Classifications

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  • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
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  • A61K31/713—Double-stranded nucleic acids or oligonucleotides
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  • A61K47/34—Macromolecular compounds obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyesters, polyamino acids, polysiloxanes, polyphosphazines, copolymers of polyalkylene glycol or poloxamers
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  • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
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  • A61K47/54—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
  • A61K47/545—Heterocyclic compounds
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  • A61K47/549—Sugars, nucleosides, nucleotides or nucleic acids
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  • A61K47/551—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound the modifying agent being also a pharmacologically or therapeutically active agent, i.e. the entire conjugate being a codrug one of the codrug's components being a vitamin, e.g. niacinamide, vitamin B3, cobalamin, vitamin B12, folate, vitamin A or retinoic acid
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  • A61K47/54—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
  • A61K47/554—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound the modifying agent being a steroid plant sterol, glycyrrhetic acid, enoxolone or bile acid
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  • A61K47/58—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule obtained by reactions only involving carbon-to-carbon unsaturated bonds, e.g. poly[meth]acrylate, polyacrylamide, polystyrene, polyvinylpyrrolidone, polyvinylalcohol or polystyrene sulfonic acid resin
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  • A61K47/64—Drug-peptide, drug-protein or drug-polyamino acid conjugates, i.e. the modifying agent being a peptide, protein or polyamino acid which is covalently bonded or complexed to a therapeutically active agent
• • A—HUMAN NECESSITIES
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  • A61K47/6905—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a colloid or an emulsion
  • A61K47/6907—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a colloid or an emulsion the form being a microemulsion, nanoemulsion or micelle
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  • A61K48/0025—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'non-active' part of the composition delivered, e.g. wherein such 'non-active' part is not delivered simultaneously with the 'active' part of the composition wherein the non-active part clearly interacts with the delivered nucleic acid
  • A61K48/0041—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'non-active' part of the composition delivered, e.g. wherein such 'non-active' part is not delivered simultaneously with the 'active' part of the composition wherein the non-active part clearly interacts with the delivered nucleic acid the non-active part being polymeric
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  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
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  • C12N2320/32—Special delivery means, e.g. tissue-specific

Definitions

• Targeted nucleic acid conjugates are effective drug delivery systems for biologically active nucleic acids (see WO2017/177326).
• Drugs based on nucleic acids which include large nucleic acid molecules such as, e.g., in vitro transcribed messenger RNA (mRNA) as well as smaller polynucleotides that interact with a messenger RNA or a gene, have to be delivered to the proper cellular compartment in order to be effective.
• mRNA messenger RNA
• double-stranded nucleic acids such as double-stranded RNA molecules (dsRNA), including, e.g., siRNAs
• dsRNA double-stranded RNA molecules
• siRNAs Upon delivery into the proper compartment, siRNAs block gene expression through a highly conserved regulatory mechanism known as RNA interference (RNAi).
• RNAi RNA interference
• siRNAs are large in size with a molecular weight ranging from 12-17 kDa, and are highly anionic due to their phosphate backbone with up to 50 negative charges.
• the two complementary RNA strands result in a rigid helix.
• siRNAs are rapidly degraded by nucleases present in blood and other fluids or in tissues, and have been shown to stimulate strong immune responses in vitro and in vivo. See, e.g., Robbins et al., Oligonucleotides 19:89-102, 2009. mRNA molecules suffer from similar issues of impermeability, fragility, and immunogenicity.
• siRNA conjugates are efficacious in a specific down regulation of a gene expressed in hepatocytes of rodents. However, in order to elicit the desired biologic effect, a large dose is needed. See Soutschek et al, Nature 432: 173-178, 2004.
• the invention provides a method for delivering a nucleic acid to a cell comprising contacting the cell with, 1) a membrane-destabilizing polymer; and 2) a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid
• the invention provides a method for delivering a nucleic acid to the cytosol of a target cell within a subject, the method comprising: administering to the subject (a) a membrane-destabilizing polymer, and (b) a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid, wherein the nucleic acid is delivered to the cytosol of the target cell.
• the invention provides a method comprising administering to an animal, 1) a membrane-destabilizing polymer; and 2) a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid
• the invention provides a composition comprising: a) a
• composition is formulated for administration by injection. In one embodiment the composition is formulated for administration by subcutaneous injection.
• the invention provides a method for treating a disease characterized by overexpression of a polypeptide, comprising administering to an animal having the disease a therapeutically effective amount of (a) a membrane-destabilizing polymer; and b) a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is an siRNA that targets expression of the overexpressed polypeptide.
• the invention provides a method to deliver an siRNA to the liver of an animal, comprising administering to the animal, (a) a membrane-destabilizing polymer that comprises a targeting moiety (T 5 ) selected to promote hepatocyte-specific delivery of the polymer; and b) a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is the siRNA
• the invention provides a method to treat a hepatitis B viral infection in an animal, comprising administering to the animal: (a) a membrane-destabilizing polymer, comprising a targeting moiety (T 5 ) selected to promote hepatocyte-specific delivery of the polymer, and (b) a nucleic acid conjugate of formula (X):
• A is a targeting ligand selected to promote hepatocyte-specific delivery of the conjugate
• B is an optional linker
• C is an siRNA that is effective to treat the hepatitis B viral infection.
• the invention provides a kit comprising: 1) a membrane- destabilizing polymer; 2) a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid
• the invention provides a kit comprising: 1) a membrane- destabilizing polymer; 2) a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid
• the invention provides a kit comprising: 1) a membrane- destabilizing polymer; 2) a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid
• the invention provides a membrane-destabilizing polymer and a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid; for use in medical therapy.
• the invention provides a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid
• the invention provides the use of a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid
• the invention provides a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid, wherein the nucleic acid conjugate is associated non-covalently with a membrane-destabilizing polymer.
• the invention provides a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid, wherein the nucleic acid conjugate is partially or fully encapsulated by a micelle that comprises a plurality of membrane-destabilizing polymers.
• the invention provides a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid, wherein the nucleic acid conjugate is partially encapsulated by a micelle that comprises a plurality of membrane-destabilizing polymers.
• the invention provides a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid, wherein the nucleic acid conjugate is fully encapsulated by a micelle that comprises a plurality of membrane-destabilizing polymers.
• the invention provides a pharmaceutical composition
• a pharmaceutical composition comprising a pharmaceutically acceptable carrier, and a nucleic acid conjugate of Formula (X):
• A is a targeting ligand
• B is an optional linker
• C is a nucleic acid, wherein the nucleic acid conjugate is partially or fully encapsulated by a micelle that comprises a plurality of membrane-destabilizing polymers.
• the invention provides compounds, compositions, and methods that can be used to target delivery of therapeutic nucleic acids (e.g. to the liver). Specifically, it includes the use of a polymer micelle as a potency enhancer to a subcutaneously-administered conjugate platform for targeted delivery of nucleci acid therapeutics to the liver.
• the polymer micelles typically remain intact during delivery to hepatocytes and exert their functionality, for example, when administered subcutaneously.
• Gene silencing is examined by measuring the inhibition or reduction in expression of the target gene relative to the vehicle control.
• Membrane destabilizing polymers are reported in United States Patent Application Publication Numbers: US2010/0160216, US2010/0210504, US2011/0143434,
• the membrane destabilizing polymer comprises three distinct regions:
• hepatocyte targeting can be achieved with a targeting moiety such as a single N- Acetylgalactoseamine monosaccharide unit that interacts with one of the three trivalent domains of the ASGPr receptor which is highly expressed on the surface of hepatocytes.
• This monosaccharide unit forms the“head’ of the polymer chain.
• the N-acetyl galactose amine (GalNAc or NAG) can be attached to the second functional domain of the polymer via a PEG12 amino acid spacer coupled to ethyl carbonotrithioate (ECT). This represents the starting“chain transfer agent” or CTA. Subsequent polymerization reactions can take place on the fully deprotected monosaccharide.
• the second“solubilizing” or hydrophilic region is comprised of polyethyleneglycol methacrylate 4-5 (PEGMA 4-5)
• the number 4 and 5 refers to the number of ethylene glycol repeats in the monomer) and hydroxyethyl methacrylate (HMA). Usually in a ratio around 75/25 PEGMA/HMA.
• the polymerization can occur using reversible addition-fragmentation chain transfer (RAFT) which allows control over the generated molecular weight and polydispersity during a free-radical polymerization initiated with azobisisobutyronitrile (AIBN).
• RAFT reversible addition-fragmentation chain transfer
• AIBN azobisisobutyronitrile
• the reaction can proceed at a fixed time at a certain concentration and temperature to produce a hydrophilic polymer around 4kDa capped with a terminal trithiocarbonate functionality that allows further polymerization.
• the third region of the polymer provides the endosomal release functionality. It can also be synthesized using RAFT polymersiation, however in this case the monomeric units in the reaction are dimethylaminoethyl acrylate (DMAEA), butyl methyacrylate (BMA) and propylacrylic acid (PAA) (typically in ratios of about 33%/55%/12%).
• DAEA dimethylaminoethyl acrylate
• BMA butyl methyacrylate
• PAA propylacrylic acid
• the polymer end group (trithiocarbonate) can be removed by radical induced reduction and the final polymer characterized by 1H NMR, HPLC and GPC (to determine MW and polydispersity)
• the combination of the two polymeric regions helps maximize efficacy.
• the polymer is typically neutral. Morever at neutral pH the second endosomal release region displays hydrophobic character.
• CMC critical micelle concentration
• small micelle structures will spontaneously form.
• the a membrane-destabilizing polymer is a polymer of formula (XX):
• PEGMA polyethyleneglycol methacrylate residue with 2-20 ethylene glycol units
• M 2 is a methacrylate residue selected from the group consisting of
• BMA is butyl methacrylate residue
• PAA is propyl acrylic acid residue
• DMAEMA is dimethylaminoethyl methacrylate residue
• s is a mole fraction of 0.2 to 0.75
• v 1 to 25 kDa
• w 1 to 25 kDa
• T 5 is a targeting moiety (e.g., a peptide, polymer or saccharide).
• L is absent or is a linking moiety.
• M 2 is selected from the group consisting of:
• Targeting moiety T 5 is a moiety that can be, e.g., a peptide, polymer or saccharide.
• the targeting moiety T 5 in certain embodiments targets delivery to a location in the body, e.g., targets delivery to a specific organ or cell type.
• T 5 is a peptide.
• T 5 is a polymer.
• T 5 is a saccharide.
• the a membrane-destabilizing polymer is a polymer of formula
• px is an integer of from about 2 to about 50, e.g., from about 2 to about 20, e.g., from 4 to 12 (e.g., 2, 3, 4, 5, 6, 7, 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 or 50).
• px is an integer of from about 8 to about 16 (e.g., 8, 9, 10, 11, 12, 13, 14, 15, or 16). In some embodiments, px is about 12.
• py is an integer of from about 2 to about 20 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20). In some embodiments, py is an integer of from about 2 to about 10 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10). In some embodiments, py is an integer of from about 4 to about 5 (e.g., 4 or 5).
• alkoxy and“alkylthio”, are used in their conventional sense, and refer to those alkyl groups attached to the remainder of the molecule via an oxygen atom (“oxy”) or thio group, and further include mono- and poly-halogenated variants thereof.
• alkyl by itself or as part of another substituent, means, unless otherwise stated, a straight or branched chain hydrocarbon radical, having the number of carbon atoms designated (i.e., C1-8 means one to eight carbons).
• alkyl groups include methyl, ethyl, n-propyl, iso-propyl, n-butyl, t-butyl, iso-butyl, sec-butyl, n-pentyl, n-hexyl, n-heptyl, n- octyl, and the like.
• alkenyl refers to an unsaturated alkyl radical having one or more double bonds.
• alkynyl refers to an unsaturated alkyl radical having one or more triple bonds.
• unsaturated alkyl groups include vinyl, 2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl), 2,4-pentadienyl, 3-(1,4-pentadienyl), ethynyl, 1- and 3- propynyl, 3-butynyl, and the higher homologs and isomers.
• animal includes mammalian species, such as a human, mouse, rat, dog, cat, hamster, guinea pig, rabbit, livestock, and the like.
• aryl refers to a single all carbon aromatic ring or a multiple condensed all carbon ring system wherein at least one of the rings is aromatic.
• an aryl group has 6 to 20 carbon atoms, 6 to 14 carbon atoms, 6 to 12 carbon atoms, or 6 to 10 carbon atoms.
• Aryl includes a phenyl radical.
• Aryl also includes multiple condensed carbon ring systems (e.g., ring systems comprising 2, 3 or 4 rings) having about 9 to 20 carbon atoms in which at least one ring is aromatic and wherein the other rings may be aromatic or not aromatic (e.g., cycloalkyl.
• the rings of the multiple condensed ring system can be connected to each other via fused, spiro and bridged bonds when allowed by valency requirements. It is to be understood that the point of attachment of a multiple condensed ring system, as defined above, can be at any position of the ring system including an aromatic or a carbocycle portion of the ring.
• aryl groups include, but are not limited to, phenyl, indenyl, indanyl, naphthyl, 1, 2, 3, 4-tetrahydronaphthyl, anthracenyl, and the like.
• cycloalkyl refers to a saturated or partially unsaturated (non-aromatic) all carbon ring having 3 to 8 carbon atoms (i.e., (C3-C8)carbocycle).
• the term also includes multiple condensed, saturated all carbon ring systems (e.g., ring systems comprising 2, 3 or 4 carbocyclic rings).
• carbocycle includes multicyclic carbocyles such as a bicyclic carbocycles (e.g., bicyclic carbocycles having about 3 to 15 carbon atoms , about 6 to 15 carbon atoms, or 6 to 12 carbon atoms such as bicyclo[3.1.0]hexane and bicyclo[2.1.1]hexane), and polycyclic carbocycles (e.g tricyclic and tetracyclic carbocycles with up to about 20 carbon atoms).
• the rings of the multiple condensed ring system can be connected to each other via fused, spiro and bridged bonds when allowed by valency requirements.
• multicyclic carbocyles can be connected to each other via a single carbon atom to form a spiro connection (e.g., spiropentane, spiro[4,5]decane, etc), via two adjacent carbon atoms to form a fused connection (e.g., carbocycles such as decahydronaphthalene, norsabinane, norcarane) or via two non-adjacent carbon atoms to form a bridged connection (e.g., norbornane,
• cycloalkyls include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, bicyclo[2.2.1]heptane, pinane, and adamantane.
• the term“gene” refers to a nucleic acid (e.g., DNA or RNA) sequence that comprises partial length or entire length coding sequences necessary for the production of a polypeptide or precursor polypeptide.
• Gene product refers to a product of a gene such as an RNA transcript or a polypeptide.
• heteroaryl refers to a single aromatic ring that has at least one atom other than carbon in the ring, wherein the atom is selected from the group consisting of oxygen, nitrogen and sulfur;“heteroaryl” also includes multiple condensed ring systems that have at least one such aromatic ring, which multiple condensed ring systems are further described below.
• “heteroaryl” includes single aromatic rings of from about 1 to 6 carbon atoms and about 1-4 heteroatoms selected from the group consisting of oxygen, nitrogen and sulfur. The sulfur and nitrogen atoms may also be present in an oxidized form provided the ring is aromatic.
• heteroaryl ring systems include but are not limited to pyridyl, pyrimidinyl, oxazolyl and furyl.“Heteroaryl” also includes multiple condensed ring systems (e.g., ring systems comprising 2, 3 or 4 rings) wherein a heteroaryl group, as defined above, is condensed with one or more rings selected from cycloalkyl, aryl, heterocycle, and heteroaryl. It is to be understood that the point of attachment for a heteroaryl or heteroaryl multiple condensed ring system can be at any suitable atom of the heteroaryl or heteroaryl multiple condensed ring system including a carbon atom and a heteroatom (e.g., a nitrogen).
• a heteroaryl e.g., a nitrogen
• heteroaryls include but are not limited to pyridyl, pyrrolyl, pyrazinyl, pyrimidinyl, pyridazinyl, pyrazolyl, thienyl, indolyl, imidazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, thiazolyl, furyl, oxadiazolyl, thiadiazolyl, quinolyl, isoquinolyl, benzothiazolyl, benzoxazolyl, indazolyl, quinoxalyl, and quinazolyl.
• heterocycle refers to a single saturated or partially unsaturated ring that has at least one atom other than carbon in the ring, wherein the atom is selected from the group consisting of oxygen, nitrogen and sulfur; the term also includes multiple condensed ring systems that have at least one such saturated or partially unsaturated ring, which multiple condensed ring systems are further described below.
• the term includes single saturated or partially unsaturated rings (e.g., 3, 4, 5, 6 or 7-membered rings) from about 1 to 6 carbon atoms and from about 1 to 3 heteroatoms selected from the group consisting of oxygen, nitrogen and sulfur in the ring.
• the sulfur and nitrogen atoms may also be present in their oxidized forms.
• heterocycles include but are not limited to azetidinyl, tetrahydrofuranyl and piperidinyl.
• the term“heterocycle” also includes multiple condensed ring systems (e.g., ring systems comprising 2, 3 or 4 rings) wherein a single heterocycle ring (as defined above) can be condensed with one or more groups selected from cycloalkyl, aryl, and heterocycle to form the multiple condensed ring system.
• the rings of the multiple condensed ring system can be connected to each other via fused, spiro and bridged bonds when allowed by valency requirements. It is to be understood that the individual rings of the multiple condensed ring system may be connected in any order relative to one another.
• the point of attachment of a multiple condensed ring system can be at any position of the multiple condensed ring system including a heterocycle, aryl and carbocycle portion of the ring.
• heterocycle includes a 3-15 membered heterocycle.
• heterocycle includes a 3-10 membered heterocycle.
• heterocycle includes a 3- 8 membered heterocycle.
• heterocycle includes a 3-7 membered heterocycle.
• heterocycle includes a 3-6 membered heterocycle.
• the term heterocycle includes a 4-6 membered heterocycle.
• heterocycle includes a 3-10 membered monocyclic or bicyclic heterocycle comprising 1 to 4 heteroatoms. In one embodiment the term heterocycle includes a 3-8 membered monocyclic or bicyclic heterocycle heterocycle comprising 1 to 3
• heterocycle includes a 3-6 membered monocyclic heterocycle comprising 1 to 2 heteroatoms. In one embodiment the term heterocycle includes a 4-6 membered monocyclic heterocycle comprising 1 to 2 heteroatoms.
• Exemplary heterocycles include, but are not limited to aziridinyl, azetidinyl, pyrrolidinyl, piperidinyl, homopiperidinyl, morpholinyl, thiomorpholinyl, piperazinyl, tetrahydrofuranyl,
• dihydrooxazolyl tetrahydropyranyl, tetrahydrothiopyranyl, 1,2,3,4- tetrahydroquinolyl, benzoxazinyl, dihydrooxazolyl, chromanyl, 1,2-dihydropyridinyl, 2,3-dihydrobenzofuranyl, 1,3-benzodioxolyl, 1,4-benzodioxanyl, spiro[cyclopropane-1,1'-isoindolinyl]-3'-one, isoindolinyl-1-one, 2-oxa-6-azaspiro[3.3]heptanyl, imidazolidin-2-one imidazolidine, pyrazolidine, butyrolactam, valerolactam, imidazolidinone, hydantoin, dioxolane, phthalimide, and 1,4-dioxane.
• saccharide includes monosaccharides, disaccharides and trisaccharides, all of which can be optionally substituted.
• the term includes glucose, sucrose fructose, galactose and ribose, as well as deoxy sugars such as deoxyribose and amino sugar such as
• Saccharide derivatives can conveniently be prepared as described in
• a saccharide can conveniently be linked to the remainder of a compound of formula I through an ether bond, a thioether bond (e.g. an S-glycoside), an amine nitrogen (e.g., an N-glycoside ), or a carbon-carbon bond (e.g. a C-glycoside).
• a thioether bond e.g. an S-glycoside
• an amine nitrogen e.g., an N-glycoside
• a carbon-carbon bond e.g. a C-glycoside
• small-interfering RNA or“siRNA” as used herein refers to double stranded RNA (i.e., duplex RNA) that is capable of reducing or inhibiting the expression of a target gene or sequence (e.g., by mediating the degradation or inhibiting the translation of mRNAs which are complementary to the siRNA sequence) when the siRNA is in the same cell as the target gene or sequence.
• the siRNA may have substantial or complete identity to the target gene or sequence, or may comprise a region of mismatch (i.e., a mismatch motif).
• the siRNAs may be about 19-25 (duplex) nucleotides in length, and is preferably about 20-24, 21-22, or 21-23 (duplex) nucleotides in length.
• siRNA duplexes may comprise 3’ overhangs of about 1 to about 4 nucleotides or about 2 to about 3 nucleotides and 5’ phosphate termini.
• Examples of siRNA include, without limitation, a double-stranded polynucleotide molecule assembled from two separate stranded molecules, wherein one strand is the sense strand and the other is the complementary antisense strand.
• the 5' and/or 3' overhang on one or both strands of the siRNA comprises 1-4 (e.g., 1, 2, 3, or 4) modified and/or unmodified deoxythymidine (t or dT) nucleotides, 1-4 (e.g., 1, 2, 3, or 4) modified (e.g., 2'OMe) and/or unmodified uridine (U) ribonucleotides, and/or 1-4 (e.g., 1, 2, 3, or 4) modified (e.g., 2'OMe) and/or unmodified ribonucleotides or deoxyribonucleotides having complementarity to the target sequence (e.g., 3'overhang in the antisense strand) or the complementary strand thereof (e.g., 3' overhang in the sense strand).
• 1-4 e.g., 1, 2, 3, or 4 modified and/or unmodified deoxythymidine (t or dT) nucleotides
• 1-4
• siRNA are chemically synthesized.
• siRNA can also be generated by cleavage of longer dsRNA (e.g., dsRNA greater than about 25 nucleotides in length) with the E. coli RNase III or Dicer. These enzymes process the dsRNA into biologically active siRNA (see, e.g., Yang et al., Proc. Natl. Acad. Sci. USA, 99:9942-9947 (2002); Calegari et al., Proc. Natl. Acad. Sci.
• dsRNA are at least 50 nucleotides to about 100, 200, 300, 400, or 500 nucleotides in length.
• a dsRNA may be as long as 1000, 1500, 2000, 5000 nucleotides in length, or longer.
• the dsRNA can encode for an entire gene transcript or a partial gene transcript.
• siRNA may be encoded by a plasmid (e.g., transcribed as sequences that automatically fold into duplexes with hairpin loops).
• the phrase“inhibiting expression of a target gene” refers to the ability of a siRNA of the invention to silence, reduce, or inhibit expression of a target gene.
• a test sample e.g., a biological sample from an organism of interest expressing the target gene or a sample of cells in culture expressing the target gene
• a siRNA that silences, reduces, or inhibits expression of the target gene.
• Expression of the target gene in the test sample is compared to expression of the target gene in a control sample (e.g., a biological sample from an organism of interest expressing the target gene or a sample of cells in culture expressing the target gene) that is not contacted with the siRNA.
• Control samples may be assigned a value of 100%.
• silencing, inhibition, or reduction of expression of a target gene is achieved when the value of the test sample relative to the control sample (e.g., buffer only, an siRNA sequence that targets a different gene, a scrambled siRNA sequence, etc.) is about 100%, 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%, 79%, 78%, 77%, 76%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, or 0%.
• Suitable assays include, without limitation, examination of protein or mRNA levels using techniques known to those of skill in the art, such as, e.g., dot blots, Northern blots, in situ hybridization, ELISA, immunoprecipitation, enzyme function, as well as phenotypic assays known to those of skill in the art.
• an“effective amount” or“therapeutically effective amount” of a therapeutic nucleic acid such as siRNA is an amount sufficient to produce the desired effect, e.g., an inhibition of expression of a target sequence in comparison to the normal expression level detected in the absence of a siRNA.
• inhibition of expression of a target gene or target sequence is achieved when the value obtained with a siRNA relative to the control (e.g., buffer only, an siRNA sequence that targets a different gene, a scrambled siRNA sequence, etc.) is about 100%, 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%, 79%, 78%, 77%, 76%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, or 0%.
• a siRNA relative to the control e.g., buffer only, an siRNA sequence that targets a different gene, a scrambled siRNA sequence, etc.
• Suitable assays for measuring the expression of a target gene or target sequence include, but are not limited to, examination of protein or mRNA levels using techniques known to those of skill in the art, such as, e.g., dot blots, Northern blots, in situ hybridization, ELISA, immunoprecipitation, enzyme function, as well as phenotypic assays known to those of skill in the art.
• nucleic acid refers to a polymer containing at least two nucleotides (i.e., deoxyribonucleotides or ribonucleotides) in either single- or double-stranded form and includes DNA and RNA.
• Nucleotides contain a sugar deoxyribose (DNA) or ribose (RNA), a base, and a phosphate group.
• Nucleotides are linked together through the phosphate groups.“Bases” include purines and pyrimidines, which further include natural compounds adenine, thymine, guanine, cytosine, uracil, inosine, and natural analogs, and synthetic derivatives of purines and pyrimidines, which include, but are not limited to, modifications which place new reactive groups such as, but not limited to, amines, alcohols, thiols, carboxylates, and alkylhalides. Nucleic acids include nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, and which have similar binding properties as the reference nucleic acid.
• nucleic acids can include one or more UNA moieties.
• protecting group refers to a substituent that is commonly employed to block or protect a particular functional group on a compound.
• an “amino-protecting group” is a substituent attached to an amino group that blocks or protects the amino
• Suitable amino-protecting groups include acetyl,
• hydroxy-protecting group refers to a substituent of a hydroxy group that blocks or protects the hydroxy functionality. Suitable protecting groups include acetyl, silyl and 2,2-dimethoxy propene.
• a “carboxy-protecting group” refers to a substituent of the carboxy group that blocks or protects the carboxy functionality.
• Common carboxy-protecting groups include phenylsulfonylethyl, cyanoethyl, 2- (trimethylsilyl)ethyl, 2-(trimethylsilyl)ethoxymethyl, 2-(p-toluenesulfonyl)ethyl, 2-(p- nitrophenylsulfenyl)ethyl, 2-(diphenylphosphino)-ethyl, nitroethyl and the like.
• protecting groups and their use see P.G.M. Wuts and T.W. Greene, Greene's Protective Groups in Organic Synthesis 4 th edition, Wiley-Interscience, New York, 2006.
• synthetic activating group refers to a group that can be attached to an atom to activate that atom to allow it to form a covalent bond with another reactive group. It is understood that the nature of the synthetic activating group may depend on the atom that it is activating. For example, when the synthetic activating group is attached to an oxygen atom, the synthetic activating group is a group that will activate that oxygen atom to form a bond (e.g. an ester, carbamate, or ether bond) with another reactive group. Such synthetic activating groups are known. Examples of synthetic activating groups that can be attached to an oxygen atom include, but are not limited to, acetate, succinate, triflate, and mesylate.
• the synthetic activating group When the synthetic activating group is attached to an oxygen atom of a carboxylic acid, the synthetic activating group can be a group that is derivable from a known coupling reagent (e.g. a known amide coupling reagent).
• a known coupling reagent e.g. a known amide coupling reagent
• Such coupling reagents are known. Examples of such coupling reagents include, but are not limited to, N,N’-Dicyclohexylcarbodimide (DCC),
• hydroxybenzotriazole HABt
• EDC N-(3-Dimethylaminopropyl)-N’-ethylcarbonate
• BOP Benzotriazol-1-yloxy
• PyBOP benzotriazol-1-yl-oxytripyrrolidinophosphonium hexafluorophosphate
• HATU hexafluorophosphate
• T3P propylphosphonic anhydride solution
• HBTU O-benzotriazol- 1-yl-N,N,N’,N’-tetramethyluronium hexafluorophosphate
• nucleic acid includes any oligonucleotide or polynucleotide, with fragments containing up to 60 nucleotides generally termed oligonucleotides, and longer fragments termed polynucleotides.
• a deoxyribooligonucleotide consists of a 5-carbon sugar called deoxyribose joined covalently to phosphate at the 5’ and 3’ carbons of this sugar to form an alternating, unbranched polymer.
• DNA may be in the form of, e.g., antisense molecules, plasmid DNA, pre-condensed DNA, a PCR product, vectors, expression cassettes, chimeric sequences, chromosomal DNA, or derivatives and combinations of these groups.
• a ribooligonucleotide consists of a similar repeating structure where the 5-carbon sugar is ribose.
• RNA may be in the form, for example, of small interfering RNA (siRNA), Dicer-substrate dsRNA, small hairpin RNA (shRNA), asymmetrical interfering RNA (aiRNA), microRNA (miRNA), mRNA, tRNA, rRNA, tRNA, viral RNA (vRNA), self-amplifying RNA (sa-RNA), and combinations thereof.
• siRNA small interfering RNA
• Dicer-substrate dsRNA small hairpin RNA
• aiRNA asymmetrical interfering RNA
• miRNA microRNA
• miRNA microRNA
• mRNA microRNA
• mRNA microRNA
• mRNA microRNA
• mRNA microRNA
• mRNA microRNA
• mRNA microRNA
• mRNA mRNA
• tRNA tRNA
• rRNA tRNA
• vRNA viral RNA
• sa-RNA self-amplifying RNA
• polynucleotide and“oligonucleotide” also include polymers or oligomers comprising non-naturally occurring monomers, or portions thereof, which function similarly. Such modified or substituted oligonucleotides are often preferred over native forms because of properties such as, for example, enhanced cellular uptake, reduced immunogenicity, and increased stability in the presence of nucleases. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions), alleles, orthologs, SNPs, and complementary sequences as well as the sequence explicitly indicated.
• degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res., 19:5081 (1991); Ohtsuka et al., J. Biol. Chem., 260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes, 8:91- 98 (1994)).
• the nucleic acid is a nucleic acid described herein.
• the nucleic acids used herein can be single- stranded DNA or RNA, or double-stranded DNA or RNA, or DNA-RNA hybrids. Examples of double-stranded RNA are described herein and include, e.g., siRNA and other RNAi agents such as aiRNA and pre-miRNA.
• Single-stranded nucleic acids include, e.g., antisense oligonucleotides, ribozymes, mature miRNA, and triplex-forming oligonucleotides.
• the nucleic acid is an oligonucleotide.
• the oligonucleotide ranges from about 10 to about 100 nucleotides in length.
• oligonucleotides, both single-stranded, double-stranded, and triple-stranded may range in length from about 10 to about 60 nucleotides, from about 15 to about 60 nucleotides, from about 20 to about 50 nucleotides, from about 15 to about 30 nucleotides, or from about 20 to about 30 nucleotides in length.
• the nucleic acid is selected from the group consisting of small interfering RNA (siRNA), Dicer-substrate dsRNA, small hairpin RNA (shRNA), asymmetrical interfering RNA (aiRNA), microRNA (miRNA), tRNA, rRNA, tRNA, viral RNA (vRNA), self-amplifying RNA (sa-RNA), and combinations thereof.
• siRNA small interfering RNA
• Dicer-substrate dsRNA small hairpin RNA
• aiRNA asymmetrical interfering RNA
• miRNA microRNA
• tRNA tRNA
• rRNA tRNA
• vRNA viral RNA
• sa-RNA self-amplifying RNA
• the nucleic acid is an antisense molecule. In certain embodiments, the nucleic acid is a miRNA molecule. In certain embodiments, the nucleic acid is a siRNA. Suitable siRNA, as well as method and intermediates useful for their preparation are reported in International Patent Application Publication Number WO2016/054421.
• the nucleic acid may be used to downregulate or silence the translation (i.e., expression) of a gene of interest.
• Genes of interest include, but are not limited to, genes associated with viral infection and survival, genes associated with metabolic diseases and disorders (e.g., liver diseases and disorders), genes associated with tumorigenesis and cell transformation (e.g., cancer), angiogenic genes, immunomodulator genes such as those associated with inflammatory and autoimmune responses, ligand receptor genes, and genes associated with neurodegenerative disorders.
• the gene of interest is expressed in hepatocytes.
• Genes associated with viral infection and survival include those expressed by a virus in order to bind, enter, and replicate in a cell.
• viral sequences associated with chronic viral diseases include sequences of
• Filoviruses such as Ebola virus and Marburg virus (see, e.g., Geisbert et al., J. Infect. Dis., 193:1650-1657 (2006)); Arenaviruses such as Lassa virus, Junin virus, Machupo virus, Guanarito virus, and Sabia virus (Buchmeier et al., Arenaviridae: the viruses and their replication, In: FIELDS VIROLOGY, Knipe et al. (eds.), 4th ed., Lippincott-Raven,
• Influenza viruses such as Influenza A, B, and C viruses, (see, e.g., Steinhauer et al., Annu Rev Genet., 36:305-332 (2002); and Neumann et al., J Gen Virol., 83:2635-2662 (2002)); Hepatitis viruses (see, e.g., Hamasaki et al., FEBS Lett., 543:51 (2003); Yokota et al., EMBO Rep., 4:602 (2003); Schlomai et al., Hepatology, 37:764 (2003); Wilson et al., Proc. Natl. Acad. Sci.
• Herpes viruses Jia et al., J. Virol., 77:3301 (2003)
• HPV Human Papilloma Viruses
• Exemplary Filovirus nucleic acid sequences that can be silenced include, but are not limited to, nucleic acid sequences encoding structural proteins (e.g., VP30, VP35,
• NP nucleoprotein
• L-pol polymerase protein
• GP glycoprotein
• VP24 membrane-associated proteins
• Ebola virus VP24 sequences are set forth in, e.g., Genbank Accession Nos.
• Ebola virus L-pol sequences are set forth in, e.g., Genbank Accession No. X67110.
• Ebola virus VP40 sequences are set forth in, e.g., Genbank Accession No.
• Ebola virus NP sequences are set forth in, e.g., Genbank Accession No.
• Ebola virus GP sequences are set forth in, e.g., Genbank Accession No.
• Ebola virus sequences are set forth in, e.g., Genbank Accession Nos. L11365 and X61274.
• Complete genome sequences for Marburg virus are set forth in, e.g., Genbank Accession Nos. NC — 001608; AY430365; AY430366; and AY358025.
• Marburg virus GP sequences are set forth in, e.g., Genbank Accession Nos. AF005734; AF005733; and
• Marburg virus VP35 sequences are set forth in, e.g., Genbank Accession Nos. AF005731 and AF005730. Additional Marburg virus sequences are set forth in, e.g., Genbank Accession Nos. X64406; Z29337; AF005735; and Z12132.
• Non-limiting examples of siRNA molecules targeting Ebola virus and Marburg virus nucleic acid sequences include those described in U.S. Patent Publication No.20070135370, the disclosure of which is herein incorporated by reference in its entirety for all purposes.
• Influenza virus nucleic acid sequences that can be silenced include, but are not limited to, nucleic acid sequences encoding nucleoprotein (NP), matrix proteins (M1 and M2), nonstructural proteins (NS1 and NS2), RNA polymerase (PA, PB1, PB2), neuraminidase (NA), and haemagglutinin (HA).
• NP nucleoprotein
• M1 and M2 matrix proteins
• NS1 and NS2 nonstructural proteins
• NA neuraminidase
• HA haemagglutinin
• Influenza A NP sequences are set forth in, e.g., Genbank Accession Nos.
• Influenza A PA sequences are set forth in, e.g., Genbank Accession Nos. AY818132; AY790280; AY646171; AY818132; AY818133; AY646179; AY818134; AY551934; AY651613; AY651610; AY651620; AY651617;
• Non-limiting examples of siRNA molecules targeting Influenza virus nucleic acid sequences include those described in U.S. Patent Publication No. 20070218122, the disclosure of which is herein incorporated by reference in its entirety for all purposes.
• Exemplary hepatitis virus nucleic acid sequences that can be silenced include, but are not limited to, nucleic acid sequences involved in transcription and translation (e.g., En1, En2, X, P) and nucleic acid sequences encoding structural proteins (e.g., core proteins including C and C-related proteins, capsid and envelope proteins including S, M, and/or L proteins, or fragments thereof) (see, e.g., FIELDS VIROLOGY, supra).
• structural proteins e.g., core proteins including C and C-related proteins, capsid and envelope proteins including S, M, and/or L proteins, or fragments thereof
• HCV nucleic acid sequences that can be silenced include, but are not limited to, the 5 - untranslated region (5 -UTR), the 3 -untranslated region (3 -UTR), the polyprotein translation initiation codon region, the internal ribosome entry site (IRES) sequence, and/or nucleic acid sequences encoding the core protein, the E1 protein, the E2 protein, the p7 protein, the NS2 protein, the NS3 protease/helicase, the NS4A protein, the NS4B protein, the NS5A protein, and/or the NS5B RNA-dependent RNA polymerase.
• 5 -UTR 5 - untranslated region
• 3 -UTR 3 -untranslated region
• the polyprotein translation initiation codon region the internal ribosome entry site (IRES) sequence
• IRS internal ribosome entry site
• HCV genome sequences are set forth in, e.g., Genbank Accession Nos. NC—004102 (HCV genotype 1a), AJ238799 (HCV genotype 1b), NC — 009823 (HCV genotype 2), NC — 009824 (HCV genotype 3), NC — 009825 (HCV genotype 4), NC—009826 (HCV genotype 5), and NC—009827 (HCV genotype 6).
• Hepatitis A virus nucleic acid sequences are set forth in, e.g., Genbank Accession No. NC—001489;
• Hepatitis B virus nucleic acid sequences are set forth in, e.g., Genbank Accession No. NC — 003977; Hepatitis D virus nucleic acid sequence are set forth in, e.g., Genbank Accession No. NC—001653; Hepatitis E virus nucleic acid sequences are set forth in, e.g., Genbank Accession No. NC — 001434; and Hepatitis G virus nucleic acid sequences are set forth in, e.g., Genbank Accession No. NC — 001710. Silencing of sequences that encode genes associated with viral infection and survival can conveniently be used in combination with the administration of conventional agents used to treat the viral condition.
• Non-limiting examples of siRNA molecules targeting hepatitis virus nucleic acid sequences include those described in U.S. Patent Publication Nos.20060281175, 20050058982, and 20070149470; U.S. Pat. No.
• Genes associated with metabolic diseases and disorders include, for example, genes expressed in dyslipidemia (e.g., liver X receptors such as LXRa and LXRb (Genback Accession No. NM — 007121), farnesoid X receptors (FXR) (Genbank Accession No. NM—005123), sterol- regulatory element binding protein (SREBP), site-1 protease (SIP), 3-hydroxy-3- methylglutaryl coenzyme-A reductase (HMG coenzyme-A reductase), apolipoprotein B (ApoB) (Genbank Accession No.
• dyslipidemia e.g., liver X receptors such as LXRa and LXRb (Genback Accession No. NM — 007121), farnesoid X receptors (FXR) (Genbank Accession No. NM—005123), sterol- regulatory element binding protein (SREBP), site-1 protease (
• NM—000384 apolipoprotein CIII (ApoC3) (Genbank Accession Nos. NM—000040 and NG—008949 REGION: 5001.8164), and apolipoprotein E (ApoE) (Genbank Accession Nos. NM — 000041 and NG — 007084 REGION: 5001.8612)); and diabetes (e.g., glucose 6-phosphatase) (see, e.g., Forman et al., Cell, 81:687 (1995); Seol et al., Mol. Endocrinol., 9:72 (1995), Zavacki et al., Proc. Natl. Acad. Sci.
• diabetes e.g., glucose 6-phosphatase
• genes associated with metabolic diseases and disorders include genes that are expressed in the liver itself as well as and genes expressed in other organs and tissues. Silencing of sequences that encode genes associated with metabolic diseases and disorders can conveniently be used in combination with the
• Non-limiting examples of siRNA molecules targeting the ApoB gene include those described in U.S. Patent Publication No.20060134189, the disclosure of which is herein incorporated by reference in its entirety for all purposes.
• Non-limiting examples of siRNA molecules targeting the ApoC3 gene include those described in U.S. Provisional Application No.61/147,235, filed Jan.26, 2009, the disclosure of which is herein incorporated by reference in its entirety for all purposes.
• Examples of gene sequences associated with tumorigenesis and cell transformation include mitotic kinesins such as Eg5 (KSP, KIF11; Genbank Accession No. NM—004523); serine/threonine kinases such as polo-like kinase 1 (PLK-1) (Genbank Accession No. NM — 005030; Barr et al., Nat. Rev. Mol. Cell. Biol., 5:429-440 (2004)); tyrosine kinases such as WEE1 (Genbank Accession Nos.
• mitotic kinesins such as Eg5 (KSP, KIF11; Genbank Accession No. NM—004523
• serine/threonine kinases such as polo-like kinase 1 (PLK-1) (Genbank Accession No. NM — 005030; Barr et al., Nat. Rev. Mol. Cell. Biol., 5:429-440 (2004)
• NM — 003390 and NM — 001143976 inhibitors of apoptosis such as XIAP (Genbank Accession No. NM—001167); COP9 signalosome subunits such as CSN1, CSN2, CSN3, CSN4, CSN5 (JAB1; Genbank Accession No. NM — 006837); CSN6, CSN7A, CSN7B, and CSN8; ubiquitin ligases such as COP1 (RFWD2; Genbank Accession Nos. NM—022457 and NM—001001740); and histone deacetylases such as HDAC1, HDAC2 (Genbank Accession No.
• Non-limiting examples of siRNA molecules targeting the Eg5 and XIAP genes include those described in U.S. patent application Ser. No.11/807,872, filed May 29, 2007, the disclosure of which is herein incorporated by reference in its entirety for all purposes.
• Non-limiting examples of siRNA molecules targeting the PLK-1 gene include those described in U.S. Patent Publication Nos.20050107316 and 20070265438; and U.S. patent application Ser. No.12/343,342, filed Dec.23, 2008, the disclosures of which are herein incorporated by reference in their entirety for all purposes.
• Non-limiting examples of siRNA molecules targeting the CSN5 gene include those described in U.S. Provisional Application No.61/045,251, filed Apr.15, 2008, the disclosure of which is herein incorporated by reference in its entirety for all purposes.
• translocation sequences such as MLL fusion genes, BCR-ABL (Wilda et al., Oncogene, 21:5716 (2002); Scherr et al., Blood, 101:1566 (2003)), TEL-AML1, EWS- FLI1, TLS-FUS, PAX3-FKHR, BCL-2, AML1-ETO, and AML1-MTG8 (Heidenreich et al., Blood, 101:3157 (2003)); overexpressed sequences such as multidrug resistance genes (Nieth et al., FEBS Lett., 545:144 (2003); Wu et al, Cancer Res.63:1515 (2003)), cyclins (Li et al., Cancer Res., 63:3593 (2003); Zou et al., Genes Dev., 16:2923 (2002)), beta-catenin (Verma et al., Clin Cancer Res.
• Non-limiting examples of siRNA molecules targeting the EGFR gene include those described in U.S. patent application Ser. No.11/807,872, filed May 29, 2007, the disclosure of which is herein incorporated by reference in its entirety for all purposes.
• Angiogenic genes are able to promote the formation of new vessels.
• vascular endothelial growth factor VEGF
• VEGFR vascular endothelial growth factor
• siRNA sequences that target VEGFR are set forth in, e.g., GB 2396864; U.S. Patent Publication No.20040142895; and CA 2456444, the disclosures of which are herein incorporated by reference in their entirety for all purposes.
• Anti-angiogenic genes are able to inhibit neovascularization. These genes are particularly useful for treating those cancers in which angiogenesis plays a role in the pathological development of the disease.
• anti-angiogenic genes include, but are not limited to, endostatin (see, e.g., U.S. Pat. No.6,174,861), angiostatin (see, e.g., U U.S. Pat. No.5,639,725), and VEGFR2 (see, e.g., Decaussin et al., J. Pathol., 188: 369-377 (1999)), the disclosures of which are herein incorporated by reference in their entirety for all purposes.
• Immunomodulator genes are genes that modulate one or more immune responses.
• immunomodulator genes include, without limitation, cytokines such as growth factors (e.g., TGF-a, TGF-b, EGF, FGF, IGF, NGF, PDGF, CGF, GM-CSF, SCF, etc.), interleukins (e.g., IL-2, IL-4, IL-12 (Hill et al., J. Immunol., 171:691 (2003)), IL-15, IL-18, IL-20, etc.), interferons (e.g., IFN-a, IFN-b, IFN-g, etc.) and TNF.
• cytokines such as growth factors (e.g., TGF-a, TGF-b, EGF, FGF, IGF, NGF, PDGF, CGF, GM-CSF, SCF, etc.), interleukins (e.g., IL-2, IL-4, IL-12 (
• Fas and Fas ligand genes are also immunomodulator target sequences of interest (Song et al., Nat. Med., 9:347 (2003)).
• Genes encoding secondary signaling molecules in hematopoietic and lymphoid cells are also included in the present invention, for example, Tec family kinases such as Bruton's tyrosine kinase (Btk) (Heinonen et al., FEBS Lett., 527:274 (2002)).
• Cell receptor ligands include ligands that are able to bind to cell surface receptors (e.g., insulin receptor, EPO receptor, G-protein coupled receptors, receptors with tyrosine kinase activity, cytokine receptors, growth factor receptors, etc.), to modulate (e.g., inhibit, activate, etc.) the physiological pathway that the receptor is involved in (e.g., glucose level modulation, blood cell development, mitogenesis, etc.).
• cell receptor ligands include, but are not limited to, cytokines, growth factors, interleukins, interferons, erythropoietin (EPO), insulin, glucagon, G-protein coupled receptor ligands, etc.
• Templates coding for an expansion of trinucleotide repeats find use in silencing pathogenic sequences in neurodegenerative disorders caused by the expansion of trinucleotide repeats, such as spinobulbular muscular atrophy and Huntington's Disease (Caplen et al., Hum. Mol. Genet., 11:175 (2002)).
• target genes which may be targeted by a nucleic acid (e.g., by siRNA) to downregulate or silence the expression of the gene, include but are not limited to, Actin, Alpha 2, Smooth Muscle, Aorta (ACTA2), Alcohol dehydrogenase 1A (ADH1A), Alcohol dehydrogenase 4 (ADH4), Alcohol dehydrogenase 6 (ADH6), Afamin (AFM),
• ACTA2 Alcohol dehydrogenase 1A
• ADH4 Alcohol dehydrogenase 4
• ADH6 Alcohol dehydrogenase 6
• Afamin Afamin
• Angiotensinogen AAT
• Serine-pyruvate aminotransferase AXT
• Alpha-2-HS- glycoprotein AHSG
• Aldo-keto reductase family 1 member C4 ARB
• Serum albumin ABP
• alpha-1-microglobulin/bikunin precursor ABP
• Angiopoietin-related protein 3 ANGPTL3
• Serum amyloid P-component APCS
• Apolipoprotein A-II APOA2
• Apolipoprotein B-100 APOB
• Apolipoprotein C3 APOC3
• Apolipoprotein C-IV APOC4
• Apolipoprotein F APOF
• Beta-2-glycoprotein 1 APOH
• Aquaporin-9 AQP9
• Bile acid- CoA:amino acid N-acyltransferase BAAT
• C4b-binding protein beta chain C4BPB
• Putative uncharacterized protein encoded by LINC01554 C5orf27
• Complement factor 3 C3
• Complement Factor 5 C5
• C6 C6
• C8 alpha chain C8A
• C8 beta chain C8B
• C8G Complement component C8G
• C9 C9
• CYP4F2 Phylloquinone omega-hydroxylase CYP4F2
• CYP8B1 Dipeptidyl peptidase 4
• DPP4 Dipeptidyl peptidase 4
• F12 coagulation factor 12
• thrombin thrombin
• F9 coagulation factor IX
• fibrinogen alpha chain FGA
• fibrinogen beta chain FGB
• fibrinogen gamma chain FGG
• fibrinogen-like 1 FGL1
• FMO3 flavin containing monooxygenase 3
• FMO5 flavin containing monooxygenase 5
• group-specific component vitamin D binding protein
• GC Growth hormone receptor
• GHR glycine N-methyltransferase
• HBP2 hepcidin antimicrobial peptide
• HAMP hepcidin antimicrobial peptide
• GEO1 hydroxyacid oxidase 1
• HFAC HGF activator
• haptoglobin-related protein haptoglobin (HPR), hemopexin (HPX), histidine-rich glycoprotein (HRG), hydroxysteroid (11-beta)
• HSD11B1 hydroxysteroid (17-beta) dehydrogenase 13
• HSD17B13 Inter- alpha-trypsin inhibitor heavy chain H1
• IIH2 Inter-alpha-trypsin inhibitor heavy chain H2
• IIH3 Inter-alpha-trypsin inhibitor heavy chain H3
• IIH4 Inter-alpha-trypsin inhibitor heavy chain H4
• KLKB1 Prekallikrein
• KLKB1 Lactate dehydrogenase A
• LECT2 liver expressed antimicrobial peptide 2
• LECT2 leukocyte cell-derived chemotaxin 2
• LECT2 lipoprotein
• LPA lipoprotein
• MASP2 mannan-binding lectin serine peptidase 2
• MASP2 S- adenosylmethionine synthase isoform type-1
• MAT1A NADPH Oxidase 4
• NOX4 Poly [ADP-ribose]
• SERPINA6 Antithrombin-III (SERPINC1), Heparin cofactor 2 (SERPIND1), Serpin Family H Member 1 (SERPINH1), Solute Carrier Family 5 Member 2 (SLC5A2), Sodium/bile acid cotransporter (SLC10A1), Solute carrier family 13 member 5 (SLC13A5), Solute carrier family 22 member 1 (SLC22A1), Solute carrier family 25 member 47 (SLC25A47), Solute carrier family 2, facilitated glucose transporter member 2 (SLC2A2), Sodium-coupled neutral amino acid transporter 4 (SLC38A4), Solute carrier organic anion transporter family member 1B1 (SLCO1B1), Sphingomyelin Phosphodiesterase 1 (SMPD1), Bile salt sulfotransferase (SULT2A1), tyrosine aminotransferase (TAT), tryptophan 2,3-dioxygenase (TDO2), UDP glucuronosyltrans
• nucleic acids e.g., siRNA
• certain nucleic acids can be used in target validation studies directed at testing whether a gene of interest has the potential to be a therapeutic target.
• Certain nucleic acids e.g., siRNA
• target identification studies aimed at discovering genes as potential therapeutic targets.
• siRNA can be provided in several forms including, e.g., as one or more isolated small- interfering RNA (siRNA) duplexes, as longer double-stranded RNA (dsRNA), or as siRNA or dsRNA transcribed from a transcriptional cassette in a DNA plasmid.
• siRNA may be produced enzymatically or by partial/total organic synthesis, and modified ribonucleotides can be introduced by in vitro enzymatic or organic synthesis.
• each strand is prepared chemically. Methods of synthesizing RNA molecules are known in the art, e.g., the chemical synthesis methods as described in Verma and Eckstein (1998) or as described herein.
• RNA, synthesizing RNA, hybridizing nucleic acids, making and screening cDNA libraries, and performing PCR are well known in the art (see, e.g., Gubler and Hoffman, Gene, 25:263-269 (1983); Sambrook et al., supra; Ausubel et al., supra), as are PCR methods (see, U.S. Patent Nos.4,683,195 and 4,683,202; PCR Protocols: A Guide to Methods and Applications (Innis et al., eds, 1990)).
• Expression libraries are also well known to those of skill in the art.
• siRNA are chemically synthesized.
• the oligonucleotides that comprise the siRNA molecules of the invention can be synthesized using any of a variety of techniques known in the art, such as those described in Usman et al., J. Am. Chem. Soc., 109:7845 (1987); Scaringe et al., Nucl. Acids Res., 18:5433 (1990); Wincott et al., Nucl. Acids Res., 23:2677- 2684 (1995); and Wincott et al., Methods Mol. Bio., 74:59 (1997).
• oligonucleotides makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5’-end and phosphoramidites at the 3’-end.
• small scale syntheses can be conducted on an Applied Biosystems synthesizer using a 0.2 ⁇ mol scale protocol.
• syntheses at the 0.2 ⁇ mol scale can be performed on a 96-well plate synthesizer from Protogene (Palo Alto, CA).
• Protogene Protogene
• a larger or smaller scale of synthesis is also within the scope of this invention.
• Suitable reagents for oligonucleotide synthesis, methods for RNA deprotection, and methods for RNA purification are known to those of skill in the art.
• siRNA molecules can be assembled from two distinct oligonucleotides, wherein one oligonucleotide comprises the sense strand and the other comprises the antisense strand of the siRNA.
• each strand can be synthesized separately and joined together by hybridization or ligation following synthesis and/or deprotection.
• the conjugates of the invention may include one or more linking groups (e.g. L 3 or L 4 ).
• the structure of each linking group can vary, provided the conjugate functions as described herein.
• the structure of each linking group vary in length and atom composition, and each linking group can be branched, non-branched, cyclic, or a combination thereof.
• the linking group may also modulate the solubility, stability, or aggregation properties of the conjugate.
• each linking group comprises about 3-1000 atoms. In one embodiment each linking group comprises about 3-500 atoms. In one embodiment each linking group comprises about 3-200 atoms. In one embodiment each linking group comprises about 3-50 atoms. In one embodiment each linking group comprises about 10-1000 atoms. In one embodiment each linking group comprises about 10-500 atoms. In one embodiment each linking group comprises about 10-200 atoms. In one embodiment each linking group comprises about 10-50 atoms.
• each linking group comprises atoms selected from H, C, N, S and O.
• each linking group comprises atoms selected from H, C, N, S, P and O.
• each linking group comprises a branched or unbranched, saturated or unsaturated, hydrocarbon chain, having from about 1 to 1000 (or 1-750, 1-500, 1-250, 1- 100, 1-50, 1-25, 1-10, 1-5, 5-1000, 5-750, 5-500, 5-250, 5-100, 5-50, 5-25, 5-10 or 2-5 carbon atoms) wherein one or more of the carbon atoms is optionally replaced independently by -O-, -S, -N(R a )-, 3-7 membered heterocycle, 5-6-membered heteroaryl or carbocycle and wherein each chain, 3-7 membered heterocycle, 5-6-membered heteroaryl or carbocycle is optionally and independently substituted with one or more (e.g.1, 2, 3, 4, 5 or more) substituents selected from (C1-C6)alkyl, (C1-C6)alkoxy, (C3-C6)cycl
• each R a is independently H or (C 1 -C 6 )alkyl.
• the linker comprises a branched or unbranched, saturated or unsaturated, hydrocarbon chain, having from about 1 to 1000 (or 1-750, 1-500, 1-250, 1-100, 1-50, 1-25, 1-10, 1-5, 5-1000, 5-750, 5-500, 5-250, 5- 100, 5-50, 5-25, 5-10 or 2-5 carbon atoms) wherein one or more of the carbon atoms is optionally replaced independently by -O-, -S, -N(R a )-, , wherein each R a is independently H or (C 1 -C 6 )alkyl.
• each linking group comprises a polyethylene glycol.
• the linking group comprises a polyethylene glycol linked to the remainder of the targeted conjugate by a carbonyl group.
• the polyethylene glycol comprises about 1 to about 500 or about 5 to about 500 or about 3 to about 100 repeat (e.g., -CH 2 CH 2 O-) units (Greenwald, R.B., et al., Poly (ethylene glycol) Prodrugs: Altered Pharmacokinetics and Pharmacodynamics, Chapter, 2.3.1., 283-338; Filpula, D., et al., Releasable PEGylation of proteins with customized linkers, Advanced Drug Delivery, 60, 2008, 29-49; Zhao, H., et al., Drug Conjugates with Poly(Ethylene Glycol), Drug Delivery in Oncology, 2012, 627-656).
• A is a targeting ligand that specifically binds to a molecule on the surface of the target cell.
• nucleic acid conjugate and the membrane- destabilizing polymer are administered separately.
• the membrane-destabilizing polymer is administered after administration of the nucleic acid conjugate.
• the nucleic acid conjugate and the membrane- destabilizing polymer are administered together within a single composition.
• the targeting ligand and T 5 are different and either (i) specifically bind to the same cell surface molecule or (ii) specifically bind to a different cell surface molecule on the target cell.
• the targeting ligand and the T 5 are the same and each specifically binds to the same cell surface molecule.
• the cell is a secretory cell, a chondrocyte, an epithelial cell, a nerve cell, a muscle cell, a blood cell, an endothelial cell, a pericyte, a fibroblast, a glial cell, or a dendritic cell.
• the cell is a cancer cell, an immune cell, a bacterially-infected cell, a virally-infected cell, or a cell having an abnormal metabolic activity.
• the targeting ligand specifically binds to a cell surface molecule selected from the group consisting of transferrin receptor type 1, transferrin receptor type 2, the EGF receptor, HER2/Neu, a VEGF receptor, a PDGF receptor, an integrin, an NGF receptor, CD2, CD3, CD4, CD8, CD19, CD20, CD22, CD33, CD43, CD38, CD56, CD69, the asialoglycoprotein receptor (ASGPR), prostate-specific membrane antigen (PSMA), a folate receptor, and a sigma receptor.
• a cell surface molecule selected from the group consisting of transferrin receptor type 1, transferrin receptor type 2, the EGF receptor, HER2/Neu, a VEGF receptor, a PDGF receptor, an integrin, an NGF receptor, CD2, CD3, CD4, CD8, CD19, CD20, CD22, CD33, CD43, CD38, CD56, CD69, the asialoglycoprotein receptor (ASGPR), prostate-specific membrane antigen (PSMA),
• the targeting ligand comprises a small molecule targeting moiety.
• the small molecule targeting moiety is a sugar, a vitamin, a bisphosphonate, or an analogue thereof.
• the sugar is selected from lactose, galactose, N- acetyl
• NAG galactosamine
• M6P mannose-6-phosphate
• the vitamin is folate.
• the targeting ligand comprises a protein.
• the protein is an antibody, a peptide aptamer, or a protein derived from a natural ligand of the cell surface molecule.
• the targeting ligand comprises a peptide
• the peptide is an integrin-binding peptide, a LOX- 1 -binding peptide, and epidermal growth factor (EGF) peptide, a neurotensin peptide, an NL4 peptide, or a YIGSR laminin peptide.
• EGF epidermal growth factor
• the cell is a hepatocyte.
• the targeting ligand specifically binds to the asialoglycoprotein receptor (ASGPR).
• ASGPR asialoglycoprotein receptor
• the targeting ligand comprises an N- acetylgalactosamine (NAG) residue.
• the membrane destabilizing polymer comprises of three regions: a monosaccharide,
• hydrophilic region comprising polyethyleneglycol methacrylate 4-5 (PEGMA 4-5) and hydroxyethyl methacrylate (HMA); and
• the membrane destabilizing polymer is a polymer of
• PEGMA polyethyleneglycol methacrylate residue with 2-20 ethylene glycol units
• M 2 is a methacrylate residue selected from the group consisting of
• BMA is butyl methacrylate residue
• PAA is propyl acrylic acid residue
• DMAEMA is dimethylaminoethyl methacrylate residue
• q is a mole fraction of 0.2 to 0.75
• r is a mole fraction of 0.05 to 0.6
• s is a mole fraction of 0.2 to 0.75
• v 1 to 25 kDa
• w 1 to 25 kDa
• T 5 is a targeting moiety (e.g., a peptide, polymer or saccharide).
• L is absent or is a linking moiety.
• M 2 is selected from the group consisting of:
• PEGMA has 4-5 ethylene glycol units or 7-8 ethylene glycol units.
• T l and L are present and T l comprises an N-acetylgalactosamine (NAG) residue.
• L is comprises a polyethylene glycol (PEG) moiety having 2-20 ethylene glycol units.
• the membrane destabilizing polymer is a polymer of
• px is an integer of from about 2 to about 50, e.g., from about 2 to about 20, e.g., from 4 to 12 (e.g., 2, 3, 4, 5, 6, 7, 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 or 50).
• px is an integer of from about 8 to about 16 (e.g., 8, 9, 10, 11, 12, 13, 14, 15, or 16). In some embodiments, px is about 12.
• py is an integer of from about 2 to about 20 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20). In some embodiments, py is an integer of from about 2 to about 10 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10). In some embodiments, py is an integer of from about 4 to about 5 (e.g., 4 or 5).
• the compound of formula (X) is a compound of formula (I):
• R 1 a is targeting ligand
• L 1 is absent or a linking group
• L 2 is absent or a linking group
• R 2 is the nucleic acid
• the ring A is absent, a 3-20 membered cycloalkyl, a 5-20 membered aryl, a 5-20 membered heteroaryl, or a 3-20 membered heterocycloalkyl;
• each R A is independently selected from the group consisting of hydrogen, hydroxy, CN, F, Cl, Br, I, -C1-2 alkyl-OR B , C1-10 alkyl C2-10 alkenyl, and C2-10 alkynyl; wherein the C1-10 alkyl C 2-10 alkenyl, and C 2-10 alkynyl are optionally substituted with one or more groups independently selected from halo, hydroxy, and C1-3 alkoxy;
• R B is hydrogen, a protecting group, a covalent bond to a solid support, or a bond to a linking group that is bound to a solid support;
• n 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;
• R 1 a is targeting ligand
• L 1 is absent or a linking group
• L 2 is absent or a linking group
• R 2 is the nucleic acid
• the ring A is absent, a 3-20 membered cycloalkyl, a 5-20 membered aryl, a 5-20 membered heteroaryl, or a 3-20 membered heterocycloalkyl;
• each R A is independently selected from the group consisting of hydrogen, hydroxy, CN, F, Cl, Br, I, -C1-2 alkyl-OR B and C1-8 alkyl that is optionally substituted with one or more groups independently selected from halo, hydroxy, and C 1-3 alkoxy;
• R B is hydrogen, a protecting group, a covalent bond to a solid support, or a bond to a linking group that is bound to a solid support;
• n 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
• R 1 is–C(H) (3-p) (L 3 -saccharide) p ,
• each L 3 is independently a linking group
• p is 1, 2, or 3;
• saccharide is a monosaccharide or disaccharide.
• the saccharide is:
• R 3 is hydrogen or (C1-C4)alkyl
• R 4 , R 5 , R 6 , R 7 , R 8 and R 9 are each independently selected from the group consisting of hydrogen, (C 1 -C 8 )alkyl, (C 1 -C 8 )haloalkyl, (C 1 -C 8 )alkoxy and (C 3 -C 6 )cycloalkyl that is optionally substituted with one or more groups independently selected from the group consisting of halo, (C1-C4)alkyl, (C1-C4)haloalkyl, (C1-C4)alkoxy and (C1-C4)haloalkoxy;
• R 10 is -OH, -NR 8 R 9 or– F;
• R 11 is -OH, -NR 8 R 9 , -F or 5 membered heterocycle that is optionally substituted with one or more groups independently selected from the group consisting of halo, hydroxyl, carboxyl, amino, (C1-C4)alkyl, (C1-C4)haloalkyl, (C1-C4)alkoxy and (C1-C4)haloalkoxy
• the saccharide is selected from the group consisting of:
• the saccharide is:
• L 3 is: .
• R 1 is:
• G is—NH- or–O-;
• R C is hydrogen, (C1-C8)alkyl, (C1-C8)haloalkyl, (C1-C8)alkoxy, (C1-C6)alkanoyl, (C3- C 20 )cycloalkyl, (C 3 -C 20 )heterocycle, aryl, heteroaryl, monosaccharide, disaccharide or trisaccharide; and wherein the cycloalkyl, heterocyle, ary, heteroaryl and saccharide are optionally substituted with one or more groups independently selected from the group consisting of halo, carboxyl, hydroxyl, amino, (C 1 -C 4 )alkyl, (C 1 -C 4 )haloalkyl, (C 1 -C 4 )alkoxy and (C1-C4)haloalkoxy.
• R C is:
• R 1 is:
• R C is: .
• G is–NH-.
• R 1 is:
• R 1 is:
• each R D is independently selected from the group consisting of hydrogen, (C1- C 6 )alkyl, (C 9 -C 20 )alkylsilyl, (R W ) 3 Si-, (C 2 -C 6 )alkenyl, tetrahydropyranyl, (C 1 -C 6 )alkanoyl, benzoyl, aryl(C 1 -C 3 )alkyl, TMTr (Trimethoxytrityl), DMTr (Dimethoxytrityl), MMTr
• each R W is independently selected from the group consisting of (C 1 -C 4 )alkyl and aryl.
• L 2 is connected to R 2 through -O-.
• L 1 is selected from the group consisting of:
• L 2 is–CH 2 -O- or–CH 2 -CH 2 -O-.
• the compound of formula (I) is a compound of formula (Ia):
• the compound of formula (I) is selected from the group consisting of:
• Q 1 is hydrogen and Q 2 is R 2 ; or Q 1 is R 2 and Q 2 is hydrogen;
• Z is–L 1 -R 1 .
• the compound of formula (I) is a compound of formula (Ib):
• the compound of formula (I) is selected from the group consisting of:
• Q 1 is hydrogen and Q 2 is R 2 ; or Q 1 is R 2 and Q 2 is hydrogen;
• Z is–L 1 -R 1 .
• the compound of formula (I) is a compound of formula (Ic):
• E is–O- or -CH 2 -;
• n is selected from the group consisting of 0, 1, 2, 3, and 4;
• n1 and n2 are each independently selected from the group consisting of 0, 1, 2, and 3.
• the compound of formula (I) is selected from the group consisting of:
• Z is–L 1 -R 1 .
• -A-L 2 -R 2 is:
• Q 1 is hydrogen and Q 2 is R 2 ; or Q 1 is R 2 and Q 2 is hydrogen;
• each q is independently 0, 1, 2, 3, 4 or 5.
• the compound of formula (I) is selected from the group consisting of:
• R 1 is selected from the group consisting of:
• n 2, 3, or 4;
• x is 1 or 2.
• L 1 is selected from the group consisting of:
• A is absent, phenyl, pyrrolidinyl, or cyclopentyl.
• L 2 is C1-4 alkylene-O- that is optionally substituted with hydroxy. In one embodiment, L 2 is–CH 2 O-, -CH 2 CH 2 O-, or -CH(OH)CH 2 O-. In one embodiment, each R A is independently hydroxy or C 1-8 alkyl that is optionally substituted with hydroxyl.
• each R A is independently selected from the group consisting of hydroxy, methyl and–CH 2 OH.
• the compound of formula (I) is a compound formula (Ig):
• B is–N- or -CH-
• L 2 is C1-4 alkylene-O- that is optionally substituted with hydroxyl or halo; and n is 0, 1, 2, 3, 4, 5, 6, or 7.
• the compound of formula (I) is selected from the group consisting of:
• R’ is C 1-9 alkyl, C 2-9 alkenyl or C 2-9 alkynyl; wherein the C 1-9 alkyl, C 2-9 alkenyl or C 2-9 alkynyl are optionally substituted with halo or hydroxyl.
• the compound of formula (I) is selected from the group consisting of:
• the compound of formula (I) is selected from the group consisting of:
• the compound of formula (I) is a compound formula (Id):
• R 1d is selected from:
• X d is C 2 - 10 alkylene
• n d is 0 or 1;
• R 2d is a nucleic acid
• R 3d is H.
• R 1d is:
• X d is C8alkylene.
• n d is 0.
• R 3d is H.
• the compound of formula (I) is selected from the group consisting of:
• the compound of formula (I) is a compound of formula (Ig):
• B is–N- or -CH-
• L 2 is C 1-4 alkylene-O- that is optionally substituted with hydroxyl or halo; and n is 0, 1, 2, 3, 4, 5, 6, or 7.
• the compound of formula (I) is selected from the group consisting of:
• R’ is C1-9 alkyl, C2-9 alkenyl or C2-9 alkynyl; wherein the C1-9 alkyl, C2-9 alkenyl or C2-9 alkynyl are optionally substituted with halo or hydroxy.
• the compound of formula (I) is selected from the group consisting of:
• the compound of formula (X) is a compound of formula (XX):
• R 1 a is targeting ligand
• L 1 is absent or a linking group
• L 2 is absent or a linking group
• R 2 is a nucleic acid
• B is divalent and is selected from the group consisting of:
• each R’ is independently C 1-9 alkyl, C 2-9 alkenyl or C 2-9 alkynyl; wherein the C 1-9 alkyl, C 2-9 alkenyl or C 2-9 alkynyl are optionally substituted with halo or hydroxyl;
• the valence marked with * is attached to L 1 or is attached to R 1 if L 1 is absent; and the valence marked with ** is attached to L 2 or is attached to R 2 if L 2 is absent.
• R 1 comprises 2-8 saccharides.
• R 1 comprises 2-4 saccharides.
• R 1 comprises 3-8 saccharides.
• R 1 comprises 3-6 saccharides.
• R 1 comprises 3-4 saccharides.
• R 1 comprises 2 saccharides.
• R 1 comprises 3 saccharides.
• R 1 comprises 4 saccharides.
• R 1 has the following formula:
• B 1 is a trivalent group comprising about 1 to about 20 atoms and is covalently bonded to L 1 , T 1 , and T 2 .
• B 2 is a trivalent group comprising about 1 to about 20 atoms and is covalently bonded to T 1 , T 3 , and T 4 ;
• B 3 is a trivalent group comprising about 1 to about 20 atoms and is covalently bonded to T 2 , T 5 , and T 6 ;
• T 1 is absent or a linking group;
• T 2 is absent or a linking group
• T 3 is absent or a linking group
• T 4 is absent or a linking group
• T 5 is absent or a linking group
• T 6 is absent or a linking group.
• each saccharide is independently selected from:
• R 3 is hydrogen or (C1-C4)alkyl
• R 4 , R 5 , R 6 , R 7 , R 8 and R 9 are each independently selected from the group consisting of hydrogen, (C 1 -C 8 )alkyl, (C 1 -C 8 )haloalkyl, (C 1 -C 8 )alkoxy and (C 3 -C 6 )cycloalkyl that is optionally substituted with one or more groups independently selected from the group consisting of halo, (C1-C4)alkyl, (C1-C4)haloalkyl, (C1-C4)alkoxy and (C1-C4)haloalkoxy;
• R 10 is -OH, -NR 8 R 9 or– F;
• R 11 is -OH, -NR 8 R 9 , -F or 5 membered heterocycle that is optionally substituted with one or more groups independently selected from the group consisting of halo, hydroxyl, carboxyl, amino, (C 1 -C 4 )alkyl, (C 1 -C 4 )haloalkyl, (C 1 -C 4 )alkoxy and (C 1 -C 4 )haloalkoxy.
• each saccharide is independently selected from the group consisting of:
• each saccharide is independently:
• one of T 1 and T 2 is absent.
• both T 1 and T 2 are absent.
• At least one of T 3 , T 4 , T 5 , and T 6 is:
• each of T 3 , T 4 , T 5 , and T 6 is independently selected from the group consisting of:
• At least one of T 1 and T 2 is glycine.
• each of T 1 and T 2 is glycine.
• B 1 is a trivalent group comprising 1 to 15 atoms and is covalently bonded to L 1 , T 1 , and T 2 .
• B 1 is a trivalent group comprising 1 to 10 atoms and is covalently bonded to L 1 , T 1 , and T 2 .
• B 1 comprises a (C 1 -C 6 )alkyl.
• B 1 comprises a C 3-8 cycloalkyl.
• B 1 comprises a silyl group.
• B 1 comprises a D- or L-amino acid.
• B 1 comprises a saccharide
• B 1 comprises a phosphate group.
• B 1 comprises a phosphonate group.
• B 1 comprises an aryl. In one embodiment, B 1 comprises a phenyl ring.
• B 1 is a phenyl ring.
• B 1 is CH.
• B 1 comprises a heteroaryl
• B 1 is seleced from:
• B 2 is a trivalent group comprising 1 to 15 atoms and is covalently bonded to T 2 , T 5 , and T 6 .
• B 2 is a trivalent group comprising 1 to 10 atoms and is covalently bonded to T 2 , T 5 , and T 6 .
• B 2 comprises a (C1-C6)alkyl.
• B 2 comprises a C 3-8 cycloalkyl.
• B 2 comprises a silyl group.
• B 2 comprises a D- or L-amino acid.
• B 2 comprises a saccharide
• B 2 comprises a phosphate group.
• B 2 comprises a phosphonate group.
• B 2 comprises an aryl
• B 2 comprises a phenyl ring.
• B 2 is a phenyl ring.
• B 2 is CH.
• B 2 comprises a heteroaryl
• B 2 is selected from the group consisting of:
• B 3 is a trivalent group comprising 1 to 15 atoms and is covalently bonded to L 1 , T 1 , and T 2 .
• B 3 is a trivalent group comprising 1 to 10 atoms and is covalently bonded to L 1 , T 1 , and T 2 .
• B 3 comprises a (C1-C6)alkyl.
• B 3 comprises a C3-8 cycloalkyl.
• B 3 comprises a silyl group.
• B 3 comprises a D- or L-amino acid.
• B 3 comprises a saccharide
• B 3 comprises a phosphate group.
• B 3 comprises a phosphonate group.
• B 3 comprises an aryl
• B 3 comprises a phenyl ring.
• B 3 is a phenyl ring.
• B 3 is CH.
• B 3 comprises a heteroaryl
• B 3 is selected from the group consisting of:
• B 3 is selected from the group consisting of:
• L 1 is selected from the group consisting of:
• L 1 is selected from the group consisting of:
• L 2 is connected to R 2 through -O-.
• L 2 is C 1-4 alkylene-O- that is optionally substituted with hydroxy. In one embodiment, L 2 is connected to R 2 through -O-.
• L 2 is absent.
• the compound of formula (I) is selected from the group consisting of:
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• L 1 is absent or a linking group
• L 2 is absent or a linking group
• R 2 is a nucleic acid
• the ring A is absent, a 3-20 membered cycloalkyl, a 5-20 membered aryl, a 5-20 membered heteroaryl, or a 3-20 membered heterocycloalkyl;
• each R A is independently selected from the group consisting of hydrogen, hydroxy, CN, F, Cl, Br, I, -C 1-2 alkyl-OR B , C 1-10 alkyl C 2-10 alkenyl, and C 2-10 alkynyl; wherein the C 1-10 alkyl C 2-10 alkenyl, and C 2-10 alkynyl are optionally substituted with one or more groups
• R B is hydrogen, a protecting group, a covalent bond to a solid support, or a bond to a linking group that is bound to a solid support;
• n 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
• the compound of formula (I) is the compound,
• L 2 is absent or a linking group
• R 2 is a nucleic acid
• the ring A is absent, a 3-20 membered cycloalkyl, a 5-20 membered aryl, a 5-20 membered heteroaryl, or a 3-20 membered heterocycloalkyl;
• each R A is independently selected from the group consisting of hydrogen, hydroxy, CN, F, Cl, Br, I, -C1-2 alkyl-OR B , C1-10 alkyl C2-10 alkenyl, and C2-10 alkynyl; wherein the C1-10 alkyl C2-10 alkenyl, and C2-10 alkynyl are optionally substituted with one or more groups
• R B is hydrogen, a protecting group, a covalent bond to a solid support, or a bond to a linking group that is bound to a solid support;
• n 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;
• the compound of formula (I) is the compound,
• R 2 is a nucleic acid
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• the compound of formula (I) is the compound,
• R 1c is a saccharide
• B c is a 5-10 membered aryl or a 5-10 membered heteroaryl, which 5-10 membered aryl or 5-10 membered heteroaryl is optionally substituted with one or more groups independently selected from the group consisting of halo, hydroxy, cyano, trifluoromethyl, trifluoromethoxy, (C1-C6)alkyl, (C1-C6)alkoxy, (C1-C6)alkoxycarbonyl, (C1-C6)alkanoyloxy, (C3-C6)cycloalkyl, and (C3-C6)cycloalkyl(C1-C6)alkyl
• R 2c is a saccharide
• L 3c is absent or a linking group
• a c is a 3-20 membered cycloalkyl, a 5-20 membered aryl, a 5-20 membered heteroaryl, or a 3-20 membered heterocycloalkyl;
• each R Ac is independently selected from the group consisting of hydrogen, hydroxy, CN, F, Cl, Br, I, -C1-2 alkyl-OR a , C1-10 alkyl C2-10 alkenyl, and C2-10 alkynyl; wherein the C1-10 alkyl C2-10 alkenyl, and C2-10 alkynyl are optionally substituted with one or more groups independently selected from halo, hydroxy, and C 1-3 alkoxy;
• nc 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;
• L 4c is absent or a linking group
• R 3c is a nucleic acid
• R ac is hydrogen
• L 5c is a linking group
• B c is a 5-10 membered aryl.
• B c is naphthyl or phenyl.
• B c is phenyl
• B c is a 5-10 membered heteroaryl.
• B c is pyridyl, pyrimidyl, quinolyl, isoquinolyl, imidazolyl, thiazolyl, oxadiazolyl or oxazolyl.
• L 1c is:
• L 2c is:
• R 1c is:
• R 20 is hydrogen or (C1-C4)alkyl
• R 21 , R 22 , R 23 , R 24 , R 25 and R 26 are each independently selected from the group consisting of hydrogen, (C 1 -C 8 )alkyl, (C 1 -C 8 )alkoxy and (C 3 -C 6 )cycloalkyl, wherein any (C 1 - C8)alkyl, (C1-C8)alkoxy and (C3-C6)cycloalkyl is optionally substituted with one or more groups independently selected from the group consisting of halo, (C 1 -C 4 )alkyl, and (C 1 - C 4 )alkoxy;
• R 27 is–OH, -NR 25 R 26 or–F;
• R 28 is–OH, -NR 25 R 26 or–F;
• R 29 is–OH, -NR 25 R 26 , -F, -N 3 , -NR 35 R 36 , or 5 membered heterocycle that is optionally substituted with one or more groups independently selected from the group consisting of halo, hydroxyl, carboxyl, amino, (C1-C4)alkyl, aryl, and (C1-C4)alkoxy, wherein any (C1-C4)alkyl, and (C 1 -C 4 )alkoxy is optionally substituted with one or more groups independently selected from the group consisting of halo, and wherein any aryl is optionally substituted with one or more groups independently selected from the group consisting of halo, hydroxyl, nitro, cyano, amino, (C 1 -C 8 )alkyl, (C 1 -C 8 )alkoxy, (C 1 -C 8 )alkanoyl, (C 1 -C 8 )alkoxycarbonyl, (C 1 - C 8 )al
• each R 35 and R 36 is independently selected from the group consisting of hydrogen, (C1- C8)alkyl, (C1-C8)alkoxy and (C3-C6)cycloalkyl, wherein any (C1-C8)alkyl, (C1-C8)alkoxy and (C 3 -C 6 )cycloalkyl is optionally substituted with one or more groups independently selected from the group consisting of halo and (C1-C4)alkoxy; or R 35 and R 36 taken together with the nitrogen to which they are attached form a 5-6 membered heteroaryl ring, which heteroaryl ring is optionally substituted with one or more groups independently selected from the group consisting of (C 1 -C 8 )alkyl, (C 1 -C 8 )alkoxy, aryl, and (C 3 -C 6 )cycloalkyl, wherein any aryl, and (C3-C6)cycloalkyl is optionally substituted with one or more groups R 39 ;
• each R 37 and R 38 is independently selected from the group consisting of hydrogen, (C 1 - C 8 )alkyl, (C 1 -C 8 )alkoxy, (C 1 -C 8 )alkanoyl, (C 1 -C 8 )alkoxycarbonyl, (C 1 -C 8 )alkanoyloxy, and (C3-C6)cycloalkyl, wherein any (C1-C8)alkyl, (C1-C8)alkoxy, (C1-C8)alkanoyl, (C1- C 8 )alkoxycarbonyl, (C 1 -C 8 )alkanoyloxy, and (C 3 -C 6 )cycloalkyl is optionally substituted with one or more groups independently selected from the group consisting of halo, (C 1 -C 4 )alkyl, and (C1-C4)alkoxy; or R 37 and R 38 taken together with the nitrogen to which they are attached form a 5-8 membered
• each R 39 is independently selected from the group consisting of (C 1 -C 8 )alkyl, (C 1 - C8)alkoxy and (C3-C6)cycloalkyl, wherein any (C1-C8)alkyl, (C1-C8)alkoxy and (C3- C6)cycloalkyl is optionally substituted with one or more groups independently selected from halo.
• R 1c is:
• R 1c is:
• R 2c is:
• R 20 is hydrogen or (C 1 -C 4 )alkyl
• R 21 , R 22 , R 23 , R 24 , R 25 and R 26 are each independently selected from the group consisting of hydrogen, (C1-C8)alkyl, (C1-C8)alkoxy and (C3-C6)cycloalkyl, wherein any (C1- C 8 )alkyl, (C 1 -C 8 )alkoxy and (C 3 -C 6 )cycloalkyl is optionally substituted with one or more groups independently selected from the group consisting of halo, (C1-C4)alkyl, and (C1- C4)alkoxy;
• R 27 is -OH, -NR 25 R 26 or -F;
• R 28 is -OH, -NR 25 R 26 or -F;
• R 29 is -OH, -NR 25 R 26 , -F, -N3, -NR 35 R 36 , or 5 membered heterocycle that is optionally substituted with one or more groups independently selected from the group consisting of halo, hydroxyl, carboxyl, amino, (C 1 -C 4 )alkyl, aryl, and (C 1 -C 4 )alkoxy, wherein any (C 1 -C 4 )alkyl, and (C1-C4)alkoxy is optionally substituted with one or more groups independently selected from the group consisting of halo, and wherein any aryl is optionally substituted with one or more groups independently selected from the group consisting of halo, hydroxyl, nitro, cyano, amino, (C1-C8)alkyl, (C1-C8)alkoxy, (C1-C8)alkanoyl, (C1-C8)alkoxycarbonyl, (C1- C 8 )alkanoyloxy, and (
• each R 35 and R 36 is independently selected from the group consisting of hydrogen, (C 1 - C8)alkyl, (C1-C8)alkoxy and (C3-C6)cycloalkyl, wherein any (C1-C8)alkyl, (C1-C8)alkoxy and (C3-C6)cycloalkyl is optionally substituted with one or more groups independently selected from the group consisting of halo and (C 1 -C 4 )alkoxy; or R 35 and R 36 taken together with the nitrogen to which they are attached form a 5-6 membered heteroaryl ring, which heteroaryl ring is optionally substituted with one or more groups independently selected from the group consisting of (C 1 -C 8 )alkyl, (C 1 -C 8 )alkoxy, aryl, and (C 3 -C 6 )cycloalkyl, wherein any aryl, and (C3-C6)cycloalkyl is optionally substituted with one or more groups R 39 ;
• each R 37 and R 38 is independently selected from the group consisting of hydrogen, (C1- C 8 )alkyl, (C 1 -C 8 )alkoxy, (C 1 -C 8 )alkanoyl, (C 1 -C 8 )alkoxycarbonyl, (C 1 -C 8 )alkanoyloxy, and (C3-C6)cycloalkyl, wherein any (C1-C8)alkyl, (C1-C8)alkoxy, (C1-C8)alkanoyl, (C1- C8)alkoxycarbonyl, (C1-C8)alkanoyloxy, and (C3-C6)cycloalkyl is optionally substituted with one or more groups independently selected from the group consisting of halo, (C 1 -C 4 )alkyl, and (C1-C4)alkoxy; or R 37 and R 38 taken together with the nitrogen to which they are attached form a 5-8 membered heterocycle that is optionally substituted with
• each R 39 is independently selected from the group consisting of (C 1 -C 8 )alkyl, (C 1 - C 8 )alkoxy and (C 3 -C 6 )cycloalkyl, wherein any (C 1 -C 8 )alkyl, (C 1 -C 8 )alkoxy and (C 3 - C6)cycloalkyl is optionally substituted with one or more groups independently selected from halo.
• R 2c is:
• R 2c is:
• substituents selected from (C 1 -C 6 )alkoxy, (C 3 -C 6 )cycloalkyl, (C 1 -C 6 )alkanoyl, (C 1 -C 6 )alkanoyloxy, (C 1 - C 6 )alkoxycarbonyl, (C 1 -C 6 )alkylthio, azido, cyano, nitro, halo, hydroxy, oxo ( O), carboxy, aryl, aryloxy, heteroaryl, and heteroaryloxy.
• L 3c is:
• each R’ is independently C 1-9 alkyl, C 2-9 alkenyl or C 2-9 alkynyl; wherein the C 1-9 alkyl, C2-9 alkenyl or C2-9 alkynyl are optionally substituted with halo or hydroxyl.
• the group is selected from the group consisting of:
• each R’ is independently C1-9 alkyl, C2-9 alkenyl or C2-9 alkynyl; wherein the C1-9 alkyl, C2-9 alkenyl or C2-9 alkynyl are optionally substituted with halo or hydroxyl;
• L 4c is connected to R 3c through -O-. In one embodiment, R 3c is attached to the reminder of the conjugate through the oxygen of a phosphate of the nucleic acid molecule.
• R 3c is attached to the reminder of the conjugate through the oxygen of a phosphate at the 5’-end of a sense or the antisense strand.
• R 3c is attached to the reminder of the conjugate through the oxygen of a phosphate at the 3’-end of a sense or the antisense strand.
• R 3c is attached to the reminder of the conjugate through the oxygen of a phosphate at the 3’-end of a sense strand.
• the compound of formula (I) is selected from the group consisting of:
• the targeted nucleic acid conjugate is a targeted nucleic acid conjugate as described in WO2015/006740, WO2016/028649, US8,106,022B2,
• Membrane destabilizing polymers can be prepared using starting materials and synthetic methods that are similar to those described in International Patent Application Publication Numbers WO2015/017519 and WO2016/118697.
• Targeted nucleic acid conjugates can be prepared as described in International Patent Application Publication Number WO2017/177326 and as described below.
• the succinate 20 was loaded onto 1000 ⁇ LCAA (long chain aminoalkyl) CPG (control pore glass) using standard amide coupling chemistry.
• a solution of diisopropylcarbodiimide (52.6 ⁇ mol), N-hydroxy succinimide (0.3 mg, 2.6 ⁇ mol) and pyridine (10 ⁇ L) in anhydrous acetonitrile (0.3 mL) was added to 20 (20.6 mg, 8 ⁇ mol) in anhydrous dichloromethane (0.2 mL). This mixture was added to LCAA CPG (183 mg). The suspension was gently mixed overnight at room temperature.
• the reaction mixture was filtered and the CPG was washed with 1 mL of each dichloromethane, acetonitrile, a solution of 5% acetic anhydride / 5% N-methylimidazole / 5% pyridine in THF, then THF, acetonitrile and dichloromethane.
• the CPG was then dried overnight under high vacuum. Loading was determined by standard DMTr assay by UV/Vis (504 nm) to be 25 ⁇ mol/g.
• the resulting GalNAc loaded CPG solid support was employed in automated oligonucleotide synthesis using standard procedures. Nucleotide deprotection followed by removal from the solid support (with concurrent galactosamine acetate deprotection) afforded the GalNAc-oligonucleotide conjugate 1 as a representative example.
• a suspension of lithium aluminum hydride (13.6 g, 358 mmol) in anhydrous tetrahydrofuran (450 mL) was brought to reflux under a nitrogen atmosphere and treated, dropwise, with a solution of dimethyl-5-aminoisophthalte 25 (20 g, 96 mmol) in anhydrous tetrahydrofuran (350 mL). After the addition was complete the mixture was heated to reflux for an additional 2 hours. Upon completion, the solution was cooled to room temperature and quenched by the slow addition of MeOH (27 mL) then water (40 mL).
• Conjugate 36 was prepared using identical procedures as used to synthesize compound 34 and all corresponding intermediates. The only exception being the synthesis of compound 6 where propanoic anhydride was used in place of acetic anhydride.
• Example 4 Synthesis of conjugate 42 Scheme 9.
• Conjugate 142 was prepared from compound 141 (200 mg) and 1000A lcaa CPG (1.8 g) using an identical procedure to that used for compound 1. Yield: 1.9 g, 22 mol/g CPG loading.
• the resulting GalNAc loaded CPG solid support was employed in automated oligonucleotide synthesis using standard procedures. Nucleotide deprotection followed by removal from the solid support (with concurrent galactosamine acetate deprotection) afforded the GalNAc-oligonucleotide conjugate 142.
• Example 9 Synthesis of conjugate 145 Scheme 19.
• dichloromethane 75 mL was slowly added trifluoroacetic acid (75 ⁇ L). Stir overnight allowing the solution to slowly warm to room temperature as the ice bath melted. The reaction mixture was concentrated to dryness, dissolved in ethyl acetate (100 mL), washed with saturated sodium bicarbonate (2 x 100mL), dried on magnesium sulfate, filtered and concentrated to dryness.
• Conjugate 145 was prepared from compound 144 (200 mg) and 1000A lcaa CPG (1.8 g) using an identical procedure to that used for compound 1. Yield: 1.9 g, 20 mol/g CPG loading.
• the resulting GalNAc loaded CPG solid support was employed in automated oligonucleotide synthesis using standard procedures. Nucleotide deprotection followed by removal from the solid support (with concurrent galactosamine acetate deprotection) afforded the GalNAc-oligonucleotide conjugate 145.
• Example 10 Synthesis of conjugate 150 Scheme 21.
• Compound 146-5 was prepared from 2-amino-4-(hydroxymethyl)cyclopentanol 146-4 and 1-(2,5-dioxopyrrolidin-1-yl) 12-methyl dodecanedioate 146-1, using the same procedure as described in the synthesis of 12-(2-(tert-butoxycarbonylamino)ethylamino)-12- oxododecanoate (3-2). Methyl 12-(2-hydroxy-4-(hydroxymethyl)cyclopentylamino)-12- oxododecanoate 146-5 was obtained in 87.4% yield as an off-white solid. Step 6. Preparation of compound 147
• Compound 150 was prepared from compound 149 (436mg) and 1000A lcaa CPG (2.62g) using an identical procedure to that used for compound 1. Yield: 2.7g, 21.3 mol/g CPG loading.
• the resulting GalNAc loaded CPG solid support was employed in automated oligonucleotide synthesis using standard procedures. Nucleotide deprotection followed by removal from the solid support (with concurrent galactosamine acetate deprotection) afforded the GalNAc-oligonucleotide conjugate 150.
• Example 11 Synthesis of conjugates 153, 158, 163, 168 and 173 Scheme 22.
• AD-mix-b 47.4 g
• methanesulfonamide 2.89 g, 30.4 mmol
• the reaction was stirred at room temperature for 30 min and was then cooled to 0 o C.
• tert-Butyl 3-vinylpyrrolidine-1-carboxylate 164-1 (6.00g, 30.4 mmol) was added.
• the reaction was stirred at room temperature overnight.
• the reaction mixture was cooled to 0 o C.
• Sodium thiosulfate pentahydrate (96 g, 387 mmol) was added and the temperature was allowed to warm to room temperature.
• This substance was prepared from methyl 12-(3-(1,2-dihydroxyethyl)pyrrolidin-1-yl)- 12-oxododecanoate 164-4 and 4,4-dimethoxytrityl chloride (1 eq) using the same procedure as described in the synthesis of 2-(2-(bis(4-methoxyphenyl)(phenyl)methoxy)ethyl)isoindoline- 1,3-dione 138. The product was purified by column chromatography (1.5%
• Methyl 12-(3-(2-(bis(4-methoxyphenyl)(phenyl)methoxy)-1- hydroxyethyl)pyrrolidin-1-yl)-12-oxododecanoate 164 was obtained in 51% yield as a yellow oil.
• Compound 170-4 was synthesized from (S)-2,2-dimethyl-1,3-dioxolane-4-carboxylic acid 170-3 and N-hydroxysuccinimide in 86% yield, using the same procedure as described in the synthesis of 1-(2,5-dioxopyrrolidin-1-yl) 12-methyl dodecanedioate 146-1.
• (S)-2,5- Dioxopyrrolidin-1-yl 2,2-dimethyl-1,3-dioxolane-4-carboxylate 170-4 was obtained in 86% yield as a white solid. Step 20. Preparation of Compound 170-5
• Conjugates 153, 158, 163, 168 and 173 were prepared from compound 139, 154, 159, 164 and 169 using an identical procedure to that used for compound 1.
• Conjugate 176 was prepared from compounds 24 and 130 using an identical procedure to that used for compound 1.
• Example 13 Synthesis of conjugate 179 Scheme 29.
• Conjugate 179 was prepared from compounds 18 and 81 using an identical procedure to that used for compound 1.
• Example 14 Synthesis of conjugate 182 Scheme 31.

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