Oligonucleotide compositions and methods thereof
Inventors
Vargeese, Chandra • Zhong, Zhong • Iwamoto, Naoki • Zhang, Jason Jingxin • Dodart, Jean-Cosme • Liu, Yuanjing • Kandasamy, Pachamuthu • Divakaramenon, Sethumadhavan • Lu, Genliang • Marappan, Subramanian
Assignees
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Publication Number
US-11739325-B2
Publication Date
2023-08-29
Expiration Date
Abstract
Among other things, the present disclosure provides oligonucleotides, compositions, and methods thereof. Among other things, the present disclosure encompasses the recognition that structural elements of oligonucleotides, such as base sequence, chemical modifications (e.g., modifications of sugar, base, and/or internucleotidic linkages) or patterns thereof, conjugation with additional chemical moieties, and/or stereochemistry [e.g., stereochemistry of backbone chiral centers (chiral internucleotidic linkages)], and/or patterns thereof, can have significant impact on oligonucleotide properties and activities, e.g., knockdown ability, stability, delivery, etc. In some embodiments, the oligonucleotides decrease the expression, activity and/or level of a C9orf72 gene, including but not limited to, one comprising a repeat expansion, or a gene product thereof. In some embodiments, the present disclosure provides methods for treatment of diseases using provided oligonucleotide compositions, for example, in treatment of C9orf72-related disorders.
Core Innovation
The invention relates to an oligonucleotide composition comprising oligonucleotides of a particular oligonucleotide type characterized by a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers. The composition is enriched, relative to a substantially racemic preparation of oligonucleotides having the same common base sequence, for oligonucleotides of the particular oligonucleotide type. This defines a chirally controlled asymmetric format rather than a substantially racemic mixture.
Each oligonucleotide of the particular oligonucleotide type independently comprises a first wing, a second wing and a core in a format of first wing-core-second wing or second wing-core-first wing. The first wing and the second wing comprise different sugar modifications, and the core comprises (Op)n(Sp)m, where Sp indicates the S configuration of a chiral linkage phosphorus of a chiral modified internucleotidic linkage and Op indicates an achiral linkage phosphorus of a natural phosphate linkage with a 5′-modification on its sugar. Each of n and m is independently 1-20.
The disclosure further describes chirally controlled internucleotidic linkages and related structural definitions, including phosphodiester linkage, phosphorothioate linkage, and non-negatively-charged internucleotidic linkage. The compositions are presented in connection with selective transcript suppression and allele-specific suppression, as well as reported effects on RNase H-like cleavage, translation inhibition, exon skipping, gene knockdown, cell uptake, endosomal escape, and delivery to the cellular nucleus.
Claims Coverage
The independent claim coverage centers on one enriched, chirally controlled oligonucleotide composition with a common base sequence, common backbone linkage and chiral-center patterns, and an asymmetric wing-core format. Four inventive features are consistently presented across the inputs, with dependent refinements to selective and allele-specific transcript suppression.
Enriched chirally controlled oligonucleotide type relative to substantially racemic preparation
The composition comprises oligonucleotides of a particular oligonucleotide type characterized by a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers, and is enriched relative to a substantially racemic preparation of oligonucleotides having the same common base sequence.
Asymmetric wing-core format with different sugar modifications
Each oligonucleotide independently comprises a first wing, a second wing and a core in a format of first wing-core-second wing or second wing-core-first wing, wherein the first wing and the second wing comprise different sugar modifications.
Core defined by (Op)n(Sp)m linkage phosphorus pattern
Oligonucleotides comprise (Op)n(Sp)m in the core, where Sp indicates the S configuration of a chiral linkage phosphorus of a chiral modified internucleotidic linkage and Op indicates an achiral linkage phosphorus of a natural phosphate linkage, with the nucleotidic unit comprising Op having a 5′-modification on its sugar, and each of n and m independently 1-20.
Selective transcript suppression by complementary common base sequence
A method is described to selectively suppress a transcript from a target nucleic acid sequence by contacting a transcript-containing sample with a chirally controlled oligonucleotide composition whose common base sequence is complementary to the characteristic sequence element defining the target relative to similar sequences.
Allele-specific transcript suppression by allele-defining complementarity
A method is described to suppress a target transcript allele-specifically by contacting a sample’s target transcripts with a chirally controlled oligonucleotide composition whose common base sequence is complementary to an allele-defining characteristic nucleotide sequence element.
The claims center on an enriched, chirally controlled oligonucleotide composition defined by a shared base sequence, shared backbone linkage and chiral-center patterns, and a wing-core-wing architecture with different sugar modifications in the wings and a core containing a defined Op/Sp stereochemical linkage pattern. The same composition is extended to selective and allele-specific transcript suppression by complementarity to characteristic sequence elements.
Stated Advantages
Improved knockdown, including RNase H-mediated transcript knockdown and/or cleavage outcomes.
Potential increased cell uptake and endosomal escape.
Potential modulation of melting temperature.
Potential enhancement of exon skipping and gene knockdown.
Controlled cleavage.
Allele-specific transcript suppression and transcript/protein level reduction.
Reduction of transcripts and related protein levels in the described biological context.
Preferentially enhance RNase H-like cleavage at specific sites, including newly created sites, by increasing cleavage rate and/or extent.
Suppress cleavage at specific sites to increase allele selectivity near mutations and/or SNPs.
Provide reduction of transcript/protein levels in systems including cell, tissue, organ, or organism.
Improved biological activity, including delivery to the cellular nucleus.
Target gene / gene product decrease.
Translation inhibition (steric hindrance).
RNaseH mechanism via DNA-RNA duplex.
Supports properties and outcomes described as cell uptake, endosomal escape, exon skipping, and gene knockdown.
Documented Applications
Selective suppression of a transcript from a target nucleic acid sequence by contacting a transcript-containing sample with a chirally controlled oligonucleotide composition.
Allele-specific suppression of a target transcript by contacting a sample’s target transcripts with a chirally controlled oligonucleotide composition complementary to an allele-defining characteristic nucleotide sequence element.
RNase H-mediated transcript knockdown, including for mutant C9orf72 repeat-expansion transcripts.
Targeting C9orf72 gene expression, including repeat expansion, for C9orf72-related disorders.
Preferential knockdown of C9orf72 repeat-expansion transcripts, with transcript and protein reduction, in a therapeutic evaluation context for neurodegeneration including ALS and FTD.
Experimental activity for oligonucleotides targeting C9orf72 V3 transcripts, intron 1/AS, and all V transcripts in ALS motor neurons in vitro and in C9-BAC mice in vivo.
In vivo and pharmacodynamic statements linking oligonucleotide treatment to reduced polyGP dipeptide repeat protein levels.
Extended efficacy data for PNPLA3 oligonucleotides showing knockdown in hepatic cells/hepatocytes for wild-type versus I148M mutant allele contexts.
Use with conjugates and delivery using lipid-nucleic acid particles, with pharmaceutical formulations and administration in a CNS delivery context.
Subject treatment methods for diseases and conditions including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), corticobasal degeneration syndrome (CBD), atypical Parkinsonian syndrome, olivopontocerebellar degeneration (OPCD), and Alzheimer’s disease.
Preferential reduction of C9orf72 repeat transcripts (GGGGCC expansion), Malat1, PNPLA3, and ApoC3 transcripts, including associated reduction context involving C9orf72-expanded repeat foci and dipeptide repeat proteins.
CNS delivery exemplification using conjugation-related chemistry including 5′/3′ conjugation strategies and chemical moieties/targeting ligands.
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