene was deleted to restore the reading frame and remove the premature termination codon (PTC).
  • This minigene was designated as mt19-22FC minigene ( FIG. 3 ).
  • the three minigenes, wt19-22, mt19-22 and mt19-22FC, were individually transfected into HEK-293 cells using the same protocol as described above.
  • the expressed RNA was analyzed by RT-PCR. Consistent with the observation made in the study with antisense oligonucleotide transfection described above, the skipped mRNAs with or without the PTC were equally stable ( FIG. 5 ). This confirms that at least in HEK-293 cells, the skipped mRNA isoform is not subject to NMD.
  • oligonucleotides were designed targeting the first 30-nucleotide stretch of ISS-40. These oligonucleotides were designed by choosing sequences shifted in one nucleotide increments upstream and downstream (i.e., a “microwalk”) of ISS-40, starting from the +6 position in exon 20.
  • the antisense oligonucleotides are presented in Table 2 and FIG. 4D , and were designed as uniform 2′- ⁇ -methoxyethyl ribose (MOE) oligonucleotides with phosphate backbones. Each oligonucleotide is 20 nucleosides in length.
  • cytosine residues throughout the oligonucleotide are 5-methylcytosines.
  • ‘Start Site’ indicates the 5′-most nucleoside to which the oligonucleotide is targeted in the human gene sequence.
  • “Stop site” indicates the 3′-most nucleoside to which the oligonucleotide is targeted in the human gene sequence.
  • Each oligonucleotide listed in Table 2 is targeted to intron 20 of the human IKBKAP genomic sequence (the complement of GENBANK Accession No NT 008470.16 truncated from nucleotides 13290828 to 13358424, designated herein as SEQ ID NO: 1). These oligonucleotides were tested in vitro. ISIS 414161, ISIS 414162, ISIS 414163, ISIS 414163, ISIS 414164, ISIS 414165, and ISIS 414166, which showed a high percentage of inclusion, were also included in the assay.
  • HEK-293 cells harboring the mt19-21 minigene vector construct at a density of 7 ⁇ 10 5 cells per well were transfected using electroporation (Gene Pulsar II apparatus, Bio-Rad) with 0.007 nmol antisense oligonucleotide, as previously described (Hua, Y., et al., 2007 . PLoS Biol 5:e73).
  • Control oligonucleotides that do not cause any exon skipping were similarly transfected and served as controls for non-specific effects of uniform MOE oligonucleotides with phosphate backbones.
  • the patient skin fibroblast line GM04899 (Coriell Cell Repository) was utilized.
  • the cell line was derived from an individual homozygous for the major FD mutation.
  • GM04899 was cultured in minimal essential medium (Invitrogen) supplemented with non-essential amino acids (Invitrogen) and 20% (v/v) fetal bovine serum. The cells were grown to 40-50% confluence in 10-cm dishes. Cells were transfected with 2 nM, 5 nM, 25 nM, or 125 nM concentrations of ISIS 421992 using 12 ⁇ L Lipofectamine 2000 transfection reagent (Invitrogen). Two days later, cDNA synthesized from total RNA extracted from HEK-293 cells was amplified using the forward primer pcDNAF and reverse primer sequence LKAP21R4 to assay the splicing pattern of expressed RNAs by RT-PCR.
  • Invitrogen minimal essential medium
  • LKAP21R4 reverse primer sequence
  • ISIS 421992 Treatment with ISIS 421992 almost completely suppressed the splicing defect, as demonstrated by the percent inclusion of exon 20 in Table 3 and the left panel of FIG. 1A .
  • Kinetin (6-furfurylaminopurine) has been shown to improve splicing and increase wild-type IKBKAP mRNA and IKAP protein expression in FD cell lines (Hims, M. M. et al., 2007 . J. Mol. Med. 85: 149-161).
  • Treatment with ISIS 421992 was as effective as treatment with kinetin for 3 days in restoring full-length mRNA levels ( FIG. 1A , right panel).
  • a batch of cells was treated with solvent (NaOH) only of the kinetin solution as a control.
  • RNA from IMR90 a wild-type normal diploid lung fibroblast cell line was used as positive control. The results are expressed as percent inclusion of exon 20 compared to the exon 20 inclusion (100%) of IKBKAP mRNA
  • transgenic mice that carry the entire human IKBKAP gene with the major FD mutation, in addition to being homozygous wild type at the mouse Ikbkap locus, were obtained from an NIH core facility. Though the transgenic mice do not show any overt disease phenotype, due to the presence of the wild-type mouse Ikbkap gene, the mRNA expressed by the mutant human IKBKAP transgene does show a pattern of skipping similar to that of FD patients (Hims, M. M. et al., 2007 . Genomics. 90: 389-396).
  • mice were treated with ISIS 421992 administered by intracerebroventricular infusion at the rate of 50 ⁇ g/day, 100 ⁇ g/day, or 200 ⁇ g/day.
  • the protocol has been previously described by Hua et al. ( Genes Dev. 2010. 24: 1634-1644).
  • a small burr hole at the surgical site 1.8 mm lateral to the sagittal suture and 0.3 mm posterior to the bregma suture was drilled through the skull above the right lateral ventricle.
  • a cannula with a 2.2 mm stylet was positioned in the hole.
  • the cannula was connected to an Alzet micro-osmotic pump (model 1007D, Durect Corporation) with a vinyl catheter.
  • the pump prefilled with the oligonucleotide solution or PBS only was implanted subcutaneously on the back and continuously infused the solution through the cannula into the lateral ventricle at a rate of 0.5 ⁇ L per hour.
  • the mice were euthanized on day 8 and RNA from the thoracic spinal cord of the transgenic mice was extracted using Trizol and following the manufacturer's protocol. Human IKBKAP mRNA levels were measured and the results are presented in Table 5 and FIG. 2A . Multiple lanes for each condition represent independent experiments. The data indicate that there was a dose-dependent increase in the inclusion of exon 20 in human IKBKAP mRNA levels in these mice.
  • Neonatal transgenic mice were also treated with ISIS 421992 administered as a single ICV injection dose of 2.5 ⁇ g, 5 ⁇ g, 10 ⁇ g, 20 ⁇ g, or 30 ⁇ g.
  • a group of neonatal mice were treated with ISIS 421992 administered subcutaneously using a 10 ⁇ L micro syringe (Hamilton) and a 33-gauge needle. In all cases, the injections were administered at P1 and the RNA was assayed at P8. The RNA splicing patterns in the various tissues after administering ISIS 421992 in neonate mice were then observed.
  • the results of the ICV administration are presented in FIG. 2B and Table 6. Multiple lanes for each condition represent independent experiments.
  • ICV administration primarily resulted in increased full-length IKBKAP mRNA in the brain and spinal cord, with moderate effects in the peripheral tissues, whereas subcutaneous administration primarily affected expression in the liver, skeletal muscle, and heart with moderate effects in the CNS ( FIGS. 2C , 2 F, and Table 7).
  • the plot shows inclusion percentages of IKBKAP exon 20 in different tissues from five independent ICV or subcutaneous injections.

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