US20170369872A1 - Reversir tm compounds - Google Patents

Reversir tm compounds Download PDF

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US20170369872A1
US20170369872A1 US15/537,083 US201515537083A US2017369872A1 US 20170369872 A1 US20170369872 A1 US 20170369872A1 US 201515537083 A US201515537083 A US 201515537083A US 2017369872 A1 US2017369872 A1 US 2017369872A1
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reversir
certain embodiments
sirna
compounds
compound
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Vasant Jadhav
John MARAGANORE
Martin Maier
Kallanthottathil G. Rajeev
Muthiah Manoharan
Akin Akinc
Ivan ZLATEV
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Alnylam Pharmaceuticals Inc
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Alnylam Pharmaceuticals Inc
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Assigned to ALNYLAM PHARMACEUTICALS, INC. reassignment ALNYLAM PHARMACEUTICALS, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: JADHAV, VASANT, ZLATEV, IVAN, RAJEEV, KALLANTHOTTATHIL G., AKINC, AKIN, MARAGANORE, JOHN, MAIER, MARTIN, MANOHARAN, MUTHIAH
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    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
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    • C12N2310/31—Chemical structure of the backbone
    • C12N2310/318—Chemical structure of the backbone where the PO2 is completely replaced, e.g. MMI or formacetal
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    • C12N2320/53—Methods for regulating/modulating their activity reducing unwanted side-effects

Definitions

  • the present disclosure relates generally to oligomeric compounds (oligomers), which target siRNAs (e.g. conjugated or unconjugated siRNAs) in vivo, thereby providing a method of tailored control of RNAi pharmacology and therefore the therapeutic activity and/or side effects of siRNA based therapeutics in vivo.
  • target siRNAs e.g. conjugated or unconjugated siRNAs
  • Conjugated and unconjugated siRNA compounds have been used to modulate target nucleic acids. Conjugated and unconjugated siRNAs comprising a variety of modifications and motifs have been reported. In certain instances, such compounds are useful as research tools and as therapeutic agents.
  • REVERSIR compounds are provided herein.
  • REVERSIR is a trademark of Alnylam Pharmaceuticals, Inc.
  • Such compounds reduce RNAi activity of a siRNA compound, for example conjugated siRNA or unconjugated siRNA.
  • the REVERSIR compounds modulate hybridize or bind siRNA molecule in a sequence dependent manner and modulate (e.g., inhibit or reverse) their activity.
  • the present invention provides REVERSIR compounds that are complementary to at least one strand of siRNA compounds (e.g. conjugated or unconjugated siRNA).
  • the REVERSIR compounds are complementary to the antisense strand of siRNA compounds.
  • the REVERSIR compounds are complementary to the sense strand of siRNA compounds.
  • the present invention provides REVERSIR compounds comprising a modified oligonucleotide consisting of 6 to 30 linked nucleosides and having a nucleobase sequence substantially complementary to at least one strand of siRNA compounds (e.g. conjugated or unconjugated siRNA).
  • the REVERSIR compounds comprise a modified oligonucleotide consisting of 6 to 30 linked nucleosides and having a nucleobase sequence substantially complementary to the antisense strand of siRNA compounds.
  • the REVERSIR compounds comprise a modified oligonucleotide consisting of 6 to 30 linked nucleosides and having a nucleobase sequence substantially complementary to the sense strand of siRNA compounds.
  • the modified oligonucleotide is a single-stranded oligonucleotide and/or is at least 90% complementary to at least one strand of the siRNA. In some embodiments, the modified oligonucleotide is a single-stranded oligonucleotide and/or is at least 90% complementary to the antisense strand of the siRNA. In some other embodiments, the modified oligonucleotide is a single-stranded oligonucleotide and/or is at least 90% complementary to the sense strand of the siRNA.
  • the REVERSIR compound is fully complementary to at least one strand of the conjugated or unconjugated siRNA. In some embodiments, the REVERSIR compound is fully complementary to the antisense strand of the siRNA. In some other embodiments, the REVERSIR compound is fully complementary to the sense strand of the siRNA.
  • REVERSIR compounds comprise at least one modified internucleoside or intersugar linkage.
  • at least one e.g., one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen or more and upto and including all
  • internucleoside linkage is a phosphorothioate internucleoside linkage.
  • REVERSIR compounds comprise at least one nucleoside comprising a modified sugar.
  • the modified sugar is a bicyclic sugar or sugar comprising a 2′-O-methyl or a 2′-O-methoxyethyl.
  • REVERSIR compounds comprise one or more (e.g., one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen or more and upto and including all) locked nucleic acid (LNA) monomers.
  • LNA locked nucleic acid
  • REVERSIR compounds comprise at least one (e.g., one, two, three, four, five, six, seven, eight, nine, ten or more) nucleotide that does not comprise a 2′-O-methyl group, i.e., the REVERSIR compound is not fully 2′-O-methyl.
  • each nucleoside in the REVERSIR compound is a 2′-O-methyl nucleoside and the REVERSIR compound comprises at least one (e.g., one, two, three, four, five, six, seven, eight, nine, ten or more) G-clamp nucleobases.
  • REVERSIR compounds comprise at least one nucleoside comprising a modified nucleobase.
  • the modified nucleobase is a 5-methylcytosine.
  • REVERSIR compounds comprise at least one modification.
  • REVERSIR compounds comprise one or more nucleoside modifications and or one or more linkage modifications.
  • REVERSIR compounds comprise one or more modifications selected from: sugar modifications, linkage modifications, nucleobase modifications, conjugates (e.g., ligands), and any combinations thereof.
  • REVERSIR compounds comprise a modified oligonucleotide comprising: a gap segment consisting of linked deoxynucleosides; a 5′ wing segment consisting of linked nucleosides; a 3′ wing segment consisting of linked nucleosides; wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.
  • REVERSIR compounds comprise a modified oligonucleotide comprising: a gap segment consisting of ten linked deoxynucleosides; a 5′ wing segment consisting of five linked nucleosides; a 3′ wing segment consisting of five linked nucleosides; wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment, wherein each nucleoside of each wing segment comprises a 2′-O-methoxyethyl sugar; and wherein each internucleoside linkage is a phosphorothioate linkage.
  • REVERSIR compound comprises a modified oligonucleotide consisting of 6-17, 7-16 8-15 or 6-25 linked nucleosides. In some embodiments, REVERSIR compound comprises a modified oligonucleotide consisting of 8, 9, 10, 11, 12, 13, 14, 15 or 20 linked nucleosides.
  • REVERSIR compound comprises a modified oligonucleotide wherein each nucleoside is modified.
  • REVERSIR compound comprises or consists of nine linked nucleosides.
  • REVERSIR compound has low PS content.
  • low PS content is meant that the REVERSIR compound has 1, 2, 3, 4 or 5 phosphorothioate linkages per nine nucleoides of the REVERSIR compound.
  • REVERSIR compound comprises or consists of nine linked nucleosides and has low PS content.
  • REVERSIR compound consists of nine linked nucleosides and comprises five phosphorothioate linkages.
  • REVERSIR compound consists of nine linked nucleosides, comprises five phosphorothioate linkages and is linked to a ligand.
  • REVERSIR compounds are complementary to the antisense or sense strand of a conjugated or unconjugated siRNA, wherein the siRNA is targeted to an mRNA.
  • the siRNA is targeted to an mRNA encoding a blood factor.
  • the siRNA is targeted to an mRNA encoding a protein involved in metabolism.
  • the siRNA is targeted to an mRNA encoding a protein involved in diabetes.
  • the siRNA is targeted to an mRNA encoding a protein involved in cardiopathology.
  • the siRNA is targeted to an mRNA encoding a protein expressed in nerve cells.
  • the siRNA is targeted to an mRNA encoding a protein expressed in the central nervous system.
  • the siRNA is targeted to an mRNA expressed in peripheral nerves.
  • the conjugated or unconjugated siRNA is targeted to an mRNA encoding a protein expressed in the liver. In certain embodiments, the siRNA is targeted to an mRNA encoding a protein expressed in the kidney.
  • the conjugated or unconjugated siRNA is targeted to a pre-mRNA. In certain embodiments, the conjugated or unconjugated siRNA is targeted to a micro-RNA. In certain embodiments, the conjugated or unconjugated siRNA activates the RISC pathway. In some embodiments, the conjugated or unconjugated siRNA inhibits the expression of a target nucleic acid.
  • REVERSIR compounds modulate the RISC pathway. In some embodiments, REVERSIR compounds inhibit the RISC pathway.
  • the invention provides a composition comprising a REVERSIR compound or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable carrier or diluent.
  • the invention provides methods comprising administering to a subject (e.g., an animal) a REVERSIR compound or composition comprising same.
  • a subject e.g., an animal
  • the administering is oral, topical, or parenteral.
  • the invention provides methods of inhibiting RNAi activity of a conjugated or unconjugated siRNA in a cell.
  • the method generally, comprises contacting the cell with a REVERSIR compound according the present invention and thereby inhibiting the RNAi activity in the cell.
  • the cell is in in vivo.
  • the cell is in vitro.
  • the cell is ex vivo.
  • the cell is in a subject.
  • the cell is an animal.
  • the animal is a human.
  • the invention provides methods comprising: contacting a cell with a conjugated or unconjugated siRNA; detecting RNAi activity; and contacting the cell with a REVERSIR compound.
  • the method the detecting RANi activity comprises measuring the amount of target mRNA present, the amount of target protein present, and/or the activity of a target protein.
  • such methods comprise detecting REVERSIR activity by measuring RNAi activity after contacting the cell with the REVERSIR compound.
  • the cell is in vivo.
  • the cell is in an animal. In certain embodiments, the animal is a human.
  • the invention provides methods of ameliorating a side-effect of siRNA treatment comprising: contacting a cell with a conjugated or unconjugated siRNA; detecting a side-effect; contacting the cell with a REVERSIR compound; and thereby ameliorating the side effect of the siRNA.
  • the invention provides methods of treating a patient comprising: administering to the patient a conjugated or unconjugated siRNA; monitoring the patient for siRNA activity; and if the siRNA activity becomes higher than desired, administrating a REVERSIR compound.
  • the monitoring siRNA activity comprises measuring the amount of target mRNA present, measuring the amount of target protein present and/or measuring the activity of a target protein.
  • such methods include detecting REVERSIR activity by measuring siRNA activity after administration of the REVERSIR compound.
  • the patient is a mammal. In some embodiments, the patient is a human.
  • the invention provides methods of treating a patient comprising: administering to the patient a conjugated or unconjugated siRNA; monitoring the patient for one or more side effect; and if the one or more side effect reaches an undesirable level, administrating a REVERSIR compound.
  • the patient is a mammal. In some embodiments, the patient is a human.
  • the invention provides a kit comprising a conjugated or unconjugated siRNA and a REVERSIR compound; REVERSIR compound and a non-oligomeric REVERSIR; or conjugated or unconjugated siRNA compound, REVERSIR compound, and a non-oligomeric REVERSIR.
  • the non-oligomeric REVERSIR is a target protein.
  • FIG. 1 shows in vivo activity of exemplary REVERSIR compounds targeting antithrombin (AT) siRNAs.
  • FIG. 2 shows that reversal of activity of siRNAs by REVERSIR compounds in vivo is rapid and dose-dependent. Full reversal can be seen within 4-days of dosing.
  • FIG. 3 shows the effect of REVERSIR compound length on the in vivo activity of exemplary REVERSIR compounds. As seen, shorter REVERSIR compounds showed better in vivo activity than the longer REVERSIR compounds.
  • FIG. 4 shows the effect of exemplary nucleic acid modifications on the in vivo activity of REVERSIR compounds.
  • FIG. 5 shows the effect of number of phosphorothioate internucleoside linkages on the in vivo activity of REVERSIR compounds.
  • FIGS. 6 and 7 show that REVERSIR compounds have increased in vivo potency with decreasing length
  • FIGS. 8 and 9 shows effect of number phosphorothioate linkages on the activity of REVERSIR compounds.
  • FIG. 10 shows further improvement in potency for exemplary REVERSIR compounds.
  • FIG. 11 shows in vitro reversal of siRNA activity by free uptake of exemplary REVERSIR compounds targeting antithrombin siRNA in primary mouse hepatocytes.
  • FIG. 12 shows in vitro reversal of siRNA activity by free uptake of exemplary REVERSIR compounds targeting antithrombin siRNA in primary mouse hepatocytes at various concentrations.
  • FIGS. 13 and 14 show in vitro reversal of siRNA activity by free uptake of exemplary REVERSIR compounds targeting Factor IX siRNAs in primary mouse hepatocytes at various concentrations.
  • FIG. 15 shows the effect of high-affinity chemistry on the in vivo activity of exemplary REVERSIR compounds targeting Factor IX siRNAs.
  • FIGS. 16 and 17 show the effect of REVERSIR compound length on the in vivo activity of exemplary REVERSIR compounds targeting Factor IX siRNAs.
  • REVERSIR compounds were administered at 3 mg/kg ( FIG. 16 ) and 1 mg/kg ( FIG. 17 )
  • FIG. 18 shows the effect of linker, between the REVERSIR compound and the ligand conjugated with the REVERSIR compound, on the in vivo activity of exemplary REVERSIR compounds targeting Factor IX siRNAs.
  • FIG. 19 shows the effect of phosphorothioate linkages in the REVERSIR compound on the in vivo activity of exemplary REVERSIR compounds targeting Factor IX siRNAs.
  • FIG. 20 shows the effect of linker, between the REVERSIR compound and the ligand conjugated with the REVERSIR compound, on the in vitro activity of exemplary REVERSIR compounds targeting Factor IX siRNAs.
  • FIG. 21 shows the effect on activity of siRNA by exemplary REVERSIR compounds matching certain portion of the antisense strand of the siRNA.
  • FIG. 22 shows in vivo dos-dependent effect of exemplary REVERSIR compounds targeting Factor IX siRNA.
  • FIG. 23 shows that REVERSIR compounds are tolerated in vivo.
  • FIGS. 24A and 24B show in vivo reversal of siRNA activity by some exemplary REVERSIR compounds in non-human primates.
  • nucleoside means a glycosylamine comprising a nucleobase and a sugar. Nucleosides includes, but are not limited to, naturally occurring nucleosides, abasic nucleosides, modified nucleosides, and nucleosides having mimetic bases and/or sugar groups.
  • nucleotide refers to a glycosomine comprising a nucleobase and a sugar having a phosphate group covalently linked to the sugar. Nucleotides may be modified with any of a variety of substituents.
  • nucleobase refers to the base portion of a nucleoside or nucleotide.
  • a nucleobase may comprise any atom or group of atoms capable of hydrogen bonding to a base of another nucleic acid.
  • heterocyclic base moiety refers to a nucleobase comprising a heterocycle.
  • oligomeric compound refers to a polymeric structure comprising two or more sub-structures and capable of hybridizing to a region of a nucleic acid molecule.
  • oligomeric compounds are oligonucleosides.
  • oligomeric compounds are oligonucleotides.
  • oligomeric compounds are antisense compounds.
  • oligomeric compounds are REVERSIR compounds.
  • oligomeric compounds comprise conjugate groups.
  • oligonucleoside refers to an oligonucleotide in which the internucleoside linkages do not contain a phosphorus atom.
  • oligonucleotide refers to an oligomeric compound comprising a plurality of linked nucleosides.
  • one or more nucleotides of an oligonucleotide is modified.
  • an oligonucleotide comprises ribonucleic acid (RNA) or deoxyribonucleic acid (DNA).
  • oligonucleotides are composed of naturally- and/or non-naturally-occurring nucleobases, sugars and covalent internucleoside linkages, and may further include non-nucleic acid conjugates.
  • nucleoside linkage refers to a covalent linkage between adjacent nucleosides.
  • naturally occurring internucleoside linkage refers to a 3′ to 5′ phosphodiester linkage.
  • detecting siRNA activity or “measuring siRNA activity” means that a test for detecting or measuring siRNA activity is performed on a particular sample and compared to that of a control sample. Such detection and/or measuring can include values of zero. Thus, if a test for detection of siRNA activity results in a finding of no siRNA activity (siRNA activity of zero), the step of “detecting siRNA activity” has nevertheless been performed.
  • control sample refers to a sample that has not been contacted with a reporter oligomeric compound.
  • motif refers to the pattern of unmodified and modified nucleotides in an oligomeric compound.
  • REVERSIR compound refers to an oligomeric compound that is complementary to and capable of hybridizing with at least one strand of a conjugated or unconjugated siRNA. Without limitations, the REVERSIR compound could not only block unintended target PD effect but also block any potential off-target activity that could happen with a conjugated or unconjugated siRNA.
  • non-oligomeric REVERSIR refers to a compound that does not hybridize with a strand of siRNA and that reduces the amount or duration of a siRNA activity.
  • a non-oligomeric REVERSIR is a target protein.
  • REVERSIR activity refers to any decrease in intensity or duration of any siRNA activity attributable to hybridization of a REVERSIR compound to one of the strands of the siRNA.
  • chimeric oligomer refers to an oligomeric compound, having at least one sugar, nucleobase or internucleoside linkage that is differentially modified as compared to at least on other sugar, nucleobase or internucleoside linkage within the same oligomeric compound.
  • the remainder of the sugars, nucleobases and internucleoside linkages can be independently modified or unmodified, the same or different.
  • chimeric oligonucleotide refers to an oligonucleotide, having at least one sugar, nucleobase or internucleoside linkage that is differentially modified as compared to at least on other sugar, nucleobase or internucleoside linkage within the same oligonucleotide.
  • the remainder of the sugars, nucleobases and internucleoside linkages can be independently modified or unmodified, the same or different.
  • mixed-backbone oligomeric compound refers to an oligomeric compound wherein at least one internucleoside linkage of the oligomeric compound is different from at least one other internucleoside linkage of the oligomeric compound.
  • target protein refers to a protein, the modulation of which is desired.
  • target gene refers to a gene encoding a target protein.
  • target nucleic acid refers to any nucleic acid molecule the expression or activity of which is capable of being modulated by a conjugated or unconjugated siRNA compound.
  • Target nucleic acids include, but are not limited to, RNA (including, but not limited to pre-mRNA and mRNA or portions thereof) transcribed from DNA encoding a target protein, and also cDNA derived from such RNA, and miRNA.
  • the target nucleic acid can be a cellular gene (or mRNA transcribed from the gene) whose expression is associated with a particular disorder or disease state, or a nucleic acid molecule from an infectious agent.
  • target siRNA refers to a siRNA compound that is targeted by a REVERSIR compound.
  • targeting refers to the association of antisense strand of a siRNA to a particular target nucleic acid molecule or a particular region of nucleotides within a target nucleic acid molecule.
  • nucleobase complementarity refers to 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 refers to a nucleobase of an antisense compound that is capable of base pairing with a nucleobase of its target nucleic acid.
  • nucleobase at a certain position of an antisense compound is 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.
  • non-complementary nucleobase refers to a pair of nucleobases that do not form hydrogen bonds with one another or otherwise support hybridization.
  • the term “complementary” refers to the capacity of an oligomeric compound to hybridize to another oligomeric compound or nucleic acid through nucleobase complementarity.
  • an oligomeric compound and its target are complementary to each other when a sufficient number of corresponding positions in each molecule are occupied by nucleobases that can bond with each other to allow stable association between the antisense compound and the target.
  • nucleobases that can bond with each other to allow stable association between the antisense compound and the target.
  • oligomeric compounds e.g., REVERSIR compounds, siRNAs, and the like
  • oligomeric compounds may comprise up to about 20% nucleotides that are mismatched (i.e., are not nucleobase complementary to the corresponding nucleotides of the target).
  • the oligomeric compounds such as REVERSIR compounds and siRNAs, contain no more than about 15%, more preferably not more than about 10%, most preferably not more than 5% or no mismatches.
  • the remaining nucleotides are nucleobase complementary or otherwise do not disrupt hybridization (e.g., universal bases).
  • hybridization means the pairing of complementary oligomeric compounds (e.g., an antisense strand of a siRNA and its target nucleic acid or a REVERSIR to its target siRNA). 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 nucleoside or nucleotide bases (nucleobases).
  • the natural base adenine is nucleobase complementary to the natural nucleobases thymidine and uracil which pair through the formation of hydrogen bonds.
  • the natural base guanine is nucleobase complementary to the natural bases cytosine and 5-methyl cytosine. Hybridization can occur under varying circumstances.
  • the term “specifically hybridizes” refers to the ability of an oligomeric compound to hybridize to one nucleic acid site with greater affinity than it hybridizes to another nucleic acid site.
  • the antisense strand of an siRNA specifically hybridizes to more than one target site.
  • design or “designed to” refer to the process of designing an oligomeric compound that specifically hybridizes with a selected nucleic acid molecule.
  • modulation refers to a perturbation of function or activity when compared to the level of the 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 perturbing splice site selection of pre-mRNA processing.
  • expression refers to all the functions and steps by which a gene's coded information is converted into structures present and operating in a cell. Such structures include, but are not limited to the products of transcription and translation.
  • variant refers to an alternative RNA transcript that can be produced from the same genomic region of DNA. Variants include, but are not limited to “pre-mRNA variants” which are transcripts produced from the same genomic DNA that differ from other transcripts produced from the same genomic DNA in either their start or stop position and contain both intronic and exonic sequence. Variants also include, but are not limited to, those with alternate splice junctions, or alternate initiation and termination codons.
  • high-affinity modified monomer refers to a monomer having at least one modified nucleobase, internucleoside linkage or sugar moiety, when compared to naturally occurring monomers, such that the modification increases the affinity of an antisense compound comprising the high-affinity modified monomer to its target nucleic acid.
  • High-affinity modifications include, but are not limited to, monomers (e.g., nucleosides and nucleotides) comprising 2′-modified sugars.
  • 2′-modified or “2′-substituted” means a sugar comprising substituent at the 2′ position other than H or OH.
  • 2′-modified monomers include, but are not limited to, BNA's and monomers (e.g., nucleosides and nucleotides) with 2′-substituents, such as allyl, amino, azido, thio, O-allyl, O—C 1 -C 10 alkyl, —OCF3, O—(CH 2 ) 2 —O—CH 3 , 2′-O(CH 2 ) 2 SCH 3 , O—(CH 2 ) 2 —O—N(Rm)(Rn), or 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.
  • oligomeric compounds comprise a 2′ modified monomer that does not have the formula 2′-O(CH 2 )—H, wherein n is one to six. In certain embodiments, oligomeric compounds comprise a 2′ modified monomer that does not have the formula 2′-OCH 3 . In certain embodiments, oligomeric compounds comprise a 2′ modified monomer that does not have the formula or, in the alternative, 2′-O(CH 2 ) 2 OCH 3 .
  • locked nucleic acid or “LNA” or “locked nucleoside” or “locked nucleotide” refers to a nucleoside or nucleotide wherein the furanose portion of the nucleoside includes a bridge connecting two carbon atoms on the furanose ring, thereby forming a bicyclic ring system.
  • Locked nucleic acids are also referred to as bicyclic nucleic acids (BNA).
  • methyleneoxy LNA alone refers to ⁇ -D-methyleneoxy LNA.
  • MOE refers to a 2′-O-methoxyethyl substituent.
  • the term “gapmer” refers to a chimeric oligomeric compound comprising a central region (a “gap”) and a region on either side of the central region (the “wings”), wherein the gap comprises at least one modification that is different from that of each wing.
  • modifications include nucleobase, monomeric linkage, and sugar modifications as well as the absence of modification (unmodified).
  • the nucleotide linkages in each of the wings are different than the nucleotide linkages in the gap.
  • each wing comprises nucleotides with high affinity modifications and the gap comprises nucleotides that do not comprise that modification.
  • nucleotides in the gap and the nucleotides in the wings all comprise high affinity modifications, but the high affinity modifications in the gap are different than the high affinity modifications in the wings.
  • the modifications in the wings are the same as one another. In certain embodiments, the modifications in the wings are different from each other.
  • nucleotides in the gap are unmodified and nucleotides in the wings are modified.
  • the modification(s) in each wing are the same.
  • the modification(s) in one wing are different from the modification(s) in the other wing.
  • oligomeric compounds are gapmers having 2′-deoxynucleotides in the gap and nucleotides with high-affinity modifications in the wing.
  • prodrug refers to a therapeutic agent that is prepared in an inactive form that is converted to an active form (i.e., drug) within the body or cells thereof by the action of endogenous enzymes or other chemicals and/or conditions.
  • pharmaceutically acceptable salts refers to salts of active compounds that retain the desired biological activity of the active compound and do not impart undesired toxicological effects thereto.
  • cap structure or “terminal cap moiety” refers to chemical modifications, which have been incorporated at either terminus of an antisense compound.
  • prevention refers to delaying or forestalling the onset or development of a condition or disease for a period of time from hours to days, preferably weeks to months.
  • the term “amelioration” refers to a lessening of at least one activity or one indicator of the severity of a condition or disease.
  • the severity of indicators may be determined by subjective or objective measures which are known to those skilled in the art.
  • treatment refers to administering a composition of the invention to effect an alteration or improvement of the disease or condition.
  • Prevention, amelioration, and/or treatment may require administration of multiple doses at regular intervals, or prior to onset of the disease or condition to alter the course of the disease or condition.
  • a single agent may be used in a single individual for each prevention, amelioration, and treatment of a condition or disease sequentially, or concurrently.
  • a pharmaceutical agent refers to a substance that provides a therapeutic benefit when administered to a subject.
  • a pharmaceutical agent is an active pharmaceutical agent.
  • a pharmaceutical agent is a prodrug.
  • terapéuticaally effective amount refers to an amount of a pharmaceutical agent that provides a therapeutic benefit to an animal.
  • administering means providing a pharmaceutical agent to an animal, and includes, but is not limited to administering by a medical professional and self-administering.
  • the term “co-administering” means providing more than one pharmaceutical agent to an animal. In certain embodiments, such more than one pharmaceutical agents are administered together. In certain embodiments, such more than one pharmaceutical agents are administered separately. In certain embodiments, such more than one pharmaceutical agents are administered at the same time. In certain embodiments, such more than one pharmaceutical agents are administered at different times. In certain embodiments, such more than one pharmaceutical agents are administered through the same route of administration. In certain embodiments, such more than one pharmaceutical agents are administered through different routes of administration. In certain embodiments, such more than one pharmaceutical agents are contained in the same pharmaceutical formulation. In certain embodiments, such more than one pharmaceutical agents are in separate formulations.
  • a pharmaceutical composition refers to a mixture of substances suitable for administering to an individual.
  • a pharmaceutical composition may comprise an antisense oligonucleotide and a sterile aqueous solution.
  • a pharmaceutical composition includes a pharmaceutical agent and a diluent and/or carrier.
  • in vitro refers to events that occur in an artificial environment, e.g., in a test tube or reaction vessel, in cell culture, etc., rather than within an organism (e.g. animal or a plant).
  • ex vivo refers to cells which are removed from a living organism and cultured outside the organism (e.g., in a test tube).
  • in vivo refers to events that occur within an organism (e.g. animal, plant, and/or microbe).
  • the term “subject” or “patient” refers to any organism to which a composition disclosed herein can be administered, e.g., for experimental, diagnostic, and/or therapeutic purposes.
  • Typical subjects include animals (e.g., mammals such as mice, rats, rabbits, non-human primates, and humans) and/or plants.
  • animals e.g., mammals such as mice, rats, rabbits, non-human primates, and humans
  • the animal is a vertebrate such as a primate, rodent, domestic animal or game animal.
  • Primates include chimpanzees, cynomologous monkeys, spider monkeys, and macaques, e.g., Rhesus.
  • Rodents include mice, rats, woodchucks, ferrets, rabbits and hamsters.
  • Domestic and game animals include cows, horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, canine species, e.g., dog, fox, wolf, avian species, e.g., chicken, emu, ostrich, and fish, e.g., trout, catfish and salmon.
  • Patient or subject includes any subset of the foregoing, e.g., all of the above, but excluding one or more groups or species such as humans, primates or rodents.
  • the subject is a mammal, e.g., a primate, e.g., a human.
  • the terms, “patient” and “subject” are used interchangeably herein.
  • a subject can be male or female.
  • the subject is a mammal.
  • the mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but are not limited to these examples. Mammals other than humans can be advantageously used as subjects that represent animal models of human diseases and disorders.
  • compounds, compositions and methods described herein can be used to with domesticated animals and/or pets.
  • the subject is human. In another embodiment, the subject is an experimental animal or animal substitute as a disease model.
  • the term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be covered. Examples of subjects include humans, dogs, cats, cows, goats, and mice.
  • the term subject is further intended to include transgenic species.
  • the subject can be of European ancestry.
  • the subject can be of African American ancestry.
  • the subject can be of Asian ancestry.
  • parenteral administration refers to administration through injection or infusion.
  • Parenteral administration includes, but is not limited to, subcutaneous administration, intravenous administration, or intramuscular administration.
  • subcutaneous administration refers to administration just below the skin.
  • Intravenous administration means administration into a vein.
  • a dose refers to a specified quantity of a pharmaceutical agent provided in a single administration.
  • a dose may be administered in two or more boluses, tablets, or injections.
  • the desired dose requires a volume not easily accommodated by a single injection.
  • two or more injections may be used to achieve the desired dose.
  • a dose may be administered in two or more injections to minimize injection site reaction in an individual.
  • a dosage unit refers to a form in which a pharmaceutical agent is provided.
  • a dosage unit is a vial comprising lyophilized antisense oligonucleotide.
  • a dosage unit is a vial comprising reconstituted antisense oligonucleotide.
  • active pharmaceutical ingredient refers to the substance in a pharmaceutical composition that provides a desired effect.
  • side effects refers to physiological responses attributable to a treatment other than desired effects.
  • side effects include, without limitation, injection site reactions, liver function test abnormalities, renal function abnormalities, liver toxicity, renal toxicity, central nervous system abnormalities, and myopathies.
  • increased aminotransferase levels in serum may indicate liver toxicity or liver function abnormality.
  • increased bilirubin may indicate liver toxicity or liver function abnormality.
  • alkyl refers to a saturated straight or branched hydrocarbon radical containing up to twenty four carbon atoms.
  • alkyl groups include, but are not limited to, 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 (C1-C12 alkyl) with from 1 to about 6 carbon atoms being more preferred.
  • the term “lower alkyl” as used herein includes from 1 to about 6 carbon atoms.
  • Alkyl groups as used herein may optionally include one or more further substituent groups.
  • alkenyl refers to 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, but are not limited to, 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 refers to 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, but are not limited to, 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 substitutent groups.
  • aminoalkyl refers to an amino substituted alkyl radical. This term is meant to include C1-C12 alkyl groups having an amino substituent at any position and wherein the alkyl group attaches the aminoalkyl group to the parent molecule. The alkyl and/or amino portions of the aminoalkyl group can be further substituted with substituent groups.
  • aliphatic refers to 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 substitutent groups.
  • alicyclic refers to 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 substitutent groups.
  • alkoxy refers to 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, but are not limited to, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, sec-butoxy, tert-butoxy, n-pentoxy, neopentoxy, n-hexoxy and the like.
  • Alkoxy groups as used herein may optionally include further substitutent groups.
  • halo and “halogen,” as used herein, refer to an atom selected from fluorine, chlorine, bromine and iodine.
  • aryl and “aromatic,” as used herein, refer to a mono- or polycyclic carbocyclic ring system radicals having one or more aromatic rings.
  • aryl groups include, but are not limited to, 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 substitutent groups.
  • aralkyl and arylalkyl refer to a radical formed between an alkyl group and an aryl group wherein the alkyl group is used to attach the aralkyl group to a parent molecule. Examples include, but are not limited to, benzyl, phenethyl and the like. Aralkyl groups as used herein may optionally include further substitutent groups attached to the alkyl, the aryl or both groups that form the radical group.
  • heterocyclic radical refers to a radical mono-, or poly-cyclic ring system that includes at least one heteroatom and is unsaturated, partially saturated or fully saturated, thereby including heteroaryl groups. Heterocyclic is also meant to include fused ring systems wherein one or more of the fused rings contain at least one heteroatom and the other rings can contain one or more heteroatoms or optionally contain no heteroatoms.
  • a heterocyclic group typically includes at least one atom selected from sulfur, nitrogen or oxygen.
  • heterocyclic groups include, [1,3]dioxolane, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuryl and the like.
  • Heterocyclic groups as used herein may optionally include further substitutent groups.
  • heteroaryl refers to a radical comprising a mono- or poly-cyclic aromatic ring, ring system or fused ring system wherein at least one of the rings is aromatic and includes one or more heteroatom. 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, but are not limited to, 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 substitutent groups.
  • heteroarylalkyl refers to a heteroaryl group as previously defined having an alky radical that can attach the heteroarylalkyl group to a parent molecule. Examples include, but are not limited to, pyridinylmethyl, pyrimidinylethyl, napthyridinylpropyl and the like. Heteroarylalkyl groups as used herein may optionally include further substitutent groups on one or both of the heteroaryl or alkyl portions.
  • the term “mono or poly cyclic structure” as used in the present invention includes all ring systems that are single or polycyclic having rings that are fused or linked and is meant to be inclusive of single and mixed ring systems individually selected from aliphatic, alicyclic, aryl, heteroaryl, aralkyl, arylalkyl, heterocyclic, heteroaryl, heteroaromatic, heteroarylalkyl.
  • Such mono and poly cyclic structures can contain rings that are uniform or have varying degrees of saturation including fully saturated, partially saturated or fully unsaturated.
  • Each ring can comprise ring atoms selected from C, N, O and S to give rise to heterocyclic rings as well as rings comprising only C ring atoms which can be present in a mixed motif such as for example benzimidazole wherein one ring has only carbon ring atoms and the fused ring has two nitrogen atoms.
  • the mono or poly cyclic structures can be further substituted with substituent groups such as for example phthalimide which has two ⁇ O groups attached to one of the rings.
  • mono or poly cyclic structures can be attached to a parent molecule directly through a ring atom, through a substituent group or a bifunctional linking moiety.
  • acyl refers to 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 substitutent groups.
  • hydrocarbyl includes groups comprising C, O and H. Included are straight, branched and cyclic groups having any degree of saturation. Such hydrocarbyl groups can include one or more heteroatoms selected from N, O and S and can be further mono or poly substituted with one or more substituent groups.
  • substituted and substituteduent group include groups that are typically added to other groups or parent compounds to enhance desired properties or give desired effects.
  • Substituent groups can be protected or unprotected and can be added to one available site or to many available sites in a parent compound.
  • Substituent groups 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.
  • each Raa, Rbb and Rcc is, independently, H, an optionally linked chemical functional group or a further substituent group with a preferred list including without limitation H, alkyl, alkenyl, alkynyl, aliphatic, alkoxy, acyl, aryl, aralkyl, heteroaryl, alicyclic, heterocyclic and heteroarylalkyl.
  • the REVERSIR compounds disclosed herein are particularly effective in reducing the activity of siRNAs.
  • the REVERSIR compounds disclosed herein can reduce the activity of an siRNA by at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90%, or at least about 95%, or at least about 97%, or at least about 99% or up to and including a 100% decrease (i.e., absent level as compared to a reference sample), or any decrease between 50-100% as compared to a reference level.
  • the reference level can be siRNA activity in absence of the REVERSIR compound.
  • the REVERSIR compounds describe herein can reduce the activity of the siRNA by at least 75%, for example by 80%, 85%, 90%, 95% or more and upto and including completer reduction or inhibition of siRNA activity, within less than seven (e.g., within 6 days, five days, four days, three days, two days or one day) of administering or use of the REVERSIR compound.
  • the REVERSIR compounds can completely reduce the siRNA activity within four days of administering or use of the REVERSIR compound.
  • complete reduction of siRNA activity is meant a reduction of the siRNA activity by at least 80% relative to a reference level.
  • the siRNA and/or the REVERSIR compounds are oligomeric compounds.
  • oligomeric compounds comprise one or more modified monomer.
  • oligomeric compounds comprise one or more high affinity monomer.
  • such high-affinity monomer is selected from monomers (e.g., nucleosides and nucleotides) comprising 2′-modified sugars, including, but not limited to: BNA's and monomers (e.g., nucleosides and nucleotides) with 2′-substituents such as allyl, amino, azido, thio, O-allyl, O—C 1 -C 10 alkyl, —OCF 3 , O—(CH 2 ) 2 —O—CH3, 2′-O(CH 2 ) 2 SCH 3 , O—(CH 2 ) 2 —O—N(Rm)(Rn), or O—CH 2 —C( ⁇ O)—N(Rm)(Rn), where each Rm and Rn is, independently, H or substituted or unsubstituents such as allyl,
  • the oligomeric compounds including, but not limited to REVERSIR compounds and siRNAs of the present invention, comprise one or more high affinity monomers.
  • the oligomeric compounds including, but not limited to REVERSIR compounds and siRNAs of the present invention, comprise one or more ⁇ -D-Methyleneoxy (4′-CH 2 —O-2′) LNA monomers.
  • the oligomeric compounds including, including, but not limited to REVERSIR compounds and siRNAs of the present invention, comprise one or more ⁇ -D-Methyleneoxy (4′-CH 2 —O-2′) LNA monomers.
  • the oligomeric compounds including, including, but not limited to REVERSIR compounds and siRNAs of the present invention, comprise one or more (S)-cEt monomers.
  • the oligomeric compounds including, but not limited to REVERSIR compounds and siRNAs of the present invention, comprise one or more high affinity monomers provided that the oligomeric compound does not comprise a nucleotide comprising a 2′-O(CH 2 ) n H, wherein n is one to six.
  • the oligomeric compounds including, but not limited to REVERSIR compounds and siRNAs, comprise one or more high affinity monomer provided that the oligomeric compound does not comprise a nucleotide comprising a 2′-OCH 3 or a 2′-O(CH 2 ) 2 OCH 3 .
  • the oligomeric compounds including, but not limited to REVERSIR compounds and siRNAs, comprise one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more) high affinity monomer provided that the oligomeric compound does not comprise a ⁇ -L-Methyleneoxy (4′-CH 2 —O-2′) LNA.
  • the oligomeric compounds including, but no limited to REVERSIR compounds and siRNAs, comprise one or more high affinity monomer provided that the oligomeric compound does not comprise a ⁇ -D-Methyleneoxy (4′-CH 2 —O-2′) LNA.
  • the oligomeric compounds including, but no limited to REVERSIR compound and siRNAs, comprise one or more high affinity monomer provided that the oligomeric compound does not comprise a ⁇ -L-Methyleneoxy (4′-CH 2 —O-2′) LNA or 3-D-Methyleneoxy (4′-CH 2 —O-2′) LNA.
  • the naturally occurring base portion of a nucleoside is typically a heterocyclic base.
  • the two most common classes of such heterocyclic bases are the purines and the pyrimidines.
  • a phosphate group can be linked to the 2′, 3′ or 5′ hydroxyl moiety of the sugar.
  • those phosphate groups covalently link adjacent nucleosides to one another to form a linear polymeric compound.
  • the phosphate groups are commonly referred to as forming the internucleoside backbone of the oligonucleotide.
  • the naturally occurring linkage or backbone of RNA and of DNA is a 3′ to 5′ phosphodiester linkage.
  • nucleobases such as the purine nucleobases adenine (A) and guanine (G), and the pyrimidine nucleobases thymine (T), cytosine (C) and uracil (U)
  • A purine nucleobase
  • G guanine
  • T pyrimidine nucleobase
  • T thymine
  • C cytosine
  • U uracil
  • modified nucleobases or nucleobase mimetics known to those skilled in the art are amenable with the compounds described herein.
  • the unmodified or natural nucleobases can be modified or replaced to provide oligonucleotides having improved properties.
  • nuclease resistant oligonucleotides can be prepared with these bases or with synthetic and natural nucleobases (e.g., inosine, xanthine, hypoxanthine, nubularine, isoguanisine, or tubercidine) and any one of the oligomer modifications described herein.
  • nucleobases e.g., inosine, xanthine, hypoxanthine, nubularine, isoguanisine, or tubercidine
  • substituted or modified analogs of any of the above bases and “universal bases” can be employed.
  • the nucleotide is said to comprise a modified nucleobase and/or a nucleobase modification herein.
  • Modified nucleobase and/or nucleobase modifications also include natural, non-natural and universal bases, which comprise conjugated moieties, e.g. a ligand described herein.
  • Preferred conjugate moieties for conjugation with nucleobases include cationic amino groups which can be conjugated to the nucleobase via an appropriate alkyl, alkenyl or a linker with an amide linkage.
  • nucleobase often referred to in the art simply as “base” modifications or substitutions.
  • “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U).
  • modified nucleobases include, but are not limited to, other synthetic and natural nucleobases such as inosine, xanthine, hypoxanthine, nubularine, isoguanisine, tubercidine, 2-(halo)adenine, 2-(alkyl)adenine, 2-(propyl)adenine, 2-(amino)adenine, 2-(aminoalkyll)adenine, 2-(aminopropyl)adenine, 2-(methylthio)-N 6 -(isopentenyl)adenine, 6-(alkyl)adenine, 6-(methyl)adenine, 7-(deaza)adenine, 8-(alkenyl)adenine, 8-(alkyl)adenine, 8-(alkynyl)adenine, 8-(amino)adenine, 8-(halo)adenine, 8-(hydroxyl)adenine, 8-(thioalkyl)adenine,
  • a universal nucleobase is any nucleobase that can base pair with all of the four naturally occurring nucleobases without substantially affecting the melting behavior, recognition by intracellular enzymes or activity of the oligonucleotide duplex.
  • Some exemplary universal nucleobases include, but are not limited to, 2,4-difluorotoluene, nitropyrrolyl, nitroindolyl, 8-aza-7-deazaadenine, 4-fluoro-6-methylbenzimidazle, 4-methylbenzimidazle, 3-methyl isocarbostyrilyl, 5-methyl isocarbostyrilyl, 3-methyl-7-propynyl isocarbostyrilyl, 7-azaindolyl, 6-methyl-7-azaindolyl, imidizopyridinyl, 9-methyl-imidizopyridinyl, pyrrolopyrizinyl, isocarbostyrilyl, 7-propynyl
  • nucleobases include those disclosed in U.S. Pat. No. 3,687,808; those disclosed in International Application No. PCT/US09/038425, filed Mar. 26, 2009; those disclosed in the Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. I., ed. John Wiley & Sons, 1990; those disclosed by English et al., Angewandte Chemie, International Edition, 1991, 30, 613; those disclosed in Modified Nucleosides in Biochemistry, Biotechnology and Medicine, Herdewijin, P. Ed. Wiley-VCH, 2008; and those disclosed by Sanghvi, Y. S., Chapter 15, dsRNA Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., Eds., CRC Press, 1993. Contents of all of the above are herein incorporated by reference.
  • a modified nucleobase is a nucleobase that is fairly similar in structure to the parent nucleobase, such as for example a 7-deaza purine, a 5-methyl cytosine, or a G-clamp.
  • nucleobase mimetic include more complicated structures, such as for example a tricyclic phenoxazine nucleobase mimetic. Methods for preparation of the above noted modified nucleobases are well known to those skilled in the art.
  • the REVERSIR compound comprises at least one (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more) G-clamp nucleobase selected from the following:
  • n 0, 1, 2, 3, 4, 5 or 6.
  • Oligomeric compounds provided herein can comprise one or more monomer, including a nucleoside or nucleotide, having a modified sugar moiety.
  • the furanosyl sugar ring of a nucleoside can be modified in a number of ways including, but not limited to, addition of a substituent group, bridging of two non-geminal ring atoms to form a locked nucleic acid or bicyclic nucleic acid.
  • oligomeric compounds comprise one or more monomers that are LNA.
  • x 0, 1, or 2;
  • n 1, 2, 3, or 4;
  • each R1 and R2 is, independently, H, a protecting group, hydroxyl, C1-C12 alkyl, substituted C1-C12 alkyl, C2-C12 alkenyl, substituted C2-C12 alkenyl, C2-C12 alkynyl, substituted C2-C12 alkynyl, C5-C20 aryl, substituted C5-C20 aryl, heterocycle radical, substituted heterocycle radical, heteroaryl, substituted heteroaryl, C5-C7 alicyclic radical, substituted C5-C7 alicyclic radical, halogen, OJ1, NJ1J2, SJ1, N3, COOJ1 acyl (C( ⁇ O)—H), substituted acyl, CN, sulfonyl (S( ⁇ O)2-J1), or sulfoxyl (S( ⁇ O)-J1); and
  • each J1 and J2 is, independently, H, C1-C12 alkyl, substituted C1-C12 alkyl, C2-C12 alkenyl, substituted C2-C12 alkenyl, C2-C12 alkynyl, substituted C2-C12 alkynyl, C5-C20 aryl, substituted C5-C20 aryl, acyl (C( ⁇ O)—H), substituted acyl, a heterocycle radical, a substituted heterocycle radical, C1-C12 aminoalkyl, substituted C1-C12 aminoalkyl or a protecting group.
  • each of the linkers of the LNA compounds is, independently, —[C(R1)(R2)]n-, —[C(R1)(R2)]n-O—, —C(R1R2)-N(R1)-O— or —C(R1R2)-O—N(R1)-.
  • each of said linkers is, independently, 4′-CH 2 -2′, 4′-(CH 2 ) 2 -2′, 4′-(CH 2 ) 3 -2′, 4′-CH 2 —O-2′, 4′-(CH 2 ) 2 —O-2′, 4′-CH 2 -O—N(R1)-2′ and 4′-CH 2 —N(R1)-O-2′- wherein each R1 is, independently, H, a protecting group or C1-C12 alkyl.
  • LNAs in which the 2′-hydroxyl group of the ribosyl sugar ring is linked to the 4′ carbon atom of the sugar ring thereby forming a methyleneoxy (4′-CH 2 —O-2′) linkage to form the bicyclic sugar moiety
  • 4′-CH 2 —O-2′ linkage to form the bicyclic sugar moiety
  • the linkage can be a methylene (—CH 2 —) group bridging the 2′ oxygen atom and the 4′ carbon atom, for which the term methyleneoxy (4′-CH 2 —O-2′) LNA is used for the bicyclic moiety; in the case of an ethylene group in this position, the term ethyleneoxy (4′-CH 2 CH 2 —O-2′) LNA is used (Singh et al., Chem. Commun., 1998, 4, 455-456: Morita et al., Bioorganic Medicinal Chemistry, 2003, 11, 2211-2226).
  • Potent and nontoxic antisense oligonucleotides comprising BNAs have been described (Wahlestedt et al., Proc. Natl. Acad. Sci. U.S.A., 2000, 97, 5633-5638).
  • alpha-L-methyleneoxy (4′-CH 2 —O-2′) LNA which has been shown to have superior stability against a 3′-exonuclease.
  • the alpha-L-methyleneoxy (4′-CH 2 —O-2′) LNA's were incorporated into antisense gapmers and chimeras that showed potent antisense activity (Frieden et al., Nucleic Acids Research, 2003, 21, 6365-6372).
  • 2′-amino-LNA a novel comformationally restricted high-affinity oligonucleotide analog has been described in the art (Singh et al., J. Org. Chem., 1998, 63, 10035-10039).
  • 2′-Amino- and 2′-methylamino-LNA's have been prepared and the thermal stability of their duplexes with complementary RNA and DNA strands has been previously reported.
  • Modified sugar moieties are well known and can be used to alter, typically increase, the affinity of the antisense compound for its target and/or increase nuclease resistance.
  • a representative list of preferred modified sugars includes but is not limited to bicyclic modified sugars, including methyleneoxy (4′-CH 2 —O-2′) LNA and ethyleneoxy (4′-(CH 2 ) 2 —O-2′ bridge) ENA; substituted sugars, especially 2′-substituted sugars having a 2′-F, 2′-OCH 3 or a 2′-O(CH 2 ) 2 —OCH 3 substituent group; and 4′-thio modified sugars. Sugars can also be replaced with sugar mimetic groups among others.
  • OR polyethylene
  • a modification at the 2′ position can be present in the arabinose configuration
  • the term “arabinose configuration” refers to the placement of a substituent on the C2′ of ribose in the same configuration as the 2′-OH is in the arabinose.
  • the sugar can comprise two different modifications at the same carbon in the sugar, e.g., gem modification.
  • the sugar group can also contain one or more carbons that possess the opposite stereochemical configuration than that of the corresponding carbon in ribose.
  • an oligomeric compound can include one or more monomers containing e.g., arabinose, as the sugar.
  • the monomer can have an alpha linkage at the 1′ position on the sugar, e.g., alpha-nucleosides.
  • the monomer can also have the opposite configuration at the 4′-position, e.g., C5′ and H4′ or substituents replacing them are interchanged with each other. When the C5′ and H4′ or substituents replacing them are interchanged with each other, the sugar is said to be modified at the 4′ position.
  • Oligomeric compounds can also include abasic sugars, i.e., a sugar which lack a nucleobase at C-1′ or has other chemical groups in place of a nucleobase at C1′. See for example U.S. Pat. No. 5,998,203, content of which is herein incorporated in its entirety. These abasic sugars can also be further containing modifications at one or more of the constituent sugar atoms. Oligomeric compounds can also contain one or more sugars that are the L isomer, e.g. L-nucleosides. Modification to the sugar group can also include replacement of the 4′-O with a sulfur, optionally substituted nitrogen or CH 2 group. In some embodiments, linkage between C1′ and nucleobase is in a configuration.
  • abasic sugars i.e., a sugar which lack a nucleobase at C-1′ or has other chemical groups in place of a nucleobase at C1′. See for example U.S. Pat. No.
  • Sugar modifications can also include acyclic nucleotides, wherein a C—C bonds between ribose carbons (e.g., C1′-C2′, C2′-C3′, C3′-C4′, C4′-O4′, C1′-O4′) is absent and/or at least one of ribose carbons or oxygen (e.g., C1′, C2′, C3′, C4′ or O4′) are independently or in combination absent from the nucleotide.
  • acyclic nucleotide is
  • R 1 and R 2 independently are H, halogen, OR 3 , or alkyl;
  • R 3 is H, alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar).
  • xylose configuration refers to the placement of a substituent on the C3′ of ribose in the same configuration as the 3′-OH is in the xylose sugar.
  • the hydrogen attached to C4′ and/or C1′ can be replaced by a straight- or branched-optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, wherein backbone of the alkyl, alkenyl and alkynyl can contain one or more of O, S, S(O), SO 2 , N(R′), C(O), N(R′)C(O)O, OC(O)N(R′), CH(Z′), phosphorous containing linkage, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclic or optionally substituted cycloalkyl, where R′ is hydrogen, acyl or optionally substituted aliphatic, Z′ is selected from the group consisting of OR 11 , COR 11 , CO 2 R 11 ,
  • NR 21 R 31 CONR 21 R 31 , CON(H)NR 21 R 31 , ONR 21 R 31 , CON(H)N ⁇ CR 41 R 51 , N(R 21 )C( ⁇ NR 31 )NR 21 R 31 , N(R 21 )C(O)NR 21 R 31 , N(R 21 )C(S)NR 21 R 31 , OC(O)NR 21 R 31 , SC(O)NR 21 R 31 , N(R 21 )C(S)OR 11 , N(R 21 )C(O)OR 11 , N(R 21 )C(O)SR 11 , N(R 21 )N ⁇ CR 41 R 51 , ON ⁇ CR 41 R 51 , SO 2 R 11 , SOR 11 , SR 11 , and substituted or unsubstituted heterocyclic; R 21 and R 31 for each occurrence are independently hydrogen, acyl, unsubstituted or substituted aliphatic, aryl, heteroaryl, heterocyclic, OR 11
  • C4′ and C5′ together form an optionally substituted heterocyclic, preferably comprising at least one —PX(Y)—, wherein X is H, OH, OM, SH, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkylthio, optionally substituted alkylamino or optionally substituted dialkylamino, where M is independently for each occurrence an alki metal or transition metal with an overall charge of +1; and Y is O, S, or NR′, where R′ is hydrogen, optionally substituted aliphatic.
  • this modification is at the 5 terminal of the oligonucleotide.
  • each of the substituted groups is, independently, mono or poly substituted with optionally protected substituent groups independently selected from halogen, oxo, hydroxyl, OJ1, NJ1J2, SJ1, N3, OC( ⁇ X)J1, OC( ⁇ X)NJ1J2, NJ3C( ⁇ X)NJ1J2 and CN, wherein each J1, J2 and J3 is, independently, H or C1-C6 alkyl, and X is O, S or NJ1.
  • each of the substituted groups is, independently, mono or poly substituted with substituent groups independently selected from halogen, oxo, hydroxyl, OJ1, NJ1J2, SJ1, N3, OC( ⁇ X)J1, and NJ3C( ⁇ X)NJ1J2, wherein each J1, J2 and J3 is, independently, H, C1-C6 alkyl, or substituted C1-C6 alkyl and X is O or NJ1.
  • the Z group is C1-C6 alkyl substituted with one or more Xx, wherein each Xx is independently OJ1, NJ1J2, SJ1, N3, OC( ⁇ X)J1, OC( ⁇ X)NJ1J2, NJ3C( ⁇ X)NJ1J2 or CN; wherein each J1, J2 and J3 is, independently, H or C1-C6 alkyl, and X is O, S or NJ1.
  • the Z group is C1-C6 alkyl substituted with one or more Xx, wherein each Xx is independently halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH3O—), substituted alkoxy or azido.
  • the Z group is —CH2Xx, wherein Xx is OJ1, NJ1J2, SJ1, N3, OC( ⁇ X)J1, OC( ⁇ X)NJ1J2, NJ3C( ⁇ X)NJ1J2 or CN; wherein each J1, J2 and J3 is, independently, H or C1-C6 alkyl, and X is O, S or NJ1.
  • the Z group is —CH2Xx, wherein Xx is halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH3O—) or azido.
  • the Z group is in the (R)-configuration:
  • the Z group is in the (S)-configuration:
  • each T1 and T2 is a hydroxyl protecting group.
  • hydroxyl protecting groups includes benzyl, benzoyl, 2,6-dichlorobenzyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, mesylate, tosylate, dimethoxytrityl (DMT), 9-phenylxanthine-9-yl (Pixyl) and 9-(p-methoxyphenyl)xanthine-9-yl (MOX).
  • T1 is a hydroxyl protecting group selected from acetyl, benzyl, t-butyldimethylsilyl, t-butyldiphenylsilyl and dimethoxytrityl wherein a more preferred hydroxyl protecting group is T1 is 4,4′-dimethoxytrityl.
  • T2 is a reactive phosphorus group wherein preferred reactive phosphorus groups include diisopropylcyanoethoxy phosphoramidite and H-phosphonate.
  • T1 is 4,4′-dimethoxytrityl and T2 is diisopropylcyanoethoxy phosphoramidite.
  • oligomeric compounds have at least one monomer of the formula:
  • each of the substituted groups is, independently, mono or poly substituted with optionally protected substituent groups independently selected from halogen, oxo, hydroxyl, OJ1, NJ1J2, SJ1, N3, OC( ⁇ X)J1, OC( ⁇ X)NJ1J2, NJ3C( ⁇ X)NJ1J2 and CN, wherein each J1, J2 and J3 is, independently, H or C1-C6 alkyl, and X is O, S or NJ1.
  • each of the substituted groups is, independently, mono or poly substituted with substituent groups independently selected from halogen, oxo, hydroxyl, OJ1, NJ1J2, SJ1, N3, OC( ⁇ X)J1, and NJ3C( ⁇ X)NJ1J2, wherein each J1, J2 and J3 is, independently, H or C1-C6 alkyl, and X is O or NJ1.
  • At least one Z is C1-C6 alkyl or substituted C1-C6 alkyl. In certain embodiments, each Z is, independently, C1-C6 alkyl or substituted C1-C6 alkyl. In certain embodiments, at least one Z is C1-C6 alkyl. In certain embodiments, each Z is, independently, C1-C6 alkyl. In certain embodiments, at least one Z is methyl. In certain embodiments, each Z is methyl. In certain embodiments, at least one Z is ethyl. In certain embodiments, each Z is ethyl. In certain embodiments, at least one Z is substituted C1-C6 alkyl.
  • each Z is, independently, substituted C1-C6 alkyl. In certain embodiments, at least one Z is substituted methyl. In certain embodiments, each Z is substituted methyl. In certain embodiments, at least one Z is substituted ethyl. In certain embodiments, each Z is substituted ethyl.
  • At least one substituent group is C1-C6 alkoxy (e.g., at least one Z is C1-C6 alkyl substituted with one or more C1-C6 alkoxy).
  • each substituent group is, independently, C1-C6 alkoxy (e.g., each Z is, independently, C1-C6 alkyl substituted with one or more C1-C6 alkoxy).
  • At least one C1-C6 alkoxy substituent group is CH3O— (e.g., at least one Z is CH 3 OCH 2 —). In another embodiment, each C1-C6 alkoxy substituent group is CH 3 O— (e.g., each Z is CH 3 OCH 2 —).
  • At least one substituent group is halogen (e.g., at least one Z is C1-C6 alkyl substituted with one or more halogen).
  • each substituent group is, independently, halogen (e.g., each Z is, independently, C1-C6 alkyl substituted with one or more halogen).
  • at least one halogen substituent group is fluoro (e.g., at least one Z is CH 2 FCH 2 —, CHF 2 CH 2 — or CF 3 CH 2 —).
  • each halo substituent group is fluoro (e.g., each Z is, independently, CH 2 FCH 2 —, CHF 2 CH 2 — or CF 3 CH 2 —).
  • At least one substituent group is hydroxyl (e.g., at least one Z is C1-C6 alkyl substituted with one or more hydroxyl). In certain embodiments, each substituent group is, independently, hydroxyl (e.g., each Z is, independently, C1-C6 alkyl substituted with one or more hydroxyl). In certain embodiments, at least one Z is HOCH 2 —. In another embodiment, each Z is HOCH 2 —.
  • At least one Z is CH 3 —, CH 3 CH 2 —, CH 2 OCH 3 —, CH 2 F— or HOCH 2 —.
  • each Z is, independently, CH 3 —, CH 3 CH 2 —, CH 2 OCH 3 —, CH 2 F— or HOCH 2 —.
  • At least one Z group is C1-C6 alkyl substituted with one or more Xx, wherein each Xx is, independently, OJ1, NJ1J2, SJ1, N3, OC( ⁇ X)J1, OC( ⁇ X)NJ1J2, NJ3C( ⁇ X)NJ1J2 or CN; wherein each J1, J2 and J3 is, independently, H or C1-C6 alkyl, and X is O, S or NJ1.
  • At least one Z group is C1-C6 alkyl substituted with one or more Xx, wherein each Xx is, independently, halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH3O—) or azido.
  • each Z group is, independently, C1-C6 alkyl substituted with one or more Xx, wherein each Xx is independently OJ1, NJ1J2, SJ1, N3, OC( ⁇ X)J1, OC( ⁇ X)NJ1J2, NJ3C( ⁇ X)NJ1J2 or CN; wherein each J1, J2 and J3 is, independently, H or C1-C6 alkyl, and X is O, S or NJ1.
  • each Z group is, independently, C1-C6 alkyl substituted with one or more Xx, wherein each Xx is independently halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH3O—) or azido.
  • Xx is independently halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH3O—) or azido.
  • At least one Z group is —CH 2 Xx, wherein Xx is OJ1, NJ1J2, SJ1, N3, OC( ⁇ X)J1, OC( ⁇ X)NJ1J2, NJ3C( ⁇ X)NJ1J2 or CN; wherein each J1, J2 and J3 is, independently, H or C1-C6 alkyl, and X is O, S or NJ1
  • at least one Z group is —CH 2 Xx, wherein Xx is halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH 3 O—) or azido.
  • each Z group is, independently, —CH 2 Xx, wherein each Xx is, independently, OJ1, NJ1J2, SJ1, N3, OC( ⁇ X)J1, OC( ⁇ X)NJ1J2, NJ3C( ⁇ X)NJ1J2 or CN; wherein each J1, J2 and J3 is, independently, H or C1-C6 alkyl, and X is O, S or NJ1.
  • each Z group is, independently, —CH 2 Xx, wherein each Xx is, independently, halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH 3 O—) or azido.
  • At least one Z is CH 3 —. In another embodiment, each Z is, CH 3 —.
  • the Z group of at least one monomer is in the (R)-configuration represented by the formula:
  • the Z group of each monomer of the formula is in the (R)-configuration.
  • the Z group of at least one monomer is in the (S)-configuration represented by the formula:
  • the Z group of each monomer of the formula is in the (S)-configuration.
  • T3 is H or a hydroxyl protecting group. In certain embodiments, T4 is H or a hydroxyl protecting group. In a further embodiment T3 is an internucleoside linking group attached to a nucleoside, a nucleotide or a monomeric subunit. In certain embodiments, T4 is an internucleoside linking group attached to a nucleoside, a nucleotide or a monomeric subunit. In certain embodiments, T3 is an internucleoside linking group attached to an oligonucleoside or an oligonucleotide. In certain embodiments, T4 is an internucleoside linking group attached to an oligonucleoside or an oligonucleotide.
  • T3 is an internucleoside linking group attached to an oligomeric compound.
  • T4 is an internucleoside linking group attached to an oligomeric compound.
  • at least one of T3 and T4 comprises an internucleoside linking group selected from phosphodiester or phosphorothioate.
  • oligomeric compounds have at least one region of at least two contiguous monomers of the formula:
  • LNAs include, but are not limited to, (A) ⁇ -L-Methyleneoxy (4′-CH2-O-2′) LNA, (B) ⁇ -D-Methyleneoxy (4′-CH2-O-2′) LNA, (C) Ethyleneoxy (4′-(CH2)2-O-2′) LNA, (D) Aminooxy (4′-CH2-O—N(R)-2′) LNA and (E) Oxyamino (4′-CH2-N(R)—O-2′) LNA, as depicted below:
  • the oligomeric compound comprises at least two regions of at least two contiguous monomers of the above formula. In certain embodiments, the oligomeric compound comprises a gapped oligomeric compound. In certain embodiments, the oligomeric compound comprises at least one region of from about 8 to about 14 contiguous ⁇ -D-2′-deoxyribofuranosyl nucleosides. In certain embodiments, the oligomeric compound comprises at least one region of from about 9 to about 12 contiguous ⁇ -D-2′-deoxyribofuranosyl nucleosides.
  • the oligomeric compound comprises at least one (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more) S-cEt monomer of the formula:
  • Bx IS heterocyclic base moiety
  • the oligomeric compound e.g. REVERSIR compound
  • B is A-001 to A-026 and n is 0-6 (e.g., 0, 1, 2, 3, 4, 5 or 6).
  • monomers include sugar mimetics.
  • a mimetic is used in place of the sugar or sugar-internucleoside linkage combination, and the nucleobase is maintained for hybridization to a selected target.
  • Representative examples of a sugar mimetics include, but are not limited to, cyclohexenyl or morpholino.
  • Representative examples of a mimetic for a sugar-internucleoside linkage combination include, but are not limited to, peptide nucleic acids (PNA) and morpholino groups linked by uncharged achiral linkages. In some instances a mimetic is used in place of the nucleobase.
  • nucleobase mimetics are well known in the art and include, but are not limited to, tricyclic phenoxazine analogs and universal bases (Berger et al., Nuc Acid Res. 2000, 28:2911-14, incorporated herein by reference). Methods of synthesis of sugar, nucleoside and nucleobase mimetics are well known to those skilled in the art.
  • the REVERSIR compound comprises at least one monomer that is LNA and at least one G-clamp nucleobase.
  • the REVERSIR compound can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more monomers that are LNA 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more G-clamp nucleobases.
  • the REVERSIR compound comprises at least one (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more) peptide nucleic acid monomer.
  • the REVERSIR compound comprises at least one monomer that is LNA and at least one monomer that is PNA.
  • the REVERSIR compound can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more monomers that are LNA 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more monomers that are PNA.
  • the REVERSIR compound comprises at least one PNA monomer and at least one G-clamp nucleobase.
  • the REVERSIR compound can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more PNA monomers and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more G-clamp nucleobases.
  • the REVERSIR compound comprises at least one LNA monomer, at least one PNA monomer and at least one G-clamp nucleobase.
  • the REVERSIR compound can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more LNA monomers; 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more PNA monomers and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more G-clamp nucleobases.
  • linking groups that link monomers (including, but not limited to, modified and unmodified nucleosides and nucleotides) together, thereby forming an oligomeric compound.
  • Such linking groups are also referred to as intersugar linkage.
  • the two main classes of linking groups are defined by the presence or absence of a phosphorus atom.
  • Representative phosphorus containing linkages include, but are not limited to, phosphodiesters (P ⁇ O), phosphotriesters, methylphosphonates, phosphoramidate, and phosphorothioates (P ⁇ S).
  • Non-phosphorus containing linking groups include, but are not limited to, methylenemethylimino (—CH2-N(CH3)-O—CH2-), thiodiester (—O—C(O)—S—), thionocarbamate (—O—C(O)(NH)—S—); siloxane (—O—Si(H)2-O—); and N,N′-dimethylhydrazine (—CH2-N(CH3)-N(CH3)-).
  • Oligomeric compounds having non-phosphorus linking groups are referred to as oligonucleosides. Modified linkages, compared to natural phosphodiester linkages, can be used to alter, typically increase, nuclease resistance of the oligomeric compound.
  • linkages having a chiral atom can be prepared a racemic mixtures, as separate enantomers.
  • Representative chiral linkages include, but are not limited to, alkylphosphonates and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing linkages are well known to those skilled in the art.
  • the phosphate group in the linking group can be modified by replacing one of the oxygens with a different substituent.
  • One result of this modification can be increased resistance of the oligonucleotide to nucleolytic breakdown.
  • modified phosphate groups include phosphorothioate, phosphoroselenates, borano phosphates, borano phosphate esters, hydrogen phosphonates, phosphoroamidates, alkyl or aryl phosphonates and phosphotriesters.
  • one of the non-bridging phosphate oxygen atoms in the linkage can be replaced by any of the following: S, Se, BR 3 (R is hydrogen, alkyl, aryl), C (i.e.
  • the phosphorous atom in an unmodified phosphate group is achiral. However, replacement of one of the non-bridging oxygens with one of the above atoms or groups of atoms renders the phosphorous atom chiral; in other words a phosphorous atom in a phosphate group modified in this way is a stereogenic center.
  • the stereogenic phosphorous atom can possess either the “R” configuration (herein Rp) or the “S” configuration (herein Sp).
  • Phosphorodithioates have both non-bridging oxygens replaced by sulfur.
  • the phosphorus center in the phosphorodithioates is achiral which precludes the formation of oligonucleotides diastereomers.
  • modifications to both non-bridging oxygens, which eliminate the chiral center, e.g. phosphorodithioate formation can be desirable in that they cannot produce diastereomer mixtures.
  • the non-bridging oxygens can be independently any one of O, S, Se, B, C, H, N, or OR (R is alkyl or aryl).
  • the phosphate linker can also be modified by replacement of bridging oxygen, (i.e. oxygen that links the phosphate to the sugar of the monomer), with nitrogen (bridged phosphoroamidates), sulfur (bridged phosphorothioates) and carbon (bridged methylenephosphonates).
  • bridging oxygen i.e. oxygen that links the phosphate to the sugar of the monomer
  • nitrogen bridged phosphoroamidates
  • sulfur bridged phosphorothioates
  • carbon bridged methylenephosphonates
  • Modified phosphate linkages where at least one of the oxygen linked to the phosphate has been replaced or the phosphate group has been replaced by a non-phosphorous group are also referred to as “non-phosphodiester intersugar linkage” or “non-phosphodiester linker.”
  • the phosphate group can be replaced by non-phosphorus containing connectors, e.g. dephospho linkers.
  • Dephospho linkers are also referred to as non-phosphodiester linkers herein. While not wishing to be bound by theory, it is believed that since the charged phosphodiester group is the reaction center in nucleolytic degradation, its replacement with neutral structural mimics should impart enhanced nuclease stability. Again, while not wishing to be bound by theory, it can be desirable, in some embodiment, to introduce alterations in which the charged phosphate group is replaced by a neutral moiety.
  • moieties which can replace the phosphate group include, but are not limited to, amides (for example amide-3 (3′-CH 2 —C( ⁇ O)—N(H)-5′) and amide-4 (3′-CH 2 —N(H)—C( ⁇ O)-5′)), hydroxylamino, siloxane (dialkylsiloxxane), carboxamide, carbonate, carboxymethyl, carbamate, carboxylate ester, thioether, ethylene oxide linker, sulfide, sulfonate, sulfonamide, sulfonate ester, thioformacetal (3′-S—CH 2 —O-5′), formacetal (3′-O—CH 2 —O-5′), oxime, methyleneimino, methykenecarbonylamino, methylenemethylimino (MMI, 3′-CH 2 —N(CH 3 )—O-5′), methylenehydrazo, methylenedimethylhydr
  • Preferred embodiments include methylenemethylimino (MMI), methylenecarbonylamino, amides, carbamate and ethylene oxide linker.
  • a modification of a non-bridging oxygen can necessitate modification of 2′-OH, e.g., a modification that does not participate in cleavage of the neighboring intersugar linkage, e.g., arabinose sugar, 2′-O-alkyl, 2′-F, LNA and ENA.
  • Preferred non-phosphodiester intersugar linkages include phosphorothioates, phosphorothioates with an at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% 95% or more enantiomeric excess of Sp isomer, phosphorothioates with an at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% 95% or more enantiomeric excess of Rp isomer, phosphorodithioates, phosphotriesters, aminoalkylphosphotrioesters, alkyl-phosphonaters (e.g., methyl-phosphonate), selenophosphates, phosphoramidates (e.g., N-alkylphosphoramidate), and boranophosphonates.
  • phosphorodithioates phosphotriesters, aminoalkylphosphotrioesters, alkyl-phosphonaters (e.g., methyl-phosphonate), sel
  • the oligomeric compound e.g., REVERSIR compound or siRNA
  • the oligomeric compound, e.g., REVERSIR compound or siRNA comprises at least one (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more and upto including all) phosphorothioate linkages.
  • all internucleoside linkages in the reverser compounds are phosphorothioate (PS) internucleoside linkages.
  • the REVERSIR compounds comprise at least one phosphorothioate (PS) internucleoside linkage, but not all internucleoside linkages in said REVERSIR compound are a phosphorothioate linkage. In other words, in some embodiments, less than 100% (e.g., 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40% or fewer) of the internucleoside linkages are phosphorothioate linkages.
  • the REVERSIR compounds comprise at least one phosphorothioate internucleoside linkage and at least one internucleoside linkage that is not a phosphorothioate.
  • the REVERSIR compounds comprise at least one phosphorothioate internucleoside linkage and at least one phosphodiester internucleoside linkage.
  • the non-phosphorothioate internucleoside linkage is between the terminus and the penultimate nucleosides.
  • the internucleoside linkage between the nucleobase at the 3′-terminus of the REVERSIR compound and the rest of the REVERSIR compound is a phosphodiester linkage. In some embodiments, all internucleoside linkages in the reverser compounds are phosphorothioate except for the internucleoside linkage between the nucleoside at the 3′-terminus of the REVERSIR compound and the rest of the REVERSIR compound.
  • Oligomeric compounds can also be constructed wherein the phosphate linker and the sugar are replaced by nuclease resistant nucleoside or nucleotide surrogates. While not wishing to be bound by theory, it is believed that the absence of a repetitively charged backbone diminishes binding to proteins that recognize polyanions (e.g. nucleases). Again, while not wishing to be bound by theory, it can be desirable in some embodiment, to introduce alterations in which the bases are tethered by a neutral surrogate backbone.
  • Examples include the morpholino, cyclobutyl, pyrrolidine, peptide nucleic acid (PNA), aminoethylglycyl PNA (aegPNA) and backnone-extended pyrrolidine PNA (bepPNA) nucleoside surrogates.
  • PNA peptide nucleic acid
  • aegPNA aminoethylglycyl PNA
  • bepPNA backnone-extended pyrrolidine PNA
  • the oligomeric compounds 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), such as for sugar anomers, or as (D) or (L) such as for amino acids et al. Included in the antisense compounds provided herein are all such possible isomers, as well as their racemic and optically pure forms.
  • Ends of the oligomeric compound can be modified. Such modifications can be at one end or both ends.
  • the 3′ and/or 5′ ends of an oligonucleotide can be conjugated to other functional molecular entities such as labeling moieties, e.g., fluorophores (e.g., pyrene, TAMRA, fluorescein, Cy3 or Cy5 dyes) or protecting groups (based e.g., on sulfur, silicon, boron or ester).
  • the functional molecular entities can be attached to the sugar through a phosphate group and/or a linker.
  • the terminal atom of the linker can connect to or replace the linking atom of the phosphate group or the C-3′ or C-5′ O, N, S or C group of the sugar.
  • the linker can connect to or replace the terminal atom of a nucleotide surrogate (e.g., PNAs).
  • this array can substitute for a hairpin loop in a hairpin-type oligomeric compound.
  • Terminal modifications useful for modulating activity include modification of the 5′ end of oligomeric compound with phosphate or phosphate analogs.
  • the 5′end of oligomeric compound is phosphorylated or includes a phosphoryl analog.
  • Exemplary 5′-phosphate modifications include those which are compatible with RISC mediated gene silencing. Modifications at the 5′-terminal end can also be useful in stimulating or inhibiting the immune system of a subject.
  • the 5′-end of the oligomeric compound comprises the modification
  • W, X and Y are each independently selected from the group consisting of O, OR (R is hydrogen, alkyl, aryl), S, Se, BR 3 (R is hydrogen, alkyl, aryl), BH 3 ⁇ , C (i.e. an alkyl group, an aryl group, etc. . . .
  • a and Z are each independently for each occurrence absent, O, S, CH 2 , NR (R is hydrogen, alkyl, aryl), or optionally substituted alkylene, wherein backbone of the alkylene can comprise one or more of O, S, SS and NR (R is hydrogen, alkyl, aryl) internally and/or at the end; and n is 0-2. In some embodiments, n is 1 or 2. It is understood that A is replacing the oxygen linked to 5′ carbon of sugar.
  • W and Y together with the P to which they are attached can form an optionally substituted 5-8 membered heterocyclic, wherein W an Y are each independently O, S, NR′ or alkylene.
  • the heterocyclic is substituted with an aryl or heteroaryl.
  • one or both hydrogen on C5′ of the 5′-terminal nucleotides are replaced with a halogen, e.g., F.
  • Exemplary 5′-modificaitons include, but are not limited to, 5′-monophosphate ((HO) 2 (O)P—O-5′); 5′-diphosphate ((HO) 2 (O)P—O—P(HO)(O)—O-5′); 5′-triphosphate ((HO) 2 (O)P—O—(HO)(O)P—O—P(HO)(O)—O-5′); 5′-monothiophosphate (phosphorothioate; (HO)2(S)P—O-5′); 5′-monodithiophosphate (phosphorodithioate; (HO)(HS)(S)P—O-5′), 5′-phosphorothiolate ((HO)2(O)P—S-5′); 5′-alpha-thiotriphosphate; 5′-beta-thiotriphosphate; 5′-gamma-thiotriphosphate; 5′-phosphoramidates ((HO) 2 (O)P—NH
  • exemplary 5′-modifications include where Z is optionally substituted alkyl at least once, e.g., ((HO) 2 (X)P—O[—(CH 2 ) a —O—P(X)(OH)—O] b -5′, ((HO)2(X)P—O[CH 2 ) a —P(X)(OH)—O] b — 5′, ((HO)2(X)P—[—(CH 2 ) a —O—P(X)(OH)—O] b -5′; dialkyl terminal phosphates and phosphate mimics: HO[—(CH 2 ) a —O—P(X)(OH)—O] b -5′, H 2 N[—(CH 2 ) a —O—P(X)(OH)—O] b -5′, H[CH 2 ) a —O—P(X)(OH)—O] b -5′, Me 2 N
  • Terminal modifications can also be useful for monitoring distribution, and in such cases the preferred groups to be added include fluorophores, e.g., fluorescein or an Alexa dye, e.g., Alexa 488. Terminal modifications can also be useful for enhancing uptake, useful modifications for this include targeting ligands. Terminal modifications can also be useful for cross-linking an oligonucleotide to another moiety; modifications useful for this include mitomycin C, psoralen, and derivatives thereof.
  • fluorophores e.g., fluorescein or an Alexa dye, e.g., Alexa 488.
  • Terminal modifications can also be useful for enhancing uptake, useful modifications for this include targeting ligands. Terminal modifications can also be useful for cross-linking an oligonucleotide to another moiety; modifications useful for this include mitomycin C, psoralen, and derivatives thereof.
  • oligomeric compounds having reactive phosphorus groups useful for forming linkages including for example phosphodiester and phosphorothioate internucleoside linkages.
  • Methods of preparation and/or purification of precursors or oligomeric compounds are not a limitation of the compositions or methods provided herein.
  • Methods for synthesis and purification of oligomeric compounds including DNA, RNA, oligonucleotides, oligonucleosides, and antisense compounds are well known to those skilled in the art.
  • oligomeric compounds comprise a plurality of monomeric subunits linked together by linking groups.
  • Non-limiting examples of oligomeric compounds include primers, probes, antisense compounds, antisense oligonucleotides, external guide sequence (EGS) oligonucleotides, alternate splicers, and siRNAs.
  • these compounds can be introduced in the form of single-stranded, double-stranded, circular, branched or hairpins and can contain structural elements such as internal or terminal bulges or loops.
  • Oligomeric double-stranded compounds can be two strands hybridized to form double-stranded compounds or a single strand with sufficient self-complementarity to allow for hybridization and formation of a fully or partially double-stranded compound.
  • the present invention provides chimeric oligomeric compounds.
  • chimeric oligomeric compounds are chimeric oligonucleotides.
  • the chimeric oligonucleotides comprise differently modified nucleotides.
  • chimeric oligonucleotides are mixed-backbone antisense oligonucleotides.
  • a chimeric oligomeric compound will have modified nucleosides that can be in isolated positions or grouped together in regions that will define a particular motif. Any combination of modifications and/or mimetic groups can comprise a chimeric oligomeric compound as described herein.
  • chimeric oligomeric compounds typically comprise at least one region modified so as to confer increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid.
  • an additional region of the oligomeric compound may serve as a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids.
  • chimeric oligomeric compounds are gapmers.
  • a mixed-backbone oligomeric compound has one type of internucleotide linkages in one or both wings and a different type of internucleoside linkages in the gap.
  • the mixed-backbone oligonucleotide has phosphodiester linkages in the wings and phosphorothioate linkages in the gap.
  • the internucleoside linkages in a wing is different from the internucleoside linkages in the gap, the internucleoside linkage bridging that wing and the gap is the same as the internucleoside linkage in the wing.
  • the internucleoside linkage bridging that wing and the gap is the same as the internucleoside linkage in the gap.
  • the present invention provides oligomeric compounds, including siRNAs and REVERSIR compounds of any of a variety of ranges of lengths.
  • the invention provides oligomeric compounds consisting of X-Y linked oligonucleosides, where 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 comprising: 8-9, 8-10, 8-11, 8-12, 8-13, 8-14, 8-15, 8-16, 8-17, 8-18, 8-19, 8-20, 8-21, 8-22, 8-23, 8-24, 8-25, 8-26, 8-27, 8-28, 8-29, 8-30, 9-10, 9-11, 9-12, 9-13, 9-14, 9-15, 9-16, 9-17, 9-18, 9-19, 9-20, 9-21, 9-22, 9-23, 9-24, 9-25, 9-26, 9-27, 9-28, 9-29, 9-30, 10-11, 10-12, 10-13, 10-14, 10-15, 10-16, 10-17, 10-18, 10-19, 10-20, 10-21, 10-22, 10-23, 10-24, 10-25, 10-26, 10-27, 10-28, 10-29, 10-30, 11-12, 11-13, 11-14, 11-15, 11-16, 11-17, 11-18, 11-19, 11-20, 11-21, 10-22, 10-23, 10-24, 10-25, 10-26,
  • REVERSIR compounds can be of any length.
  • the REVERSIR compound is a modified oligonucleotide consisting of 6-30 nucleotides.
  • the REVERSIR compound can consist of 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 linked nucleobases.
  • the REVERSIR compound consists of 6-17, 7-16 or 8-15 linked nucleobases.
  • REVERSIR compounds i.e., modified oligonucleotides, consisting of 15 or fewer nucleosides are particularly effective in reversing the siRNA activity.
  • the REVERSIR compound is a modified oligonucleotide consisting of 8-15 (e.g., 8, 9, 10, 11, 12, 13, 14 or 15) linked nucleosides.
  • the REVERSIR compound is a modified oligonucleotide consisting of 6-12, 7-11 or 8-10 linked nucleobases.
  • the REVERSIR compound consists of 8-9 linked nucleobases.
  • REVERSIR compounds are modified oligonucleotides that are substantially complementary to at least one strand of an siRNA.
  • REVERSIR compounds that are substantially complementary to the seed region of the antisense strand of the siRNA are particularly effective in reducing siRNA activity.
  • the REVERSIR compound is substantially complementary to nucleosides 2-8, 2-9, 2-10, 2-11, 2-12, 2-13, 2-14, 2-15 or 2-16 of the antisense strand of the siRNA.
  • substantially complementary in this context is meant a complementarity of at least 90%, preferably at least 95%, and more preferably complete complementarity.
  • oligomeric compounds are modified by covalent attachment of one or more conjugate groups.
  • conjugate groups modify one or more properties of the attached oligomeric compound including but not limited to pharmacodynamic, pharmacokinetic, 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 linking moiety or linking group to a parent compound such as an oligomeric compound.
  • 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.
  • Preferred conjugate groups amenable to the present invention include lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553); cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4, 1053); a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306; Manoharan et al., Bioorg. Med. Chem.
  • lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553); cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4, 1053); a thio
  • Ligands can include naturally occurring molecules, or recombinant or synthetic molecules.
  • exemplary ligands include, but are not limited to, polylysine (PLL), poly L-aspartic acid, poly L-glutamic acid, styrene-maleic acid anhydride copolymer, poly(L-lactide-co-glycolied) copolymer, divinyl ether-maleic anhydride copolymer, N-(2-hydroxypropyl)methacrylamide copolymer (HMPA), polyethylene glycol (PEG, e.g., PEG-2K, PEG-5K, PEG-10K, PEG-12K, PEG-15K, PEG-20K, PEG-40K), MPEG, [MPEG] 2 , polyvinyl alcohol (PVA), polyurethane, poly(2-ethylacryllic acid), N-is
  • psoralen mitomycin C
  • porphyrins e.g., TPPC4, texaphyrin, Sapphyrin
  • polycyclic aromatic hydrocarbons e.g., phenazine, dihydrophenazine
  • artificial endonucleases e.g., EDTA
  • lipophilic molecules e.g, steroids, bile acids, cholesterol, cholic acid, adamantane acetic acid, 1-pyrene butyric acid, dihydrotestosterone, 1,3-Bis-O(hexadecyl)glycerol, geranyloxyhexyl group, hexadecylglycerol, borneol, menthol, 1,3-propanediol, heptadecyl group, palmitic acid, myristic acid, O3-(oleoyl)lithocholic acid, O3-(oleoyl)cholenic acid, dimeth
  • biotin transport/absorption facilitators
  • transport/absorption facilitators e.g., naproxen, aspirin, vitamin E, folic acid
  • synthetic ribonucleases e.g., imidazole, bisimidazole, histamine, imidazole clusters, acridine-imidazole conjugates, Eu3+ complexes of tetraazamacrocycles), dinitrophenyl, HRP, AP, antibodies, hormones and hormone receptors, lectins, carbohydrates, multivalent carbohydrates, vitamins (e.g., vitamin A, vitamin E, vitamin K, vitamin B, e.g., folic acid, B12, riboflavin, biotin and pyridoxal), vitamin cofactors, lipopolysaccharide, an activator of p38 MAP kinase, an activator of NF- ⁇ B, taxon, vincristine, vinblastine, cytochalasin, nocodazole
  • Peptide and peptidomimetic ligands include those having naturally occurring or modified peptides, e.g., D or L peptides; ⁇ , ⁇ , or ⁇ peptides; N-methyl peptides; azapeptides; peptides having one or more amide, i.e., peptide, linkages replaced with one or more urea, thiourea, carbamate, or sulfonyl urea linkages; or cyclic peptides.
  • a peptidomimetic also referred to herein as an oligopeptidomimetic is a molecule capable of folding into a defined three-dimensional structure similar to a natural peptide.
  • the peptide or peptidomimetic ligand can be about 5-50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids long.
  • amphipathic peptides include, but are not limited to, cecropins, lycotoxins, paradaxins, buforin, CPF, bombinin-like peptide (BLP), cathelicidins, ceratotoxins, S. clava peptides, hagfish intestinal antimicrobial peptides (HFIAPs), magainines, brevinins-2, dermaseptins, melittins, pleurocidin, H 2 A peptides, Xenopus peptides, esculentinis-1, and caerins.
  • endosomolytic ligand refers to molecules having endosomolytic properties. Endosomolytic ligands promote the lysis of and/or transport of the composition of the invention, or its components, from the cellular compartments such as the endosome, lysosome, endoplasmic reticulum (ER), golgi apparatus, microtubule, peroxisome, or other vesicular bodies within the cell, to the cytoplasm of the cell.
  • Some exemplary endosomolytic ligands include, but are not limited to, imidazoles, poly or oligoimidazoles, linear or branched polyethyleneimines (PEIs), linear and brached polyamines, e.g.
  • spermine cationic linear and branched polyamines, polycarboxylates, polycations, masked oligo or poly cations or anions, acetals, polyacetals, ketals/polyketals, orthoesters, linear or branched polymers with masked or unmasked cationic or anionic charges, dendrimers with masked or unmasked cationic or anionic charges, polyanionic peptides, polyanionic peptidomimetics, pH-sensitive peptides, natural and synthetic fusogenic lipids, natural and synthetic cationic lipids.
  • Exemplary endosomolytic/fusogenic peptides include, but are not limited to,
  • AALEALAEALEALAEALEALAEAAAAGGC GALA
  • AALAEALAEALAEALAEALAEALAAAAGGC EALA
  • ALEALAEALEALAEA GLFEAIEGFIENGWEGMIWDYG (INF-7); GLFGAIAGFIENGWEGMIDGWYG (Inf HA-2); GLFEAIEGFIENGWEGMIDGWYGCGLFEAIEGFIENGWEGMID GWYGC (diINF-7); GLFEAIEGFIENGWEGMIDGGCGLFEAIEGFIENGWEGMIDGGC (diINF-3); GLFGALAEALAEALAEHLAEALAEALEALAAGGSC (GLF); GLFEAIEGFIENGWEGLAEALAEALEALAAGGSC (GALA-INF3); GLF EAI EGFI ENGW EGnI DG K GLF EAI EGFI ENGW EGnI DG (INF-5, n is norleucine); LFEALLELLESLWELLLEA (JTS-1); G
  • fusogenic lipids fuse with and consequently destabilize a membrane.
  • Fusogenic lipids usually have small head groups and unsaturated acyl chains.
  • Exemplary fusogenic lipids include, but are not limited to, 1,2-dileoyl-sn-3-phosphoethanolamine (DOPE), phosphatidylethanolamine (POPE), palmitoyloleoylphosphatidylcholine (POPC), (6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-tetraen-19-ol (Di-Lin), N-methyl(2,2-di((9Z,12Z)-octadeca-9,12-dienyl)-1,3-dioxolan-4-yl)methanamine (DLin-k-DMA) and N-methyl-2-(2,2-di((9Z,12Z)-octadeca-9,12-dienyl)-1,
  • Exemplary cell permeation peptides include, but are not limited to,
  • RQIKIWFQNRRMKWKK penetratin
  • GRKKRRQRRRPPQC Tat fragment 48-60
  • GALFLGWLGAAGSTMGAWSQPKKKRKV signal sequence based peptide
  • LLIILRRRIRKQAHAHSK PVEC
  • GWTLNSAGYLLKINLKALAALAKKIL transportan
  • KLALKLALKALKAALKLA amphiphilic model peptide
  • RRRRRRRRR Ar
  • KFFKFFKFFK Bactaserial cell wall permeating peptide
  • LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES LL-37
  • SWLSKTAKKLENSAKKRISEGIAIAIQGGPR cecropin P1
  • ACYCRIPACIAGERRYGTCIYQGRLWAFCC ⁇ -defensin
  • DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK ⁇ -defensin
  • NH 2 alkylamino, dialkylamino, heterocyclyl, arylamino, diaryl amino, heteroaryl amino, diheteroaryl amino, or amino acid
  • targeting ligand refers to any molecule that provides an enhanced affinity for a selected target, e.g., a cell, cell type, tissue, organ, region of the body, or a compartment, e.g., a cellular, tissue or organ compartment.
  • Some exemplary targeting ligands include, but are not limited to, antibodies, antigens, folates, receptor ligands, carbohydrates, aptamers, integrin receptor ligands, chemokine receptor ligands, transferrin, biotin, serotonin receptor ligands, PSMA, endothelin, GCPII, somatostatin, LDL and HDL ligands.
  • Carbohydrate based targeting ligands include, but are not limited to, D-galactose, multivalent galactose, N-acetyl-D-galactose (GalNAc), multivalent GalNAc, e.g. GalNAc2 and GalNAc3; D-mannose, multivalent mannose, multivalent lactose, N-acetyl-galactosamine, N-acetyl-gulucosamine, multivalent fucose, glycosylated polyaminoacids and lectins.
  • the term multivalent indicates that more than one monosaccharide unit is present. Such monosaccharide subunits can be linked to each other through glycosidic linkages or linked to a scaffold molecule.
  • PK modulating ligand and “PK modulator” refers to molecules which can modulate the pharmacokinetics of the composition of the invention.
  • Some exemplary PK modulator include, but are not limited to, lipophilic molecules, bile acids, sterols, phospholipid analogues, peptides, protein binding agents, vitamins, fatty acids, phenoxazine, aspirin, naproxen, ibuprofen, suprofen, ketoprofen, (S)-(+)-pranoprofen, carprofen, PEGs, biotin, and transthyretia-binding ligands (e.g., tetraiidothyroacetic acid, 2, 4, 6-triiodophenol and flufenamic acid).
  • Oligomeric compounds that comprise a number of phosphorothioate intersugar linkages are also known to bind to serum protein, thus short oligomeric compounds, e.g. oligonucleotides of comprising from about 5 to 30 nucleotides (e.g., 5 to 25 nucleotides, preferably 5 to 20 nucleotides, e.g., 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides), and that comprise a plurality of phosphorothioate linkages in the backbone are also amenable to the present invention as ligands (e.g. as PK modulating ligands).
  • ligands e.g. as PK modulating ligands
  • the PK modulating oligonucleotide can comprise at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more phosphorothioate and/or phosphorodithioate linkages. In some embodiments, all internucleotide linkages in PK modulating oligonucleotide are phosphorothioate and/or phosphorodithioates linkages.
  • aptamers that bind serum components e.g. serum proteins
  • Binding to serum components can be predicted from albumin binding assays, such as those described in Oravcova, et al., Journal of Chromatography B (1996), 677: 1-27.
  • the ligands can all have same properties, all have different properties or some ligands have the same properties while others have different properties.
  • a ligand can have targeting properties, have endosomolytic activity or have PK modulating properties.
  • all the ligands have different properties.
  • ligand on one strand of a double-stranded oligomeric compound has affinity for a ligand on the second strand.
  • a ligand is covalently linked to both strands of a double-stranded oligomeric compound.
  • point of attachment for an oligomeric compound can be an atom of the ligand self or an atom on a carrier molecule to which the ligand itself is attached.
  • Ligands can be coupled to the oligomeric compounds at various places, for example, 3′-end, 5′-end, and/or at an internal position. When two or more ligands are present, the ligand can be on opposite ends of an oligomeric compound. In preferred embodiments, the ligand is attached to the oligomeric compound via an intervening tether/linker. The ligand or tethered ligand can be present on a monomer when said monomer is incorporated into the growing strand. In some embodiments, the ligand can be incorporated via coupling to a “precursor” monomer after said “precursor” monomer has been incorporated into the growing strand.
  • a monomer having, e.g., an amino-terminated tether (i.e., having no associated ligand), e.g., monomer-linker-NH 2 can be incorporated into a growing oligomeric compound strand.
  • a ligand having an electrophilic group e.g., a pentafluorophenyl ester or aldehyde group, can subsequently be attached to the precursor monomer by coupling the electrophilic group of the ligand with the terminal nucleophilic group of the precursor monomer's tether.
  • a monomer having a chemical group suitable for taking part in Click Chemistry reaction can be incorporated e.g., an azide or alkyne terminated tether/linker.
  • a ligand having complementary chemical group e.g. an alkyne or azide can be attached to the precursor monomer by coupling the alkyne and the azide together.
  • ligands can be attached to one or both strands.
  • an siRNA comprises a ligand conjugated to the sense strand.
  • an siRNA comprises a ligand conjugated to the antisense strand.
  • ligand can be conjugated to nucleobases, sugar moieties, or internucleosidic linkages of oligomeric compound. Conjugation to purine nucleobases or derivatives thereof can occur at any position including, endocyclic and exocyclic atoms. In some embodiments, the 2-, 6-, 7-, or 8-positions of a purine nucleobase are attached to a conjugate moiety. Conjugation to pyrimidine nucleobases or derivatives thereof can also occur at any position. In some embodiments, the 2-, 5-, and 6-positions of a pyrimidine nucleobase can be substituted with a conjugate moiety. When a ligand is conjugated to a nucleobase, the preferred position is one that does not interfere with hybridization, i.e., does not interfere with the hydrogen bonding interactions needed for base pairing.
  • Conjugation to sugar moieties of nucleosides can occur at any carbon atom.
  • Example carbon atoms of a sugar moiety that can be attached to a conjugate moiety include the 2′, 3′, and 5′ carbon atoms. The 1′ position can also be attached to a conjugate moiety, such as in an abasic residue.
  • Internucleosidic linkages can also bear conjugate moieties.
  • the conjugate moiety can be attached directly to the phosphorus atom or to an O, N, or S atom bound to the phosphorus atom.
  • amine- or amide-containing internucleosidic linkages e.g., PNA
  • the conjugate moiety can be attached to the nitrogen atom of the amine or amide or to an adjacent carbon atom.
  • REVERSIR compounds conjugated with a ligand are particularly effective in reducing activity of siRNAs.
  • a ligand can increase or enhance the ability of a REVERSIR compound by delivering the REVERSIR compound to the desired location of action.
  • the REVERSIR compound is conjugated with a ligand.
  • the linkage between the ligand and the REVERSIR compound can be designed to undergo cleavage after the REVERSIR compound reaches a desired location of action. This can be accomplished in a number of ways.
  • the linker connecting the REVERSIR compound to the ligand can be a cleavable linker.
  • the nucleoside in the REVERSIR compound that is connected with the ligand can have an effect on the ability of the REVERSIR compound to reduce activity of the siRNA.
  • ligand conjugated nucleosides comprising deoxy sugars (e.g., 2′-deoxy ribose) are particularly effective in enhancing the ability of REVERSIR compounds to reduce siRNA activity.
  • the nucleoside conjugated with the ligand comprises a deoxy sugar, for example, a 2′-deoxy sugar.
  • the ligand is attached to the nucleoside at the 3′-terminus of the REVERSIR compound.
  • the inventors have discovered inter alia that internucleotide linkage between the ligand conjugated nucleotide and the rest of the REVERSIR compound can also have an effect on the ability of the REVERSIR compound to reduce siRNA activity. Without wishing to be bound by a theory, readily cleavable internucleotide linkages were found to be particularly effective in enhancing the ability of REVERSIR compounds to reduce siRNA activity.
  • the ligand conjugated nucleotide is attached to the rest of the REVERSIR compound via a cleavable internucleotide linage.
  • the cleavable internucleotide linkage is a phosphodiester internucleotide linkage.
  • the ligand conjugated nucleotide comprises a deoxy sugar and is linked to rest of the REVERSIR compound via a cleavable internucleotide linkage.
  • the cleavable internucleotide linkage is a phosphodiester linkage.
  • the ligand conjugated nucleotide comprises a deoxy sugar and is linked to rest of the REVERSIR compound via an internucleotide linkage that is not a phosphodiester linkage.
  • the ligand is conjugated to the nucleotide at the 3′-terminus of the REVERSIR compound.
  • the ligand is conjugated at the 5′-terminus of the REVERSIR compound. In some embodiments, a first ligand is conjugated at the 5′-terminus of the REVERSIR compound and a second ligand conjugated to the first ligand.
  • an oligomeric compound is attached to a conjugate moiety by contacting a reactive group (e.g., OH, SH, amine, carboxyl, aldehyde, and the like) on the oligomeric compound with a reactive group on the conjugate moiety.
  • a reactive group e.g., OH, SH, amine, carboxyl, aldehyde, and the like
  • one reactive group is electrophilic and the other is nucleophilic.
  • an electrophilic group can be a carbonyl-containing functionality and a nucleophilic group can be an amine or thiol.
  • Methods for conjugation of nucleic acids and related oligomeric compounds with and without linking groups are well described in the literature such as, for example, in Manoharan in Antisense Research and Applications, Crooke and LeBleu, eds., CRC Press, Boca Raton, Fla., 1993, Chapter 17, which is incorporated herein by reference in its entirety.
  • the oligomeric compound described herein comprises a ligand having a structure shown below:
  • the oligomeric compound described herein comprises a ligand of Formula (II), (III), (IV) or (V):
  • q 2A , q 2B , q 3A , q 3B , q4 A , q 4B , q 5A , q 5B and q 5C for each represent independently occurrence 0-20 and wherein the repeating unit can be the same or different;
  • Q and Q′ are independently for each occurrence is absent, —(P 7 -Q 7 -R 7 ) p -T 7 - or -T 7 -Q 7 -T 7′ -B-T 8′ -Q 8 -T 8 ;
  • P 2A , P 2B , P 3A , P 3B , P 4A , P 4B , P 5A , P 5B , P 5C , P 7 , T 2A , T 2B , T 3A , T 3B , T 4A , T 4B , T 4A , T 5B , T 5C , T 7 , T 7′ , T 8 and T 8′ are each independently for each occurrence absent, CO, NH, O, S, OC(O), NHC(O), CH 2 , CH 2 NH or CH 2 O;
  • B is —CH 2 —N(B L )—CH 2 —;
  • B L is -T B -Q B
  • Q 2A , Q 2B , Q 3A , Q 3B , Q 4A , Q 4B , Q 5A , Q 5B , Q 5C , Q 7 , Q 8 and Q B are independently for each occurrence absent, alkylene, substituted alkylene and wherein one or more methylenes can be interrupted or terminated by one or more of O, S, S(O), SO 2 , N(R N ), C(R′) ⁇ C(R′), C ⁇ C or C(O);
  • T B and T B′ are each independently for each occurrence absent, CO, NH, O, S, OC(O), OC(O)O, NHC(O), NHC(O)NH, NHC(O)O, CH 2 , CH 2 NH or CH 2 O;
  • R x is a lipophile (e.g., cholesterol, cholic acid, adamantane acetic acid, 1-pyrene butyric acid, dihydrotestosterone, 1,3-Bis-O(hexadecyl)glycerol, geranyloxyhexyl group, hexadecylglycerol, borneol, menthol, 1,3-propanediol, heptadecyl group, palmitic acid, myristic acid, O3-(oleoyl)lithocholic acid, O3-(oleoyl)cholenic acid, dimethoxytrityl, or phenoxazine), a vitamin (e.g., folate, vitamin A, vitamin E, biotin, pyridoxal), a peptide, a carbohydrate (e.g., monosaccharide, disaccharide, trisaccharide, tetrasaccharide,
  • R 1 , R 2 , R 2A , R 2B , R 3A , R 3B , R 4A , R 4B , R 5A , R 5B , R 5C , R 7 are each independently for each occurrence absent, NH, O, S, CH 2 , C(O)O, C(O)NH, NHCH(R a )C(O), —C(O)—CH(R a )—NH—, CO, CH ⁇ N—O,
  • L 1 , L 2A , L 2B , L 3A , L 3B , L 4A , L 4B , L 5A , L 5B and L 5C are each independently for each occurrence a carbohydrate, e.g., monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide and polysaccharide;
  • R′ and R′′ are each independently H, C 1 -C 6 alkyl, OH, SH, or N(R N ) 2 ;
  • R N is independently for each occurrence H, methyl, ethyl, propyl, isopropyl, butyl or benzyl;
  • R a is H or amino acid side chain
  • Z′, Z′′, Z′′′ and Z′′′′ are each independently for each occurrence O or S;
  • p represent independently for each occurrence 0-20.
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • both L 2A and L 2B are different.
  • both L 3A and L 3B are the same.
  • both L 3A and L 3B are different.
  • both L 4A and L 4B are the same.
  • both L 4A and L 4B are different.
  • L 5A , L 5B and L 5C are the same.
  • L 5A , L 5B and L 5C are the same
  • L 5A and L 5B are the same.
  • L 5A and L 5C are the same.
  • L 5B and L 5C are the same.
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • Y is O or S and n is 3-6.
  • the oligomeric compound described herein comprises a monomer of structure:
  • Y is O or S and n is 3-6.
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer selected from the group consisting of:
  • the oligomeric compound described herein comprises a monomer of structure:
  • R is OH or NHCOOH.
  • the oligomeric compound described herein comprises a monomer of structure:
  • R is OH or NHCOOH.
  • the oligomeric compound described herein comprises a monomer of structure:
  • R is O or S.
  • the oligomeric compound described herein comprises a monomer of structure:
  • R is OH or NHCOOH.
  • the oligomeric compound described herein comprises a monomer of structure:
  • the oligomeric compound described herein comprises a monomer of structure:
  • R is OH or NHCOOH.
  • the oligomeric compound described herein comprises a monomer of structure:
  • R is OH or NHCOOH.
  • the oligomeric compound described herein comprises a monomer of structure:
  • R is OH or NHCOOH.
  • the oligomeric compound described herein comprises a monomer of structure:
  • R is OH or NHCOOH.
  • the oligomeric compound described herein comprises a monomer of structure:
  • X and Y are each independently for each occurrence H, a protecting group, a phosphate group, a phosphodiester group, an activated phosphate group, an activated phosphite group, a phosphoramidite, a solid support, —P(Z′)(Z′′)O-nucleoside, —P(Z′)(Z′′)O-oligonucleotide, a lipid, a PEG, a steroid, a polymer, a nucleotide, a nucleoside, or an oligonucleotide; and Z′ and Z′′ are each independently for each occurrence O or S.
  • the REVERSIR compound is conjugated with a ligand of structure:
  • the conjugated siRNA comprises a ligand of structure:
  • the REVERSIR compound comprises a monomer of structure:
  • the oligomeric compound described herein comprises a ligand of structure:
  • the oligomeric compound described herein comprises a ligand from those described in U.S. Pat. No. 9,181,549 to Prakash et al., the content of which is incorporated herein by reference in its entirety.
  • Linking groups or bifunctional linking moieties such as those known in the art are amenable to the compounds provided herein. Linking groups are useful for attachment of chemical functional groups, conjugate 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 chemical functional group or a conjugate group.
  • the linker comprises a chain structure or an oligomer of repeating units such as ethylene glycol or amino acid units.
  • bifunctional linking moieties include amino, hydroxyl, carboxylic acid, thiol, unsaturations (e.g., double or triple bonds), and the like.
  • bifunctional linking moieties include 8-amino-3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) and 6-aminohexanoic acid (AHEX or AHA).
  • linking groups include, but are not limited to, substituted C1-C10 alkyl, substituted or unsubstituted C2-C10 alkenyl or substituted or unsubstituted C2-C10 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.
  • the ligand is conjugated with the oligomeric compound via a linker.
  • linker means an organic moiety that connects two parts of a compound.
  • Linkers typically comprise a direct bond or an atom such as oxygen or sulfur, a unit such as NR 1 , C(O), C(O)NH, SO, SO 2 , SO 2 NH or a chain of atoms, such as substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, arylalkyl, arylalkenyl, arylalkynyl, heteroarylalkyl, heteroarylalkenyl, heteroarylalkynyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, aryl, heteroaryl, heterocyclyl, cycloalkyl, cycloalkenyl, alkylarylalkyl, alkyl aryl alkenyl, alkylarylalkyl, alkyl
  • the linker is —[(P-Q′′-R) q -X-(P′-Q′′′-R′) q′ ] q′′ -T-, wherein: P, R, T, P′, R′ and T are each independently for each occurrence absent, CO, NH, O, S, OC(O), NHC(O), CH 2 , CH 2 NH, CH 2 O; NHCH(R a )C(O), —C(O)—CH(R a )—NH—, CH ⁇ N—O,
  • Q′′ and Q′′′ are each independently for each occurrence absent, —(CH 2 ) n —, —C(R 1 )(R 2 )(CH 2 ) n —, —(CH 2 ) n C(R 1 )(R 2 )—, —(CH 2 CH 2 O) m CH 2 CH 2 —, or —(CH 2 CH 2 O) m CH 2 CH 2 NH—;
  • X is absent or a cleavable linking group;
  • R a is H or an amino acid side chain;
  • R 1 and R 2 are each independently for each occurrence H, CH 3 , OH, SH or N(R N ) 2 ;
  • R N is independently for each occurrence H, methyl, ethyl, propyl, isopropyl, butyl or benzyl;
  • q, q′ and q′′ are each independently for each occurrence 0-20 and wherein the repeating unit can be the same or different;
  • the linker comprises at least one cleavable linking group.
  • the linker is a branched linker.
  • the branchpoint of the branched linker may be at least trivalent, but can be a tetravalent, pentavalent or hexavalent atom, or a group presenting such multiple valencies.
  • the branchpoint is, —N, —N(Q)-C, —O—C, —S—C, —SS—C, —C(O)N(Q)-C, —OC(O)N(Q)-C, —N(Q)C(O)—C, or —N(Q)C(O)O—C; wherein Q is independently for each occurrence H or optionally substituted alkyl.
  • the branchpoint is glycerol or derivative thereof.
  • a cleavable linking group is one which is sufficiently stable outside the cell, but which upon entry into a target cell is cleaved to release the two parts the linker is holding together.
  • the cleavable linking group is cleaved at least 10 times or more, preferably at least 100 times faster in the target cell or under a first reference condition (which can, e.g., be selected to mimic or represent intracellular conditions) than in the blood or serum of a subject, or under a second reference condition (which can, e.g., be selected to mimic or represent conditions found in the blood or serum).
  • Cleavable linking groups are susceptible to cleavage agents, e.g., pH, redox potential or the presence of degradative molecules. Generally, cleavage agents are more prevalent or found at higher levels or activities inside cells than in serum or blood. Examples of such degradative agents include: redox agents which are selected for particular substrates or which have no substrate specificity, including, e.g., oxidative or reductive enzymes or reductive agents such as mercaptans, present in cells, that can degrade a redox cleavable linking group by reduction; esterases; amidases; endosomes or agents that can create an acidic environment, e.g., those that result in a pH of five or lower; enzymes that can hydrolyze or degrade an acid cleavable linking group by acting as a general acid, peptidases (which can be substrate specific) and proteases, and phosphatases.
  • redox agents which are selected for particular substrates or which have no substrate specificity,
  • a linker can include a cleavable linking group that is cleavable by a particular enzyme.
  • the type of cleavable linking group incorporated into a linker can depend on the cell to be targeted. For example, liver targeting ligands can be linked to the cationic lipids through a linker that includes an ester group. Liver cells are rich in esterases, and therefore the linker will be cleaved more efficiently in liver cells than in cell types that are not esterase-rich. Other cell-types rich in esterases include cells of the lung, renal cortex, and testis.
  • Linkers that contain peptide bonds can be used when targeting cell types rich in peptidases, such as liver cells and synoviocytes.
  • cleavable linking group is cleaved at least 1.25, 1.5, 1.75, 2, 3, 4, 5, 10, 25, 50, or 100 times faster in the cell (or under in vitro conditions selected to mimic intracellular conditions) as compared to blood or serum (or under in vitro conditions selected to mimic extracellular conditions). In some embodiments, the cleavable linking group is cleaved by less than 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, 5%, or 1% in the blood (or in vitro conditions selected to mimic extracellular conditions) as compared to in the cell (or under in vitro conditions selected to mimic intracellular conditions).
  • Exemplary cleavable linking groups include, but are not limited to, redox cleavable linking groups (e.g., —S—S— and —C(R) 2 —S—S—, wherein R is H or C 1 -C 6 alkyl and at least one R is C 1 -C 6 alkyl such as CH 3 or CH 2 CH 3 ); phosphate-based cleavable linking groups (e.g., —O—P(O)(OR)—O—, —O—P(S)(OR)—O—, —O—P(S)(SR)—O—, —S—P(O)(OR)—O—, —O—P(O)(OR)—S—, —S—P(O)(OR)—S—, —O—P(S)(ORk)-S—, —S—P(S)(OR)—O—, —O—P(O)(R)—O—, —O—P
  • a peptide based cleavable linking group comprises two or more amino acids.
  • the peptide-based cleavage linkage comprises the amino acid sequence that is the substrate for a peptidase or a protease found in cells.
  • an acid cleavable linking group is cleaveable in an acidic environment with a pH of about 6.5 or lower (e.g., about 6.-, 5.5, 5.0, or lower), or by agents such as enzymes that can act as a general acid.
  • the linker is an oligonucleotide linker including, but not limited to, (N) n ; wherein N is independently a modified or unmodified nucleotide and n is 1-23. In some embodiments, n is 1-10, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, the oligonucleotide linker is selected from the group consisting of GNRA, (G) 4 , (U) 4 , and (dT) 4 , wherein N is a modified or unmodified nucleotide and R is a modified or unmodified purine nucleotide.
  • the linker is dA.
  • the present invention also includes oligomeric compounds which are chimeric oligomeric compounds.
  • “Chimeric” oligomeric compounds or “chimeras,” in the context of this invention are oligomeric compounds which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a modified or unmodified nucleotide in the case of an oligonucleotide.
  • Chimeric oligomeric compounds can be described as having a particular motif.
  • the motifs include, but are not limited to, an alternating motif, a gapped motif, a hemimer motif, a uniformly fully modified motif and a positionally modified motif.
  • the phrase “chemically distinct region” refers to an oligomeric region which is different from other regions by having a modification that is not present elsewhere in the oligomeric compound or by not having a modification that is present elsewhere in the oligomeric compound.
  • An oligomeric compound can comprise two or more chemically distinct regions.
  • a region that comprises no modifications is also considered chemically distinct.
  • a chemically distinct region can be repeated within an oligomeric compound.
  • a pattern of chemically distinct regions in an oligomeric compound can be realized such that a first chemically distinct region is followed by one or more second chemically distinct regions.
  • This sequence of chemically distinct regions can be repeated one or more times. Preferably, the sequence is repeated more than one time. Both strands of a double-stranded oligomeric compound can comprise these sequences.
  • Each chemically distinct region can actually comprise as little as a single monomers, e.g., nucleotides.
  • each chemically distinct region comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 or 18 monomers, e.g., nucleotides.
  • alternating nucleotides comprise the same modification, e.g. all the odd number nucleotides in a strand have the same modification and/or all the even number nucleotides in a strand have the similar modification to the first strand. In some embodiments, all the odd number nucleotides in an oligomeric compound have the same modification and all the even numbered nucleotides have a modification that is not present in the odd number nucleotides and vice versa.
  • nucleotides of one strand can be complementary in position to nucleotides of the second strand which are similarly modified.
  • the shift is such that the similarly modified nucleotides of the first strand and second strand are not in complementary position to each other.
  • the first strand has an alternating modification pattern wherein alternating nucleotides comprise a 2′-modification, e.g., 2′-O-Methyl modification.
  • the first strand comprises an alternating 2′-O-Methyl modification and the second strand comprises an alternating 2′-fluoro modification.
  • both strands of a double-stranded oligonucleotide comprise alternating 2′-O-methyl modifications.
  • both strands of a double-stranded oligonucleotide comprise alternating 2′-O-methyl modifications
  • such 2′-modified nucleotides can be in complementary position in the duplex region.
  • such 2′-modified nucleotides may not be in complementary positions in the duplex region.
  • the oligonucleotide comprises two chemically distinct regions, wherein each region is 1,2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides in length.
  • the oligomeric compound comprises three chemically distinct region.
  • the middle region is about 5-15, (e.g., 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15) nucleotide in length and each flanking or wing region is independently 1-10 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10) nucleotides in length. All three regions can have different modifications or the wing regions can be similarly modified to each other. In some embodiments, the wing regions are of equal length, e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides long.
  • alternating motif refers to an oligomeric compound comprising a contiguous sequence of linked monomer subunits wherein the monomer subunits have two different types of sugar groups that alternate for essentially the entire sequence of the oligomeric compound.
  • Oligomeric compounds having an alternating motif can be described by the formula: 5′-A(-L-B-L-A)n(-L-B)nn-3′ where A and B are monomelic subunits that have different sugar groups, each L is an internucleoside linking group, n is from about 4 to about 12 and nn is 0 or 1. This permits alternating oligomeric compounds from about 9 to about 26 monomer subunits in length. This length range is not meant to be limiting as longer and shorter oligomeric compounds are also amenable to the present invention.
  • one of A and B is a 2′-modified nucleoside as provided herein.
  • nucleoside having a modification of a first type may be an unmodified nucleoside.
  • type region refers to a portion of an oligomeric compound wherein the nucleosides and internucleoside linkages within the region all comprise the same type of modifications; and the nucleosides and/or the internucleoside linkages of any neighboring portions include at least one different type of modification.
  • uniformly fully modified motif refers to an oligonucleotide comprising a contiguous sequence of linked monomer subunits that each have the same type of sugar group.
  • the uniformly fully modified motif includes a contiguous sequence of nucleosides of the invention.
  • one or both of the 3′ and 5′-ends of the contiguous sequence of the nucleosides provided herein comprise terminal groups such as one or more unmodified nucleosides.
  • hemimer motif refers to an oligomeric compound having a short contiguous sequence of monomer subunits having one type of sugar group located at the 5” or the 3′ end wherein the remainder of the monomer subunits have a different type of sugar group.
  • a hemimer is an oligomeric compound of uniform sugar groups further comprising a short region (1, 2, 3, 4 or about 5 monomelic subunits) having uniform but different sugar groups and located on either the 3′ or the 5′ end of the oligomeric compound.
  • the hemimer motif comprises a contiguous sequence of from about 10 to about 28 monomer subunits of one type with from 1 to 5 or from 2 to about 5 monomer subunits of a second type located at one of the termini.
  • a hemimer is a contiguous sequence of from about 8 to about 20 ⁇ -D-2′-deoxyribonucleosides having from 1-12 contiguous nucleosides of the invention located at one of the termini.
  • a hemimer is a contiguous sequence of from about 8 to about 20 ⁇ -D-2′-deoxyribonucleosides having from 1-5 contiguous nucleosides of the invention located at one of the termini.
  • a hemimer is a contiguous sequence of from about 12 to about 18 ⁇ -D-2′-deoxyribo-nucleosides having from 1-3 contiguous nucleosides of the invention located at one of the termini. In one embodiment, a hemimer is a contiguous sequence of from about 10 to about 14 ⁇ -D-2′-deoxyribonucleosides having from 1-3 contiguous nucleosides of the invention located at one of the termini.
  • blockmer motif refers to an oligonucleotide comprising an otherwise contiguous sequence of monomer subunits wherein the sugar groups of each monomer subunit is the same except for an interrupting internal block of contiguous monomer subunits having a different type of sugar group.
  • a blockmer overlaps somewhat with a gapmer in the definition but typically only the monomer subunits in the block have non-naturally occurring sugar groups in a blockmer and only the monomer subunits in the external regions have non-naturally occurring sugar groups in a gapmer with the remainder of monomer subunits in the blockmer or gapmer being ⁇ -D-2′-deoxyribonucleosides or ⁇ -D-ribonucleosides.
  • blockmer oligonucleotides are provided herein wherein all of the monomer subunits comprise non-naturally occurring sugar groups.
  • positionally modified motif is meant to include an otherwise contiguous sequence of monomer subunits having one type of sugar group that is interrupted with two or more regions of from 1 to about 5 contiguous monomer subunits having another type of sugar group.
  • Each of the two or more regions of from 1 to about 5 contiguous monomer subunits are independently uniformly modified with respect to the type of sugar group.
  • each of the two or more regions have the same type of sugar group.
  • each of the two or more regions have a different type of sugar group.
  • positionally modified oligonucleotides comprising a sequence of from 8 to 20 ⁇ -D-2′-deoxyribonucleosides that further includes two or three regions of from 2 to about 5 contiguous nucleosides of the invention.
  • Positionally modified oligonucleotides are distinguished from gapped motifs, hemimer motifs, blockmer motifs and alternating motifs because the pattern of regional substitution defined by any positional motif does not fit into the definition provided herein for one of these other motifs.
  • the term positionally modified oligomeric compound includes many different specific substitution patterns.
  • the term “gapmer” or “gapped oligomeric compound” refers to an oligomeric compound having two external regions or wings and an internal region or gap.
  • the three regions form a contiguous sequence of monomer subunits with the sugar groups of the external regions being different than the sugar groups of the internal region and wherein the sugar group of each monomer subunit within a particular region is the same.
  • the gapmer is a symmetric gapmer and when the sugar group used in the 5′-external region is different from the sugar group used in the 3′-external region, the gapmer is an asymmetric gapmer.
  • the external regions are small (each independently 1, 2, 3, 4 or about 5 monomer subunits) and the monomer subunits comprise non-naturally occurring sugar groups with the internal region comprising ⁇ -D-2′-deoxyribonucleosides.
  • the external regions each, independently, comprise from 1 to about 5 monomer subunits having non-naturally occurring sugar groups and the internal region comprises from 6 to 18 unmodified nucleosides.
  • the internal region or the gap generally comprises ⁇ -D-2′-deoxyribo-nucleosides but can comprise non-naturally occurring sugar groups.
  • the gapped oligomeric compounds comprise an internal region of ⁇ -D-2′-deoxyribonucleosides with one of the external regions comprising nucleosides of the invention. In one embodiment, the gapped oligonucleotide comprise an internal region of ⁇ -D-2′-deoxyribonucleosides with both of the external regions comprising nucleosides of the invention. In one embodiment, the gapped oligonucleotide comprise an internal region of ⁇ -D-2′-deoxyribonucleosides with both of the external regions comprising nucleosides of the invention.
  • gapped oligonucleotides are provided herein wherein all of the monomer subunits comprise non-naturally occurring sugar groups.
  • gapped oliogonucleotides are provided comprising one or two nucleosides of the invention at the 5′-end, two or three nucleosides of the invention at the 3′-end and an internal region of from 10 to 16 ⁇ -D-2′-deoxyribonucleosides.
  • gapped oligonucleotides are provided comprising one nucleoside of the invention at the 5′-end, two nucleosides of the invention at the 3′-end and an internal region of from 10 to 16 ⁇ -D-2′-deoxyribonucleosides.
  • gapped oligonucleotides comprising two nucleosides of the invention at the 5′-end, two nucleosides of the invention at the 3′-end and an internal region of from 10 to 14 ⁇ -D-2′-deoxyribonucleosides. In one embodiment, gapped oligonucleotides are provided that are from about 10 to about 21 monomer subunits in length. In one embodiment, gapped oligonucleotides are provided that are from about 12 to about 16 monomer subunits in length. In one embodiment, gapped oligonucleotides are provided that are from about 12 to about 14 monomer subunits in length.
  • the 5′-terminal monomer of an oligomeric compound of the invention comprises a phosphorous moiety at the 5′-end.
  • the 5′-terminal monomer comprises a 2′-modification.
  • the 2′-modification of the 5′-terminal monomer is a cationic modification.
  • the 5′-terminal monomer comprises a 5′-modification.
  • the 5′-terminal monomer comprises a 2′-modification and a 5′-modification.
  • the 5′-terminal monomer is a 5′-stabilizing nucleoside.
  • the modifications of the 5′-terminal monomer stabilize the 5′-phosphate.
  • oligomeric compounds comprising modifications of the 5′-terminal monomer are resistant to exonucleases. In certain embodiments, oligomeric compounds comprising modifications of the 5′-terminal monomer have improved REVERSIR properties. In certain such embodiments, oligomeric compound comprising modifications of the 5′-terminal monomer have improved association with a strand of the siRNA.
  • the 5′terminal monomer is attached to rest of the oligomeric compound a modified linkage. In certain such embodiments, the 5′terminal monomer is attached to rest of the oligomeric compound by a phosphorothioate linkage.
  • oligomeric compounds of the present invention comprise one or more regions of alternating modifications. In certain embodiments, oligomeric compounds comprise one or more regions of alternating nucleoside modifications. In certain embodiments, oligomeric compounds comprise one or more regions of alternating linkage modifications. In certain embodiments, oligomeric compounds comprise one or more regions of alternating nucleoside and linkage modifications.
  • oligomeric compounds of the present invention comprise one or more regions of alternating 2′-F modified nucleosides and 2′-OMe modified nucleosides.
  • regions of alternating 2′F modified and 2′OMe modified nucleosides also comprise alternating linkages.
  • the linkages at the 3′ end of the 2′-F modified nucleosides are phosphorothioate linkages.
  • the linkages at the 3′end of the 2′OMe nucleosides are phosphodiester linkages.
  • such alternating regions are:
  • oligomeric compounds comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11 such alternatig regions. Such regions may be contiguous or may be interrupted by differently modified nucleosides or linkages.
  • one or more alternating regions in an alternating motif include more than a single nucleoside of a type.
  • oligomeric compounds of the present invention may include one or more regions of any of the following nucleoside motifs:
  • A is a nucleoside of a first type and B is a nucleoside of a second type.
  • a and B are each selected from 2′-F, 2′-OMe, LNA, DNA and MOE.
  • A is DNA. In certain embodiments B is DNA. In some embodiments, A is 4′-CH 2 O-2′-LNA. In certain embodiments, B is 4′-CH 2 O-2′-LNA. In certain embodiments, A is DNA and B is 4′-CH 2 O-2′-LNA. In certain embodiments A is 4′-CH 2 O-2′-LNA and B is DNA.
  • A is 2′-OMe.
  • B is 2′-OMe.
  • A is 2′-OMe and B is 4′-CH 2 O-2′-LNA.
  • A is 4′-CH 2 O-2′-LNA and B is 2′-OMe.
  • A is 2′-OMe and B is DNA.
  • A is DNA and B is 2′-OMe.
  • A is (S)-cEt.
  • B is (S)-cEt.
  • A is 2′-OMe and B is (S)-cEt.
  • A is (S)-cEt and B is 2′-OMe.
  • A is DNA and B is (S)-cEt.
  • A is (S)-cEt and B is DNA.
  • A is 2′-F. In certain embodiments B is 2′-F. In certain embodiments, A is 2′-F and B is 4′-CH 2 O-2′-LNA. In certain embodiments A is 4′-CH 2 O-2′-LNA and B is 2′-F. In certain embodiments, A is 2′-F and B is (S)-cEt. In certain embodiments A is (S)-cEt and B is 2′-F. In certain embodiments, A is 2′-F and B is DNA. In certain embodiments A is DNA and B is 2′-F. In certain embodiments, A is 2′-OMe and B is 2′-F. In certain embodiments, A is DNA and B is 2′-OMe. In certain embodiments, A is 2′-OMe and B is DNA.
  • oligomeric compounds having such an alternating motif also comprise a 5′ terminal nucleoside comprising a phosphate stabilizing modification. In certain embodiments, oligomeric compounds having such an alternating motif also comprise a 5′ terminal nucleoside comprising a 2′-cationic modification. In certain embodiments, oligomeric compounds having such an alternating motif also comprise a 5′ terminal modification.
  • oligomeric compounds of the present invention comprise a region having a 2-2-3 motif. Such regions comprises the following motif:
  • A is a first type of modifed nucleoside
  • B, C, D, and E are nucleosides that are differently modified than A, however, B, C, D, and E may have the same or different modifications as one another;
  • w and z are from 0 to 15;
  • x and y are from 1 to 15.
  • A is a 2′-OMe modified nucleoside.
  • B, C, D, and E are all 2′-F modified nucleosides.
  • A is a 2′-OMe modified nucleoside and B, C, D, and E are all 2′-F modified nucleosides.
  • the linkages of a 2-2-3 motif are all modifed linkages. In certain embodiments, the linkages are all phosphorothioate linkages. In certain embodiments, the linkages at the 3′-end of each modification of the first type are phosphodiester.
  • Z is 0.
  • the region of three nucleosides of the first type are at the 3′-end of the oligonucleotide. In certain embodiments, such region is at the 3′-end of the oligomeric compound, with no additional groups attached to the 3′ end of the region of three nucleosides of the first type.
  • an oligomeric compound comprising an oligonucleotide where Z is 0, may comprise a terminal group attached to the 3′-terminal nucleoside. Such terminal groups may include additional nucleosides. Such additional nucleosides are typically non-hybridizing nucleosides.
  • oligomeric compounds can comprise two or more motifs.
  • oligomeric compounds can have two or more nucleoside motifs selected from LNAs, phosphorthioate linkages, 2′-OMe, conjugated ligand(s).
  • Oligomeric compounds having any of the various nucleoside motifs described herein can have also have any linkage motif.
  • first 1, 2, 3, 4 or 5 at the 5′-end be modified intersugar linkages and first 4, 5, 6, 7 or 8 intersugar linkages at the 3′-end can be modified intersugar linkages.
  • the central region of such modified oligomeric compound can have intersugar linkages based on the any of the other motifs described herein, for example, uniform, alternating, hemimer, gapmer, and the like.
  • the oligomeric compound comprise a phosphorothioate linkage between the first and second monomer at the 5′-terminus, alternating phosphorothioate/phosphodiester linkages in the central region and 6, 7, or 8 phosphorothioate linkages at the 3′-terminus.
  • single-stranded oligomeric compounds or at least one strand of a double-stranded oligomeric compound includes at least one of the following motifs:
  • both strands of a double-stranded oligomeric compound independently comprise at least one of the above described motifs. In some other embodiments, both strands of a double-stranded oligomeric compound comprise at least one at least one of the above described motifs, which motifs can be same or different or some combination of same and different.
  • lengths of oligomeric compounds can be easily manipulated by lengthening or shortening one or more of the described regions, without disrupting the motif.
  • oligomeric compound comprises two or more chemically distinct regions and has a structure as described in International Application No. PCT/US09/038433, filed Mar. 26, 2009, contents of which are herein incorporated in their entirety.
  • Oligomerization of modified and unmodified nucleosides and nucleotides can be routinely performed according to literature procedures for DNA (Protocols for Oligonucleotides and Analogs, Ed. Agrawal (1993), Humana Press) and/or RNA (Scaringe, Methods (2001), 23, 206-217. Gait et al., Applications of Chemically synthesized RNA in RNA: Protein Interactions, Ed. Smith (1998), 1-36. Gallo et al., Tetrahedron (2001), 57, 5707-5713).
  • Oligomeric compounds provided herein can be conveniently and routinely made through the well-known technique of solid phase synthesis.
  • Equipment for such synthesis is sold by several vendors including, for example, Applied Biosystems (Foster City, Calif.). Any other means for such synthesis known in the art may additionally or alternatively be employed. It is well known to use similar techniques to prepare oligonucleotides such as the phosphorothioates and alkylated derivatives.
  • the invention is not limited by the method of antisense compound synthesis.
  • Analysis methods include capillary electrophoresis (CE) and electrospray-mass spectroscopy. Such synthesis and analysis methods can be performed in multi-well plates.
  • the method of the invention is not limited by the method of oligomer purification.
  • the oligomeric compounds of the invention can be prepared using solution-phase or solid-phase organic synthesis, or enzymatically by methods known in the art.
  • Organic synthesis offers the advantage that the oligomeric strands comprising non-natural or modified nucleotides can be easily prepared. Any other means for such synthesis known in the art can additionally or alternatively be employed. It is also known to use similar techniques to prepare other oligomeric compounds, such as those comprising phosphorothioates, phosphorodithioates and alkylated derivatives of intersugar linkages.
  • the double-stranded oligomeric compounds of the invention can be prepared using a two-step procedure. First, the individual strands of the double-stranded molecule are prepared separately. Then, the component strands are annealed.
  • the oligomeric compounds can be prepared in a solution (e.g., an aqueous and/or organic solution) that is appropriate for formulation.
  • a solution e.g., an aqueous and/or organic solution
  • the oligonmeric preparation can be precipitated and redissolved in pure double-distilled water, and lyophilized.
  • the dried oligomeric compound can then be resuspended in a solution appropriate for the intended formulation process.
  • 5,587,469 drawn to oligonucleotides having N-2 substituted purines
  • U.S. Pat. No. 5,587,470 drawn to oligonucleotides having 3-deazapurines
  • U.S. Pat. Nos. 5,602,240, and 5,610,289 drawn to backbone-modified oligonucleotide analogs
  • U.S. Pat. Nos. 6,262,241, and 5,459,255 drawn to, inter alia, methods of synthesizing 2′-fluoro-oligonucleotides.
  • Oligomeric compounds can 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 are dependent upon a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.
  • Oligomeric compounds can be utilized in pharmaceutical compositions by combining such oligomeric compounds with a suitable pharmaceutically acceptable diluent or carrier.
  • a pharmaceutically acceptable diluent includes phosphate-buffered saline (PBS).
  • PBS is a diluent suitable for use in compositions to be delivered parenterally.
  • employed in the methods described herein is a pharmaceutical composition comprising an antisense compound and/or antidote compound and a pharmaceutically acceptable diluent.
  • the pharmaceutically acceptable diluent is PBS.
  • compositions comprising oligomeric compounds encompass any pharmaceutically acceptable salts, esters, or salts of such esters.
  • pharmaceutical compositions comprising oligomeric 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 oligomeric compound.
  • compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (e.g., by a transdermal patch), pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal, oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; subdermal, e.g., via an implanted device; or intracranial, e.g., by intraparenchymal, intrathecal or intraventricular, administration.
  • Administration may be topical (e.g., by a transdermal patch), pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal
  • the oligomeric compounds can be delivered in a manner to target a particular tissue, such as the liver (e.g., the hepatocytes of the liver).
  • a particular tissue such as the liver (e.g., the hepatocytes of the liver).
  • compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders.
  • Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
  • Coated condoms, gloves and the like may also be useful.
  • Suitable topical formulations include those in which the iRNAs featured in the invention are in admixture with a topical delivery agent such as lipids, liposomes, fatty acids, fatty acid esters, steroids, chelating agents and surfactants.
  • Suitable lipids and liposomes include neutral (e.g., dioleoylphosphatidyl DOPE ethanolamine, dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl choline) negative (e.g., dimyristoylphosphatidyl glycerol DMPG) and cationic (e.g., dioleoyltetramethylaminopropyl DOTAP and dioleoylphosphatidyl ethanolamine DOTMA).
  • iRNAs featured in the invention may be encapsulated within liposomes or may form complexes thereto, in particular to cationic liposomes.
  • iRNAs may be complexed to lipids, in particular to cationic lipids.
  • Suitable fatty acids and esters include but are not limited to arachidonic acid, oleic acid, eicosanoic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or a C 1-20 alkyl ester (e.g., isopropylmyristate IPM), monoglyceride, diglyceride or pharmaceutically acceptable salt thereof.
  • Topical formulations are described in detail in U.S. Pat. No. 6,747,014, which is incorporated herein by reference.
  • liposome means a vesicle composed of amphiphilic lipids arranged in a spherical bilayer or bilayers.
  • Liposomes are unilamellar or multilamellar vesicles which have a membrane formed from a lipophilic material and an aqueous interior. The aqueous portion contains the composition to be delivered. Cationic liposomes possess the advantage of being able to fuse to the cell wall. Non-cationic liposomes, although not able to fuse as efficiently with the cell wall, are taken up by macrophages in vivo.
  • liposomes obtained from natural phospholipids are biocompatible and biodegradable; liposomes can incorporate a wide range of water and lipid soluble drugs; liposomes can protect encapsulated drugs in their internal compartments from metabolism and degradation (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245).
  • Important considerations in the preparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes.
  • Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomes start to merge with the cellular membranes and as the merging of the liposome and cell progresses, the liposomal contents are emptied into the cell where the active agent may act.
  • Liposomes present several advantages over other formulations. Such advantages include reduced side-effects related to high systemic absorption of the administered drug, increased accumulation of the administered drug at the desired target, and the ability to administer a wide variety of drugs, both hydrophilic and hydrophobic, into the skin.
  • liposomes to deliver agents including high-molecular weight DNA into the skin.
  • Compounds including analgesics, antibodies, hormones and high-molecular weight DNAs have been administered to the skin. The majority of applications resulted in the targeting of the upper epidermis
  • Liposomes fall into two broad classes. Cationic liposomes are positively charged liposomes which interact with the negatively charged DNA molecules to form a stable complex. The positively charged DNA/liposome complex binds to the negatively charged cell surface and is internalized in an endosome. Due to the acidic pH within the endosome, the liposomes are ruptured, releasing their contents into the cell cytoplasm (Wang et al., Biochem. Biophys. Res. Commun., 1987, 147, 980-985).
  • Liposomes which are pH-sensitive or negatively-charged, entrap DNA rather than complex with it. Since both the DNA and the lipid are similarly charged, repulsion rather than complex formation occurs. Nevertheless, some DNA is entrapped within the aqueous interior of these liposomes. pH-sensitive liposomes have been used to deliver DNA encoding the thymidine kinase gene to cell monolayers in culture. Expression of the exogenous gene was detected in the target cells (Zhou et al., Journal of Controlled Release, 1992, 19, 269-274).
  • liposomal composition includes phospholipids other than naturally-derived phosphatidylcholine.
  • Neutral liposome compositions can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl phosphatidylcholine (DPPC).
  • Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic liposomes are formed primarily from dioleoyl phosphatidylethanolamine (DOPE).
  • DOPE dioleoyl phosphatidylethanolamine
  • Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC, and egg PC.
  • PC phosphatidylcholine
  • Another type is formed from mixtures of phospholipid and/or phosphatidylcholine and/or cholesterol.
  • Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol.
  • Non-ionic liposomal formulations comprising NovasomeTM I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and NovasomeTM II (glyceryl distearate/cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver cyclosporin-A into the dermis of mouse skin. Results indicated that such non-ionic liposomal systems were effective in facilitating the deposition of cyclosporin-A into different layers of the skin (Hu et al. S. T. P. Pharma. Sci., 1994, 4, 6, 466).
  • Liposomes also include “sterically stabilized” liposomes, a term which, as used herein, refers to liposomes comprising one or more specialized lipids that, when incorporated into liposomes, result in enhanced circulation lifetimes relative to liposomes lacking such specialized lipids.
  • sterically stabilized liposomes are those in which part of the vesicle-forming lipid portion of the liposome (A) comprises one or more glycolipids, such as monosialoganglioside G M1 , or (B) is derivatized with one or more hydrophilic polymers, such as a polyethylene glycol (PEG) moiety.
  • PEG polyethylene glycol
  • Liposomes comprising (1) sphingomyelin and (2) the ganglioside G M1 or a galactocerebroside sulfate ester.
  • U.S. Pat. No. 5,543,152 discloses liposomes comprising sphingomyelin. Liposomes comprising 1,2-sn-dimyristoylphosphatidylcholine are disclosed in WO 97/13499 (Lim et al).
  • liposomes comprising lipids derivatized with one or more hydrophilic polymers, and methods of preparation thereof, are known in the art.
  • Sunamoto et al. (Bull. Chem. Soc. Jpn., 1980, 53, 2778) described liposomes comprising a nonionic detergent, 2C 1215G , that contains a PEG moiety.
  • Illum et al. (FEBS Lett., 1984, 167, 79) noted that hydrophilic coating of polystyrene particles with polymeric glycols results in significantly enhanced blood half-lives.
  • Synthetic phospholipids modified by the attachment of carboxylic groups of polyalkylene glycols (e.g., PEG) are described by Sears (U.S.
  • Liposomes having covalently bound PEG moieties on their external surface are described in European Patent No. EP 0 445 131 B1 and WO 90/04384 to Fisher.
  • Liposome compositions containing 1-20 mole percent of PE derivatized with PEG, and methods of use thereof, are described by Woodle et al. (U.S. Pat. Nos. 5,013,556 and 5,356,633) and Martin et al. (U.S. Pat. No. 5,213,804 and European Patent No. EP 0 496 813 B1).
  • Liposomes comprising a number of other lipid-polymer conjugates are disclosed in WO 91/05545 and U.S. Pat. No.
  • a number of liposomes comprising nucleic acids are known in the art.
  • WO 96/40062 to Thierry et al. discloses methods for encapsulating high molecular weight nucleic acids in liposomes.
  • U.S. Pat. No. 5,264,221 to Tagawa et al. discloses protein-bonded liposomes and asserts that the contents of such liposomes may include a dsRNA.
  • U.S. Pat. No. 5,665,710 to Rahman et al. describes certain methods of encapsulating oligodeoxynucleotides in liposomes.
  • WO 97/04787 to Love et al. discloses liposomes comprising dsRNAs targeted to the raf gene.
  • Transfersomes are yet another type of liposomes, and are highly deformable lipid aggregates which are attractive candidates for drug delivery vehicles. Transfersomes may be described as lipid droplets which are so highly deformable that they are easily able to penetrate through pores which are smaller than the droplet. Transfersomes are adaptable to the environment in which they are used, e.g., they are self-optimizing (adaptive to the shape of pores in the skin), self-repairing, frequently reach their targets without fragmenting, and often self-loading. To make transfersomes it is possible to add surface edge-activators, usually surfactants, to a standard liposomal composition. Transfersomes have been used to deliver serum albumin to the skin. The transfersome-mediated delivery of serum albumin has been shown to be as effective as subcutaneous injection of a solution containing serum albumin.
  • Liposome compositions can be prepared by a variety of methods that are known in the art. See e.g., U.S. Pat. Nos. 4,235,871; 4,737,323; 4,897,355 and 5,171,678; published International Applications WO 96/14057 and WO 96/37194; Felgner, P. L. et al., Proc. Natl. Acad. Sci., USA (1987) 8:7413-7417, Bangham, et al. M Mol. Biol . (1965) 23:238, Olson, et al. Biochim. Biophys. Acta (1979) 557:9, Szoka, et al. Proc. Natl. Acad. Sci .
  • HLB hydrophile/lipophile balance
  • Nonionic surfactants find wide application in pharmaceutical and cosmetic products and are usable over a wide range of pH values. In general their HLB values range from 2 to about 18 depending on their structure.
  • Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters.
  • Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and ethoxylated/propoxylated block polymers are also included in this class.
  • the polyoxyethylene surfactants are the most popular members of the nonionic surfactant class.
  • Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates.
  • the most important members of the anionic surfactant class are the alkyl sulfates and the soaps.
  • Cationic surfactants include quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are the most used members of this class.
  • amphoteric surfactants include acrylic acid derivatives, substituted alkylamides, N-alkylbetaines and phosphatides.
  • the REVERSIR can be fully encapsulated in a lipid formulation, e.g., a LNP, or other nucleic acid-lipid particle.
  • the REVERSIR encapsulated in the lipid formulation can be unconjugated or conjugated with a ligand (i.e., a conjugated REVERSIR).
  • LNP refers to a stable nucleic acid-lipid particle.
  • LNPs contain a cationic lipid, a non-cationic lipid, and a lipid that prevents aggregation of the particle (e.g., a PEG-lipid conjugate).
  • LNPs are extremely useful for systemic applications, as they exhibit extended circulation lifetimes following intravenous (i.v.) injection and accumulate at distal sites (e.g., sites physically separated from the administration site).
  • LNPs include “pSPLP,” which include an encapsulated condensing agent-nucleic acid complex as set forth in PCT Publication No. WO 00/03683.
  • the particles of the present invention typically have a mean diameter of about 50 nm to about 150 nm, more typically about 60 nm to about 130 nm, more typically about 70 nm to about 110 nm, most typically about 70 nm to about 90 nm, and are substantially nontoxic.
  • the nucleic acids when present in the nucleic acid-lipid particles of the present invention are resistant in aqueous solution to degradation with a nuclease. Nucleic acid-lipid particles and their method of preparation are disclosed in, e.g., U.S. Pat. Nos. 5,976,567; 5,981,501; 6,534,484; 6,586,410; 6,815,432; U.S. Publication No. 2010/0324120 and PCT Publication No. WO 96/40964.
  • the lipid to drug ratio (mass/mass ratio) (e.g., lipid to REVERSIR ratio) will be in the range of from about 1:1 to about 50:1, from about 1:1 to about 25:1, from about 3:1 to about 15:1, from about 4:1 to about 10:1, from about 5:1 to about 9:1, or about 6:1 to about 9:1. Ranges intermediate to the above recited ranges are also contemplated to be part of the invention.
  • the cationic lipid can be, for example, N,N-dioleyl-N,N-dimethylammonium chloride (DODAC), N,N-distearyl-N,N-dimethylammonium bromide (DDAB), N—(I-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP), N—(I-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA), N,N-dimethyl-2,3-dioleyloxy)propylamine (DODMA), 1,2-DiLinoleyloxy-N,N-dimethylaminopropane (DLinDMA), 1,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLenDMA), 1,2-Dilinoleylcarbamoyloxy-3-dimethylamino
  • the compound 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane can be used to prepare lipid-REVERSIR nanoparticles. Synthesis of 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane is described in International application no. PCT/US2009/061897, published as WO/2010/048536, which is herein incorporated by reference.
  • the lipid-REVERSIR particle includes 40% 2, 2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane: 10% DSPC: 40% Cholesterol: 10% PEG-C-DOMG (mole percent) with a particle size of 63.0 ⁇ 20 nm and a 0.027 REVERSIR/Lipid Ratio.
  • the ionizable/non-cationic lipid can be an anionic lipid or a neutral lipid including, but not limited to, distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol (DPPG), dioleoyl-phosphatidylethanolamine (DOPE), palmitoyloleoylphosphatidylcholine (POPC), palmitoyloleoylphosphatidylethanolamine (POPE), dioleoyl-phosphatidylethanolamine 4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (DOPE-mal), dipalmitoyl phosphatidyl ethanolamine (DPPE), dimyristoylphosphoethanolamine (DM
  • the conjugated lipid that inhibits aggregation of particles can be, for example, a polyethyleneglycol (PEG)-lipid including, without limitation, a PEG-diacylglycerol (DAG), a PEG-dialkyloxypropyl (DAA), a PEG-phospholipid, a PEG-ceramide (Cer), or a mixture thereof.
  • the PEG-DAA conjugate can be, for example, a PEG-dilauryloxypropyl (C 12 ), a PEG-dimyristyloxypropyl (C 14 ), a PEG-dipalmityloxypropyl (C 16 ), or a PEG-distearyloxypropyl (C 18 ).
  • the conjugated lipid that prevents aggregation of particles can be from 0 mol % to about 20 mol % or about 2 mol % of the total lipid present in the particle.
  • the nucleic acid-lipid particle further includes cholesterol at, e.g., about 10 mol % to about 60 mol % or about 48 mol % of the total lipid present in the particle.
  • lipid REVERSIR formulations cationic lipid/non-cationic lipid/cholesterol/PEG-lipid conjugate Formulation Ionizable/Cationic Lipid Lipid:REVERSIR ratio LNP_DLinDMA 1,2-Dilinolenyloxy-N,N- DLinDMA/DPPC/Cholesterol/PEG-cDMA dimethylaminopropane (DLinDMA) (57.1/7.1/34.4/1.4)
  • DSPC distearoylphosphatidylcholine
  • DPPC dipalmitoylphosphatidylcholine
  • PEG-DMG PEG-didimyristoyl glycerol (C14-PEG, or PEG-C14) (PEG with avg mol wt of 2000)
  • PEG-DSG PEG-distyryl glycerol (C18-PEG, or PEG-C18) (PEG with avg mol wt of 2000)
  • PEG-cDMA PEG-carbamoyl-1,2-dimyristyloxypropylamine (PEG with avg mol wt of 2000).
  • DLinDMA (1,2-Dilinolenyloxy-N,N-dimethylaminopropane) comprising formulations are described in International Publication No. WO2009/127060, filed Apr. 15, 2009, which is hereby incorporated by reference.
  • XTC comprising formulations are described, e.g., in U.S. Provisional Ser. No. 61/148,366, filed Jan. 29, 2009; U.S. Provisional Ser. No. 61/156,851, filed Mar. 2, 2009; U.S. Provisional Serial No. filed Jun. 10, 2009; U.S. Provisional Ser. No. 61/228,373, filed Jul. 24, 2009; U.S. Provisional Ser. No. 61/239,686, filed Sep. 3, 2009, and International Application No. PCT/US2010/022614, filed Jan. 29, 2010, which are hereby incorporated by reference.
  • MC3 comprising formulations are described, e.g., in U.S. Publication No. 2010/0324120, filed Jun. 10, 2010, the entire contents of which are hereby incorporated by reference.
  • Biodegradable lipid comprising formulations are described, e.g., PCT Publications No. WO2011/153493, filed Jun. 3, 2011 and WO/2013/086354, filed Dec. 7, 2012, the entire contents of which are hereby incorporated by reference.
  • the oligomeric compounds of the invention can be prepared and formulated as micelles.
  • micelles are a particular type of molecular assembly in which amphipathic molecules are arranged in a spherical structure such that all hydrophobic portions on the molecules are directed inward, leaving the hydrophilic portions in contact with the surrounding aqueous phase. The converse arrangement exists if the environment is hydrophobic.
  • the formulations comprises micelles formed from an oligonucleotide of the invention and at least one amphiphilic carrier, in which the micelles have an average diameter of less than about 100 nm, preferably. More preferred embodiments provide micelles having an average diameter less than about 50 nm, and even more preferred embodiments provide micelles having an average diameter less than about 30 nm, or even less than about 20 nm.
  • Micelle formulations can be prepared by mixing an aqueous solution of the oligonucleotide composition, an alkali metal C 8 to C 22 alkyl sulphate, and an amphiphilic carrier.
  • the amphiphilic carrier can be added at the same time or after addition of the alkali metal alkyl sulphate.
  • Micelles will form with substantially any kind of mixing of the ingredients but vigorous mixing in order to provide smaller size micelles.
  • oligomeric compounds of the present invention can be prepared and formulated as emulsions.
  • emulsion is a heterogenous system of one liquid dispersed in another in the form of droplets.
  • Emulsions are often biphasic systems comprising two immiscible liquid phases intimately mixed and dispersed with each other.
  • emulsions may be of either the water-in-oil (w/o) or the oil-in-water (o/w) variety.
  • w/o water-in-oil
  • o/w oil-in-water
  • Emulsions are often biphasic systems comprising two immiscible liquid phases intimately mixed and dispersed with each other.
  • emulsions may be of either the water-in-oil (w/o) or the oil-in-water (o/w) variety.
  • w/o water-in-oil
  • o/w oil-in-water
  • Emulsions may contain additional components in addition to the dispersed phases, and the active drug which may be present as a solution in either the aqueous phase, oily phase or itself as a separate phase.
  • Pharmaceutical excipients such as emulsifiers, stabilizers, dyes, and anti-oxidants may also be present in emulsions as needed.
  • Pharmaceutical emulsions may also be multiple emulsions that are comprised of more than two phases such as, for example, in the case of oil-in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w) emulsions.
  • Such complex formulations often provide certain advantages that simple binary emulsions do not.
  • Emulsions are characterized by little or no thermodynamic stability. Often, the dispersed or discontinuous phase of the emulsion is well dispersed into the external or continuous phase and maintained in this form through the means of emulsifiers or the viscosity of the formulation. Either of the phases of the emulsion may be a semisolid or a solid, as is the case of emulsion-style ointment bases and creams. Other means of stabilizing emulsions entail the use of emulsifiers that may be incorporated into either phase of the emulsion.
  • Emulsifiers may broadly be classified into four categories: synthetic surfactants, naturally occurring emulsifiers, absorption bases, and finely dispersed solids (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).
  • Synthetic surfactants also known as surface active agents, have found wide applicability in the formulation of emulsions and have been reviewed in the literature (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), Marcel Dekker, Inc., New York, N.Y., 1988, volume 1, p. 199).
  • Surfactants are typically amphiphilic and comprise a hydrophilic and a hydrophobic portion.
  • HLB hydrophile/lipophile balance
  • surfactants may be classified into different classes based on the nature of the hydrophilic group: nonionic, anionic, cationic and amphoteric (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285).
  • Naturally occurring emulsifiers used in emulsion formulations include lanolin, beeswax, phosphatides, lecithin and acacia.
  • Absorption bases possess hydrophilic properties such that they can soak up water to form w/o emulsions yet retain their semisolid consistencies, such as anhydrous lanolin and hydrophilic petrolatum. Finely divided solids have also been used as good emulsifiers especially in combination with surfactants and in viscous preparations.
  • polar inorganic solids such as heavy metal hydroxides, nonswelling clays such as bentonite, attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum silicate and colloidal magnesium aluminum silicate, pigments and nonpolar solids such as carbon or glyceryl tristearate.
  • non-emulsifying materials is also included in emulsion formulations and contributes to the properties of emulsions. These include fats, oils, waxes, fatty acids, fatty alcohols, fatty esters, humectants, hydrophilic colloids, preservatives and antioxidants (Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).
  • Hydrophilic colloids or hydrocolloids include naturally occurring gums and synthetic polymers such as polysaccharides (for example, acacia, agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth), cellulose derivatives (for example, carboxymethylcellulose and carboxypropylcellulose), and synthetic polymers (for example, carbomers, cellulose ethers, and carboxyvinyl polymers). These disperse or swell in water to form colloidal solutions that stabilize emulsions by forming strong interfacial films around the dispersed-phase droplets and by increasing the viscosity of the external phase.
  • polysaccharides for example, acacia, agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth
  • cellulose derivatives for example, carboxymethylcellulose and carboxypropylcellulose
  • synthetic polymers for example, carbomers, cellulose ethers, and
  • emulsions often contain a number of ingredients such as carbohydrates, proteins, sterols and phosphatides that may readily support the growth of microbes, these formulations often incorporate preservatives.
  • preservatives included in emulsion formulations include methyl paraben, propyl paraben, quaternary ammonium salts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boric acid.
  • Antioxidants are also commonly added to emulsion formulations to prevent deterioration of the formulation.
  • Antioxidants used may be free radical scavengers such as tocopherols, alkyl gallates, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium metabisulfite, and antioxidant synergists such as citric acid, tartaric acid, and lecithin.
  • free radical scavengers such as tocopherols, alkyl gallates, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium metabisulfite
  • antioxidant synergists such as citric acid, tartaric acid, and lecithin.
  • the compositions are formulated as microemulsions.
  • microemulsion refers to a system of water, oil and amphiphile which is a single optically isotropic and thermodynamically stable liquid solution. Microemuslions also include thermodynamically stable, isotropically clear dispersions of two immiscible liquids that are stabilized by interfacial films of surface-active molecules.
  • a microemulsion may be defined as a system of water, oil and amphiphile which is a single optically isotropic and thermodynamically stable liquid solution (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245).
  • microemulsions are systems that are prepared by first dispersing an oil in an aqueous surfactant solution and then adding a sufficient amount of a fourth component, generally an intermediate chain-length alcohol to form a transparent system.
  • microemulsions have also been described as thermodynamically stable, isotropically clear dispersions of two immiscible liquids that are stabilized by interfacial films of surface-active molecules (Leung and Shah, in: Controlled Release of Drugs: Polymers and Aggregate Systems, Rosoff, M., Ed., 1989, VCH Publishers, New York, pages 185-215).
  • Microemulsions commonly are prepared via a combination of three to five components that include oil, water, surfactant, cosurfactant and electrolyte.
  • microemulsion is of the water-in-oil (w/o) or an oil-in-water (o/w) type is dependent on the properties of the oil and surfactant used and on the structure and geometric packing of the polar heads and hydrocarbon tails of the surfactant molecules (Schott, in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 271).
  • microemulsions offer the advantage of solubilizing water-insoluble drugs in a formulation of thermodynamically stable droplets that are formed spontaneously.
  • Surfactants used in the preparation of microemulsions include, but are not limited to, ionic surfactants, non-ionic surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol fatty acid esters, tetraglycerol monolaurate (ML310), tetraglycerol monooleate (MO310), hexaglycerol monooleate (PO310), hexaglycerol pentaoleate (PO500), decaglycerol monocaprate (MCA750), decaglycerol monooleate (MO750), decaglycerol sequioleate (SO750), decaglycerol decaoleate (DAO750), alone or in combination with cosurfactants.
  • ionic surfactants non-ionic surfactants
  • Brij 96 polyoxyethylene oleyl ethers
  • polyglycerol fatty acid esters tetraglycerol monolaurate (ML310),
  • the cosurfactant usually a short-chain alcohol such as ethanol, 1-propanol, and 1-butanol, serves to increase the interfacial fluidity by penetrating into the surfactant film and consequently creating a disordered film because of the void space generated among surfactant molecules.
  • Microemulsions may, however, be prepared without the use of cosurfactants and alcohol-free self-emulsifying microemulsion systems are known in the art.
  • the aqueous phase may typically be, but is not limited to, water, an aqueous solution of the drug, glycerol, PEG300, PEG400, polyglycerols, propylene glycols, and derivatives of ethylene glycol.
  • the oil phase may include, but is not limited to, materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C8-C12) mono, di, and tri-glycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C8-C10 glycerides, vegetable oils and silicone oil.
  • materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C8-C12) mono, di, and tri-glycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C8-C10 glycerides, vegetable oils and silicone oil.
  • Microemulsions are particularly of interest from the standpoint of drug solubilization and the enhanced absorption of drugs.
  • Lipid based microemulsions both o/w and w/o have been proposed to enhance the oral bioavailability of drugs, including peptides (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385-1390; Ritschel, Meth. Find. Exp. Clin. Pharmacol., 1993, 13, 205).
  • Microemulsions afford advantages of improved drug solubilization, protection of drug from enzymatic hydrolysis, possible enhancement of drug absorption due to surfactant-induced alterations in membrane fluidity and permeability, ease of preparation, ease of oral administration over solid dosage forms, improved clinical potency, and decreased toxicity (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385; Ho et al., J. Pharm. Sci., 1996, 85, 138-143). Often microemulsions may form spontaneously when their components are brought together at ambient temperature. This may be particularly advantageous when formulating thermolabile drugs, peptides or dsRNAs. Microemulsions have also been effective in the transdermal delivery of active components in both cosmetic and pharmaceutical applications.
  • microemulsion compositions and formulations of the present invention will facilitate the increased systemic absorption of dsRNAs and nucleic acids from the gastrointestinal tract, as well as improve the local cellular uptake of dsRNAs and nucleic acids.
  • Microemulsions of the present invention may also contain additional components and additives such as sorbitan monostearate (Grill 3), Labrasol, and penetration enhancers to improve the properties of the formulation and to enhance the absorption of the dsRNAs and nucleic acids of the present invention.
  • Penetration enhancers used in the microemulsions of the present invention may be classified as belonging to one of five broad categories—surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92). Each of these classes has been discussed above.
  • the oligomeric compounds of the present invention can be prepared and formulated as lipid particles, e.g., formulated lipid particles (FLiPs) comprising (a) an oligonucleotide of the invention, where said oligonucleotide has been conjugated to a lipophile and (b) at least one lipid component, for example an emulsion, liposome, isolated lipoprotein, reconstituted lipoprotein or phospholipid, to which the conjugated oligonucleotide has been aggregated, admixed or associated.
  • FLiPs formulated lipid particles
  • FLiPs formulated lipid particles
  • the stoichiometry of oligonucleotide to the lipid component can be 1:1. Alternatively the stoichiometry can be 1:many, many:1 or many:many, where many is two or more.
  • the FLiP can comprise triacylglycerols, phospholipids, glycerol and one or several lipid-binding proteins aggregated, admixed or associated via a lipophilic linker molecule with an oligonucleotide.
  • the FLiPs show affinity to liver, gut, kidney, steroidogenic organs, heart, lung and/or muscle tissue. These FLiPs can therefore serve as carrier for oligonucleotides to these tissues.
  • lipid-conjugated oligonucleotides e.g., cholesterol-conjugated oligonucleotides
  • lipid-conjugated oligonucleotides bind to HDL and LDL lipoprotein particles which mediate cellular uptake upon binding to their respective receptors thus directing oligonucleotide delivery into liver, gut, kidney and steroidogenic organs, see Wolfrum et al. Nature Biotech. (2007), 25:1145-1157.
  • the FLiP can be a lipid particle comprising 15-25% triacylglycerol, about 0.5-2% phospholipids and 1-3% glycerol, and one or several lipid-binding proteins.
  • FLiPs can be a lipid particle having about 15-25% triacylglycerol, about 1-2% phospholipids, about 2-3% glycerol, and one or several lipid-binding proteins.
  • the lipid particle comprises about 20% triacylglycerol, about 1.2% phospholipids and about 2.25% glycerol, and one or several lipid-binding proteins.
  • lipoproteins for example isolated lipoproteins or more preferably reconstituted lipoprotieins.
  • exemplary lipoproteins include chylomicrons, VLDL (Very Low Density Lipoproteins), IDL (Intermediate Density Lipoproteins), LDL (Low Density Lipoproteins) and HDL (High Density Lipoproteins).
  • VLDL Very Low Density Lipoproteins
  • IDL Intermediate Density Lipoproteins
  • LDL Low Density Lipoproteins
  • HDL High Density Lipoproteins
  • Intralipid is a brand name for the first safe fat emulsion for human use.
  • Intralipid® 20% (a 20% intravenous fat emulsion) is made up of 20% soybean oil, 1.2% egg yolk phospholipids, 2.25% glycerin, and water for injection. It is further within the present invention that other suitable oils, such as saflower oil, can serve to produce the lipid component of the FLiP.
  • FLiP can range in size from about 20-50 nm or about 30-50 nm, e.g., about 35 nm or about 40 nm. In some embodiments, the FLiP has a particle size of at least about 100 nm. FLiPs can alternatively be between about 100-150 nm, e.g., about 110 nm, about 120 nm, about 130 nm, or about 140 nm, whether characterized as liposome- or emulsion-based. Multiple FLiPs can also be aggregated and delivered together, therefore the size can be larger than 100 nm.
  • the process for making the lipid particles comprises the steps of: (a) mixing a lipid components with one or several lipophile (e.g. cholesterol) conjugated oligonucleotides that can be chemically modified; and (b) fractionating this mixture.
  • the process comprises the additional step of selecting the fraction with particle size of 30-50 nm, preferably of about 40 nm in size.
  • the oligomeric compounds can be formulated in yeast cell wall particles (“YCWP”).
  • YCWP yeast cell wall particles
  • a yeast cell wall particle comprises an extracted yeast cell wall exterior and a core, the core comprising a payload (e.g., oligonucleotides). Exterior of the particle comprises yeast glucans (e.g. beta glucans, beta-1,3-glucans, beta-1,6-glucans), yeast mannans, or combinations thereof.
  • yeast cell wall particles are typically spherical particles about 1-4 ⁇ m in diameter.
  • yeast cell wall particles Preparation of yeast cell wall particles is known in the art, and is described, for example in U.S. Pat. Nos. 4,992,540; 5,082,936; 5,028,703; 5,032,401; 5,322,841; 5,401,727; 5,504,079; 5,607,677; 5,741,495; 5,830,463; 5,968,811; 6,444,448; and 6,476,003, U.S. Pat. App. Pub. Nos. 2003/0216346 and 2004/0014715, and Int. App. Pub. No. WO 2002/12348, contents of which are herein incorporated by reference in their entirety. Applications of yeast cell like particles for drug delivery are described, for example in U.S. Pat. Nos.
  • siRNA refers to an agent that mediates the targeted cleavage of an RNA transcript. These agents associate with a cytoplasmic multi-protein complex known as RNAi-induced silencing complex (RISC). Agents that are effective in inducing RNA interference are also referred to as siRNA, RNAi agent, or iRNA agent, herein. As used herein, the term siRNA includes microRNAs and pre-microRNAs.
  • RISC RNAi-induced silencing complex
  • RNA refers to an agent that mediates the targeted cleavage of an RNA transcript. These agents associate with a cytoplasmic multi-protein complex known as RNAi-induced silencing complex (RISC). Agents that are effective in inducing RNA interference are also referred to as siRNA, dsRNA, RNAi agent, or iRNA agent herein.
  • RISC RNAi-induced silencing complex
  • siRNA activity and “RNAi activity” refer to gene silencing by an siRNA.
  • RNA silencing by a RNA interference molecule refers to a decrease in the mRNA level in a cell for a target gene by at least about 5%, at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 99% up to and including 100%, and any integer in between of the mRNA level found in the cell without the presence of the miRNA or RNA interference molecule.
  • the mRNA levels are decreased by at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 99%, up to and including 100% and any integer in between 5% and 100%.”
  • modulate gene expression means that expression of the gene, or level of RNA molecule or equivalent RNA molecules encoding one or more proteins or protein subunits is up regulated or down regulated, such that expression, level, or activity is greater than or less than that observed in the absence of the modulator.
  • modulate can mean “inhibit,” but the use of the word “modulate” is not limited to this definition.
  • gene expression modulation happens when the expression of the gene, or level of RNA molecule or equivalent RNA molecules encoding one or more proteins or protein subunits is at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 2-fold, 3-fold, 4-fold, 5-fold or more different from that observed in the absence of the siRNA, e.g., RNAi agent.
  • the % and/or fold difference can be calculated relative to the control or the non-control, for example,
  • the term “inhibit”, “down-regulate”, or “reduce” in relation to gene expression means that the expression of the gene, or level of RNA molecules or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits, is reduced below that observed in the absence of modulator.
  • the gene expression is down-regulated when expression of the gene, or level of RNA molecules or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits, is reduced at least 10% lower relative to a corresponding non-modulated control, and preferably at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or most preferably, 100% (i.e., no gene expression).
  • the term “increase” or “up-regulate” in relation to gene expression means that the expression of the gene, or level of RNA molecules or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits, is increased above that observed in the absence of modulator.
  • the gene expression is up-regulated when expression of the gene, or level of RNA molecules or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits, is increased at least 10% relative to a corresponding non-modulated control, and preferably at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 100%, 1.1-fold, 1.25-fold, 1.5-fold, 1.75-fold, 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 50-fold, 100-fold or more.
  • “increased” or “increase” as used herein generally means an increase by a statically significant amount; for the avoidance of any doubt, “increased” means an increase of at least 10% as compared to a reference level, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% increase or any increase between 10-100% as compared to a reference level, or at least about a 2-fold, or at least about a 3-fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10-fold increase, or any increase between 2-fold and 10-fold or greater as compared to a reference level.
  • reduced or “reduce” as used herein generally means a decrease by a statistically significant amount. However, for avoidance of doubt, “reduced” means a decrease by at least 10% as compared to a reference level, for example a decrease by at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% decrease (i.e. absent level as compared to a reference sample), or any decrease between 10-100% as compared to a reference level.
  • double-stranded oligonucleotides comprising a duplex structure of between 20 and 23, but specifically 21, base pairs have been hailed as particularly effective in inducing RNA interference (Elbashir et al., EMBO 2001, 20:6877-6888). However, others have found that shorter or longer double-stranded oligonucleotides can be effective as well.
  • the double-stranded oligonucleotides comprise two oligonucleotide strands that are sufficiently complementary to hybridize to form a duplex structure.
  • the duplex structure is between 15 and 30, more generally between 18 and 25, yet more generally between 19 and 24, and most generally between 19 and 21 base pairs in length.
  • longer double-stranded oligonucleotides of between 25 and 30 base pairs in length are preferred.
  • shorter double-stranded oligonucleotides of between 10 and 15 base pairs in length are preferred.
  • the double-stranded oligonucleotide is at least 21 nucleotides long.
  • the double-stranded oligonucleotide comprises a sense strand and an antisense strand, wherein the antisense RNA strand has a region of complementarity which is complementary to at least a part of a target sequence, and the duplex region is 14-30 nucleotides in length.
  • the region of complementarity to the target sequence is between 14 and 30, more generally between 18 and 25, yet more generally between 19 and 24, and most generally between 19 and 21 nucleotides in length.
  • antisense strand refers to an oligomeric compound that is substantially or 100% complementary to a target sequence of interest.
  • antisense strand includes the antisense region of both oligomeric compounds that are formed from two separate strands, as well as unimolecular oligomeric compounds that are capable of forming hairpin or dumbbell type structures.
  • antisense strand and guide strand are used interchangeably herein.
  • sense strand refers to an oligomeric compound that has the same nucleoside sequence, in whole or in part, as a target sequence such as a messenger RNA or a sequence of DNA.
  • target sequence such as a messenger RNA or a sequence of DNA.
  • sense strand and passenger strand are used interchangeably herein.
  • nucleic acid can form hydrogen bond(s) with another nucleic acid sequence by either traditional Watson-Crick or other non-traditional types.
  • the binding free energy for a nucleic acid molecule with its complementary sequence is sufficient to allow the relevant function of the nucleic acid to proceed, e.g., RNAi activity. Determination of binding free energies for nucleic acid molecules is well known in the art (see, e.g., Turner et al, 1987 , CSH Symp. Quant. Biol . LII pp. 123-133; Frier et al., 1986 , Proc. Nat. Acad. Sci .
  • a percent complementarity indicates the percentage of contiguous residues in a nucleic acid molecule that can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary). “Perfectly complementary” or 100% complementarity means that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence.
  • nucleoside units of two strands can hydrogen bond with each other.
  • Substantial complementarity refers to polynucleotide strands exhibiting 90% or greater complementarity, excluding regions of the polynucleotide strands, such as overhangs, that are selected so as to be noncomplementary. Specific binding requires a sufficient degree of complementarity to avoid non-specific binding of the oligomeric compound to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, or in the case of in vitro assays, under conditions in which the assays are performed.
  • the non-target sequences typically differ by at least 5 nucleotides.
  • off-target and the phrase “off-target effects” refer to any instance in which an siRNA against a given target causes an unintended affect by interacting either directly or indirectly with another mRNA sequence, a DNA sequence or a cellular protein or other moiety.
  • an “off-target effect” may occur when there is a simultaneous degradation of other transcripts due to partial homology or complementarity between that other transcript and the sense and/or antisense strand of an siRNA.
  • the double-stranded region of a double-stranded oligomeric compound is equal to or at least, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotide pairs in length.
  • the antisense strand of a double-stranded oligomeric compound is equal to or at least 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length.
  • the sense strand of a double-stranded oligomeric compound is equal to or at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length.
  • one strand has at least one stretch of 1-5 single-stranded nucleotides in the double-stranded region.
  • stretch of single-stranded nucleotides in the double-stranded region is meant that there is present at least one nucleotide base pair at both ends of the single-stranded stretch.
  • both strands have at least one stretch of 1-5 (e.g., 1, 2, 3, 4, or 5) single-stranded nucleotides in the double stranded region.
  • both strands have a stretch of 1-5 (e.g., 1, 2, 3, 4, or 5) single-stranded nucleotides in the double stranded region
  • such single-stranded nucleotides can be opposite to each other (e.g., a stretch of mismatches) or they can be located such that the second strand has no single-stranded nucleotides opposite to the single-stranded oligonucleotides of the first strand and vice versa (e.g., a single-stranded loop).
  • the single-stranded nucleotides are present within 8 nucleotides from either end, for example 8, 7, 6, 5, 4, 3, or 2 nucleotide from either the 5′ or 3′ end of the region of complementarity between the two strands.
  • each strand of the double-stranded oligonucleotide has a ZXY structure, such as is described in PCT Publication No. 2004080406, content of which is hereby incorporated in its entireties.
  • the two strands of double-stranded oligomeric compound can be linked together.
  • the two strands can be linked to each other at both ends, or at one end only.
  • linking at one end is meant that 5′-end of first strand is linked to the 3′-end of the second strand or 3′-end of first strand is linked to 5′-end of the second strand.
  • 5′-end of first strand is linked to 3′-end of second strand and 3′-end of first strand is linked to 5′-end of second strand.
  • the two strands can be linked together by an oligonucleotide linker including, but not limited to, (N) n ; wherein N is independently a modified or unmodified nucleotide and n is 3-23. In some embodiments, n is 3-10, e.g., 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, the oligonucleotide linker is selected from the group consisting of GNRA, (G) 4 , (U) 4 , and (dT) 4 , wherein N is a modified or unmodified nucleotide and R is a modified or unmodified purine nucleotide.
  • nucleotides in the linker can be involved in base-pair interactions with other nucleotides in the linker.
  • the two strands can also be linked together by a non-nucleosidic linker, e.g. a linker described herein. It will be appreciated by one of skill in the art that any oligonucleotide chemical modifications or variations describe herein can be used in the oligonucleotide linker.
  • Hairpin and dumbbell type oligomeric compounds will have a duplex region equal to or at least 14, 15, 15, 16, 17, 18, 19, 29, 21, 22, 23, 24, or 25 nucleotide pairs.
  • the duplex region can be equal to or less than 200, 100, or 50, in length. In some embodiments, ranges for the duplex region are 15-30, 17 to 23, 19 to 23, and 19 to 21 nucleotides pairs in length.
  • the hairpin oligomeric compounds can have a single strand overhang or terminal unpaired region, in some embodiments at the 3′, and in some embodiments on the antisense side of the hairpin. In some embodiments, the overhangs are 1-4, more generally 2-3 nucleotides in length.
  • the hairpin oligomeric compounds that can induce RNA interference are also referred to as “shRNA” herein.
  • two oligomeric strands specifically hybridize when there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target nucleic acid sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and under conditions in which assays are performed in the case of in vitro assays.
  • stringent hybridization conditions or “stringent conditions” refers to conditions under which an antisense compound will hybridize to its target sequence, but to a minimal number of other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances, and “stringent conditions” under which antisense compounds hybridize to a target sequence are determined by the nature and composition of the antisense compounds and the assays in which they are being investigated.
  • Tm melting temperature
  • a target nucleic acid is a mRNA.
  • siRNAs are designed to modulate that target mRNA or its expression.
  • designing an antisense compound to a target nucleic acid molecule can be a multistep process. Typically the process begins with the identification of a target protein, the activity of which is to be modulated, and then identifying the nucleic acid the expression of which yields the target protein.
  • designing of an antisense compound results in an antisense compound that is hybridizable to the targeted nucleic acid molecule.
  • the antisense compound is an antisense oligonucleotide or antisense oligonucleoside.
  • an antisense compound and a target nucleic acid are complementary to one another. In certain such embodiments, an antisense compound is perfectly complementary to a target nucleic acid. In certain embodiments, an antisense compound includes one mismatch. In certain embodiments, an antisense compound includes two mismatches. In certain embodiments, an antisense compound includes three or more mismatches.
  • RNA to be modulated include, but are not limited to, translocation functions, which include, but are not limited to, translocation of the RNA to a site of protein translation, translocation of the RNA to sites within the cell which are distant from the site of RNA synthesis, and translation of protein from the RNA.
  • RNA processing functions that can be modulated include, but are not limited to, splicing of the RNA to yield one or more RNA species, capping of the RNA, 3′ maturation of the RNA and catalytic activity or complex formation involving the RNA which may be engaged in or facilitated by the RNA.
  • Modulation of expression can result in the increased level of one or more nucleic acid species or the decreased level of one or more nucleic acid species, either temporally or by net steady state level.
  • modulation of expression can mean increase or decrease in target RNA or protein levels.
  • modulation of expression can mean an increase or decrease of one or more RNA splice products, or a change in the ratio of two or more splice products.
  • the siRNA is a conjugated siRNA.
  • conjugated siRNA refers to an RNAi agent that is conjugated with a ligand.
  • the siRNA is an unconjugated siRNA.
  • unconjugated siRNA referes to an RNAi agent that is not conjugated with a ligand, e.g., a ligand described herein.
  • the invention relates to a double-stranded RNA (dsRNA) agent, i.e., siRNA, for inhibiting the expression of a target gene.
  • dsRNA agent comprises a sense strand and an antisense strand, each strand having 14 to 40 nucleotides.
  • the dsRNA agent is represented by formula (I):
  • B1, B2, B3, B1′, B2′, B3′, and B4′ each are independently a nucleotide containing a modification selected from the group consisting of 2′-O-alkyl, 2′-substituted alkoxy, 2′-substituted alkyl, 2′-halo, ENA, and BNA/LNA.
  • B1, B2, B3, B1′, B2′, B3′, and B4′ each contain 2′-OMe modifications.
  • C1 is a thermally destabilizing nucleotide placed at a site opposite to the seed region of the antisense strand (i.e., at positions 2-8 of the 5′-end of the antisense strand).
  • C1 is at a position of the sense strand that pairs with a nucleotide at positions 2-8 of the 5′-end of the antisense strand.
  • C1 nucleotide bears the thermally destabilizing modification which can include abasic modification; mismatch with the opposing nucleotide in the duplex; and sugar modification such as 2′-deoxy modification or acyclic nucleotide e.g., unlocked nucleic acids (UNA) or glycerol nuceltic acid (GNA).
  • C1 has thermally destabilizing modification selected from the group consisting of: i) mismatch with the opposing nucleotide in the antisense strand; ii) abasic modification selected from the group consisting of:
  • the thermally destabilizing modification in C1 is a mismatch selected from the group consisting of G:G, G:A, G:U, G:T, A:A, A:C, C:C, C:U, C:T, U:U, T:T, and U:T; and optionally, at least one nucleobase in the mismatch pair is a 2′-deoxy nucleobase.
  • the thermally destabilizing modification in C1 is GNA or
  • T1, T1′, T2′, and T3′ each independently represent a nucleotide comprising a modification providing the nucleotide a steric bulk that is less or equal to the steric bulk of a 2′-OMe modification.
  • the modification can be at the 2′ position of a ribose sugar of the nucleotide, or a modification to a non-ribose nucleotide, acyclic nucleotide, or the backbone of the nucleotide that is similar or equivalent to the 2′ position of the ribose sugar, and provides the nucleotide a steric bulk that is less than or equal to the steric bulk of a 2′-OMe modification.
  • T1, T1′, T2′, and T3′ are each independently selected from DNA, RNA, LNA, 2′-F, and 2′-F-5′-methyl.
  • T1 is DNA.
  • T1′ is DNA, RNA or LNA.
  • T2′ is DNA or RNA.
  • T3′ is DNA or RNA.
  • n 1 , n 3 , and q 1 are independently 4 to 15 nucleotides in length.
  • n 5 , q 3 , and q 7 are independently 1-6 nucleotide(s) in length.
  • n 4 , q 2 , and q 6 are independently 1-3 nucleotide(s) in length.
  • q 5 is independently 0-10 nucleotide(s) in length.
  • n 2 and q 4 are independently 0-3 nucleotide(s) in length.
  • n 4 is 0-3 nucleotide(s) in length.
  • n 4 can be 0. In one example, n 4 is 0, and q 2 and q 6 are 1. In another example, n 4 is 0, and q 2 and q 6 are 1, with two phosphorothioate internucleotide linkage modifications within position 1-5 of the sense strand (counting from the 5′-end of the sense strand), and two phosphorothioate internucleotide linkage modifications at positions 1 and 2 and two phosphorothioate internucleotide linkage modifications within positions 18-23 of the antisense strand (counting from the 5′-end of the antisense strand).
  • n 4 , q 2 , and q 6 are each 1.
  • n 2 , n 4 , q 2 , q 4 , and q 6 are each 1.
  • C1 is at position 14-17 of the 5′-end of the sense strand, when the sense strand is 19-22 nucleotides in length, and n 4 is 1.
  • T3′ starts at position 2 from the 5′ end of the antisense strand. In one example, T3′ is at position 2 from the 5′ end of the antisense strand and q 6 is equal to 1.
  • T1′ starts at position 14 from the 5′ end of the antisense strand. In one example, T1′ is at position 14 from the 5′ end of the antisense strand and q 2 is equal to 1.
  • T1′ and T3′ are separated by 11 nucleotides in length (i.e. not counting the T1′ and T3′ nucleotides.
  • T1′ is at position 14 from the 5′ end of the antisense strand. In one example, T1′ is at position 14 from the 5′ end of the antisense strand and q 2 is equal to 1, and the modification at the 2′ position or positions in a non-ribose, acyclic or backbone that provide less steric bulk than a 2′-OMe ribose.
  • T3′ is at position 2 from the 5′ end of the antisense strand. In one example, T3′ is at position 2 from the 5′ end of the antisense strand and q 6 is equal to 1, and the modification at the 2′ position or positions in a non-ribose, acyclic or backbone that provide less than or equal to steric bulk than a 2′-OMe ribose.
  • T1 is at cleavage site of the sense strand. In one example, T1 is at position 11 from the 5′ end of the sense strand, when the sense strand is 19-22 nucleotides in length, and n 2 is 1.
  • T2′ starts at position 6 from the 5′ end of the antisense strand. In one example, T2′ is at positions 6-10 from the 5′ end of the antisense strand, and q 4 is 1.
  • B1 is 2′-OMe or 2′-F
  • n 1 8
  • T1 is 2′F
  • n 2 3
  • B2 is 2′-OMe
  • n 3 7
  • n 4 is 0,
  • B3 is 2′OMe
  • n 5 3
  • B1′ is 2′-OMe or 2′-F
  • q 1 9
  • T1′ is 2′-F
  • q 2 1, B2′ is 2′-OMe or 2′-F
  • q 3 4,
  • T2′ is 2′-F
  • q 4 2,
  • B3′ 2′-OMe or 2′-F
  • q 5 5
  • T3′ is 2′-F
  • q 6 1
  • B4′ is 2′-OMe
  • q 7 1
  • B1 is 2′-OMe or 2′-F
  • n 1 8
  • T1 is 2′F
  • n 2 3
  • B2 is 2′-OMe
  • n 3 7, n 4 is 0,
  • B3 is 2′-OMe
  • n 5 3
  • B1′ 2′-OMe or 2′-F
  • q 1 9
  • T1′ is 2′-F
  • q 2 1, B2′ is 2′-OMe or 2′-F
  • q 3 4,
  • T2′ is 2′-F
  • q 4 2,
  • B3′ 2′-OMe or 2′-F
  • q 5 5
  • T3′ 2′-F
  • q 7 1; with two phosphorothioate internucleotide linkage modifications within position 1-5 of the sense strand (counting from the 5′-end of the sense strand), and two phosphorothioate internucleotide link
  • B1 is 2′-OMe or 2′-F
  • n 1 8
  • T1 is 2′F
  • n 2 3
  • B2 is 2′-OMe
  • n 3 7, n 4 is 0,
  • B3 is 2′-OMe
  • n 5 3
  • B1′ is 2′-OMe or 2′-F
  • q 1 9
  • T1′ is 2′-F
  • q 2 1, B2′ is 2′-OMe or 2′-F
  • q 3 4, q 4 is 0,
  • B3′ is 2′-OMe or 2′-F
  • q 5 7
  • T3′ 2′-F
  • q 7 1
  • B1 is 2′-OMe or 2′-F
  • n 1 8
  • T1 is 2′F
  • n 2 3
  • B2 is 2′-OMe
  • n 3 7, n 4 is 0,
  • B3 is 2′-OMe
  • n 5 3
  • B1′ is 2′-OMe or 2′-F
  • q 1 9
  • T1′ is 2′-F
  • q 2 1, B2′ is 2′-OMe or 2′-F
  • q 3 4, q 4 is 0,
  • B3′ is 2′-OMe or 2′-F
  • q 5 7
  • T3′ 2′-F
  • q 7 1; with two phosphorothioate internucleotide linkage modifications within position 1-5 of the sense strand (counting from the 5′-end), and two phosphorothioate internucleotide linkage modifications at positions 1 and 2 and two phosphorothi
  • B1 is 2′-OMe or 2′-F
  • n 1 8
  • T1 is 2′F
  • n 2 3
  • B2 is 2′-OMe
  • n 3 7
  • n 4 is 0,
  • B3 is 2′OMe
  • n 5 3
  • B1′ is 2′-OMe or 2′-F
  • q 1 9
  • T1′ is 2′-F
  • q 2 1, B2′ is 2′-OMe or 2′-F
  • q 3 4,
  • T2′ is 2′-F
  • q 4 2,
  • B3′ 2′-OMe or 2′-F
  • q 5 5
  • T3′ is 2′-F
  • q 6 1
  • B4′ is 2′-F
  • q 7 1
  • B1 is 2′-OMe or 2′-F
  • n 1 8
  • T1 is 2′F
  • n 2 3
  • B2 is 2′-OMe
  • n 3 7, n 4 is 0,
  • B3 is 2′-OMe
  • n 5 3
  • B1′ is 2′-OMe or 2′-F
  • q 1 9
  • T1′ is 2′-F
  • q 2 1, B2′ is 2′-OMe or 2′-F
  • q 3 4,
  • T2′ is 2′-F
  • q 4 2,
  • B3′ 2′-OMe or 2′-F
  • q 5 5
  • T3′ 2′-F
  • q 7 1; with two phosphorothioate internucleotide linkage modifications within position 1-5 of the sense strand (counting from the 5′-end of the sense strand), and two phosphorothioate internucleotide link
  • B1 is 2′-OMe or 2′-F
  • n 1 8
  • T1 is 2′F
  • n 2 3
  • B2 is 2′-OMe
  • n 3 7, n 4 is 0,
  • B3 is 2′-OMe
  • n 5 3
  • B1′ is 2′-OMe or 2′-F
  • q 1 9
  • T1′ is 2′-F
  • q 2 1, B2′ is 2′-OMe or 2′-F
  • q 3 4, q 4 is 0,
  • B3′ is 2′-OMe or 2′-F
  • q 5 7
  • T3′ 2′-F
  • q 7 1
  • B1 is 2′-OMe or 2′-F
  • n 1 8 T1 is 2′F
  • n 2 3
  • B2 is 2′-OMe
  • n 3 7, n 4 is 0,
  • B3 is 2′-OMe
  • n 5 3
  • B1′ 2′-OMe or 2′-F
  • q 1 9
  • T1′ is 2′-F
  • q 2 1, B2′ is 2′-OMe or 2′-F
  • q 3 4, q 4 is 0, B3′ is 2′-OMe or 2′-F
  • q 5 7
  • T3′ 2′-F
  • q 7 1; with two phosphorothioate internucleotide linkage modifications within position 1-5 of the sense strand (counting from the 5′-end of the sense strand), and two phosphorothioate internucleotide linkage modifications at positions 1 and 2 and two phosphorothio
  • 100%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35% or 30% of the dsRNA agent of the invention is modified.
  • each of the sense and antisense strands of the dsRNA agent is independently modified with acyclic nucleotides, LNA, HNA, CeNA, 2′-methoxyethyl, 2′-O-methyl, 2′-O-allyl, 2′-C-allyl, 2′-deoxy, 2′-fluoro, 2′-O—N-methylacetamido (2′-O-NMA), a 2′-O-dimethylaminoethoxyethyl (2′-O-DMAEOE), 2′-O-aminopropyl (2′-O-AP), or 2′-ara-F.
  • each of the sense and antisense strands of the dsRNA agent contains at least two different modifications.
  • the dsRNA agent of Formula (I) further comprises 3′ and/or 5′ overhang(s) of 1-10 nucleotides in length.
  • dsRNA agent of formula (I) comprises a 3′ overhang at the 3′-end of the antisense strand and a blunt end at the 5′-end of the antisense strand.
  • the dsRNA agent has a 5′ overhang at the 5′-end of the sense strand.
  • the dsRNA agent of the invention does not contain any 2′-F modification.
  • the sense strand and/or antisense strand of the dsRNA agent comprises one or more blocks of phosphorothioate or methylphosphonate internucleotide linkages.
  • the sense strand comprises one block of two phosphorothioate or methylphosphonate internucleotide linkages.
  • the antisense strand comprises two blocks of two phosphorothioate or methylphosphonate internucleotide linkages.
  • the two blocks of phosphorothioate or methylphosphonate internucleotide linkages are separated by 16-18 phosphate internucleotide linkages.
  • each of the sense and antisene strands of the dsRNA agent has 15-30 nucleotides.
  • the sense strand has 19-22 nucleotides, and the antisense strand has 19-25 nucleotides.
  • the sense strand has 21 nucleotides, and the antisense strand has 23 nucleotides.
  • the nucleotide at position 1 of the 5′-end of the antisense strand in the duplex is selected from the group consisting of A, dA, dU, U, and dT. In one embodiment, at least one of the first, second, and third base pair from the 5′-end of the antisense strand is an AU base pair.
  • the antisense strand of the dsRNA agent of the invention is 100% complementary to a target RNA to hybridize thereto and inhibits its expression through RNA interference. In another embodiment, the antisense strand of the dsRNA agent of the invention is at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 65%, at least 60%, at least 55%, or at least 50% complementary to a target RNA.
  • the invention relates to a dsRNA agent capable of inhibiting the expression of a target gene.
  • the dsRNA agent comprises a sense strand and an antisense strand, each strand having 14 to 40 nucleotides.
  • the sense strand contains at least one thermally destabilizing nucleotide, wherein at at least one said thermally destabilizing nucleotide occurs at or near the site that is opposite to the seed region of the antisense strand (i.e. at position 2-8 of the 5′-end of the antisense strand), For example, the thermally destabilizing nucleotide occurs between positions 14-17 of the 5′-end of the sense strand when the sense strand is 21 nucleotides in length.
  • the antisense strand contains at least two modified nucleic acids that are smaller than a sterically demanding 2′-OMe modification.
  • the two modified nucleic acids that is smaller than a sterically demanding 2′-OMe are separated by 11 nucleotides in length.
  • the two modified nucleic acids are at positions 2 and 14 of the 5′end of the antisense strand.
  • the sense strand sequence of the dsRNA agent is represented by formula (Is):
  • the sense strand sequence having 19, 20, 21, or 22 nucleotides in length of the dsRNA agent is represented by formula (Is):
  • the dsRNA agent of formula (Is) further comprises 3′ and/or 5′ overhang(s) of 1-10 nucleotides in length. In one example, the dsRNA agent of formula (Is) comprises a 5′ overhang.
  • C1 comprises one thermally destabilizing nucleotide at position 14, 15, 16 or 17 from the 5′-end of the sense strand.
  • C1 is an acyclic nucleotide (e.g., UNA or GNA), mismatch, abasic, or DNA.
  • C1 is a GNA.
  • T1 comprises a DNA, RNA, LNA, 2′-F, or 2′-F-5′-methyl at position 11 from the 5′-end of the sense strand.
  • the dsRNA agent of the invention comprises a sense strand (Is), wherein C1 is an acyclic nucleotide (e.g., UNA or GNA), mismatch, abasic, or DNA; and T1 comprises a DNA, RNA, LNA, 2′-F, or 2′-F-5′-methyl at position 11 from the 5′-end of the sense strand.
  • C1 is an acyclic nucleotide (e.g., UNA or GNA), mismatch, abasic, or DNA
  • T1 comprises a DNA, RNA, LNA, 2′-F, or 2′-F-5′-methyl at position 11 from the 5′-end of the sense strand.
  • the antisense strand sequence of the dsRNA agent is represented by formula (Ia):
  • the antisense strand sequence having 19, 20, 21, 22, 23, 24, or 25 nucleotides in length of the dsRNA agent is represented by formula (Ia):
  • dsRNA of formula (Ia) further comprises 3′ and/or 5′ overhang(s) of 1-10 nucleotides in length. In one example, dsRNA of formula (Ia) comprises a 3′ overhang.
  • the invention relates to a double-stranded RNA (dsRNA) agent for inhibiting the expression of a target gene.
  • dsRNA agent comprises a sense strand and an antisense strand, each strand having 14 to 40 nucleotides:
  • the invention relates to a double-stranded RNA (dsRNA) agent for inhibiting the expression of a target gene.
  • dsRNA agent comprises a sense strand and an antisense strand, each strand having 14 to 40 nucleotides:
  • the invention relates to a double-stranded RNA (dsRNA) agent for inhibiting the expression of a target gene.
  • dsRNA agent comprises a sense strand and an antisense strand, each strand having 15-30 nucleotides:
  • the invention relates to a double-stranded RNA (dsRNA) agent for inhibiting the expression of a target gene.
  • dsRNA agent comprises a sense strand and an antisense strand, each strand having 19-23 nucleotides:
  • the invention relates to a double-stranded RNA (dsRNA) agent for inhibiting the expression of a target gene.
  • dsRNA agent comprises a sense strand and an antisense strand, each strand having 14 to 40 nucleotides:
  • the invention relates to a double-stranded RNA (dsRNA) agent for inhibiting the expression of a target gene.
  • dsRNA agent comprises a sense strand and an antisense strand, each strand having 14 to 40 nucleotides:
  • the invention relates to a double-stranded RNA (dsRNA) agent for inhibiting the expression of a target gene.
  • dsRNA agent comprises a sense strand and an antisense strand, each strand having 14 to 40 nucleotides:
  • the dsRNA agent can be optimized for RNA interference by increasing the propensity of the dsRNA duplex to disassociate or melt (decreasing the free energy of duplex association) by introducing a thermally destabilizing modification in the sense strand at a site opposite to the seed region of the antisense strand (i.e., at positions 2-8 of the 5′-end of the antisense strand). This modification can increase the propensity of the duplex to disassociate or melt in the seed region of the antisense strand.
  • the thermally destabilizing modifications can include abasic modification; mismatch with the opposing nucleotide in the opposing strand; and sugar modification such as 2′-deoxy modification or acyclic nucleotide, e.g., unlocked nucleic acids (UNA) or glycerol nuceltic acid (GNA).
  • UUA unlocked nucleic acids
  • GAA glycerol nuceltic acid
  • acyclic nucleotide refers to any nucleotide having an acyclic ribose sugar, for example, where any of bonds between the ribose carbons (e.g., C1′-C2′, C2′-C3′, C3′-C4′, C4′-O4′, or C1′-O4′) is absent and/or at least one of ribose carbons or oxygen (e.g., C1′, C2′, C3′, C4′ or O4′) are independently or in combination absent from the nucleotide.
  • bonds between the ribose carbons e.g., C1′-C2′, C2′-C3′, C3′-C4′, C4′-O4′, or C1′-O4′
  • ribose carbons or oxygen e.g., C1′, C2′, C3′, C4′ or O4′
  • acyclic nucleotide is
  • B is a modified or unmodified nucleobase
  • R 1 and R 2 independently are H, halogen, OR 3 , or alkyl
  • R 3 is H, alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar).
  • the term “UNA” refers to unlocked acyclic nucleic acid, wherein any of the bonds of the sugar has been removed, forming an unlocked “sugar” residue.
  • UNA also encompasses monomers with bonds between C1′-C4′ being removed (i.e. the covalent carbon-oxygen-carbon bond between the C1′ and C4′ carbons).
  • the C2′-C3′ bond i.e.
  • the acyclic derivative provides greater backbone flexibility without affecting the Watson-Crick pairings.
  • the acyclic nucleotide can be linked via 2′-5′ or 3′-5′ linkage.
  • glycol nucleic acid refers to glycol nucleic acid which is a polymer similar to DNA or RNA but differing in the composition of its “backbone” in that is composed of repeating glycerol units linked by phosphodiester bonds:
  • the thermally destabilizing modification can be mismatches (i.e., noncomplementary base pairs) between the thermally destabilizing nucleotide and the opposing nucleotide in the opposite strand within the dsRNA duplex.
  • exemplary mismatch basepairs include G:G, G:A, G:U, G:T, A:A, A:C, C:C, C:U, C:T, U:U, T:T, U:T, or a combination thereof.
  • Other mismatch base pairings known in the art are also amenable to the present invention.
  • a mismatch can occur between nucleotides that are either naturally occurring nucleotides or modified nucleotides, i.e., the mismatch base pairing can occur between the nucleobases from respective nucleotides independent of the modifications on the ribose sugars of the nucleotides.
  • the dsRNA agent contains at least one nucleobase in the mismatch pairing that is a 2′-deoxy nucleobase; e.g., the 2′-deoxy nucleobase is in the sense strand.
  • the thermally destabilizing modifications may also include universal base with reduced or abolished capability to form hydrogen bonds with the opposing bases, and phosphate modifications.
  • nucleobase modifications with impaired or completely abolished capability to form hydrogen bonds with bases in the opposite strand have been evaluated for destabilization of the central region of the dsRNA duplex as described in WO 2010/0011895, which is herein incorporated by reference in its entirety.
  • Exemplary nucleobase modifications are:
  • Exemplary phosphate modifications known to decrease the thermal stability of dsRNA duplexes compared to natural phosphodiester linkages are:
  • the dsRNA agent of the invention can comprise 2′-5′ linkages (with 2′-H, 2′-OH and 2′-OMe and with P ⁇ O or P ⁇ S).
  • the 2′-5′ linkages modifications can be used to promote nuclease resistance or to inhibit binding of the sense to the antisense strand, or can be used at the 5′ end of the sense strand to avoid sense strand activation by RISC.
  • the dsRNA agent of the invention can comprise L sugars (e.g., L ribose, L-arabinose with 2′-H, 2′-OH and 2′-OMe).
  • L sugars e.g., L ribose, L-arabinose with 2′-H, 2′-OH and 2′-OMe.
  • these L sugars modifications can be used to promote nuclease resistance or to inhibit binding of the sense to the antisense strand, or can be used at the 5′ end of the sense strand to avoid sense strand activation by RISC.
  • the dsRNA agent is a multimer containing at least two duplexes represented by formula (I), wherein said duplexes are connected by a linker.
  • the linker can be cleavable or non-cleavable.
  • said multimer further comprise a ligand.
  • Each of the dsRNA agent can target the same gene or two different genes; or each of the dsRNA agent can target same gene at two different target sites.
  • the dsRNA agent is a multimer containing three, four, five, six or more duplexes represented by formula (I), wherein said duplexes are connected by a linker.
  • the linker can be cleavable or non-cleavable.
  • said multimer further comprises a ligand.
  • Each of the dsRNA agent can target the same gene or two different genes; or each of the dsRNA agent can target same gene at two different target sites.
  • two dsRNA agent represented by formula (I) are linked to each other at the 5′ end, and one or both of the 3′ ends of the are optionally conjugated to a ligand.
  • Each of the dsRNA can target the same gene or two different genes; or each of the dsRNA can target same gene at two different target sites.
  • the dsRNA agent that contains conjugations of one or more carbohydrate moieties to a dsRNA agent can optimize one or more properties of the dsRNA agent.
  • the carbohydrate moiety will be attached to a modified subunit of the dsRNA agent.
  • the ribose sugar of one or more ribonucleotide subunits of a dsRNA agent can be replaced with another moiety, e.g., a non-carbohydrate (preferably cyclic) carrier to which is attached a carbohydrate ligand.
  • a ribonucleotide subunit in which the ribose sugar of the subunit has been so replaced is referred to herein as a ribose replacement modification subunit (RRMS).
  • a cyclic carrier may be a carbocyclic ring system, i.e., all ring atoms are carbon atoms, or a heterocyclic ring system, i.e., one or more ring atoms may be a heteroatom, e.g., nitrogen, oxygen, sulfur.
  • the cyclic carrier may be a monocyclic ring system, or may contain two or more rings, e.g. fused rings.
  • the cyclic carrier may be a fully saturated ring system, or it may contain one or more double bonds.
  • the ligand may be attached to the polynucleotide via a carrier.
  • the carriers include (i) at least one “backbone attachment point,” preferably two “backbone attachment points” and (ii) at least one “tethering attachment point.”
  • a “backbone attachment point” as used herein refers to a functional group, e.g. a hydroxyl group, or generally, a bond available for, and that is suitable for incorporation of the carrier into the backbone, e.g., the phosphate, or modified phosphate, e.g., sulfur containing, backbone, of a ribonucleic acid.
  • a “tethering attachment point” in some embodiments refers to a constituent ring atom of the cyclic carrier, e.g., a carbon atom or a heteroatom (distinct from an atom which provides a backbone attachment point), that connects a selected moiety.
  • the moiety can be, e.g., a carbohydrate, e.g. monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide and polysaccharide.
  • the selected moiety is connected by an intervening tether to the cyclic carrier.
  • the cyclic carrier will often include a functional group, e.g., an amino group, or generally, provide a bond, that is suitable for incorporation or tethering of another chemical entity, e.g., a ligand to the constituent ring.
  • a functional group e.g., an amino group
  • another chemical entity e.g., a ligand to the constituent ring.
  • the dsRNA agent of the invention is conjugated to a ligand via a carrier, wherein the carrier can be cyclic group or acyclic group; preferably, the cyclic group is selected from pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, [1,3]dioxolane, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuryl and decalin; preferably, the acyclic group is selected from serinol backbone or diethanolamine backbone.
  • the double-stranded RNA (dsRNA) agent of the invention may optionally be conjugated to one or more ligands.
  • the ligand can be attached to the sense strand, antisense strand or both strands, at the 3′-end, 5′-end or both ends.
  • the ligand may be conjugated to the sense strand, in particular, the 3′-end of the sense strand.
  • dsRNA agents of the invention are 5′ phosphorylated or include a phosphoryl analog at the 5′ prime terminus.
  • 5′-phosphate modifications include those which are compatible with RISC mediated gene silencing. Suitable modifications include: 5′-monophosphate ((HO)2(O)P-O-5′); 5′-diphosphate ((HO)2(O)P—O—P(HO)(O)—O-5′); 5′-triphosphate ((HO)2(O)P—O—(HO)(O)P—O—P(HO)(O)—O-5′); 5′-guanosine cap (7-methylated or non-methylated) (7m-G-O-5′-(HO)(O)P—O—(HO)(O)P—O—P(HO)(O)—O-5′); 5′-adenosine cap (Appp), and any modified or unmodified nucleotide cap structure (N—O-5′-(HO)(O)P—O
  • the modification can in placed in the antisense strand of a dsRNA agent.
  • siRNA activity it is desirable to inhibit siRNA activity.
  • siRNAtarget is an mRNA
  • certain siRNAs have been used therapeutically.
  • siRNAs are long-acting.
  • long acting siRNAs are desirable, for their convenience.
  • a patient may respond poorly to treatment or receive too high a dose.
  • a reverser compound can be administered to at least partially reduce the RNAi activity of the siRNA.
  • the long-lasting effect of siRNA makes waiting for that effect to slowly diminish through natural clearance an unattractive option.
  • siRNAs are useful for inhibiting blood clotting factors (e.g., Factor II (prothrombin), Factor VII, Factor IX, etc.).
  • blood clotting factors e.g., Factor II (prothrombin), Factor VII, Factor IX, etc.
  • Such siRNAs have therapeutic potential as anticoagulants. Long half-lives make such siRNAs particularly attractive, however, if a patient receives too high a dose, has surgery (where anti-coagulation is undesirable) or otherwise desires a decrease in the anti-coagulant effect, a reverser compound to the anti-coagulant siRNA can be administered. Such REVERSIR compound will restore coagulation function more quickly than simply waiting for natural clearance of the siRNA. This example is provided for illustrative purposes.
  • siRNAs have been designed to a vast number of targets, including without limitation, a vast number of messenger RNA (mRNA) targets and pre-mRNA targets, as well as a vast number of non-coding RNA targets.
  • mRNA messenger RNA
  • REVERSIR compounds provided herein are suitable for any siRNA, regardless of the target or mechanism of the siRNA compound.
  • the invention provides REVERSIR compounds to an siRNA targeted to an mRNA.
  • the target mRNA encodes a protein involved in metabolism.
  • the target mRNA encodes a protein involved in cardiac function.
  • the target mRNA encodes a protein involved in blood-clotting.
  • Exemplary siRNA compounds targeting any of a variety of target proteins are known in the art. Further, methods for preparing siRNA against a target gene are well known in the art and readily available to one of skill in the art.
  • target genes for siRNAs include, but are not limited to genes promoting unwanted cell proliferation, growth factor gene, growth factor receptor gene, genes expressing kinases, an adaptor protein gene, a gene encoding a G protein super family molecule, a gene encoding a transcription factor, a gene which mediates angiogenesis, a viral gene, a gene required for viral replication, a cellular gene which mediates viral function, a gene of a bacterial pathogen, a gene of an amoebic pathogen, a gene of a parasitic pathogen, a gene of a fungal pathogen, a gene which mediates an unwanted immune response, a gene which mediates the processing of pain, a gene which mediates a neurological disease, an allene gene found in cells characterized by loss of heterozygosity, or one allege gene of a polymorphic gene.
  • target genes for the siRNAs include, but are not limited to, AT3, AGT, ALAS1, TMPR, HAO1, AGT, C5, CCR-5, PDGF beta gene; Erb-B gene, Src gene; CRK gene; GRB2 gene; RAS gene; MEKK gene; JNK gene; RAF gene; Erk1/2 gene; PCNA(p21) gene; MYB gene; c-MYC gene; JUN gene; FOS gene; BCL-2 gene; Cyclin D gene; VEGF gene; EGFR gene; Cyclin A gene; Cyclin E gene; WNT-1 gene; beta-catenin gene; c-MET gene; PKC gene; NFKB gene; STAT3 gene; survivin gene; Her2/Neu gene; topoisomerase I gene; topoisomerase II alpha gene; p73 gene; p21(WAF1/CIP1) gene, p27(KIP1) gene; PPM1D gene; caveolin I gene; MIB I gene; MTAI gene
  • Louis Encephalitis gene a gene that is required for St. Louis Encephalitis replication, Tick-borne encephalitis virus gene, a gene that is required for Tick-borne encephalitis virus replication, Murray Valley encephalitis virus gene, a gene that is required for Murray Valley encephalitis virus replication, dengue virus gene, a gene that is required for dengue virus gene replication, Simian Virus 40 gene, a gene that is required for Simian Virus 40 replication, Human T Cell Lymphotropic Virus gene, a gene that is required for Human T Cell Lymphotropic Virus replication, Moloney-Murine Leukemia Virus gene, a gene that is required for Moloney-Murine Leukemia Virus replication, encephalomyocarditis virus gene, a gene that is required for encephalomyocarditis virus replication, measles virus gene, a gene that is required for measles virus replication, Vericella zoster virus gene, a gene that is required for Vericella
  • the loss of heterozygosity can result in hemizygosity for sequence, e.g., genes, in the area of LOH. This can result in a significant genetic difference between normal and disease-state cells, e.g., cancer cells, and provides a useful difference between normal and disease-state cells, e.g., cancer cells. This difference can arise because a gene or other sequence is heterozygous in duploid cells but is hemizygous in cells having LOH.
  • the regions of LOH will often include a gene, the loss of which promotes unwanted proliferation, e.g., a tumor suppressor gene, and other sequences including, e.g., other genes, in some cases a gene which is essential for normal function, e.g., growth.
  • Methods of the invention rely, in part, on the specific modulation of one allele of an essential gene with a composition of the invention.
  • the invention provides REVERSIR compound to an siRNA that modulates a micro-RNA.
  • REVERSIR compounds are oligomeric compounds. Accordingly, in certain embodiments, REVERSIR compounds comprise, for example and without limitation, any of the modifications and motifs described in the discussion herein for oligomeric compounds.
  • motifs are designed with consideration given to both the siRNA and the REVERSIR compound.
  • a REVERSIR compound could comprise 4 or more contiguous DNA-like monomers.
  • the resulting RNA/DNA duplex could activate RNase H, resulting in cleavage of the RNA-like antisense compound.
  • REVERSIR activity does not depend on enzymatic activity.
  • compounds designed without regard for enzymatic compatibility may incorporate modifications to improve other attributes. For example, certain motifs yield oligomeric compounds with high affinity for a target nucleic acid, but that are unable to elicit enzymatic cleavage of that target. Such motifs may be useful for REVERSIR compounds in embodiments where cleavage of the siRNA is not necessary.
  • one strand of the siRNA e.g., the strand complementary to REVERSIR compound, and corresponding REVERSIR compound are the same length. In some embodiments, one strand of the siRNA, e.g., the strand complementary to REVERSIR compound, and corresponding REVERSIR compound are different lengths. In some embodiments, the REVERSIR compound is shorter than the corresponding complementary strand from the siRNA. In some embodiments, the REVERSIR compound is shorter by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleotides than the corresponding complementary strand from the siRNA.
  • antisense strand of the siRNA and corresponding REVERSIR compound are the same length. In some embodiments, antisense strand of the siRNA and corresponding REVERSIR compound are different lengths. In some embodiments, the REVERSIR compound is shorter than the corresponding complementary antisense strand from the siRNA. In some embodiments, the REVERSIR compound is shorter by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleotides than the corresponding complementary antisense strand from the siRNA.
  • sense strand of the siRNA and corresponding REVERSIR compound are the same length. In some embodiments, sense strand of the siRNA and corresponding REVERSIR compound are different lengths. In some embodiments, the REVERSIR compound is shorter than the corresponding complementary sense strand from the siRNA. In some embodiments, the REVERSIR compound is shorter by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleotides than the corresponding complementary sense strand from the siRNA.
  • an siRNA and a REVERSIR compound are administered to a patient.
  • pharmaceutical compositions comprising an siRNA and those comprising a REVERSIR compound comprise the same formulation.
  • pharmaceutical compositions comprising an siRNA and those comprising a REVERSIR compound comprise different formulations.
  • an siRNA and a REVERSIR compound are administered by the same route.
  • an siRNA and a REVERSIR compound are administered by different routes.
  • an siRNA is administered orally and a REVERSIR compound is administered by injection.
  • the dosages of the siRNA and the REVERSIR compound are the same.
  • the dosages of the siRNA and the REVERSIR compound are different.
  • the toxicity profiles of the siRNA and the REVERSIR compound are similar. In certain embodiments, such toxicity profiles are different.
  • an siRNA can be intended for chronic administration and the REVERSIR compound is only intended for acute use as needed. In such embodiments, the tolerance for toxic side-effects of the REVERSIR compound can be higher. Accordingly, modifications and motifs that may be too toxic for use in an siRNA can be acceptable in a REVERSIR compound.
  • oligomeric compounds comprising one or more LNA nucleoside have been shown to have high affinity for a target nucleic acid, but in certain embodiments have been shown to cause toxicity at relatively low concentrations.
  • certain such compounds comprising LNA may not be suitable.
  • LNA modifications in an antidote compound are acceptable.
  • the increased affinity of LNA can improve the REVERSIR effect and since the REVERSIR compound is only administered for a short period of time, and possibly when the patient is in distress, the increased toxicity of LNA may be justified.
  • Other high affinity, but potentially toxic modifications are also known.
  • activity of siRNA is counteracted by a non-oligomeric REVERSIR.
  • the target nucleic acid is a target mRNA encoding a protein it is desirable to reduce the activity of siRNA and to increase in the amount of the target protein (e.g., target protein amount has gone too low, or circumstances have changed resulting in the desire to restore target protein amount).
  • the target protein may have a short half-life in the animal.
  • an oligomeric REVERSIR compound is co-administered with a non-oligomeric REVERSIR.
  • the non-oligomeric REVERSIR is a target protein.
  • the non-oligomeric REVERSIR compound is a protein having similar physiological effect as a target protein or that stimulates expression of the target protein.
  • siRNAs have been used as research tools. For example, researchers investigating the function of a particular gene product can design siRNAs to reduce the amount of that gene product present in a cell or an animal and observe phenotypic changes in the cell or animal.
  • the present invention provides methods for reducing the amount of a gene product in a cell or animal through RNAi and then reducing that RNAi activity, thereby restoring the inhibited gene product.
  • investigators can use such techniques to characterize proteins or untranslated nucleic acids.
  • investigators can vary the amount of time between siRNA and REVERSIR compounds administration. In certain embodiments, such experiments are used to investigate kinetics and/or turnover of gene products and/or certain cellular functions.
  • the invention provides methods comprising administering to a subject a siRNA followed by administering a REVERSIR compound or composition comprising same.
  • the siRNA and the REVERSIR compound can be conjugated or unconjugated.
  • the siRNA and the REVERSIR compound can be independently encapsulated in a lipid formulation, e.g., a LNP, or other nucleic acid-lipid particle.
  • the siRNA and the REVERSIR compound can be administered, independently, via any appropriate route or mode of administration.
  • the siRNA and the REVERSIR compound can be independently administered via intravenous administration (IV) or via subcutaneous administration (SC).
  • the invention provides methods comprising administering to a subject an unconjugated siRNA followed by administering a conjugated REVERSIR compound, wherein the REVERSIR compound is encapsulated in a lipid formulation, e.g., a LNP, or other nucleic acid-lipid particle, and wherein the REVERSIR compound is administered via intravenous administration.
  • a conjugated REVERSIR compound wherein the REVERSIR compound is encapsulated in a lipid formulation, e.g., a LNP, or other nucleic acid-lipid particle, and wherein the REVERSIR compound is administered via intravenous administration.
  • the invention provides methods comprising administering to a subject an unconjugated siRNA followed by administering a conjugated REVERSIR compound, wherein the REVERSIR compound is encapsulated in a lipid formulation and the REVERSIR compound is administered via subcutaneous administration.
  • the invention provides methods comprising administering to a subject a conjugated siRNA followed by administering a conjugated REVERSIR compound, wherein the REVERSIR compound is encapsulated in a lipid formulation and the REVERSIR compound is administered via intravenous administration.
  • the invention provides methods comprising administering to a subject a conjugated siRNA followed by administering a conjugated REVERSIR compound, wherein the REVERSIR compound is encapsulated in a lipid formulation and the REVERSIR compound is administered via subcutaneous administration.
  • the invention provides methods comprising administering to a subject an unconjugated siRNA followed by administering an unconjugated REVERSIR compound, wherein the REVERSIR compound is encapsulated in a lipid formulation and the REVERSIR compound is administered via intravenous administration.
  • the invention provides methods comprising administering to a subject an unconjugated siRNA followed by administering an unconjugated REVERSIR compound, wherein the REVERSIR compound is encapsulated in a lipid formulation and the REVERSIR compound is administered via subcutaneous administration.
  • the invention provides methods comprising administering to a subject a conjugated siRNA followed by administering an unconjugated REVERSIR compound, wherein the REVERSIR compound is encapsulated in a lipid formulation and the REVERSIR compound is administered via intravenous administration.
  • the invention provides methods comprising administering to a subject a conjugated siRNA followed by administering an unconjugated REVERSIR compound, wherein the REVERSIR compound is encapsulated in a lipid formulation and the REVERSIR compound is administered via subcutaneous administration.
  • kits comprising one or more siRNAs and one or more corresponding REVERSIR compound.
  • such kits are intended for therapeutic application.
  • such kits are intended for research use.
  • nucleoside sequences set forth in the sequence listing and Examples are independent of any modification to a sugar moiety, a monomeric linkage, or a nucleobase.
  • oligomeric compounds defined by a SEQ ID NO can comprise, independently, one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • mice Sixty wild-type mice (C57BL/6, female) were bled on Day ⁇ 1 to obtain pre-dose blood samples. All animals were subsequently injected subcutaneously with a single dose of ALN-57213 at 3 mg/kg on Day 0. On Day 3, 3 mice per group received a single subcutaneous injection of one of 19 different reversal agents (Table 2) at a dose of 10 mg/kg. Three animals did not receive an injection on Day 3 and served as an untreated control. All animals were bled on Days 7, 11, and 15 to obtain serum samples. Serum samples were then analyzed for AT antigen level by AT ELISA and were normalized to the pre-dose AT level for each animal. FIG. 1 displays normalized group mean ( ⁇ S.D.) AT levels. As indicated in FIG. 1 , multiple reversal agents reduced the level of AT knockdown mediated by a single subcutaneous dose of ALN-57213.
  • Mouse primary hepatocytes were transfected with 1 nM siRNA by adding 4.9 ⁇ L of Opti-MEM plus 0.1 ⁇ L of Lipofectamine RNAiMax per well (Invitrogen, Carlsbad Calif. cat #13778-150) to 5 ⁇ L siRNA per well into a 384-well plate and incubated at room temperature for 15 minutes. 40 ⁇ L of William's media containing ⁇ 5 ⁇ 10 3 cells were then added to the siRNA mixture, yielding a final siRNA concentration of 1 nM. Cells were incubated at 37° C. After 4 h, hepatocytes were washed and REVERSIR compounds were added by free uptake in 50 ⁇ L media for 48 h at 37° C.
  • Results are shown in FIGS. 15-21 .
  • the various REVERSIR compounds tested for in vivo toxicity showed little or no change in body weight gain. Further, no liver enzyme elevation was observed across doses, e.g., 20 and 100 mg/kg. Moreover, no liver enzyme elevation was observed across time points, e.g., day 4 and day 8. Thus, the REVERSIR compounds of the invention have good in vivo tolerability and safety profile.
  • REVERSIR compounds A-138959, A-140340 or A-140337
  • Table 10 The dose levels of the REVERSIR compounds replicated levels previously evaluated in subcutaneous pharmacokinetic/pharmacodynamic studies in mice.
  • Hematology parameters included differential leukocyte count, erythrocyte count, hemoglobin, hemoglobin distribution width hematocrit, mean corpuscular hemoglobin, mean corpuscular volume, mean corpuscular hemoglobin concentration, platelet count, red cell distribution width, reticulocyte count and total leukocyte count.
  • Serum chemistry parameters included alanine aminotransferase, albumin, alkaline phosphatase, albumin/globulin ratio (calculated), aspartate aminotransferase, calcium chloride, creatinine, gamma glutamyltransferase, globulin (calculated), glucose, phosphorus, potassium, sodium, sorbitol dehydrogenase, total bilirubin, total cholesterol, total protein, triglycerides, urea nitrogen, and appearance.
  • the tested exemplary REVERSIR compounds reversed the activity of the antithrombin siRNA in non-human primates.
  • REVERSIR compounds were administered at a dose of 2.5 mg/kg (0.75 molar eq. of the siRNA, ALN-AT3).
  • REVERSIR compounds were administered at a dose of 0.25 mg/kg (0.075 molar eq. of the siRNA, ALN-AT3).
  • REVERSIR A-140340 (a 9-mer with low phosphorothioate content, 5 PS) showed complete reversal of ALN-AT3 activity within 4 days of dosing and was active at 30-fold lower dose than the conjugate (13 molar eq.).
  • nucleotide(s) A Adenosine-3'-phosphate Ab beta-L-adenosine-3'-phosphate Af 2'-fluoroadenosine-3'-phosphate Afs 2'-fluoroadenosine-3'-phosphorothioate As adenosine-3'-phosphorothioate C cytidine-3'-phosphate Cb beta-L-cytidine-3'-phosphate Cf 2'-fluorocytidine-3'-phosphate Cfs 2'-fluorocytidine-3'-phosphorothioate Cs cytidine-3'-phosphorothioate G guanosine-3'-phosphate Gb beta-L-guanosine-3'-phosphate Gbs beta-L-guanosine-3'-phosphorothioate Gf 2'-fluoroguanosine-3'-

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