# Patent

## Title
Oligomeric compounds comprising bicyclic nucleosides and uses thereof

## Abstract

The present invention provides oligomeric compounds. Certain such oligomeric compounds are useful for hybridizing to a complementary nucleic acid, including but not limited, to nucleic acids in a cell. In certain embodiments, hybridization results in modulation of the amount activity or expression of the target nucleic acid in a cell. In certain embodiments, the present invention provides compounds comprising oligonucleotides. In certain embodiments, such oligonucleotides comprise a region having a gapmer sugar motif. In certain embodiments, oligonucleotides comprise one or more type of modified sugar moieties and/or naturally occurring sugar moieties arranged along an oligonucleotide or region thereof in a defined pattern or sugar modification motif.

## Background
BACKGROUND OF THE INVENTION
Antisense compounds have been used to modulate target nucleic acids. Antisense compounds comprising a variety of chemical modifications and motifs have been reported. In certain instances, such compounds are useful as research tools, diagnostic reagents, and as therapeutic agents. In certain instances antisense compounds have been shown to modulate protein expression by binding to a target messenger RNA (mRNA) encoding the protein. In certain instances, such binding of an antisense compound to its target mRNA results in cleavage of the mRNA. Antisense compounds that modulate processing of a pre-mRNA have also been reported. Such antisense compounds alter splicing, interfere with polyadenlyation or prevent formation of the 5′-cap of a pre-mRNA.
Certain antisense compounds have been described previously. See for example U.S. Pat. No. 7,399,845 and published International Patent Application No. WO 2008/049085, which are hereby incorporated by reference herein in their entirety.
SUMMARY OF THE INVENTION
In certain embodiments, the present invention provides compounds comprising oligonucleotides. In certain embodiments, such oligonucleotides comprise a region having a gapmer sugar motif. In certain embodiments, such oligonucleotides consist of a region having a gapmer sugar motif.
In certain embodiments, oligonucleotides have a sugar motif selected from among:
BBB-(D)8-BBBAA; KKK-(D)8-KKKAA; LLL-(D)8-LLLAA; BBB-(D)8-BBBEE; KKK-(D)8-KKKEE; LLL-(D)8-LLLEE; BBB-(D)7-BBBAA; KKK-(D)7-KKKAA; LLL-(D)7-LLLAA; BBB-(D)7-BBBEE; KKK-(D)7-KKKEE; LLL-(D)7-LLLEE; BBB-(D)8-BBBAAA; KKK-(D)8-KKKAAA; LLL-(D)8-LLLAAA; BBB-(D)8-BBBEEE; KKK-(D)8-KKKEEE; LLL-(D)8-LLLEEE; BBB-(D)7-BBBAAA; KKK-(D)7-KKKAAA; LLL-(D)7-LLLAAA; BBB-(D)7-BBBEEE; KKK-(D)7-KKKEEE; LLL-(D)7-LLLEEE; BABA-(D)8-ABAB; KAKA-(D)8-AKAK; LALA-(D)8-ALAL; BEBE-(D)8-EBEB; KEKE-(D)8-EKEK; LELE-(D)8-ELEL; BABA-(D)7-ABAB; KAKA-(D)7-AKAK; LALA-(D)7-ALAL; BEBE-(D)7-EBEB; KEKE-(D)7-EKEK; LELE-(D)7-ELEL; ABAB-(D)8-ABAB; AKAK-(D)8-AKAK; ALAL-(D)8-ALAL; EBEB-(D)8-EBEB; EKEK-(D)8-EKEK; ELEL-(D)8-ELEL; ABAB-(D)7-ABAB; AKAK-(D)7-AKAK; ALAL-(D)7-ALAL; EBEB-(D)7-EBEB; EKEK-(D)7-EKEK; ELEL-(D)7-ELEL; AABB-(D)8-BBAA; AAKK-(D)8-KKAA; AALL-(D)8-LLAA; EEBB-(D)8-BBEE; EEKK-(D)8-KKEE; EELL-(D)8-LLEE; AABB-(D)7-BBAA; AAKK-(D)7-KKAA; AALL-(D)7-LLAA; EEBB-(D)7-BBEE; EEKK-(D)7-KKEE; EELL-(D)7-LLEE; BBB-(D)9-BBA; KKK-(D)9-KKA; LLL-(D)9-LLA; BBB-(D)9-BBE; KKK-(D)9-KKE; LLL-(D)9-LLE; BBB-(D)8-BBA; KKK-(D)8-KKA; LLL-(D)8-LLA; BBB-(D)8-BBE; KKK-(D)8-KKE; LLL-(D)8-LLE; BBB-(D)7-BBA; KKK-(D)7-KKA; LLL-(D)7-LLA; BBB-(D)7-BBE; KKK-(D)7-KKE; LLL-(D)7-LLE; ABBB-(D)8-BBBA; AKKK-(D)8-KKKA; ALLL-(D)8-LLLA; EBBB-(D)8-BBBE; EKKK-(D)8-KKKE; ELLL-(D)8-LLLE; ABBB-(D)7-BBBA; AKKK-(D)7-KKKA; ALLL-(D)7-LLLA; EBBB-(D)7-BBBE; EKKK-(D)7-KKKE; ELLL-(D)7-LLLE; ABBB-(D)8-BBBAA; AKKK-(D)8-KKKAA; ALLL-(D)8-LLLAA; EBBB-(D)8-BBBEE; EKKK-(D)8-KKKEE; ELLL-(D)8-LLLEE; ABBB-(D)7-BBBAA; AKKK-(D)7-KKKAA; ALLL-(D)7-LLLAA; EBBB-(D)7-BBBEE; EKKK-(D)7-KKKEE; ELLL-(D)7-LLLEE; AABBB-(D)8-BBB; AAKKK-(D)8-KKK; AALLL-(D)8-LLL; EEBBB-(D)8-BBB; EEKKK-(D)8-KKK; EELLL-(D)8-LLL; AABBB-(D)7-BBB; AAKKK-(D)7-KKK; AALLL-(D)7-LLL; EEBBB-(D)7-BBB; EEKKK-(D)7-KKK; EELLL-(D)7-LLL; AABBB-(D)8-BBBA; AAKKK-(D)8-KKKA; AALLL-(D)8-LLLA; EEBBB-(D)8-BBBE; EEKKK-(D)8-KKKE; EELLL-(D)8-LLLE; AABBB-(D)7-BBBA; AAKKK-(D)7-KKKA; AALLL-(D)7-LLLA; EEBBB-(D)7-BBBE; EEKKK-(D)7-KKKE; EELLL-(D)7-LLLE; ABBAABB-(D)8-BB; AKKAAKK-(D)8-KK; ALLAALLL-(D)8-LL; EBBEEBB-(D)8-BB; EKKEEKK-(D)8-KK; ELLEELL-(D)8-LL; ABBAABB-(D)7-BB; AKKAAKK-(D)7-KK; ALLAALL-(D)7-LL; EBBEEBB-(D)7-BB; EKKEEKK-(D)7-KK; ELLEELL-(D)7-LL; ABBABB-(D)8-BBB; AKKAKK-(D)8-KKK; ALLALLL-(D)8-LLL; EBBEBB-(D)8-BBB; EKKEKK-(D)8-KKK; ELLELL-(D)8-LLL; ABBABB-(D)7-BBB; AKKAKK-(D)7-KKK; ALLALL-(D)7-LLL; EBBEBB-(D)7-BBB; EKKEKK-(D)7-KKK; ELLELL-(D)7-LLL.
In certain embodiments, such oligonucleotides provide desirable properties as therapeutic agents.


DETAILED DESCRIPTION OF THE INVENTION
Unless specific definitions are provided, the nomenclature used in connection with, and the procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well known and commonly used in the art. Standard techniques may be used for chemical synthesis, and chemical analysis. Certain such techniques and procedures may be found for example in “Carbohydrate Modifications in Antisense Research” Edited by Sangvi and Cook, American Chemical Society, Washington D.C., 1994; “Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, Pa., 21st edition, 2005; and “Antisense Drug Technology, Principles, Strategies, and Applications” Edited by Stanley T. Crooke, CRC Press, Boca Raton, Fla.; and Sambrook et al., “Molecular Cloning, A laboratory Manual,” 2nd Edition, Cold Spring Harbor Laboratory Press, 1989, which are hereby incorporated by reference for any purpose. Where permitted, all patents, applications, published applications and other publications and other data referred to throughout in the disclosure are incorporated by reference herein in their entirety.
Unless otherwise indicated, the following terms have the following meanings:
As used herein, “nucleoside” means a compound comprising a nucleobase moiety and a sugar moiety. Nucleosides include, but are not limited to, naturally occurring nucleosides (as found in DNA and RNA) and modified nucleosides. Nucleosides may be linked to a phosphate moiety. Nucleosides are capable of being linked together to form an oligomeric compound, which is capable of hybridization to a complementary oligomeric compound. In certain embodiments such complementary oligomeric compound is a naturally occurring nucleic acid.
As used herein, “chemical modification” means a chemical difference in a compound when compared to a naturally occurring counterpart. In reference to an oligonucleotide, chemical modification does not include differences only in nucleobase sequence. Chemical modifications of oligonucleotides include nucleoside modifications (including sugar moiety modifications and nucleobase modifications) and internucleoside linkage modifications.
As used herein, “furanosyl” means a structure comprising a 5-membered ring comprising four carbon atoms and one oxygen atom.
As used herein, “naturally occurring sugar moiety” means a ribofuranosyl as found in naturally occurring RNA or a deoxyribofuranosyl as found in naturally occurring DNA.
As used herein, “sugar moiety” means a naturally occurring sugar moiety or a modified sugar moiety of a nucleoside.
As used herein, “modified sugar moiety” means a substituted sugar moiety or a sugar surrogate.
As used herein, “substituted sugar moiety” means a furanosyl that is not a naturally occurring sugar moiety. Substituted sugar moieties include, but are not limited to furanosyls comprising substituents at the 2′-position, the 3′-position, the 5′-position and/or the 4′-position. Certain substituted sugar moieties are bicyclic sugar moieties.
As used herein, “2′-substituted sugar moiety” means a furanosyl comprising a substituent at the 2′-position other than H or OH. Unless otherwise indicated, a 2′-substituted sugar moiety is not a bicyclic sugar moiety (i.e., the 2′-substituent of a 2′-substituted sugar moiety does not form a bridge to another atom of the furanosyl ring.
As used herein, “MOE” means —OCH2CH2OCH3.
As used herein the term “sugar surrogate” means a structure that does not comprise a furanosyl and that is capable of replacing the naturally occurring sugar moiety of a nucleoside, such that the resulting nucleoside is capable of (1) incorporation into an oligonucleotide and (2) hybridization to a complementary nucleoside. Such structures include rings comprising a different number of atoms than furanosyl (e.g., 4, 6, or 7-membered rings); replacement of the oxygen of a furanosyl with a non-oxygen atom (e.g., carbon, sulfur, or nitrogen); or both a change in the number of atoms and a replacement of the oxygen. Such structures may also comprise substitutions corresponding to those described for substituted sugar moieties (e.g., 6-membered carbocyclic bicyclic sugar surrogates optionally comprising additional substituents). Sugar surrogates also include more complex sugar replacements (e.g., the non-ring systems of peptide nucleic acid). Sugar surrogates include without limitation morpholinos, cyclohexenyls and cyclohexitols.
As used herein, “bicyclic sugar moiety” means a modified sugar moiety comprising a 4 to 7 membered ring (including but not limited to a furanosyl) comprising a bridge connecting two atoms of the 4 to 7 membered ring to form a second ring, resulting in a bicyclic structure. In certain embodiments, the 4 to 7 membered ring is a sugar ring. In certain embodiments the 4 to 7 membered ring is a furanosyl. In certain such embodiments, the bridge connects the 2′-carbon and the 4′-carbon of the furanosyl.
As used herein, “nucleotide” means a nucleoside further comprising a phosphate linking group. As used herein, “linked nucleosides” may or may not be linked by phosphate linkages and thus includes, but is not limited to “linked nucleotides.” As used herein, “linked nucleosides” are nucleosides that are connected in a continuous sequence (i.e. no additional nucleosides are present between those that are linked).
As used herein, “nucleobase” means a group of atoms that can be linked to a sugar moiety to create a nucleoside that is capable of incorporation into an oligonucleotide, and wherein the group of atoms is capable of bonding with a complementary naturally occurring nucleobase of another oligonucleotide or nucleic acid. Nucleobases may be naturally occurring or may be modified.
As used herein, “heterocyclic base” or “heterocyclic nucleobase” means a nucleobase comprising a heterocyclic structure.
As used herein the terms, “unmodified nucleobase” or “naturally occurring nucleobase” means the naturally occurring heterocyclic nucleobases of RNA or DNA: the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) (including 5-methyl C), and uracil (U).
As used herein, “modified nucleobase” means any nucleobase that is not a naturally occurring nucleobase.
As used herein, “modified nucleoside” means a nucleoside comprising at least one chemical modification compared to naturally occurring RNA or DNA nucleosides. Modified nucleosides comprise a modified sugar moiety and/or a modified nucleobase.
As used herein, “bicyclic nucleoside” or “BNA” means a nucleoside comprising a bicyclic sugar moiety.
As used herein, “constrained ethyl nucleoside” or “cEt” means a nucleoside comprising a bicyclic sugar moiety comprising a 4′-CH(CH3)—O-2′ bridge.
As used herein, “locked nucleic acid nucleoside” or “LNA” means a nucleoside comprising a bicyclic sugar moiety comprising a 4′-CH2—O-2′ bridge.
As used herein, “2′-substituted nucleoside” means a nucleoside comprising a substituent at the 2′-position other than H or OH. Unless otherwise indicated, a 2′-substituted nucleoside is not a bicyclic nucleoside.
As used herein, “2′-deoxynucleoside” means a nucleoside comprising 2′-H furanosyl sugar moiety, as found in naturally occurring deoxyribonucleosides (DNA). In certain embodiments, a 2′-deoxynucleoside may comprise a modified nucleobase or may comprise an RNA nucleobase (e.g., uracil).
As used herein, “oligonucleotide” means a compound comprising a plurality of linked nucleosides. In certain embodiments, an oligonucleotide comprises one or more unmodified ribonucleosides (RNA) and/or unmodified deoxyribonucleosides (DNA) and/or one or more modified nucleosides.
As used herein “oligonucleoside” means an oligonucleotide in which none of the internucleoside linkages contains a phosphorus atom. As used herein, oligonucleotides include oligonucleosides.
As used herein, “modified oligonucleotide” means an oligonucleotide comprising at least one modified nucleoside and/or at least one modified internucleoside linkage.
As used herein “internucleoside linkage” means a covalent linkage between adjacent nucleosides in an oligonucleotide.
As used herein “naturally occurring internucleoside linkage” means a 3′ to 5′ phosphodiester linkage.
As used herein, “modified internucleoside linkage” means any internucleoside linkage other than a naturally occurring internucleoside linkage.
As used herein, “oligomeric compound” means a polymeric structure comprising two or more sub-structures. In certain embodiments, an oligomeric compound comprises an oligonucleotide. In certain embodiments, an oligomeric compound comprises one or more conjugate groups and/or terminal groups. In certain embodiments, an oligomeric compound consists of an oligonucleotide.
As used herein, “terminal group” means one or more atom attached to either, or both, the 3′ end or the 5′ end of an oligonucleotide. In certain embodiments a terminal group is a conjugate group. In certain embodiments, a terminal group comprises one or more terminal group nucleosides.
As used herein, “conjugate” means an atom or group of atoms bound to an oligonucleotide or oligomeric compound. In general, conjugate groups modify one or more properties of the compound to which they are attached, including, but not limited to pharmacodynamic, pharmacokinetic, binding, absorption, cellular distribution, cellular uptake, charge and/or clearance properties.
As used herein, “conjugate linking group” means any atom or group of atoms used to attach a conjugate to an oligonucleotide or oligomeric compound.
As used herein, “antisense compound” means a compound comprising or consisting of an oligonucleotide at least a portion of which is complementary to a target nucleic acid to which it is capable of hybridizing, resulting in at least one antisense activity.
As used herein, “antisense activity” means any detectable and/or measurable change attributable to the hybridization of an antisense compound to its target nucleic acid.
As used herein, “detecting” or “measuring” means that a test or assay for detecting or measuring is performed. Such detection and/or measuring may result in a value of zero. Thus, if a test for detection or measuring results in a finding of no activity (activity of zero), the step of detecting or measuring the activity has nevertheless been performed.
As used herein, “detectable and/or measurable activity” means a measurable activity that is not zero.
As used herein, “essentially unchanged” means little or no change in a particular parameter, particularly relative to another parameter which changes much more. In certain embodiments, a parameter is essentially unchanged when it changes less than 5%. In certain embodiments, a parameter is essentially unchanged if it changes less than two-fold while another parameter changes at least ten-fold. For example, in certain embodiments, an antisense activity is a change in the amount of a target nucleic acid. In certain such embodiments, the amount of a non-target nucleic acid is essentially unchanged if it changes much less than the target nucleic acid does, but the change need not be zero.
As used herein, “expression” means the process by which a gene ultimately results in a protein. Expression includes, but is not limited to, transcription, post-transcriptional modification (e.g., splicing, polyadenlyation, addition of 5′-cap), and translation.
As used herein, “target nucleic acid” means a nucleic acid molecule to which an antisense compound hybridizes.
As used herein, “single nucleotide polymorphism” or “SNP” means a single nucleotide variation between the genomes of individuals of the same species. In some cases, a SNP may be a single nucleotide deletion or insertion.
As used herein, “mRNA” means an RNA molecule that encodes a protein.
As used herein, “pre-mRNA” means an RNA transcript that has not been fully processed into mRNA. Pre-RNA includes one or more intron.
As used herein, “object RNA” means an RNA molecule other than a target RNA, the amount, activity, splicing, and/or function of which is modulated, either directly or indirectly, by a target nucleic acid. In certain embodiments, a target nucleic acid modulates splicing of an object RNA. In certain such embodiments, an antisense compound modulates the amount or activity of the target nucleic acid, resulting in a change in the splicing of an object RNA and ultimately resulting in a change in the activity or function of the object RNA.
As used herein, “microRNA” means a naturally occurring, small, non-coding RNA that represses gene expression of at least one mRNA. In certain embodiments, a microRNA represses gene expression by binding to a target site within a 3′ untranslated region of an mRNA. In certain embodiments, a microRNA has a nucleobase sequence as set forth in miRBase, a database of published microRNA sequences found at http://microrna.sanger.ac.uk/sequences/. In certain embodiments, a microRNA has a nucleobase sequence as set forth in miRBase version 12.0 released September 2008, which is herein incorporated by reference in its entirety.
As used herein, “targeting” or “targeted to” means the association of an antisense compound to a particular target nucleic acid molecule or a particular region of a target nucleic acid molecule. An antisense compound targets a target nucleic acid if it is sufficiently complementary to the target nucleic acid to allow hybridization under physiological conditions.
As used herein, “nucleobase complementarity” or “complementarity” when in reference to nucleobases means a nucleobase that is capable of base pairing with another nucleobase. For example, in DNA, adenine (A) is complementary to thymine (T). For example, in RNA, adenine (A) is complementary to uracil (U). In certain embodiments, complementary nucleobase means a nucleobase of an antisense compound that is capable of base pairing with a nucleobase of its target nucleic acid. For example, if a 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, then the position of hydrogen bonding between the oligonucleotide and the target nucleic acid is considered to be complementary at that nucleobase pair. Nucleobases comprising certain modifications may maintain the ability to pair with a counterpart nucleobase and thus, are still capable of nucleobase complementarity.
As used herein, “non-complementary” in reference to nucleobases means a pair of nucleobases that do not form hydrogen bonds with one another.
As used herein, “complementary” in reference to oligomeric compounds (e.g., linked nucleosides, oligonucleotides, or nucleic acids) means the capacity of such oligomeric compounds or regions thereof to hybridize to another oligomeric compound or region thereof through nucleobase complementarity under stringent conditions. Complementary oligomeric compounds need not have nucleobase complementarity at each nucleoside. Rather, some mismatches are tolerated. In certain embodiments, complementary oligomeric compounds or regions are complementary at 70% of the nucleobases (70% complementary). In certain embodiments, complementary oligomeric compounds or regions are 80% complementary. In certain embodiments, complementary oligomeric compounds or regions are 90% complementary. In certain embodiments, complementary oligomeric compounds or regions are 95% complementary. In certain embodiments, complementary oligomeric compounds or regions are 100% complementary.
As used herein, “hybridization” means the pairing of complementary oligomeric compounds (e.g., an antisense compound and its target nucleic acid). While not limited to a particular mechanism, the most common mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases.
As used herein, “specifically hybridizes” means the ability of an oligomeric compound to hybridize to one nucleic acid site with greater affinity than it hybridizes to another nucleic acid site. In certain embodiments, an antisense oligonucleotide specifically hybridizes to more than one target site.
As used herein, “fully complementary” in reference to an oligonucleotide or portion thereof means that each nucleobase of the oligonucleotide or portion thereof is capable of pairing with a nucleobase of a complementary nucleic acid or contiguous portion thereof. Thus, a fully complementary region comprises no mismatches or unhybridized nucleobases in either strand.
As used herein, “percent complementarity” means the percentage of nucleobases of an oligomeric compound that are complementary to an equal-length portion of a target nucleic acid. Percent complementarity is calculated by dividing the number of nucleobases of the oligomeric compound that are complementary to nucleobases at corresponding positions in the target nucleic acid by the total length of the oligomeric compound.
As used herein, “percent identity” means the number of nucleobases in a first nucleic acid that are the same type (independent of chemical modification) as nucleobases at corresponding positions in a second nucleic acid, divided by the total number of nucleobases in the first nucleic acid.
As used herein, “modulation” means a change of amount or quality of a molecule, function, or activity when compared to the amount or quality of a molecule, function, or activity prior to modulation. For example, modulation includes the change, either an increase (stimulation or induction) or a decrease (inhibition or reduction) in gene expression. As a further example, modulation of expression can include a change in splice site selection of pre-mRNA processing, resulting in a change in the absolute or relative amount of a particular splice-variant compared to the amount in the absence of modulation.
As used herein, “motif” means a pattern of chemical modifications in an oligomeric compound or a region thereof. Motifs may be defined by modifications at certain nucleosides and/or at certain linking groups of an oligomeric compound.
As used herein, “nucleoside motif” means a pattern of nucleoside modifications in an oligomeric compound or a region thereof. The linkages of such an oligomeric compound may be modified or unmodified. Unless otherwise indicated, motifs herein describing only nucleosides are intended to be nucleoside motifs. Thus, in such instances, the linkages are not limited.
As used herein, “sugar motif” means a pattern of sugar modifications in an oligomeric compound or a region thereof.
As used herein, “linkage motif” means a pattern of linkage modifications in an oligomeric compound or region thereof. The nucleosides of such an oligomeric compound may be modified or unmodified. Unless otherwise indicated, motifs herein describing only linkages are intended to be linkage motifs. Thus, in such instances, the nucleosides are not limited.
As used herein, “nucleobase modification motif” means a pattern of modifications to nucleobases along an oligonucleotide. Unless otherwise indicated, a nucleobase modification motif is independent of the nucleobase sequence.
As used herein, “sequence motif” means a pattern of nucleobases arranged along an oligonucleotide or portion thereof. Unless otherwise indicated, a sequence motif is independent of chemical modifications and thus may have any combination of chemical modifications, including no chemical modifications.
As used herein, “type of modification” in reference to a nucleoside or a nucleoside of a “type” means the chemical modification of a nucleoside and includes modified and unmodified nucleosides. Accordingly, unless otherwise indicated, a “nucleoside having a modification of a first type” may be an unmodified nucleoside.
As used herein, “differently modified” mean chemical modifications or chemical substituents that are different from one another, including absence of modifications. Thus, for example, a MOE nucleoside and an unmodified DNA nucleoside are “differently modified,” even though the DNA nucleoside is unmodified. Likewise, DNA and RNA are “differently modified,” even though both are naturally-occurring unmodified nucleosides. Nucleosides that are the same but for comprising different nucleobases are not differently modified. For example, a nucleoside comprising a 2′-OMe modified sugar and an unmodified adenine nucleobase and a nucleoside comprising a 2′-OMe modified sugar and an unmodified thymine nucleobase are not differently modified.
As used herein, “the same type of modifications” refers to modifications that are the same as one another, including absence of modifications. Thus, for example, two unmodified DNA nucleoside have “the same type of modification,” even though the DNA nucleoside is unmodified. Such nucleosides having the same type modification may comprise different nucleobases.
As used herein, “separate regions” means portions of an oligonucleotide wherein the chemical modifications or the motif of chemical modifications of any neighboring portions include at least one difference to allow the separate regions to be distinguished from one another.
As used herein, “pharmaceutically acceptable carrier or diluent” means any substance suitable for use in administering to an animal. In certain embodiments, a pharmaceutically acceptable carrier or diluent is sterile saline. In certain embodiments, such sterile saline is pharmaceutical grade saline.
As used herein, “substituent” and “substituent group,” means an atom or group that replaces the atom or group of a named parent compound. For example a substituent of a modified nucleoside is any atom or group that differs from the atom or group found in a naturally occurring nucleoside (e.g., a modified 2′-substituent is any atom or group at the 2′-position of a nucleoside other than H or OH). Substituent groups can be protected or unprotected. In certain embodiments, compounds of the present invention have substituents at one or at more than one position of the parent compound. Substituents may also be further substituted with other substituent groups and may be attached directly or via a linking group such as an alkyl or hydrocarbyl group to a parent compound.
Likewise, as used herein, “substituent” in reference to a chemical functional group means an atom or group of atoms differs from the atom or a group of atoms normally present in the named functional group. In certain embodiments, a substituent replaces a hydrogen atom of the functional group (e.g., in certain embodiments, the substituent of a substituted methyl group is an atom or group other than hydrogen which replaces one of the hydrogen atoms of an unsubstituted methyl group). Unless otherwise indicated, groups amenable for use as substituents include without limitation, halogen, hydroxyl, alkyl, alkenyl, alkynyl, acyl (—C(O)Raa), carboxyl (—C(O)O—Raa), aliphatic groups, alicyclic groups, alkoxy, substituted oxy (—O—Raa), aryl, aralkyl, heterocyclic radical, heteroaryl, heteroarylalkyl, amino (—N(Rbb)(Rcc)), imino (═NRbb), amido (—C(O)N(Rbb)(Rcc) or —N(Rbb)C(O)Ra), azido (—N3), nitro (—NO2), cyano (—CN), carbamido (—OC(O)N(Rbb)(Rcc) or —N(Rbb)C(O)ORaa), ureido (—N(Rbb)C(O)N(Rbb)(Rcc)), thioureido (—N(Rbb)C(S)N(Rbb)—(Rcc)), guanidinyl (—N(Rbb)C(═NRbb)N(Rbb)(Rcc)), amidinyl (—C(═NRbb)N(Rbb)(Rcc) or —N(Rbb)C(═NRbb)(Raa)), thiol (—SRbb), sulfinyl (—S(O)Rbb), sulfonyl (—S(O)2Rbb) and sulfonamidyl (—S(O)2N(Rbb)(Rcc) or —N(Rbb)S—(O)2Rbb). Wherein 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, alkyl, alkenyl, alkynyl, aliphatic, alkoxy, acyl, aryl, aralkyl, heteroaryl, alicyclic, heterocyclic and heteroarylalkyl. Selected substituents within the compounds described herein are present to a recursive degree.
As used herein, “alkyl,” as used herein, means a saturated straight or branched hydrocarbon radical containing up to twenty four carbon atoms. Examples of alkyl groups include without limitation, methyl, ethyl, propyl, butyl, isopropyl, n-hexyl, octyl, decyl, dodecyl and the like. Alkyl groups typically include from 1 to about 24 carbon atoms, more typically from 1 to about 12 carbon atoms (C1-C12 alkyl) with from 1 to about 6 carbon atoms being more preferred.
As used herein, “alkenyl,” means a straight or branched hydrocarbon chain radical containing up to twenty four carbon atoms and having at least one carbon-carbon double bond. Examples of alkenyl groups include without limitation, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, dienes such as 1,3-butadiene and the like. Alkenyl groups typically include from 2 to about 24 carbon atoms, more typically from 2 to about 12 carbon atoms with from 2 to about 6 carbon atoms being more preferred. Alkenyl groups as used herein may optionally include one or more further substituent groups.
As used herein, “alkynyl,” means a straight or branched hydrocarbon radical containing up to twenty four carbon atoms and having at least one carbon-carbon triple bond. Examples of alkynyl groups include, without limitation, ethynyl, 1-propynyl, 1-butyryl, and the like. Alkynyl groups typically include from 2 to about 24 carbon atoms, more typically from 2 to about 12 carbon atoms with from 2 to about 6 carbon atoms being more preferred. Alkynyl groups as used herein may optionally include one or more further substituent groups.
As used herein, “acyl,” means a radical formed by removal of a hydroxyl group from an organic acid and has the general Formula —C(O)—X where X is typically aliphatic, alicyclic or aromatic. Examples include aliphatic carbonyls, aromatic carbonyls, aliphatic sulfonyls, aromatic sulfinyls, aliphatic sulfinyls, aromatic phosphates, aliphatic phosphates and the like. Acyl groups as used herein may optionally include further substituent groups.
As used herein, “alicyclic” means a cyclic ring system wherein the ring is aliphatic. The ring system can comprise one or more rings wherein at least one ring is aliphatic. Preferred alicyclics include rings having from about 5 to about 9 carbon atoms in the ring. Alicyclic as used herein may optionally include further substituent groups.
As used herein, “aliphatic” means a straight or branched hydrocarbon radical containing up to twenty four carbon atoms wherein the saturation between any two carbon atoms is a single, double or triple bond. An aliphatic group preferably contains from 1 to about 24 carbon atoms, more typically from 1 to about 12 carbon atoms with from 1 to about 6 carbon atoms being more preferred. The straight or branched chain of an aliphatic group may be interrupted with one or more heteroatoms that include nitrogen, oxygen, sulfur and phosphorus. Such aliphatic groups interrupted by heteroatoms include without limitation, polyalkoxys, such as polyalkylene glycols, polyamines, and polyimines. Aliphatic groups as used herein may optionally include further substituent groups.
As used herein, “alkoxy” means a radical formed between an alkyl group and an oxygen atom wherein the oxygen atom is used to attach the alkoxy group to a parent molecule. Examples of alkoxy groups include without limitation, 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 substituent groups.
As used herein, “aminoalkyl” means an amino substituted C1-C12 alkyl radical. The alkyl portion of the radical forms a covalent bond with a parent molecule. The amino group can be located at any position and the aminoalkyl group can be substituted with a further substituent group at the alkyl and/or amino portions.
As used herein, “aralkyl” and “arylalkyl” mean an aromatic group that is covalently linked to a C1-C12 alkyl radical. The alkyl radical portion of the resulting aralkyl (or arylalkyl) group forms a covalent bond with a parent molecule. Examples include without limitation, benzyl, phenethyl and the like. Aralkyl groups as used herein may optionally include further substituent groups attached to the alkyl, the aryl or both groups that form the radical group.
As used herein, “aryl” and “aromatic” mean a mono- or polycyclic carbocyclic ring system radicals having one or more aromatic rings. Examples of aryl groups include without limitation, phenyl, naphthyl, tetrahydronaphthyl, indanyl, idenyl and the like. Preferred aryl ring systems have from about 5 to about 20 carbon atoms in one or more rings. Aryl groups as used herein may optionally include further substituent groups.
As used herein, “halo” and “halogen,” mean an atom selected from fluorine, chlorine, bromine and iodine.
As used herein, “heteroaryl,” and “heteroaromatic,” mean 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 heteroatoms. Heteroaryl is also meant to include fused ring systems including systems where one or more of the fused rings contain no heteroatoms. Heteroaryl groups typically include one ring atom selected from sulfur, nitrogen or oxygen. Examples of heteroaryl groups include without limitation, pyridinyl, pyrazinyl, pyrimidinyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl, quinolinyl, isoquinolinyl, benzimidazolyl, benzooxazolyl, quinoxalinyl and the like. Heteroaryl radicals can be attached to a parent molecule directly or through a linking moiety such as an aliphatic group or hetero atom. Heteroaryl groups as used herein may optionally include further substituent groups.
Oligomeric Compounds
In certain embodiments, the present invention provides oligomeric compounds. In certain embodiments, such oligomeric compounds comprise oligonucleotides optionally comprising one or more conjugate and/or terminal groups. In certain embodiments, an oligomeric compound consists of an oligonucleotide. In certain embodiments, oligonucleotides comprise one or more chemical modifications. Such chemical modifications include modifications one or more nucleoside (including modifications to the sugar moiety and/or the nucleobase) and/or modifications to one or more internucleoside linkage.
Certain Sugar Moieties
In certain embodiments, oligomeric compounds of the invention comprise one or more modified nucleosides comprising a modified sugar moiety. Such oligomeric compounds comprising one or more sugar-modified nucleosides may have desirable properties, such as enhanced nuclease stability or increased binding affinity with a target nucleic acid relative to oligomeric compounds comprising only nucleosides comprising naturally occurring sugar moieties. In certain embodiments, modified sugar moieties are substituted sugar moieties. In certain embodiments, modified sugar moieties are sugar surrogates. Such sugar surrogates may comprise one or more substitutions corresponding to those of substituted sugar moieties.
In certain embodiments, modified sugar moieties are substituted sugar moieties comprising one or more non-bridging sugar substituent, including but not limited to substituents at the 2′ and/or 5′ positions. Examples of sugar substituents suitable for the 2′-position, include, but are not limited to: 2′-F, 2′-OCH3 (“OMe” or “O-methyl”), and 2′-O(CH2)2OCH3 (“MOE”). In certain embodiments, sugar substituents at the 2′ position is selected from allyl, amino, azido, thio, O-allyl, O—C1-C10 alkyl, O—C1-C10 substituted alkyl; OCF3, O(CH2)2SCH3, O(CH2)2—O—N(Rm)(Rn), and O—CH2—C(═O)—N(Rm)(Rn), where each Rm and Rn is, independently, H or substituted or unsubstituted C1-C10 alkyl. Examples of sugar substituents at the 5′-position, include, but are not limited to: 5′-methyl (R or S); 5′-vinyl, and 5′-methoxy. In certain embodiments, substituted sugars comprise more than one non-bridging sugar substituent, for example, 2′-F-5′-methyl sugar moieties (see, e.g., PCT International Application WO 2008/101157, for additional 5′,2′-bis substituted sugar moieties and nucleosides).
Nucleosides comprising 2′-substituted sugar moieties are referred to as 2′-substituted nucleosides. In certain embodiments, a 2′-substituted nucleoside comprises a 2′-substituent group selected from halo, allyl, amino, azido, SH, CN, OCN, CF3, OCF3, O, S, or N(Rm)-alkyl; O, S, or N(Rm)-alkenyl; O, S or N(Rm)-alkynyl; O-alkylenyl-O-alkyl, alkynyl, alkaryl, aralkyl, O-alkaryl, O-aralkyl, O(CH2)2SCH3, O—(CH2)2—O—N(Rm)(Rn) or O—CH2—C(═O)—N(Rm)(Rn), where each Rm and Rn is, independently, H, an amino protecting group or substituted or unsubstituted C1-C10 alkyl. These 2′-substituent groups can be further substituted with one or more substituent groups independently selected from hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO2), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.
In certain embodiments, a 2′-substituted nucleoside comprises a 2′-substituent group selected from F, NH2, N3, OCF3, O—CH3, O(CH2)3NH2, CH2—CH═CH2, O—CH2—CH═CH2, OCH2CH2OCH3, O(CH2)2SCH3, O—(CH2)2—O—N(Rm)(Rn), O(CH2)2O(CH2)2N(CH3)2, and N-substituted acetamide (O—CH2—C(═O)—N(Rm)(Rn) where each Rm and Rn is, independently, H, an amino protecting group or substituted or unsubstituted C1-C10 alkyl.
In certain embodiments, a 2′-substituted nucleoside comprises a sugar moiety comprising a 2′-substituent group selected from F, OCF3, O—CH3, OCH2CH2OCH3, O(CH2)2SCH3, O—(CH2)2—O—N(CH3)2, —O(CH2)2O(CH2)2N(CH3)2, and O—CH2—C(═O)—N(H)CH3.
In certain embodiments, a 2′-substituted nucleoside comprises a sugar moiety comprising a 2′-substituent group selected from F, O—CH3, and OCH2CH2OCH3.
Certain modified sugar moieties comprise a bridging sugar substituent that forms a second ring resulting in a bicyclic sugar moiety. In certain such embodiments, the bicyclic sugar moiety comprises a bridge between the 4′ and the 2′ furanose ring atoms. Examples of such 4′ to 2′ sugar substituents, include, but are not limited to: —[C(Ra)(Rb)]n—, —[C(Ra)(Rb)]n—O—, —C(RaRb)—N(R)—O— or, —C(RaRb)—O—N(R)—; 4′-CH2-2′,4′-(CH2)2-2′,4′-(CH2)3-2′. 4′-(CH2)—O-2′ (LNA); 4′-(CH2)—S-2; 4′-(CH2)2—O-2′ (ENA); 4′-CH(CH3)—O-2′ (cEt) and 4′-CH(CH2OCH3)—O-2′, and analogs thereof (see, e.g., U.S. Pat. No. 7,399,845, issued on Jul. 15, 2008); 4′-C(CH3)(CH3)—O-2′ and analogs thereof, (see, e.g., WO2009/006478, published Jan. 8, 2009); 4′-CH2—N(OCH3)-2′ and analogs thereof (see, e.g., WO2008/150729, published Dec. 11, 2008); 4′-CH2—O—N(CH3)-2′ (see, e.g., US2004/0171570, published Sep. 2, 2004); 4′-CH2—O—N(R)-2′, and 4′-CH2—N(R)—O-2′-, wherein each R is, independently, H, a protecting group, or C1-C12 alkyl; 4′-CH2—N(R)—O-2′, wherein R is H, C1-C12 alkyl, or a protecting group (see, U.S. Pat. No. 7,427,672, issued on Sep. 23, 2008); 4′-CH2—C(H)(CH3)-2′ (see, e.g., Chattopadhyaya, et al., J. Org. Chem., 2009, 74, 118-134); and 4′-CH2—C(═CH2)-2′ and analogs thereof (see, published PCT International Application WO 2008/154401, published on Dec. 8, 2008) and 4′-CH2—O—CH2-2′.
In certain embodiments, such 4′ to 2′ bridges independently comprise from 1 to 4 linked groups independently selected from —[C(Ra)(Rb)]n—, —C(Ra)═C(Rb)—, —C(Ra)═N—, —C(═NRa)—, —C(═O)—, —C(═S)—, —O—, —Si(Ra)2—, —S(═O)x—, and —N(Ra)—;
wherein:
x is 0, 1, or 2;
n is 1, 2, 3, or 4;
each Ra and Rb 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.
Nucleosides comprising bicyclic sugar moieties are referred to as bicyclic nucleosides or BNAs. Bicyclic nucleosides include, but are not limited to, (A) α-L-Methyleneoxy (4′-CH2—O-2′) BNA, (B) 13-D-Methyleneoxy (4′-CH2—O-2′) BNA (also referred to as locked nucleic acid or LNA), (C) Ethyleneoxy (4′-(CH2)2—O-2′) BNA, (D) Aminooxy (4′-CH2—O—N(R)-2′) BNA, (E) Oxyamino (4′-CH2—N(R)—O-2′) BNA, (F) Methyl(methyleneoxy) (4′-CH(CH3)—O-2′) BNA (also referred to as constrained ethyl or cEt), (G) methylene-thio (4′-CH2—S-2′) BNA, (H) methylene-amino (4′-CH2-N(R)-2′) BNA, (I) methyl carbocyclic (4′-CH2—CH(CH3)-2′) BNA, (J) propylene carbocyclic (4′-(CH2)3-2′) BNA, and (M) 4′-CH2—O—CH2-2′ as depicted below.







wherein Bx is a nucleobase moiety and R is, independently, H, a protecting group, or C1-C12 alkyl.

Additional bicyclic sugar moieties are known in the art, for example: Singh et al., Chem. Commun., 1998, 4, 455-456; Koshkin et al., Tetrahedron, 1998, 54, 3607-3630; Wahlestedt et al., Proc. Natl. Acad. Sci. U.S.A., 2000, 97, 5633-5638; Kumar et al., Bioorg. Med. Chem. Lett., 1998, 8, 2219-2222; Singh et al., J. Org. Chem., 1998, 63, 10035-10039; Srivastava et al., J. Am. Chem. Soc., 129(26) 8362-8379 (Jul. 4, 2007); Elayadi et al., Curr. Opinion Invens. Drugs, 2001, 2, 558-561; Braasch et al., Chem. Biol., 2001, 8, 1-7; Orum et al., Curr. Opinion Mol. Ther., 2001, 3, 239-243; U.S. Pat. Nos. 7,053,207, 6,268,490, 6,770,748, 6,794,499, 7,034,133, 6,525,191, 6,670,461, and 7,399,845; WO 2004/106356, WO 1994/14226, WO 2005/021570, and WO 2007/134181; U.S. Patent Publication Nos. US2004/0171570, US2007/0287831, and US2008/0039618; U.S. patent Ser. Nos. 12/129,154, 60/989,574, 61/026,995, 61/026,998, 61/056,564, 61/086,231, 61/097,787, and 61/099,844; and PCT International Applications Nos. PCT/US2008/064591, PCT/US2008/066154, and PCT/US2008/068922.
In certain embodiments, bicyclic sugar moieties and nucleosides incorporating such bicyclic sugar moieties are further defined by isomeric configuration. For example, a nucleoside comprising a 4′-2′ methylene-oxy bridge, may be in the α-L configuration or in the β-D configuration. Previously, α-L-methyleneoxy (4′-CH2—O-2′) bicyclic nucleosides have been incorporated into antisense oligonucleotides that showed antisense activity (Frieden et al., Nucleic Acids Research, 2003, 21, 6365-6372).
In certain embodiments, substituted sugar moieties comprise one or more non-bridging sugar substituent and one or more bridging sugar substituent (e.g., 5′-substituted and 4′-2′ bridged sugars). (see, PCT International Application WO 2007/134181, published on Nov. 22, 2007, wherein LNA is substituted with, for example, a 5′-methyl or a 5′-vinyl group).
In certain embodiments, modified sugar moieties are sugar surrogates. In certain such embodiments, the oxygen atom of the naturally occurring sugar is substituted, e.g., with a sulfer, carbon or nitrogen atom. In certain such embodiments, such modified sugar moiety also comprises bridging and/or non-bridging substituents as described above. For example, certain sugar surrogates comprise a 4′-sulfer atom and a substitution at the 2′-position (see, e.g., published U.S. Patent Application US2005/0130923, published on Jun. 16, 2005) and/or the 5′ position. By way of additional example, carbocyclic bicyclic nucleosides having a 4′-2′ bridge have been described (see, e.g., Freier et al., Nucleic Acids Research, 1997, 25(22), 4429-4443 and Albaek et al., J. Org. Chem., 2006, 71, 7731-7740).
In certain embodiments, sugar surrogates comprise rings having other than 5-atoms. For example, in certain embodiments, a sugar surrogate comprises a six-membered tetrahydropyran. Such tetrahydropyrans may be further modified or substituted. Nucleosides comprising such modified tetrahydropyrans include, but are not limited to, hexitol nucleic acid (HNA), anitol nucleic acid (ANA), manitol nucleic acid (MNA) (see Leumann, C J. Bioorg. & Med. Chem. (2002) 10:841-854), fluoro HNA (F-HNA), and those compounds having Formula VII:




wherein independently for each of said at least one tetrahydropyran nucleoside analog of Formula VII:

Bx is a nucleobase moiety;
T3 and T4 are each, independently, an internucleoside linking group linking the tetrahydropyran nucleoside analog to the antisense compound or one of T3 and T4 is an internucleoside linking group linking the tetrahydropyran nucleoside analog to the antisense compound and the other of T3 and T4 is H, a hydroxyl protecting group, a linked conjugate group, or a 5′ or 3′-terminal group;
q1, q2, q3, q4, q5, q6 and q7 are each, independently, H, C1-C6 alkyl, substituted C1-C6 alkyl, C2-C6 alkenyl, substituted C2-C6 alkenyl, C2-C6 alkynyl, or substituted C2-C6 alkynyl; and
one of R1 and R2 is hydrogen and the other is selected from halogen, substituted or unsubstituted alkoxy, NJ1J2, SJ1, N3, OC(═X)J1, OC(═X)NJ1J2, NJ3C(═X)NJ1J2, and CN, wherein X is O, S or NJ1, and each J1, J2, and J3 is, independently, H or C1-C6 alkyl.
In certain embodiments, the modified THP nucleosides of Formula VII are provided wherein q1, q2, q3, q4, q5, q6 and q7 are each H. In certain embodiments, at least one of q1, q2, q3, q4, q5, q6 and q7 is other than H. In certain embodiments, at least one of q1, q2, q3, q4, q5, q6 and q7 is methyl. In certain embodiments, THP nucleosides of Formula VII are provided wherein one of R1 and R2 is F. In certain embodiments, R1 is fluoro and R2 is H, R1 is methoxy and R2 is H, and R1 is methoxyethoxy and R2 is H.
Many other bicyclo and tricyclo sugar surrogate ring systems are also known in the art that can be used to modify nucleosides for incorporation into antisense compounds (see, e.g., review article: Leumann, J. C, Bioorganic & Medicinal Chemistry, 2002, 10, 841-854).
Combinations of modifications are also provided without limitation, such as 2′-F-5′-methyl substituted nucleosides (see PCT International Application WO 2008/101157 Published on Aug. 21, 2008 for other disclosed 5′,2′-bis substituted nucleosides) and replacement of the ribosyl ring oxygen atom with S and further substitution at the 2′-position (see published U.S. Patent Application US2005-0130923, published on Jun. 16, 2005) or alternatively 5′-substitution of a bicyclic nucleic acid (see PCT International Application WO 2007/134181, published on Nov. 22, 2007 wherein a 4′-CH2—O-2′ bicyclic nucleoside is further substituted at the 5′ position with a 5′-methyl or a 5′-vinyl group). The synthesis and preparation of carbocyclic bicyclic nucleosides along with their oligomerization and biochemical studies have also been described (see, e.g., Srivastava et al., J. Am. Chem. Soc. 2007, 129(26), 8362-8379).
Certain Nucleobases
In certain embodiments, nucleosides of the present invention comprise one or more unmodified nucleobases. In certain embodiments, nucleosides of the present invention comprise one or more modified nucleobases.
In certain embodiments, modified nucleobases are selected from: universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases as defined herein. 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil; 5-propynylcytosine; 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl CH3) uracil and cytosine and other alkynyl derivatives of pyrimidine bases, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 2-F-adenine, 2-amino-adenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine, 3-deazaguanine and 3-deazaadenine, universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases as defined herein. Further modified nucleobases include tricyclic pyrimidines such as phenoxazine cytidine([5,4-b][1,4]benzoxazin-2(3H)-one), phenothiazine cytidine (1H-pyrimido[5,4-b][1,4]benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g. 9-(2-aminoethoxy)-H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one), carbazole cytidine (2H-pyrimido[4,5-b]indol-2-one), pyridoindole cytidine (H-pyrido[3′,2′:4,5]pyrrolo[2,3-d]pyrimidin-2-one). Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, Kroschwitz, J. I., Ed., John Wiley & Sons, 1990, 858-859; those disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613; and those disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, Crooke, S. T. and Lebleu, B., Eds., CRC Press, 1993, 273-288.
Representative United States patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include without limitation, U.S. Pat. Nos. 3,687,808; 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121; 5,596,091; 5,614,617; 5,645,985; 5,681,941; 5,750,692; 5,763,588; 5,830,653 and 6,005,096, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference in its entirety.
Certain Internucleoside Linkages
In certain embodiments, the present invention provides oligomeric compounds comprising linked nucleosides. In such embodiments, nucleosides may be linked together using any internucleoside linkage. The two main classes of internucleoside linking groups are defined by the presence or absence of a phosphorus atom. Representative phosphorus containing internucleoside linkages include, but are not limited to, phosphodiesters (P═O), phosphotriesters, methylphosphonates, phosphoramidate, and phosphorothioates (P═S). Representative non-phosphorus containing internucleoside 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)—). Modified linkages, compared to natural phosphodiester linkages, can be used to alter, typically increase, nuclease resistance of the oligomeric compound. In certain embodiments, internucleoside linkages having a chiral atom can be prepared as a racemic mixture, or as separate enantiomers. Representative chiral linkages include, but are not limited to, alkylphosphonates and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing internucleoside linkages are well known to those skilled in the art.
The oligonucleotides described herein contain one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric configurations that may be defined, in terms of absolute stereochemistry, as (R) or (S), α or β such as for sugar anomers, or as (D) or (L) such as for amino acids etc. Included in the antisense compounds provided herein are all such possible isomers, as well as their racemic and optically pure forms.
Neutral internucleoside linkages include without limitation, phosphotriesters, methylphosphonates, MMI (3′-CH2—N(CH3)—O-5′), amide-3 (3′-CH2—C(═O)—N(H)-5′), amide-4 (3′-CH2—N(H)—C(═O)-5′), formacetal (3′-O—CH2—O-5′), and thioformacetal (3′-S—CH2—O-5′). Further neutral internucleoside linkages include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides (See for example: Carbohydrate Modifications in Antisense Research; Y. S. Sanghvi and P. D. Cook, Eds., ACS Symposium Series 580; Chapters 3 and 4, 40-65). Further neutral internucleoside linkages include nonionic linkages comprising mixed N, O, S and CH2 component parts.
Certain Motifs
In certain embodiments, the present invention provides oligomeric compounds comprising oligonucleotides. In certain embodiments, such oligonucleotides comprise one or more chemical modification. In certain embodiments, chemically modified oligonucleotides comprise one or more modified sugars. In certain embodiments, chemically modified oligonucleotides comprise one or more modified nucleobases. In certain embodiments, chemically modified oligonucleotides comprise one or more modified internucleoside linkages. In certain embodiments, the chemically modifications (sugar modifications, nucleobase modifications, and/or linkage modifications) define a pattern or motif. In certain embodiments, the patterns of chemical modifications of sugar moieties, internucleoside linkages, and nucleobases are each independent of one another. Thus, an oligonucleotide may be described by its sugar modification motif, internucleoside linkage motif and/or nucleobase modification motif (as used herein, nucleobase modification motif describes the chemical modifications to the nucleobases independent of the sequence of nucleobases).
Certain Sugar Motifs
In certain embodiments, oligonucleotides comprise one or more type of modified sugar moieties and/or naturally occurring sugar moieties arranged along an oligonucleotide or region thereof in a defined pattern or sugar modification motif. Such motifs may include any of the sugar modifications discussed herein and/or other known sugar modifications.
In certain embodiments, the oligonucleotides comprise or consist of a region having a gapmer sugar modification motif, which comprises two external regions or “wings” and an internal region or “gap.” The three regions of a gapmer motif (the 5′-wing, the gap, and the 3′-wing) form a contiguous sequence of nucleosides wherein at least some of the sugar moieties of the nucleosides of each of the wings differ from at least some of the sugar moieties of the nucleosides of the gap. Specifically, at least the sugar moieties of the nucleosides of each wing that are closest to the gap (the 3′-most nucleoside of the 5′-wing and the 5′-most nucleoside of the 3′-wing) differ from the sugar moiety of the neighboring gap nucleosides, thus defining the boundary between the wings and the gap. In certain embodiments, the sugar moieties within the gap are the same as one another. In certain embodiments, the gap includes one or more nucleoside having a sugar moiety that differs from the sugar moiety of one or more other nucleosides of the gap. In certain embodiments, the sugar modification motifs of the two wings are the same as one another (symmetric gapmer). In certain embodiments, the sugar modification motifs of the 5′-wing differs from the sugar modification motif of the 3′-wing (asymmetric gapmer).
Certain 5′-Wings
In certain embodiments, the 5′-wing of a gapmer consists of 1 to 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 2 to 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 3 to 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 4 or 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 to 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 to 3 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 or 2 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 2 to 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 2 or 3 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 3 or 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 nucleoside. In certain embodiments, the 5′-wing of a gapmer consists of 2 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 3 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 5 linked nucleosides.
In certain embodiments, the 5′-wing of a gapmer has a sugar motif selected from among those listed in the following non-limiting table:







TABLE 1







Certain 5′-Wing Sugar Motifs










5′-wing




sugar motif #
motif







1a
BBB



2a
ABBB



3a
AABB



4a
BABA



5a
ABAB



6a
ABB



7a
AABBB



8a
ABBAABB



9a
ABBABB



1b
BBB



2b
EBBB



3b
EEBB



4b
BEBE



5b
EBEB



6b
EBB



7b
EEBBB



8b
EBBEEBB



9b
EBBEBB



1c
LLL



2c
ALLL



3c
AALL



4c
LALA



5c
ALAL



6c
ALL



7c
AALLL



8c
ALLAALL



9c
ALLALL



1d
LLL



2d
ELLL



3d
EELL



4d
LELE



5d
ELEL



6d
ELL



7d
EELLL



8d
ELLEELL



9d
ELLELL



1e
KKK



2e
AKKK



3e
AAKK



4e
KAKA



5e
AKAK



6e
AKK



7e
AAKKK



8e
AKKAAKK



9e
AKKAKK



1f
KKK



2f
EKKK



3f
EEKK



4f
KEKE



5f
EKEK



6f
EKK



7f
EEKKK



8f
EKKEEKK



9f
EKKEKK







In the above table, “A” represents a modified nucleoside comprising a non-bicyclic sugar moiety. In certain embodiments, such “A” nucleosides comprise a 2′-substituted sugar moiety; “B” represents a bicyclic nucleoside; “K” represents a constrained ethyl nucleoside; “L” represents an LNA nucleoside; and “E” represents a 2′-MOE nucleoside.






Certain 3′-Wings
In certain embodiments, the 3′-wing of a gapmer consists of 1 to 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 2 to 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 3 to 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 4 or 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 to 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 to 3 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 or 2 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 2 to 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 2 or 3 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 3 or 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 nucleoside. In certain embodiments, the 3′-wing of a gapmer consists of 2 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 3 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 5 linked nucleosides.
In certain embodiments, the 3′-wing of a gapmer has a sugar motif selected from among those listed in the following non-limiting table:







TABLE 2







Certain 3′-Wing Sugar Motifs










3′-wing




sugar motif #
motif







1a
BBB



2a
BBBA



3a
BBBAA



4a
BBBAAA



5a
BBAA



6a
ABAB



7a
BBA



8a
BBA



1b
BBB



2b
BBBE



3b
BBBEE



4b
BBBEEE



5b
BBEE



6b
EBEB



7b
BBE



8b
BBE



1c
LLL



2c
LLLA



3c
LLLAA



4c
LLLAAA



5c
LLAA



6c
ALAL



7c
LLA



8c
LLA



1d
LLL



2d
LLLE



3d
LLLEE



4d
LLLEEE



5d
LLEE



6d
ELEL



7d
LLE



8d
LLE



1e
KKK



2e
KKKA



3e
KKKAA



4e
KKKAAA



5e
KKAA



6e
AKAK



7e
KKA



8e
KKA



1f
KKK



2f
KKKE



3f
KKKEE



4f
KKKEEE



5f
KKEE



6f
EKEK



7f
KKE



8f
KKE







In the above table, “A” represents a modified nucleoside comprising a modified non-bicyclic sugar moiety. In certain embodiments, such “A” nucleosides comprise a 2′-substituted sugar moiety; “B” represents a bicyclic nucleoside; “K” represents a constrained ethyl nucleoside; “L” represents an LNA nucleoside; and “E” represents a 2′-MOE nucleoside.






In certain embodiments, an oligonucleotide comprises any 3′-wing motif provided herein. In certain such embodiments, the oligonucleotide is a 3′-hemimer (does not comprise a 5′-wing). In certain embodiments, such an oligonucleotide is a gapmer. In certain such embodiments, the 5′-wing of the gapmer may comprise any sugar modification motif.
Certain Gaps
In certain embodiments, the gap of a gapmer consists of 6 to 20 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 15 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 12 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 8 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 or 7 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 to 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 to 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 or 8 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 8 to 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 8 or 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 8 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 11 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 12 linked nucleosides.
In certain embodiments, each nucleotide of the gap of a gapmer is a 2′-deoxynucleoside. In certain embodiments, the gap comprises one or more modified nucleosides. In certain embodiments, each nucleotide of the gap of a gapmer is a 2′-deoxynucleoside or is a modified nucleoside that is “DNA-like.” In such embodiments, “DNA-like” means that the nucleoside has similar characteristics to DNA, such that a duplex comprising the gapmer and an RNA molecule is capable of activating RNase H. For example, under certain conditions, 2′-fluoro (arabino) nucleosides (also referred to as FANA) have been shown to support RNase H activation, and thus is DNA-like. In certain embodiments, one or more nucleosides of the gap of a gapmer is not a 2′-deoxynucleoside and is not DNA-like. In certain such embodiments, the gapmer nonetheless supports RNase H activation (e.g., by virtue of the number or placement of the non-DNA nucleosides).
Certain Gapmer Motifs
In certain embodiments, a gapmer comprises a 5′-wing, a gap, and a 3′ wing, wherein the 5′-wing, gap, and 3′ wing are independently selected from among those discussed above.
In certain embodiments, a gapmer comprises a 5′-wing, a gap, and a 3′ wing, independently selected from among those proved in the above tables, for example as provided in the following table:







TABLE 3







Certain Gapmer Sugar Motifs










Gapmer
5-wing sugar motif

3′-wing sugar motif


motif #
(from table 1)
Gap
(from table 2)













1
1a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
1a, b, c, d, e, or f


2
2a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
1a, b, c, d, e, or f


3
3a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
1a, b, c, d, e, or f


4
4a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
1a, b, c, d, e, or f


5
5a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
1a, b, c, d, e, or f


6
6a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
1a, b, c, d, e, or f


7
7a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
1a, b, c, d, e, or f


8
8a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
1a, b, c, d, e, or f


9
9a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
1a, b, c, d, e, or f


10
1a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
2a, b, c, d, e, or f


11
2a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
2a, b, c, d, e, or f


12
3a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
2a, b, c, d, e, or f


13
4a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
2a, b, c, d, e, or f


14
5a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
2a, b, c, d, e, or f


15
6a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
2a, b, c, d, e, or f


16
7a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
2a, b, c, d, e, or f


17
8a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
2a, b, c, d, e, or f


18
9a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
2a, b, c, d, e, or f


19
1a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
3a, b, c, d, e, or f


20
2a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
3a, b, c, d, e, or f


21
3a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
3a, b, c, d, e, or f


22
4a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
3a, b, c, d, e, or f


23
5a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
3a, b, c, d, e, or f


24
6a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
3a, b, c, d, e, or f


25
7a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
3a, b, c, d, e, or f


26
8a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
3a, b, c, d, e, or f


27
9a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
3a, b, c, d, e, or f


28
1a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
4a, b, c, d, e, or f


29
2a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
4a, b, c, d, e, or f


30
3a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
4a, b, c, d, e, or f


31
4a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
4a, b, c, d, e, or f


32
5a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
4a, b, c, d, e, or f


33
6a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
4a, b, c, d, e, or f


34
7a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
4a, b, c, d, e, or f


35
8a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
4a, b, c, d, e, or f


36
9a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
4a, b, c, d, e, or f


37
1a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
5a, b, c, d, e, or f


38
2a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
5a, b, c, d, e, or f


39
3a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
5a, b, c, d, e, or f


40
4a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
5a, b, c, d, e, or f


41
5a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
5a, b, c, d, e, or f


42
6a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
5a, b, c, d, e, or f


43
7a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
5a, b, c, d, e, or f


44
8a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
5a, b, c, d, e, or f


45
9a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
5a, b, c, d, e, or f


46
1a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
6a, b, c, d, e, or f


47
2a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
6a, b, c, d, e, or f


48
3a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
6a, b, c, d, e, or f


49
4a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
6a, b, c, d, e, or f


50
5a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
6a, b, c, d, e, or f


51
6a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
6a, b, c, d, e, or f


52
7a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
6a, b, c, d, e, or f


53
8a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
6a, b, c, d, e, or f


54
9a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
6a, b, c, d, e, or f


55
1a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
7a, b, c, d, e, or f


56
2a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
7a, b, c, d, e, or f


57
3a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
7a, b, c, d, e, or f


58
4a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
7a, b, c, d, e, or f


59
5a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
7a, b, c, d, e, or f


60
6a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
7a, b, c, d, e, or f


61
7a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
7a, b, c, d, e, or f


62
8a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
7a, b, c, d, e, or f


63
9a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
7a, b, c, d, e, or f


64
1a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
8a, b, c, d, e, or f


65
2a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
8a, b, c, d, e, or f


66
3a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
8a, b, c, d, e, or f


67
4a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
8a, b, c, d, e, or f


68
5a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
8a, b, c, d, e, or f


69
6a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
8a, b, c, d, e, or f


70
7a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
8a, b, c, d, e, or f


71
8a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
8a, b, c, d, e, or f


72
9a, b, c, d, e, or f
7, 8, or 9 2′-deoxynucleosides
8a, b, c, d, e, or f









In certain embodiments, a gapmer comprises a 5′-wing selected from among the 5′-wings provided herein and any 3′-wing.
In certain embodiments, the gapmer oligonucleotides provided herein are useful in therapy. In certain such embodiments, a sugar motif is selected to provide antisense activity. In such embodiments, the antisense compound is potent. In certain embodiments, an antisense compound is well tolerated when administered to an animal. In certain embodiments, an antisense compound is active and potent and well tolerated. Therapeutic index is a measure of potency divided by a measure of toxicity. In certain embodiments, therapeutic indication informs the relative importance of potency, activity, and tolerability. For example, for treatment of aggressive and lethal diseases, one may select a highly active and potent compound, even if its tolerability is not ideal. For other indications, safety/tolerability may be paramount, even if it means selecting a compound that is not the most active/potent. Accordingly, in certain embodiments, antisense compounds comprising the sugar motifs provided herein have therapeutic profiles suitable for a variety of indications.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)8-BBBAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)8-KKKAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)8-LLLAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)8-BBBEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)8-KKKEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)8-LLLEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)7-BBBAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)7-KKKAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)7-LLLAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)7-BBBEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)7-KKKEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)7-LLLEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)8-BBBAAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)8-KKKAAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)8-LLLAAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)8-BBBEEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)8-KKKEEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)8-LLLEEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)7-BBBAAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)7-KKKAAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)7-LLLAAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)7-BBBEEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)7-KKKEEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)7-LLLEEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BABA-(D)8-ABAB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KAKA-(D)8-AKAK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LALA-(D)8-ALAL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BEBE-(D)8-EBEB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KEKE-(D)8-EKEK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LELE-(D)8-ELEL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BABA-(D)7-ABAB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KAKA-(D)7-AKAK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LALA-(D)7-ALAL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BEBE-(D)7-EBEB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KEKE-(D)7-EKEK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LELE-(D)7-ELEL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ABAB-(D)8-ABAB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AKAK-(D)8-AKAK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ALAL-(D)8-ALAL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EBEB-(D)8-EBEB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EKEK-(D)8-EKEK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ELEL-(D)8-ELEL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ABAB-(D)7-ABAB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AKAK-(D)7-AKAK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ALAL-(D)7-ALAL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EBEB-(D)7-EBEB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EKEK-(D)7-EKEK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ELEL-(D)7-ELEL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AABB-(D)8-BBAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AAKK-(D)8-KKAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AALL-(D)8-LLAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEBB-(D)8-BBEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEKK-(D)8-KKEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EELL-(D)8-LLEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AABB-(D)7-BBAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AAKK-(D)7-KKAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AALL-(D)7-LLAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEBB-(D)7-BBEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEKK-(D)7-KKEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EELL-(D)7-LLEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)9-BBA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)9-KKA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)9-LLA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)9-BBE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)9-KKE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)9-LLE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)8-BBA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)8-KKA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)8-LLA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)8-BBE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)8-KKE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)8-LLE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)7-BBA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)7-KKA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)7-LLA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif BBB-(D)7-BBE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif KKK-(D)7-KKE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif LLL-(D)7-LLE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ABBB-(D)8-BBBA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AKKK-(D)8-KKKA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ALLL-(D)8-LLLA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EBBB-(D)8-BBBE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EKKK-(D)8-KKKE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ELLL-(D)8-LLLE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ABBB-(D)7-BBBA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AKKK-(D)7-KKKA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ALLL-(D)7-LLLA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EBBB-(D)7-BBBE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EKKK-(D)7-KKKE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ELLL-(D)7-LLLE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ABBB-(D)8-BBBAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AKKK-(D)8-KKKAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ALLL-(D)8-LLLAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EBBB-(D)8-BBBEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EKKK-(D)8-KKKEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ELLL-(D)8-LLLEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ABBB-(D)7-BBBAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AKKK-(D)7-KKKAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ALLL-(D)7-LLLAA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EBBB-(D)7-BBBEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EKKK-(D)7-KKKEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ELLL-(D)7-LLLEE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AABBB-(D)8-BBB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AAKKK-(D)8-KKK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AALLL-(D)8-LLL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEBBB-(D)8-BBB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEKKK-(D)8-KKK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EELLL-(D)8-LLL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AABBB-(D)7-BBB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AAKKK-(D)7-KKK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AALLL-(D)7-LLL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEBBB-(D)7-BBB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEKKK-(D)7-KKK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EELLL-(D)7-LLL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AABBB-(D)8-BBBA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AAKKK-(D)8-KKKA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AALLL-(D)8-LLLA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEBBB-(D)8-BBBE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEKKK-(D)8-KKKE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EELLL-(D)8-LLLE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AABBB-(D)7-BBBA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AAKKK-(D)7-KKKA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AALLL-(D)7-LLLA has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEBBB-(D)7-BBBE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EEKKK-(D)7-KKKE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EELLL-(D)7-LLLE has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ABBAABB-(D)8-BB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AKKAAKK-(D)8-KK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ALLAALLL-(D)8-LL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EBBEEBB-(D)8-BB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EKKEEKK-(D)8-KK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ELLEELL-(D)8-LL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ABBAABB-(D)7-BB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AKKAAKK-(D)7-KK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ALLAALL-(D)7-LL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EBBEEBB-(D)7-BB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EKKEEKK-(D)7-KK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ELLEELL-(D)7-LL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ABBABB-(D)8-BBB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AKKAKK-(D)8-KKK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ALLALLL-(D)8-LLL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EBBEBB-(D)8-BBB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EKKEKK-(D)8-KKK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ELLELL-(D)8-LLL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ABBABB-(D)7-BBB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif AKKAKK-(D)7-KKK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ALLALL-(D)7-LLL has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EBBEBB-(D)7-BBB has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif EKKEKK-(D)7-KKK has a desirable therapeutic profile.
In certain embodiments, an antisense oligonucleotide having a sugar motif ELLELL-(D)7-LLL has a desirable therapeutic profile.
In the above embodiments, A represents a modified nucleoside comprising a non-bicyclic modified sugar. In certain embodiments, A comprises a substituted sugar moiety. In certain embodiments, A comprises a 2′-substituted sugar moiety.
In the above embodiments, B represents a modified nucleoside comprising a bicyclic sugar moiety. In certain embodiments, B comprises a sugar moiety comprising a 4′-2′ bridge. In certain such embodiments, the sugar moiety of B is selected from: α-L-Methyleneoxy (4′-CH2—O-2′), β-D-Methyleneoxy (4′-CH2—O-2′), Ethyleneoxy (4′-(CH2)2—O-2′), Aminooxy (4′-CH2—O—N(R)-2′), Oxyamino (4′-CH2—N(R)—O-2′), Methyl(methyleneoxy) (4′-CH(CH3)—O-2′), methylene-thio (4′-CH2—S-2′), methylene-amino (4′-CH2-N(R)-2′), methyl carbocyclic (4′-CH2—CH(CH3)-2′), propylene carbocyclic (4′-(CH2)3-2′), and 4′-CH2—O—CH2-2′.
In the above embodiments, E represents a nucleoside having a 2′-MOE.
In the above embodiments, L represents an LNA nucleoside (i.e., a bicyclic sugar comprising a 4′-CH2—O-2′ bridge.
In the above embodiments, K represents an cEt nucleoside (i.e., a bicyclic sugar comprising a 4′-CH(CH3)—O-2′ bridge.
In the above embodiments, D represents a nucleoside having an unmodified DNA sugar moiety.
Certain Internucleoside Linkage Motifs
In certain embodiments, oligonucleotides comprise modified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or modified internucleoside linkage motif. In certain embodiments, internucleoside linkages are arranged in a gapped motif, as described above for sugar modification motif. In such embodiments, the internucleoside linkages in each of two wing regions are different from the internucleoside linkages in the gap region. In certain embodiments the internucleoside linkages in the wings are phosphodiester and the internucleoside linkages in the gap are phosphorothioate. The sugar modification motif is independently selected, so such oligonucleotides having a gapped internucleoside linkage motif may or may not have a gapped sugar modification motif and if it does have a gapped sugar motif, the wing and gap lengths may or may not be the same.
In certain embodiments, oligonucleotides comprise a region having an alternating internucleoside linkage motif. In certain embodiments, oligonucleotides of the present invention comprise a region of uniformly modified internucleoside linkages. In certain such embodiments, the oligonucleotide comprises a region that is uniformly linked by phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide is uniformly linked by phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate and at least one internucleoside linkage is phosphorothioate.
In certain embodiments, the oligonucleotide comprises at least 6 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 8 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 10 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 6 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 8 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 10 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least block of at least one 12 consecutive phosphorothioate internucleoside linkages. In certain such embodiments, at least one such block is located at the 3′ end of the oligonucleotide. In certain such embodiments, at least one such block is located within 3 nucleosides of the 3′ end of the oligonucleotide.
Certain Nucleobase Modification Motifs
In certain embodiments, oligonucleotides comprise chemical modifications to nucleobases arranged along the oligonucleotide or region thereof in a defined pattern or nucleobases modification motif. In certain such embodiments, nucleobase modifications are arranged in a gapped motif. In certain embodiments, nucleobase modifications are arranged in an alternating motif. In certain embodiments, each nucleobase is modified. In certain embodiments, none of the nucleobases is chemically modified.
In certain embodiments, oligonucleotides comprise a block of modified nucleobases. In certain such embodiments, the block is at the 3′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleotides of the 3′-end of the oligonucleotide. In certain such embodiments, the block is at the 5′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleotides of the 5′-end of the oligonucleotide.
In certain embodiments, nucleobase modifications are a function of the natural base at a particular position of an oligonucleotide. For example, in certain embodiments each purine or each pyrimidine in an oligonucleotide is modified. In certain embodiments, each adenine is modified. In certain embodiments, each guanine is modified. In certain embodiments, each thymine is modified. In certain embodiments, each cytosine is modified. In certain embodiments, each uracil is modified.
In certain embodiments, some, all, or none of the cytosine moieties in an oligonucleotide are 5-methyl cytosine moieties. Herein, 5-methyl cytosine is not a “modified nucleobase.” Accordingly, unless otherwise indicated, unmodified nucleobases include both cytosine residues having a 5-methyl and those lacking a 5 methyl. In certain embodiments, the methylation state of all or some cytosine nucleobases is specified.
Certain Overall Lengths
In certain embodiments, the present invention provides oligomeric compounds including oligonucleotides of any of a variety of ranges of lengths. In certain embodiments, the invention provides oligomeric compounds or oligonucleotides consisting of X to Y linked nucleosides, where X represents the fewest number of nucleosides in the range and Y represents the largest number of nucleosides in the range. In certain such embodiments, 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. For example, in certain embodiments, the invention provides oligomeric compounds which comprise oligonucleotides consisting of 8 to 9, 8 to 10, 8 to 11, 8 to 12, 8 to 13, 8 to 14, 8 to 15, 8 to 16, 8 to 17, 8 to 18, 8 to 19, 8 to 20, 8 to 21, 8 to 22, 8 to 23, 8 to 24, 8 to 25, 8 to 26, 8 to 27, 8 to 28, 8 to 29, 8 to 30, 9 to 10, 9 to 11, 9 to 12, 9 to 13, 9 to 14, 9 to 15, 9 to 16, 9 to 17, 9 to 18, 9 to 19, 9 to 20, 9 to 21, 9 to 22, 9 to 23, 9 to 24, 9 to 25, 9 to 26, 9 to 27, 9 to 28, 9 to 29, 9 to 30, 10 to 11, 10 to 12, 10 to 13, 10 to 14, 10 to 15, 10 to 16, 10 to 17, 10 to 18, 10 to 19, 10 to 20, 10 to 21, 10 to 22, 10 to 23, 10 to 24, 10 to 25, 10 to 26, 10 to 27, 10 to 28, 10 to 29, 10 to 30, 11 to 12, 11 to 13, 11 to 14, 11 to 15, 11 to 16, 11 to 17, 11 to 18, 11 to 19, 11 to 20, 11 to 21, 11 to 22, 11 to 23, 11 to 24, 11 to 25, 11 to 26, 11 to 27, 11 to 28, 11 to 29, 11 to 30, 12 to 13, 12 to 14, 12 to 15, 12 to 16, 12 to 17, 12 to 18, 12 to 19, 12 to 20, 12 to 21, 12 to 22, 12 to 23, 12 to 24, 12 to 25, 12 to 26, 12 to 27, 12 to 28, 12 to 29, 12 to 30, 13 to 14, 13 to 15, 13 to 16, 13 to 17, 13 to 18, 13 to 19, 13 to 20, 13 to 21, 13 to 22, 13 to 23, 13 to 24, 13 to 25, 13 to 26, 13 to 27, 13 to 28, 13 to 29, 13 to 30, 14 to 15, 14 to 16, 14 to 17, 14 to 18, 14 to 19, 14 to 20, 14 to 21, 14 to 22, 14 to 23, 14 to 24, 14 to 25, 14 to 26, 14 to 27, 14 to 28, 14 to 29, 14 to 30, 15 to 16, 15 to 17, 15 to 18, 15 to 19, 15 to 20, 15 to 21, 15 to 22, 15 to 23, 15 to 24, 15 to 25, 15 to 26, 15 to 27, 15 to 28, 15 to 29, 15 to 30, 16 to 17, 16 to 18, 16 to 19, 16 to 20, 16 to 21, 16 to 22, 16 to 23, 16 to 24, 16 to 25, 16 to 26, 16 to 27, 16 to 28, 16 to 29, 16 to 30, 17 to 18, 17 to 19, 17 to 20, 17 to 21, 17 to 22, 17 to 23, 17 to 24, 17 to 25, 17 to 26, 17 to 27, 17 to 28, 17 to 29, 17 to 30, 18 to 19, 18 to 20, 18 to 21, 18 to 22, 18 to 23, 18 to 24, 18 to 25, 18 to 26, 18 to 27, 18 to 28, 18 to 29, 18 to 30, 19 to 20, 19 to 21, 19 to 22, 19 to 23, 19 to 24, 19 to 25, 19 to 26, 19 to 29, 19 to 28, 19 to 29, 19 to 30, 20 to 21, 20 to 22, 20 to 23, 20 to 24, 20 to 25, 20 to 26, 20 to 27, 20 to 28, 20 to 29, 20 to 30, 21 to 22, 21 to 23, 21 to 24, 21 to 25, 21 to 26, 21 to 27, 21 to 28, 21 to 29, 21 to 30, 22 to 23, 22 to 24, 22 to 25, 22 to 26, 22 to 27, 22 to 28, 22 to 29, 22 to 30, 23 to 24, 23 to 25, 23 to 26, 23 to 27, 23 to 28, 23 to 29, 23 to 30, 24 to 25, 24 to 26, 24 to 27, 24 to 28, 24 to 29, 24 to 30, 25 to 26, 25 to 27, 25 to 28, 25 to 29, 25 to 30, 26 to 27, 26 to 28, 26 to 29, 26 to 30, 27 to 28, 27 to 29, 27 to 30, 28 to 29, 28 to 30, or 29 to 30 linked nucleosides. In embodiments where the number of nucleosides of an oligomeric compound or oligonucleotide is limited, whether to a range or to a specific number, the oligomeric compound or oligonucleotide may, nonetheless further comprise additional other substituents. For example, an oligonucleotide comprising 8-30 nucleosides excludes oligonucleotides having 31 nucleosides, but, unless otherwise indicated, such an oligonucleotide may further comprise, for example one or more conjugates, terminal groups, or other substituents. In certain embodiments, a gapmer oligonucleotide has any of the above lengths.
In certain embodiments, any of the gapmer motifs provided above, including but not limited to gapmer motifs 1-278 provided in Tables 3 and 4, may have any of the above lengths. One of skill in the art will appreciate that certain lengths may not be possible for certain motifs. For example: a gapmer having a 5′-wing region consisting of four nucleotides, a gap consisting of at least six nucleotides, and a 3′-wing region consisting of three nucleotides cannot have an overall length less than 13 nucleotides. Thus, one would understand that the lower length limit is 13 and that the limit of 10 in “10-20” has no effect in that embodiment.
Further, where an oligonucleotide is described by an overall length range and by regions having specified lengths, and where the sum of specified lengths of the regions is less than the upper limit of the overall length range, the oligonucleotide may have additional nucleosides, beyond those of the specified regions, provided that the total number of nucleosides does not exceed the upper limit of the overall length range. For example, an oligonucleotide consisting of 20-25 linked nucleosides comprising a 5′-wing consisting of 5 linked nucleosides; a 3′-wing consisting of 5 linked nucleosides and a central gap consisting of 10 linked nucleosides (5+5+10=20) may have up to 5 nucleosides that are not part of the 5′-wing, the 3′-wing, or the gap (before reaching the overall length limitation of 25). Such additional nucleosides may be 5′ of the 5′-wing and/or 3′ of the 3′ wing.
Certain Oligonucleotides
In certain embodiments, oligonucleotides of the present invention are characterized by their sugar motif, internucleoside linkage motif, nucleobase modification motif and overall length. In certain embodiments, such parameters are each independent of one another. Thus, each internucleoside linkage of an oligonucleotide having a gapmer sugar motif may be modified or unmodified and may or may not follow the gapmer modification pattern of the sugar modifications. Thus, the internucleoside linkages within the wing regions of a sugar-gapmer may be the same or different from one another and may be the same or different from the internucleoside linkages of the gap region. Likewise, such sugar-gapmer oligonucleotides may comprise one or more modified nucleobase independent of the gapmer pattern of the sugar modifications.
Certain Conjugate Groups
In certain embodiments, oligomeric compounds are modified by attachment of one or more conjugate groups. In general, conjugate groups modify one or more properties of the attached oligomeric compound including but not limited to pharmacodynamics, pharmacokinetics, stability, binding, absorption, cellular distribution, cellular uptake, charge and clearance. Conjugate groups are routinely used in the chemical arts and are linked directly or via an optional conjugate linking moiety or conjugate linking group to a parent compound such as an oligomeric compound, such as an oligonucleotide. Conjugate groups includes without limitation, intercalators, reporter molecules, polyamines, polyamides, polyethylene glycols, thioethers, polyethers, cholesterols, thiocholesterols, cholic acid moieties, folate, lipids, phospholipids, biotin, phenazine, phenanthridine, anthraquinone, adamantane, acridine, fluoresceins, rhodamines, coumarins and dyes. Certain conjugate groups have been described previously, for example: cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Let., 1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g., do-decan-diol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimie, 1993, 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923-937).
In certain embodiments, a conjugate group comprises an active drug substance, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fen-bufen, ketoprofen, (S)-(+)-pranoprofen, carprofen, dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indo-methicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic.
In certain embodiments, conjugate groups are directly attached to oligonucleotides in oligomeric compounds. In certain embodiments, conjugate groups are attached to oligonucleotides by a conjugate linking group. In certain such embodiments, conjugate linking groups, including, but not limited to, bifunctional linking moieties such as those known in the art are amenable to the compounds provided herein. Conjugate linking groups are useful for attachment of conjugate groups, such as chemical stabilizing groups, functional groups, reporter groups and other groups to selective sites in a parent compound such as for example an oligomeric compound. In general 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. In some embodiments, the conjugate linker comprises a chain structure or an oligomer of repeating units such as ethylene glycol or amino acid units. Examples of functional groups that are routinely used in a bifunctional linking moiety include, but are not limited to, electrophiles for reacting with nucleophilic groups and nucleophiles for reacting with electrophilic groups. In some embodiments, bifunctional linking moieties include amino, hydroxyl, carboxylic acid, thiol, unsaturations (e.g., double or triple bonds), and the like.
Some nonlimiting examples of conjugate linking moieties include pyrrolidine, 8-amino-3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) and 6-aminohexanoic acid (AHEX or AHA). Other 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.
Conjugate groups may be attached to either or both ends of an oligonucleotide (terminal conjugate groups) and/or at any internal position.
In certain embodiments, conjugate groups are at the 3′-end of an oligonucleotide of an oligomeric compound. In certain embodiments, conjugate groups are near the 3′-end. In certain embodiments, conjugates are attached at the 3′ end of an oligomeric compound, but before one or more terminal group nucleosides. In certain embodiments, conjugate groups are placed within a terminal group. In certain embodiments, the present invention provides oligomeric compounds. In certain embodiments, oligomeric compounds comprise an oligonucleotide. In certain embodiments, an oligomeric compound comprises an oligonucleotide and one or more conjugate and/or terminal groups. Such conjugate and/or terminal groups may be added to oligonucleotides having any of the chemical motifs discussed above. Thus, for example, an oligomeric compound comprising an oligonucleotide having region of alternating nucleosides may comprise a terminal group.
Antisense Compounds
In certain embodiments, oligomeric compounds of the present invention are antisense compounds. Such antisense compounds are capable of hybridizing to a target nucleic acid, resulting in at least one antisense activity. In certain embodiments, antisense compounds specifically hybridize to one or more target nucleic acid. In certain embodiments, a specifically hybridizing antisense compound has a nucleobase sequence comprising a region having sufficient complementarity to a target nucleic acid to allow hybridization and result in antisense activity and insufficient complementarity to any non-target so as to avoid non-specific hybridization to any non-target nucleic acid sequences under conditions in which specific hybridization is desired (e.g., under physiological conditions for in vivo or therapeutic uses, and under conditions in which assays are performed in the case of in vitro assays).
In certain embodiments, the present invention provides antisense compounds comprising oligonucleotides that are fully complementary to the target nucleic acid over the entire length of the oligonucleotide. In certain embodiments, oligonucleotides are 99% complementary to the target nucleic acid. In certain embodiments, oligonucleotides are 95% complementary to the target nucleic acid. In certain embodiments, such oligonucleotides are 90% complementary to the target nucleic acid.
In certain embodiments, such oligonucleotides are 85% complementary to the target nucleic acid. In certain embodiments, such oligonucleotides are 80% complementary to the target nucleic acid. In certain embodiments, an antisense compound comprises a region that is fully complementary to a target nucleic acid and is at least 80% complementary to the target nucleic acid over the entire length of the oligonucleotide. In certain such embodiments, the region of full complementarity is from 6 to 14 nucleobases in length.
Certain Antisense Activities and Mechanisms
In certain antisense activities, hybridization of an antisense compound results in recruitment of a protein that cleaves of the target nucleic acid. For example, certain antisense compounds result in RNase H mediated cleavage of target nucleic acid. RNase H is a cellular endonuclease that cleaves the RNA strand of an RNA:DNA duplex. The “DNA” in such an RNA:DNA duplex, need not be unmodified DNA. In certain embodiments, the invention provides antisense compounds that are sufficiently “DNA-like” to elicit RNase H activity. Such DNA-like antisense compounds include, but are not limited to gapmers having unmodified deoxyfuronose sugar moieties in the nucleosides of the gap and modified sugar moieties in the nucleosides of the wings.
Antisense activities may be observed directly or indirectly. In certain embodiments, observation or detection of an antisense activity involves observation or detection of a change in an amount of a target nucleic acid or protein encoded by such target nucleic acid; a change in the ratio of splice variants of a nucleic acid or protein; and/or a phenotypic change in a cell or animal.
In certain embodiments, compounds comprising oligonucleotides having a gapmer motif described herein have desirable properties compared to non-gapmer oligonucleotides or to gapmers having other motifs. In certain circumstances, it is desirable to identify motifs resulting in a favorable combination of potent antisense activity and relatively low toxicity. In certain embodiments, compounds of the present invention have a favorable therapeutic index (measure of potency divided by measure of toxicity).
Certain Target Nucleic Acids
In certain embodiments, antisense compounds comprise or consist of an oligonucleotide comprising a region that is complementary to a target nucleic acid. In certain embodiments, the target nucleic acid is an endogenous RNA molecule. In certain embodiments, the target nucleic acid is a non-coding RNA. In certain such embodiments, the target non-coding RNA is selected from: a long-non-coding RNA, a short non-coding RNA, an intronic RNA molecule, a snoRNA, a scaRNA, a microRNA (including pre-microRNA and mature microRNA), a ribosomal RNA, and promoter directed RNA. In certain embodiments, the target nucleic acid encodes a protein. In certain such embodiments, the target nucleic acid is selected from: an mRNA and a pre-mRNA, including intronic, exonic and untranslated regions. In certain embodiments, oligomeric compounds are at least partially complementary to more than one target nucleic acid. For example, antisense compounds of the present invention may mimic microRNAs, which typically bind to multiple targets.
In certain embodiments, the target nucleic acid is a nucleic acid other than a mature mRNA. In certain embodiments, the target nucleic acid is a nucleic acid other than a mature mRNA or a microRNA. In certain embodiments, the target nucleic acid is a non-coding RNA other than a microRNA. In certain embodiments, the target nucleic acid is a non-coding RNA other than a microRNA or an intronic region of a pre-mRNA. In certain embodiments, the target nucleic acid is a long non-coding RNA. In certain embodiments, the target RNA is an mRNA. In certain embodiments, the target nucleic acid is a pre-mRNA. In certain such embodiments, the target region is entirely within an intron. In certain embodiments, the target region spans an intron/exon junction. In certain embodiments, the target region is at least 50% within an intron. In certain embodiments, the target nucleic acid is selected from among non-coding RNA, including exonic regions of pre-mRNA. In certain embodiments, the target nucleic acid is a ribosomal RNA (rRNA). In certain embodiments, the target nucleic acid is a non-coding RNA associated with splicing of other pre-mRNAs. In certain embodiments, the target nucleic acid is a nuclear-retained non-coding RNA.
In certain embodiments, antisense compounds described herein are complementary to a target nucleic acid comprising a single-nucleotide polymorphism. In certain such embodiments, the antisense compound is capable of modulating expression of one allele of the single-nucleotide polymorphism-containing-target nucleic acid to a greater or lesser extent than it modulates another allele. In certain embodiments an antisense compound hybridizes to a single-nucleotide polymorphism-containing-target nucleic acid at the single-nucleotide polymorphism site. In certain embodiments an antisense compound hybridizes to a single-nucleotide polymorphism-containing-target nucleic acid near the single-nucleotide polymorphism site. In certain embodiments, the target nucleic acid is a Huntingtin gene transcript. In certain embodiments, the target nucleic acid is a single-nucleotide polymorphism-containing-target nucleic acid other than a Huntingtin gene transcript. In certain embodiments, the target nucleic acid is any nucleic acid other than a Huntingtin gene transcript.
Certain Pharmaceutical Compositions
In certain embodiments, the present invention provides pharmaceutical compositions comprising one or more antisense compound. In certain embodiments, such pharmaceutical composition comprises a suitable pharmaceutically acceptable diluent or carrier. In certain embodiments, a pharmaceutical composition comprises a sterile saline solution and one or more antisense compound. In certain embodiments, such pharmaceutical composition consists of a sterile saline solution and one or more antisense compound. In certain embodiments, the sterile saline is pharmaceutical grade saline. In certain embodiments, a pharmaceutical composition comprises one or more antisense compound and sterile water. In certain embodiments, a pharmaceutical composition consists of one or more antisense compound and sterile water. In certain embodiments, the sterile saline is pharmaceutical grade water. In certain embodiments, a pharmaceutical composition comprises one or more antisense compound and phosphate-buffered saline (PBS). In certain embodiments, a pharmaceutical composition consists of one or more antisense compound and sterile phosphate-buffered saline (PBS). In certain embodiments, the sterile saline is pharmaceutical grade PBS.
In certain embodiments, antisense compounds may be admixed with pharmaceutically acceptable active and/or inert substances for the preparation of pharmaceutical compositions or formulations. Compositions and methods for the formulation of pharmaceutical compositions depend on a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.
Pharmaceutical compositions comprising antisense compounds encompass any pharmaceutically acceptable salts, esters, or salts of such esters. In certain embodiments, pharmaceutical compositions comprising antisense compounds comprise one or more oligonucleotide which, upon administration to an animal, including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. Accordingly, for example, the disclosure is also drawn to pharmaceutically acceptable salts of antisense compounds, prodrugs, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents. Suitable pharmaceutically acceptable salts include, but are not limited to, sodium and potassium salts.
A prodrug can include the incorporation of additional nucleosides at one or both ends of an oligomeric compound which are cleaved by endogenous nucleases within the body, to form the active antisense oligomeric compound.
Lipid moieties have been used in nucleic acid therapies in a variety of methods. In certain such methods, the nucleic acid is introduced into preformed liposomes or lipoplexes made of mixtures of cationic lipids and neutral lipids. In certain methods, DNA complexes with mono- or poly-cationic lipids are formed without the presence of a neutral lipid. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to a particular cell or tissue. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to fat tissue. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to muscle tissue.
In certain embodiments, pharmaceutical compositions provided herein comprise one or more modified oligonucleotides and one or more excipients. In certain such embodiments, excipients are selected from water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylase, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose and polyvinylpyrrolidone.
In certain embodiments, a pharmaceutical composition provided herein comprises a delivery system. Examples of delivery systems include, but are not limited to, liposomes and emulsions. Certain delivery systems are useful for preparing certain pharmaceutical compositions including those comprising hydrophobic compounds. In certain embodiments, certain organic solvents such as dimethylsulfoxide are used.
In certain embodiments, a pharmaceutical composition provided herein comprises one or more tissue-specific delivery molecules designed to deliver the one or more pharmaceutical agents of the present invention to specific tissues or cell types. For example, in certain embodiments, pharmaceutical compositions include liposomes coated with a tissue-specific antibody.
In certain embodiments, a pharmaceutical composition provided herein comprises a co-solvent system. Certain of such co-solvent systems comprise, for example, benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase. In certain embodiments, such co-solvent systems are used for hydrophobic compounds. A non-limiting example of such a co-solvent system is the VPD co-solvent system, which is a solution of absolute ethanol comprising 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant Polysorbate 80TM and 65% w/v polyethylene glycol 300. The proportions of such co-solvent systems may be varied considerably without significantly altering their solubility and toxicity characteristics. Furthermore, the identity of co-solvent components may be varied: for example, other surfactants may be used instead of Polysorbate 80TM; the fraction size of polyethylene glycol may be varied; other biocompatible polymers may replace polyethylene glycol, e.g., polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose.
In certain embodiments, a pharmaceutical composition provided herein is prepared for oral administration. In certain embodiments, pharmaceutical compositions are prepared for buccal administration.
In certain embodiments, a pharmaceutical composition is prepared for administration by injection (e.g., intravenous, subcutaneous, intramuscular, etc.). In certain of such embodiments, a pharmaceutical composition comprises a carrier and is formulated in aqueous solution, such as water or physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer. In certain embodiments, other ingredients are included (e.g., ingredients that aid in solubility or serve as preservatives). In certain embodiments, injectable suspensions are prepared using appropriate liquid carriers, suspending agents and the like. Certain pharmaceutical compositions for injection are presented in unit dosage form, e.g., in ampoules or in multi-dose containers. Certain pharmaceutical compositions for injection are suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Certain solvents suitable for use in pharmaceutical compositions for injection include, but are not limited to, lipophilic solvents and fatty oils, such as sesame oil, synthetic fatty acid esters, such as ethyl oleate or triglycerides, and liposomes. Aqueous injection suspensions may contain substances that increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, such suspensions may also contain suitable stabilizers or agents that increase the solubility of the pharmaceutical agents to allow for the preparation of highly concentrated solutions.
In certain embodiments, a pharmaceutical composition is prepared for transmucosal administration. In certain of such embodiments penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
In certain embodiments, a pharmaceutical composition provided herein comprises an oligonucleotide in a therapeutically effective amount. In certain embodiments, the therapeutically effective amount is sufficient to prevent, alleviate or ameliorate symptoms of a disease or to prolong the survival of the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art.
In certain embodiments, one or more modified oligonucleotide provided herein is formulated as a prodrug. In certain embodiments, upon in vivo administration, a prodrug is chemically converted to the biologically, pharmaceutically or therapeutically more active form of an oligonucleotide. In certain embodiments, prodrugs are useful because they are easier to administer than the corresponding active form. For example, in certain instances, a prodrug may be more bioavailable (e.g., through oral administration) than is the corresponding active form. In certain instances, a prodrug may have improved solubility compared to the corresponding active form. In certain embodiments, prodrugs are less water soluble than the corresponding active form. In certain instances, such prodrugs possess superior transmittal across cell membranes, where water solubility is detrimental to mobility. In certain embodiments, a prodrug is an ester. In certain such embodiments, the ester is metabolically hydrolyzed to carboxylic acid upon administration. In certain instances the carboxylic acid containing compound is the corresponding active form. In certain embodiments, a prodrug comprises a short peptide (polyaminoacid) bound to an acid group. In certain of such embodiments, the peptide is cleaved upon administration to form the corresponding active form.
In certain embodiments, the present invention provides compositions and methods for reducing the amount or activity of a target nucleic acid in a cell. In certain embodiments, the cell is in an animal. In certain embodiments, the animal is a mammal. In certain embodiments, the animal is a rodent. In certain embodiments, the animal is a primate. In certain embodiments, the animal is a non-human primate. In certain embodiments, the animal is a human.
In certain embodiments, the present invention provides methods of administering a pharmaceutical composition comprising an oligomeric compound of the present invention to an animal. Suitable administration routes include, but are not limited to, oral, rectal, transmucosal, intestinal, enteral, topical, suppository, through inhalation, intrathecal, intracerebroventricular, intraperitoneal, intranasal, intraocular, intratumoral, and parenteral (e.g., intravenous, intramuscular, intramedullary, and subcutaneous). In certain embodiments, pharmaceutical intrathecals are administered to achieve local rather than systemic exposures.
Nonlimiting Disclosure and Incorporation by Reference
While certain compounds, compositions and methods described herein have been described with specificity in accordance with certain embodiments, the following examples serve only to illustrate the compounds described herein and are not intended to limit the same. Each of the references, GenBank accession numbers, and the like recited in the present application is incorporated herein by reference in its entirety.
EXAMPLES
The following examples illustrate certain embodiments of the present invention and are not limiting. Moreover, where specific embodiments are provided, the inventors have contemplated generic application of those specific embodiments. For example, disclosure of an oligonucleotide having a particular motif provides reasonable support for additional oligonucleotides having the same or similar motif. And, for example, where a particular high-affinity modification appears at a particular position, other high-affinity modifications at the same position are considered suitable, unless otherwise indicated.
Where nucleobase sequences are not provided, to allow assessment of the relative effects of nucleobase sequence and chemical modification, throughout the examples, oligomeric compounds are assigned a “Sequence Code.” Oligomeric compounds having the same Sequence Code have the same nucleobase sequence. Oligomeric compounds having different Sequence Codes have different nucleobase sequences.
Example 1: Antisense Inhibition of Human Target X in HuVEC Cells
Antisense oligonucleotides were designed to target a messenger RNA molecule (Target X) and were tested for their effects on target X mRNA in vitro. Cultured HuVEC cells at a density of 20,000 cells per well were transfected using electroporation with 250 nM antisense oligonucleotide. After a treatment period of approximately 24 hours, RNA was isolated from the cells and Target X mRNA levels were measured by quantitative real-time PCR. Target X mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented as percent inhibition of Target X, relative to untreated control cells. A total of 40 oligonucleotides were tested. Only those oligonucleotides which were selected for further study are shown in Table 4.
The ‘Chemistry’ column describes the sugar modifications of each oligonucleotide. ‘k’ indicates an (S)-cEt sugar modification; the number indicates the number of deoxynucleosides; and ‘e’ indicates a MOE modification. The internucleoside linkages throughout each gapmer are phosphorothioate linkages. All cytosine residues throughout each gapmer are 5-methylcytosines. “Start site” indicates the 5′-most nucleoside to which the gapmer is targeted in the human gene sequence of Target X. “Stop site” indicates the 3′-most nucleoside to which the gapmer is targeted human gene sequence of Target X. Each gapmer listed in Table 4 is targeted to the human Target X genomic sequence. Oligonucleotides having the same start site and stop site as one another have the identical nucleobase sequence.











TABLE 4





Target
Target


%


Start Site
Stop Site
ISIS No
Chemistry
inhibition







58721
58736
549457
kkk-10-kkk
67


58751
58766


58722
58737
549458
kkk-10-kkk
71


58752
58767


58720
58735
560098
kkk-10-kkk
69


58750
58765


58751
58766


58721
58736
560131
kkk-9-kkke
74


58751
58766


58721
58736
560137
ekkk-8-kkke
66


58751
58766


58750
58765


58720
58735
569213
kkk-9-kkke
69


58750
58765


58720
58735
569216
ekkk-8-kkke
68


58750
58765


58721
58736
569222
eekkk-8-kkk
74


58751
58766


58721
58736
569228
eekkk-7-kkke
67


58751
58766


58720
58735
569236
ekkk-7-kkkee
66


58750
58765









Example 2: Dose-Dependent Antisense Inhibition of Human Target X in HuVEC Cells
Gapmers from the studies described above exhibiting significant in vitro inhibition of Target X mRNA were selected and tested at various doses in HuVEC cells. Cells were plated at a density of 20,000 cells per well and transfected using electroporation with 31.3 μM, 62.5 μM, 125.0 μM, 250.0 μM, 500.0 μM, and 1000.0 μM concentrations of antisense oligonucleotide, as specified in Table 5. After a treatment period of approximately 16 hours, RNA was isolated from the cells and Target X mRNA levels were measured by quantitative real-time PCR. Target X mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented as percent inhibition of Target X, relative to untreated control cells. The antisense oligonucleotides were tested in a series of experiments that had similar culture conditions. The results for each experiment are presented in separate tables shown below.
The half maximal inhibitory concentration (IC50) of each oligonucleotide is also presented in Table 5. As illustrated, Target X mRNA levels were reduced in a dose-dependent manner in the antisense oligonucleotide treated cells.














TABLE 5






31.25
62.5
125.0
250.0
500.0
1000.0
IC50


ISIS No
nM
nM
nM
nM
nM
nM
(μM)







549457
34
44
75
82
93
96
0.06


549458
30
36
54
70
85
90
0.10


560098
30
54
65
78
89
97
0.07


560131
16
48
65
82
89
97
0.09


560137
35
39
64
73
89
94
0.08


569213
35
53
65
83
94
96
0.06


569216
38
51
68
83
91
96
0.05


569222
36
48
67
83
91
98
0.06


569228
26
43
62
78
88
92
0.09


569236
17
39
54
79
84
92
0.11









Example 3: Dose-Dependent Antisense Inhibition of Human Target X in HuVEC Cells
Additional antisense oligonucleotides were designed as deoxy, MOE and (S)-cEt oligonucleotides targeting Target X gene sequences and were tested at various doses in HuVEC cells. The ‘Chemistry’ column describes the sugar modifications of each oligonucleotide. ‘k’ indicates an (S)-cEt sugar modification; the number indicates the number of deoxynucleosides; otherwise indicates deoxyribose; and ‘e’ indicates a MOE modification. The internucleoside linkages throughout each gapmer are phosphorothioate linkages. All cytosine residues throughout each gapmer are 5-methylcytosines. “Start site” indicates the 5′-most nucleoside to which the gapmer is targeted in the human gene sequence. “Stop site” indicates the 3′-most nucleoside to which the gapmer is targeted human gene sequence. Each gapmer listed in Table 6 is targeted to the human Target X genomic sequence. Oligonucleotides having the same start site and stop site as one another have the identical nucleobase sequence.










TABLE 6





Target
Target




Start Site
Stop Site
ISIS No
Chemistry







58720
58735
569221
eekkk-8-kkk


58750
58765


58720
58735
569227
eekkk-7-kkke


58750
58765


58720
58735
569236
ekkk-7-kkkee


58750
58765


58720
58735
579666
ekkeekk-7-kk


58750
58765


58721
58736
579667
ekkeekk-7-kk


58751
58766


58720
58735
579670
ekkekk-7-kkk


58750
58765


58721
58736
579671
ekkekk-7-kkk


58751
58766


58721
58736
569228
eekkk-7-kkke


58751
58766


58723
58738
579669
ekkeekk-7-kk


58753
58768


58722
58737
579672
ekkekk-7-kkk


58752
58767


58722
58737
569217
ekkk-8-kkke


58752
58767


58723
58738
569214
kkk-9-kkke


58753
58768


58723
58738
560099
kkk-10-kkk


58753
58768









Cells were plated at a density of 20,000 cells per well and transfected using electroporation with 62.5 μM, 125.0 μM, 250.0 μM, 500.0 μM, and 1000.0 μM concentrations of antisense oligonucleotide, as specified in Tables 10-12. After a treatment period of approximately 16 hours, RNA was isolated from the cells and Target X mRNA levels were measured by quantitative real-time PCR. Target X mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented as percent inhibition of Target X, relative to untreated control cells. The antisense oligonucleotides were tested in a series of experiments that had similar culture conditions. The results for each experiment are presented in separate tables shown below.
The half maximal inhibitory concentration (IC50) of each oligonucleotide is also presented in Tables 7-9. As illustrated, Target X mRNA levels were reduced in a dose-dependent manner in some of the antisense oligonucleotide treated cells.













TABLE 7






62.5
125.0
250.0
500.0
1000.0
IC50


ISIS No
nM
nM
nM
nM
nM
(nM)





















549458
25
46
55
64
78
203


569227
8
40
33
51
73
388


569228
29
44
63
77
87
158


569236
4
35
54
68
88
252


579666
33
34
47
64
80
229


579667
30
29
44
36
76
411






















TABLE 8






62.5
125.0
250.0
500.0
1000.0
IC50


ISIS No
nM
nM
nM
nM
nM
(nM)





















549458
16
22
44
64
74
324


579669
24
39
45
74
91
207


579670
27
28
55
75
70
236


579671
6
40
54
57
77
288


579672
9
30
50
72
86
258






















TABLE 9






62.5
125.0
250.0
500.0
1000.0
IC50


ISIS No
nM
nM
nM
nM
nM
(nM)





















549458
19
22
45
38
71
470


569214
20
26
61
62
76
265


569217
34
39
49
64
64
247


569221
12
32
59
57
73
294









Example 4: Antisense Inhibition of Human Target X in HuVEC Cells
Additional antisense oligonucleotides were designed targeting Target X nucleic acid and were tested for their effects on Target X mRNA in vitro. Cultured HuVEC cells at a density of 20,000 cells per well were transfected using electroporation with 1,000 nM antisense oligonucleotide. After a treatment period of approximately 24 hours, RNA was isolated from the cells and Target X mRNA levels were measured by quantitative real-time PCR. Target X mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented as percent inhibition of Target X, relative to untreated control cells. A total of 75 oligonucleotides were tested. Only those oligonucleotides which were selected for further study are shown in Table 10.
The ‘Chemistry’ column describes the sugar modifications of each oligonucleotide. ‘k’ indicates an (S)-cEt sugar modification; the number indicates the number of deoxynucleosides; otherwise ‘d.’ indicates deoxyribose; and ‘e’ indicates a MOE modification. The internucleoside linkages throughout each gapmer are phosphorothioate linkages. All cytosine residues throughout each gapmer are 5-methylcytosines.
The “Start site” indicates the 5′-most nucleoside to which the gapmer is targeted in the human gene sequence. “Stop site” indicates the 3′-most nucleoside to which the gapmer is targeted human gene sequence. Each gapmer listed in Table 10 is targeted to the human Target X genomic sequence. Oligonucleotides having the same start site and stop site as one another have the identical nucleobase sequence.











TABLE 10





Target
Target


%


Start Site
Stop Site
ISIS No
Chemistry
inhibition



















5062
5077
549372
kkk-10-kkk
64


5061
5076
585233
kkk-8-keeee
69


5062
5077
585259
ekkk-9-kkk
71


5062
5077
585262
kkk-9-kkke
77


5062
5077
585263
kkk-8-kkkee
69


5062
5077
585264
kkk-7-kkkeee
62


5062
5077
585265
eekk-8-kkee
69


5062
5077
585268
keke-8-ekek
72


5062
5077
585269
ekek-8-ekek
73


5062
5077
585271
ekk-10-kke
57


5062
5077
585274
kkk-10-kke
65


58719
58734
586124
kkk-10-kkk
82


58720
58735
569227
eekkk-7-kkke
51


58750
58765


58722
58737
560132
kkk-9-kkke
58


58752
58767


58722
58737
569229
eekkk-7-kkke
57


58752
58767


58722
58737
569238
ekkk-7-kkkee
51


58752
58767


58722
58737
549458
kkk-10-kkk
87


58752
58767


58722
58737
569223
eekkk-8-kkk
59


58752
58767


58724
58739
569215
kkk-9-kkke
59


58754
58769


58725
58740
560133
kkk-9-kkke
53


58755
58770


58725
58740
569220
ekkk-8-kkke
58


58755
58770


58721
58736
586224
kkkkk-8-kkk
90


58751
58766


58722
58737
586225
kkkkk-8-kkk
88


58752
58767


58720
58735
586227
kkkkk-8-kkk
87


58750
58765









Example 5: Dose-Dependent Antisense Inhibition of Human Target X in HuVEC Cells
Antisense oligonucleotides from the studies described above exhibiting significant in vitro inhibition of Target X mRNA were selected and tested at various doses in HuVEC cells. Cells were plated at a density of 20,000 cells per well and transfected using electroporation with 31.25 μM, 62.5 μM, 125.0 μM, 250.0 μM, 500.0 μM, and 1000.0 μM concentrations of antisense oligonucleotide, as specified in Table 11. After a treatment period of approximately 16 hours, RNA was isolated from the cells and Target X mRNA levels were measured by quantitative real-time PCR. Target X mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented as percent inhibition of Target X, relative to untreated control cells. The antisense oligonucleotides were tested in a series of experiments that had similar culture conditions. The results for each experiment are presented in separate tables shown below.
The half maximal inhibitory concentration (IC50) of each oligonucleotide is also presented in Table 11. As illustrated, Target X mRNA levels were reduced in a dose-dependent manner in the antisense oligonucleotide treated cells.














TABLE 11






31.25
62.5
125.0
250.0
500.0
1000.0
IC50


ISIS No
nM
nM
nM
nM
nM
nM
nM






















549372
2
17
31
51
61
80
271


549458
0
19
40
63
74
90
196


560132
8
19
21
53
65
85
252


560133
17
15
24
35
58
79
336


569215
12
2
26
55
71
90
234


569220
11
29
34
43
59
78
275


569223
21
20
30
59
73
87
191


569227
13
22
45
46
61
74
255


569229
16
14
36
47
74
84
220


569238
4
32
33
54
71
88
202









Example 6: Dose-Dependent Antisense Inhibition of Human Target X in HuVEC Cells
Gapmers from Example 8 exhibiting significant in vitro inhibition of Target X mRNA were selected and tested at various doses in HuVEC cells. Cells were plated at a density of 20,000 cells per well and transfected using electroporation with 46.9 μM, 187.5 μM, 750.0 μM, and 3000.0 μM concentrations of antisense oligonucleotide, as specified in Table 12. After a treatment period of approximately 16 hours, RNA was isolated from the cells and Target X mRNA levels were measured by quantitative real-time PCR. Target X mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented as percent inhibition of AR, relative to untreated control cells.
The half maximal inhibitory concentration (IC50) of each oligonucleotide is also presented in Table 12. As illustrated, Target X mRNA levels were reduced in a dose-dependent manner in antisense oligonucleotide treated cells.














TABLE 12








46.9
187.5
750.0
3000.0
IC50



ISIS No
nM
nM
nM
nM
(μM)























549372
9
41
66
87
0.29



549458
15
50
85
96
0.19



586124
28
47
84
94
0.13



586224
39
75
93
98
0.05



586225
17
61
89
97
0.13



586227
20
60
88
96
0.13










Example 7: Tolerability of Antisense Oligonucleotides Targeting Human Target X in CD1 Mice
CD1® mice (Charles River, Mass.) are a multipurpose mice model, frequently utilized for safety and efficacy testing. The mice were treated with ISIS antisense oligonucleotides presented in Table 13 and evaluated for changes in the levels of various plasma chemistry markers.








TABLE 13





ISIS No
Chemistry







549372
kkk-10-kkk


585233
kkk-8-keeee


585259
ekkk-9-kkk


585262
kkk-9-kkke


585263
kkk-8-kkkee


585264
kkk-7-kkkeee


585265
eekk-8-kkee


585268
keke-8-ekek


585269
ekek-8-ekek









Treatment

Groups of 4-6-week old male CD1 mice were injected subcutaneously twice a week for 4 weeks with 100 mg/kg of ISIS 549372, ISIS 585233, ISIS 585259, ISIS 585262, ISIS 585263, ISIS 585264, ISSI 585265, ISSI 585268, ISIS 585269, ISIS 585271, or ISIS 585274 (weekly dose of 200 mg/kg). One group of 4-6-week old male CD1 mice was injected subcutaneously twice a week for 4 weeks with PBS. Mice were euthanized 48 hours after the last dose, and organs and plasma were harvested for further analysis.
Organ Weights
To evaluate the effect of ISIS oligonucleotides on organ weights, mice were euthanized and the liver, kidney and spleen for mice from all groups were weighed. The results are presented in Table 14. ISIS oligonucleotides that caused changes in the weights of any of the organs outside the expected range for antisense oligonucleotides were excluded in further studies.







TABLE 14







Organ weights











Liver
Kidney
Spleen
















PBS
201
64
15



ISIS 549372
244
52
45



ISIS 585233
241
46
14



ISIS 585259
261
49
15



ISIS 585262
257
57
35



ISIS 585263
206
52
14



ISIS 585264
237
50
17



ISIS 585265
219
45
14



ISIS 585268
218
50
21



ISIS 585269
214
48
16










Plasma Chemistry Markers

To evaluate the effect of ISIS oligonucleotides on liver and kidney function, plasma levels of transaminases, bilirubin, albumin, cholesterol, and BUN were measured using an automated clinical chemistry analyzer (Hitachi Olympus AU400e, Melville, N.Y.). The results are presented in Table 15. ISIS oligonucleotides that caused changes in the levels of any of the liver or kidney function markers outside the expected range for antisense oligonucleotides were excluded in further studies.







TABLE 15







Plasma chemistry markers in CD1 mice plasma
















Albu-

Choles-




ALT
AST
min
BUN
terol
Bilirubin



(IU/L)
(IU/L)
(g/dL)
(mg/dL)
(mg/dL)
(mg/dL)

















PBS
40
62
2.6
26
112
0.19


ISIS 549372
116
151
2
25.4
40
0.16


ISIS 585233
884
716
1.8
23
93
0.94


ISIS 585259
2858
1302
2.3
24.4
93
0.39


ISIS 585262
860
823
2
25.1
48
0.25


ISIS 585263
133
113
2.4
28.3
82
0.21


ISIS 585264
134
108
2.2
28.2
109
0.17


ISIS 585265
404
229
2
24.5
98
0.19


ISIS 585268
105
140
2.1
23.7
75
0.13


ISIS 585269
354
202
2.1
25.8
94
0.15









Hematology Assays

Blood obtained from all mice groups were analyzed for hematocrit (HCT), and hemoglobin content measurements, as well as measurements of the various blood cells, such as WBC, RBC, and platelets. The results are presented in Tables 16. ISIS oligonucleotides that caused changes in the levels of any of the blood cell counts outside the expected range for antisense oligonucleotides were excluded in further studies.







TABLE 16







Complete blood count in CD1 mice













HCT
Hemoglobin
Platelets
RBC
WBC



(%)
(g/dL)
(103/μL)
(106/μL)
(103/μL)
















PBS
45
13.9
844
8.4
6.1


ISIS 549372
42
13
425
8.4
2.9


ISIS 585233
34
10.2
877
6.5
14.8


ISIS 585259
36
10.9
1055
7
9.8


ISIS 585262
44
13.3
497
8.5
7.5


ISIS 585263
45
14
706
8.8
7.3


ISIS 585264
43
13.1
659
8.3
3.6


ISIS 585265
42
12.7
732
8.2
7.3


ISIS 585268
44
13.3
872
8.3
6.8


ISIS 585269
46
14.2
730
8.9
6









RNA Analysis

RNA was isolated from the liver and muscle. Mouse Target X mRNA expression was analyzed by RT-PCR. The data is presented in Table 17. The results indicate that antisense oligonucleotides targeting Target X inhibited the expression of Target X mRNA in treated mice compared to the control group.







TABLE 17







% inhibition of Target X mRNA levels


compared to the PBS control










Liver (%)
Muscle (%)













ISIS 549372
99
97


ISIS 585262
98
98


ISIS 585263
92
97


ISIS 585264
76
97


ISIS 585265
99
98


ISIS 585268
98
97


ISIS 585269
99
98

## Claims

1. A compound comprising:
a modified oligonucleotide consisting of 10 to 20 linked nucleosides, wherein the modified oligonucleotide has a motif selected from: BBB-(D)8-BBBAA; BBB-(D)7-BBBAA; BBB-(D)8-BBBAAA; BBB-(D)7-BBBAAA; BABA-(D)8-ABAB; BABA-(D)7-ABAB; ABAB-(D)8-ABAB; ABAB-(D)7-ABAB; AABB-(D)8-BBAA; AABB-(D)7-BBAA; BBB-(D)9-BBA; BBB-(D)8-BBA; BBB-(D)7-BBA; ABBB-(D)8-BBBA; ABBB-(D)7-BBBA; ABBB-(D)8-BBBAA; ABBB-(D)7-BBBAA; AABBB-(D)8-BBB; AABBB-(D)7-BBB; AABBB-(D)8-BBBA; AABBB-(D)7-BBBA; ABBAABB-(D)8-BB; ABBAABB-(D)7-BB; ABBABB-(D)8-BBB; and ABBABB-(D)7-BBB;
wherein each B is a bicyclic nucleoside, each A is a non-bicyclic modified nucleoside, and each D is a 2′-deoxynucleoside.

2. The compound of claim 1, wherein at least one B is a cEt nucleoside.

3. The compound of claim 2, wherein each B is a cEt nucleoside.

4. The compound of claim 1, wherein at least one B is a LNA nucleoside.

5. The compound of claim 4, wherein each B is a LNA nucleoside.

6. The compound of claim 1, wherein each B is either a cEt nucleoside or a LNA nucleoside.

7. The compound of claim 1, wherein each B comprises the same bicyclic sugar moiety.

8. The compound of claim 1, wherein at least one A is a 2′-MOE nucleoside.

9. The compound of claim 1, wherein at least one A is a 2′-OMe nucleoside.

10. The compound of claim 1, wherein each A comprises the same non-bicyclic modified sugar moiety.

11. The compound of claim 1 comprising at least one modified internucleoside linkage.

12. The compound of claim 11 comprising at least one phosphorothioate internucleoside linkage.

13. A method of modulating expression of a target nucleic acid in a cell comprising contacting the cell with a compound according to claim 1.

14. The method of claim 13, wherein the cell is in an animal.

15. The method of claim 14, wherein the animal is a human.

16. A pharmaceutical composition comprising the compound according to claim 1 and a pharmaceutically acceptable diluent.

17. A method of modulating expression of a target nucleic acid in an animal comprising administering to the animal a pharmaceutical composition according to claim 16.