Oligonucleotide compositions and methods of use thereof
Inventors
Vargeese, Chandra • Iwamoto, Naoki • Butler, David Charles Donnell • Marappan, Subramanian • Lu, Genliang • Zhang, Jason Jingxin • VATHIPADIEKAL, Vinod • Apponi, Luciano Henrique • Wisniewska, Hanna Maria • Cheng, Xiayun • Cho, Young Jin
Assignees
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Publication Number
US-11597927-B2
Publication Date
2023-03-07
Expiration Date
Abstract
Among other things, the present disclosure provides designed PNPLA3 oligonucleotides, compositions, and methods thereof. In some embodiments, provided oligonucleotide compositions provide improved single-stranded RNA interference and/or RNase H-mediated knockdown. 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 N 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., RNA interference (RNAi) activity, stability, delivery, etc. In some embodiments, the present disclosure provides methods for treatment of diseases using provided oligonucleotide compositions, for example, in RNA interference and/or RNase H-mediated knockdown.
Core Innovation
The invention relates to chirally controlled oligonucleotide compositions that target PNPLA3. The compositions are defined by oligonucleotides of a particular oligonucleotide type that share a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers, and comprise at least one internucleotidic linkage including a linkage phosphorus in the Sp configuration. The composition is enriched, relative to a substantially racemic preparation of oligonucleotides having the same common base sequence, for the specified oligonucleotide type.
The common base sequence has over 50% identity with TACUGUAGAAAGGCAUGAATU (SEQ ID NO: 153), wherein each U can be optionally and independently replaced with T. The disclosure also refers to higher identity thresholds over 60% and over 70%, shared chirally controlled internucleotidic linkages with the same linkage phosphorus stereochemistry at five or more chiral linkages, and complementarity to a 15-or-more-nucleobase portion of a PNPLA3 transcript.
The document further describes PNPLA3-targeting ssRNAi and oligonucleotide conjugate embodiments, including seed and post-seed region arrangements, 3′-end cap structures, RCD connected to the oligonucleotide through a linker, and targeting moieties such as GalNAc, ASGPR-binding targeting moieties, lipid moieties, and other ligand or linker configurations. It also describes chirally controlled phosphorothioate linkages, Rp/Sp configurations, and structural features intended to support ssRNAi, RNase H-mediated knockdown, stability, and tissue delivery.
Claims Coverage
The claim coverage centers on chirally controlled PNPLA3-targeting oligonucleotide compositions defined by shared base sequence identity, shared backbone linkage and backbone chiral-center patterns, and enrichment relative to substantially racemic preparations. The independent claim features one core inventive combination, with dependent claims adding sequence-identity refinements, chirality and complementarity constraints, linker connectivity, and human therapeutic use.
Chirally controlled PNPLA3-targeting oligonucleotide composition
A composition comprising oligonucleotides of a particular oligonucleotide type having a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers, wherein the oligonucleotide comprises at least one internucleotidic linkage comprising a linkage phosphorus in the Sp configuration, and wherein the composition is chirally controlled in that it is enriched, relative to a substantially racemic preparation of oligonucleotides having the same common base sequence, for oligonucleotides of the particular oligonucleotide type.
Common base sequence identity to TACUGUAGAAAGGCAUGAATU
The oligonucleotide targets PNPLA3, and the common base sequence has over 50% identity with TACUGUAGAAAGGCAUGAATU (SEQ ID NO: 153), wherein each U can be optionally and independently replaced with T.
Sequence identity threshold refinements
The common base sequence has over 60% identity with TACUGUAGAAAGGCAUGAATU (SEQ ID NO: 153), and over 70% identity with TACUGUAGAAAGGCAUGAATU (SEQ ID NO: 153), wherein each U can be optionally and independently replaced with T.
Shared chirally controlled internucleotidic linkages and transcript complementarity
The oligonucleotides share chirally controlled internucleotidic linkages with the same linkage phosphorus stereochemistry at five or more chiral linkages, at least about 10% of oligonucleotides with the common base sequence are members of the plurality, and the common base sequence is complementary to a 15-or-more-nucleobase portion of a PNPLA3 transcript.
RCD connected through a linker
The composition is configured so that RCD is connected to the oligonucleotide or oligonucleotides through a linker.
Human therapeutic use for fatty liver and NAFLD/NASH conditions
A method for treating fatty liver, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis, nonalcoholic steatohepatitis with liver fibrosis, nonalcoholic steatohepatitis with cirrhosis, or nonalcoholic steatohepatitis with cirrhosis and hepatocellular carcinoma in humans by administering to a human in need of such treatment a therapeutically effective amount of a composition of claim 2.
Overall, the claims emphasize chirally controlled PNPLA3-targeting oligonucleotides enriched relative to substantially racemic preparations, with at least one internucleotidic linkage having linkage phosphorus in the Sp configuration and a common base sequence defined by identity to TACUGUAGAAAGGCAUGAATU with optional U-to-T substitution. Dependent features further tighten identity thresholds, add chirality and complementarity constraints, require RCD connection through a linker, and extend to human treatment of fatty liver and NAFLD/NASH-related conditions.
Stated Advantages
Decrease PNPLA3 gene expression via RNase H, steric hindrance, and/or RNA interference.
Improve ssRNAi and/or RNase H-mediated knockdown.
Improve stability.
Reduce nuclease susceptibility versus stereorandom/racemic preparations.
Improve tissue delivery, especially to muscle tissue.
Improve activity (including ssRNAi) and/or tissue delivery.
Support micelle formation.
Improve stability in plasma and tissue homogenates.
Improves distribution and pharmacokinetics, including Cmax, Tmax, Cmin, elimination half-life, AUC, and clearance.
Enriched chirality relative to a substantially racemic preparation for oligonucleotides of the particular oligonucleotide type.
Increased stability and/or RNAi-mediated knockdown and RNase H-mediated effects are indicated.
Documented Applications
Decreasing PNPLA3 gene expression in cells/patients using PNPLA3-targeting oligonucleotide compositions.
Treating fatty liver, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis, nonalcoholic steatohepatitis with liver fibrosis, nonalcoholic steatohepatitis with cirrhosis, and nonalcoholic steatohepatitis with cirrhosis and hepatocellular carcinoma in humans.
Extra-hepatic delivery of PNPLA3 oligonucleotide compositions using lipids for tissues including muscle.
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