Classifications

• • C—CHEMISTRY; METALLURGY
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
  • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
• • C—CHEMISTRY; METALLURGY
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  • C12N2310/00—Structure or type of the nucleic acid
  • C12N2310/10—Type of nucleic acid
  • C12N2310/11—Antisense
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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  • C12N2310/00—Structure or type of the nucleic acid
  • C12N2310/30—Chemical structure
  • C12N2310/31—Chemical structure of the backbone
  • C12N2310/315—Phosphorothioates
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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  • C12N2310/00—Structure or type of the nucleic acid
  • C12N2310/30—Chemical structure
  • C12N2310/33—Chemical structure of the base
  • C12N2310/334—Modified C
  • C12N2310/3341—5-Methylcytosine
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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  • C12N2310/00—Structure or type of the nucleic acid
  • C12N2310/30—Chemical structure
  • C12N2310/34—Spatial arrangement of the modifications
  • C12N2310/341—Gapmers, i.e. of the type ===---===

Definitions

• Such oligomeric agents, oligomeric compounds, methods, and pharmaceutical compositions are useful to ameliorate at least one symptom or hallmark of a neurodevelopmental disease or disorder.
• Such neurodevelopmental diseases or disorders include MECP2 duplication syndrome.
• Such symptoms or hallmarks include autism, intellectual disability, motor dysfunction, hypotonia, global developmental delays, gastrointestinal symptoms, anxiety, epilepsy, recurrent respiratory tract infections, epileptic encephalopathy, and early death.
• Methyl CpG binding protein 2 (MECP2) is located on chromosome Xq28 and plays a fundamental role in epigenetics, controlling chromatin states, and expression of thousands of genes (Chahrour et al., Science, 2008, 320:1224-1229; Nan et al., Nature, 1998, 393:386-389; Jones et al., Nat. Genet., 1998, 19:187-191).
• MECP2 duplication syndrome caused by overexpression of MECP2 is characterized by autism, intellectual disability, motor dysfunction, hypotonia, global developmental delays, gastrointestinal symptoms, anxiety, epilepsy, recurrent respiratory tract infections, epileptic encephalopathy, and early death, typically in males (Ramocki et al., Am J Med Genet A, 2010, 152A:1079-1088).
• MECP2 RNA or protein levels can be reduced in a cell or animal. Also provided are methods of treating MECP2 Duplication Syndrome. Detailed Description It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive. Herein, the use of the singular includes the plural unless specifically stated otherwise. As used herein, the use of “or” means “and/or” unless stated otherwise. Furthermore, the use of the term “including” as well as other forms, such as “includes” and “included” is not limiting. Also, terms such as “element” or “component” encompass both elements and components comprising one unit and elements and components that comprise more than one subunit, unless specifically stated otherwise.
• 2’-deoxynucleoside means a nucleoside comprising a 2’-H(H) deoxyfuranosyl sugar moiety.
• a 2’-deoxynucleoside is a 2’- ⁇ -D-deoxynucleoside and comprises a 2’- ⁇ -D-deoxyribosyl sugar moiety, which has the ⁇ -D ribosyl configuration as found in naturally occurring deoxyribonucleic acids (DNA).
• a 2’-deoxynucleoside may comprise a modified nucleobase or may comprise an RNA nucleobase (uracil).
• “2’-MOE” means a OCH 2 CH 2 OCH 3 group in place of the 2’-OH group of a furanosyl sugar moiety.
• a “2’-MOE sugar moiety” or a “2’-O-methoxyethyl sugar moiety” or “2’-MOE ribosyl sugar moiety” means a sugar moiety with a OCH 2 CH 2 OCH 3 group in place of the 2’-OH group of a furanosyl sugar moiety.
• a 2’-MOE sugar moiety is in the ⁇ -D-ribosyl configuration.
• MOE means O-methoxyethyl.
• 2’-MOE nucleoside means a nucleoside comprising a 2’-MOE sugar moiety.
• 2’-OMe means a 2’-OCH 3 group in place of the 2’-OH group of a furanosyl sugar moiety.
• a “2’-O-methyl sugar moiety” or “2’-OMe sugar moiety” means a sugar moiety with a 2’-OCH 3 group in place of the 2’- OH group of a furanosyl sugar moiety.
• a 2’-OMe sugar moiety is in the ⁇ -D-ribosyl configuration.
• “2’-OMe nucleoside” means a nucleoside comprising a 2’-OMe sugar moiety.
• “2’-F” means a 2’-fluoro group in place of the 2’-OH group of a furanosyl sugar moiety.
• a “2’- F sugar moiety” means a sugar moiety with a 2’-F group in place of the 2’-OH group of a furanosyl sugar moiety.
• a 2’-F sugar moiety is in the ⁇ -D ribosyl stereochemical configuration.
• 2’-F nucleoside means a nucleoside comprising a 2’-F sugar moiety.
• “2’-NMA sugar moiety” means the sugar moiety of a 2’-NMA nucleoside.
• “2’-substituted nucleoside” means a nucleoside comprising a 2’-substituted furanosyl sugar moiety.
• “2’-substituted” in reference to a sugar moiety means a sugar moiety comprising at least one 2'- substituent group other than H or OH.
• 3’ target site refers to the 3’-most nucleotide of a target nucleic acid which is complementary to an antisense oligonucleotide, when the antisense oligonucleotide is hybridized to the target nucleic acid.
• 5’ target site refers to the 5’-most nucleotide of a target nucleic acid which is complementary to an antisense oligonucleotide, when the antisense oligonucleotide is hybridized to the target nucleic acid.
• 5-methylcytosine means a cytosine modified with a methyl group attached to the 5 position.
• a 5-methylcytosine is a modified nucleobase.
• abasic sugar moiety means a sugar moiety of a nucleoside that is not attached to a nucleobase. Such abasic sugar moieties are sometimes referred to in the art as “abasic nucleosides.”
• “ameliorate” in reference to a treatment means improvement in at least one symptom or hallmark relative to the same symptom or hallmark in the absence of the treatment. In certain embodiments, amelioration is the reduction in the severity or frequency of a symptom or hallmark or the delayed onset or slowing of progression in the severity or frequency of a symptom or hallmark.
• the symptom or hallmark is one or more of autism, intellectual disability, motor dysfunction, hypotonia, global developmental delays, gastrointestinal symptoms, anxiety, epilepsy, recurrent respiratory tract infections, epileptic encephalopathy, and early death.
• the progression or severity of indicators may be determined by subjective or objective measures, which are known to those skilled in the art.
• “bicyclic sugar” or “bicyclic sugar moiety” means a modified sugar moiety comprising two rings, wherein the second ring is formed via a bridge connecting two of the atoms in the first ring thereby forming a bicyclic structure.
• the first ring of the bicyclic sugar moiety is a furanosyl sugar moiety.
• the furanosyl sugar moiety is a ribosyl sugar moiety.
• the bicyclic sugar moiety does not comprise a furanosyl moiety.
• Examples of bicyclic sugar moieties include LNA (locked nucleic acid) sugar moiety and cEt sugar moiety as defined herein.
• LNA locked nucleic acid
• cEt sugar moiety as defined herein.
• bicyclic nucleoside” or “BNA” means a nucleoside comprising a bicyclic sugar moiety.
• “blunt” or “blunt ended” in reference to an oligomeric duplex formed by two oligonucleotides mean that there are no terminal unpaired nucleotides (i.e., no overhanging nucleotides).
• cell-targeting moiety means a conjugate moiety or portion of a conjugate moiety that is capable of binding to a particular cell type or particular cell types.
• CSF Cerebrospinal fluid
• Artificial cerebrospinal fluid” or “aCSF” means a prepared or manufactured fluid that has certain properties (e.g., osmolarity, pH, and/or electrolytes) similar to cerebrospinal fluid and is biocompatible with CSF.
• chirally controlled in reference to an internucleoside linkage means chirality at that linkage is enriched for a particular stereochemical configuration.
• chirally enriched in reference to a population means a plurality of molecules of identical molecular formula, wherein the number or percentage of molecules within the population that contain a particular stereochemical configuration at a particular chiral center is greater than the number or percentage of molecules expected to contain the same particular stereochemical configuration at the same particular chiral center within the population if the particular chiral center were stereorandom as defined herein.
• Chirally enriched populations of molecules having multiple chiral centers within each molecule may contain one or more stereorandom chiral centers.
• the molecules are modified oligonucleotides. In certain embodiments, the molecules are oligomeric compounds comprising modified oligonucleotides. In certain embodiments, the chiral center is at the phosphorous atom of a phosphorothioate internucleoside linkage. In certain embodiments, the chiral center is at the phosphorous atom of a mesyl phosphoramidate internucleoside linkage.
• “cleavable moiety” means a bond or group of atoms that is cleaved under physiological conditions, for example, inside a cell, an animal, or a human.
• oligonucleotide in reference to an oligonucleotide means that at least 70% of the nucleobases of the oligonucleotide and the nucleobases of another nucleic acid or one or more regions thereof are capable of hydrogen bonding with one another when the nucleobase sequence of the oligonucleotide and the other nucleic acid are aligned in opposing directions.
• “Complementary region” in reference to a region of an oligonucleotide means that at least 70% of the nucleobases of that region and the nucleobases of another nucleic acid or one or more regions thereof are capable of hydrogen bonding with one another when the nucleobase sequence of the oligonucleotide and the other nucleic acid are aligned in opposing directions.
• Complementary nucleobases mean nucleobases that are capable of forming hydrogen bonds with one another.
• Complementary nucleobase pairs include adenine (A) and thymine (T), adenine (A) and uracil (U), cytosine (C) and guanine (G), 5-methylcytosine (mC) and guanine (G).
• Certain modified nucleobases that pair with unmodified nucleobases or with other modified nucleobases are known in the art and are not considered complementary nucleobases as defined herein unless indicated otherwise.
• inosine can pair, but is not considered complementary, with adenosine, cytosine, or uracil.
• Complementary oligonucleotides and/or nucleic acids need not have nucleobase complementarity at each nucleoside.
• oligonucleotide is complementary to another oligonucleotide or nucleic acid at each nucleobase of the shorter of the two oligonucleotides, or at each nucleoside if the oligonucleotides are the same length.
• complementary region in reference to an oligonucleotide is the range of nucleobases of the oligonucleotide that is complementary with a second oligonucleotide or target nucleic acid.
• conjugate group means a group of atoms that is directly attached to an oligonucleotide.
• Conjugate groups include a conjugate moiety and a conjugate linker that attaches the conjugate moiety to the oligonucleotide.
• conjugate linker means a single bond or a group of atoms comprising at least one bond that connects a conjugate moiety to an oligonucleotide.
• conjugate moiety means a group of atoms that modifies one or more properties of a molecule compared to the identical molecule lacking the conjugate moiety, wherein such properties include, but are not limited to, pharmacodynamics, pharmacokinetics, stability, binding, absorption, tissue distribution, cellular distribution, cellular uptake, charge, and clearance.
• constraining ethyl or “cEt” or “cEt sugar moiety” means a ⁇ -D ribosyl bicyclic sugar moiety wherein the second ring of the bicyclic sugar is formed via a bridge connecting the 4’-carbon and the 2’-carbon of the ⁇ - D ribosyl sugar moiety, wherein the bridge has the formula 4'-CH(CH 3 )-O-2', and wherein the methyl group of the bridge is in the S configuration.
• cEt nucleoside means a nucleoside comprising a cEt sugar moiety.
• oligonucleotide refers to nucleosides, nucleobases, sugar moieties, or internucleoside linkages that are immediately adjacent to each other.
• contiguous nucleobases means nucleobases that are immediately adjacent to each other in a sequence.
• deoxy region means a region of 5-12 contiguous nucleotides, wherein at least 70% of the nucleosides comprise a ⁇ -D-2’-deoxyribosyl sugar moiety.
• a deoxy region supports RNase H activity.
• a deoxy region is the gap of a gapmer.
• diluent means an ingredient in a composition that lacks pharmacological activity but is pharmaceutically necessary or desirable.
• the diluent in an injected composition can be a liquid, e.g., aCSF, PBS, or saline solution.
• double-stranded in reference to a region or an oligonucleotide, means a duplex formed by complementary strands of nucleic acids (including, but not limited to oligonucleotides) hybridized to one another. In certain embodiments, the two strands of a double-stranded region are separate molecules.
• the two strands are regions of the same molecule that has folded onto itself (e.g., a hairpin structure).
• duplex or “duplex region” means the structure formed by two oligonucleotides or portions thereof that are hybridized to one another.
• gapmer means a modified oligonucleotide comprising an internal region positioned between external regions having one or more nucleosides, wherein the nucleosides comprising the internal region are chemically distinct from the nucleoside or nucleosides comprising the external regions, and wherein the modified oligonucleotide supports RNAse H cleavage.
• the internal region may be referred to as the “gap” and the external regions may be referred to as the “wings.”
• the internal region is a deoxy region.
• the positions of the internal region or gap refer to the order of the nucleosides of the internal region and are counted starting from the 5’-end of the internal region. Unless otherwise indicated, “gapmer” refers to a sugar motif.
• the internal region is a “deoxy region”. In certain embodiments, each nucleoside of the gap is a 2’- ⁇ -D-deoxynucleoside.
• the gap comprises one 2’-substituted nucleoside at position 1, 2, 3, 4, or 5 of the gap, and the remainder of the nucleosides of the gap are 2’- ⁇ -D-deoxynucleosides.
• MOE gapmer indicates a gapmer having a gap comprising 2’- ⁇ -D-deoxynucleosides and wings comprising 2’-MOE nucleosides.
• mixed wing gapmer indicates a gapmer having wings comprising modified nucleosides comprising at least two different sugar modifications.
• a gapmer may comprise one or more modified internucleoside linkages and/or modified nucleobases and such modifications do not necessarily follow the gapmer pattern of the sugar modifications.
• hotspot region is a range of nucleobases on a target nucleic acid that is amenable to reduction of the amount or activity of the target nucleic acid by the action of an oligomeric agent, oligomeric compound, modified oligonucleotide, antisense compound, or antisense agent.
• hybridization means the annealing of oligonucleotides and/or nucleic acids.
• complementary nucleic acid molecules include, but are not limited to, an antisense compound and a nucleic acid target.
• complementary nucleic acid molecules include, but are not limited to, an oligonucleotide and a nucleic acid target.
• internucleoside linkage is the covalent linkage between adjacent nucleosides in an oligonucleotide.
• modified internucleoside linkage means any internucleoside linkage other than a phosphodiester internucleoside linkage.
• Phosphorothioate internucleoside linkage or “PS internucleoside linkage” is a modified internucleoside linkage in which one of the non-bridging oxygen atoms of a phosphodiester internucleoside linkage is replaced with a sulfur atom.
• inverted nucleoside means a nucleotide having a 3’ to 3’ and/or 5’ to 5’ internucleoside linkage, as shown herein.
• inverted sugar moiety means the sugar moiety of an inverted nucleoside or an abasic sugar moiety having a 3’ to 3’ and/or 5’ to 5’ internucleoside linkage.
• linked nucleosides are nucleosides that are connected in a contiguous sequence (i.e., no additional nucleosides are presented between those that are linked).
• linker-nucleoside means a nucleoside that links, either directly or indirectly, an oligonucleotide to a conjugate moiety. Linker-nucleosides are located within the conjugate linker of an oligomeric compound.
• Linker-nucleosides are not considered part of the oligonucleotide portion of an oligomeric compound even if they are contiguous with the oligonucleotide.
• mis or “non-complementary” means a nucleobase of a first nucleic acid sequence that is not complementary with the corresponding nucleobase of a second nucleic acid sequence or target nucleic acid when the first and second nucleic acid sequences are aligned in opposing directions.
• motif means the pattern of unmodified and/or modified sugar moieties, nucleobases, and/or internucleoside linkages, in an oligonucleotide.
• modified nucleoside means a nucleoside comprising a modified nucleobase and/or a modified sugar moiety.
• non-bicyclic modified sugar moiety means a modified sugar moiety that comprises a modification, such as a substituent, that does not form a bridge between two atoms of the sugar to form a second ring.
• nucleobase means an unmodified nucleobase or a modified nucleobase.
• a nucleobase is a heterocyclic moiety.
• an “unmodified nucleobase” is adenine (A), thymine (T), cytosine (C), uracil (U), or guanine (G).
• a “modified nucleobase” is a group of atoms other than unmodified A, T, C, U, or G capable of pairing with at least one other nucleobase.
• a “5-methylcytosine” is a modified nucleobase.
• a universal base is a modified nucleobase that can pair with any one of the five unmodified nucleobases.
• nucleobase sequence means the order of contiguous nucleobases in a nucleic acid or oligonucleotide independent of any sugar or internucleoside linkage modification.
• nucleobase sequence of a reference SEQ ID NO, refers only to the nucleobase sequence provided in such SEQ ID NO and therefore, unless otherwise indicated, includes compounds wherein each sugar moiety and each internucleoside linkage, independently, is modified or unmodified, irrespective of the presence or absence of modifications indicated in the referenced SEQ ID NO.
• nucleoside means a compound or fragment of a compound comprising a nucleobase and a sugar moiety.
• oligomeric agent means an oligomeric compound and optionally one or more additional features, such as a second oligomeric compound.
• An oligomeric agent may be a single-stranded oligomeric compound or may be an oligomeric duplex formed by two complementary oligomeric compounds.
• oligomeric compound means an oligonucleotide and optionally one or more additional features, such as a conjugate group or terminal group.
• An oligomeric compound may be paired with a second oligomeric compound that is complementary to the first oligomeric compound or may be unpaired.
• a “singled-stranded oligomeric compound” is an unpaired oligomeric compound.
• the term “oligomeric duplex” means a duplex formed by two oligomeric compounds having complementary nucleobase sequences. Each oligomeric compound of an oligomeric duplex may be referred to as a “duplexed oligomeric compound.”
• “oligonucleotide” means a strand of linked nucleosides connected via internucleoside linkages, wherein each nucleoside and internucleoside linkage may be modified or unmodified. Unless otherwise indicated, oligonucleotides consist of 8-50 linked nucleosides.
• modified oligonucleotide means an oligonucleotide, wherein at least one nucleoside or internucleoside linkage is modified.
• unmodified oligonucleotide means an oligonucleotide that does not comprise any nucleoside modifications or internucleoside modifications.
• An oligonucleotide may be paired with a second oligonucleotide that is complementary to the oligonucleotide or it may be unpaired.
• a “single-stranded oligonucleotide” is an unpaired oligonucleotide.
• a “double- stranded oligonucleotide” is an oligonucleotide that is paired with a second oligonucleotide.
• pharmaceutically acceptable carrier or diluent means any substance suitable for use in administering to an animal. Certain such carriers enable pharmaceutical compositions to be formulated as, for example, tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and lozenges for the oral ingestion by a subject.
• a pharmaceutically acceptable carrier or diluent is sterile water, sterile saline, sterile buffer solution or sterile artificial cerebrospinal fluid.
• pharmaceutically acceptable salt(s) means physiologically and pharmaceutically acceptable salts of compounds. Pharmaceutically acceptable salts retain the desired biological activity of the parent compound and do not impart undesired toxicological effects thereto.
• pharmaceutical composition means a mixture of substances suitable for administering to a subject.
• a pharmaceutical composition may comprise an oligomeric compound and a sterile aqueous solution.
• a pharmaceutical composition shows activity in free uptake assay in certain cell lines.
• “population” means a plurality of molecules of identical molecular formula.
• prodrug means an inactive or less active form of a compound which, when administered to a subject, is metabolized to form the active, or more active, compound.
• a prodrug comprises a cell-targeting moiety and at least one active compound.
• RNA means an RNA transcript and includes pre-mRNA and mature mRNA unless otherwise specified.
• RNAi agent means an antisense agent that acts, at least in part, through RISC or Ago2 to modulate a target nucleic acid and/or protein encoded by a target nucleic acid.
• RNAi agents include, but are not limited to double-stranded siRNA, single-stranded RNAi (ssRNAi), and microRNA, including microRNA mimics. RNAi agents may comprise conjugate groups and/or terminal groups. In certain embodiments, an RNAi agent modulates the amount and/or activity, of a target nucleic acid.
• RNAi agent excludes antisense agents that act through RNase H.
• RNase H agent means an antisense agent that acts through RNase H to modulate a target nucleic acid and/or protein encoded by a target nucleic acid. In certain embodiments, RNase H agents are single- stranded. In certain embodiments, RNase H agents are double-stranded.
• RNase H compounds may comprise conjugate groups and/or terminal groups.
• an RNase H agent modulates the amount and/or activity of a target nucleic acid.
• RNase H agent excludes antisense agents that act principally through RISC/Ago2.
• antisense RNase H oligonucleotide means an oligonucleotide comprising a region that is complementary to a target sequence, and which includes at least one chemical modification suitable for RNase H- mediated nucleic acid reduction.
• RNAi oligonucleotide means an oligonucleotide comprising a region that is complementary to a target sequence, and which includes at least one chemical modification suitable for RNAi-mediated nucleic acid reduction.
• self-complementary in reference to an oligonucleotide means an oligonucleotide that at least partially hybridizes to itself.
• single-stranded means a nucleic acid (including but not limited to an oligonucleotide) that is unpaired and is not part of a duplex.
• Single-stranded compounds are capable of hybridizing with complementary nucleic acids to form duplexes, at which point they are no longer single-stranded.
• “stabilized phosphate group” refers to a 5’-chemical moiety that results in stabilization of a 5’- phosphate moiety of the 5’-terminal nucleoside of an oligonucleotide, relative to the stability of an unmodified 5’- phosphate of an unmodified nucleoside under biologic conditions. Such stabilization of a 5’-phosphate group includes but is not limited to resistance to removal by phosphatases.
• Stabilized phosphate groups include, but are not limited to, 5’-vinyl phosphonates and 5’-cyclopropyl phosphonate.
• standard cell assay means the in vitro assays described in Examples 1 and 2 and reasonable variations thereof.
• stereoorandom or “stereorandom chiral center” in the context of a population of molecules of identical molecular formula means a chiral center that is not controlled during synthesis, or enriched following synthesis, for a particular absolute stereochemical configuration. The stereochemical configuration of a chiral center is random when it is the result of a synthetic method that is not designed to control the stereochemical configuration.
• the number of molecules having the (S) configuration of the stereorandom chiral center may be but is not necessarily the same as the number of molecules having the (R) configuration of the stereorandom chiral center (“racemic”).
• the stereorandom chiral center is not racemic because one absolute configuration predominates following synthesis, e.g., due to the action of non-chiral reagents near the enriched stereochemistry of an adjacent sugar moiety.
• a stereorandom chiral center is at the phosphorous atom of a stereorandom phosphorothioate or mesyl phosphoroamidate internucleoside linkage.
• “subject” means a human or non-human animal.
• the terms “subject”, “animal”, and “individual” are used interchangeably.
• the subject is human.
• “sugar moiety” means an unmodified sugar moiety or a modified sugar moiety.
• “unmodified sugar moiety” means a 2’-OH(H) ribosyl moiety, as found in RNA (an “unmodified RNA sugar moiety”), or a 2’-H(H) deoxyribosyl sugar moiety, as found in DNA (an “unmodified DNA sugar moiety”).
• Unmodified sugar moieties have one hydrogen at each of the 1’, 3’, and 4’ positions, an oxygen at the 3’ position, and two hydrogens at the 5’ position.
• modified sugar moiety or “modified sugar” means a modified furanosyl sugar moiety or a sugar surrogate.
• sugar surrogate means a modified sugar moiety having other than a furanosyl moiety that can link a nucleobase to another group, such as an internucleoside linkage, conjugate group, or terminal group in an oligonucleotide, but which is not a furanosyl sugar moiety or a bicyclic sugar moiety.
• Modified nucleosides comprising sugar surrogates can be incorporated into one or more positions within an oligonucleotide and such oligonucleotides are capable of hybridizing to complementary oligomeric compounds or target nucleic acids.
• sugar surrogates include GNA (glycol nucleic acid), FHNA (fluoro hexitol nucleic acid), morpholino, and other structures described herein and known in the art.
• “symptom or hallmark” means any physical feature or test result that indicates the existence or extent of a disease or disorder. In certain embodiments, a symptom is apparent to a subject or to a medical professional examining or testing said subject.
• a hallmark is apparent upon invasive diagnostic testing, including, but not limited to, post-mortem tests. In certain embodiments, a hallmark is apparent on a brain MRI scan. In certain embodiments, symptoms and hallmarks include autism, intellectual disability, motor dysfunction, hypotonia, global developmental delays, gastrointestinal symptoms, anxiety, epilepsy, recurrent respiratory tract infections, epileptic encephalopathy, and early death.
• target nucleic acid and “target RNA” mean a nucleic acid that an oligomeric compound is designed to affect. Target RNA means an RNA transcript and includes pre-mRNA and mature mRNA unless otherwise specified.
• target region means a portion of a target nucleic acid to which an oligomeric compound is designed to hybridize.
• terminal group means a chemical group or group of atoms that is covalently linked to a terminus of an oligonucleotide.
• treating means improving a subject’s disease or condition by administering an oligomeric agent, an oligomeric compound, an oligomeric duplex, or an antisense agent described herein. In certain embodiments, treating a subject improves a symptom relative to the same symptom in the absence of the treatment.
• treatment reduces the severity or frequency of a symptom, delays the onset of a symptom, slows the progression of a symptom, or slows the severity or frequency of a symptom.
• therapeutically effective amount means an amount of a pharmaceutical agent or composition that provides a therapeutic benefit to an animal.
• a therapeutically effective amount improves a symptom of a disease.
• antisense activity means any detectable and/or measurable change attributable to the hybridization of an antisense compound to its target nucleic acid.
• antisense activity is a decrease in the amount or expression of a target nucleic acid or protein encoded by such target nucleic acid compared to target nucleic acid levels or target protein levels in the absence of the antisense compound.
• antisense activity is the modulation of splicing of a target pre-mRNA.
• antisense agent means an antisense compound and optionally one or more additional features, such as a sense compound.
• antisense compound means an antisense oligonucleotide and optionally one or more additional features, such as a conjugate group.
• sense compound means a sense oligonucleotide and optionally one or more additional features, such as a conjugate group.
• antisense oligonucleotide means an oligonucleotide, including the oligonucleotide portion of an antisense compound, that is capable of hybridizing to a target nucleic acid and is capable of at least one antisense activity.
• Antisense oligonucleotides include but are not limited to antisense RNAi oligonucleotides and antisense RNase H oligonucleotides.
• sense oligonucleotide means an oligonucleotide, including the oligonucleotide portion of a sense compound, that is capable of hybridizing to an antisense oligonucleotide.
• CERTAIN EMBODIMENTS The present disclosure provides the following non-limiting numbered embodiments: Embodiment 1.
• An oligomeric compound comprising a modified oligonucleotide consisting of 8 to 80 linked nucleosides wherein the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion of a MECP2 nucleic acid, and wherein the modified oligonucleotide has at least one modification selected from a modified sugar moiety and a modified internucleoside linkage.
• Embodiment 2 The oligomeric compound of embodiment 1, wherein the MECP2 nucleic acid has the nucleobase sequence of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 2340.
• nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion within nucleobases 10858-10885, 11534-11588, 11597-11620, 12936-12962, 13599-13641, 13669-13711, 14716-14746, 15883-15905, 16362-16396, 18941-18975, 19046-19091, 20216-20271, 21505-21532, 21945-21976, 23689-23713, 24791-24833, 24901-24930, 24970-24995, 32385-32414, 32447-32508, 32588-32671, 35116-35158, 43248-43273, 43863-43923, or 64179-64202 of SEQ ID NO: 1.
• Embodiment 4 The oligomeric compound of any of embodiments 1-3, wherein the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion within nucleobases 32588-32671 of SEQ ID NO: 1.
• Embodiment 5. The oligomeric compound of any of embodiments 1-3, wherein the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion within nucleobases 32611-32630 of SEQ ID NO: 1.
• An oligomeric compound comprising a modified oligonucleotide consisting of 8 to 80 linked nucleosides and having a nucleobase sequence comprising at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or at least 20 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 18-2339, and wherein the modified oligonucleotide has at least one modification selected from a modified sugar and a modified internucleoside linkage.
• Embodiment 8 Embodiment 8.
• Embodiment 9. The oligomeric compound of embodiment 7 or embodiment 8, wherein the modified oligonucleotide has a nucleobase sequence consisting of the nucleobase sequence of any of SEQ ID NOs: 18-2339.
• Embodiment 11 is a nucleobase sequence comprising at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases of any of the nucleobase sequences of ⁇ SEQ ID NOs: 18-2335.
• the oligomeric compound of any of embodiments 7-10, wherein the modified oligonucleotide has a nucleobase sequence comprising the nucleobase sequence of SEQ ID NO: 1197.
• Embodiment 14 The oligomeric compound of any of embodiments 1-13, wherein the modified oligonucleotide is at least 80%, at least 85%, at least 90%, at least 95%, or 100% complementary to an equal length portion of a MECP2 nucleic acid, wherein the MECP2 nucleic acid has the nucleobase sequence of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 2340.
• the oligomeric compound of any of embodiments 1-14, wherein the modified oligonucleotide consists of 10 to 25, 10 to 30, 10 to 50, 12 to 20, 12 to 25, 12 to 30, 12 to 50, 13 to 20, 13 to 25, 13 to 30, 13 to 50, 14 to 20, 14 to 25, 14 to 30, 14 to 50, 15 to 20, 15 to 25, 15 to 30, 15 to 50, 16 to 18,16 to 20, 16 to 25, 16 to 30, 16 to 50, 17 to 20, 17 to 25, 17 to 30, 17 to 50, 18 to 20, 18 to 22, 18 to 25, 18 to 30, 18 to 50, 19 to 20, 19 to 25, 19 to 30, 19 to 50, 20 to 25, 20 to 30, 20 to 50, 21 to 25, 21 to 30, 21 to 50, 22 to 25, 22 to 30, 22 to 50, 23 to 25, 23 to 30, or 23 to 50 linked nucleosides.
• Embodiment 16 The oligomeric compound of any of embodiments 1-15, wherein the modified oligonucleotide consists of 18 linked nucleosides.
• Embodiment 17. The oligomeric compound of any of embodiments 1-15, wherein the modified oligonucleotide consists of 20 linked nucleosides.
• Embodiment 18. The oligomeric compound of any of embodiments 1-17, wherein the modified oligonucleotide comprises at least one modified nucleoside.
• Embodiment 19 The oligomeric compound of embodiment 18, wherein the at least one modified nucleoside comprises a modified sugar moiety.
• Embodiment 20. The oligomeric compound of embodiment 19, wherein the modified sugar moiety comprises a bicyclic sugar moiety.
• Embodiment 21 The oligomeric compound of embodiment 20, wherein the bicyclic sugar moiety comprises a 2’-4’ bridge selected from –O-CH 2 - and –O-CH(CH 3 )-.
• Embodiment 22 The oligomeric compound of embodiment 19, wherein the modified sugar moiety comprises a non-bicyclic modified sugar moiety.
• Embodiment 23 The oligomeric compound of embodiment 22, wherein the non-bicyclic modified sugar moiety is a 2’-MOE sugar moiety, a 2’-F sugar moiety, or a 2’-OMe sugar moiety.
• Embodiment 24 Embodiment 24.
• Embodiment 29. The oligomeric compound of embodiment 26 or embodiment 27, wherein at least one internucleoside linkage of the modified oligonucleotide is a phosphodiester internucleoside linkage.
• Embodiment 30. The oligomeric compound of any of embodiments 26 or 28-29, wherein each internucleoside linkage of the modified oligonucleotide is independently selected from a phosphodiester internucleoside linkage and a phosphorothioate internucleoside linkage.
• the oligomeric compound of any of embodiments 26 or 28-30, wherein at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, or at least 19 internucleoside linkages of the modified oligonucleotide are phosphorothioate internucleoside linkages.
• Embodiment 32. The oligomeric compound of any of embodiments 26-28 or 30-31, wherein each internucleoside linkage is a phosphorothioate internucleoside linkage.
• Embodiment 33 Embodiment 33.
• Embodiment 34 The oligomeric compound of any of embodiments 1-33, wherein the modified oligonucleotide comprises at least one modified nucleobase.
• Embodiment 35 The internucleoside linkage motif of the modified oligonucleotide is selected from 5’-soooosssssssssooss-3’ and 5’- sooosssssssooss -3’; wherein each ‘o’ represents a phosphodiester intern
• Embodiment 36. The oligomeric compound of embodiment 35, wherein each cytosine is a 5-methylcytosine.
• Embodiment 37. The oligomeric compound of any of embodiments 1-36, wherein the oligomeric compound comprises a modified oligonucleotide consisting of 12-22, 12-20, 14-18, 14-20, 15-17, 15-25, 16-20, 16-18, 18-20, 18- 22, 18-25, 18-20, 20-25, or 21-23 linked nucleosides, or a pharmaceutically acceptable salt thereof.
• Embodiment 39. The oligomeric compound of embodiment 38, wherein each nucleoside of the deoxy region is a 2’- ⁇ -D-deoxynucleoside.
• Embodiment 40. The oligomeric compound of embodiment 38 or embodiment 39, wherein the deoxy region consists of 6, 7, 8, 9, 10, or 6-10 linked nucleosides.
• Embodiment 41 The oligomeric compound of any of embodiments 38-40, wherein each nucleoside immediately adjacent to the deoxy region comprises a modified sugar moiety.
• oligomeric compound of any of embodiments 38-41 wherein the deoxy region is flanked on the 5’-side by a 5’-external region consisting of 1-6 linked 5’-external region nucleosides and on the 3’-side by a 3’- external region consisting of 1-6 linked 3’-external region nucleosides; wherein the 3’-most nucleoside of the 5’ external region nucleosides comprises a modified sugar moiety; and the 5’-most nucleoside of the 3’ external region nucleosides comprises a modified sugar moiety.
• Embodiment 43 Embodiment 43.
• each of the 3’ external region nucleosides comprises a modified sugar moiety.
• Embodiment 44. The oligomeric compound of embodiment 43, wherein the modified oligonucleotide has: a 5’ external region consisting of 5 linked nucleosides; a deoxy region consisting of 10 linked nucleosides; and a 3’ external region consisting of 5 linked nucleosides; wherein each of the 5’ external region nucleosides and each of the 3’ external region nucleosides is a 2’-MOE nucleoside.
• the oligomeric compound of embodiment 42 or embodiment 43, wherein the modified oligonucleotide has: a 5’ external region consisting of 5 linked 5’-external region nucleosides; a deoxy region consisting of 8 linked nucleosides; and a 3’ external region consisting of 5 linked 3’-external region nucleosides; wherein each of the 5’ external region nucleosides and each of the 3’ external region nucleosides is a 2’-MOE nucleoside.
• Embodiment 46 Embodiment 46.
• a sugar motif comprising: a 5’ external -region consisting of 1-6 linked nucleosides; a deoxy region consisting of 6-10 linked nucleosides; and a 3’ external region consisting of 1-6 linked nucleosides; wherein each of the 5’ external region nucleosides and each of the 3’
• a sugar motif 5’ to 3’
• T a thymine nucleobase
• e a 2’-MOE sugar moiety
• d a 2’- ⁇ -D-deoxyribosyl sugar moiety
• s a phosphorothioate internucleoside linkage
• o a phosphodiester internucle
• Embodiment 50. The oligomeric compound of any of embodiments 1-48, wherein the oligomeric compound comprises a conjugate group.
• Embodiment 51. The oligomeric compound of embodiment 50, wherein the conjugate group comprises a conjugate linker and a conjugate moiety.
• Embodiment 52. The oligomeric compound of embodiment 51, wherein the conjugate linker consists of a single bond.
• Embodiment 57 The oligomeric compound of any of embodiments 50-55, wherein the conjugate group is attached to the modified oligonucleotide at the 3’-end of the modified oligonucleotide.
• Embodiment 58 The oligomeric compound of any of embodiments 1 to 57, wherein the oligomeric compound comprises a terminal group.
• Embodiment 59 The oligomeric compound of embodiment 58, wherein the terminal group is an abasic sugar moiety.
• Embodiment 60 The oligomeric compound of any of embodiments 1-59, wherein the oligomeric compound is a singled-stranded oligomeric compound.
• Embodiment 61 A modified oligonucleotide according to the following chemical structure:
• Embodiment 62 The modified oligonucleotide of embodiment 61, which is a pharmaceutically acceptable salt comprising one or more cations selected from sodium, potassium, calcium and magnesium.
• Embodiment 63 The modified oligonucleotide of embodiment 61, which is the sodium salt or the potassium salt.
• Embodiment 64 A modified oligonucleotide according to the following chemical structure:
• Embodiment 65 A chirally enriched population of oligomeric compounds of any of embodiments 1-60 or a chirally enriched population of modified oligonucleotides of any of embodiments 61-64, wherein the population is enriched for modified oligonucleotides comprising at least one particular phosphorothioate internucleoside linkage having a particular stereochemical configuration.
• Embodiment 66 The chirally enriched population of embodiment 65, wherein the population is enriched for modified oligonucleotides comprising at least one particular phosphorothioate internucleoside linkage having the (Sp) or (Rp) configuration.
• Embodiment 67 The chirally enriched population of embodiment 65, wherein the population is enriched for modified oligonucleotides having a particular, independently selected stereochemical configuration at each phosphorothioate internucleoside linkage.
• Embodiment 68 The chirally enriched population of embodiment 65, wherein the population is enriched for modified oligonucleotides having the (Rp) configuration at one particular phosphorothioate internucleoside linkage and the (Sp) configuration at each of the remaining phosphorothioate internucleoside linkages.
• Embodiment 69 Embodiment 69.
• Embodiment 70 A population of oligomeric compounds of any of embodiments 1-60 or a population of modified oligonucleotides of any of embodiments 61-64, wherein all of the phosphorothioate internucleoside linkages of the modified oligonucleotide are stereorandom.
• Embodiment 71 A population of oligomeric compounds of any of embodiments 1-60 or a population of modified oligonucleotides of any of embodiments 61-64, wherein all of the phosphorothioate internucleoside linkages of the modified oligonucleotide are stereorandom.
• An oligomeric duplex comprising a first oligomeric compound comprising a first modified oligonucleotide and a second oligomeric compound comprising a second modified oligonucleotide, wherein the first oligomeric compound is an oligomeric compound of any of embodiments 1-60.
• Embodiment 73 Embodiment 73.
• the oligomeric duplex of any of embodiments 71-74, wherein the first modified oligonucleotide comprises a glycol nucleic acid (GNA) sugar surrogate.
• GNA glycol nucleic acid
• Embodiment 77. The oligomeric duplex of any of embodiments 71-76, wherein at least one nucleoside of the second modified oligonucleotide comprises a modified sugar moiety.
• Embodiment 78. The oligomeric duplex of embodiment 77, wherein the modified sugar moiety of the second modified oligonucleotide comprises a bicyclic sugar moiety.
• the oligomeric duplex of embodiment 78 wherein the bicyclic sugar moiety of the second modified oligonucleotide comprises a 2’-4’ bridge selected from –O-CH 2 - and –O-CH(CH 3 )-.
• Embodiment 80 The oligomeric duplex of embodiment 77, wherein the modified sugar moiety of the second modified oligonucleotide comprises a non-bicyclic modified sugar moiety.
• Embodiment 81. The oligomeric duplex of embodiment 80, wherein the non-bicyclic modified sugar moiety of the second modified oligonucleotide is a 2’-MOE sugar moiety, a 2’-F sugar moiety, or a 2’-OMe sugar moiety.
• Embodiment 82 The oligomeric duplex of any of embodiments 71-81, wherein at least one nucleoside of the second modified oligonucleotide comprises a sugar surrogate.
• Embodiment 83 The oligomeric duplex of any of embodiments 71-82, wherein at least one internucleoside linkage of the second modified oligonucleotide is a modified internucleoside linkage.
• Embodiment 84 The oligomeric duplex of embodiment 83, wherein at least one modified internucleoside linkage of the second modified oligonucleotide is a phosphorothioate internucleoside linkage.
• Embodiment 85 The oligomeric duplex of any of embodiments 71-81, wherein at least one nucleoside of the second modified oligonucleotide comprises a sugar surrogate.
• Embodiment 83 The oligomeric duplex of any of embodiments 71-82,
• Embodiment 86. The oligomeric duplex of any of embodiments 71-85, wherein each internucleoside linkage of the second modified oligonucleotide is independently selected from a phosphodiester internucleoside linkage and a phosphorothioate internucleoside linkage.
• the oligomeric duplex of any of embodiments 71-86, wherein the second modified oligonucleotide comprises at least one modified nucleobase.
• Embodiment 89. The oligomeric duplex of any of embodiments 71-88, wherein the second modified oligonucleotide comprises a conjugate group.
• Embodiment 90. The oligomeric duplex of embodiment 89, wherein the conjugate group comprises a conjugate linker and a conjugate moiety.
• Embodiment 91. The oligomeric duplex of embodiment 89 or embodiment 90, wherein the conjugate group is attached to the second modified oligonucleotide at the 5’-end of the second modified oligonucleotide.
• Embodiment 92 The oligomeric duplex of embodiment 89 or embodiment 90, wherein the conjugate group is attached to the second modified oligonucleotide at the 3’-end of the second modified oligonucleotide.
• Embodiment 93 The oligomeric duplex of embodiment 89 or embodiment 90, wherein the conjugate group is attached via the 2’ position of a ribosyl sugar moiety at an internal position of the second modified oligonucleotide.
• Embodiment 94 The oligomeric duplex of any of embodiments 89-93, wherein the conjugate group comprises a lipid.
• Embodiment 95 The oligomeric duplex of any of embodiments 89-93, wherein the conjugate group comprises a lipid.
• Embodiment 96. The oligomeric duplex of embodiment 95, wherein the terminal group is an abasic sugar moiety.
• Embodiment 98 An antisense agent comprising an antisense compound, wherein the antisense compound is the oligomeric compound of any of embodiments 1-60 or the modified oligonucleotide of any of embodiments 61-64.
• Embodiment 99 An antisense agent, wherein the antisense agent is the oligomeric duplex of any of embodiments 71-97.
• Embodiment 100 The antisense agent of embodiment 98 or embodiment 99, wherein the antisense agent is: i. an RNase H agent capable of reducing the amount of MECP2 nucleic acid through the activation of RNase H; or ii.
• Embodiment 101 The antisense agent of any of embodiments 98-100, wherein the antisense agent comprises a conjugate group, wherein the conjugate group is a cell-targeting moiety.
• Embodiment 102 A pharmaceutical composition comprising an oligomeric compound of any of embodiments 1-60, a modified oligonucleotide of any of embodiments 61-64, a population of any of embodiments 65-70, an oligomeric duplex of any of embodiments 71-97, or an antisense agent of any of embodiments 98-101, and a pharmaceutically acceptable diluent.
• Embodiment 103 The pharmaceutical composition of embodiment 102, wherein the pharmaceutically acceptable diluent is phosphate-buffered saline or artificial cerebrospinal fluid.
• Embodiment 104 The pharmaceutical composition of embodiment 103, wherein the pharmaceutical composition consists essentially of the oligomeric compound, the modified oligonucleotide, the population, the oligomeric duplex, or the antisense agent and the phosphate-buffered saline or the artificial cerebrospinal fluid.
• Embodiment 105 Embodiment 105.
• a method comprising administering to a subject an oligomeric compound of any of embodiments 1-60, a modified oligonucleotide of any of embodiments 61-64, a population of any of embodiments 65- 70, an oligomeric duplex of any of embodiments 71-97, an antisense agent of any of embodiments 98-101, or a pharmaceutical composition of any of embodiments 102-104.
• Embodiment 106 The method of embodiment 105, wherein the subject has a disease or disorder associated with MECP2.
• Embodiment 108 is a neurodevelopmental disease or disorder.
• Embodiment 109 A method of treating a disease or disorder associated with MECP2 comprising administering to a subject having or at risk for developing a disease or disorder associated with MECP2 a therapeutically effective amount of an oligomeric compound of any of embodiments 1-60, a modified oligonucleotide of any of embodiments 61- 64, a population of any of embodiments 65-70, an oligomeric duplex of any of embodiments 71-97, an antisense agent of any of embodiments 98-101, or a pharmaceutical composition of any of embodiments 102-104; and thereby treating the disease or disorder associated with MECP2.
• Embodiment 110 The method of embodiment 109, wherein the disease or disorder associated with MECP2 is a neurodevelopmental disease or disorder.
• Embodiment 111. The method of embodiment 109 or embodiment 110, wherein the disease or disorder associated with MECP2 is MECP2 Duplication Syndrome.
• Embodiment 112. The method of any of embodiments 109-111, wherein at least one symptom or hallmark of the disease or disorder associated with MECP2 is ameliorated.
• Embodiment 113 The method of embodiment 112, wherein the symptom or hallmark is autism, intellectual disability, motor dysfunction, hypotonia, global developmental delays, gastrointestinal symptoms, anxiety, epilepsy, recurrent respiratory tract infections, epileptic encephalopathy, or early death.
• Embodiment 115 The method of any of embodiments 105-114, wherein administering the oligomeric compound, the modified oligonucleotide, the population, the oligomeric duplex, the antisense agent, or the pharmaceutical composition reduces seizures, reduces or delays cognitive impairment, reduces or delays intellectual disabilities, reduces or delays symptoms of autism, reduces anxiety, or reduces gastrointestinal symptoms in the subject; or improves motor function, motor development, muscle tone, cognitive development, speech, or social skill development in the subject.
• Embodiment 116 The method of any of embodiments 105-115, wherein the subject is human.
• Embodiment 117 The method of any of embodiments 105-115, wherein the subject is human.
• a method of reducing expression of MECP2 in a cell comprising contacting the cell with an oligomeric compound of any of embodiments 1-60, a modified oligonucleotide of any of embodiments 61-64, a population of any of embodiments 65-70, an oligomeric duplex of any of embodiments 71-97, an antisense agent of any of embodiments 98-101, or a pharmaceutical composition of any of embodiments 102-104.
• Embodiment 118. The method of embodiment 117, wherein the cell is a neuron.
• Embodiment 119. The method of embodiment 117 or embodiment 118, wherein the cell is a human cell.
• Embodiment 121 Embodiment 121.
• Embodiment 122 The use of embodiment 120 or embodiment 121, wherein the disease or disorder is associated with an elevated level of MECP2.
• Embodiment 123 The use of any of embodiments 120-122, wherein the disease or disorder is MECP2 duplication syndrome.
• the MECP2 nucleic acid has the sequence set forth in SEQ ID NO: 1 (GenBank Accession No. NC_000023.11 truncated from nucleosides 154019001 to 154101000) or SEQ ID NO: 2 (GenBank Accession No. NM_004992.3) or SEQ ID NO: 2340 (the complement of GenBank Accession No. NT_167198.1 truncated from nucleosides 4203000 to 4283000), each of which is incorporated by reference in its entirety.
• the oligomeric agent is a single-stranded oligomeric compound. In certain embodiments, the oligomeric agent is an oligomeric duplex. Certain embodiments provide an oligomeric compound comprising a modified oligonucleotide consisting of 8 to 80 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion of a MECP2 nucleic acid, and wherein the modified oligonucleotide has at least one modification selected from a modified sugar moiety and a modified internucleoside linkage. In certain embodiments, the MECP2 nucleic acid has the nucleobase sequence of SEQ ID NOs: 1 or 2.
• the nucleobase sequence of the modified oligonucleotide is at least 85%, at least 90%, at least 95%, or 100% complementary to an equal length portion of the MECP2 nucleic acid. In certain embodiments, the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion within nucleobases 2055-2074, 2267-2286, 2321-2340, 2411-2430, 2485- 2504, 2536-2555, 2547-2566, 2553-2572, 2683-2702, 2840-2859, 3060-3079, 3075-3094, 3701-3719, 3703-3722, 4286- 4305, 4302-4321, 4327-4346, 4456-4475, 4482-4501, 4509-4528, 4511-4530, 4531-4550, 4550-4569, 4560-4579, 4574- 4593, 4575-4594, 4659-4678, 4820-4839, 4823-4842, 4825
• the nucleobase sequence of the modified oligonucleotide is at least 85%, at least 90%, at least 95%, or 100% complementary to the equal length portion of the MECP2 nucleic acid. In certain embodiments, the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion within nucleobases 129-148, 154-173, 156-175, 217-236, 218-237, 219-238, 232-251, 301-320, 315-334, 317-336, 545-564, 552-571, 572-591, 859-878, 860-879, 1561-1580, 1565-1584, 1595- 1614, 1597-1616, 1603-1622, 1668-1687, 1669-1688, 1714-1733, 1715-1734, 1753-1772, 1755-1774, 1757-1776, 1759- 1778, 1761-1780, 1763-1782, 1840-1859, 1884-1903, 1906-1925,
• the nucleobase sequence of the modified oligonucleotide is at least 85%, at least 90%, at least 95%, or 100% complementary to the equal length portion of the MECP2 nucleic acid. In certain embodiments, the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion within nucleobases 2305-2324 of SEQ ID NO: 2340.
• the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion within nucleobases 10858-10885, 11534-11588, 11597-11620, 12936-12962, 13599-13641, 13669-13711, 14716-14746, 15883-15905, 16362-16396, 18941-18975, 19046-19091, 20216-20271, 21505-21532, 21945-21976, 23689-23713, 24791-24833, 24901-24930, 24970-24995, 32385-32414, 32447-32508, 32588-32671, 35116-35158, 43248-43273, 43863-43923, or 64179-64202 of SEQ ID NO: 1.
• the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion within nucleobases 32588-32671 of SEQ ID NO: 1. In certain embodiments, the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion within nucleobases 32611-32630 of SEQ ID NO: 1. In certain embodiments, the nucleobase sequence of the modified oligonucleotide is at least 85%, at least 90%, at least 95%, or 100% complementary to the equal length portion of the MECP2 nucleic acid.
• an oligomeric compound comprising a modified oligonucleotide consisting of 8 to 80 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide comprises at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or at least 20 contiguous nucleobases of any of SEQ ID NOs: 18-2339.
• Certain embodiments provide an oligomeric compound comprising a modified oligonucleotide consisting of 18 to 80 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide comprises the nucleobase sequence of any of SEQ ID NOs: 18-2339.
• an oligomeric compound comprising a modified oligonucleotide consisting of 18 to 80 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide consists of the nucleobase sequence of any of SEQ ID NOs: 18-2339. Certain embodiments provide an oligomeric compound comprising a modified oligonucleotide consisting of 20 to 80 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide comprises the nucleobase sequence of any of SEQ ID NOs: 18-2335.
• an oligomeric compound comprising a modified oligonucleotide consisting of 20 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide consists of the nucleobase sequence of any of SEQ ID NOs: 18-2335.
• Certain embodiments provide an oligomeric compound comprising a modified oligonucleotide consisting of 18 to 80 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide comprises the nucleobase sequence of any of SEQ ID NOs: 2336-2339.
• an oligomeric compound comprising a modified oligonucleotide consisting of 20 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide consists of the nucleobase sequence of SEQ ID NO: 1197.
• the nucleobase sequence of the modified oligonucleotide can be at least 85%, at least 90%, at least 95%, or 100% complementary to an equal length portion of a MECP2 nucleic acid, wherein the MECP2 nucleic acid has the nucleobase sequence of SEQ ID NOs: 1 or 2.
• the modified oligonucleotide can consist of 10 to 25, 10 to 30, 10 to 50, 12 to 20, 12 to 25, 12 to 30, 12 to 50, 13 to 20, 13 to 25, 13 to 30, 13 to 50, 14 to 20, 14 to 25, 14 to 30, 14 to 50, 15 to 20, 15 to 25, 15 to 30, 15 to 50, 16 to 18,16 to 20, 16 to 25, 16 to 30, 16 to 50, 17 to 20, 17 to 25, 17 to 30, 17 to 50, 18 to 20, 18 to 22, 18 to 25, 18 to 30, 18 to 50, 19 to 20, 19 to 25, 19 to 30, 19 to 50, 20 to 25, 20 to 30, 20 to 50, 21 to 25, 21 to 30, 21 to 50, 22 to 25, 22 to 30, 22 to 50, 23 to 25, 23 to 30, or 23 to 50 linked nucleosides.
• At least one nucleoside of the modified oligonucleotide can comprise a modified sugar moiety.
• the modified sugar moiety comprises a bicyclic sugar moiety, such as a 2’-4’ bridge selected from –O-CH 2 - and –O-CH(CH 3 )-.
• the modified sugar moiety comprises a non-bicyclic sugar moiety, such as a 2’-MOE sugar moiety or 2’-OMe sugar moiety.
• at least one nucleoside of the modified oligonucleotide compound can comprise a sugar surrogate.
• At least one internucleoside linkage of the modified oligonucleotide can comprise a modified internucleoside linkage, such as a phosphorothioate internucleoside linkage.
• each internucleoside linkage of the modified oligonucleotide can be a modified internucleoside linkage.
• each internucleoside linkage of the modified oligonucleotide can be a phosphorothioate internucleoside linkage.
• at least one internucleoside linkage of the modified oligonucleotide can be a phosphodiester internucleoside linkage.
• each internucleoside linkage of the modified oligonucleotide can be independently selected from a phosphodiester internucleoside linkage or a phosphorothioate internucleoside linkage.
• at least 2, at least 3, at least 4, at least 5, or at least 6 internucleoside linkages of the modified oligonucleotide can be phosphodiester internucleoside linkages.
• at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, or 19 internucleoside linkages of the modified oligonucleotide can be phosphorothioate internucleoside linkages.
• At least one nucleobase of the modified oligonucleotide can be a modified nucleobase, such as 5-methylcytosine.
• each cytosine is 5-methylcytosine.
• the modified oligonucleotide can comprise a deoxy region consisting of 5-12 contiguous 2’-deoxynucleosides.
• each nucleoside of the deoxy region is a 2’- ⁇ -D-deoxynucleoside.
• the deoxy region consists of 6, 7, 8, 9, 10, or 6-10 linked nucleosides.
• each nucleoside immediately adjacent to the deoxy region comprises a modified sugar moiety.
• the deoxy region is flanked on the 5’-side by a 5’-external region consisting of 1- 6 linked 5’-external region nucleosides and on the 3’-side by a 3’-external region consisting of 1-6 linked 3’-external region nucleosides; wherein the 3’-most nucleoside of the 5’-region comprises a modified sugar moiety, and the 5’-most nucleoside of the 3’-region comprises a modified sugar moiety.
• each nucleoside of the 3’- region comprises a modified sugar moiety.
• each nucleoside of the 5’-region comprises a modified sugar moiety.
• Compound No.1435454 is characterized as a 5-10-5 MOE gapmer of linked nucleosides having a nucleobase sequence (from 5’ to 3’) of GCAACATTTTCAGTTTCAGC (SEQ ID NO: 1197), wherein each of nucleosides 1-5 and 16-20 (from 5’ to 3’) are 2’-MOE nucleosides and each of nucleosides 6-15 are 2’- ⁇ -D-deoxynucleosides, wherein the internucleoside linkages between nucleosides 2-3, 3-4, 4-5, 5-6, 16-17, and 17-18 are phosphodiester internucleoside linkages, the internucleoside linkages between nucleosides 1-2, 6-7, 7-8, 8-9, 9-10, 10-11, 11-12, 12-13, 13-14, 14-15, 15-16, 18-19
• the oligomeric compound comprises a pharmaceutically acceptable salt of the modified oligonucleotide represented by Structure 1 comprising one or more cations selected from sodium, potassium, calcium, and magnesium.
• the sodium salt of Compound No.1435454 is represented by the following chemical structure:
• Certain Oligomeric Duplexes Certain embodiments are directed to oligomeric duplexes comprising a first oligomeric compound and a second oligomeric compound.
• an oligomeric duplex comprises: a first oligomeric compound comprising a first modified oligonucleotide consisting of 8 to 80 linked nucleosides, wherein the nucleobase sequence of the first modified oligonucleotide is at least 80% complementary to the nucleobase sequence of an equal length portion within nucleobases 2055-2074, 2267-2286, 2321-2340, 2411-2430, 2485-2504, 2536-2555, 2547-2566, 2553-2572, 2683-2702, 2840-2859, 3060-3079, 3075-3094, 3701-3719, 3703-3722, 4286-4305, 4302-4321, 4327-4346, 4456-4475, 4482-4501, 4509-4528, 4511-4530, 4531-4550, 4550-4569, 4560-4579, 4574-4593, 4575-4594, 4659-4678, 4820-4839, 4823-4842, 4825-48
• an oligomeric duplex comprises: a first oligomeric compound comprising a first modified oligonucleotide consisting of 8 to 80 linked nucleosides, wherein the nucleobase sequence of the first modified oligonucleotide is at least 80% complementary to the nucleobase sequence of an equal length portion within nucleobases 10858-10885, 11534-11588, 11597-11620, 12936- 12962, 13599-13641, 13669-13711, 14716-14746, 15883-15905, 16362-16396, 18941-18975, 19046-19091, 20216- 20271, 21505-21532, 21945-21976, 23689-237
• an oligomeric duplex comprises: a first oligomeric compound comprising a first modified oligonucleotide consisting of 8 to 80 linked nucleosides, wherein the nucleobase sequence of the first modified oligonucleotide comprises at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases of the nucleobase sequence of any of SEQ ID NOs: 18-2339, wherein each thymine is replaced by uracil; and a second oligomeric compound comprising a second modified oligonucleotide consisting of 8 to 80 linked nucleosides, wherein the nucleobase sequence of the second
• an oligomeric duplex comprises: a first oligomeric compound comprising a first modified oligonucleotide consisting of 8 to 80 linked nucleosides, wherein the nucleobase sequence of the first modified oligonucleotide comprises at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases of the nucleobase sequence of any of SEQ ID NOs: 18-2339, wherein each thymine is replaced by uracil; and a second oligomeric compound comprising a second modified oligonucleotide consisting of 8 to 80 linked nucleosides, wherein the nucleobase sequence of the second
• an oligomeric duplex comprises: a first oligomeric compound comprising a first modified oligonucleotide consisting of 8 to 80 linked nucleosides, wherein the nucleobase sequence of the first modified oligonucleotide comprises at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases of the nucleobase sequence of any of SEQ ID NOs: 18-2335, wherein each thymine is replaced by uracil; and a second oligomeric compound comprising a second modified oligonucleotide consisting of 8 to 80 linked nucleosides, wherein the nucleobase sequence of the second modified
• an oligomeric duplex comprises: a first oligomeric compound comprising a first modified oligonucleotide consisting of 8 to 80 linked nucleosides wherein the nucleobase sequence of the first modified oligonucleotide comprises at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, or at least 16, at least 17, or 18 contiguous nucleobases of the nucleobase sequence of any of SEQ ID NOs: 2336-2339, wherein each thymine is replaced by uracil; and a second oligomeric compound comprising a second modified oligonucleotide consisting of 8 to 80 linked nucleosides wherein the nucleobase sequence of the second modified oligonucle
• the nucleobase sequence of the first modified oligonucleotide is at least 85%, at least 90%, at least 95%, or 100% complementary to an equal length portion of the MECP2 nucleic acid.
• the first oligomeric compound is an antisense compound.
• the first modified oligonucleotide is an antisense oligonucleotide.
• the second oligomeric compound is a sense compound. In certain embodiments, the second modified oligonucleotide is a sense oligonucleotide.
• At least one nucleoside of the first modified oligonucleotide and/or at least one nucleoside of the second modified oligonucleotide can comprise a modified sugar moiety.
• suitable modified sugar moieties include, but are not limited to, a bicyclic sugar moiety, such as a 2’-4’ bridge selected from –O-CH 2 - and –O-CH(CH 3 )-, and a non-bicyclic sugar moiety, such as a 2’-MOE sugar moiety, a 2’-F sugar moiety, a 2’-OMe sugar moiety, or a 2’-NMA sugar moiety.
• At least 80%, at least 90%, or 100% of the nucleosides of the first modified oligonucleotide and/or the second modified oligonucleotide comprises a modified sugar moiety selected from 2’-F and 2’-OMe.
• at least one nucleoside of the first modified oligonucleotide and/or at least one nucleoside of the second modified oligonucleotide can comprise a sugar surrogate.
• suitable sugar surrogates include, but are not limited to, morpholino, peptide nucleic acid (PNA), glycol nucleic acid (GNA), and unlocked nucleic acid (UNA).
• At least one nucleoside of the first modified oligonucleotide comprises a sugar surrogate, which can be a GNA.
• at least one internucleoside linkage of the first modified oligonucleotide and/or at least one internucleoside linkage of the second modified oligonucleotide can comprise a modified internucleoside linkage.
• the modified internucleoside linkage is a phosphorothioate internucleoside linkage.
• At least one of the first, second, or third internucleoside linkages from the 5’ end and/or the 3’ end of the first modified oligonucleotide comprises a phosphorothioate linkage. In certain embodiments, at least one of the first, second, or third internucleoside linkages from the 5’ end and/or the 3’ end of the second modified oligonucleotide comprises a phosphorothioate linkage.
• At least one internucleoside linkage of the first modified oligonucleotide and/or at least one internucleoside linkage of the second modified oligonucleotide can comprise a phosphodiester internucleoside linkage.
• each internucleoside linkage of the first modified oligonucleotide and/or each internucleoside linkage of the second modified oligonucleotide can be independently selected from a phosphodiester or a phosphorothioate internucleoside linkage.
• At least one nucleobase of the first modified oligonucleotide and/or at least one nucleobase of the second modified oligonucleotide can be a modified nucleobase.
• the modified nucleobase is 5-methylcytosine.
• the first modified oligonucleotide can comprise a stabilized phosphate group attached to the 5’ position of the 5’-most nucleoside.
• the stabilized phosphate group comprises a cyclopropyl phosphonate or an (E)-vinyl phosphonate.
• the first modified oligonucleotide can comprise a conjugate group.
• the conjugate group comprises a conjugate linker and a conjugate moiety.
• the conjugate group is attached to the first modified oligonucleotide at the 5’-end of the first modified oligonucleotide.
• the conjugate group is attached to the first modified oligonucleotide at the 3’- end of the modified oligonucleotide.
• the conjugate group comprises N-acetyl galactosamine.
• the conjugate group comprises a cell-targeting moiety having an affinity for transferrin receptor (TfR), also known as TfR1 and CD71.
• TfR transferrin receptor
• the conjugate group comprises an anti-TfR1 antibody or fragment thereof.
• the conjugate group comprises a protein or peptide capable of binding TfR1.
• the conjugate group comprises an aptamer capable of binding TfR1.
• conjugate groups may be selected from any of a C22 alkyl, C20 alkyl, C16 alkyl, C10 alkyl, C21 alkyl, C19 alkyl, C18 alkyl, C17 alkyl, C15 alkyl, C14 alkyl, C13 alkyl, C12 alkyl, C11 alkyl, C9 alkyl, C8 alkyl, C7 alkyl, C6 alkyl, C5 alkyl, C22 alkenyl, C20 alkenyl, C16 alkenyl, C10 alkenyl, C21 alkenyl, C19 alkenyl, C18 alkenyl, C17 alkenyl, C15 alkenyl, C14 alkenyl, C13 alkenyl, C12 alkenyl, C11 alkenyl, C9 alkenyl, C8 alkenyl, C7 alkenyl, C6 alkenyl, or C5 alkenyl.
• conjugate groups may be selected from any of C22 alkyl, C20 alkyl, C16 alkyl, C10 alkyl, C21 alkyl, C19 alkyl, C18 alkyl, C17 alkyl, C15 alkyl, C14 alkyl, C13 alkyl, C12 alkyl, C11 alkyl, C9 alkyl, C8 alkyl, C7 alkyl, C6 alkyl, and C5 alkyl, where the alkyl chain has one or more unsaturated bonds.
• the second modified oligonucleotide can comprise a conjugate group.
• the conjugate group comprises a conjugate linker and a conjugate moiety. In certain embodiments, the conjugate group is attached to the second modified oligonucleotide at the 5’-end of the second modified oligonucleotide. In certain embodiments, the conjugate group is attached to the second modified oligonucleotide at the 3’-end of the modified oligonucleotide. In certain embodiments, the conjugate group comprises N-acetyl galactosamine. In certain embodiments, the conjugate group comprises a cell-targeting moiety having an affinity for transferrin receptor (TfR), also known as TfR1 and CD71.
• TfR transferrin receptor
• the conjugate group comprises an anti-TfR1 antibody or fragment thereof. In certain embodiments, the conjugate group comprises a protein or peptide capable of binding TfR1. In certain embodiments, the conjugate group comprises an aptamer capable of binding TfR1.
• conjugate groups may be selected from any of a C22 alkyl, C20 alkyl, C16 alkyl, C10 alkyl, C21 alkyl, C19 alkyl, C18 alkyl, C17 alkyl, C15 alkyl, C14 alkyl, C13 alkyl, C12 alkyl, C11 alkyl, C9 alkyl, C8 alkyl, C7 alkyl, C6 alkyl, C5 alkyl, C22 alkenyl, C20 alkenyl, C16 alkenyl, C10 alkenyl, C21 alkenyl, C19 alkenyl, C18 alkenyl, C17 alkenyl, C15 alkenyl, C14 alkenyl, C13 alkenyl, C12 alkenyl, C11 alkenyl, C9 alkenyl, C8 alkenyl, C7 alkenyl, C6 alkenyl, or C5 alkenyl.
• conjugate groups may be selected from any of C22 alkyl, C20 alkyl, C16 alkyl, C10 alkyl, C21 alkyl, C19 alkyl, C18 alkyl, C17 alkyl, C15 alkyl, C14 alkyl, C13 alkyl, C12 alkyl, C11 alkyl, C9 alkyl, C8 alkyl, C7 alkyl, C6 alkyl, and C5 alkyl, where the alkyl chain has one or more unsaturated bonds.
• an antisense agent comprises an antisense compound, which comprises an oligomeric compound or an oligomeric duplex described herein.
• an antisense agent which can comprise an oligomeric compound or an oligomeric duplex described herein, is an RNAi agent capable of reducing the amount of MECP2 nucleic acid through the activation of RISC/Ago2.
• an antisense agent which can comprise an oligomeric compound or an oligomeric duplex described herein, is an RNAse H agent capable of reducing the amount of MECP2 nucleic acid through the activation of RNAse H.
• Certain embodiments provide an oligomeric agent comprising two or more oligomeric duplexes.
• an oligomeric agent comprises two or more of any of the oligomeric duplexes described herein.
• an oligomeric agent comprises two or more of the same oligomeric duplex, which can be any of the oligomeric duplexes described herein.
• the two or more oligomeric duplexes are linked together.
• the two or more oligomeric duplexes are covalently linked together.
• the second modified oligonucleotides of two or more oligomeric duplexes are covalently linked together.
• the second modified oligonucleotides of two or more oligomeric duplexes are covalently linked together at their 3’ ends.
• the two or more oligomeric duplexes are covalently linked together by a glycol linker, such as a tetraethylene glycol linker.
• a glycol linker such as a tetraethylene glycol linker.
• oligomeric compounds comprising oligonucleotides, which consist of linked nucleosides. Oligonucleotides may be unmodified oligonucleotides (RNA or DNA) or may be modified oligonucleotides. Modified oligonucleotides comprise at least one modification relative to unmodified RNA or DNA.
• modified oligonucleotides comprise at least one modified nucleoside (comprising a modified sugar moiety and/or a modified nucleobase) and/or at least one modified internucleoside linkage.
• modified nucleosides and modified internucleoside linkages suitable for use in modified oligonucleotides are described below.
• A. Certain Modified Nucleosides Modified nucleosides comprise a modified sugar moiety or a modified nucleobase or both a modified sugar moiety and a modified nucleobase. In certain embodiments, modified nucleosides comprising the following modified sugar moieties and/or the following modified nucleobases may be incorporated into modified oligonucleotides. 1.
• modified sugar moieties are non-bicyclic modified sugar moieties.
• modified sugar moieties are bicyclic or tricyclic sugar moieties.
• modified sugar moieties are sugar surrogates. Such sugar surrogates may comprise one or more substitutions corresponding to those of other types of modified sugar moieties.
• modified sugar moieties are non-bicyclic modified sugar moieties comprising a furanosyl ring with one or more substituent groups none of which bridges two atoms of the furanosyl ring to form a bicyclic structure.
• non bridging substituents may be at any position of the furanosyl, including but not limited to substituents at the 2’, 3’, 4’, and/or 5’ positions.
• one or more non-bridging substituent of non- bicyclic modified sugar moieties is branched.
• non-bicyclic modifed sugar moieties comprise a substituent group at the 2’-position. Examples of substituent groups suitable for the 2’-position of non-bicyclic modified sugar moieties include but are not limited to: -F, -OCH 3 (“OMe” or “O-methyl”), and -O(CH 2 ) 2 OCH 3 (“MOE” or “O-methoxyethyl”).
• 2’-substituent groups are selected from among: halo, allyl, amino, azido, SH, CN, OCN, CF 3 , OCF 3 , O- C 1 -C 10 alkoxy, O-C 1 -C 10 substituted alkoxy, O-C 1 -C 10 alkyl, O-C 1 -C 10 substituted alkyl, S-alkyl, N(R m )-alkyl, O-alkenyl, S-alkenyl, N(R m )-alkenyl, O-alkynyl, S-alkynyl, N(R m )-alkynyl, O-alkylenyl-O-alkyl, alkynyl, alkaryl, aralkyl, O- alkaryl, O-aralkyl, O(CH 2 ) 2 SCH 3 , O(CH 2 ) 2 ON(R m )(R n ) or
• non-bicyclic modified sugar moieties comprise a substituent group at the 3’-position.
• substituent groups suitable for the 3’-position of modified sugar moieties include but are not limited to alkoxy (e.g., methoxy), alkyl (e.g., methyl, ethyl).
• non-bicyclic modified sugar moieties comprise a substituent group at the 4’-position.
• 4’-substituent groups suitable for non-bicyclic modified sugar moieties include but are not limited to alkoxy (e.g., methoxy), alkyl, and those described in Manoharan et al., WO 2015/106128.
• non-bicyclic modified sugar moieties comprise a substituent group at the 5’-position.
• non-bicyclic modified sugar moieties examples include but are not limited to: methyl (R or S), vinyl, ethyl, and methoxy.
• non-bicyclic modified sugar moieties comprise more than one non-bridging sugar substituent, for example, 2'-F-5'-methyl sugar moieties and the modified sugar moieties and modified nucleosides described in Migawa et al., WO 2008/101157 and Rajeev et al., US2013/0203836.
• a non-bridging 2’-substituent group selected from: F, OCF 3, OCH 3 , O(CH 2 ) 2 OCH 3 (MOE), O(CH 2 ) 2 SCH 3 , O(CH 2 ) 2 O(CH 2 ) 2 N(CH 3 ) 2 , O(CH 2
• a 2’-substituted non-bicyclic modified nucleoside comprises a sugar moiety comprising a non-bridging 2’-substituent group selected from: F, OCH 3 , and OCH 2 CH 2 OCH 3 .
• modified furanosyl sugar moieties and nucleosides incorporating such modified furanosyl sugar moieties are further defined by isomeric configuration.
• a 2’-deoxyfuranosyl sugar moiety may be in seven isomeric configurations other than the naturally occurring ⁇ -D-deoxyribosyl configuration.
• modified sugar moieties are described in, e.g., WO 2019/157531.
• a 2’-modified sugar moiety has an additional stereocenter at the 2’-position relative to a 2’-deoxyfuranosyl sugar moiety; therefore, such sugar moieties have a total of sixteen possible isomeric configurations.
• 2’-modified sugar moieties described herein are in the ⁇ -D-ribosyl isomeric configuration unless otherwise specified.
• sugars are linked to one another 3’ to 5’.
• oligonucleotides include one or more nucleoside or sugar moiety linked at an alternative position, for example at the 2’ or inverted 5’ to 3’.
• the 2’-substituent groups may instead be at the 3’-position.
• Certain modified sugar moieties comprise a substituent that bridges two atoms of the furanosyl ring to form a second ring, resulting in a bicyclic sugar moiety.
• the bicyclic sugar moiety comprises a bridge between the 4' and the 2' furanose ring atoms.
• Nucleosides comprising such bicyclic sugar moieties have been referred to as bicyclic nucleosides (BNAs), locked nucleosides (LNA), or conformationally restricted nucleotides (CRN).
• the bicyclic sugar moiety comprises a bridge between the 4' and the 2' furanose ring atoms.
• the furanose ring is a ribose ring.
• Examples of such 4’ to 2’ bridging sugar substituents include but are not limited to: 4'-CH 2 -2', 4'-(CH 2 ) 2 -2', 4'-(CH 2 ) 3 -2', 4'-CH 2 -O-2' (“LNA”), 4'-CH 2 -S-2', 4'-(CH 2 ) 2 -O-2' (“ENA”), 4'-CH(CH 3 )-O-2' (referred to as “constrained ethyl” or “cEt” when in the S configuration), 4’-CH 2 -O-CH 2 -2’, 4’-CH 2 -N(R)-2’, 4'-CH(CH 2 OCH 3 )-O-2' (“constrained MOE” or “cMOE”) and analogs thereof (see, e.g., Seth et al., U.S.7,399,845, Bhat et al., U.S.7,569,686, Swayze et
• bicyclic sugar moieties and nucleosides incorporating such bicyclic sugar moieties are further defined by isomeric configuration.
• an LNA nucleoside (described herein) may be in the ⁇ -L configuration or in the ⁇ - D configuration.
• ⁇ -L-methyleneoxy (4’-CH 2 -O-2’) or ⁇ -L-LNA bicyclic nucleosides have been incorporated into oligonucleotides that showed antisense activity (Frieden et al., Nucleic Acids Research, 2003, 21, 6365-6372).
• the addition of locked nucleic acids to siRNAs has been shown to increase siRNA stability in serum, and to reduce off-target effects (Elmen, J. et al., (2005) Nucleic Acids Research, 33(1):439-447; Mook, OR. et al., (2007) Mal Cane Ther., 6(3):833-843; Grunweller, A.
• modified 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).
• modified sugar moieties are sugar surrogates.
• the oxygen atom of the sugar moiety is replaced, e.g., with a sulfur, carbon or nitrogen atom.
• modified sugar moieties also comprise bridging and/or non-bridging substituents as described herein.
• certain sugar surrogates comprise a 4’-sulfur atom and a substitution at the 2'-position (see, e.g., Bhat et al., U.S. 7,875,733 and Bhat et al., U.S.7,939,677) and/or the 5’ position.
• sugar surrogates comprise rings having other than 5 atoms.
• a sugar surrogate comprises a six-membered tetrahydropyran (“THP”).
• TTP tetrahydropyrans
• 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”), mannitol nucleic acid (“MNA”) (see, e.g., Leumann, CJ. Bioorg. & Med.
• F-HNA fluoro HNA
• F-HNA can also be referred to as a F-THP or 3'-fluoro tetrahydropyran
• nucleosides comprising additional modified THP compounds having the formula: q 1 q2 T 3 O q O 3
• modified THP nucleoside: Bx is a T 3 and T 4 are each, independently, an internucleoside linking group linking the modified THP nucleoside to the remainder of an oligonucleotide or one of T 3 and T 4 is an internucleoside linking group linking the modified THP nucleoside to the
• modified THP nucleosides are provided wherein q 1 , q 2 , q 3 , q 4 , q 5 , q 6 and q 7 are each H. In certain embodiments, at least one of q 1 , q 2 , q 3 , q 4 , q 5 , q 6 and q 7 is other than H. In certain embodiments, at least one of q 1 , q 2 , q 3 , q 4 , q 5 , q 6 and q 7 is methyl. In certain embodiments, modified THP nucleosides are provided wherein one of R 1 and R 2 is F.
• R 1 is F and R 2 is H
• R 1 is methoxy and R 2 is H
• R 1 is methoxyethoxy and R 2 is H
• sugar surrogates comprise rings having more than 5 atoms and more than one heteroatom.
• nucleosides comprising morpholino sugar moieties and their use in oligonucleotides have been reported (see, e.g., Braasch et al., Biochemistry, 2002, 41, 4503-4510 and Summerton et al., U.S.5,698,685; Summerton et al., U.S.5,166,315; Summerton et al., U.S.5,185,444; and Summerton et al., U.S.5,034,506).
• morpholino means a sugar surrogate having the following structure: O O Bx .
• sugar surrogates may be modified, for example by adding or altering various substituent groups from the above morpholino structure.
• Such sugar surrogates are referred to herein as “modified morpholinos.”
• sugar surrogates comprise acyclic moieties.
• nucleosides and oligonucleotides comprising such acyclic sugar surrogates include but are not limited to peptide nucleic acid (“PNA”), acyclic butyl nucleic acid (see, e.g., Kumar et al., Org. Biomol.
• sugar surrogates comprise acyclic moieties.
• nucleosides and oligonucleotides comprising such acyclic sugar surrogates include, but are not limited to: peptide nucleic acid (“PNA”), acyclic butyl nucleic acid (see, e.g., Kumar et al., Org. Biomol. Chem., 2013, 11, 5853-5865), and nucleosides and oligonucleotides described in Manoharan et al., US 2013/130378.
• sugar surrogates are the “unlocked” sugar structure of UNA (unlocked nucleic acid) nucleosides.
• UNA is an unlocked acyclic nucleic acid, wherein any of the bonds of the sugar has been removed, forming an unlocked sugar surrogate.
• sugar surrogates are the glycerol as found in GNA (glycol nucleic acid) nucleosides as depicted below: (S)-GNA Bx where Bx represents Many other bicyclic sugar and sugar surrogates are known in the art that can be used in modified nucleosides.
• GNA glycol nucleic acid
• Bx represents Many other bicyclic sugar and sugar surrogates are known in the art that can be used in modified nucleosides.
• modified oligonucleotides comprise one or more nucleosides comprising an unmodified nucleobase.
• modified oligonucleotides comprise one or more nucleosides comprising a modified nucleobase. In certain embodiments, modified oligonucleotides comprise one or more nucleosides that does not comprise a nucleobase, referred to as an abasic nucleoside. In certain embodiments, modified oligonucleotides comprise one or more inosine nucleosides (i.e., nucleosides comprising a hypoxanthine nucleobase).
• An “unmodified nucleobase” is adenine (A), thymine (T), cytosine (C), uracil (U), or guanine (G).
• a modified nucleobase is a group of atoms other than unmodified A, T, C, U, or G capable of pairing with at least one other nucleobase.
• a 5-methylcytosine is an example of a modified nucleobase.
• a universal base is a modified nucleobase that can pair with any one of the five unmodified nucleobases.
• modified adenine has structure (I): I wherein: R 2A is H, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 thioalkyl, or substituted C 1 -C 6 thioalkyl, C 1 -C 6 alkyloxy, or substituted C 1 -C 6 alkyloxy; R 6A is H, N(R a )(R b ), oxo, acetyl, formyl, or O-phenyl; Y 7A is N and R 7A is absent or is C 1 -C 6 alkyl; or Y 7A is C and R 7A is selected from H, C 1 -C 6 alkyl, or CN(R a )(R b ); Y 8A is N and R 8A is absent, or Y 8A is C and R 8A is selected from H, a halogen, OH, C 1 -C 6 alkyl
• modified guanine has structure (II): II and R 1G is H, or R 6G is selected from O-C 1 -C 6 alkyl or S-C 1 -C 6 alkyl and R 1G is absent; Y 7G is N and R 7A is absent or is C 1 -C 6 alkyl; or Y 7G is C and R 7G is selected from H, C 1 -C 6 alkyl, or CN(R a )(R b ); Y 8G is N and R 8G is absent, or Y 8G is C and R 8G is selected from H, a halogen, OH, C 1 -C 6 alkyl, or substituted C 1 -C 6 alkyl; R a and R b are independently selected from H, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkenyl, substituted C 1 -C 6 alkenyl, acetyl, formy
• modified thymine or modified uracil has structure (III): X or S and R 5U is selected from H, OH, halogen, O-C 1 -C 12 alkyl, O-C 1 -C 12 substituted alkyl, C 1 -C 12 alkyl , substituted C 1 -C 12 alkyl, C 1 -C 12 alkenyl, substituted C 1 -C 12 alkenyl; wherein if each X is O, R 5U is not H or CH 3 (unmodified uracil and unmodified thymine, respectively).
• modified cytosine has structure (IV): R 4C O or S, R 4C is N(R a )(R b ); R 5C is selected from H, OH, halogen, O-C 1 -C 12 alkyl, O- C 1 -C 12 substituted alkyl, C 1 -C 12 alkyl , substituted C 1 -C 12 alkyl, C 1 -C 12 alkenyl, substituted C 1 -C 12 alkenyl; R a and R b are independently selected from H, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkenyl, substituted C 1 -C 6 alkenyl, acetyl, formyl, or together form a 5-7-membered heterocycle; excluding where X is O, R 4C is NH 2 and R 5C is H (unmodified cytosine).
• modified nucleobases are selected from: 5-substituted pyrimidines, 6-azapyrimidines, alkyl or alkynyl substituted pyrimidines, alkyl substituted purines, and N-2, N-6 and O-6 substituted purines.
• modified nucleobases are selected from: 5-methylcytosine, 2-aminopropyladenine, 5- hydroxymethylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-N-methylguanine, 6-N-methyladenine, 2- propyladenine , 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-propynyl (-C ⁇ C-CH 3 ) uracil, 5-propynylcytosine, 6- azouracil, 6-azocytosine, 6-azothymine, 5-ribosyluracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8- thioalkyl, 8-hydroxyl, 8-aza and other 8-substituted purines, 5-halo, particularly 5-bromo, 5-trifluoromethyl, 5- halouracil, and 5-halocytosine,
• modified nucleobases include tricyclic pyrimidines, such as 1,3-diazaphenoxazine-2-one, 1,3-diazaphenothiazine-2-one and 9-(2-aminoethoxy)-1,3- diazaphenoxazine-2-one (G-clamp).
• 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.
• nucleobases include those disclosed in Merigan et al., U.S.3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, Kroschwitz, J.I., Ed., John Wiley & Sons, 1990, 858-859; Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613; Sanghvi, Y.S., Chapter 15, Antisense Research and Applications, Crooke, S.T. and Lebleu, B., Eds., CRC Press, 1993, 273-288; and those disclosed in Chapters 6 and 15, Antisense Drug Technology, Crooke S.T., Ed., CRC Press, 2008, 163-166 and 442-443.
• each nucleobase of a modified oligonucleotide is selected from unmodified A, unmodified G, unmodified C, unmodified T, unmodified U, m C, or hypoxanthine.
• Certain Modified Internucleoside Linkages The naturally occurring internucleoside linkage of RNA and DNA is a 3' to 5' phosphodiester linkage.
• nucleosides of modified oligonucleotides may be linked together using one or more modified internucleoside linkages.
• the two main classes of internucleoside linking groups are defined by the presence or absence of a phosphorus atom.
• Modified internucleoside linkages compared to naturally occurring phosphate linkages, can be used to alter, typically increase, nuclease resistance of the oligonucleotide.
• internucleoside linkages having a chiral atom can be prepared as a racemic mixture, or as separate enantiomers. Methods of preparation of phosphorous-containing and non-phosphorous- containing internucleoside linkages are well known to those skilled in the art. In certain embodiments, a modified internucleoside linkage is any of those described in WO 2021/030778.
• a modified internucleoside linkage comprises a mesyl phosphoramidate linking group having a formula:
• a mesyl phosphoramidate internucleoside linkage may comprise a chiral center.
• modified oligonucleotides comprising (Rp) and/or (Sp) mesyl phosphoramidates comprise one or more of the following formulas, respectively, wherein “B” indicates a nucleobase: .
• alkylphosphonates and linkages having a chiral center can be prepared as populations of modified oligonucleotides comprising stereorandom internucleoside linkages, or as populations of modified oligonucleotides comprising phosphorothioate linkages in particular stereochemical configurations.
• populations of modified oligonucleotides comprise phosphorothioate internucleoside linkages wherein all of the phosphorothioate internucleoside linkages are stereorandom.
• Such modified oligonucleotides can be generated using synthetic methods that result in random selection of the stereochemical configuration of each phosphorothioate linkage.
• each individual phosphorothioate of each individual oligonucleotide molecule has a defined stereoconfiguration.
• populations of modified oligonucleotides are enriched for modified oligonucleotides comprising one or more particular phosphorothioate internucleoside linkages in a particular, independently selected stereochemical configuration.
• the particular configuration of the particular phosphorothioate linkage is present in at least 65% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 70% of the molecules in the population.
• a population of modified oligonucleotides is enriched for modified oligonucleotides having at least one indicated phosphorothioate in the (Sp) configuration. In certain embodiments, a population of modified oligonucleotides is enriched for modified oligonucleotides having at least one phosphorothioate in the (Rp) configuration. In certain embodiments, modified oligonucleotides comprising (Rp) and/or (Sp) phosphorothioates comprise one or more of the following formulas, respectively, wherein “B” indicates a nucleobase:
• chiral internucleoside linkages of modified oligonucleotides described herein can be stereorandom or in a particular stereochemical configuration.
• Further neutral internucleoside linkages include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides (See for example: Carbohydrate Modifications in Antisense Research; Y.S. Sanghvi and P.D. Cook, Eds., ACS Symposium Series 580; Chapters 3 and 4, 40-65). Further neutral internucleoside linkages include nonionic linkages comprising mixed N, O, S and CH 2 component parts.
• modified oligonucleotides comprise one or more inverted nucleoside, as shown below: , wherein any nucleobase.
• an inverted nucleoside is terminal (i.e., the last nucleoside on one end of an oligonucleotide) and so only one internucleoside linkage depicted above will be present.
• additional features such as a conjugate group may be attached to the inverted nucleoside.
• Such terminal inverted nucleosides can be attached to either or both ends of an oligonucleotide.
• such groups lack a nucleobase and are referred to herein as inverted sugar moieties.
• an inverted sugar moiety is terminal (i.e., attached to the last nucleoside on one end of an oligonucleotide) and so only one internucleoside linkage above will be present.
• additional features such as a conjugate group
• Such terminal inverted sugar moieties can be attached to either or both ends of an oligonucleotide.
• nucleic acids can be linked 2’ to 5’ rather than the standard 3’ to 5’ linkage. Such a linkage is illustrated below. , wherein B.
• modified oligonucleotides comprise one or more modified nucleosides comprising a modified sugar moiety.
• modified oligonucleotides comprise one or more modified nucleosides comprising a modified nucleobase.
• modified oligonucleotides comprise one or more modified internucleoside linkage.
• the modified, unmodified, and differently modified sugar moieties, nucleobases, and/or internucleoside linkages of a modified oligonucleotide define a pattern or motif. Unless otherwise indicated, the patterns of sugar moieties, nucleobases, and internucleoside linkages are each independent of one another.
• a modified oligonucleotide may be described by its sugar motif, nucleobase motif and/or internucleoside linkage motif (as used herein, nucleobase motif describes the modifications to the nucleobases independent of the sequence of nucleobases).
• nucleobase motif describes the modifications to the nucleobases independent of the sequence of nucleobases.
• each nucleoside of the deoxy region is a 2’- ⁇ -D-deoxynucleoside.
• the deoxy region consists of 5-12 linked nucleosides.
• the deoxy region consists of 6, 7, 8, 9, 10, or 6-10 linked nucleosides.
• at least one nucleoside within the deoxy region comprises a modified sugar moiety.
• exactly one nucleoside within the deoxy region comprises a modified sugar moiety.
• two or three nucleosides within the deoxy region comprise a modified sugar moiety.
• the deoxy region is flanked on the 5’-side by a 5’-region consisting of linked 5’-region nucleosides and on the 3’-side by a 3’-region consisting of linked 3’-region nucleosides; wherein the 3’-most nucleoside of the 5’-region is a modified nucleoside and the 5’-most nucleoside of the 3’-region is a modified nucleoside. At least one nucleoside of the 5’-region comprises a modified sugar moiety; and at least one nucleoside of the 3’-region comprises a modified sugar moiety.
• the three regions form a contiguous sequence of nucleosides.
• the sugar moiety of the 3’-most nucleoside of the 5’-region and the sugar moiety of the 5’-most nucleoside of the 3’-region each differ from the sugar moiety of the respective adjacent nucleoside of the deoxy region, thus defining the boundary between the 5’-region, the deoxy region, and the 3’- region.
• each nucleoside of the 5’-region and each nucleoside of the 3’-region comprises a modified sugar moiety.
• the nucleosides within the 5’-region comprise the same sugar modification.
• the nucleosides within the 5’-region comprise two or more different sugar modifications. In certain embodiments, the nucleosides within the 3’-region comprise the same sugar modification. In certain embodiments, the nucleosides within the 3’-region comprise two or more different sugar modifications. In certain embodiments, the 5’-region and the 3’-region of a modified oligonucleotide each comprises 1-8 nucleosides. In certain embodiments, the 5’-region comprises 1-7 nucleosides. In certain embodiments, the 5’-region comprises 1-6 nucleosides. In certain embodiments, the 5’-region comprises 1, 2, 3, 4, 5, 6, 7, or 8 nucleosides.
• the 3’-region comprises 1-7 nucleosides. In certain embodiments, the 3’-region comprises 1-6 nucleosides. In certain embodiments, the 3’-region comprises 1, 2, 3, 4, 5, 6, 7, or 8 nucleosides.
• modified oligonucleotides comprise or consist of a region having a gapmer motif, which is defined by two external regions or “wings” and a central or internal region or “gap.”
• the three regions of a gapmer motif (the 5’-wing, the gap, and the 3’-wing) form a contiguous sequence of nucleosides wherein at least some of the sugar moieties of the nucleosides of each of the wings differ from at least some of the sugar moieties of the nucleosides of the gap.
• the sugar moieties of the nucleosides of each wing that are closest to the gap differ from the sugar moiety of the neighboring gap nucleosides, thus defining the boundary between the wings and the gap (i.e., the wing/gap junction).
• the sugar moieties within the gap are the same as one another.
• the gap includes one or more nucleoside having a sugar moiety that differs from the sugar moiety of one or more other nucleosides of the gap.
• the sugar motifs of the two wings are the same as one another (symmetric gapmer).
• the sugar motif of the 5'-wing differs from the sugar motif of the 3'-wing (asymmetric gapmer).
• the wings of a gapmer comprise 1-6 nucleosides.
• each nucleoside of each wing of a gapmer comprises a modified sugar moiety.
• at least one nucleoside of each wing of a gapmer comprises a modified sugar moiety.
• at least two nucleosides of each wing of a gapmer comprises a modified sugar moiety.
• at least three nucleosides of each wing of a gapmer comprises a modified sugar moiety.
• each wing of a gapmer comprises a modified sugar moiety.
• the gap of a gapmer comprises 7-12 nucleosides.
• each nucleoside of the gap of a gapmer comprises a 2’- ⁇ -D-deoxyribosyl sugar moiety.
• at least one nucleoside of the gap of a gapmer comprises a modified sugar moiety.
• the gapmer is a deoxy gapmer.
• the nucleosides on the gap side of each wing/gap junction comprise 2’- deoxyribosyl sugar moieties and the nucleosides on the wing sides of each wing/gap junction comprise modified sugar moieties.
• each nucleoside of the gap comprises a 2’- ⁇ -D-deoxyribosyl sugar moiety.
• each nucleoside of each wing of a gapmer comprises a modified sugar moiety.
• at least one nucleoside of the gap of a gapmer comprises a modified sugar moiety.
• one nucleoside of the gap comprises a modified sugar moiety and each remaining nucleoside of the gap comprises a 2’-deoxyribosyl sugar moiety.
• at least one nucleoside of the gap of a gapmer comprises a 2’-OMe sugar moiety.
• the lengths (number of nucleosides) of the three regions of a gapmer may be provided using the notation [# of nucleosides in the 5’-wing] – [# of nucleosides in the gap] – [# of nucleosides in the 3’-wing].
• a 3- 10-3 gapmer consists of 3 linked nucleosides in each wing and 10 linked nucleosides in the gap.
• a 5-10-5 MOE gapmer consists of 5 linked 2’-MOE nucleosides in the 5’-wing, 10 linked 2’- ⁇ -D-deoxynucleosides in the gap, and 5 linked 2’-MOE nucleosides in the 3’-wing.
• a 5-8-5 MOE gapmer consists of 5 linked 2’-MOE nucleosides in the 5’-wing, 8 linked 2’- ⁇ -D-deoxynucleosides in the gap, and 5 linked 2’-MOE nucleosides in the 3’-wing.
• modified oligonucleotides disclosed herein are modified by a specific sugar modification.
• modified oligonucleotides are 5-10-5 MOE gapmers.
• modified oligonucleotides are 5-8-5 MOE gapmers.
• modified oligonucleotides have a sugar motif of (from 5’ to 3’): eeeeeddddddddddeeeee; wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’- MOE ribosyl sugar moiety.
• modified oligonucleotides have a sugar motif of (from 5’ to 3’): eeeeeddddddddeeee; wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE ribosyl sugar moiety.
• oligonucleotides comprise modified and/or unmodified nucleobases arranged along the oligonucleotide or region thereof in a defined pattern or motif.
• each nucleobase is modified.
• none of the nucleobases are modified.
• each purine or each pyrimidine is modified.
• each adenine is modified.
• each guanine is modified.
• each thymine is modified.
• each uracil is modified.
• each cytosine is modified.
• modified 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 nucleosides of the 3’-end of the oligonucleotide.
• the block is at the 5’-end of the oligonucleotide. In certain embodiments the block is within 3 nucleosides of the 5’-end of the oligonucleotide.
• oligonucleotides having a gapmer motif comprise a nucleoside comprising a modified nucleobase. In certain such embodiments, one nucleoside comprising a modified nucleobase is in the central gap of an oligonucleotide having a gapmer motif.
• the sugar moiety of said nucleoside is a 2’- deoxyribosyl sugar moiety.
• the modified nucleobase is selected from a 2-thiopyrimidine and a 5-propynepyrimidine. 3. Certain Internucleoside Linkage Motifs
• oligonucleotides comprise modified and/or unmodified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or motif.
• each internucleoside linkage of a modified oligonucleotide is independently selected from a phosphorothioate internucleoside linkage and phosphodiester internucleoside linkage.
• each phosphorothioate internucleoside linkage is independently selected from a stereorandom phosphorothioate a (Sp) phosphorothioate, and a (Rp) phosphorothioate.
• the sugar motif of a modified oligonucleotide is a gapmer and the internucleoside linkages within the gap are all modified.
• the internucleoside linkages in the wings are unmodified phosphodiester internucleoside linkages.
• the terminal internucleoside linkages are modified.
• the sugar motif of a modified oligonucleotide is a gapmer, and the internucleoside linkage motif comprises at least one phosphodiester internucleoside linkage in at least one wing, wherein the at least one phosphodiester linkage is not a terminal internucleoside linkage, and the remaining internucleoside linkages are phosphorothioate internucleoside linkages.
• all of the phosphorothioate linkages are stereorandom.
• all of the phosphorothioate linkages in the wings are (Sp) phosphorothioates, and the gap comprises at least one Sp, Sp, Rp motif.
• populations of modified oligonucleotides are enriched for modified oligonucleotides comprising such internucleoside linkage motifs.
• modified oligonucleotides have an internucleoside linkage motif of (from 5’ to 3’) soooossssssssooss and sooosssssssooss, wherein each “s” represents a phosphorothioate internucleoside linkage and each “o” represents a phosphodiester internucleoside linkage.
• modified oligonucleotides have an internucleoside linkage motif comprising one or more mesyl phosphoramidate linking groups.
• one or more phosphorothioate internucleoside linkages or one or more phosphodiester internucleoside linkages of the internucleoside linkage motifs described herein is substituted with a mesyl phosphoramidate internucleoside linkage.
• C. Certain Lengths It is possible to increase or decrease the length of an oligonucleotide without eliminating activity. For example, in Woolf et al. (Proc. Natl. Acad. Sci. USA 89:7305-7309, 1992), a series of oligonucleotides 13-25 nucleobases in length were tested for their ability to induce cleavage of a target RNA in an oocyte injection model.
• Oligonucleotides 25 nucleobases in length with 8 or 11 mismatch bases near the ends of the oligonucleotides were able to direct specific cleavage of the target RNA, albeit to a lesser extent than the oligonucleotides that contained no mismatches. Similarly, target specific cleavage was achieved using 13 nucleobase oligonucleotides, including those with 1 or 3 mismatches. In certain embodiments, oligonucleotides (including modified oligonucleotides) can have any of a variety of ranges of lengths.
• oligonucleotides consist of X to Y linked nucleosides, where X represents the fewest number of nucleosides in the range and Y represents the largest number nucleosides in the range.
• X and Y are each independently selected from 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, and 50; provided that X ⁇ Y.
• oligonucleotides consist of 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, 15 to 28, 15 to 29, 15 to 30, 16 to 17, 16
• oligonucleotides consist of 18 linked nucleosides. In certain embodiments, oligonucleotides (including modified oligonucleotides) consist of 20 linked nucleosides.
• D. Certain Modified Oligonucleotides In certain embodiments, the above modifications (sugar, nucleobase, internucleoside linkage) are incorporated into a modified oligonucleotide. In certain embodiments, modified oligonucleotides are characterized by their modification motifs and overall lengths. In certain embodiments, such parameters are each independent of one another.
• 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.
• 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 of the sugar motif.
• such sugar gapmer oligonucleotides may comprise one or more modified nucleobase independent of the gapmer pattern of the sugar modifications. Unless otherwise indicated, all modifications are independent of nucleobase sequence.
• Modified Oligonucleotides Populations of modified oligonucleotides in which all of the modified oligonucleotides of the population have the same molecular formula can be stereorandom populations or chirally enriched populations. All of the chiral centers of all of the modified oligonucleotides are stereorandom in a stereorandom population. In a chirally enriched population, at least one particular chiral center is not stereorandom in the modified oligonucleotides of the population.
• the modified oligonucleotides of a chirally enriched population are enriched for ⁇ -D ribosyl sugar moieties, and all of the phosphorothioate internucleoside linkages are stereorandom. In certain embodiments, the modified oligonucleotides of a chirally enriched population are enriched for both ⁇ -D ribosyl sugar moieties and at least one, particular phosphorothioate internucleoside linkage in a particular stereochemical configuration.
• F. Nucleobase Sequence In certain embodiments, oligonucleotides (unmodified or modified oligonucleotides) are further described by their nucleobase sequence.
• oligonucleotides have a nucleobase sequence that is complementary to a second oligonucleotide or an identified reference nucleic acid, such as a target nucleic acid.
• a region of an oligonucleotide has a nucleobase sequence that is complementary to a second oligonucleotide or an identified reference nucleic acid, such as a target nucleic acid.
• the nucleobase sequence of a region or entire length of an oligonucleotide is at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% complementary to the second oligonucleotide or nucleic acid, such as a target nucleic acid.
• oligomeric compounds which consist of an oligonucleotide (modified or unmodified) and optionally one or more conjugate groups and/or terminal groups.
• Conjugate groups consist of one or more conjugate moiety and a conjugate linker which links the conjugate moiety to the oligonucleotide.
• Conjugate groups may be attached to either or both ends of an oligonucleotide and/or at any internal position. In certain embodiments, conjugate groups are attached to the 2'-position of a nucleoside of a modified oligonucleotide. In certain embodiments, conjugate groups that are attached to either or both ends of an oligonucleotide are terminal groups. In certain such embodiments, conjugate groups or terminal groups are attached at the 3’ and/or 5’-end of oligonucleotides. In certain such embodiments, conjugate groups (or terminal groups) are attached at the 3’-end of oligonucleotides. In certain embodiments, conjugate groups are attached near the 3’-end of oligonucleotides.
• conjugate groups are attached at the 5’-end of oligonucleotides. In certain embodiments, conjugate groups are attached near the 5’-end of oligonucleotides.
• A. Certain Conjugate Groups In certain embodiments, oligonucleotides are covalently attached to one or more conjugate groups. In certain embodiments, conjugate groups modify one or more properties of the attached oligonucleotide, including but not limited to pharmacodynamics, pharmacokinetics, stability, binding, absorption, tissue distribution, cellular distribution, cellular uptake, charge and clearance.
• conjugation of one or more carbohydrate moieties to a modified oligonucleotide can alter one or more properties of the modified oligonucleotide.
• the carbohydrate moiety is attached to a modified subunit of the modified oligonucleotide.
• the ribose sugar of one or more ribonucleotide subunits of a modified oligonucleotide can be replaced with another moiety, e.g., a non-carbohydrate (preferably cyclic) carrier to which is attached a carbohydrate ligand.
• a ribonucleotide subunit in which the ribose sugar of the subunit has been so replaced is referred to herein as a ribose replacement modification subunit (RRMS), which is a modified sugar moiety.
• RRMS ribose replacement modification subunit
• a cyclic carrier may be a carbocyclic ring system, i.e., one or more ring atoms may be a heteroatom, e.g., nitrogen, oxygen, sulphur.
• the cyclic carrier may be a monocyclic ring system, or may contain two or more rings, e.g., fused rings.
• the cyclic carrier may be a fully saturated ring system, or it may contain one or more double bonds.
• the modified oligonucleotide is a gapmer.
• conjugate groups impart a new property on the attached oligonucleotide, e.g., fluorophores or reporter groups that enable detection of the oligonucleotide.
• Certain conjugate groups and conjugate moieties 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. Lett., 1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y.
• 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 a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp.
• conjugate groups may be selected from any of a C22 alkyl, C20 alkyl, C16 alkyl, C10 alkyl, C21 alkyl, C19 alkyl, C18 alkyl, C17 alkyl, C15 alkyl, C14 alkyl, C13 alkyl, C12 alkyl, C11 alkyl, C9 alkyl, C8 alkyl, C7 alkyl, C6 alkyl, C5 alkyl, C22 alkenyl, C20 alkenyl, C16 alkenyl, C10 alkenyl, C21 alkenyl, C19 alkenyl, C18 alkenyl, C17 alkenyl, C15 alkenyl, C14 alkenyl, C13 alkenyl, C12 alkenyl, C11 alkenyl, C9 alkenyl, C8 alkenyl, C7 alkenyl, C6 alkenyl, or C5 alkenyl.
• conjugate groups may be selected from any of C22 alkyl, C20 alkyl, C16 alkyl, C10 alkyl, C21 alkyl, C19 alkyl, C18 alkyl, C17 alkyl, C15 alkyl, C14 alkyl, C13 alkyl, C12 alkyl, C11 alkyl, C9 alkyl, C8 alkyl, C7 alkyl, C6 alkyl, and C5 alkyl, where the alkyl chain has one or more unsaturated bonds.
• a conjugate group has the following structure: . 1.
• Conjugate moieties include, without limitation, intercalators, reporter molecules, polyamines, polyamides, peptides, carbohydrates (e.g., GalNAc), vitamin moieties, polyethylene glycols, thioethers, polyethers, cholesterols, thiocholesterols, cholic acid moieties, folate, lipids, phospholipids, biotin, phenazine, phenanthridine, anthraquinone, adamantane, acridine, fluoresceins, rhodamines, coumarins, fluorophores, and dyes.
• intercalators include, without limitation, intercalators, reporter molecules, polyamines, polyamides, peptides, carbohydrates (e.g., GalNAc), vitamin moieties, polyethylene glycols, thioethers, polyethers, cholesterols, thiocholesterols, cholic acid moieties, folate, lipids, phospholipids, bio
• a conjugate moiety comprises an active drug substance, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fen-bufen, ketoprofen, (S)-(+)-pranoprofen, carprofen, dansylsarcosine, 2,3,5- triiodobenzoic acid, fingolimod, 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.
• an active drug substance for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fen-bufen, ketoprofen, (S)-(+)-pranoprofen, car
• Conjugate Linkers Conjugate moieties are attached to oligonucleotides through conjugate linkers.
• the conjugate linker is a single chemical bond (i.e., the conjugate moiety is attached directly to an oligonucleotide through a single bond).
• the conjugate linker comprises a chain structure, such as a hydrocarbyl chain, or an oligomer of repeating units such as ethylene glycol, nucleosides, or amino acid units.
• a conjugate linker comprises pyrrolidine.
• a conjugate linker comprises one or more groups selected from alkyl, amino, oxo, amide, disulfide, polyethylene glycol, ether, thioether, and hydroxylamino. In certain such embodiments, the conjugate linker comprises groups selected from alkyl, amino, oxo, amide and ether groups. In certain embodiments, the conjugate linker comprises groups selected from alkyl and amide groups. In certain embodiments, the conjugate linker comprises groups selected from alkyl and ether groups. In certain embodiments, the conjugate linker comprises at least one phosphorus moiety. In certain embodiments, the conjugate linker comprises at least one phosphate group. In certain embodiments, the conjugate linker includes at least one neutral linking group.
• conjugate linkers are bifunctional linking moieties, e.g., those known in the art to be useful for attaching conjugate groups to compounds, such as the oligonucleotides provided herein.
• a bifunctional linking moiety comprises at least two functional groups. One of the functional groups is selected to bind to a particular site on a compound and the other is selected to bind to a conjugate group. Examples of functional groups used in a bifunctional linking moiety include but are not limited to electrophiles for reacting with nucleophilic groups and nucleophiles for reacting with electrophilic groups.
• bifunctional linking moieties comprise one or more groups selected from amino, hydroxyl, carboxylic acid, thiol, alkyl, alkenyl, and alkynyl.
• conjugate linkers include but are not limited to pyrrolidine, 8-amino-3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) and 6-aminohexanoic acid (AHEX or AHA).
• conjugate linkers include but are not limited to substituted or unsubstituted C 1 -C 10 alkyl, substituted or unsubstituted C 2 -C 10 alkenyl or substituted or unsubstituted C 2 -C 10 alkynyl, wherein a nonlimiting list of preferred substituent groups includes hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl and alkynyl.
• conjugate linkers comprise 1-10 linker-nucleosides. In certain embodiments, conjugate linkers comprise 1-5 linker-nucleosides.
• conjugate linkers comprise 1-3 linker- nucleosides. In certain embodiments, conjugate linkers comprise exactly 3 linker-nucleosides. In certain embodiments, conjugate linkers comprise the TCA motif. In certain embodiments, such linker-nucleosides are modified nucleosides. In certain embodiments such linker-nucleosides comprise a modified sugar moiety. In certain embodiments, linker- nucleosides are unmodified. In certain embodiments, linker-nucleosides comprise an optionally protected heterocyclic base selected from a purine, substituted purine, pyrimidine or substituted pyrimidine.
• a cleavable moiety is a nucleoside selected from uracil, thymine, cytosine, 4-N-benzoylcytosine, 5-methylcytosine, 4-N- benzoyl-5-methylcytosine, adenine, 6-N-benzoyladenine, guanine and 2-N-isobutyrylguanine. It is typically desirable for linker-nucleosides to be cleaved from the oligomeric compound after it reaches a target tissue. Accordingly, linker- nucleosides are typically linked to one another and to the remainder of the oligomeric compound through cleavable bonds. In certain embodiments, such cleavable bonds are phosphodiester bonds.
• linker-nucleosides are not considered to be part of the oligonucleotide. Accordingly, in embodiments in which an oligomeric compound comprises an oligonucleotide consisting of a specified number or range of linked nucleosides and/or a specified percent complementarity to a reference nucleic acid and the oligomeric compound also comprises a conjugate group comprising a conjugate linker comprising linker-nucleosides, those linker-nucleosides are not counted toward the length of the oligonucleotide and are not used in determining the percent complementarity of the oligonucleotide for the reference nucleic acid.
• an oligomeric compound may comprise (1) a modified oligonucleotide consisting of 8-30 nucleosides and (2) a conjugate group comprising 1-10 linker-nucleosides that are contiguous with the nucleosides of the modified oligonucleotide.
• the total number of contiguous linked nucleosides in such an oligomeric compound is more than 30.
• an oligomeric compound may comprise a modified oligonucleotide consisting of 8-30 nucleosides and no conjugate group. The total number of contiguous linked nucleosides in such an oligomeric compound is no more than 30.
• conjugate linkers comprise no more than 10 linker-nucleosides.
• conjugate linkers comprise no more than 5 linker- nucleosides. In certain embodiments, conjugate linkers comprise no more than 3 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 2 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 1 linker-nucleoside. In certain embodiments, it is desirable for a conjugate group to be cleaved from the oligonucleotide.
• conjugate linkers may comprise one or more cleavable moieties.
• a cleavable moiety is a cleavable bond.
• a cleavable moiety is a group of atoms comprising at least one cleavable bond.
• a cleavable moiety comprises a group of atoms having one, two, three, four, or more than four cleavable bonds.
• a cleavable moiety is selectively cleaved inside a cell or subcellular compartment, such as a lysosome.
• a cleavable moiety is selectively cleaved by endogenous enzymes, such as nucleases.
• a cleavable bond is selected from an amide, an ester, an ether, one or both esters of a phosphodiester, a phosphate ester, a carbamate, and a disulfide.
• a cleavable bond is one or both of the esters of a phosphodiester.
• a cleavable moiety comprises a phosphate or phosphodiester.
• the cleavable moiety is a phosphate linkage between an oligonucleotide and a conjugate moiety or conjugate group.
• a cleavable moiety comprises or consists of one or more linker-nucleosides. In certain such embodiments, the one or more linker-nucleosides are linked to one another and/or to the remainder of the oligomeric compound through cleavable bonds.
• cleavable bonds are unmodified phosphodiester bonds.
• a cleavable moiety is 2'-deoxynucleoside that is attached to either the 3' or 5'-terminal nucleoside of an oligonucleotide by a phosphate internucleoside linkage and covalently attached to the remainder of the conjugate linker or conjugate moiety by a phosphate or phosphorothioate linkage.
• the cleavable moiety is 2'-deoxyadenosine.
• a conjugate group has the general formula: wherein n is from 1 to 3, m is 0 when n is 1, m is 1 when n is 2 or greater, j is 1 or 0, and k is 1 or 0. In certain embodiments, n is 1, j is 1 and k is 0. In certain embodiments, n is 1, j is 0 and k is 1. In certain embodiments, n is 1, j is 1 and k is 1. In certain embodiments, n is 2, j is 1 and k is 0. In certain embodiments, n is 2, j is 0 and k is 1. In certain embodiments, n is 2, j is 1 and k is 1. In certain embodiments, n is 3, j is 1 and k is 0.
• conjugate groups comprise cell-targeting moieties that have at least one tethered ligand.
• cell-targeting moieties comprise two tethered ligands covalently attached to a branching group.
• cell-targeting moieties comprise three tethered ligands covalently attached to a branching group.
• the cell-targeting moiety targets neurons.
• the cell-targeting moiety targets a neurotransmitter receptor.
• the cell targeting moiety targets a neurotransmitter transporter.
• the cell targeting moiety targets a GABA transporter. See e.g., WO 2011/131693, WO 2014/064257.
• conjugate groups comprise cell-targeting moieties that have affinities for transferrin receptor (TfR) (also referred to herein as TfR1 and CD71).
• TfR transferrin receptor
• a conjugate group described herein comprises an anti-TfR1 antibody or fragment thereof.
• the conjugate group comprises a protein or peptide capable of binding TfR1.
• the conjugate group comprises an aptamer capable of binding TfR1.
• the anti-TfR1 antibody or fragment thereof can be any known in the art including but not limited to those described in WO 1991/004753; WO2013/103800; WO 2014/144060; WO 2016/081643; WO 2016/179257; WO 2016/207240; WO 2017/221883; WO 2018/129384; WO 2018/124121; WO 2019/151539; WO 2020/132584; WO 2020/028864; U.S.7,208,174; U.S.9,034,329; and U.S.10,550,188.
• a fragment of an anti-TfR1 antibody is F(ab') 2 , Fab, Fab', Fv, or scFv.
• the conjugate group comprises a protein or peptide capable of binding TfR1.
• the protein or peptide capable of binding TfR1 can be any known in the art including but not limited to those described in WO 2019/140050; WO 2020/037150; WO 2020/124032; and U.S.10,138,483.
• the conjugate group comprises an aptamer capable of binding TfR1.
• oligomeric compounds comprise one or more terminal groups. Examples of terminal groups include but are not limited to conjugate groups, capping groups, phosphate moieties, protecting groups, modified or unmodified nucleosides, and two or more nucleosides that are independently modified or unmodified. In some embodiments, oligomeric compounds comprise a stabilized 5’-phosphate.
• Stabilized 5’-phosphates include, but are not limited to 5’-phosphonates, including, but not limited to 5’-vinylphosphonates.
• terminal groups comprise one or more abasic sugar moieties and/or inverted nucleosides.
• terminal groups comprise one or more 2’-linked nucleosides or sugar moieties.
• the 2’-linked group is an abasic sugar moiety.
• antisense agents have antisense activity when they reduce or inhibit the amount or activity of a target nucleic acid by 25% or more in the standard cell assay. In certain embodiments, antisense agents selectively affect one or more target nucleic acid.
• antisense agents comprise a nucleobase sequence that hybridizes to one or more target nucleic acid, resulting in one or more desired antisense activity and does not hybridize to one or more non-target nucleic acid or does not hybridize to one or more non-target nucleic acid in such a way that results in significant undesired antisense activity.
• hybridization of an antisense agents or a portion of an antisense agent to a target nucleic acid results in recruitment of a protein that cleaves the target nucleic acid.
• certain antisense agents result in RNase H mediated cleavage of the 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.
• described herein are antisense agents comprising antisense oligomeric compounds comprising antisense oligonucleotidesthat are sufficiently “DNA-like” to elicit RNase H activity.
• one or more non- DNA-like nucleoside in the gap of a gapmer is tolerated.
• an antisense agent or a portion of an antisense agent is loaded into an RNA- induced silencing complex (RISC), ultimately resulting in cleavage of the target nucleic acid.
• RISC RNA- induced silencing complex
• certain antisense agents result in cleavage of the target nucleic acid by Argonaute.
• Antisense agents that are loaded into RISC are RNAi agents.
• RNAi agents may be double-stranded (siRNA or dsRNAi) or single-stranded (ssRNAi).
• hybridization of an antisense agent or portion thereof to a target nucleic acid does not result in recruitment of a protein that cleaves that target nucleic acid. In certain embodiments, hybridization of the antisense agent or portion thereof to the target nucleic acid results in alteration of splicing of the target nucleic acid. In certain embodiments, hybridization of an antisense agent or a portion thereof to a target nucleic acid results in inhibition of a binding interaction between the target nucleic acid and a protein or other nucleic acid. In certain embodiments, hybridization of an antisense agent or a portion thereof to a target nucleic acid results in alteration of translation of the target nucleic acid. Antisense activities may be observed directly or indirectly.
• 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.
• oligomeric compounds comprise or consist of an oligonucleotide comprising a region that is complementary to a target nucleic acid.
• the target nucleic acid is an endogenous RNA molecule.
• the target nucleic acid encodes a protein.
• the target nucleic acid is selected from: a mature mRNA and a pre-mRNA, including intronic, exonic and untranslated regions.
• the target RNA is a mature mRNA.
• the target nucleic acid is a pre- mRNA.
• the target region is entirely within an intron.
• the target region spans an intron/exon junction.
• the target region is at least 50% within an intron.
• the target nucleic acid is a non-coding RNA.
• the target non-coding RNA is selected from: a long non-coding RNA, a short non-coding RNA, an intronic RNA molecule.
• oligonucleotides are complementary to the target nucleic acid over the entire length of the oligonucleotide. In certain embodiments, oligonucleotides are 99%, 95%, 90%, 85%, or 80% complementary to the target nucleic acid. In certain embodiments, oligonucleotides are at least 80% complementary to the target nucleic acid over the entire length of the oligonucleotide and comprise a region that is 100% or fully complementary to a target nucleic acid. In certain embodiments, the region of full complementarity is from 6 to 20, 10 to 18, or 18 to 20 nucleobases in length.
• Gautschi et al J. Natl. Cancer Inst. 93:463-471, March 2001
• this oligonucleotide demonstrated potent anti-tumor activity in vivo. Maher and Dolnick (Nuc. Acid. Res.
• oligonucleotides 16:3341-3358, 1988) tested a series of tandem 14 nucleobase oligonucleotides, and 28 and 42 nucleobase oligonucleotides comprised of the sequence of two or three of the tandem oligonucleotides, respectively, for their ability to arrest translation of human DHFR in a rabbit reticulocyte assay.
• Each of the three 14 nucleobase oligonucleotides alone was able to inhibit translation, albeit at a more modest level than the 28 or 42 nucleobase oligonucleotides.
• oligonucleotides comprise one or more mismatched nucleobases relative to the target nucleic acid.
• the mismatch is specifically positioned within an oligonucleotide having a gapmer motif. In certain embodiments, the mismatch is at position 1, 2, 3, 4, 5, 6, 7, or 8 from the 5’-end of the gap region. In certain embodiments, the mismatch is at position 9, 8, 7, 6, 5, 4, 3, 2, 1 from the 3’-end of the gap region. In certain embodiments, the mismatch is at position 1, 2, 3, or 4 from the 5’-end of the wing region.
• oligomeric agents, oligomeric compounds, oligomeric duplexes, or antisense agents comprise or consist of an oligonucleotide comprising a region that is complementary to a target nucleic acid, wherein the target nucleic acid is a MECP2 nucleic acid.
• the MECP2 nucleic acid has the nucleobase sequence set forth in SEQ ID NO: 1 (GenBank Accession No. NC_000023.11 truncated from nucleosides 154019001 to 154101000) or SEQ ID NO: 2 (GenBank Accession No.
• contacting a cell with an oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent complementary to SEQ ID NO: 1 or SEQ ID NO: 2 reduces the amount of MECP2 RNA, and in certain embodiments reduces the amount of MECP2 protein.
• the oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent consists of a modified oligonucleotide.
• the oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent consists of a modified oligonucleotide and a conjugate group.
• contacting a cell with an oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent complementary to SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 2340 reduces the amount of MECP2 RNA in a cell.
• contacting a cell with an oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent complementary to SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 2340 reduces the amount of MECP2 protein in a cell.
• the cell is in vitro.
• contacting a cell in a subject with an oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent complementary to SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 2340 ameliorates one or more symptoms or hallmarks of a neurodegenerative disease or disorder associated with MECP2.
• the neurodegenerative disease or disorder associated with MECP2 is MECP duplication syndrome.
• the symptom or hallmark is any of autism, intellectual disability, motor dysfunction, hypotonia, global developmental delays, gastrointestinal symptoms, anxiety, epilepsy, recurrent respiratory tract infections, epileptic encephalopathy, and early death.
• administering the oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent reduces seizures, reduces or delays cognitive impairment, reduces or delays intellectual disabilities, reduces or delays symptoms of autism, reduces anxiety, or reduces gastrointestinal symptoms in the subject; or improves motor function, motor development, muscle tone, cognitive development, speech, or social skill development in the subject.
• an oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent complementary to SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 2340 is capable of reducing the detectable amount of MECP2 RNA in vitro by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% in the standard cell assay.
• an oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent complementary to SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 2340 is capable of reducing the detectable amount of MECP2 protein in vitro by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%.
• an oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent complementary to SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 2340 is capable of reducing the detectable amount of MECP2 RNA in vivo by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%.
• an oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent complementary to SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 2340 is capable of reducing the detectable amount of MECP2 protein in vivo by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%.
• an oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent complementary to SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 2340 is capable of reducing the detectable amount of MECP2 RNA in the CSF of an animal by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%.
• an oligomeric agent, oligomeric compound, oligomeric duplex, or antisense agent complementary to SEQ ID NO: 1, SEQ ID NO: 2, , or SEQ ID NO: 2340 is capable of reducing the detectable amount of MECP2 protein in the CSF of an animal by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%.
• oligomeric compounds comprise or consist of an oligonucleotide comprising a region that is complementary to a target nucleic acid, wherein the target nucleic acid is expressed in a pharmacologically relevant tissue.
• the pharmacologically relevant tissues are the brain and spinal cord.
• the target nucleic acid is expressed in a pharmacologically relevant cell.
• the pharmacologically relevant cell is a MECP2-expressing cell.
• the pharmacologically relevant cell is a neuron or glial cell.
• the pharmacologically relevant cell is a neuronal cell.
• the pharmacologically relevant cell is an astrocyte, an oligodendrocyte or a microglial cell. IV.
• Certain embodiments provided herein relate to methods of reducing or inhibiting MECP2 expression or activity, which can be useful for treating, preventing, or ameliorating a disease or disorder associated with overexpression of MECP2 in a subject, by administration of an oligomeric agent, oligomeric compound, modified oligonucleotide, or oligomeric duplex, any of which comprise a modified oligonucleotide having a nucleobase sequence complementary to a MECP2 nucleic acid.
• the disease or disorder associated with overexpression of MECP2 is a neurodegenerative disease or disorder.
• the neurodegenerative disease or disorder is MECP2 Duplication Syndrome.
• a method comprises administering to a subject an oligomeric agent, an oligomeric compound, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a MECP2 nucleic acid.
• the subject has or is at risk for developing a disease or disorder associated with MECP2.
• the subject has or is at risk for developing MECP2 Duplication Syndrome.
• a method of treating a neurodegenerative disease or disorder associated with MECP2 comprises administering to a subject a therapeutically effective amount of an oligomeric agent, an oligomeric compound, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to an MECP2 nucleic acid, thereby treating the subject.
• the subject has or is at risk for developing a neurodegenerative disease or disorder associated with MECP2.
• the disease or disorder is associated with an elevated level of MECP2 in the subject.
• the subject has or is at risk for developing MECP2 Duplication Syndrome.
• At least one symptom or hallmark of the neurodegenerative disease or disorder associated with MECP2 Duplication Syndrome is ameliorated.
• exemplary symptoms or hallmarks include, but are not limited to, autism, intellectual disability, motor dysfunction, hypotonia, global developmental delays, gastrointestinal symptoms, anxiety, epilepsy, recurrent respiratory tract infections, epileptic encephalopathy, and early death.
• a method of reducing expression of MECP2 nucleic acid, for example RNA, or reducing the expression of MECP2 protein in a cell comprises administering to the subject an oligomeric agent, an oligomeric compound, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to an MECP2 nucleic acid, thereby inhibiting expression of MECP2 nucleic acid in the subject.
• administering the oligomeric agent, the oligomeric compound, the oligomeric duplex, or the antisense agent inhibits expression of MECP2 in the brain or the spinal cord of the subject.
• the subject has or is at risk for developing a neurological disease or condition associated with MECP2.
• a method of inhibiting expression of MECP2 nucleic acid in a cell comprises contacting the cell with an oligomeric agent, an oligomeric compound, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a MECP2 nucleic acid, thereby inhibiting expression of MECP2 nucleic acid in the cell.
• the cell is a human cell.
• the cell is a brain cell.
• the cell is a neuron or a glial cell (e.g., an astrocyte, an oligodendrocyte, a microglial cell).
• the cell is obtained from a subject, e.g., a subject, that has or is at risk for developing a disease or disorder associated with MECP2.
• the cell is in a subject having or at risk for developing a disease or condition associated with MECP2, such as MECP2 Duplication Syndrome.
• a method of reducing expression of MECP2, for example RNA, or reducing the expression of MECP2 protein in a cell comprises contacting the cell with an oligomeric compound, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to an ATN1 nucleic acid.
• the subject has or is at risk for developing MECP2 Duplication Syndrome (MDS).
• MDS MECP2 Duplication Syndrome
• the subject has MDS.
• the cell is a neuron or glial cell.
• the cell is a human cell.
• Certain embodiments are drawn to an oligomeric agent, an oligomeric compound, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to an MECP2 nucleic acid, for use in treating a disease or disorder associated with elevated MECP2 signaling, or with over-expression of MECP2.
• the disease or disorder is MECP2 Duplication Syndrome.
• an oligomeric agent, an oligomeric compound, an oligomeric duplex, or an antisense agent is for use in improving a symptom or hallmark of a disease or condition associated with MECP2 Duplication Syndrome.
• the symptom or hallmark is selected from autism, intellectual disability, motor dysfunction, hypotonia, global developmental delays, gastrointestinal symptoms, anxiety, epilepsy, recurrent respiratory tract infections, epileptic encephalopathy, and early death.
• an oligomeric compound, a modified oligonucleotide, an oligomeric duplex, or an antisense agent is for use in reducing MECP2 expression in a subject.
• Certain embodiments are drawn to an oligomeric agent, an oligomeric compound, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to an MECP2 nucleic acid, for the manufacture or preparation of a medicament for treating a disease associated with MECP2.
• the disease is MECP2 Duplication Syndrome.
• an oligomeric agent, an oligomeric compound, an oligomeric duplex, or an antisense agent is for the manufacture or preparation of a medicament for improving symptoms or hallmarks associated with MECP2 Duplication Syndrome.
• the symptom or hallmark is selected from autism, intellectual disability, motor dysfunction, hypotonia, global developmental delays, gastrointestinal symptoms, anxiety, epilepsy, recurrent respiratory tract infections, epileptic encephalopathy, and early death.
• an oligomeric agent, an oligomeric compound, an oligomeric duplex, or an antisense agent is for the manufacture or preparation of a medicament for use in reducing MECP2 expression in a subject.
• the oligomeric agent, oligomeric compound, modified oligonucleotide, or oligomeric duplex can be any described herein. V.
• compositions comprising one or more oligomeric compounds.
• the one or more oligomeric compounds each comprise a modified oligonucleotide.
• the one or more oligomeric compounds each consists of a modified oligonucleotide.
• the pharmaceutical composition comprises a pharmaceutically acceptable diluent or carrier.
• a pharmaceutical composition comprises or consists of a sterile saline solution and one or more oligomeric compounds.
• the sterile saline is pharmaceutical grade saline.
• a pharmaceutical composition comprises or consists of one or more oligomeric compound and sterile water.
• the sterile water is pharmaceutical grade water.
• a pharmaceutical composition comprises or consists of one or more oligomeric compounds and phosphate-buffered saline (PBS).
• the sterile PBS is pharmaceutical grade PBS.
• a pharmaceutical composition comprises or consists of one or more oligomeric compounds and artificial cerebrospinal fluid (“artificial CSF” or “aCSF”).
• artificial cerebrospinal fluid is pharmaceutical grade artificial cerebrospinal fluid.
• a pharmaceutical composition comprises an oligomeric compound and PBS.
• a pharmaceutical composition consists of an oligomeric compound and PBS.
• a pharmaceutical composition consists essentially of an oligomeric compound and PBS.
• the PBS is pharmaceutical grade.
• a pharmaceutical composition comprises a modified oligonucleotide and PBS.
• a pharmaceutical composition consists of a modified oligonucleotide and PBS.
• a pharmaceutical composition consists essentially of a modified oligonucleotide and PBS.
• the PBS is pharmaceutical grade.
• a pharmaceutical composition comprises an oligomeric compound and artificial cerebrospinal fluid.
• a pharmaceutical composition consists of an oligomeric compound and artificial cerebrospinal fluid.
• a pharmaceutical composition consists essentially of an oligomeric compound and artificial cerebrospinal fluid.
• the artificial cerebrospinal fluid is pharmaceutical grade.
• a pharmaceutical composition comprises a modified oligonucleotide and aCSF.
• a pharmaceutical composition consists of a modified oligonucleotide and aCSF.
• a pharmaceutical composition consists essentially of a modified oligonucleotide and aCSF.
• the aCSF is pharmaceutical grade.
• aCSF comprises sodium chloride, potassium chloride, sodium dihydrogen phosphate dihydrate, sodium phosphate dibasic anhydrous, calcium chloride dihydrate, and magnesium chloride hexahydrate.
• the pH of an aCSF solution is modulated with a suitable pH- adjusting agent, for example, with acids such as hydrochloric acid and alkalis such as sodium hydroxide, to a range of from about 7.1-7.3, or to about 7.2.
• pharmaceutical compositions comprise one or more oligomeric compounds and one or more excipients.
• excipients are selected from water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylase, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose and polyvinylpyrrolidone.
• oligomeric compounds may be admixed with pharmaceutically acceptable active and/or inert substances for the preparation of pharmaceutical compositions or formulations. Compositions and methods for the formulation of pharmaceutical compositions depend on a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.
• compositions comprising an oligomeric compound encompass any pharmaceutically acceptable salts of the oligomeric compound, esters of the the oligomeric compound, or salts of such esters.
• pharmaceutical compositions comprising oligomeric compounds comprising one or more modified oligonucleotide upon administration to an subject, including a human subject, are 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 oligomeric compounds, prodrugs, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents.
• pharmaceutically acceptable salts comprise inorganic salts, such as monovalent or divalent inorganic salts.
• Suitable pharmaceutically acceptable salts include, but are not limited to, sodium, potassium, calcium, and magnesium salts.
• prodrugs comprise one or more conjugate group attached to an oligonucleotide, wherein the conjugate group is cleaved by endogenous nucleases within the body.
• oligomeric compounds are lyophilized and isolated as sodium salts.
• the sodium salt of an oligomeric compound is mixed with a pharmaceutically acceptable diluent.
• the pharmaceutically acceptable diluent comprises sterile saline, sterile water, PBS, or aCSF.
• the sodium salt of an oligomeric compound is mixed with PBS.
• the sodium salt of an oligomeric compound is mixed with aCSF. In certain embodiments, the sodium salt of the oligomeric compound is a sodium salt of a modified oligonucleotide.
• Lipid moieties have been used in nucleic acid therapies in a variety of methods. In certain such methods, the nucleic acid, such as an oligomeric compound, 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.
• 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.
• pharmaceutical compositions comprise 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, pharmaceutical compositions comprise one or more tissue-specific delivery molecules designed to deliver the one or more pharmaceutical agents comprising an oligomeric compound provided herein to specific tissues or cell types.
• compositions include liposomes coated with a tissue-specific antibody.
• pharmaceutical compositions comprise a co-solvent system.
• co-solvent systems comprise, for example, benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase.
• co-solvent systems are used for hydrophobic compounds.
• VPD co-solvent system 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.
• co-solvent systems may be varied considerably without significantly altering their solubility and toxicity characteristics.
• 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.
• pharmaceutical compositions are prepared for oral administration. In certain embodiments, pharmaceutical compositions are prepared for buccal administration.
• a pharmaceutical composition is prepared for administration by injection (e.g., intravenous, subcutaneous, intramuscular, intrathecal (IT), intracerebroventricular (ICV), etc.).
• a pharmaceutical composition comprises a carrier and is formulated in an aqueous solution, such as water or a physiologically compatible buffer such as Hanks's solution, Ringer's solution, or physiological saline buffer.
• other ingredients are included (e.g., ingredients that aid in solubility or serve as preservatives).
• injectable suspensions are prepared using appropriate liquid carriers, suspending agents and the like.
• compositions for injection are 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. Under certain conditions, certain compounds disclosed herein act as acids.
• aqueous solutions of such compounds exist in equilibrium among such forms.
• a phosphate linkage of an oligonucleotide in aqueous solution exists in equilibrium among free acid, anion and salt forms.
• compounds described herein are intended to include all such forms.
• certain oligonucleotides have several such linkages, each of which is in equilibrium.
• oligonucleotides in solution exist in an ensemble of forms at multiple positions all at equilibrium.
• the term “oligonucleotide” is intended to include all such forms.
• Drawn structures necessarily depict a single form.
• modified oligonucleotides or oligomeric compounds are in aqueous solution with sodium.
• modified oligonucleotides or oligomeric compounds are in PBS.
• modified oligonucleotides or oligomeric compounds are in water.
• the pH of the solution is adjusted with NaOH and/or HCl to achieve a desired pH.
• certain specific doses are described.
• a dose may be in the form of a dosage unit.
• a dose (or dosage unit) of a modified oligonucleotide or oligomeric compound in milligrams indicates the mass of the free acid form of the modified oligonucleotide or oligomeric compound.
• the free acid is in equilibrium with anionic and salt forms.
• the modified oligonucleotide or oligomeric compound exists as a solvent-free, sodium-acetate free, anhydrous, free acid.
• a modified oligonucleotide or an oligomeric compound may be partially or fully de-protonated and in association with sodium ions.
• the mass of the protons is nevertheless counted toward the weight of the dose, and the mass of the sodium ions is not counted toward the weight of the dose.
• a dose, or dosage unit, of 10 mg of Compound No.1435454 equals the number of fully protonated molecules that weighs 10 mg. This would be equivalent to 10.59 mg of solvent-free, sodium acetate-free, anhydrous sodiated Compound No.1435454.
• a modified oligonucleotide or oligomeric compound where a modified oligonucleotide or oligomeric compound is in a solution, such as aCSF, comprising sodium, potassium, calcium, and magnesium, the modified oligonucleotide or oligomeric compound may be partially or fully de-protonated and in association with sodium, potassium, calcium, and/or magnesium.
• the mass of the protons is nevertheless counted toward the weight of the dose, and the mass of the sodium, potassium, calcium, and magnesium ions is not counted toward the weight of the dose.
• an oligomeric compound comprises a conjugate group
• the mass of the conjugate group is included in calculating the dose of such oligomeric compound.
• nucleobases 10,858-10,885 of SEQ ID NO: 1 In certain embodiments, nucleobases 10,858-10,885 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 10,858-10,885 of SEQ ID NO: 1. In certain embodiments, the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length.
• oligomeric compounds or antisense oligonucleotides are gapmers.
• the gapmers are MOE gapmers.
• the MOE gapmers are 5-10-5 MOE gapmers.
• the sugar motif for the gapmers is (from 5’ to 3’): eeeeeddddddddddeeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 188, 673, 1893, 2012, 2031, 2104, 2233, and 2311 are complementary to a portion of nucleobases 10,858-10,885 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985840, 1434926, 1435030, 1435374, 1435535, 1436154, 1436207, and 1436353 are complementary to a portion of nucleobases 10,858-10,885 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 10,858-10,885 of SEQ ID NO: 1 achieve at least 68% reduction of MECP2 RNA in a standard cell assay. In certain embodiments, oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 10,858-10,885 of SEQ ID NO: 1 achieve an average of 84.5% reduction of MECP2 RNA in a standard cell assay. 2. Nucleobases 11,534-11,588 of SEQ ID NO: 1 In certain embodiments, nucleobases 11,534-11,588 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 11,534-11,588 of SEQ ID NO: 1. In certain embodiments, the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers.
• the sugar motif for the gapmers is (from 5’ to 3’) eeeeeddddddddddeeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’) soooossssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• the nucleobase sequences of SEQ ID NOs: 35, 342, 419, 496, 573, 870, 975, 1030, and 1130 are complementary to a portion of nucleobases 11,534-11,588 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985842, 985843, 985844, 985845, 985846, 1434938, 1435167, 1435529, and 1435649 are complementary to a portion of nucleobases 11,534-11,588 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 11,534-11,588 of SEQ ID NO: 1 achieve at least 58% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 11,534-11,588 of SEQ ID NO: 1 achieve an average of 84.3% reduction of MECP2 RNA in a standard cell assay.
• Nucleobases 11,597-11,620 of SEQ ID NO: 1 In certain embodiments, nucleobases 11,597-11,620 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 11,597-11,620 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’) eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’) soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 1589, 1652, 1780, 1823, and 1882 are complementary to a portion of nucleobases 11,597-11,620 of SEQ ID NO: 1.
• the nucleobase sequences of Compound Nos: 1435121, 1435143, 1435440, 1435634, and 1436258 are complementary to a portion of nucleobases 11,597-11,620 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 11,597-11,620 of SEQ ID NO: 1 achieve at least 76% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 11,597-11,620 of SEQ ID NO: 1 achieve an average of 84% reduction of MECP2 RNA in a standard cell assay. 4.
• Nucleobases 12,936-12,962 of SEQ ID NO: 1 In certain embodiments, nucleobases 12,936-12,962 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 12,936-12,962 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 964, 1058, 1106, 1192, and 1276 are complementary to a portion of nucleobases 12,936-12,962 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 1434953, 1435202, 1435393, 1435409, and 1435737 are complementary to a portion of nucleobases 12,936-12,962 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 12,936-12,962 of SEQ ID NO: 1 achieve at least 82% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 12,936-12,962 of SEQ ID NO: 1 achieve an average of 88.2% reduction of MECP2 RNA in a standard cell assay. 5.
• Nucleobases 13,599-13,641 of SEQ ID NO: 1 In certain embodiments, nucleobases 13,599-13,641 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 13,599-13,641 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 344, 1303, 1333, 1407, 1545, 1561, 1724, and 1648 are complementary to a portion of nucleobases 13,599-13,641 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985858, 1434886, 1434892, 1434988, 1435017, 1435123, 1435927, and 1436211 are complementary to a portion of nucleobases 13,599-13,641 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 13,599-13,641 of SEQ ID NO: 1 achieve at least 67% reduction of MECP2 RNA in a standard cell assay. In certain embodiments, oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 13,599-13,641 of SEQ ID NO: 1 achieve an average of 87.9% reduction of MECP2 RNA in a standard cell assay. 6. Nucleobases 13,669-13,711 of SEQ ID NO: 1 In certain embodiments, nucleobases 13,669-13,711 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 13,669-13,711 of SEQ ID NO: 1. In certain embodiments, the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers.
• the sugar motif for the gapmers is (from 5’ to 3’): eeeeeddddddddddeeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooossssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• the nucleobase sequences of SEQ ID NOs: 421, 663, 765, 835, 912, 990, 1042, 1096, and 2291 are complementary to a portion of nucleobases 13,669-13,711 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985859, 1434822, 1435372, 1435404, 1435762, 1435891, 1435913, 1435934, and 1436156 are complementary to a portion of nucleobases 13,669-13,711 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 13,669-13,711 of SEQ ID NO: 1 achieve at least 61% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 13,669-13,711 of SEQ ID NO: 1 achieve an average of 79.1% reduction of MECP2 RNA in a standard cell assay.
• Nucleobases 14,716-14,746 of SEQ ID NO: 1 In certain embodiments, nucleobases 14,716-14,746 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 14,716-14,746 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 191, 268, 345, 422, 499, 1335, 1425, 1539, 1573, and 1705 are complementary to a portion of nucleobases 14,716-14,746 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985864, 985865, 985866, 985867, 985868, 1435005, 1435124, 1435310, 1436093, and 1436367 are complementary to a portion of nucleobases 14,716-14,746 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 14,716-14,746 of SEQ ID NO: 1 achieve at least 57% reduction of MECP2 RNA in a standard cell assay. In certain embodiments, oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 14,716-14,746 of SEQ ID NO: 1 achieve an average of 76.1% reduction of MECP2 RNA in a standard cell assay. 8. Nucleobases 15,883-15,905 of SEQ ID NO: 1 In certain embodiments, nucleobases 15,883-15,905 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 15,883-15,905 of SEQ ID NO: 1. In certain embodiments, the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers.
• the sugar motif for the gapmers is (from 5’ to 3’): eeeeeddddddddddeeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooossssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• the nucleobase sequences of SEQ ID NOs: 840, 914, 977, and 1085 are complementary to a portion of nucleobases 15,883-15,905 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 1435682, 1435914, 1435974, and 1436202 are complementary to a portion of nucleobases 15,883-15,905 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 15,883-15,905 of SEQ ID NO: 1 achieve at least 85% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 15,883-15,905 of SEQ ID NO: 1 achieve an average of 94.8% reduction of MECP2 RNA in a standard cell assay.
• Nucleobases 16,362-16,396 of SEQ ID NO: 1 In certain embodiments, nucleobases 16,362-16,396 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 16,362-16,396 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 346, 1954, 2046, 2135, and 2183 are complementary to a portion of nucleobases 16,362-16,396 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985874, 1435003, 1435056, 1435298, and 1435688 are complementary to a portion of nucleobases 16,362-16,396 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 16,362-16,396 of SEQ ID NO: 1 achieve at least 64% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 16,362-16,396 of SEQ ID NO: 1 achieve an average of 88.8% reduction of MECP2 RNA in a standard cell assay. 10.
• Nucleobases 18,941-18,975 of SEQ ID NO: 1 In certain embodiments, nucleobases 18,941-18,975 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 18,941-18,975 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 580, 1806, 1869, 1949, 2054, 2111, and 2199 are complementary to a portion of nucleobases 18,941-18,975 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985901, 1434874, 1434934, 1435116, 1435198, 1435424, and 1435426 are complementary to a portion of nucleobases 18,941- 18,975 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 18,941-18,975 of SEQ ID NO: 1 achieve at least 65% reduction of MECP2 RNA in a standard cell assay. In certain embodiments, oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 18,941-18,975 of SEQ ID NO: 1 achieve an average of 91% reduction of MECP2 RNA in a standard cell assay. 11. Nucleobases 19,046-19,091 of SEQ ID NO: 1 In certain embodiments, nucleobases 19,046-19,091 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 19,046-19,091 of SEQ ID NO: 1. In certain embodiments, the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers.
• the sugar motif for the gapmers is (from 5’ to 3’): eeeeeddddddddddeeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooossssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• the nucleobase sequences of SEQ ID NOs: 1428, 1518, 1591, 1677, 1736, 1790, 1914, 2016, 2045, 2161, 2189, and 2313 are complementary to a portion of nucleobases 19,046-19,091 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 1434868, 1435190, 1435276, 1435308, 1435328, 1435475, 1435622, 1435650, 1435969, 1436193, 1436230, and 1436403 are complementary to a portion of nucleobases 19,046-19,091 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 19,046-19,091 of SEQ ID NO: 1 achieve at least 62% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 19,046-19,091 of SEQ ID NO: 1 achieve an average of 80% reduction of MECP2 RNA in a standard cell assay. 12.
• Nucleobases 20,216-20,271 of SEQ ID NO: 1 In certain embodiments, nucleobases 20,216-20,271 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 20,216-20,271 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 428, 1710, 1741, 1834, 1904, 1953, 2062, 2149, and 2175 are complementary to a portion of nucleobases 20,216-20,271 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985915, 1434860, 1434986, 1435359, 1435559, 1435747, 1435855, 1435956, and 1436440 are complementary to a portion of nucleobases 20,216-20,271 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 20,216-20,271 of SEQ ID NO: 1 achieve at least 75% reduction of MECP2 RNA in a standard cell assay. In certain embodiments, oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 20,216-20,271 of SEQ ID NO: 1 achieve an average of 88.2% reduction of MECP2 RNA in a standard cell assay. 13. Nucleobases 21,505-21,532 of SEQ ID NO: 1 In certain embodiments, nucleobases 21,505-21,532 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 21,505-21,532 of SEQ ID NO: 1. In certain embodiments, the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers.
• the sugar motif for the gapmers is (from 5’ to 3’): eeeeeddddddddddeeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooossssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• the nucleobase sequences of SEQ ID NOs: 430, 650, 733, 817, 2071, 2134, 2224, and 2316 are complementary to a portion of nucleobases 21,505-21,532 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985930, 1435139, 1435251, 1435453, 1435687, 1435800, 1435885, and 1436303 are complementary to a portion of nucleobases 21,505-21,532 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 21,505-21,532 of SEQ ID NO: 1 achieve at least 73% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 21,505-21,532 of SEQ ID NO: 1 achieve an average of 85% reduction of MECP2 RNA in a standard cell assay. 14.
• Nucleobases 21,945-21,976 of SEQ ID NO: 1 In certain embodiments, nucleobases 21,945-21,976 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 21,945-21,976 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 46, 653, 770, 831, 1962, 2055, 2157, 2186, and 2327 are complementary to a portion of nucleobases 21,945-21,976 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985933, 1435150, 1435185, 1435243, 1435431, 1435756, 1436047, 1436210, and 1436478 are complementary to a portion of nucleobases 21,945-21,976 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 21,945-21,976 of SEQ ID NO: 1 achieve at least 58% reduction of MECP2 RNA in a standard cell assay. In certain embodiments, oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 21,945-21,976 of SEQ ID NO: 1 achieve an average of 85.2% reduction of MECP2 RNA in a standard cell assay. 15. Nucleobases 23,689-23,713 of SEQ ID NO: 1 In certain embodiments, nucleobases 23,689-23,713 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 23,689-23,713 of SEQ ID NO: 1. In certain embodiments, the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers.
• the sugar motif for the gapmers is (from 5’ to 3’): eeeeeddddddddddeeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooossssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• the nucleobase sequences of SEQ ID NOs: 278, 1687, 1756, 1855, 1932, and 1952 are complementary to a portion of nucleobases 23,689-23,713 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985943, 1434976, 1435679, 1435846, 1436265, and 1436330 are complementary to a portion of nucleobases 23,689-23,713 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 23,689-23,713 of SEQ ID NO: 1 achieve at least 76% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 23,689-23,713 of SEQ ID NO: 1 achieve an average of 89.3% reduction of MECP2 RNA in a standard cell assay. 16.
• Nucleobases 24,791-24,833 of SEQ ID NO: 1 In certain embodiments, nucleobases 24,791-24,833 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 24,791-24,833 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 434, 1647, 1749, and 1801 are complementary to a portion of nucleobases 24,791-24,833 of SEQ ID NO: 1.
• the nucleobase sequences of Compound Nos: 985961, 1435051, 1435091, and 1435574 are complementary to a portion of nucleobases 24,791-24,833 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 24,791-24,833 of SEQ ID NO: 1 achieve at least 69% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 24,791-24,833 of SEQ ID NO: 1 achieve an average of 79.8% reduction of MECP2 RNA in a standard cell assay. 17.
• Nucleobases 24,901-24,930 of SEQ ID NO: 1 In certain embodiments, nucleobases 24,901-24,930 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 24,901-24,930 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 635, 760, 807, and 2293 are complementary to a portion of nucleobases 24,901-24,930 of SEQ ID NO: 1.
• the nucleobase sequences of Compound Nos: 1434808, 1435218, 1435824, and 1436028 are complementary to a portion of nucleobases 24,901-24,930 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 24,901-24,930 of SEQ ID NO: 1 achieve at least 83% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 24,901-24,930 of SEQ ID NO: 1 achieve an average of 84.5% reduction of MECP2 RNA in a standard cell assay. 18.
• Nucleobases 24,970-24,995 of SEQ ID NO: 1 In certain embodiments, nucleobases 24,970-24,995 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 24,970-24,995 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 509, 1769, 1837, 1897, 1964, 2026, and 2150 are complementary to a portion of nucleobases 24,970-24,995 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 985962, 1434946, 1435273, 1435478, 1435902, 1435958, and 1436004 are complementary to a portion of nucleobases 24,970- 24,995 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 24,970-24,995 of SEQ ID NO: 1 achieve at least 71% reduction of MECP2 RNA in a standard cell assay. In certain embodiments, oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 24,970-24,995 of SEQ ID NO: 1 achieve an average of 86.1% reduction of MECP2 RNA in a standard cell assay. 19.
• nucleobases 32,385-32,414 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 32,385-32,414 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length.
• oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers.
• the MOE gapmers are 5-10-5 MOE gapmers.
• the sugar motif for the gapmers is (from 5’ to 3’): eeeeeddddddddddeeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooossssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• the nucleobase sequences of SEQ ID NOs: 441, 919, 944, 1034, 1159, 1232, 1270, and 1361 are complementary to a portion of nucleobases 32,385-32,414 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 986016, 1434812, 1435204, 1435287, 1435503, 1436016, 1436137, and 1436175 are complementary to a portion of nucleobases 32,385-32,414 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 32,385-32,414 of SEQ ID NO: 1 achieve at least 63% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 32,385-32,414 of SEQ ID NO: 1 achieve an average of 77.5% reduction of MECP2 RNA in a standard cell assay.
• Nucleobases 32,447-32,508 of SEQ ID NO: 1 In certain embodiments, nucleobases 32,447-32,508 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 32,447-32,508 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 699, 1774, 1847, 1867, 1983, 2044, 2125, 2241, and 2312 are complementary to a portion of nucleobases 32,447-32,508 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 1434836, 1435240, 1435495, 1435763, 1436075, 1436111, 1436217, 1436232, and 1436289 are complementary to a portion of nucleobases 32,447-32,508 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 32,447-32,508 of SEQ ID NO: 1 achieve at least 67% reduction of MECP2 RNA in a standard cell assay. In certain embodiments, oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 32,447-32,508 of SEQ ID NO: 1 achieve an average of 84.6% reduction of MECP2 RNA in a standard cell assay. 21.
• nucleobases 32,588-32,671 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 32,588-32,671 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length.
• oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers.
• the MOE gapmers are 5-10-5 MOE gapmers.
• the sugar motif for the gapmers is (from 5’ to 3’): eeeeeddddddddddeeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooossssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 57, 134, 211, 516, 595, 640, 751, 795, 931, 980, 1073, 1120, 1197, 1266, 1341, 1448, 1500, 1582, 1663, 1722, 1814, 1881, and 2320 are complementary to a portion of nucleobases 32,588-32,671 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 986017, 986018, 986019, 986020, 986021, 1434897, 1434978, 1435012, 1435088, 1435101, 1435118, 1435267, 1435319, 1435334, 1435366, 1435412, 1435454, 1435755, 1435757, 1435879, 1435987, 1436284, and 1436337 are complementary to a portion of nucleobases 32,588-32,671 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 32,588-32,671 of SEQ ID NO: 1 achieve at least 44% reduction of MECP2 RNA in a standard cell assay. In certain embodiments, oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 32,588-32,671 of SEQ ID NO: 1 achieve an average of 81.1% reduction of MECP2 RNA in a standard cell assay. 22.
• nucleobases 35,116-35,158 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 35,116-35,158 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length.
• oligomeric compounds or antisense oligonucleotides are gapmers.
• the gapmers are MOE gapmers.
• the MOE gapmers are 5-10-5 MOE gapmers.
• the sugar motif for the gapmers is (from 5’ to 3’): eeeeeddddddddddeeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooossssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• the nucleobase sequences of SEQ ID NOs: 599, 1070, 1145, 1210, 1320, 1402, and 1427 are complementary to a portion of nucleobases 35,116-35,158 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 986050, 1435325, 1435773, 1435831, 1435930, 1436357, and 1436420 are complementary to a portion of nucleobases 35,116- 35,158 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 35,116-35,158 of SEQ ID NO: 1 achieve at least 60% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 35,116-35,158 of SEQ ID NO: 1 achieve an average of 86.4% reduction of MECP2 RNA in a standard cell assay.
• Nucleobases 43,248-43,273 of SEQ ID NO: 1 In certain embodiments, nucleobases 43,248-43,273 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 43,248-43,273 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 527, 1910, 1982, 2086, 2103, and 2200 are complementary to a portion of nucleobases 43,248-43,273 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 986111, 1434901, 1435434, 1435749, 1435870, and 1436041 are complementary to a portion of nucleobases 43,248-43,273 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 43,248-43,273 of SEQ ID NO: 1 achieve at least 68% reduction of MECP2 RNA in a standard cell assay. In certain embodiments, oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 43,248-43,273 of SEQ ID NO: 1 achieve an average of 82.3% reduction of MECP2 RNA in a standard cell assay. 24.
• nucleobases 43,863-43,923 of SEQ ID NO: 1 comprise a hotspot region.
• oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 43,863-43,923 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length.
• oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers.
• the MOE gapmers are 5-10-5 MOE gapmers.
• the sugar motif for the gapmers is (from 5’ to 3’): eeeeeddddddddddeeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooossssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• the nucleobase sequences of SEQ ID NOs: 454, 719, 834, 936, 1004, 1045, 1172, 1176, 1324, and 1391 are complementary to a portion of nucleobases 43,863-43,923 of SEQ ID NO: 1.
• nucleobase sequences of Compound Nos: 986118, 1434824, 1434955, 1435458, 1435906, 1436182, 1436206, 1436404, 1436436, and 1436474 are complementary to a portion of nucleobases 43,863-43,923 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 43,863-43,923 of SEQ ID NO: 1 achieve at least 62% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 43,863-43,923 of SEQ ID NO: 1 achieve an average of 79.3% reduction of MECP2 RNA in a standard cell assay.
• Nucleobases 64,179-64,202 of SEQ ID NO: 1 In certain embodiments, nucleobases 64,179-64,202 of SEQ ID NO: 1 comprise a hotspot region. In certain embodiments, oligomeric compounds or antisense oligonucleotides are complementary to a portion of nucleobases 64,179-64,202 of SEQ ID NO: 1.
• the oligomeric compounds or antisense oligonucleotides are 20 nucleobases in length. In certain embodiments, oligomeric compounds or antisense oligonucleotides are gapmers. In certain embodiments, the gapmers are MOE gapmers. In certain embodiments, the MOE gapmers are 5-10-5 MOE gapmers. In certain embodiments, the sugar motif for the gapmers is (from 5’ to 3’): eeeeedddddddddddeeee, wherein each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety and each “e” represents a 2’-MOE sugar moiety.
• the internucleoside linkages of the oligomeric compounds or antisense oligonucleotides are phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages.
• the internucleoside linkage motif for the gapmers is (from 5’ to 3’): soooosssssssssooss, wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage.
• nucleobase sequences of SEQ ID NOs: 472, 1933, 2002, 2023, and 2144 are complementary to a portion of nucleobases 64,179-64,202 of SEQ ID NO: 1.
• the nucleobase sequences of Compound Nos: 986259, 1434900, 1435924, 1436130, and 1436301 are complementary to a portion of nucleobases 64,179-64,202 of SEQ ID NO: 1.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 64,179-64,202 of SEQ ID NO: 1 achieve at least 64% reduction of MECP2 RNA in a standard cell assay.
• oligomeric compounds or antisense oligonucleotides complementary to a portion of nucleobases 64,179-64,202 of SEQ ID NO: 1 achieve an average of 80% reduction of MECP2 RNA in a standard cell assay.
• Nonlimiting disclosure and incorporation by reference Each of the literature and patent publications listed herein is incorporated by reference in its entirety. 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.
• GenBank accession numbers, and the like recited in the present application is incorporated herein by reference in its entirety.
• nucleobase sequence of a SEQ ID NO describes only the nucleobase sequence. Accordingly, absent additional description, such description of compounds by reference to a nucleobase sequence of a SEQ ID NO does not limit sugar or internucleoside linkage modifications or presence or absence of additional substituents such as a conjugate group. Further, absent additional description, the nucleobases of a compound “having the nucleobase sequence of” a SEQ ID NO include such compounds having modified forms of the identified nucleobases as described herein.
• an oligonucleotide comprising a nucleoside comprising a 2’-OH sugar moiety and a thymine base could be described as a DNA having a modified sugar moiety (2’-OH in place of one 2’-H of DNA) or as an RNA having a modified base (thymine (methylated uracil) in place of a uracil of RNA); and certain nucleic acid compounds described herein comprise one or more nucleosides comprising modified sugar moieties having 2’-substituent(s) that are neither OH nor H.
• labeling such nucleic acid compounds “RNA” or “DNA” does not alter or limit the description of such nucleic acid compounds.
• nucleic acid sequences provided herein are intended to encompass nucleic acids containing any combination of natural or modified RNA and/or DNA, unless otherwise stated, including, but not limited to such nucleic acids having modified nucleobases.
• an oligomeric compound having the nucleobase sequence “ATCGATCG” encompasses any oligomeric compounds having such nucleobase sequence, whether modified or unmodified, including, but not limited to, such compounds comprising RNA bases, such as those having sequence “AUCGAUCG” and those having some DNA bases and some RNA bases such as “AUCGATCG” and oligomeric compounds having other modified nucleobases, such as “AT m CGAUCG,” wherein m C indicates a cytosine base comprising a methyl group at the 5- position.
• nucleobase sequence of SEQ ID NO: X refers only to the sequence of nucleobases in that SEQ ID NO.: X, independent of any sugar or internucleoside linkage modifications also described in such SEQ ID.
• Certain compounds described herein e.g., modified oligonucleotides
• the chemical notation of “A es T ko m C ez G ds C” indicates a compound wherein the first nucleoside comprises a 2’-MOE sugar moiety (indicated by the “e” subscript) and an unmodified adenine nucleobase linked to the second nucleoside via a phosphorothioate linkage (indicated by the “s” subscript); the second nucleoside comprises a cEt sugar moiety (indicated by the “k” subscript) and an unmodified thymine nucleobase linked to the third nucleoside via a phosphodiester linkage (indicated by the “o” subscript); the third nucleoside comprises a 2’-MOE sugar moiety and a 5-methyl modified cytosine nucleobase (indicated by the “m” superscript) linked to the fourth nucleoside via a mesylphosphoramidate linkage (indicated by the “z” subscript); the
• “A es T ko m C ez G ds C” indicates a compound wherein the first nucleoside comprises a 2’-MOE sugar moiety (indicated by the “e” subscript) and an unmodified adenine nucleobase linked to the second nucleoside via a phosphorothioate linkage (indicated by the “s” subscript); the second nucleoside comprises a cEt sugar moiety (indicated by the “k” subscript) and an unmodified thymine nucleobase linked to the third nucleoside via a phosphodiester linkage (indicated by the “o” subscript); the third nucleoside comprises a 2’-MOE sugar moiety and a 5-methyl modified cytosine nucleobase (indicated by the “m” superscript) linked to the fourth nucleoside via a mesylphosphorami
• sugar, internucleoside linkage, and nucleobase modifications may be indicated within a nucleotide or nucleobase sequence (e.g., by superscript or subscript, as shown above) or may be indicated in text accompanying a sequence (e.g., in separate text that appears within or above or below a table of compounds).
• each nucleobase, sugar, and internucleoside linkage of such a specific compound includes only the modifications indicated in the drawn chemical structure.
• drawn compounds may exist in equilibrium between tautomeric forms and/or as salts in equilibrium with protonated or ionic forms. Drawn structures are intended to capture all such forms of such compounds.
• Isotopic substitutions encompassed by the compounds herein include but are not limited to: 2 H or 3 H in place of 1 H, 13 C or 14 C in place of 12 C, 15 N in place of 14 N, 17 O or 18 O in place of 16 O, and 33 S, 34 S, 35 S, or 36 S in place of 32 S.
• non-radioactive isotopic substitutions may impart new properties on the oligomeric compound that are beneficial for use as a therapeutic or research tool.
• radioactive isotopic substitutions may make the compound suitable for research or diagnostic purposes such as imaging.
• oligonucleotide having a particular motif provides reasonable support for additional oligonucleotides having the same or similar motif.
• a particular high- affinity modification appears at a particular position
• other high-affinity modifications at the same position are considered suitable, unless otherwise indicated.
• Example 1 Effect of 5-10-5 MOE gapmers complementary to human MECP2 RNA in vitro, single dose
• Modified oligonucleotides complementary to a human MECP2 nucleic acid were designed and tested for their single dose effects on MECP2 RNA in vitro. The modified oligonucleotides were tested in a series of experiments that had the same culture conditions.
• the modified oligonucleotides in the tables below are 5-10-5 MOE gapmers with mixed PO/PS linkages.
• the modified oligonucleotides in the tables below are 20 nucleosides in length, wherein the sugar motif for the modified oligonucleotides is (from 5’ to 3’): eeeeeddddddddddeeeee; wherein each “e” represents a 2’-MOE ribosyl sugar moiety and each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety.
• the internucleoside linkage motif for the modified oligonucleotides is (from 5’ to 3’): soooossssssssooss; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester linkage. Each cytosine residue is a 5-methylcytosine.
• Each modified oligonucleotide listed in the tables below is 100% complementary to SEQ ID NO: 1 (the complement of GenBank Accession No. NC_000023.11 truncated from nucleosides 154019001 to 154101000), to SEQ ID NO: 2 (GenBank Accession No. NM_004992.3), or to both.
• “Start site” indicates the 5’-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. “Stop site” indicates the 3’-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. ‘N/A’ indicates that the modified oligonucleotide is not 100% complementary to that particular target nucleic acid sequence.
• A431 cells were treated with modified oligonucleotide at a concentration of 4,000 nM by free uptake at a density of 10,000 cells per well. After a treatment period of approximately 48 hours, total RNA was isolated from the cells and MECP2 RNA levels were measured by quantitative real-time RT-PCR.
• MECP2 RNA levels were measured by human primer-probe set RTS37209 (forward sequence CAAGGCCAAACAGAGAGGA, designated herein as SEQ ID NO: 3; reverse sequence TTGTCAGAGCCCTACCCATA, designated herein as SEQ ID NO: 4; probe sequence AGAATAAAGGCAGCTGTTGTCTCTTCTCC, designated herein as SEQ ID NO: 5).
• MECP2 RNA levels were normalized to total RNA content, as measured by RIBOGREEN®. Reduction of MECP2 RNA is presented in the tables below as percent MECP2 RNA relative to the amount of MECP2 RNA in untreated control cells (% UTC).
• the values marked with a “ ⁇ ” indicate that the modified oligonucleotide is complementary to the amplicon region of the primer probe set. Additional assays may be used to measure the potency and efficacy of the modified oligonucleotides complementary to the amplicon region. Each separate experiment described in this example is identified by an Assay Identification letter in the table column labeled “AID”.
• MECP2 RNA levels were measured by quantitative real-time RTPCR.
• MECP2 RNA levels were measured by human primer-probe set RTS37209 (described herein above).
• MECP2 RNA levels were normalized to total RNA content, as measured by RIBOGREEN®. Reduction of MECP2 RNA is presented in the table below as percent MECP2 RNA relative to the amount of MECP2 RNA in untreated control cells (% UTC). AID refers to Analysis ID.
• the modified oligonucleotide in the table below is a 5-10-5 MOE gapmer with mixed PO/PS linkages.
• the modified oligonucleotide in the table below is 20 nucleosides in length, wherein the sugar motif for the modified oligonucleotide is (from 5’ to 3’): eeeeeddddddddddeeeee; wherein each “e” represents a 2’-MOE ribosyl sugar moiety and each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety.
• the internucleoside linkage motif for the modified oligonucleotide is (from 5’ to 3’): soooossssssssooss; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester linkage. Each cytosine residue is a 5-methylcytosine.
• the modified oligonucleotide listed in the table below is 100% complementary to SEQ ID NO: 2340 (the complement of GenBank Accession No. NT_167198.1 truncated from nucleosides 4203000 to 4283000).
• “Start site” indicates the 5’-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. “Stop site” indicates the 3’-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence.
• A431 cells were treated with modified oligonucleotide at a concentration of 4,000 nM using free uptake at a density of 10,000 cells per well. After a treatment period of approximately 48 hours, total RNA was isolated from the cells and MECP2 RNA levels were measured by quantitative real-time RTPCR. MECP2 RNA levels were measured by human primer-probe set RTS37209 (described herein above).
• MECP2 RNA levels were normalized to total RNA content, as measured by RIBOGREEN®. Reduction of MECP2 RNA is presented in the table below as percent MECP2 RNA relative to the amount of MECP2 RNA in untreated control cells (% UTC). Each separate experiment described in this example is identified by an Assay Identification letter in the table column labeled “AID”.
• RNA was isolated from the cells and MECP2 RNA levels were measured by quantitative real-time RTPCR.
• Human MECP2 primer-probe set RTS37209 (described herein above) was used to measure RNA levels as described above.
• MECP2 RNA levels were normalized to total RNA content, as measured by RIBOGREEN®. Reduction of MECP2 RNA is presented in the tables below as percent MECP2 RNA, relative to untreated control cells (% UTC).
• the half maximal inhibitory concentration (IC 50 ) of each modified oligonucleotide was calculated using a linear regression on a log/linear plot of the data in Excel and is also presented in the tables below. Each experiment is presented in a separate table.
• oligonucleotides complementary to a human MECP2 RNA were designed as described in the tables below. “Start site” indicates the 5’-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. “Stop site” indicates the 3’-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence.
• Each modified oligonucleotide listed in the tables below is 100% complementary to SEQ ID NO: 1 (described herein above), to SEQ ID NO: 2 (described herein above), or to both. ‘N/A’ indicates that the modified oligonucleotide is not 100% complementary to that particular target nucleic acid sequence.
• the modified oligonucleotides in the table below are 20 nucleosides in length, wherein the sugar motif for the modified oligonucleotides is (from 5’ to 3’): eeeeeddddddddddeeeee; wherein each “e” represents a 2’-MOE ribosyl sugar moiety and each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety.
• the internucleoside linkage motif for the modified oligonucleotides is (from 5’ to 3’): soooossssssssooss; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester linkage.
• Each cytosine residue is a 5-methylcytosine.
• the internucleoside linkage motif for the modified oligonucleotides is (from 5’ to 3’): sooosssssssooss; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester linkage.
• Each cytosine residue is a 5-methylcytosine.
• mice received a single ICV bolus injection of either 350 ⁇ g or 500 ⁇ g of modified oligonucleotide as specified in the tables below.
• a group of 2-4 mice received a single ICV bolus injection with PBS as a negative control.
• Two weeks post treatment mice were sacrificed and RNA was extracted from cortical brain tissue and spinal cord for quantitative real-time RTPCR analysis of RNA expression of MECP2 using human primer probe set RTS4253 (forward sequence TGAAGGAGTCTTCTATCCGATCTGT, designated herein as SEQ ID NO: 6; reverse sequence CACTTCCTTGACCTCGATGCT, designated herein as SEQ ID NO: 7; probe sequence AGACCGTACTCCCCATCAAGAAGCGC, designated herein as SEQ ID NO: 8) or human primer probe set RTS37209 (described herein above).
• RTS4253 forward sequence TGAAGGAGTCTTCTATCCGATCTGT, designated herein as SEQ ID NO: 6
• MECP2 RNA levels were normalized to mouse GAPDH.
• Mouse GAPDH was amplified using primer probe set mGapdh_LTS00102 (forward sequence GGCAAATTCAACGGCACAGT, designated herein as SEQ ID NO: 9; reverse sequence GGGTCTCGCTCCTGGAAGAT, designated herein as SEQ ID NO: 10; probe sequence AAGGCCGAGAATGGGAAGCTTGTCATC, designated herein as SEQ ID NO: 11).
• Results are presented as percent human MECP2 RNA relative to the amount of MECP2 RNA in PBS treated animals, (% control).
• mice received a single ICV bolus injection of modified oligonucleotide at various concentrations defined in the table below.
• a group of 4 mice received PBS as a negative control.
• mice were sacrificed, and RNA was extracted from cortical brain tissue, spinal cord, hippocampus, and cerebellum for quantitative real-time RT-PCR analysis to measure the amount of MECP2 RNA using human primer probe set RTS4253 (described herein above).
• MECP2 RNA levels were normalized to mouse GAPDH.
• Mouse GAPDH was amplified using primer probe set mGapdh_2 (described herein above). Results are presented as percent human MECP2 RNA relative to the amount of MECP2 RNA in PBS treated animals, (% control).
• Compound No.1435454 is a modified oligonucleotide having a nucleobase sequence of (from 5’ to 3’) GCAACATTTTCAGTTTCAGC (SEQ ID NO: 1197), wherein each of nucleosides 1-5 and 16-20 (from 5’ to 3’) are 2’-MOE nucleosides and each of nucleosides 6-15 are 2’- ⁇ -D-deoxynucleosides, wherein the internucleoside linkages between nucleosides 2-3, 3-4, 4-5, 5-6, 16-17, and 17-18 are phosphodiester internucleoside linkages, the internucleoside linkages between nucleosides 1-2, 6-7, 7-8, 8-9, 9-10, 10-11, 11-12, 12-13, 13-14, 14-15, 15-16, 18-19, and 19-20 are phosphorothioate internucleoside linkages, and wherein each cytosine is a 5-methylcytosine.
• Comparator Compound No.628785 is a 5-10-5 MOE gapmer, having a nucleobase sequence of: (from 5’ to 3’) GGTTTTTCTCCTTTATTATC (incorporated herein as SEQ ID NO: 18), wherein the sugar motif for Compound No.628785 is (from 5’ to 3’): eeeeeddddddddddeeeee; wherein each “e” represents a 2’-MOE ribosyl sugar moiety and each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety, wherein the internucleoside linkage motif is (from 5’ to 3’): soooossssssssssooss; wherein each “s” represents a phosphoroth
• Comparator Compound No.912669 described herein above and previously described in Shao et al., Sci. Trans. Med.13(583) (2021) is a 5-10-5 MOE gapmer, having a nucleobase sequence of (from 5’ to 3’): TATGGTTTTTCTCCTTTATT (incorporated herein as SEQ ID NO: 2332, wherein the sugar motif for Compound No.
• 912669 is (from 5’ to 3’): eeeeeddddddddddeeeee; wherein each “e” represents a 2’-MOE ribosyl sugar moiety and each “d” represents a 2’- ⁇ -D-deoxyribosyl sugar moiety, wherein the internucleoside linkage motif is (from 5’ to 3’): soooosssssssssooss, wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester linkage, and wherein each cytosine residue is a 5-methylcytosine.
• SHSY5Y cells plated at a density of 12,500 cells per well, were differentiated in Neurobasal media supplemented with B27 (ThermoFisher), GlutaMAX (ThermoFisher), and 10 ⁇ M retinoic acid (Sigma) for 10 days.
• Differentiated SH- SY5Y cells were treated with modified oligonucleotides at concentrations indicated in the tables below by free uptake. After a treatment period of 5 days, total RNA was isolated from the cells and MECP2 RNA levels were measured by quantitative real-time RTPCR.
• Human MECP2 primer-probe set RTS52360 (forward sequence GATCAATCCCCAGGGAAAAGC, designated herein as SEQ ID NO: 12; reverse sequence CCTCTCCCAGTTACCGTGAAG, designated herein as SEQ ID NO: 13; probe sequence CATTAGGGTCCAGGGATGTGTCGC, designated herein as SEQ ID NO: 14) was used to measure RNA levels as described above. MECP2 RNA levels were normalized to human GAPDH.
• Human GAPDH was amplified using human primer probe set RTS104 (forward sequence GAAGGTGAAGGTCGGAGTC, designated herein as SEQ ID NO: 15; reverse sequence GAAGATGGTGATGGGATTTC, designated herein as SEQ ID NO: 16; probe sequence CAAGCTTCCCGTTCTCAGCC, designated herein as SEQ ID NO: 17).
• Reduction of MECP2 RNA is presented in the table below as percent MECP2 RNA, relative to the amount of MECP2 RNA in untreated control cells (% UTC).
• the half maximal inhibitory concentration (IC 50 ) of each modified oligonucleotide was calculated with GraphPad Prism software. As shown in the table below, Compound No.

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• Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)

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• 2023
  • 2023-09-22 EP EP23869210.7A patent/EP4590308A2/de active Pending
  • 2023-09-22 JP JP2025517347A patent/JP2025532128A/ja active Pending
  • 2023-09-22 WO PCT/US2023/074829 patent/WO2024064854A2/en not_active Ceased

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