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Iwamoto N, Liu Y, Frank-Kamenetsky M, Maguire A, Tseng WC, Taborn K, Kothari N, Akhtar A, Bowman K, Shelke JD, Lamattina A, Hu XS, Jang HG, Kandasamy P, Liu F, Longo K, Looby R, Meena, Metterville J, Pan Q, Purcell-Estabrook E, Shimizu M, Prakasha PS, Standley S, Upadhyay H, Yang H, Yin Y, Zhao A, Francis C, Byrne M, Dale E, Verdine GL, Vargeese C. Preclinical evaluation of stereopure antisense oligonucleotides for allele-selective lowering of mutant HTT. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102246. [PMID: 39027419 PMCID: PMC11255113 DOI: 10.1016/j.omtn.2024.102246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/07/2024] [Indexed: 07/20/2024]
Abstract
Huntington's disease (HD) is an autosomal dominant disease caused by the expansion of cytosine-adenine-guanine (CAG) repeats in one copy of the HTT gene (mutant HTT, mHTT). The unaffected HTT gene encodes wild-type HTT (wtHTT) protein, which supports processes important for the health and function of the central nervous system. Selective lowering of mHTT for the treatment of HD may provide a benefit over nonselective HTT-lowering approaches, as it aims to preserve the beneficial activities of wtHTT. Targeting a heterozygous single-nucleotide polymorphism (SNP) where the targeted variant is on the mHTT gene is one strategy for achieving allele-selective activity. Herein, we investigated whether stereopure phosphorothioate (PS)- and phosphoryl guanidine (PN)-containing oligonucleotides can direct allele-selective mHTT lowering by targeting rs362273 (SNP3). We demonstrate that our SNP3-targeting molecules are potent, durable, and selective for mHTT in vitro and in vivo in mouse models. Through comparisons with a surrogate for the nonselective investigational compound tominersen, we also demonstrate that allele-selective molecules display equivalent potency toward mHTT with improved durability while sparing wtHTT. Our preclinical findings support the advancement of WVE-003, an investigational allele-selective compound currently in clinical testing (NCT05032196) for the treatment of patients with HD.
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Affiliation(s)
| | | | | | | | | | | | | | - Ali Akhtar
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | | | | | | | | | | | - Fangjun Liu
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Ken Longo
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | - Meena
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | - Qianli Pan
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | | | | | | | | | - Hailin Yang
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Yuan Yin
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | | | - Mike Byrne
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Elena Dale
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Gregory L. Verdine
- Department of Stem Cell and Regenerative Biology, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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2
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Zharkov TD, Markov OV, Zhukov SA, Khodyreva SN, Kupryushkin MS. Influence of Combinations of Lipophilic and Phosphate Backbone Modifications on Cellular Uptake of Modified Oligonucleotides. Molecules 2024; 29:452. [PMID: 38257365 PMCID: PMC10818405 DOI: 10.3390/molecules29020452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Numerous types of oligonucleotide modifications have been developed since automated synthesis of DNA/RNA became a common instrument in the creation of synthetic oligonucleotides. Despite the growing number of types of oligonucleotide modifications under development, only a few of them and, moreover, their combinations have been studied widely enough in terms of their influence on the properties of corresponding NA constructions. In the present study, a number of oligonucleotides with combinations of 3'-end lipophilic (a single cholesteryl or a pair of dodecyl residues) and phosphate backbone modifications were synthesized. The influence of the combination of used lipophilic groups with phosphate modifications of various natures and different positions on the efficiency of cell penetration was evaluated. The obtained results indicate that even a couple of phosphate modifications are able to affect a set of oligonucleotide properties in a complex manner and can remarkably change cellular uptake. These data clearly show that the strategy of using different patterns of modification combinations has great potential for the rational design of oligonucleotide structures with desired predefined properties.
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Affiliation(s)
| | | | | | | | - Maxim S. Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (T.D.Z.); (O.V.M.); (S.A.Z.); (S.N.K.)
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3
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Ota K, Nagao K, Hata D, Sugiyama H, Segawa Y, Tokunoh R, Seki T, Miyamoto N, Sasaki Y, Ohmiya H. Synthesis of tertiary alkylphosphonate oligonucleotides through light-driven radical-polar crossover reactions. Nat Commun 2023; 14:6856. [PMID: 37907473 PMCID: PMC10618202 DOI: 10.1038/s41467-023-42639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023] Open
Abstract
Chemical modification of nucleotides can improve the metabolic stability and target specificity of oligonucleotide therapeutics, and alkylphosphonates have been employed as charge-neutral replacements for naturally-occurring phosphodiester backbones in these compounds. However, at present, the alkyl moieties that can be attached to phosphorus atoms in these compounds are limited to methyl groups or primary/secondary alkyls, and such alkylphosphonate moieties can degrade during oligonucleotide synthesis. The present work demonstrates the tertiary alkylation of the phosphorus atoms of phosphites bearing two 2'-deoxynuclosides. This process utilizes a carbocation generated via a light-driven radical-polar crossover mechanism. This protocol provides tertiary alkylphosphonate structures that are difficult to synthesize using existing methods. The conversion of these species to oligonucleotides having charge-neutral alkylphosphonate linkages through a phosphoramidite-based approach was also confirmed in this study.
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Affiliation(s)
- Kenji Ota
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Kazunori Nagao
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
| | - Dai Hata
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan.
| | - Haruki Sugiyama
- Institute for Molecular Science Myodaiji, Okazaki, Japan
- Comprehensive Research Organization for Science and Society Neutron Industrial Application Promotion Center, Tokai, Ibaraki, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Myodaiji, Okazaki, Japan
| | - Yasutomo Segawa
- Institute for Molecular Science Myodaiji, Okazaki, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Myodaiji, Okazaki, Japan
| | - Ryosuke Tokunoh
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Tomohiro Seki
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Naoya Miyamoto
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Yusuke Sasaki
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Hirohisa Ohmiya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, Japan.
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4
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Zharkov TD, Mironova EM, Markov OV, Zhukov SA, Khodyreva SN, Kupryushkin MS. Fork- and Comb-like Lipophilic Structures: Different Chemical Approaches to the Synthesis of Oligonucleotides with Multiple Dodecyl Residues. Int J Mol Sci 2023; 24:14637. [PMID: 37834092 PMCID: PMC10572690 DOI: 10.3390/ijms241914637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Lipophilic oligonucleotide conjugates represent a powerful tool for nucleic acid cellular delivery, and many methods for their synthesis have been developed over the past few decades. In the present study, a number of chemical approaches for the synthesis of different fork- and comb-like dodecyl-containing oligonucleotide structures were performed, including use of non-nucleotide units and different types of phosphate modifications such as alkyl phosphoramidate, phosphoryl guanidine, and triazinyl phosphoramidate. The influence of the number of introduced lipophilic residues, their mutual arrangement, and the type of formed modification backbone on cell penetration was evaluated. The results obtained indicate great potential in the developed chemical approaches, not only for the synthesis of complex oligonucleotide structures but also for the fine-tuning of their properties.
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Affiliation(s)
| | | | | | | | | | - Maxim S. Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (T.D.Z.); (E.M.M.); (O.V.M.); (S.A.Z.); (S.N.K.)
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5
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Hall J. Future directions for medicinal chemistry in the field of oligonucleotide therapeutics. RNA (NEW YORK, N.Y.) 2023; 29:423-433. [PMID: 36693762 PMCID: PMC10019366 DOI: 10.1261/rna.079511.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 05/13/2023]
Abstract
In the last decade, the field of oligonucleotide therapeutics has matured, with the regulatory approval of several single-stranded and double-stranded RNA drugs. In this Perspective, I discuss enabling developments and likely future directions in the field from the perspective of oligonucleotide chemistry.
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Affiliation(s)
- Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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6
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Vasilyeva SV, Baranovskaya EE, Dyudeeva ES, Lomzov AA, Pyshnyi DV. Synthesis of Oligonucleotides Carrying Inter-nucleotide N-(Benzoazole)-phosphoramide Moieties. ACS OMEGA 2023; 8:1556-1566. [PMID: 36643477 PMCID: PMC9835791 DOI: 10.1021/acsomega.2c07083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
In this work, we present new oligonucleotide derivatives containing inter-nucleotide N-benzimidazole, N-benzoxazole, N-benzothiazole, and 1,3-dimethyl-N-benzimidazole (benzoazoles) phosphoramide groups. These modifications were introduced via the Staudinger reaction with appropriate azides during standard automated solid-phase oligonucleotide synthesis. The principal structural difference between the new azido modifiers and those already known is that they are bulk heterocyclic structures, similar to purine nucleoside bases. Modified oligonucleotides with one and two modifications at different positions and multiple modified heteronucleotide sequences were obtained with high yields. The possibility of multiple modifications in the process of automatic DNA synthesis is fundamental and critical for further application of our oligonucleotide derivatives. Initial studies on the properties of new oligonucleotides were carried out. The stability of the oligodeoxyribonucleotide duplex containing phosphoramide groups of N-benzoazoles with complementary DNA or RNA is slightly lower than that of native complexes.
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Affiliation(s)
| | | | - Evgeniya S. Dyudeeva
- Institute of Chemical Biology and Fundamental
Medicine, SB of RAS, pr. Lavrent’eva 8, 630090 Novosibirsk, Russia
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental
Medicine, SB of RAS, pr. Lavrent’eva 8, 630090 Novosibirsk, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental
Medicine, SB of RAS, pr. Lavrent’eva 8, 630090 Novosibirsk, Russia
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Kandasamy P, McClorey G, Shimizu M, Kothari N, Alam R, Iwamoto N, Kumarasamy J, Bommineni GR, Bezigian A, Chivatakarn O, Butler DC, Byrne M, Chwalenia K, Davies KE, Desai J, Shelke JD, Durbin AF, Ellerington R, Edwards B, Godfrey J, Hoss A, Liu F, Longo K, Lu G, Marappan S, Oieni J, Paik IH, Estabrook EP, Shivalila C, Tischbein M, Kawamoto T, Rinaldi C, Rajão-Saraiva J, Tripathi S, Yang H, Yin Y, Zhao X, Zhou C, Zhang J, Apponi L, Wood MJ, Vargeese C. Control of backbone chemistry and chirality boost oligonucleotide splice switching activity. Nucleic Acids Res 2022; 50:5443-5466. [PMID: 35061895 PMCID: PMC9178015 DOI: 10.1093/nar/gkac018] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/18/2021] [Accepted: 01/07/2022] [Indexed: 01/04/2023] Open
Abstract
Although recent regulatory approval of splice-switching oligonucleotides (SSOs) for the treatment of neuromuscular disease such as Duchenne muscular dystrophy has been an advance for the splice-switching field, current SSO chemistries have shown limited clinical benefit due to poor pharmacology. To overcome limitations of existing technologies, we engineered chimeric stereopure oligonucleotides with phosphorothioate (PS) and phosphoryl guanidine-containing (PN) backbones. We demonstrate that these chimeric stereopure oligonucleotides have markedly improved pharmacology and efficacy compared with PS-modified oligonucleotides, preventing premature death and improving median survival from 49 days to at least 280 days in a dystrophic mouse model with an aggressive phenotype. These data demonstrate that chemical optimization alone can profoundly impact oligonucleotide pharmacology and highlight the potential for continued innovation around the oligonucleotide backbone. More specifically, we conclude that chimeric stereopure oligonucleotides are a promising splice-switching modality with potential for the treatment of neuromuscular and other genetic diseases impacting difficult to reach tissues such as the skeletal muscle and heart.
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Affiliation(s)
| | - Graham McClorey
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | | | | | | | | | | | | | | | | | | | | | - Katarzyna Chwalenia
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Kay E Davies
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | | | | | | | - Ruth Ellerington
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Ben Edwards
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | | | | | | | - Kenneth Longo
- Wave Life Sciences, Cambridge, MA, USA
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX2 9DU, UK
| | | | | | - Jacopo Oieni
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | | | | | | | | | | | - Carlo Rinaldi
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX2 9DU, UK
| | - Joana Rajão-Saraiva
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | | | | | - Yuan Yin
- Wave Life Sciences, Cambridge, MA, USA
| | | | - Cong Zhou
- Wave Life Sciences, Cambridge, MA, USA
| | | | | | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX2 9DU, UK
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8
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Kandasamy P, Liu Y, Aduda V, Akare S, Alam R, Andreucci A, Boulay D, Bowman K, Byrne M, Cannon M, Chivatakarn O, Shelke JD, Iwamoto N, Kawamoto T, Kumarasamy J, Lamore S, Lemaitre M, Lin X, Longo K, Looby R, Marappan S, Metterville J, Mohapatra S, Newman B, Paik IH, Patil S, Purcell-Estabrook E, Shimizu M, Shum P, Standley S, Taborn K, Tripathi S, Yang H, Yin Y, Zhao X, Dale E, Vargeese C. Impact of guanidine-containing backbone linkages on stereopure antisense oligonucleotides in the CNS. Nucleic Acids Res 2022; 50:5401-5423. [PMID: 35106589 PMCID: PMC9177980 DOI: 10.1093/nar/gkac037] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/17/2021] [Accepted: 01/13/2022] [Indexed: 12/02/2022] Open
Abstract
Attaining sufficient tissue exposure at the site of action to achieve the desired pharmacodynamic effect on a target is an important determinant for any drug discovery program, and this can be particularly challenging for oligonucleotides in deep tissues of the CNS. Herein, we report the synthesis and impact of stereopure phosphoryl guanidine-containing backbone linkages (PN linkages) to oligonucleotides acting through an RNase H-mediated mechanism, using Malat1 and C9orf72 as benchmarks. We found that the incorporation of various types of PN linkages to a stereopure oligonucleotide backbone can increase potency of silencing in cultured neurons under free-uptake conditions 10-fold compared with similarly modified stereopure phosphorothioate (PS) and phosphodiester (PO)-based molecules. One of these backbone types, called PN-1, also yielded profound silencing benefits throughout the mouse brain and spinal cord at low doses, improving both the potency and durability of response, especially in difficult to reach brain tissues. Given these benefits in preclinical models, the incorporation of PN linkages into stereopure oligonucleotides with chimeric backbone modifications has the potential to render regions of the brain beyond the spinal cord more accessible to oligonucleotides and, consequently, may also expand the scope of neurological indications amenable to oligonucleotide therapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xuena Lin
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | | | | | | | | | | | | | | | | | | | - Pochi Shum
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | - Kris Taborn
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | - Hailin Yang
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Yuan Yin
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Xiansi Zhao
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Elena Dale
- Wave Life Sciences, Cambridge, MA 02138, USA
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