WO2025228429A1 - Oligonucléotide ciblant le gène de la protéine précurseur de l'amyloïde et son utilisation - Google Patents
Oligonucléotide ciblant le gène de la protéine précurseur de l'amyloïde et son utilisationInfo
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/70—Carbohydrates; Sugars; Derivatives thereof
- A61K31/7088—Compounds having three or more nucleosides or nucleotides
- A61K31/712—Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/70—Carbohydrates; Sugars; Derivatives thereof
- A61K31/7088—Compounds having three or more nucleosides or nucleotides
- A61K31/7125—Nucleic acids or oligonucleotides having modified internucleoside linkage, i.e. other than 3'-5' phosphodiesters
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P25/00—Drugs for disorders of the nervous system
- A61P25/28—Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
- C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
Definitions
- This disclosure relates to an oligonucleotide, particularly to the inhibition of amyloid precursor protein (APP) gene expression and the treatment of diseases caused by APP cleavage product ⁇ -amyloid protein.
- APP amyloid precursor protein
- Amyloid precursor protein is a single transmembrane protein that is widely distributed in cells throughout the body. After being cleaved by proteases, it produces toxic ⁇ -amyloid protein. To date, little is known about the true physiological function of APP. Many researchers believe that the senile plaques formed by A ⁇ deposition after APP cleavage are an important cause of Alzheimer's disease (AD).
- AD Alzheimer's disease
- AD Alzheimer's disease
- a ⁇ ⁇ -amyloid protein
- APP ⁇ -amyloid protein
- a ⁇ undergoes two main degradation pathways: most is hydrolyzed by ⁇ -secretase to generate sAPP ⁇ and C-terminal ⁇ fragments; a smaller portion is cleaved by ⁇ -secretase and ⁇ -secretase to generate A ⁇ (mainly A ⁇ 40 and A ⁇ 42) capable of forming amyloid aggregates.
- a ⁇ monomers and oligomers can produce neurocytotoxic effects under different in vivo and in vitro conditions.
- Tau protein is a microtubule-binding protein involved in neuronal axonal transport and polarity establishment.
- AD Alzheimer's disease
- Tau protein undergoes extensive post-translational modifications, such as phosphorylation, which reduces the binding of Tau protein to microtubules, affects the formation and stability of neuronal microtubules, and participates in neurodegenerative diseases.
- AD Alzheimer's disease
- memory loss a neurodegenerative disorder that affects approximately 35 million people worldwide, primarily those over 65.
- age-related pathological manifestations are becoming increasingly frequent, and some studies suggest this number will triple by 2050.
- Common clinical features of AD include cognitive impairment, memory loss, language difficulties, aberrations in mood and behavior, and disorientation in time and space, all of which hinder patients' ability to perform normal daily activities.
- NFTs neurofibrillary tangles
- SPs senile plaques
- Figure 1 neuronal loss, ultimately leading to brain atrophy
- NFTs consist of aberrant Tau protein aggregates.
- Tau protein contributes to cytoskeleton structure by stabilizing the microtubule network through interaction with tubulin.
- it may undergo various post-transcriptional modifications, such as breakage or hyperphosphorylation.
- breakage or hyperphosphorylation Although the reasons for activating these modifications remain elusive, there is evidence that this hyperphosphorylated form is prone to aggregation, leading to the formation of toxic NFTs that accumulate intracellularly, primarily in the hippocampus.
- a ⁇ ⁇ -amyloid
- APP a transmembrane protein found in neurons, can be processed through two different pathways: the amyloid-beta (A ⁇ ) synthesis pathway and the non-amyloid-beta (NAB) synthesis pathway, both mediated by secreted enzymes. Its deposition and neurotoxicity are mainly caused by three factors: abnormal A ⁇ anabolic metabolism, decreased A ⁇ catabolism, and A ⁇ transport imbalance.
- a ⁇ neurotoxicity involves complex molecular mechanisms, primarily including promoting free radical formation, disrupting intracellular Ca2+ homeostasis, reducing K+ channel function, enhancing inflammatory responses induced by pro-inflammatory cytokines, damaging small blood vessels causing ischemia and activating amyloid enzymes, inhibiting neural stem cell proliferation and differentiation, and potentially inducing apoptosis. These toxic factors can also interact, creating a vicious cycle, especially the relationship between A ⁇ neurotoxicity and oxidative stress, ultimately leading to neuronal apoptosis and dementia.
- CAA cerebral amyloid angiopathy
- EFAD early-onset familial Alzheimer's disease
- a ⁇ -guided immunotherapies are at various stages of development, and many human ⁇ -secretase inhibitor programs have been discontinued due to toxicity (Selkoe and Hardy.
- APP-related diseases or conditions are symptomatic treatments, not preventative or curative, and their effectiveness is limited, especially when APP-related diseases or conditions develop in affected individuals. Therefore, treatment is needed for individuals with APP-related diseases and conditions, including, in particular, individuals with hereditary CAA and EOFAD.
- the purpose of this disclosure is to provide an inhibitor of APP expression that is effective, safe, and has a long-lasting effect.
- This document also provides compositions and methods for treating pathological conditions and diseases in mammals caused by the deposition of APP cleavage product ⁇ -amyloid protein.
- the oligonucleotides are double-stranded RNAs (dsRNAs), which direct sequence-specific degradation of mRNA through a process called RNA interference (RNAi).
- this disclosure provides an oligonucleotide or a pharmaceutically acceptable salt thereof for inhibiting APP gene expression, the oligonucleotide comprising a sense strand and an antisense strand, the sense strand having at least 60% sequence identity with any sequence or fragment thereof shown in SEQ ID NO. 1-141, or a modified sequence thereof, preferably having at least 65%, 70%, 75%, 80%, 85%, 90%, or 95% sequence identity; the antisense strand having at least 60% sequence identity with any sequence or fragment thereof shown in SEQ ID NO. 144-284, or a modified sequence thereof, preferably having at least 65%, 70%, 75%, 80%, 85%, 90%, or 95% sequence identity.
- this disclosure provides a conjugate or a pharmaceutically acceptable salt thereof for inhibiting APP gene expression.
- this disclosure provides a composition
- a composition comprising the aforementioned oligonucleotide or a pharmaceutically acceptable salt thereof, or the aforementioned conjugate or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable carrier.
- this disclosure provides the use of the aforementioned oligonucleotides or pharmaceutically acceptable salts thereof, conjugates thereof, or compositions in the preparation of medicaments for the treatment and/or prevention of APP-related conditions.
- this disclosure provides a method for treating and/or preventing APP-related conditions in a subject by administering a therapeutic agent (e.g., the aforementioned oligonucleotide or a pharmaceutically acceptable salt thereof, or the aforementioned conjugate or a pharmaceutically acceptable salt thereof, or the aforementioned composition, or a vector or transgene encoding an oligonucleotide) to the subject.
- a therapeutic agent e.g., the aforementioned oligonucleotide or a pharmaceutically acceptable salt thereof, or the aforementioned conjugate or a pharmaceutically acceptable salt thereof, or the aforementioned composition, or a vector or transgene encoding an oligonucleotide
- this disclosure provides a method for treating and/or preventing APP-related conditions in subjects in combination with other drugs and/or other treatments.
- oligonucleotides disclosed herein can effectively reduce the level of APP in the body and are an effective inhibitor of ⁇ -amyloid protein.
- Figure 1 illustrates the pathogenesis of Alzheimer's disease, where mTORC1: mammalian target of rapamycin complex 1; ULK1: unc-51-like autophagy-activated kinase 1; NOS: nitric oxide synthase; SOD: superoxide dismutase; catalase: catalase; NOS: nitric oxide synthase; Beclin1: a protein that regulates autophagy; mTORC1: target of rapamycin 1; ULK1: protein kinase of upstream autophagy signaling; COX-2: cyclooxygenase-2; NF- ⁇ B: nuclear factor ⁇ B; iNOS: inducible nitric oxide synthase.
- mTORC1 mammalian target of rapamycin complex 1
- ULK1 unc-51-like autophagy-activated kinase 1
- NOS nitric oxide synthase
- SOD super
- Figure 2 shows a flowchart of oligonucleotide solid-phase synthesis.
- the term “about” or “approximately” when applied to one or more target values refers to a value similar to a reference value.
- the term “approximately” or “about” refers to a range of values falling within 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1% or less of the reference value in any direction (unless such a number would exceed 100% of the possible value).
- nucleotides e.g., two nucleotides on opposing nucleic acids or on opposing regions of a single nucleic acid strand
- nucleotides e.g., two nucleotides on opposing nucleic acids or on opposing regions of a single nucleic acid strand
- a purine nucleotide complementary to a pyrimidine nucleotide of an opposing nucleic acid can be base-paired together by forming hydrogen bonds with each other.
- complementary nucleotides may be base-paired in a Watson-Crick manner or in any other manner that allows the formation of a stable duplex.
- the two nucleic acids may have nucleotide sequences that are complementary to each other to form complementary regions, as described herein.
- chain refers to a single, continuous sequence of nucleotides linked together by internucleotide bonds (e.g., phosphodiester bonds, thiophosphate bonds). In some embodiments, the chain has two free ends, such as a 5'-end and a 3'-end.
- deoxyribonucleotide refers to a nucleotide that has a hydrogen atom at the 2' position of its pentose sugar compared to a ribonucleotide.
- a modified deoxyribonucleotide is a deoxyribonucleotide that has one or more modifications or substitutions (including modifications or substitutions in sugars, phosphate groups, or bases) other than at the 2' position.
- oligonucleotide refers to a short nucleic acid, such as a short nucleic acid less than 100 nucleotides in length. Oligonucleotides may comprise ribonucleotides, deoxyribonucleotides, and/or modified nucleotides, including, for example, modified ribonucleotides. Oligonucleotides may be single-stranded or double-stranded. Oligonucleotides may or may not have a double-stranded region.
- oligonucleotides may be, but are not limited to, small interfering RNA (siRNA), microRNA (miRNA), short hairpin RNA (shRNA), Dicer substrate interfering RNA (dsiRNA), antisense oligonucleotides, short siRNA, or single-stranded siRNA.
- the double-stranded oligonucleotide is an RNAi oligonucleotide.
- double-stranded oligonucleotide refers to an oligonucleotide that is substantially in a double-stranded form.
- complementary base pairings are formed between antiparallel sequences of nucleotides in covalently separated nucleic acid chains, forming one or more double-stranded regions of the double-stranded oligonucleotide.
- complementary base pairings are formed between antiparallel sequences of nucleotides in covalently linked nucleic acid chains.
- complementary base pairings of one or more double-stranded regions of the double-stranded oligonucleotide are formed from a single nucleic acid chain folded (e.g., via a hairpin) to provide complementary antiparallel sequences of nucleotides that are base-paired together.
- the double-stranded oligonucleotide comprises two covalently separated nucleic acid chains that are fully double-stranded with each other.
- the double-stranded oligonucleotide comprises two covalently separated nucleic acid chains that are partially double-stranded, for example, having overhangs at one or both ends.
- the double-stranded oligonucleotide comprises antiparallel sequences of nucleotides that are partially complementary, and therefore may have one or more mismatches, which may include internal mismatches or terminal mismatches.
- double-stranded RNA refers to a complex of ribonucleic acid molecules having a double-stranded structure comprising two antiparallel and substantially complementary nucleic acid strands with "sense” and “antisense” orientations relative to the target RNA (i.e., the APP gene).
- the double-stranded RNA dsRNA
- the double-stranded RNA triggers the degradation of the target RNA (e.g., mRNA) through a post-transcriptional gene silencing mechanism referred to herein as RNA interference or RNAi.
- RNAi may contain chemically modified ribonucleotides; RNAi may include substantial modifications at multiple nucleotide sites.
- RNAi As used herein, the terms “RNAi,” “iRNA,” “RNAi agent,” and “RNA interfering agent” are used interchangeably to refer to an RNA containing the terms defined herein and an agent that mediates the targeted cleavage of RNA transcripts via the RNA-inducible silencing complex (RISC) pathway.
- RISC RNA-inducible silencing complex
- RNA interference is a process that directs the specific degradation of mRNA sequences. RNAi regulates, for example, the inhibition of APP expression in cells, such as within an individual, such as a mammalian individual.
- conjugation refers to the covalent connection between two or more chemical moieties, each with a specific function; correspondingly, “conjugated compound” refers to a compound formed by the covalent connection of these chemical moieties.
- siRNA conjugated compound refers to a compound formed by the covalent attachment of one or more chemical moieties with specific functions to siRNA.
- siRNA conjugated compounds of this disclosure will sometimes be simply referred to as “conjugated compounds.”
- siRNA conjugated compound should be understood, depending on the context, as a general term for siRNA conjugated compounds, including first-type or second-type siRNA conjugated compounds, or siRNA sense strand conjugated compounds or siRNA antisense strand conjugated compounds.
- naked sequence refers to an unmodified nucleotide sequence.
- inhibitortion is used interchangeably with “knockdown,” “reduction,” “silence,” “downregulation,” “suppression,” and other similar terms, and includes any degree of inhibition.
- inhibitor APP expression is intended to refer to the suppression of the expression of any APP gene (e.g., mouse APP gene, rat APP gene, monkey APP gene, or human APP gene) and variants or mutants of the APP gene. Therefore, in the context of gene manipulation of cells, cell populations, or organisms, the APP gene can be a wild-type APP gene, a mutant APP gene, or a transgenic APP gene.
- APP gene e.g., mouse APP gene, rat APP gene, monkey APP gene, or human APP gene
- “Suppression of APP gene expression” includes suppression of the APP gene at any level, such as at least partial suppression of APP gene expression.
- APP gene expression can be assessed based on the level or changes in the level of any variable associated with APP gene expression, such as APP mRNA level or APP protein level, or indirectly by suppressing the mRNA level of the Gluc and APP fusion protein gene, thereby suppressing the Gluc protein level.
- salts derived from inorganic bases include, but are not limited to, alkali metal salts (such as sodium, potassium, and lithium salts), ammonium salts, and alkaline earth metal salts (such as calcium and magnesium salts).
- Salts derived from organic bases include, but are not limited to, salts formed with organic bases such as organic amines: primary amines, secondary amines, and tertiary amines.
- Substituted amines include naturally occurring substituted amines, cyclic amines, and basic ion exchange resins such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, ethanolamine, lysine, arginine, N-ethylpiperidine, piperidine, and polyamine resins.
- the oligonucleotides of this disclosure may also exist in zwitterionic form.
- Particularly preferred pharmaceutical salts of this disclosure are sodium salts, lithium salts, potassium salts, and trialkylammonium salts.
- the term "subject" refers to an animal that expresses the target gene endogenously or heterologously, such as a mammal, including primates (e.g., humans, non-human primates such as monkeys and chimpanzees), non-primates (e.g., cattle, pigs, horses, goats, rabbits, sheep, hamsters, guinea pigs, cats, dogs, rats, or mice), or birds.
- the subject is a human.
- RNAi agent As used herein, the term "therapeutic effective amount” is intended to encompass the amount of RNAi agent that, when administered to a subject with APP-related conditions, is sufficient to affect the treatment of the disease (e.g., by reducing, improving, or maintaining existing disease or symptoms of one or more diseases). "Therapeutic effective amount” may vary depending on the RNAi agent, how the agent is administered, the disease and its severity, as well as medical history, age, weight, family history, genetic makeup, type of prior or concomitant treatment (if any), and other individual characteristics of the subject being treated.
- the term "preventive effective dose” is intended to encompass the amount of RNAi agent sufficient to prevent or improve the condition or one or more symptoms of the condition when administered to a subject with APP-related disease. Improving the disease includes slowing its progression or reducing the severity of later-stage disease. "Preventive effective dose” may vary depending on the RNAi agent, how it is administered, the degree of disease risk, and factors such as medical history, age, weight, family history, genetic makeup, type of prior or concomitant treatment (if any), and other individual characteristics of the patient to be treated.
- the term "pharmaceutically acceptable carrier” refers to a pharmaceutically acceptable material, composition, or medium, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, magnesium talc, calcium stearate, zinc stearate, or stearic acid), or solvent encapsulation material (involving the carrying or delivery of a subject compound from one organ or part of the body to another organ or part of the body).
- manufacturing aid e.g., lubricant, magnesium talc, calcium stearate, zinc stearate, or stearic acid
- solvent encapsulation material involving the carrying or delivery of a subject compound from one organ or part of the body to another organ or part of the body.
- Each carrier must be “acceptable” in the sense that it is compatible with the other components of the formulation and harmless to the treated subject.
- Pharmaceutically acceptable carriers include carriers intended for administration by injection.
- APP is a systemically expressed protein, does not exhibit tissue-specific expression, and is present in circulation.
- Inhibition can be assessed by a reduction in the absolute or relative level of one or more variables associated with APP expression compared to a control level.
- the control level can be any type of control level used in the art, such as baseline levels before administration, or levels determined from similar subjects who were untreated or treated with a control (e.g., a buffer-only control or an inactive agent control).
- this disclosure provides an oligonucleotide or a pharmaceutically acceptable salt thereof for inhibiting APP expression, the oligonucleotide comprising a sense strand and an antisense strand, the sense strand having at least 60% sequence identity with any sequence or fragment thereof shown in SEQ ID NO. 1-141, or a modified sequence thereof, preferably having at least 65%, 70%, 75%, 80%, 85%, 90%, or 95% sequence identity; the antisense strand having at least 60% sequence identity with any sequence or fragment thereof shown in SEQ ID NO. 144-284, or a modified sequence thereof, preferably having at least 65%, 70%, 75%, 80%, 85%, 90%, or 95% sequence identity.
- the sense strand and/or antisense strand are 15-30, 17-25, or 19 to 25 nucleotides in length.
- the antisense strand is 19 to 23 nucleotides in length.
- the justice chain has one or two protruding ends.
- the oligonucleotide comprises a 3'-overhang sequence of one or two nucleotides in length.
- the oligonucleotide comprises a 5'-protruding sequence of one or two nucleotides in length.
- the 3′-protruding sequence is present on the antisense strand.
- the protruding sequence is selected from: AA, AC, AG, AU, CA, CC, CG, CU, GA, GC, GG, GU, UA, UC, UG, UU.
- the 5′-protrusion sequence is present on the antisense strand. In some implementations, the protrusion sequence is selected from A and G.
- the oligonucleotide comprises an antisense strand and a sense strand, each ranging in length from 19 to 25 nucleotides.
- the oligonucleotide comprises an antisense strand and a sense strand, each ranging in length from 19 to 23 nucleotides.
- the justice chain and the antisense chain form a dual-chain region.
- the justice chain and the antisense chain are bichain structures with 19/21 pairing, 21/21 pairing, 21/23 pairing, or 23/23 pairing, respectively.
- the oligonucleotide comprises a 5' overhang and a 3' overhang sequence of length 1 nucleotide, wherein the 5' overhang and the 3' overhang sequence are present on the antisense strand, and wherein the sense strand is 19 nucleotides long and the antisense strand is 21 nucleotides long, such that the sense strand and the antisense strand form a double helix of length 19 nucleotides.
- the oligonucleotide includes a 3'-overhang sequence of 2 nucleotides in length, wherein the 3'-overhang sequence is present on the antisense strand, and wherein the sense strand is 19 nucleotides in length and the antisense strand is 21 nucleotides in length, such that the sense strand and the antisense strand form a double helix of 19 nucleotides in length.
- the oligonucleotide includes a 3'-overhang sequence of 2 nucleotides in length, wherein the 3'-overhang sequence is present on both the antisense and sense strands, and wherein the sense strand is 21 nucleotides in length and the antisense strand is 21 nucleotides in length, such that the sense and antisense strands form a doublet of 19 nucleotides in length.
- the oligonucleotide includes a 3'-overhang sequence of 2 nucleotides in length, wherein the 3'-overhang sequence is present on the antisense strand, and wherein the sense strand is 21 nucleotides in length and the antisense strand is 23 nucleotides in length, such that the sense strand and the antisense strand form a double helix of 21 nucleotides in length.
- the oligonucleotide includes a 3'-overhang sequence of 2 nucleotides in length, wherein the 3'-overhang sequence is present on both the antisense and sense strands, and wherein the sense strand is 23 nucleotides in length and the antisense strand is 23 nucleotides in length, such that the sense and antisense strands form a doublet of 21 nucleotides in length.
- pharmaceutically acceptable salts of oligonucleotides can be prepared by adding an inorganic or organic base to a free acid.
- Salts derived from inorganic bases include, but are not limited to, alkali metal salts (such as sodium, potassium, and lithium salts), ammonium salts, and alkaline earth metal salts (such as calcium and magnesium salts).
- Salts derived from organic bases include, but are not limited to, salts formed with the following organic bases: primary amines, secondary amines, and tertiary amines; substituted amines include naturally occurring substituted amines, cyclic amines, and basic ion exchange resins such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, ethanolamine, lysine, arginine, N-ethylpiperidine, piperidine, and polyamine resins.
- organic bases e.g., organic amines
- substituted amines include naturally occurring substituted amines, cyclic amines, and basic ion exchange resins such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, ethanolamine, lysine, arginine, N-ethylpiperidine, piperidine, and polyamine resins.
- pharmaceutically acceptable salts of oligonucleotides include, but are not limited to, ammonium salts, such as salts of tertiary alkylamine compounds (e.g., triethylamine salts), metal salts such as sodium, potassium, and magnesium salts, etc.
- ammonium salts such as salts of tertiary alkylamine compounds (e.g., triethylamine salts)
- metal salts such as sodium, potassium, and magnesium salts, etc.
- the oligonucleotide or its salt may be in the form of a hydrate or a solvate.
- the oligonucleotide contains at least one modified nucleotide.
- At least one of the modified nucleotides is selected from the group consisting of: deoxynucleotides, 3′-terminal deoxythymidine (dT) nucleotides, 2′-O-methyl modified nucleotides, 2′-fluorine modified nucleotides, 2′-deoxy modified nucleotides, locked nucleotides, 2′-5′-linked ribonucleotides (3′-RNA), unlocked nucleotides, conformation-restricted nucleotides, restricted ethyl nucleotides, base-free nucleotides, 2′-amino modified nucleotides, 2′-O-allyl modified nucleotides, 2′-O-alkyl modified nucleotides, 2′-hydroxy modified nucleotides, 2′- Nucleotides modified with methoxyethyl, 2′-O-alkyl, morpholinonucleotides, aminophosphates
- At least one of the modified nucleotides is selected from the group consisting of: LNA-modified nucleotides, HNA-modified nucleotides, CeNA-modified nucleotides, 2′-methoxyethyl-modified nucleotides, 2′-O-alkyl-modified nucleotides, 2′-O-allyl-modified nucleotides, 2′-C-allyl-modified nucleotides, 2′-fluorine-modified nucleotides, 2′-deoxy-modified nucleotides, 2′-hydroxy-modified nucleotides, and ethylene glycol-modified nucleotides; and combinations thereof.
- At least one of the modified nucleotides is selected from the group consisting of: deoxynucleotides, 2′-O-methyl modified nucleotides, 2′-fluorine modified nucleotides, 2′-deoxy modified nucleotides, ethylene glycol modified nucleotides (GNA), nucleotides comprising 2′ phosphate esters, and nucleotides comprising thiophosphate ester groups; and combinations thereof.
- the oligonucleotide contains at least one 2′-modified nucleotide.
- the 2′-modified nucleotide is selected from the group consisting of: 2′-alkoxy-modified nucleotides, 2′-substituted alkoxy-modified nucleotides, 2′-alkyl-modified nucleotides, 2′-substituted alkyl-modified nucleotides, 2′-fluorine-modified nucleotides, 2′-acylamino-modified nucleotides, 2′-deoxy-modified nucleotides, 2′-O-allyl-modified nucleotides, 2′-O-alkyl-modified nucleotides, 2′-hydroxy-modified nucleotides, 2′-methoxyethyl-modified nucleotides, 2′-amino-modified nucleotides, 2′-substituted amino-modified nucleotides, 2′-deoxynucleotides, nucleotides
- Examples include C1-C3 alkoxy groups (e.g., methoxy); substituted alkoxy groups (e.g., C1 - C3 alkoxy-substituted C1 - C3 alkoxy groups, such as methoxyethoxy); alkyl groups (e.g., C1 - C3 alkyl groups, such as methyl); substituted alkyl groups (e.g., C1 - C3 alkoxy-substituted C1 - C3 alkyl groups, such as methoxymethyl, methoxyethyl); amino groups ( -NH2 ); substituted amino groups (e.g., C1 - C3 alkyl mono- or di-substituted amino groups, such as methylamino, ethylamino), but not limited thereto.
- alkyl groups e.g., C1 - C3 alkyl groups, such as methyl
- substituted alkyl groups e.g., C1
- the 2′-modified nucleotide is selected from the group consisting of: 2′-alkoxy-modified nucleotides, 2′-substituted alkoxy-modified nucleotides, 2′-alkyl-modified nucleotides, 2′-substituted alkyl-modified nucleotides, 2′-amino-modified nucleotides, 2′-substituted amino-modified nucleotides, 2′-deoxynucleotides; and combinations thereof.
- the 2′-modification is selected from the group consisting of 2′-methoxy, 2′-acetamido, 2′-aminoethyl, 2′-fluoro, 2′-O-methyl and 2′-O-methoxyethyl modifications; and combinations thereof.
- the 2′-modification is a 2′-methoxy modification.
- the 2′-modification is a 2′-acetamido modification.
- all nucleotides of the oligonucleotide are modified.
- the oligonucleotide includes a modification at the 5' end, which contains a 5′-phosphate analog or 6-(3-(2-carboxyethyl)phenyl)purine (6-mCEPh-purine).
- the oligonucleotide has a 5'-phosphate analog modified nucleotide at its 5' end.
- the 5′-phosphate analogue is modified to 5′-(E)-vinylphosphonate (5′-VP).
- the 5′ end of the nucleotide containing 5′-(E)-vinylphosphonate modification has the structure shown in formula (I); wherein, Base represents a natural or modified base; preferably Base is selected from A, G, C and U; and R is selected from H, fluorine, 2′-methoxy, 2′-acetamido, 2′-aminoethyl and 2′-O-methoxyethyl.
- the oligonucleotide comprises a 5'-(E)-vinylphosphonate-modified nucleotide at its 5' end, having the structure shown in formula (II); wherein R is selected from H, fluorine, 2′-methoxy, 2′-acetamido, 2′-aminoethyl, and 2′-O-methoxyethyl.
- the oligonucleotide has an APU at its 5' end, which is a uridine monophosphate (2′-acetamido-5′-vinylphosphonate-uridine monophosphate) modified with a 5'-phosphate analog as shown in formula (III).
- the oligonucleotide has a VPUm at its 5' end, which is a uridine monophosphate (2′-methoxy-5′-vinylphosphonate-uridine monophosphate) modified with a 5'-phosphate analog as shown in formula (IV).
- the modification is selected from the following: 5'-phosphate analog modification, 2′-methoxy ( CH3O- , m), 2′-fluorine (f), 2′-acetamido ( CH3CO -NH-), and thiophosphate (s).
- the oligonucleotide comprises a 6-(3-(2-carboxyethyl)phenyl)purine-modified nucleotide at its 5' end.
- the oligonucleotide comprises formula M, which is a 2'-O-methyl-6-(3-(2-carboxyethyl)phenyl)-purine nucleotide as shown in formula (V);
- the oligonucleotide comprises uridine-2'-phosphate (U-2'5') as shown in formula (VI), guanosine-2'-phosphate (G-2'5') as shown in formula (VII); cytidine-2'-phosphate (C-2'5') as shown in formula (VIII); adenosine-2'-phosphate (A-2'5') as shown in formula (IX); and thymidine-2'-phosphate (T-2'5') as shown in formula (X).
- U-2'5' uridine-2'-phosphate
- G-2'5' guanosine-2'-phosphate
- C-2'5' cytidine-2'-phosphate
- A-2'5' as shown in formula (IX)
- T-2'5' thymidine-2'-phosphate
- the oligonucleotide contains at least one modified nucleotide inter-bond.
- At least one modified nucleotide inter-bond is a phosphate-thioester bond.
- Phospho-thioester inter-bond modification can occur at any position on any nucleotide of the sense strand, antisense strand, or both strands.
- the inter-bond modification can occur on each nucleotide of the sense strand or antisense strand; each inter-bond modification can occur in an alternating pattern on the sense strand or antisense strand; or the sense strand or antisense strand can contain two inter-bond modifications in an alternating pattern.
- the alternating pattern of the inter-bond modification on the sense strand can be the same as or different from that on the antisense strand, and the alternating pattern of the inter-bond modification on the sense strand can be offset relative to the alternating pattern of the inter-bond on the antisense strand.
- the double-stranded RNAi agent comprises 6 to 8 phosphate-thioester inter-bonds.
- the antisense strand comprises two phosphate-thioester inter-bonds at the 5' end and two phosphate-thioester inter-bonds at the 3' end, and the sense strand comprises at least two phosphate-thioester inter-bonds at either the 5' or 3' end.
- the aforementioned positive chain comprises an unmodified oligonucleotide selected from any of SEQ ID NO. 15, 25, 26, 27, 29, 31, 49, 50, 51, 53, 54, 55, 60, 62, 64, 98, 101, 102, 103, 105, 106, 107, 112, 113, 119, 123, 124, 125, 127, 128, 129, 130, 131, 132, or 133, or a modified oligonucleotide selected from any of SEQ ID NO: 287-427; the aforementioned anti The sense strand comprises an unmodified oligonucleotide selected from any of SEQ ID NO.
- the aforementioned chain of justice includes modifications selected from any one of SEQ ID NO. 301, 311, 312, 313, 315, 317, 335, 336, 337, 339, 340, 341, 346, 348, 350, 384, 387, 388, 389, 391, 392, 393, 398, 399, 405, 409, 410, 411, 413, 414, 415, 416, 417, 418, or 419.
- Oligonucleotides; the aforementioned antisense strand comprises a modified oligonucleotide selected from any one of SEQ ID NO.
- the aforementioned oligonucleotide is selected from any of the following combinations of sense and antisense strands:
- the positive chain contains the sequence shown in SEQ ID NO.15, and the negative chain contains the sequence shown in SEQ ID NO.158;
- the positive chain contains the sequence shown in SEQ ID NO.27, and the negative chain contains the sequence shown in SEQ ID NO.170;
- the positive chain contains the sequence shown in SEQ ID NO.29, and the negative chain contains the sequence shown in SEQ ID NO.172;
- the positive chain contains the sequence shown in SEQ ID NO.31, and the negative chain contains the sequence shown in SEQ ID NO.174;
- the positive chain contains the sequence shown in SEQ ID NO.49, and the negative chain contains the sequence shown in SEQ ID NO.192;
- the sense chain contains the sequence shown in SEQ ID NO.50, and the antisense chain contains the sequence shown in SEQ ID NO.193;
- the positive chain contains the sequence shown in SEQ ID NO. 51, and the negative chain contains the sequence shown in SEQ ID NO. 194;
- the positive chain contains the sequence shown in SEQ ID NO.53, and the negative chain contains the sequence shown in SEQ ID NO.196;
- the positive chain contains the sequence shown in SEQ ID NO.54, and the negative chain contains the sequence shown in SEQ ID NO.197;
- the positive chain contains the sequence shown in SEQ ID NO.55, and the negative chain contains the sequence shown in SEQ ID NO.198;
- the positive chain contains the sequence shown in SEQ ID NO. 60, and the negative chain contains the sequence shown in SEQ ID NO. 203;
- the positive chain contains the sequence shown in SEQ ID NO. 62, and the negative chain contains the sequence shown in SEQ ID NO. 205;
- the positive chain contains the sequence shown in SEQ ID NO. 64, and the negative chain contains the sequence shown in SEQ ID NO. 207;
- the positive chain contains the sequence shown in SEQ ID NO.98, and the negative chain contains the sequence shown in SEQ ID NO.241;
- the positive chain contains the sequence shown in SEQ ID NO.102, and the negative chain contains the sequence shown in SEQ ID NO.245;
- the positive chain contains the sequence shown in SEQ ID NO.106, and the negative chain contains the sequence shown in SEQ ID NO.249;
- the positive chain contains the sequence shown in SEQ ID NO.107, and the negative chain contains the sequence shown in SEQ ID NO.250;
- the positive chain contains the sequence shown in SEQ ID NO.112, and the negative chain contains the sequence shown in SEQ ID NO.255;
- the positive chain contains the sequence shown in SEQ ID NO.113, and the negative chain contains the sequence shown in SEQ ID NO.256;
- the positive chain contains the sequence shown in SEQ ID NO.119, and the negative chain contains the sequence shown in SEQ ID NO.262;
- the positive chain contains the sequence shown in SEQ ID NO.123, and the negative chain contains the sequence shown in SEQ ID NO.266;
- the positive chain contains the sequence shown in SEQ ID NO.124, and the negative chain contains the sequence shown in SEQ ID NO.267;
- the positive chain contains the sequence shown in SEQ ID NO.125, and the negative chain contains the sequence shown in SEQ ID NO.268;
- the sense chain contains the sequence shown in SEQ ID NO.127, and the antisense chain contains the sequence shown in SEQ ID NO.270;
- the positive chain contains the sequence shown in SEQ ID NO.128, and the negative chain contains the sequence shown in SEQ ID NO.271;
- the positive chain contains the sequence shown in SEQ ID NO.129, and the negative chain contains the sequence shown in SEQ ID NO.272;
- the sense chain contains the sequence shown in SEQ ID NO.130, and the antisense chain contains the sequence shown in SEQ ID NO.273;
- the positive chain contains the sequence shown in SEQ ID NO.131, and the negative chain contains the sequence shown in SEQ ID NO.274;
- the sense chain contains the sequence shown in SEQ ID NO. 132, and the antisense chain contains the sequence shown in SEQ ID NO. 275;
- the positive chain contains the sequence shown in SEQ ID NO.133, and the negative chain contains the sequence shown in SEQ ID NO.276.
- the aforementioned oligonucleotide is selected from any of the following combinations of sense and antisense strands:
- the positive chain contains the sequence shown in SEQ ID NO.15, and the negative chain contains the sequence shown in SEQ ID NO.158;
- the positive chain contains the sequence shown in SEQ ID NO.27, and the negative chain contains the sequence shown in SEQ ID NO.170;
- the positive chain contains the sequence shown in SEQ ID NO.29, and the negative chain contains the sequence shown in SEQ ID NO.172;
- the positive chain contains the sequence shown in SEQ ID NO.31, and the negative chain contains the sequence shown in SEQ ID NO.174;
- the positive chain contains the sequence shown in SEQ ID NO. 62, and the negative chain contains the sequence shown in SEQ ID NO. 205;
- the positive chain contains the sequence shown in SEQ ID NO.101, and the negative chain contains the sequence shown in SEQ ID NO.244;
- the positive chain contains the sequence shown in SEQ ID NO.106, and the negative chain contains the sequence shown in SEQ ID NO.249;
- the positive chain contains the sequence shown in SEQ ID NO.125, and the negative chain contains the sequence shown in SEQ ID NO.268;
- the positive chain contains the sequence shown in SEQ ID NO.127, and the negative chain contains the sequence shown in SEQ ID NO.270;
- the positive chain contains the sequence shown in SEQ ID NO.131, and the negative chain contains the sequence shown in SEQ ID NO.274;
- the sense chain contains the sequence shown in SEQ ID NO. 132, and the antisense chain contains the sequence shown in SEQ ID NO. 275;
- the positive chain contains the sequence shown in SEQ ID NO.133, and the negative chain contains the sequence shown in SEQ ID NO.276.
- the aforementioned oligonucleotide is selected from any of the following combinations of sense and antisense strands:
- the positive chain contains the sequence shown in SEQ ID NO.301, and the negative chain contains the sequence shown in SEQ ID NO.446;
- the positive chain contains the sequence shown in SEQ ID NO.313, and the negative chain contains the sequence shown in SEQ ID NO.458;
- the sense chain contains the sequence shown in SEQ ID NO.315, and the antisense chain contains the sequence shown in SEQ ID NO.460;
- the positive chain contains the sequence shown in SEQ ID NO.317, and the negative chain contains the sequence shown in SEQ ID NO.462;
- the positive chain contains the sequence shown in SEQ ID NO.335, and the negative chain contains the sequence shown in SEQ ID NO.480;
- the positive chain contains the sequence shown in SEQ ID NO.336, and the negative chain contains the sequence shown in SEQ ID NO.481;
- the positive chain contains the sequence shown in SEQ ID NO.337, and the negative chain contains the sequence shown in SEQ ID NO.482;
- the positive chain contains the sequence shown in SEQ ID NO.339, and the negative chain contains the sequence shown in SEQ ID NO.484;
- the positive chain contains the sequence shown in SEQ ID NO.340, and the negative chain contains the sequence shown in SEQ ID NO.485;
- the positive chain contains the sequence shown in SEQ ID NO.341, and the negative chain contains the sequence shown in SEQ ID NO.486;
- the positive chain contains the sequence shown in SEQ ID NO.346, and the negative chain contains the sequence shown in SEQ ID NO.491;
- the positive chain contains the sequence shown in SEQ ID NO.348, and the negative chain contains the sequence shown in SEQ ID NO.493;
- the sense chain contains the sequence shown in SEQ ID NO.350, and the antisense chain contains the sequence shown in SEQ ID NO.495;
- the positive chain contains the sequence shown in SEQ ID NO.384, and the negative chain contains the sequence shown in SEQ ID NO.529;
- the positive chain contains the sequence shown in SEQ ID NO.387, and the negative chain contains the sequence shown in SEQ ID NO.532;
- the positive chain contains the sequence shown in SEQ ID NO.388, and the negative chain contains the sequence shown in SEQ ID NO.533;
- the positive chain contains the sequence shown in SEQ ID NO.389, and the negative chain contains the sequence shown in SEQ ID NO.534;
- the positive chain contains the sequence shown in SEQ ID NO.391, and the negative chain contains the sequence shown in SEQ ID NO.536;
- the positive chain contains the sequence shown in SEQ ID NO.392, and the negative chain contains the sequence shown in SEQ ID NO.537;
- the sense chain contains the sequence shown in SEQ ID NO.393, and the antisense chain contains the sequence shown in SEQ ID NO.538;
- the sense chain contains the sequence shown in SEQ ID NO.398, and the antisense chain contains the sequence shown in SEQ ID NO.543;
- the sense chain contains the sequence shown in SEQ ID NO.399, and the antisense chain contains the sequence shown in SEQ ID NO.544;
- the sense chain contains the sequence shown in SEQ ID NO.405, and the antisense chain contains the sequence shown in SEQ ID NO.550;
- the positive chain contains the sequence shown in SEQ ID NO.409, and the negative chain contains the sequence shown in SEQ ID NO.554;
- the positive chain contains the sequence shown in SEQ ID NO.410, and the negative chain contains the sequence shown in SEQ ID NO.555;
- the positive chain contains the sequence shown in SEQ ID NO.411, and the negative chain contains the sequence shown in SEQ ID NO.556;
- the positive chain contains the sequence shown in SEQ ID NO.413, and the negative chain contains the sequence shown in SEQ ID NO.558;
- the positive chain contains the sequence shown in SEQ ID NO.414, and the negative chain contains the sequence shown in SEQ ID NO.559;
- the positive chain contains the sequence shown in SEQ ID NO.415, and the negative chain contains the sequence shown in SEQ ID NO.560;
- the positive chain contains the sequence shown in SEQ ID NO.416, and the negative chain contains the sequence shown in SEQ ID NO.561;
- the positive chain contains the sequence shown in SEQ ID NO.417, and the negative chain contains the sequence shown in SEQ ID NO.562;
- the sense chain contains the sequence shown in SEQ ID NO. 418, and the antisense chain contains the sequence shown in SEQ ID NO. 563; and
- the positive chain contains the sequence shown in SEQ ID NO.419, and the negative chain contains the sequence shown in SEQ ID NO.564.
- the aforementioned oligonucleotide is selected from any of the following combinations of sense and antisense strands:
- the positive chain contains the sequence shown in SEQ ID NO.301, and the negative chain contains the sequence shown in SEQ ID NO.446;
- the positive chain contains the sequence shown in SEQ ID NO.313, and the negative chain contains the sequence shown in SEQ ID NO.458;
- the sense chain contains the sequence shown in SEQ ID NO.315, and the antisense chain contains the sequence shown in SEQ ID NO.460;
- the positive chain contains the sequence shown in SEQ ID NO.317, and the negative chain contains the sequence shown in SEQ ID NO.462;
- the positive chain contains the sequence shown in SEQ ID NO.348, and the negative chain contains the sequence shown in SEQ ID NO.493;
- the positive chain contains the sequence shown in SEQ ID NO.387, and the negative chain contains the sequence shown in SEQ ID NO.532;
- the positive chain contains the sequence shown in SEQ ID NO.392, and the negative chain contains the sequence shown in SEQ ID NO.537;
- the positive chain contains the sequence shown in SEQ ID NO.411, and the negative chain contains the sequence shown in SEQ ID NO.556;
- the positive chain contains the sequence shown in SEQ ID NO.413, and the negative chain contains the sequence shown in SEQ ID NO.558;
- the positive chain contains the sequence shown in SEQ ID NO.417, and the negative chain contains the sequence shown in SEQ ID NO.562;
- the sense chain contains the sequence shown in SEQ ID NO. 418, and the antisense chain contains the sequence shown in SEQ ID NO. 563; and
- the positive chain contains the sequence shown in SEQ ID NO.419, and the negative chain contains the sequence shown in SEQ ID NO.564.
- This disclosure also provides a conjugate or a pharmaceutically acceptable salt thereof for inhibiting APP expression, comprising: (i) the aforementioned oligonucleotide or a pharmaceutically acceptable salt thereof, and (ii) a targeting ligand, wherein at least one of the sense strand and antisense strand of the oligonucleotide is conjugated to the targeting ligand.
- the target ligand is conjugated at the 3' or 5' end of the positive-angle strand.
- the aforementioned targeting ligand comprises an N-acetylgalactosamine (GalNAc) moiety.
- the aforementioned GalNAc moiety is a monovalent GalNAc moiety, a divalent GalNAc moiety, a trivalent GalNAc moiety, or a tetravalent GalNAc moiety.
- the aforementioned targeting ligand is L96.
- This disclosure also provides a conjugate or a pharmaceutically acceptable salt thereof for inhibiting APP expression, comprising: (i) the aforementioned oligonucleotide or a pharmaceutically acceptable salt thereof, and (ii) a lipophilic moiety, wherein at least one of the sense and antisense strands of the oligonucleotide is conjugated to one or more lipophilic moieties, optionally, the lipophilic moieties being conjugated via a linker or a vector.
- the aforementioned lipophilic moiety is conjugated at the 2'-position of a nucleotide or modified nucleotide within the sense or antisense strand.
- Internal positions include all positions except the two terminal positions at each end of at least one strand of the aforementioned oligonucleotide.
- the lipophilic moiety is conjugated at position 6 of the sense strand, meaning the lipophilic moiety is located at position 6 of the sense strand.
- the aforementioned lipophilic moiety comprises one to four 2'-O-alkyl modifications.
- the 2'-O-alkyl modified nucleotide is a 2'-C16-modified nucleotide.
- the RNAi agent comprises a single 2'-O-C16-modified nucleotide.
- the single 2'-C16-modified nucleotide is located at the 6th nucleotide position at the 5' end of the positive strand.
- another modification to the RNA of the RNAi agent chemically links one or more ligands, moieties, or conjugates that enhance RNAi activity, cellular distribution, or cellular uptake.
- moieties include, but are not limited to, lipid moieties, such as cholesterol moieties (Letsinger et al., (1989) Proc. Natl. Acid. Sci. USA, 86:6553-6556), bile acids (Manoharan et al., (1994) Biorg. Med. Chem. Let., 4:1053-1060), and thioethers, such as beryl-S-triphenylmethylthiol (Manoharan et al., (1992) Ann. N.Y. Acad.
- phospholipids such as di-hexadecyl-racemic-glycerol or triethyl-ammonium 1,2-di-O-hexadecyl-racemic-glycerol-3-phosphate (Manoharan et al., (1995) Tetrahedron Lett., 36:3651-3654; Shea et al., (1990) Nucl.
- the lipophilic moiety is an aliphatic, cyclic (e.g., alicyclic) or polycyclic (e.g., polyalicyclic) compound, such as a steroid (e.g., a sterol) or a straight-chain or branched aliphatic hydrocarbon.
- the lipophilic moiety may typically comprise a hydrocarbon chain, which may be cyclic or acyclic.
- the hydrocarbon chain may contain various substituents and/or one or more heteroatoms, such as oxygen or nitrogen atoms.
- Such lipophilic aliphatic moiety includes, but is not limited to, saturated or unsaturated C4 - C30 hydrocarbons (e.g., C6 - C22 hydrocarbons), saturated or unsaturated fatty acids, waxes (e.g., monohydric esters of fatty acids and fatty diamides), terpenes (e.g., C10 terpenes, C15 sesquiterpenes, C20 diterpenes, C30 triterpenes, and C40 tetraterpenes), and other polyalicyclic hydrocarbons.
- the lipophilic moiety may comprise a C4 to C30 hydrocarbon chain (e.g., C4 to C30 alkyl or alkenyl groups).
- the lipophilic moiety comprises a saturated or unsaturated C6 to C18 hydrocarbon chain (e.g., a straight-chain C6 to C22 alkyl or alkenyl group). In one embodiment, the lipophilic moiety comprises a saturated or unsaturated C16 hydrocarbon chain (e.g., a straight-chain C16 alkyl or alkenyl group).
- the lipid moiety is a 2'-O-alkyl group comprising 10-30 hydrocarbon chains, including single-chain and/or branched chains.
- the lipophilic portion comprises lipids, cholesterol, retinoic acid, cholic acid, adamantaneacetic acid, 1-pyrenebutyric acid, dihydrotestosterone, 1,3-bis-O-(hexadecyl)glycerol, geranyloxyhexanol, hexadecylglycerol, borneol, menthol, 1,3-propanediol, heptadecanyl, palmitic acid, myristic acid, O3-(oleoyl)lithocholic acid, O3-(oleoyl)cholenic acid, ibuprofen, naproxen, dimethoxytriphenylmethyl, or phenoxazine.
- the lipophilic moiety is bound to the double-stranded RNAi agent via a linker, which may contain ether, thioether, urea, carbonate, amine, amide, maleimide-thioether, disulfide, phosphate diester, sulfonamide bond, click reaction (e.g., triazole from azide-alkynyl cycloaddition), or carbamate.
- a linker which may contain ether, thioether, urea, carbonate, amine, amide, maleimide-thioether, disulfide, phosphate diester, sulfonamide bond, click reaction (e.g., triazole from azide-alkynyl cycloaddition), or carbamate.
- the aforementioned ligands that enhance RNAi activity, cell distribution, or cell uptake comprise C12 alkyl, C16 alkyl, C18 alkyl, C22 alkyl, or branched lipids such as DDA (cationic dimethyl dioctadecyl ammonium) and TDB (trehalose 6,6,9-disorbate).
- DDA cationic dimethyl dioctadecyl ammonium
- TDB trehalose 6,6,9-disorbate
- the straight-chain lipophilic portion (C16) attached to a position on the chain has the following structure:
- Base is a nucleotide base or a nucleotide base analogue.
- Base is selected from the group consisting of adenine, guanine, cytosine, thymine, and uracil.
- 2′-O-hexadecyluridine has the following structure:
- This disclosure also provides a conjugate or a pharmaceutically acceptable salt thereof for inhibiting APP expression, wherein the lipid conjugate has the following structure:
- A is a modified double-stranded oligonucleotide or a modified single-stranded oligonucleotide, wherein the modified double-stranded oligonucleotide or the modified single-stranded oligonucleotide is conjugated to a lipid-containing moiety at the 3' end of one strand of the modified double-stranded oligonucleotide or the 3' end of the modified single-stranded nucleic acid.
- X 1 is:
- L1 is -( CH2 )n-, -(CH2) nL2 ( CH2 ) n- or a bond;
- Each m is an integer from 10 to 18, and each n is an integer from 1 to 6.
- This disclosure also provides a conjugate or a pharmaceutically acceptable salt thereof for inhibiting APP expression, comprising: (i) the aforementioned oligonucleotide or a pharmaceutically acceptable salt thereof, and (ii) a targeting ligand and a lipophilic moiety, wherein at least one of the sense strand and antisense strand of the oligonucleotide is conjugated to the targeting ligand, and at least one of the sense strand and antisense strand of the oligonucleotide is conjugated to one or more lipophilic moieties.
- APP gene expression is suppressed by at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%, or below a detectable level. In a preferred embodiment, APP expression is suppressed by at least 70%. It should also be understood that it may be desirable to suppress APP expression in some tissues (e.g., the brain) without significantly suppressing expression in other tissues. In a preferred embodiment, expression levels are determined in suitable species-matched cell lines using the assay method provided in Example 2 with siRNA concentrations of 50 nM, 10 nM, 1 nM, and 0.1 nM.
- Inhibition of APP gene expression can be represented by a reduction in the amount of mRNA expressed in a cell line (such cells may be present, for example, in a sample derived from a subject), in which the APP gene has been transcribed and treated (e.g., by contacting one or more cells with the iRNA of this disclosure, or by administering the RNAi of this disclosure to a subject in which cells are present or were previously present), such that APP gene expression is inhibited compared to a substantially identical cell line that has not been treated (control cells not treated with RNAi or not treated with RNAi targeting the target gene).
- inhibition of APP gene expression can be assessed based on a decrease in parameters associated with APP gene expression function, such as APP protein levels in the blood or serum of a subject.
- APP gene silencing can be determined in any APP-expressing cell, whether endogenous or heterologous from the expression construct, and by any assay known in the art.
- Inhibition of APP protein expression can be demonstrated by a decrease in the level of APP protein or secreted luciferase expressed in cells or cell populations, or in a subject sample (e.g., protein levels in a blood sample from a subject).
- a subject sample e.g., protein levels in a blood sample from a subject.
- inhibition of protein expression levels in treated cells or cell populations can similarly be expressed as a percentage of protein levels in control cells or cell populations, or as a change in protein levels in a subject sample (e.g., blood or serum from which it is expressed), using the following formula, expressed as a percentage of APP or Gluc expression in the treated sample (e.g., blood or serum from which it is expressed) relative to APP or Gluc expression in control cells.
- Control cells, cell populations, or subject samples that can be used to assess the inhibition of APP gene expression include cells, cell populations, or subject samples that have not yet been exposed to the RNAi agent of this disclosure.
- control cells, cell lines, or subject samples may be derived from individual subjects (e.g., human or animal subjects) before treating subjects or appropriately matched cohorts with the RNAi agent.
- RNAi is administered to a subject to deliver RNAi to a specific site within the subject.
- Inhibition of APP expression can be assessed by measuring the level or changes in APP mRNA or APP protein or fusion secreted luciferase in a fluid or tissue sample from a specific site in the subject (e.g., the brain or blood).
- This disclosure also provides methods for using the RNAi of this disclosure or compositions containing the RNAi of this disclosure to inhibit APP expression, thereby preventing or treating APP-related conditions, such as cerebral amyloid angiopathy (CAA) or Alzheimer's disease (AD), including early-onset familial Alzheimer's disease (EOFAD), dementia, etc.
- CAA cerebral amyloid angiopathy
- AD Alzheimer's disease
- EFAD early-onset familial Alzheimer's disease
- dementia etc.
- Cells suitable for treatment using the methods of this disclosure can be any cell expressing the APP gene, such as hepatocytes, nerve cells, gallbladder cells, heart cells, or kidney cells, but preferably nerve cells.
- Cells suitable for use in the methods of this disclosure can be mammalian cells, such as primate cells (e.g., human cells, including human cells in chimeric nonhuman animals, or nonhuman primate cells, such as monkey cells or chimpanzee cells) or non-primate cells.
- the cells are human cells, such as human nerve cells.
- the expression of APP in the cells is inhibited by at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%, or below a measured detection level.
- the in vivo methods of this disclosure may include administering a composition comprising RNAi to a subject, wherein the RNAi comprises a nucleotide sequence complementary to at least a portion of the RNA transcript of the APP gene of the mammal to which the RNAi agent is administered.
- the composition may be administered in any manner known in the art, including but not limited to oral, intraperitoneal, or parenteral routes, including intracranial (e.g., intraventricular, intraparenchymal, and intrathecal), intravenous, intramuscular, subcutaneous, transdermal, airway (aerosol), nasal, rectal, and local (including oral and sublingual) administration.
- the composition is administered by intravenous infusion or injection.
- the composition is administered subcutaneously.
- the composition is administered by intrathecal injection.
- this disclosure also provides a method for inhibiting APP gene expression in mammals.
- the method comprises administering an oligonucleotide or a pharmaceutically acceptable salt thereof, or a combination thereof, to a mammal.
- the oligonucleotide is a double-stranded RNA (dsRNA) that targets the APP gene in mammalian cells and sustains the mammal for sufficient time to allow degradation of the APP gene mRNA transcript, thereby inhibiting APP protein expression in the cells.
- dsRNA double-stranded RNA
- the reduction in gene expression can be assessed by any method known in the art, and by methods such as qRT-PCR as described herein, for example, as in Example 2.
- the reduction in protein product can be assessed by any method known in the art (e.g., ELISA).
- a blood sample is used as a subject sample to monitor the reduction in APP protein expression.
- This disclosure also provides methods of treatment in subjects who require it, such as subjects diagnosed with APP-related conditions, cerebral amyloid angiopathy (CAA), or Alzheimer's disease (AD), including early-onset familial Alzheimer's disease (EOFAD), dementia, etc.
- subjects diagnosed with APP-related conditions cerebral amyloid angiopathy (CAA), or Alzheimer's disease (AD), including early-onset familial Alzheimer's disease (EOFAD), dementia, etc.
- CAA cerebral amyloid angiopathy
- AD Alzheimer's disease
- EFAD early-onset familial Alzheimer's disease
- dementia dementia
- the APP-related disease is cerebral amyloid angiopathy (CAA) or Alzheimer's disease (AD), including early-onset familial Alzheimer's disease (EOFAD), dementia, etc.
- CAA cerebral amyloid angiopathy
- AD Alzheimer's disease
- EFAD early-onset familial Alzheimer's disease
- dementia etc.
- RNAi disclosed herein can be administered as “free RNAi.” Free RNAi is administered in the absence of a pharmaceutical composition. Naked RNAi can be administered in a suitable buffer solution.
- the buffer solution may contain acetate, citrate, lactate, tartrate, carbonate, or phosphate, or any combination thereof.
- the buffer solution is phosphate-buffered saline (PBS).
- PBS phosphate-buffered saline
- the pH and osmotic pressure of the buffer solution containing RNAi can be adjusted to suit its administration to the subject.
- RNAi can lead to the prevention or treatment of APP-related conditions, such as cerebral amyloid angiopathy (CAA) or Alzheimer's disease (AD), including early-onset familial Alzheimer's disease (EOFAD), dementia, etc.
- a therapeutic dose of RNAi can be administered to the subject, such as from about 0.01 mg/kg to about 200 mg/kg. Preferably, it is from 1 mg/kg to about 50 mg/kg.
- RNAi is preferably administered subcutaneously, i.e., by intrathecal injection.
- One or more injections can be used to deliver the desired dose of RNAi to the subject. Injections can be repeated over a period of time.
- RNAi is administered approximately once a month to approximately every three months, or approximately every three months to approximately every six months, or even once a year.
- RNAi agents or pharmaceutical compositions thereof in combination with other drugs and/or other treatments (e.g., known drugs and/or known treatments, such as those currently used to treat these conditions) to treat subjects who would benefit from reduced and/or suppressed APP gene expression, such as subjects with APP-related diseases.
- Other therapeutic agents and treatments suitable for treating subjects who would benefit from reduced APP expression include tacolin, donepezil, rivastigmine, galantamine, memantine and memantine-donepezil combination preparations, cholinesterase inhibitors donepezil, huperzine A, galantamine hydrobromide, rivastigmine bitartrate, etc.
- such reagents can be obtained from any molecular biology reagent supplier, and their quality/purity standards are applicable to molecular biology.
- nucleotide monomers used in nucleic acid sequence representation. It should be understood that when a nucleotide contains a 2'-fluorine modification, the fluorine replaces the hydroxyl group at that position in the parent nucleotide (i.e., it is a 2'-deoxy-2'-fluorine nucleotide).
- L96 was prepared according to the method described in patent CN104717982B.
- C16 was purchased from Chengdu Pioneer Pharmaceuticals Co., Ltd.
- a computer-based algorithm was used to generate candidate oligonucleotide sequences complementary to human APP mRNA (NM_201414.3, Table 1). Some of these sequences were also complementary to or had no more than two mismatches with cynomolgus monkey APP mRNA (XM_005548883.3, Table 1). Some were designed as double-stranded siRNAs with 19/21 pairings on the sense and antisense strands, with the antisense strand having two dangling ends complementary to the mRNA sequence. In some cases, the dangling ends of the antisense strand were non-complementary UU.
- sequences were designed as double-stranded siRNAs with 21/23 pairings on the sense and antisense strands, with the antisense strand having two dangling ends complementary to the mRNA sequence. Some sequences were designed as double-stranded siRNAs with 21/21 and 23/23 pairings. In some complementary pairing sequences, the 5' end of the antisense strand (the last 3' end of the sense strand) was replaced with a base that did not match the APP mRNA.
- siRNA sequence was synthesized separately on a solid support via a sense strand (SS) and an antisense strand (AS), and was obtained after deprotection, cleavage, purification, annealing, purification and lyophilization.
- SS sense strand
- AS antisense strand
- Solid-phase synthesis ( Figure 2): The sense and antisense strands were synthesized separately on a solid support using an automated oligonucleotide synthesizer, employing phosphoramide technology.
- the synthesizer used was, for example, an AKTA Oligopilot (Cytiva) or Dr. Oligo 192XLc (Kunshan Berlik Precision Instruments Co., Ltd.).
- Solid-phase synthesis began at the 3' end of the sequence, with monomers sequentially coupled into the sequence. Each coupling of a phosphoramide monomer involved four chemical steps: 1) unblocking or deprotection (de-hydroxyl protecting group); 2) coupling; 3) oxidation; and 4) end-capping.
- phosphoramidite monomers All phosphoramidite monomers, reagents, and purification consumables used were commercially available.
- various phosphoramidite monomers such as 5'-O-(4,4′-Dimethoxytrityl)-2'-O-methyl-Uridine-3′-CE-Phosphoramidite
- reaction reagents such as 40wt% methylamine aqueous solution, 28wt% ammonium hydroxide aqueous solution, etc.
- Sigma-Aldrich LLC All phosphoramidite monomers, reagents, and purification consumables used were commercially available.
- various phosphoramidite monomers such as 5'-O-(4,4′-Dimethoxytrityl)-2'-O-methyl-Uridine-3′-CE-Phosphoramidite
- reaction reagents such as 40wt% methylamine aqueous solution, 28wt% ammonium hydroxide aqueous solution, etc.
- siRNA synthesis and purification methods used in this paper are as described in US20130178612A1 and US2015100197A1; the synthesis methods for VPUm and APU structural sequences are as described in J.Med.Chem.2018,61,734-744.
- Solid-phase phosphoramide synthesis is a mature method for synthesizing oligonucleotides.
- a computer-controlled synthesizer is used, and the reaction takes place in a stainless steel column.
- the positive chain synthesis begins with a solid support loaded with a targeting ligand (e.g., L96), or directly with the solid support.
- a targeting ligand e.g., L96
- Different starting materials, reagents, and solvents are injected sequentially from the 3' to 5' positions through different tubing lines controlled by the solid-phase synthesizer, linking phosphoramide nucleoside monomers one by one.
- the reaction process involves four cyclic steps: DMT protection removal, condensation, oxidation or thiolation, and end-capping.
- One nucleotide unit is linked in each cycle, yielding an oligonucleotide sequence of 19 or 21 nucleotides.
- the protecting group (2-cyanoethyl) is removed on the solid-phase column, and the synthesized sequence is cleaved from the solid support via ammonolysis.
- the sequence is filtered, the filter cake is washed with ethanol, and the filtrate and washings are collected and concentrated to obtain the crude positive chain.
- the crude product is purified by chromatography (SOURCE 15Q) and lyophilized to obtain the target product, the positive chain.
- siRNA positive strand conjugates were synthesized starting with a solid support loaded with a targeting ligand (e.g., L96); siRNA was synthesized directly starting with a solid support.
- the antisense strand is synthesized using a solid-phase synthesizer. Different starting materials, reagents, and solvents are injected sequentially from the 3' to 5' ends of the sequence through different tubing, linking phosphoramidine nucleoside monomers one by one.
- the reaction process involves four cyclic steps: DMT protection removal, condensation, oxidation or thiolation, and end-capping. One nucleotide unit is linked in each cycle, yielding an oligonucleotide sequence of 21 or 23 nucleotides.
- the protecting group (2-cyanoethyl) is removed on a solid-phase column, and the synthesized sequence is cleaved from the solid support via ammonolysis.
- the sequence is filtered, the filter cake is washed with ethanol, and the filtrate and washings are collected and concentrated to obtain the crude antisense strand.
- the crude product is purified by chromatography (SOURCE 15Q), ultrafiltered, and lyophilized to obtain the target product, antisense strand siRNA.
- the AS and SS strands were dissolved separately in injection water and mixed in a defined ratio (1.01:1.0-1.2:1.0). The mixture was incubated at 30-50°C for 30-90 minutes and then cooled to room temperature. The double-stranded siRNA product was obtained by freeze-drying.
- the double-stranded siRNA reagents listed in Tables 2, 3, and 4 below were prepared using the same method.
- G”, “C”, “A”, “U”, and “T” usually represent nucleotides with guanine, cytosine, adenine, uracil, and thymine as bases, respectively.
- Human neuroblastoma cells also known as Be2C cells (Tongpai (Shanghai) Biotechnology Co., Ltd., catalog number BE(2)-C cell identification) were collected and placed in a 37°C, 5% CO2 incubator. They were cultured in DMEM, high glucose (Thermo, catalog number 11965-092), with 10% FBS (GIBCO, 12483020) and 1% penicillin-streptomycin (GIBCO, 15140-122) added. When the cell confluence reached 90%, they were digested with trypsin-EDTA (Thermo, 25200-072) and counted with a counter (Countstar, IC1000). 190 ⁇ l of cell suspension/well was seeded into 96-well plates. The seeding number of Be2C cells was 1* 104 cells/well. The cells were transfected the next day after they adhered to the plate.
- RNAiMAX LipofectamineTM RNAiMAX (thermofisher, 13778150).
- a transfection complex was prepared by mixing 2.2 ⁇ l (2 ⁇ M) of the diluted compound, 19.1 ⁇ l of Opti-MEM (thermofisher, 1105821), and 0.7 ⁇ l of RNAiMAX. After incubation for 5 minutes, the transfection complex was added to the cells (two replicates per complex), 10 ⁇ l per well, with a final siRNA concentration of 10 nM. The cells were incubated at 37°C in a 5% CO2 incubator for 24 hours.
- Tables 5 and 6 The results of the two screenings of Be2C cells are shown in Tables 5 and 6.
- the data in each table are from individual experiments. Due to different cell batches, the silencing efficiency of the target gene may vary. In some experiments, low concentrations may occur due to cell condition. The deviation between biological replicates is relatively large. Data with smaller errors at other concentrations and the same concentration should be referred to.
- the results show that the dual concentration screening results of AL0235015, AL0235025, AL0235026, AL0235027, AL0235029, AL0235031, AL0235062, AL0235101, AL0235106, AL0235107, AL0235112, AL0235113, AL0235123, AL0235125, AL0235127, AL0235131, AL0235132, and AL0235133 are better, with inhibition rates of 10 nM reaching or approaching 60%, and the highest reaching greater than 80%.
- Table 4 shows the APP siRNA sequence knockdown level in Be2C cells.
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Abstract
L'invention concerne un agent ARNi ciblant une protéine précurseur de l'amyloïde, tel qu'un agent de petit ARN interférent à double brin (ARNsi). L'invention concerne un procédé d'inhibition de l'expression du gène APP à l'aide de l'agent ARNi et une méthode de prévention et de traitement de maladies liées à l'APP, telles que l'angiopathie amyloïde cérébrale (CAA) ou la maladie d'Alzheimer (AD), y compris la maladie d'Alzheimer familiale à début précoce (EOFAD). L'ARNsi inhibe significativement le niveau d'expression du gène APP et a un effet médicamenteux durable.
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| CN110559454A (zh) * | 2019-09-29 | 2019-12-13 | 中山大学孙逸仙纪念医院 | 一种用于诊疗阿尔兹海默症的纳米复合药物 |
| WO2020160163A1 (fr) * | 2019-01-29 | 2020-08-06 | Ionis Pharmaceuticals, Inc. | Composés et méthodes permettant de réduire l'expression de l'app |
| CN113454222A (zh) * | 2018-12-19 | 2021-09-28 | 阿尼拉制药公司 | 淀粉样前体蛋白(APP)RNAi剂组成物及其使用方法 |
| WO2023173061A2 (fr) * | 2022-03-11 | 2023-09-14 | University Of Massachusetts | Oligonucléotides pour moduler app |
| CN117003704A (zh) * | 2023-08-07 | 2023-11-07 | 山东大学 | 一种靶向β淀粉样蛋白的近红外荧光探针及其在阿尔兹海默症诊断中的应用 |
| CN117064894A (zh) * | 2023-09-05 | 2023-11-17 | 浙江大学 | Stm2457在制备防治阿尔茨海默症的药物中的应用 |
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| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN113454222A (zh) * | 2018-12-19 | 2021-09-28 | 阿尼拉制药公司 | 淀粉样前体蛋白(APP)RNAi剂组成物及其使用方法 |
| WO2020160163A1 (fr) * | 2019-01-29 | 2020-08-06 | Ionis Pharmaceuticals, Inc. | Composés et méthodes permettant de réduire l'expression de l'app |
| CN110559454A (zh) * | 2019-09-29 | 2019-12-13 | 中山大学孙逸仙纪念医院 | 一种用于诊疗阿尔兹海默症的纳米复合药物 |
| WO2023173061A2 (fr) * | 2022-03-11 | 2023-09-14 | University Of Massachusetts | Oligonucléotides pour moduler app |
| CN117003704A (zh) * | 2023-08-07 | 2023-11-07 | 山东大学 | 一种靶向β淀粉样蛋白的近红外荧光探针及其在阿尔兹海默症诊断中的应用 |
| CN117064894A (zh) * | 2023-09-05 | 2023-11-17 | 浙江大学 | Stm2457在制备防治阿尔茨海默症的药物中的应用 |
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