1
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Yu M, Qin J, Liu X, Ramsden D, Williams B, Zlatev I, Guenther D, Matsuda S, Tymon R, Darcy J, Wong C, Tsung J, Zawaneh P, Chong S, Theile C, Taneja N, Rogers A, Liu J, Castellanos-Rizaldos E, Bond S, So K, Denoncourt J, Castoreno A, Manoharan M, Wu JT, Fitzgerald K, Maier MA, Jadhav V, Nair J. Evaluating the oral delivery of GalNAc-conjugated siRNAs in rodents and non-human primates. Nucleic Acids Res 2024; 52:5423-5437. [PMID: 38742636 PMCID: PMC11162796 DOI: 10.1093/nar/gkae350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
Oral delivery is the most widely used and convenient route of administration of medicine. However, oral administration of hydrophilic macromolecules is commonly limited by low intestinal permeability and pre-systemic degradation in the gastrointestinal (GI) tract. Overcoming some of these challenges allowed emergence of oral dosage forms of peptide-based drugs in clinical settings. Antisense oligonucleotides (ASOs) have also been investigated for oral administration but despite the recent progress, the bioavailability remains low. Given the advancement with highly potent and durable trivalent N-acetylgalactosamine (GalNAc)-conjugated small interfering RNAs (siRNAs) via subcutaneous (s.c.) injection, we explored their activities after oral administration. We report robust RNA interference (RNAi) activity of orally administrated GalNAc-siRNAs co-formulated with permeation enhancers (PEs) in rodents and non-human primates (NHPs). The relative bioavailability calculated from NHP liver exposure was <2.0% despite minimal enzymatic degradation in the GI. To investigate the impact of oligonucleotide size on oral delivery, highly specific GalNAc-conjugated single-stranded oligonucleotides known as REVERSIRs with different lengths were employed and their activities for reversal of RNAi effect were monitored. Our data suggests that intestinal permeability is highly influenced by the size of oligonucleotides. Further improvements in the potency of siRNA and PE could make oral delivery of GalNAc-siRNAs as a practical solution.
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Affiliation(s)
- Mikyung Yu
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - June Qin
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Xiumin Liu
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Diane Ramsden
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Ivan Zlatev
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Dale Guenther
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Roxanne Tymon
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Justin Darcy
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Catrina Wong
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Jamie Tsung
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Peter Zawaneh
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Saeho Chong
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Nathan Taneja
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Arlin Rogers
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Ju Liu
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Sarah Bond
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Kawai So
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | | | - Jing-Tao Wu
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
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2
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Pottenger AE, Roy D, Srinivasan S, Chavas TEJ, Vlaskin V, Ho DK, Livingston VC, Maktabi M, Lin H, Zhang J, Pybus B, Kudyba K, Roth A, Senter P, Tyson G, Huber HE, Wesche D, Rochford R, Burke PA, Stayton PS. Liver-targeted polymeric prodrugs delivered subcutaneously improve tafenoquine therapeutic window for malaria radical cure. SCIENCE ADVANCES 2024; 10:eadk4492. [PMID: 38640243 PMCID: PMC11029812 DOI: 10.1126/sciadv.adk4492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/19/2024] [Indexed: 04/21/2024]
Abstract
Approximately 3.3 billion people live with the threat of Plasmodium vivax malaria. Infection can result in liver-localized hypnozoites, which when reactivated cause relapsing malaria. This work demonstrates that an enzyme-cleavable polymeric prodrug of tafenoquine addresses key requirements for a mass administration, eradication campaign: excellent subcutaneous bioavailability, complete parasite control after a single dose, improved therapeutic window compared to the parent oral drug, and low cost of goods sold (COGS) at less than $1.50 per dose. Liver targeting and subcutaneous dosing resulted in improved liver:plasma exposure profiles, with increased efficacy and reduced glucose 6-phosphate dehydrogenase-dependent hemotoxicity in validated preclinical models. A COGS and manufacturability analysis demonstrated global scalability, affordability, and the ability to redesign this fully synthetic polymeric prodrug specifically to increase global equity and access. Together, this polymer prodrug platform is a candidate for evaluation in human patients and shows potential for P. vivax eradication campaigns.
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Affiliation(s)
- Ayumi E. Pottenger
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Debashish Roy
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Selvi Srinivasan
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Thomas E. J. Chavas
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Vladmir Vlaskin
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Duy-Khiet Ho
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | | | - Mahdi Maktabi
- Department of Immunology and Microbiology, University of Colorado Anschutz School of Medicine, Aurora, CO 80045, USA
| | - Hsiuling Lin
- Department of Drug Discovery, Experimental Therapeutics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Jing Zhang
- Department of Drug Discovery, Experimental Therapeutics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Brandon Pybus
- Department of Drug Discovery, Experimental Therapeutics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Karl Kudyba
- Department of Drug Discovery, Experimental Therapeutics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Alison Roth
- Department of Drug Discovery, Experimental Therapeutics Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | | | - George Tyson
- George Tyson Consulting, Los Altos Hills, CA 94022, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hans E. Huber
- BioTD Strategies LLC, 213 Abbey Ln., Lansdale, PA 19446, USA
| | | | - Rosemary Rochford
- Department of Immunology and Microbiology, University of Colorado Anschutz School of Medicine, Aurora, CO 80045, USA
| | - Paul A. Burke
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Burke Bioventures LLC, 1 Broadway 14th Floor, Cambridge, MA 02142, USA
| | - Patrick S. Stayton
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
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3
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Li Q, Yin K, Ma HP, Liu HH, Li S, Luo X, Hu R, Zhang WW, Lv ZS, Niu XL, Gu MH, Li CL, Liu YS, Liu YJ, Li HB, Li N, Li C, Gu WW, Li JJ. Application of improved GalNAc conjugation in development of cost-effective siRNA therapies targeting cardiovascular diseases. Mol Ther 2024; 32:637-645. [PMID: 38204163 PMCID: PMC10928129 DOI: 10.1016/j.ymthe.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/08/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024] Open
Abstract
N-Acetylgalactosamine (GalNAc)-conjugated small interfering RNA (siRNA) therapies have received approval for treating both orphan and prevalent diseases. To improve in vivo efficacy and streamline the chemical synthesis process for efficient and cost-effective manufacturing, we conducted this study to identify better designs of GalNAc-siRNA conjugates for therapeutic development. Here, we present data on redesigned GalNAc-based ligands conjugated with siRNAs against angiopoietin-like 3 (ANGPTL3) and lipoprotein (a) (Lp(a)), two target molecules with the potential to address large unmet medical needs in atherosclerotic cardiovascular diseases. By attaching a novel pyran-derived scaffold to serial monovalent GalNAc units before solid-phase oligonucleotide synthesis, we achieved increased GalNAc-siRNA production efficiency with fewer synthesis steps compared to the standard triantennary GalNAc construct L96. The improved GalNAc-siRNA conjugates demonstrated equivalent or superior in vivo efficacy compared to triantennary GalNAc-conjugated siRNAs.
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Affiliation(s)
- Qian Li
- Genoval Therapeutics Co., Ltd, Shanghai, China
| | - Ke Yin
- Genoval Therapeutics Co., Ltd, Shanghai, China
| | - Hai-Ping Ma
- Genoval Therapeutics Co., Ltd, Shanghai, China
| | - Hui-Hui Liu
- Cardiometabolic Center, State Key Laboratory of Cardiovascular Disease, FuWai Hospital, National Center for Cardiovascular Diseases, National Clinical Research Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Heart Failure Center, State Key Laboratory of Cardiovascular Disease, FuWai Hospital, National Center for Cardiovascular Diseases, National Clinical Research Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sha Li
- Cardiometabolic Center, State Key Laboratory of Cardiovascular Disease, FuWai Hospital, National Center for Cardiovascular Diseases, National Clinical Research Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao Luo
- Genoval Therapeutics Co., Ltd, Shanghai, China
| | - Rong Hu
- Genoval Therapeutics Co., Ltd, Shanghai, China
| | | | | | | | - Mei-Hua Gu
- Genoval Therapeutics Co., Ltd, Shanghai, China
| | - Cheng-Lu Li
- Genoval Therapeutics Co., Ltd, Shanghai, China
| | | | | | - Hai-Bo Li
- Genoval Therapeutics Co., Ltd, Shanghai, China
| | - Nancy Li
- Genoval Therapeutics Co., Ltd, Shanghai, China
| | - Chong Li
- Genoval Therapeutics Co., Ltd, Shanghai, China
| | | | - Jian-Jun Li
- Cardiometabolic Center, State Key Laboratory of Cardiovascular Disease, FuWai Hospital, National Center for Cardiovascular Diseases, National Clinical Research Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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4
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Jadhav V, Vaishnaw A, Fitzgerald K, Maier MA. RNA interference in the era of nucleic acid therapeutics. Nat Biotechnol 2024; 42:394-405. [PMID: 38409587 DOI: 10.1038/s41587-023-02105-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/15/2023] [Indexed: 02/28/2024]
Abstract
Two decades of research on RNA interference (RNAi) have transformed a breakthrough discovery in biology into a robust platform for a new class of medicines that modulate mRNA expression. Here we provide an overview of the trajectory of small-interfering RNA (siRNA) drug development, including the first approval in 2018 of a liver-targeted siRNA interference (RNAi) therapeutic in lipid nanoparticles and subsequent approvals of five more RNAi drugs, which used metabolically stable siRNAs combined with N-acetylgalactosamine ligands for conjugate-based liver delivery. We also consider the remaining challenges in the field, such as delivery to muscle, brain and other extrahepatic organs. Today's RNAi therapeutics exhibit high specificity, potency and durability, and are transitioning from applications in rare diseases to widespread, chronic conditions.
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Affiliation(s)
- Vasant Jadhav
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA.
| | - Akshay Vaishnaw
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Kevin Fitzgerald
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Martin A Maier
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA.
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5
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An G. Pharmacokinetics and Pharmacodynamics of GalNAc-Conjugated siRNAs. J Clin Pharmacol 2024; 64:45-57. [PMID: 37589246 DOI: 10.1002/jcph.2337] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/13/2023] [Indexed: 08/18/2023]
Abstract
Small interfering RNAs (siRNAs) represent a new class of drugs with tremendous potential for battling previously "undruggable" diseases. After nearly 2 decades of efforts in addressing the problems of the poor drug profile of naked unmodified siRNAs, this new modality has finally come to fruition, with 5 agents (patisiran, givosiran, lumasiran, inclisiran, and vutrisiran) being approved since 2018, and with many others in the different phases of clinical development. Unlike small-molecule drugs and protein therapeutics, siRNAs have different sizes, distinct mechanisms of action, differing physicochemical and pharmacological properties, and, accordingly, a unique pharmacokinetic/pharmacodynamic (PK/PD) relationship. To support the continuous development of siRNAs, it is important to have a thorough and deep understanding of the PK/PD and clinical pharmacology related features of siRNAs. As most of the current siRNA products are conjugated by N-acetylgalactosamine (GalNAc), this review focuses on the PK/PD relationships and clinical pharmacology of GalNAc-conjugated siRNAs, including their absorption, distribution, metabolism, excretion (ADME) properties, PK/PD models, drug-drug interactions, clinical pharmacology in special populations, and safety evaluation. In addition, necessary background information related to the development of siRNAs as a therapeutic modality, including the mechanisms of action, the advantages of siRNAs, the problems of naked siRNAs, as well as the strategies used to enhance the clinical utility of siRNAs, have also been covered. The goal of this review is to serve as a "primer" on siRNA PK/PD, and I hope the readers, especially those who have a limited background on siRNA therapeutics, will have a fundamental understanding of siRNA PK/PD and clinical pharmacology after reading this review.
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Affiliation(s)
- Guohua An
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA, USA
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6
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Sparmann A, Vogel J. RNA-based medicine: from molecular mechanisms to therapy. EMBO J 2023; 42:e114760. [PMID: 37728251 PMCID: PMC10620767 DOI: 10.15252/embj.2023114760] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
RNA-based therapeutics have the potential to revolutionize the treatment and prevention of human diseases. While early research faced setbacks, it established the basis for breakthroughs in RNA-based drug design that culminated in the extraordinarily fast development of mRNA vaccines to combat the COVID-19 pandemic. We have now reached a pivotal moment where RNA medicines are poised to make a broad impact in the clinic. In this review, we present an overview of different RNA-based strategies to generate novel therapeutics, including antisense and RNAi-based mechanisms, mRNA-based approaches, and CRISPR-Cas-mediated genome editing. Using three rare genetic diseases as examples, we highlight the opportunities, but also the challenges to wide-ranging applications of this class of drugs.
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Affiliation(s)
- Anke Sparmann
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
| | - Jörg Vogel
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
- Institute of Molecular Infection Biology (IMIB)University of WürzburgWürzburgGermany
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7
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Rocamora F, Peralta AG, Shin S, Sorrentino J, Wu MYM, Toth EA, Fuerst TR, Lewis NE. Glycosylation shapes the efficacy and safety of diverse protein, gene and cell therapies. Biotechnol Adv 2023; 67:108206. [PMID: 37354999 PMCID: PMC11168894 DOI: 10.1016/j.biotechadv.2023.108206] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 06/26/2023]
Abstract
Over recent decades, therapeutic proteins have had widespread success in treating a myriad of diseases. Glycosylation, a near universal feature of this class of drugs, is a critical quality attribute that significantly influences the physical properties, safety profile and biological activity of therapeutic proteins. Optimizing protein glycosylation, therefore, offers an important avenue to developing more efficacious therapies. In this review, we discuss specific examples of how variations in glycan structure and glycoengineering impacts the stability, safety, and clinical efficacy of protein-based drugs that are already in the market as well as those that are still in preclinical development. We also highlight the impact of glycosylation on next generation biologics such as T cell-based cancer therapy and gene therapy.
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Affiliation(s)
- Frances Rocamora
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angelo G Peralta
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Seunghyeon Shin
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - James Sorrentino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mina Ying Min Wu
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric A Toth
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Thomas R Fuerst
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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8
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Zanchi C, Locatelli M, Corna D, Cerullo D, Fishilevich E, Desai D, Rottoli D, Donadelli R, Noris M, Zoja C, Remuzzi G, Benigni A. Liver factor B silencing to cure C3 glomerulopathy: Evidence from a mouse model of complement dysregulation. Mol Immunol 2023; 161:25-32. [PMID: 37481826 DOI: 10.1016/j.molimm.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/28/2023] [Accepted: 07/18/2023] [Indexed: 07/25/2023]
Abstract
Uncontrolled activation of the alternative pathway (AP) of complement, due to genetic and/or acquired defects, plays a primary pathogenetic role in C3 glomerulopathy (C3G), a rare and heterogeneous disease characterised by predominant C3 fragment deposition within the glomerulus, as well as glomerular damage. There are currently no approved disease-specific treatments for C3G, but new drugs that directly counteract AP dysregulation, targeting components of the pathway, have opened promising new perspectives for managing the disease. Complement factor B (FB), which is primarily synthesised by hepatocytes, is a key component of the AP, as it drives the central amplification loop of the complement system. In this study we used a GalNAc (N-Acetylgalactosamine)-conjugated siRNA to selectively target and suppress liver FB expression in two mouse models characterised by the complete (Cfh-/- mice) or partial (Cfh+/-) loss of function of complement factor H (FH). Homozygous deletion of FH induced a severe C3G phenotype, with strong dysregulation of the AP of complement, glomerular C3 deposition and almost complete C3 consumption. Mice with a heterozygous deletion of FH had intermediate C3 levels and exhibited slower disease progression, resembling human C3G more closely. Here we showed that FB siRNA treatment did not improve serum C3 levels, nor limit glomerular C3 deposition in Cfh-/- mice, while it did normalise circulating C3 levels, reduce glomerular C3 deposits, and limit mesangial electron-dense deposits in Cfh+/- mice. The present data provide important insights into the potential benefits and limitations of FB-targeted inhibition strategies and suggest RNA interference-mediated FB silencing in the liver as a possible therapeutic approach for treating C3G patients with FH haploinsufficiency.
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Affiliation(s)
- Cristina Zanchi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Centro Anna Maria Astori Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Monica Locatelli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Centro Anna Maria Astori Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Daniela Corna
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Centro Anna Maria Astori Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Domenico Cerullo
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Centro Anna Maria Astori Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | | | - Dhruv Desai
- Alnylam Pharmaceuticals Inc., Boston, MA, United States
| | - Daniela Rottoli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Centro Anna Maria Astori Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Roberta Donadelli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Centro Anna Maria Astori Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Marina Noris
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Centro Anna Maria Astori Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Carlamaria Zoja
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Centro Anna Maria Astori Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Centro Anna Maria Astori Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Ariela Benigni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Centro Anna Maria Astori Science and Technology Park Kilometro Rosso, Bergamo, Italy.
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9
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Koyasu K, Chandela A, Ueno Y. Non-terminal conjugation of small interfering RNAs with spermine improves duplex binding and serum stability with position-specific incorporation. RSC Adv 2023; 13:25169-25181. [PMID: 37622021 PMCID: PMC10445083 DOI: 10.1039/d3ra04918c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023] Open
Abstract
The conjugation of small interfering RNAs (siRNAs) has been studied using lipid and ligand conjugates for efficient delivery. However, most conjugates have been inserted at the terminal position; very few have been inserted at non-terminal positions. Herein, we synthesized a 4'-C-propyllevulinate-2'-O-methyluridine analog for non-terminal conjugation of spermine into the passenger strand of siRNA. Solid-phase oligonucleotide synthesis using this analog was successful, with the conjugation of one or two spermine molecules. The siRNAs conjugated with spermine displayed improved thermodynamic stability and resistance against nucleases, which depended on the site of conjugation in each case. Circular dichroism spectroscopy revealed that the A-type helical structure of the RNA duplex was not altered by these modifications. However, the gene-silencing activity of conjugated siRNAs was reduced and further decreased when the number of spermine molecules was increased. Hence, this work supplies valuable information and provides scope for the further development of drug-delivery systems through non-terminal conjugation.
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Affiliation(s)
- Keisuke Koyasu
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University Japan +81-58-293-2919 +81-58-293-2919
| | - Akash Chandela
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University Japan
| | - Yoshihito Ueno
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University Japan +81-58-293-2919 +81-58-293-2919
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University Japan
- United Graduate School of Agricultural Science, Gifu University 1-1 Yanagido Gifu 501-1193 Japan
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10
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Biebuyck N, Destombes C, Prakash R, Boyer O. Is withdrawal of nocturnal hyperhydration possible in children with primary hyperoxaluria treated with RNAi? J Nephrol 2023; 36:1473-1476. [PMID: 37209362 DOI: 10.1007/s40620-023-01611-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/23/2023] [Indexed: 05/22/2023]
Abstract
Primary hyperoxaluria type 1 is a rare genetic disorder caused by bi-allelic pathogenic variants in the AGXT gene leading to an overproduction of oxalate which accumulates in the kidneys in the form of calcium oxalate crystals. Thus, patients may present with recurrent nephrocalcinosis and lithiasis, with progressive impairment of the renal function and eventually kidney failure. There is no specific treatment besides liver-kidney transplantation, and pre-transplantation management by 24 h-hyperhydration, crystallisation inhibitors and high-dose pyridoxine has a high negative impact on quality of life, especially because of the discomfort due to nocturnal hyperhydration. Since 2020, lumasiran, an RNA-interfering therapy, has been approved for the treatment of primary hyperoxaluria type 1 in adults and children. However, to date, there are no recommendations regarding the discontinuation of other supportive measures during RNAi therapy. In this report, we present two patients with primary hyperoxaluria type 1 who were treated with lumasiran and stopped nocturnal hyperhydration with positive outcomes, i.e. normal urinary oxalate, absence of crystalluria, stable kidney function and improved well-being. These data suggest that discontinuing nocturnal hydration may be safe in children responding to lumasiran, and may have a positive impact on their quality of life. Additional data are needed to update treatment recommendations.
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Affiliation(s)
- Nathalie Biebuyck
- Paediatric Nephrology, Necker Enfants Malades Hospital, MARHEA, APHP, Imagine Institute, Paris Cité University, 149 rue de Sèvres, 75015, Paris, France
| | - Camille Destombes
- Paediatric Nephrology, Necker Enfants Malades Hospital, MARHEA, APHP, Imagine Institute, Paris Cité University, 149 rue de Sèvres, 75015, Paris, France
| | - Richa Prakash
- Paediatric Nephrology, Necker Enfants Malades Hospital, MARHEA, APHP, Imagine Institute, Paris Cité University, 149 rue de Sèvres, 75015, Paris, France
| | - Olivia Boyer
- Paediatric Nephrology, Necker Enfants Malades Hospital, MARHEA, APHP, Imagine Institute, Paris Cité University, 149 rue de Sèvres, 75015, Paris, France.
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11
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Egli M, Schlegel MK, Manoharan M. Acyclic ( S)-glycol nucleic acid ( S-GNA) modification of siRNAs improves the safety of RNAi therapeutics while maintaining potency. RNA (NEW YORK, N.Y.) 2023; 29:402-414. [PMID: 36725319 PMCID: PMC10019370 DOI: 10.1261/rna.079526.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Glycol nucleic acid (GNA) is an acyclic nucleic acid analog connected via phosphodiester bonds. Crystal structures of RNA-GNA chimeric duplexes indicated that nucleotides of the right-handed (S)-GNA were better accommodated in the right-handed RNA duplex than were the left-handed (R)-isomers. GNA nucleotides adopt a rotated nucleobase orientation within all duplex contexts, pairing with complementary RNA in a reverse Watson-Crick mode, which explains the inabilities of GNA C and G to form strong base pairs with complementary nucleotides. Transposition of the hydrogen bond donor and acceptor pairs using novel (S)-GNA isocytidine and isoguanosine nucleotides resulted in stable base-pairing with the complementary G and C ribonucleotides, respectively. GNA nucleotide or dinucleotide incorporation into an oligonucleotide increased resistance against 3'-exonuclease-mediated degradation. Consistent with the structural observations, small interfering RNAs (siRNAs) modified with (S)-GNA had greater in vitro potencies than identical sequences containing (R)-GNA. (S)-GNA is well tolerated in the seed regions of antisense and sense strands of a GalNAc-conjugated siRNA in vitro. The siRNAs containing a GNA base pair in the seed region had in vivo potency when subcutaneously injected into mice. Importantly, seed pairing destabilization resulting from a single GNA nucleotide at position 7 of the antisense strand mitigated RNAi-mediated off-target effects in a rodent model. Two GNA-modified siRNAs have shown an improved safety profile in humans compared with their non-GNA-modified counterparts, and several additional siRNAs containing the GNA modification are currently in clinical development.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Mark K Schlegel
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, USA
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12
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Virus-Induced Gene Silencing (VIGS): A Powerful Tool for Crop Improvement and Its Advancement towards Epigenetics. Int J Mol Sci 2023; 24:ijms24065608. [PMID: 36982682 PMCID: PMC10057534 DOI: 10.3390/ijms24065608] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/17/2023] Open
Abstract
Virus-induced gene silencing (VIGS) is an RNA-mediated reverse genetics technology that has evolved into an indispensable approach for analyzing the function of genes. It downregulates endogenous genes by utilizing the posttranscriptional gene silencing (PTGS) machinery of plants to prevent systemic viral infections. Based on recent advances, VIGS can now be used as a high-throughput tool that induces heritable epigenetic modifications in plants through the viral genome by transiently knocking down targeted gene expression. As a result of the progression of DNA methylation induced by VIGS, new stable genotypes with desired traits are being developed in plants. In plants, RNA-directed DNA methylation (RdDM) is a mechanism where epigenetic modifiers are guided to target loci by small RNAs, which play a major role in the silencing of the target gene. In this review, we described the molecular mechanisms of DNA and RNA-based viral vectors and the knowledge obtained through altering the genes in the studied plants that are not usually accessible to transgenic techniques. We showed how VIGS-induced gene silencing can be used to characterize transgenerational gene function(s) and altered epigenetic marks, which can improve future plant breeding programs.
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13
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Fernandez C, Giorgees I, Goss E, Desaulniers JP. Effective carrier-free gene-silencing activity of sphingosine-modified siRNAs. Org Biomol Chem 2023; 21:2107-2117. [PMID: 36645381 DOI: 10.1039/d2ob02099h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
RNA interference (RNAi) is a natural cellular process that silences the expression of target genes in a sequence-specific way by mediating targeted mRNA degradation. One of the main challenges in RNAi research is developing an effective career-free delivery system and targeting cells in the central nervous system (CNS). Recently, lipid-conjugated systems involving fatty acids have shown promising potential as safe and effective delivery systems of oligonucleotides to CNS cells due to their hydrophobic tails and interactions with the cell's hydrophobic membrane. Therefore, in this study, we are interested in creating career-free siRNA therapeutics for potential applications in drug delivery to the CNS. Here we explore different synthetic pathways of conjugating sphingolipids containing long-carbon chains to siRNA and assess their effectiveness as career-free delivery systems. In this project, a library of sphingosine-modified siRNAs was created, and their gene-silencing effect was evaluated in both the presence and absence of a transfection carrier. siRNAs modified with one or two sphingosine moieties resulted in dose-dependent gene knockdown while demonstrating promising results for their use as carrier-free agents. The IC50 values of single-modified siRNAs ranged from 49.9 nM to 670.7 nM, whereas double-modified siRNAs had IC50 values in the range of 49.9 nM to 66.4 nM. In conclusion, sphingosine-modified siRNAs show promising results in advancing carrier-free siRNA therapeutics.
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Affiliation(s)
- Charlene Fernandez
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, L1G 0C5, Canada.
| | - Ifrodet Giorgees
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, L1G 0C5, Canada.
| | - Eva Goss
- Synthose Inc., 50 Viceroy Road Unit 7, Concord, Ontario, L4K 3A7 Canada
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, L1G 0C5, Canada.
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14
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Kandasamy P, Mori S, Matsuda S, Erande N, Datta D, Willoughby JLS, Taneja N, O'Shea J, Bisbe A, Manoharan RM, Yucius K, Nguyen T, Indrakanti R, Gupta S, Gilbert JA, Racie T, Chan A, Liu J, Hutabarat R, Nair JK, Charisse K, Maier MA, Rajeev KG, Egli M, Manoharan M. Metabolically Stable Anomeric Linkages Containing GalNAc-siRNA Conjugates: An Interplay among ASGPR, Glycosidase, and RISC Pathways. J Med Chem 2023; 66:2506-2523. [PMID: 36757090 DOI: 10.1021/acs.jmedchem.2c01337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Conjugation of synthetic triantennary N-acetyl-d-galactosamine (GalNAc) to small interfering RNA (siRNA) mediates binding to the asialoglycoprotein receptor (ASGPR) on the surface of hepatocytes, facilitating liver-specific uptake and siRNA-mediated gene silencing. The natural β-glycosidic bond of the GalNAc ligand is rapidly cleaved by glycosidases in vivo. Novel GalNAc ligands with S-, and C-glycosides with both α- and β-anomeric linkages, N-glycosides with β-anomeric linkage, and the O-glycoside with α-anomeric linkage were synthesized and conjugated to siRNA either on-column during siRNA synthesis or through a high-throughput, post-synthetic method. Unlike natural GalNAc, modified ligands were resistant to glycosidase activity. The siRNAs conjugated to newly designed ligands had similar affinities for ASGPR and similar silencing activity in mice as the parent GalNAc-siRNA conjugate. These data suggest that other factors, such as protein-nucleic acid interactions and loading of the antisense strand into the RNA-induced silencing complex (RISC), are more critical to the duration of action than the stereochemistry and stability of the anomeric linkage between the GalNAc moiety of the ligand conjugated to the sense strand of the siRNA.
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Affiliation(s)
| | - Shohei Mori
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Namrata Erande
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Dhrubajyoti Datta
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | | | - Nate Taneja
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Jonathan O'Shea
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Anna Bisbe
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Kristina Yucius
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Tuyen Nguyen
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Ramesh Indrakanti
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Swati Gupta
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Jason A Gilbert
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Tim Racie
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Amy Chan
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Ju Liu
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Renta Hutabarat
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Jayaprakash K Nair
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | - Martin A Maier
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
| | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, United States
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15
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Kumar V, Turnbull WB. Targeted delivery of oligonucleotides using multivalent protein-carbohydrate interactions. Chem Soc Rev 2023; 52:1273-1287. [PMID: 36723021 PMCID: PMC9940626 DOI: 10.1039/d2cs00788f] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Indexed: 02/02/2023]
Abstract
Cell surface protein-carbohydrate interactions are essential for tissue-specific recognition and endocytosis of viruses, some bacteria and their toxins, and many glycoproteins. Often protein-carbohydrate interactions are multivalent - multiple copies of glycans bind simultaneously to multimeric receptors. Multivalency enhances both affinity and binding specificity, and is of interest for targeted delivery of drugs to specific cell types. The first such example of carbohydrate-mediated drug delivery to reach the clinic is Givosiran, a small interfering ribonucleic acid (siRNA) that is conjugated to a trivalent N-acetylgalactosamine (GalNAc) ligand. This ligand enables efficient uptake of the nucleic acid by the asialoglycoprotein receptor (ASGP-R) on hepatocytes. Synthetic multivalent ligands for ASGP-R were among the first 'cluster glycosides' developed at the birth of multivalent glycoscience around 40 years ago. In this review we trace the history of 'GalNAc targeting' from early academic studies to current pharmaceuticals and consider what other opportunities could follow the success of this delivery technology.
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Affiliation(s)
- Vajinder Kumar
- Department of Chemistry, Akal University, Talwandi Sabo, Bathinda, Punjab, India.
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
| | - W Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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16
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Suppressing Hepatic UGT1A1 Increases Plasma Bilirubin, Lowers Plasma Urobilin, Reorganizes Kinase Signaling Pathways and Lipid Species and Improves Fatty Liver Disease. Biomolecules 2023; 13:biom13020252. [PMID: 36830621 PMCID: PMC9953728 DOI: 10.3390/biom13020252] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Several population studies have observed lower serum bilirubin levels in patients with non-alcoholic fatty liver disease (NAFLD). Yet, treatments to target this metabolic phenotype have not been explored. Therefore, we designed an N-Acetylgalactosamine (GalNAc) labeled RNAi to target the enzyme that clears bilirubin from the blood, the UGT1A1 glucuronyl enzyme (GNUR). In this study, male C57BL/6J mice were fed a high-fat diet (HFD, 60%) for 30 weeks to induce NAFLD and were treated subcutaneously with GNUR or sham (CTRL) once weekly for six weeks while continuing the HFD. The results show that GNUR treatments significantly raised plasma bilirubin levels and reduced plasma levels of the bilirubin catabolized product, urobilin. We show that GNUR decreased liver fat content and ceramide production via lipidomics and lowered fasting blood glucose and insulin levels. We performed extensive kinase activity analyses using our PamGene PamStation kinome technology and found a reorganization of the kinase pathways and a significant decrease in inflammatory mediators with GNUR versus CTRL treatments. These results demonstrate that GNUR increases plasma bilirubin and reduces plasma urobilin, reducing NAFLD and inflammation and improving overall liver health. These data indicate that UGT1A1 antagonism might serve as a treatment for NAFLD and may improve obesity-associated comorbidities.
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17
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Shivatare SS, Shivatare VS, Wong CH. Glycoconjugates: Synthesis, Functional Studies, and Therapeutic Developments. Chem Rev 2022; 122:15603-15671. [PMID: 36174107 PMCID: PMC9674437 DOI: 10.1021/acs.chemrev.1c01032] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycoconjugates are major constituents of mammalian cells that are formed via covalent conjugation of carbohydrates to other biomolecules like proteins and lipids and often expressed on the cell surfaces. Among the three major classes of glycoconjugates, proteoglycans and glycoproteins contain glycans linked to the protein backbone via amino acid residues such as Asn for N-linked glycans and Ser/Thr for O-linked glycans. In glycolipids, glycans are linked to a lipid component such as glycerol, polyisoprenyl pyrophosphate, fatty acid ester, or sphingolipid. Recently, glycoconjugates have become better structurally defined and biosynthetically understood, especially those associated with human diseases, and are accessible to new drug, diagnostic, and therapeutic developments. This review describes the status and new advances in the biological study and therapeutic applications of natural and synthetic glycoconjugates, including proteoglycans, glycoproteins, and glycolipids. The scope, limitations, and novel methodologies in the synthesis and clinical development of glycoconjugates including vaccines, glyco-remodeled antibodies, glycan-based adjuvants, glycan-specific receptor-mediated drug delivery platforms, etc., and their future prospectus are discussed.
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Affiliation(s)
- Sachin S Shivatare
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vidya S Shivatare
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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18
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Hofmeister A, Jahn-Hofmann K, Brunner B, Helms M, Metz-Weidmann C, Krack A, Kurz M, Heubel C, Scheidler S. Small Interfering RNAs Containing Dioxane- and Morpholino-Derived Nucleotide Analogues Show Improved Off-Target Profiles and Chirality-Dependent In Vivo Knock-Down. J Med Chem 2022; 65:13736-13752. [PMID: 36223135 DOI: 10.1021/acs.jmedchem.2c00873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To expand the applicability of recently developed dioxane- and morpholino-based nucleotide analogues, their seed region destabilizing properties in small interfering RNAs (siRNAs) were investigated in order to improve potential off-target profiles. For this purpose, the corresponding adenosine analogues were synthesized in two diastereomeric series as building blocks for the automated oligonucleotide synthesis. The obtained nucleotide precursors were integrated at position 7 of an siRNA antisense strand, targeting transthyretin messenger RNA. Evaluation of the melting temperatures revealed significant differences in the obtained duplex stabilities between the two diastereomeric series, while the influence of the central scaffold was small. All siRNAs containing these novel nucleotide structures showed improved off-target profiles in vitro compared to their parent sequence with the common 2'-OMe-modified adenosine at the same position. In contrast, in vivo potencies were highly dependent on the chirality within the six-membered nucleotide scaffolds and showed high mRNA downregulations for the (2R,6R)-configured diastereomers.
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Affiliation(s)
- Armin Hofmeister
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | | | - Bodo Brunner
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Mike Helms
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | | | - Arne Krack
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Michael Kurz
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Christoph Heubel
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Sabine Scheidler
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
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19
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Vaillant A. Oligonucleotide-Based Therapies for Chronic HBV Infection: A Primer on Biochemistry, Mechanisms and Antiviral Effects. Viruses 2022; 14:v14092052. [PMID: 36146858 PMCID: PMC9502277 DOI: 10.3390/v14092052] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/21/2022] Open
Abstract
Three types of oligonucleotide-based medicines are under clinical development for the treatment of chronic HBV infection. Antisense oligonucleotides (ASOs) and synthetic interfering RNA (siRNA) are designed to degrade HBV mRNA, and nucleic acid polymers (NAPs) stop the assembly and secretion of HBV subviral particles. Extensive clinical development of ASOs and siRNA for a variety of liver diseases has established a solid understanding of their pharmacodynamics, accumulation in different tissue types in the liver, pharmacological effects, off-target effects and how chemical modifications and delivery approaches affect these parameters. These effects are highly conserved for all ASO and siRNA used in human studies to date. The clinical assessment of several ASO and siRNA compounds in chronic HBV infection in recent years is complicated by the different delivery approaches used. Moreover, these assessments have not considered the large clinical database of ASO/siRNA function in other liver diseases and known off target effects in other viral infections. The goal of this review is to summarize the current understanding of ASO/siRNA/NAP pharmacology and integrate these concepts into current clinical results for these compounds in the treatment of chronic HBV infection.
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Affiliation(s)
- Andrew Vaillant
- Replicor Inc., 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada
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20
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Xie J, Hu Y, Sun D, Liu C, Li Z, Zhu J. Targeting non-coding RNA H19: A potential therapeutic approach in pulmonary diseases. Front Pharmacol 2022; 13:978151. [PMID: 36188624 PMCID: PMC9523668 DOI: 10.3389/fphar.2022.978151] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Non-coding RNA is still one of the most popular fields in biology research. In recent years, people paid more attention to the roles of H19 in lung diseases, which expressed abnormally in various pathological process. Therefore, this review focus on the regulatory role of H19 in asthma, pulmonary arterial hypertension (PAH), idiopathic pulmonary fibrosis (IPF), lung injury, pneumonia, lung cancer, etc. And the potential therapeutic agents and molecular treatments of H19 are collected. The aim is to demonstrate its underlying mechanism in pulmonary diseases and to guide the basic research targeting H19 into clinical drug translation.
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Affiliation(s)
- Jinghui Xie
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yuedi Hu
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Dengdi Sun
- The Key Laboratory of Intelligent Computing and Signal Processing (ICSP), Ministry of Education, School of Artificial Intelligence, Anhui University, Hefei, China
| | - Changan Liu
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Zegeng Li
- Institute of Traditional Chinese Medicine Prevention and Control on Respiratory Disease, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
- Department of Respiratory Medicine, First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, Anhui, China
| | - Jie Zhu
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Traditional Chinese Medicine Prevention and Control on Respiratory Disease, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
- Institutes of Integrative Medicine, Fudan University, Shanghai, China
- *Correspondence: Jie Zhu,
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21
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Chemical optimization of siRNA for safe and efficient silencing of placental sFLT1. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 29:135-149. [PMID: 35847173 PMCID: PMC9263991 DOI: 10.1016/j.omtn.2022.06.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022]
Abstract
Preeclampsia (PE) is a rising, potentially lethal complication of pregnancy. PE is driven primarily by the overexpression of placental soluble fms-like tyrosine kinase 1 (sFLT1), a validated diagnostic and prognostic marker of the disease when normalized to placental growth factor (PlGF) levels. Injecting cholesterol-conjugated, fully modified, small interfering RNAs (siRNAs) targeting sFLT1 mRNA into pregnant mice or baboons reduces placental sFLT1 and ameliorates clinical signs of PE, providing a strong foundation for the development of a PE therapeutic. siRNA delivery, potency, and safety are dictated by conjugate chemistry, siRNA duplex structure, and chemical modification pattern. Here, we systematically evaluate these parameters and demonstrate that increasing 2'-O-methyl modifications and 5' chemical stabilization and using sequence-specific duplex asymmetry and a phosphocholine-docosanoic acid conjugate enhance placental accumulation, silencing efficiency and safety of sFLT1-targeting siRNAs. The optimization strategy here provides a framework for the chemical optimization of siRNAs for PE as well as other targets and clinical indications.
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22
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Engineered ionizable lipid siRNA conjugates enhance endosomal escape but induce toxicity in vivo. J Control Release 2022; 349:831-843. [PMID: 35917865 DOI: 10.1016/j.jconrel.2022.07.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/29/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022]
Abstract
Lipid conjugation supports delivery of small interfering RNAs (siRNAs) to extrahepatic tissues, expanding the therapeutic potential of siRNAs beyond liver indications. However, siRNA silencing efficacy in extrahepatic tissues remains inferior to that routinely achieved in liver, partially due to the low rate of endosomal escape following siRNA internalization. Improving siRNA endosomal release into cytoplasm is crucial to improving efficacy of lipid-conjugated siRNAs. Given the ability of ionizable lipids to enhance endosomal escape in a context of lipid nanoparticles (LNP), here, we provide the first report on the effect of an ionizable lipid conjugate on siRNA endosomal escape, tissue distribution, efficacy, and toxicity in vivo. After developing a synthetic route to covalently attach the ionizable lipid, DLin-MC3-DMA, to siRNAs, we demonstrate that DLin-MC3-DMA enhances endosomal escape in cell culture without compromising siRNA efficacy. In mice, DLin-MC3-DMA conjugated siRNAs exhibit a similar overall tissue distribution profile to the similarly hydrophobic cholesterol-conjugated siRNA. However, only DLin-MC3-DMA conjugated siRNAs accumulated in vascular compartments, suggesting an effect of conjugate structure on intratissue distribution. Interestingly, we observed non-specific modulation of gene expression in tissues with high accumulation of DLin-MC3-DMA siRNAs (>20 pmol/mg of tissue) while limited non-specific gene modulation has been observed in tissues with lower siRNA accumulation. These findings suggest modulating the nature of the conjugate is a promising strategy to alter siRNA intratissue and intracellular trafficking. Fine-tuning the nature of the conjugate to optimize endosomal escape while minimizing toxicity will be critical for the progression of therapeutic siRNA applications beyond the liver.
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Abstract
The highly specific induction of RNA interference-mediated gene knockdown, based on the direct application of small interfering RNAs (siRNAs), opens novel avenues towards innovative therapies. Two decades after the discovery of the RNA interference mechanism, the first siRNA drugs received approval for clinical use by the US Food and Drug Administration and the European Medicines Agency between 2018 and 2022. These are mainly based on an siRNA conjugation with a targeting moiety for liver hepatocytes, N-acetylgalactosamine, and cover the treatment of acute hepatic porphyria, transthyretin-mediated amyloidosis, hypercholesterolemia, and primary hyperoxaluria type 1. Still, the development of siRNA therapeutics faces several challenges and issues, including the definition of optimal siRNAs in terms of target, sequence, and chemical modifications, siRNA delivery to its intended site of action, and the absence of unspecific off-target effects. Further siRNA drugs are in clinical studies, based on different delivery systems and covering a wide range of different pathologies including metabolic diseases, hematology, infectious diseases, oncology, ocular diseases, and others. This article reviews the knowledge on siRNA design and chemical modification, as well as issues related to siRNA delivery that may be addressed using different delivery systems. Details on the mode of action and clinical status of the various siRNA therapeutics are provided, before giving an outlook on issues regarding the future of siRNA drugs and on their potential as one emerging standard modality in pharmacotherapy. Notably, this may also cover otherwise un-druggable diseases, the definition of non-coding RNAs as targets, and novel concepts of personalized and combination treatment regimens.
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Affiliation(s)
- Maik Friedrich
- Faculty of Leipzig, Institute of Clinical Immunology, Max-Bürger-Forschungszentrum (MBFZ), University of Leipzig, Leipzig, Germany.,Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Achim Aigner
- Rudolf-Boehm Institute for Pharmacology and Toxicology, Clinical Pharmacology, University of Leipzig, Haertelstrasse 16-18, 04107, Leipzig, Germany.
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24
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Properties of Parallel Tetramolecular G-Quadruplex Carrying N-Acetylgalactosamine as Potential Enhancer for Oligonucleotide Delivery to Hepatocytes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123944. [PMID: 35745067 PMCID: PMC9228010 DOI: 10.3390/molecules27123944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 01/09/2023]
Abstract
The development of oligonucleotide conjugates for in vivo targeting is one of the most exciting areas for oligonucleotide therapeutics. A major breakthrough in this field was the development of multifunctional GalNAc-oligonucleotides with high affinity to asialoglycoprotein receptors (ASGPR) that directed therapeutic oligonucleotides to hepatocytes. In the present study, we explore the use of G-rich sequences functionalized with one unit of GalNAc at the 3'-end for the formation of tetrameric GalNAc nanostructures upon formation of a parallel G-quadruplex. These compounds are expected to facilitate the synthetic protocols by providing the multifunctionality needed for the binding to ASGPR. To this end, several G-rich oligonucleotides carrying a TGGGGGGT sequence at the 3'-end functionalized with one molecule of N-acetylgalactosamine (GalNAc) were synthesized together with appropriate control sequences. The formation of a self-assembled parallel G-quadruplex was confirmed through various biophysical techniques such as circular dichroism, nuclear magnetic resonance, polyacrylamide electrophoresis and denaturation curves. Binding experiments to ASGPR show that the size and the relative position of the therapeutic cargo are critical for the binding of these nanostructures. The biological properties of the resulting parallel G-quadruplex were evaluated demonstrating the absence of the toxicity in cell lines. The internalization preferences of GalNAc-quadruplexes to hepatic cells were also demonstrated as well as the enhancement of the luciferase inhibition using the luciferase assay in HepG2 cell lines versus HeLa cells. All together, we demonstrate that tetramerization of G-rich oligonucleotide is a novel and simple route to obtain the beneficial effects of multivalent N-acetylgalactosamine functionalization.
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Cordeiro R, Carvalho A, Durães L, Faneca H. Triantennary GalNAc-Functionalized Multi-Responsive Mesoporous Silica Nanoparticles for Drug Delivery Targeted at Asialoglycoprotein Receptor. Int J Mol Sci 2022; 23:ijms23116243. [PMID: 35682920 PMCID: PMC9181004 DOI: 10.3390/ijms23116243] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 02/01/2023] Open
Abstract
In recent years, mesoporous silica particles have been revealed as promising drug delivery systems combining high drug loading capacity, excellent biocompatibility, and easy and affordable synthetic and post-synthetic procedures. In fact, the straightforward functionalization approaches of these particles allow their conjugation with targeting moieties in order to surpass one of the major challenges in drug administration, the absence of targeting ability of free drugs that reduces their therapeutic efficacy and causes undesired side effects. In this context, the main goal of this work was to develop a new targeted mesoporous silica nanoparticle formulation with the capability to specifically and efficiently deliver an anticancer drug to hepatocellular carcinoma (HCC) cells. To this purpose, and as proof of concept, we developed redox-responsive mesoporous silica nanoparticles functionalized with the targeting ligand triantennary N-acetylgalactosamine (GalNAc) cluster, which has high affinity to asialoglycoprotein receptors overexpressed in HCC cells, and loaded them with epirubicin, an anthracycline drug. The produced nanocarrier exhibits suitable physicochemical properties for drug delivery, high drug loading capacity, high biocompatibility, and targeting ability to HCC cells, revealing its biopharmaceutical potential as a targeted drug carrier for therapeutic applications in liver diseases.
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Affiliation(s)
- Rosemeyre Cordeiro
- CNC—Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Polo I, 3004-517 Coimbra, Portugal; (R.C.); (A.C.)
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Ana Carvalho
- CNC—Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Polo I, 3004-517 Coimbra, Portugal; (R.C.); (A.C.)
| | - Luísa Durães
- CIEPQPF, Department of Chemical Engineering, University of Coimbra, Rua Sílvio Lima, Polo II, 3030-790 Coimbra, Portugal;
| | - Henrique Faneca
- CNC—Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Polo I, 3004-517 Coimbra, Portugal; (R.C.); (A.C.)
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
- Correspondence: ; Tel.: +35-12-398-20190
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26
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A novel aptamer-based small RNA delivery platform and its application to cancer therapy. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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27
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O'Sullivan J, Muñoz-Muñoz J, Turnbull G, Sim N, Penny S, Moschos S. Beyond GalNAc! Drug delivery systems comprising complex oligosaccharides for targeted use of nucleic acid therapeutics. RSC Adv 2022; 12:20432-20446. [PMID: 35919168 PMCID: PMC9281799 DOI: 10.1039/d2ra01999j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/06/2022] [Indexed: 12/12/2022] Open
Abstract
Nucleic Acid Therapeutics (NATs) are establishing a leading role for the management and treatment of genetic diseases following FDA approval of nusinersen, patisiran, and givosiran in the last 5 years, the breakthrough of milasen, with more approvals undoubtedly on the way. Givosiran takes advantage of the known interaction between the hepatocyte specific asialoglycoprotein receptor (ASGPR) and N-acetyl galactosamine (GalNAc) ligands to deliver a therapeutic effect, underscoring the value of targeting moieties. In this review, we explore the history of GalNAc as a ligand, and the paradigm it has set for the delivery of NATs through precise targeting to the liver, overcoming common hindrances faced with this type of therapy. We describe various complex oligosaccharides (OSs) and ask what others could be used to target receptors for NAT delivery and the opportunities awaiting exploration of this chemical space. Tapping the glycome space for targeted delivery. We explore GalNAc for targeting oligonucleotides to the liver and ask what other oligosaccharides could expand targeting options for other tissues.![]()
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Affiliation(s)
- Joseph O'Sullivan
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK, NE1 8ST
| | - Jose Muñoz-Muñoz
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK, NE1 8ST
| | - Graeme Turnbull
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK, NE1 8ST
| | - Neil Sim
- High Force Research Ltd, Bowburn North Industrial Estate, Durham, UK, DH6 5PF
| | - Stuart Penny
- High Force Research Ltd, Bowburn North Industrial Estate, Durham, UK, DH6 5PF
| | - Sterghios Moschos
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK, NE1 8ST
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28
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Bakowski K, Vogel S. Evolution of complexity in non-viral oligonucleotide delivery systems: from gymnotic delivery through bioconjugates to biomimetic nanoparticles. RNA Biol 2022; 19:1256-1275. [PMID: 36411594 PMCID: PMC9683052 DOI: 10.1080/15476286.2022.2147278] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
From the early days of research on RNA biology and biochemistry, there was an interest to utilize this knowledge and RNA itself for therapeutic applications. Today, we have a series of oligonucleotide therapeutics on the market and many more in clinical trials. These drugs - exploit different chemistries of oligonucleotides, such as modified DNAs and RNAs, peptide nucleic acids (PNAs) or phosphorodiamidate morpholino oligomers (PMOs), and different mechanisms of action, such as RNA interference (RNAi), targeted RNA degradation, splicing modulation, gene expression and modification. Despite major successes e.g. mRNA vaccines developed against SARS-CoV-2 to control COVID-19 pandemic, development of therapies for other diseases is still limited by inefficient delivery of oligonucleotides to specific tissues and organs and often prohibitive costs for the final drug. This is even more critical when targeting multifactorial disorders and patient-specific biological variations. In this review, we will present the evolution of complexity of oligonucleotide delivery methods with focus on increasing complexity of formulations from gymnotic delivery to bioconjugates and to lipid nanoparticles in respect to developments that will enable application of therapeutic oligonucleotides as drugs in personalized therapies.
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Affiliation(s)
- Kamil Bakowski
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark,CONTACT Stefan Vogel Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230Odense, Denmark
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29
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Hill A, van Leeuwen D, Schlösser V, Behera A, Mateescu B, Hall J. Chemically synthesized, self-assembling small interfering RNA-prohead RNA molecules trigger Dicer-independent gene silencing. Chemistry 2021; 28:e202103995. [PMID: 34879171 PMCID: PMC9305526 DOI: 10.1002/chem.202103995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Indexed: 11/07/2022]
Abstract
RNA interference (RNAi) mediated by small interfering RNA (siRNA) duplexes is a powerful therapeutic modality, but the translation of siRNAs from the bench into clinical application has been hampered by inefficient delivery in vivo. An innovative delivery strategy involves fusing siRNAs to a three‐way junction (3WJ) motif derived from the phi29 bacteriophage prohead RNA (pRNA). Chimeric siRNA‐3WJ molecules are presumed to enter the RNAi pathway through Dicer cleavage. Here, we fused siRNAs to the phi29 3WJ and two phylogenetically related 3WJs. We confirmed that the siRNA‐3WJs are substrates for Dicer in vitro. However, our results reveal that siRNA‐3WJs transfected into Dicer‐deficient cell lines trigger potent gene silencing. Interestingly, siRNA‐3WJs transfected into an Argonaute 2‐deficient cell line also retain some gene silencing activity. siRNA‐3WJs are most efficient when the antisense strand of the siRNA duplex is positioned 5′ of the 3WJ (5′‐siRNA‐3WJ) relative to 3′ of the 3WJ (3′‐siRNA‐3WJ). This work sheds light on the functional properties of siRNA‐3WJs and offers a design rule for maximizing their potency in the human RNAi pathway.
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Affiliation(s)
- Alyssa Hill
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, SWITZERLAND
| | - Daniël van Leeuwen
- ETH Zürich D-BIOL: Eidgenossische Technische Hochschule Zurich Departement Biologie, Department of Biology, SWITZERLAND
| | - Verena Schlösser
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
| | - Alok Behera
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
| | - Bogdan Mateescu
- ETH Zürich D-BIOL: Eidgenossische Technische Hochschule Zurich Departement Biologie, Department of Biology, SWITZERLAND
| | - Jonathan Hall
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
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30
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Wada F, Yamamoto T, Kobayashi T, Tachibana K, Ito KR, Hamasaki M, Kayaba Y, Terada C, Yamayoshi A, Obika S, Harada-Shiba M. Drug discovery and development scheme for liver-targeting bridged nucleic acid antisense oligonucleotides. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:957-969. [PMID: 34760338 PMCID: PMC8560717 DOI: 10.1016/j.omtn.2021.10.008] [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: 03/05/2021] [Revised: 08/15/2021] [Accepted: 10/06/2021] [Indexed: 11/21/2022]
Abstract
Antisense oligonucleotides (ASOs) containing bridged nucleic acids (BNAs) have been proven to be very powerful. However, ensuring a reliable discovery and translational development scheme for this class of ASOs with wider therapeutic windows remains a fundamental challenge. We here demonstrate the robustness of our scheme in the context of the selection of ASOs having two different BNA chemistries (2,′4′-BNA/locked nucleic acid [LNA] and amido-bridged nucleic acid [AmNA]) targeting human proprotein convertase subtilisin/kexin type 9 (PCSK9). The scheme features a two-step process, including (1) a unique and sensitive in vitro screening approach, called Ca2+ enrichment of medium (CEM) transfection, and (2) a ligand-targeted drug delivery approach to better reach target tissues, averting unintended accumulation of ASOs. Using CEM screening, we identified a candidate ASO that shows >70% cholesterol-lowering action in monkeys. An N-acetylgalactosamine (GalNAc) ligand then was appended to the candidate ASO to further broaden the therapeutic margin by altering the molecule’s pharmacokinetics. The GalNAc conjugate, HsPCSK9-1811-LNA, was found to be at least ten times more potent in non-human primates (compared with the unconjugated counterpart), with reduced nephrotoxicity in rats. Overall, we successfully showed that our drug development scheme is better suited for selecting clinically relevant BNA-based ASOs, especially for the treatment of liver-associated diseases.
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Affiliation(s)
- Fumito Wada
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Tadayuki Kobayashi
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keisuke Tachibana
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kosuke Ramon Ito
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mayumi Hamasaki
- Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Yukina Kayaba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Chisato Terada
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
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31
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Yamada K, Hildebrand S, Davis SM, Miller R, Conroy F, Sapp E, Caiazzi J, Alterman JF, Roux L, Echeverria D, Hassler MR, Pfister EL, DiFiglia M, Aronin N, Khvorova A. Structurally constrained phosphonate internucleotide linkage impacts oligonucleotide-enzyme interaction, and modulates siRNA activity and allele specificity. Nucleic Acids Res 2021; 49:12069-12088. [PMID: 34850120 PMCID: PMC8643693 DOI: 10.1093/nar/gkab1126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/09/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Oligonucleotides is an emerging class of chemically-distinct therapeutic modalities, where extensive chemical modifications are fundamental for their clinical applications. Inter-nucleotide backbones are critical to the behaviour of therapeutic oligonucleotides, but clinically explored backbone analogues are, effectively, limited to phosphorothioates. Here, we describe the synthesis and bio-functional characterization of an internucleotide (E)-vinylphosphonate (iE-VP) backbone, where bridging oxygen is substituted with carbon in a locked stereo-conformation. After optimizing synthetic pathways for iE-VP-linked dimer phosphoramidites in different sugar contexts, we systematically evaluated the impact of the iE-VP backbone on oligonucleotide interactions with a variety of cellular proteins. Furthermore, we systematically evaluated the impact of iE-VP on RNA-Induced Silencing Complex (RISC) activity, where backbone stereo-constraining has profound position-specific effects. Using Huntingtin (HTT) gene causative of Huntington's disease as an example, iE-VP at position 6 significantly enhanced the single mismatch discrimination ability of the RISC without negative impact on silencing of targeting wild type htt gene. These findings suggest that the iE-VP backbone can be used to modulate the activity and specificity of RISC. Our study provides (i) a new chemical tool to alter oligonucleotide-enzyme interactions and metabolic stability, (ii) insight into RISC dynamics and (iii) a new strategy for highly selective SNP-discriminating siRNAs.
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Affiliation(s)
- Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Sarah M Davis
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Faith Conroy
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA, USA
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Edith L Pfister
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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32
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Jahns H, Degaonkar R, Podbevsek P, Gupta S, Bisbe A, Aluri K, Szeto J, Kumar P, LeBlanc S, Racie T, Brown CR, Castoreno A, Guenther DC, Jadhav V, Maier MA, Plavec J, Egli M, Manoharan M, Zlatev I. Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing. Nucleic Acids Res 2021; 49:10250-10264. [PMID: 34508350 PMCID: PMC8501968 DOI: 10.1093/nar/gkab724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022] Open
Abstract
In order to achieve efficient therapeutic post-transcriptional gene-silencing mediated by the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) must be chemically modified. Several supra-RNA structures, with the potential to stabilize siRNAs metabolically have been evaluated for their ability to induce gene silencing, but all have limitations or have not been explored in therapeutically relevant contexts. Covalently closed circular RNA transcripts are prevalent in eukaryotes and have potential as biomarkers and disease targets, and circular RNA mimics are being explored for use as therapies. Here we report the synthesis and evaluation of small circular interfering RNAs (sciRNAs). To synthesize sciRNAs, a sense strand functionalized with the trivalent N-acetylgalactosamine (GalNAc) ligand and cyclized using ‘click’ chemistry was annealed to an antisense strand. This strategy was used for synthesis of small circles, but could also be used for synthesis of larger circular RNA mimics. We evaluated various sciRNA designs in vitro and in vivo. We observed improved metabolic stability of the sense strand upon circularization and off-target effects were eliminated. The 5′-(E)-vinylphosphonate modification of the antisense strand resulted in GalNAc-sciRNAs that are potent in vivo at therapeutically relevant doses. Physicochemical studies and NMR-based structural analysis, together with molecular modeling studies, shed light on the interactions of this novel class of siRNAs, which have a partial duplex character, with the RNAi machinery.
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Affiliation(s)
- Hartmut Jahns
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Peter Podbevsek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, EU
| | - Swati Gupta
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Anna Bisbe
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Krishna Aluri
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - John Szeto
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Pawan Kumar
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Sarah LeBlanc
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Tim Racie
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, EU
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Ivan Zlatev
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
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33
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Thangamani L, Balasubramanian B, Easwaran M, Natarajan J, Pushparaj K, Meyyazhagan A, Piramanayagam S. GalNAc-siRNA conjugates: Prospective tools on the frontier of anti-viral therapeutics. Pharmacol Res 2021; 173:105864. [PMID: 34474100 PMCID: PMC8405237 DOI: 10.1016/j.phrs.2021.105864] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 12/19/2022]
Abstract
The growing use of short-interfering RNA (siRNA)-based therapeutics for viral diseases reflects the most recent innovations in anti-viral vaccines and drugs. These drugs play crucial roles in the fight against many hitherto incurable diseases, the causes, pathophysiologies, and molecular processes of which remain unknown. Targeted liver drug delivery systems are in clinical trials. The receptor-mediated endocytosis approach involving the abundant asialoglycoprotein receptors (ASGPRs) on the surfaces of liver cells show great promise. We here review N-acetylgalactosamine (GalNAc)-siRNA conjugates that treat viral diseases such as hepatitis B infection, but we also mention that novel, native conjugate-based, targeted siRNA anti-viral drugs may also cure several life-threatening diseases such as hemorrhagic cystitis, multifocal leukoencephalopathy, and severe acute respiratory syndrome caused by coronaviruses and human herpes virus.
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Affiliation(s)
- Lokesh Thangamani
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | | | - Murugesh Easwaran
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Karthika Pushparaj
- Department of Zoology, School of Biosciences, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore 641043, Tamil Nadu, India
| | - Arun Meyyazhagan
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru 560029, Karnataka, India.
| | - Shanmughavel Piramanayagam
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore 641046, Tamil Nadu, India.
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34
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Terada C, Wada F, Uchida M, Yasutomi Y, Oh K, Kawamoto S, Kayaba Y, Yamayoshi A, Harada-Shiba M, Obika S, Yamamoto T. Programmed Instability of Ligand Conjugation Manifold for Efficient Hepatocyte Delivery of Therapeutic Oligonucleotides. Nucleic Acid Ther 2021; 31:404-416. [PMID: 34468210 DOI: 10.1089/nat.2021.0036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ligand-targeted drug delivery (LTDD) has gained more attention in the field of nucleic acid therapeutics. To further elicit the potential of therapeutic oligonucleotides by means of LTDD, we newly developed (R)- and (S)-3-amino-1,2-propanediol (APD) manifold for ligand conjugation. N-acetylgalactosamine (GalNAc)/asialoglycoprotein receptor (ASGPr) system has been shown to be a powerful and robust paradigm of LTDD. Our novel APD-based GalNAc (GalNAcAPD) was shown to have intrinsic chemical instability that could play a role in better manipulation of active drug release. The APD manifold also enables facile production of conjugates through an on-support ligand cluster synthesis. We showed in a series of in vivo studies that while the knockdown activity of antisense oligonucleotides (ASOs) bearing 5'-GalNAcAPD was comparable to the conventional hydroxy-L-prolinol-linked GalNAc (GalNAcHP), 3'-GalNAcAPD elicited ASO activity by more than twice as much as the conventional 3'-GalNAcHP. This was ascribed partly to the GalNAcAPD's ideal susceptibility to nucleolytic digestion, which is expected to facilitate cytosolic internalization of ASO drugs. Moreover, an in vivo/ex vivo imaging study visualized the enhancement effect of monoantennary GalNAcAPD on liver localization of ASOs. This versatile manifold with chemical and biological instability would benefit therapeutic oligonucleotides that target both the liver and extrahepatic tissues.
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Affiliation(s)
- Chisato Terada
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Fumito Wada
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Mei Uchida
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yukari Yasutomi
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kaho Oh
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Seiya Kawamoto
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yukina Kayaba
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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35
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Schmidt S, Gallego SF, Zelnik ID, Kovalchuk S, Albæk N, Sprenger RR, Øverup C, Pewzner-Jung Y, Futerman AH, Lindholm MW, Jensen ON, Ejsing CS. Silencing of ceramide synthase 2 in hepatocytes modulates plasma ceramide biomarkers predictive of cardiovascular death. Mol Ther 2021; 30:1661-1674. [PMID: 34400330 PMCID: PMC9077316 DOI: 10.1016/j.ymthe.2021.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/26/2021] [Accepted: 08/08/2021] [Indexed: 12/15/2022] Open
Abstract
Emerging clinical data show that three ceramide molecules, Cer d18:1/16:0, Cer d18:1/24:1, and Cer d18:1/24:0, are biomarkers of a fatal outcome in patients with cardiovascular disease. This finding raises basic questions about their metabolic origin, their contribution to disease pathogenesis, and the utility of targeting the underlying enzymatic machinery for treatment of cardiometabolic disorders. Here, we outline the development of a potent N-acetylgalactosamine-conjugated antisense oligonucleotide engineered to silence ceramide synthase 2 specifically in hepatocytes in vivo. We demonstrate that this compound reduces the ceramide synthase 2 mRNA level and that this translates into efficient lowering of protein expression and activity as well as Cer d18:1/24:1 and Cer d18:1/24:0 levels in liver. Intriguingly, we discover that the hepatocyte-specific antisense oligonucleotide also triggers a parallel modulation of blood plasma ceramides, revealing that the biomarkers predictive of cardiovascular death are governed by ceramide biosynthesis in hepatocytes. Our work showcases a generic therapeutic framework for targeting components of the ceramide enzymatic machinery to disentangle their roles in disease causality and to explore their utility for treatment of cardiometabolic disorders.
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Affiliation(s)
- Steffen Schmidt
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Sandra F Gallego
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Iris Daphne Zelnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Kovalchuk
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Nanna Albæk
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Richard R Sprenger
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Charlotte Øverup
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Yael Pewzner-Jung
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Marie W Lindholm
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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36
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Oyama S, Yamamoto T, Yamayoshi A. Recent Advances in the Delivery Carriers and Chemical Conjugation Strategies for Nucleic Acid Drugs. Cancers (Basel) 2021; 13:3881. [PMID: 34359781 PMCID: PMC8345803 DOI: 10.3390/cancers13153881] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/30/2021] [Indexed: 01/01/2023] Open
Abstract
With the development of new anticancer medicines, novel modalities are being explored for cancer treatment. For many years, conventional modalities, such as small chemical drugs and antibody drugs, have worked by "inhibiting the function" of target proteins. In recent years, however, nucleic acid drugs, such as ASOs and siRNAs, have attracted attention as a new modality for cancer treatment because nucleic acid drugs can directly promote the "loss of function" of target genes. Recently, nucleic acid drugs for use in cancer therapy have been extensively developed and some of them have currently been under investigation in clinical trials. To develop novel nucleic acid drugs for cancer treatment, it is imperative that cancer researchers, including ourselves, cover and understand those latest findings. In this review, we introduce and provide an overview of various DDSs and ligand modification technologies that are being employed to improve the success and development of nucleic acid drugs, then we also discuss the future of nucleic acid drug developments for cancer therapy. It is our belief this review will increase the awareness of nucleic acid drugs worldwide and build momentum for the future development of new cancer-targeted versions of these drugs.
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Affiliation(s)
- Shota Oyama
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Nagasaki 852-8521, Japan; (S.O.); (T.Y.)
| | - Tsuyoshi Yamamoto
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Nagasaki 852-8521, Japan; (S.O.); (T.Y.)
| | - Asako Yamayoshi
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Nagasaki 852-8521, Japan; (S.O.); (T.Y.)
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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37
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Murray JK, Long J, Liu L, Singh S, Pruitt D, Ollmann M, Swearingen E, Hardy M, Homann O, Wu B, Holder JR, Sham K, Herberich B, Lo MC, Dou H, Shkumatov A, Florio M, Rulifson IC. Identification and Optimization of a Minor Allele-Specific Small Interfering RNA to Prevent PNPLA3 I148M-Driven Nonalcoholic Fatty Liver Disease. Nucleic Acid Ther 2021; 31:324-340. [PMID: 34297902 DOI: 10.1089/nat.2021.0026] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human genome wide association studies confirm the association of the rs738409 single nucleotide polymorphism (SNP) in the gene encoding protein patatin like phospholipase domain containing 3 (PNPLA3) with nonalcoholic fatty liver disease (NAFLD); the presence of the resulting mutant PNPLA3 I148M protein is a driver of nonalcoholic steatohepatitis (NASH). While Pnpla3-deficient mice do not display an adverse phenotype, the safety of knocking down endogenous wild type PNPLA3 in humans remains unknown. To expand the scope of a potential targeted NAFLD therapeutic to both homozygous and heterozygous PNPLA3 rs738409 populations, we sought to identify a minor allele-specific small interfering RNA (siRNA). Limiting our search to SNP-spanning triggers, a series of chemically modified siRNA were tested in vitro for activity and selectivity toward PNPLA3 rs738409 mRNA. Conjugation of the siRNA to a triantennary N-acetylgalactosamine (GalNAc) ligand enabled in vivo screening using adeno-associated virus to overexpress human PNPLA3I148M versus human PNPLA3I148I in mouse livers. Structure-activity relationship optimization yielded potent and minor allele-specific compounds that achieved high levels of mRNA and protein knockdown of human PNPLA3I148M but not PNPLA3I148I. Testing of the minor allele-specific siRNA in PNPLA3I148M-expressing mice fed a NASH-inducing diet prevented PNPLA3I148M-driven disease phenotypes, thus demonstrating the potential of a precision medicine approach to treating NAFLD.
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Affiliation(s)
- Justin K Murray
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Jason Long
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Lei Liu
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
| | - Shivani Singh
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
| | - Danielle Pruitt
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
| | - Michael Ollmann
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Elissa Swearingen
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Miki Hardy
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Oliver Homann
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Bin Wu
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Jerry Ryan Holder
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Kelvin Sham
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Brad Herberich
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Mei-Chu Lo
- Therapeutic Discovery, Amgen Research, South San Francisco, California, USA
| | - Hui Dou
- Therapeutic Discovery, Amgen Research, South San Francisco, California, USA
| | - Artem Shkumatov
- Translational Safety and Bioanalytical Sciences, Amgen Research, South San Francisco, California, USA
| | - Monica Florio
- Cardiometabolic Disorders, Amgen Research, Thousand Oaks, California, USA
| | - Ingrid C Rulifson
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
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38
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Jahns H, Taneja N, Willoughby JLS, Akabane-Nakata M, Brown CR, Nguyen T, Bisbe A, Matsuda S, Hettinger M, Manoharan RM, Rajeev KG, Maier MA, Zlatev I, Charisse K, Egli M, Manoharan M. Chirality matters: stereo-defined phosphorothioate linkages at the termini of small interfering RNAs improve pharmacology in vivo. Nucleic Acids Res 2021; 50:1221-1240. [PMID: 34268578 PMCID: PMC8860597 DOI: 10.1093/nar/gkab544] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/29/2021] [Accepted: 06/30/2021] [Indexed: 12/04/2022] Open
Abstract
A critical challenge for the successful development of RNA interference-based therapeutics therapeutics has been the enhancement of their in vivo metabolic stability. In therapeutically relevant, fully chemically modified small interfering RNAs (siRNAs), modification of the two terminal phosphodiester linkages in each strand of the siRNA duplex with phosphorothioate (PS) is generally sufficient to protect against exonuclease degradation in vivo. Since PS linkages are chiral, we systematically studied the properties of siRNAs containing single chiral PS linkages at each strand terminus. We report an efficient and simple method to introduce chiral PS linkages and demonstrate that Rp diastereomers at the 5′ end and Sp diastereomers at the 3′ end of the antisense siRNA strand improved pharmacokinetic and pharmacodynamic properties in a mouse model. In silico modeling studies provide mechanistic insights into how the Rp isomer at the 5′ end and Sp isomer at the 3′ end of the antisense siRNA enhance Argonaute 2 (Ago2) loading and metabolic stability of siRNAs in a concerted manner.
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Affiliation(s)
- Hartmut Jahns
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Nate Taneja
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | | | | | | | - Tuyen Nguyen
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Anna Bisbe
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Matt Hettinger
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | | | - Martin A Maier
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 W. Kendall St, Cambridge, MA 02142, USA
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39
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Yamamoto T, Mukai Y, Wada F, Terada C, Kayaba Y, Oh K, Yamayoshi A, Obika S, Harada–Shiba M. Highly Potent GalNAc-Conjugated Tiny LNA Anti-miRNA-122 Antisense Oligonucleotides. Pharmaceutics 2021; 13:817. [PMID: 34072682 PMCID: PMC8228246 DOI: 10.3390/pharmaceutics13060817] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
The development of clinically relevant anti-microRNA antisense oligonucleotides (anti-miRNA ASOs) remains a major challenge. One promising configuration of anti-miRNA ASOs called "tiny LNA (tiny Locked Nucleic Acid)" is an unusually small (~8-mer), highly chemically modified anti-miRNA ASO with high activity and specificity. Within this platform, we achieved a great enhancement of the in vivo activity of miRNA-122-targeting tiny LNA by developing a series of N-acetylgalactosamine (GalNAc)-conjugated tiny LNAs. Specifically, the median effective dose (ED50) of the most potent construct, tL-5G3, was estimated to be ~12 nmol/kg, which is ~300-500 times more potent than the original unconjugated tiny LNA. Through in vivo/ex vivo imaging studies, we have confirmed that the major advantage of GalNAc over tiny LNAs can be ascribed to the improvement of their originally poor pharmacokinetics. We also showed that the GalNAc ligand should be introduced into its 5' terminus rather than its 3' end via a biolabile phosphodiester bond. This result suggests that tiny LNA can unexpectedly be recognized by endogenous nucleases and is required to be digested to liberate the parent tiny LNA at an appropriate time in the body. We believe that our strategy will pave the way for the clinical application of miRNA-targeting small ASO therapy.
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Affiliation(s)
- Tsuyoshi Yamamoto
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; (C.T.); (Y.K.); (K.O.); (A.Y.)
| | - Yahiro Mukai
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; (Y.M.); (F.W.); (S.O.)
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan;
| | - Fumito Wada
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; (Y.M.); (F.W.); (S.O.)
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan;
| | - Chisato Terada
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; (C.T.); (Y.K.); (K.O.); (A.Y.)
| | - Yukina Kayaba
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; (C.T.); (Y.K.); (K.O.); (A.Y.)
| | - Kaho Oh
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; (C.T.); (Y.K.); (K.O.); (A.Y.)
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; (C.T.); (Y.K.); (K.O.); (A.Y.)
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; (Y.M.); (F.W.); (S.O.)
| | - Mariko Harada–Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan;
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40
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Forbes TA, Brown BD, Lai C. Therapeutic RNA interference: A novel approach to the treatment of primary hyperoxaluria. Br J Clin Pharmacol 2021; 88:2525-2538. [PMID: 34022071 PMCID: PMC9291495 DOI: 10.1111/bcp.14925] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/19/2021] [Accepted: 05/08/2021] [Indexed: 12/13/2022] Open
Abstract
RNA interference (RNAi) is a natural biological pathway that inhibits gene expression by targeted degradation or translational inhibition of cytoplasmic mRNA by the RNA induced silencing complex. RNAi has long been exploited in laboratory research to study the biological consequences of the reduced expression of a gene of interest. More recently RNAi has been demonstrated as a therapeutic avenue for rare metabolic diseases. This review presents an overview of the cellular RNAi machinery as well as therapeutic RNAi design and delivery. As a clinical example we present primary hyperoxaluria, an ultrarare inherited disease of increased hepatic oxalate production which leads to recurrent calcium oxalate kidney stones. In the most common form of the disease (Type 1), end‐stage kidney disease occurs in childhood or young adulthood, often necessitating combined kidney and liver transplantation. In this context we discuss nedosiran (Dicerna Pharmaceuticals, Inc.) and lumasiran (Alnylam Pharmaceuticals), which are both novel RNAi therapies for primary hyperoxaluria that selectively reduce hepatic expression of lactate dehydrogenase and glycolate oxidase respectively, reducing hepatic oxalate production and urinary oxalate levels. Finally, we consider future optimizations advances in RNAi therapies.
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Affiliation(s)
- Thomas A Forbes
- Royal Children's Hospital, Parkville, Victoria, Australia.,Murdoch Children's Research Institute, Parkville, Victoria, Australia.,University of Melbourne, Parkville, Victoria, Australia
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41
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Hofmeister A, Jahn-Hofmann K, Brunner B, Helms MW, Metz-Weidmann C, Krack A, Kurz M, Li Z, Weitzenberg MM, Pflimlin E, Plettenburg O, Scheidler S. Syntheses of Morpholine-Based Nucleotide Analogs for Hepatic siRNA Targeting and Stabilization. J Med Chem 2021; 64:6838-6855. [PMID: 33950677 DOI: 10.1021/acs.jmedchem.1c00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A morpholine-based nucleotide analog was developed as a building block for hepatic siRNA targeting and stabilization. Attachment of an asialoglycoprotein-binding GalNAc ligand at the morpholine nitrogen was realized with different linkers. The obtained morpholino GalNAc scaffolds were coupled to the sense strand of a transthyretin-targeting siRNA and tested for their knockdown potency in vitro and in vivo. A clear structure-activity relationship was developed with regard to the linker type and length as well as the attachment site of the morpholino GalNAc moieties at the siRNA sense strand. Further, simple alkylation of the morpholine nitrogen led to a nucleotide analog, which increased siRNA stability, when used as a double 3'-overhang at the sense strand sequence. Combination of the best morpholino GalNAc building blocks as targeting nucleotides with an optimized stabilizing alkyl-substituted morpholine as 3'-overhangs resulted in siRNAs without any phosphorothioate stabilization in the sense strand and clearly improved the duration of action in vivo.
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Affiliation(s)
- Armin Hofmeister
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | | | - Bodo Brunner
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | - Mike W Helms
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | | | - Arne Krack
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | - Michael Kurz
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | - Ziyu Li
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | - Merle M Weitzenberg
- Institute of Organic Chemistry, Center of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Hannover 30167, Germany.,Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Institute of Medicinal Chemistry (IMC), Neuherberg 85764, Germany
| | | | - Oliver Plettenburg
- Institute of Organic Chemistry, Center of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Hannover 30167, Germany.,Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Institute of Medicinal Chemistry (IMC), Neuherberg 85764, Germany
| | - Sabine Scheidler
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
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42
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Biscans A, Caiazzi J, McHugh N, Hariharan V, Muhuri M, Khvorova A. Docosanoic acid conjugation to siRNA enables functional and safe delivery to skeletal and cardiac muscles. Mol Ther 2021; 29:1382-1394. [PMID: 33348054 PMCID: PMC8058398 DOI: 10.1016/j.ymthe.2020.12.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/24/2020] [Accepted: 12/15/2020] [Indexed: 01/20/2023] Open
Abstract
Oligonucleotide therapeutics hold promise for the treatment of muscle- and heart-related diseases. However, oligonucleotide delivery across the continuous endothelium of muscle tissue is challenging. Here, we demonstrate that docosanoic acid (DCA) conjugation of small interfering RNAs (siRNAs) enables efficient (~5% of injected dose), sustainable (>1 month), and non-toxic (no cytokine induction at 100 mg/kg) gene silencing in both skeletal and cardiac muscles after systemic injection. When designed to target myostatin (muscle growth regulation gene), siRNAs induced ~55% silencing in various muscle tissues and 80% silencing in heart, translating into a ~50% increase in muscle volume within 1 week. Our study identifies compounds for RNAi-based modulation of gene expression in skeletal and cardiac muscles, paving the way for both functional genomics studies and therapeutic gene modulation in muscle and heart.
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Affiliation(s)
- Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Vignesh Hariharan
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Manish Muhuri
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01604, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01604, USA; VIDE Program, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA.
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43
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Alkhouri N, Reddy GK, Lawitz E. Oligonucleotide-Based Therapeutics: An Emerging Strategy for the Treatment of Chronic Liver Diseases. Hepatology 2021; 73:1581-1593. [PMID: 32978989 DOI: 10.1002/hep.31569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Naim Alkhouri
- Texas Liver Institute, University of Texas Health San Antonio, San Antonio, TX
| | - G Kesava Reddy
- Texas Liver Institute, University of Texas Health San Antonio, San Antonio, TX
| | - Eric Lawitz
- Texas Liver Institute, University of Texas Health San Antonio, San Antonio, TX
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44
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Alkhouri N, Gawrieh S. A perspective on RNA interference-based therapeutics for metabolic liver diseases. Expert Opin Investig Drugs 2021; 30:237-244. [PMID: 33470860 DOI: 10.1080/13543784.2021.1879792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Therapeutic oligonucleotides have emerged as a promising new class of drug that could silence undruggable targets; they can potentially treat metabolic liver diseases such as nonalcoholic fatty liver disease (NAFLD), hereditary hemochromatosis and alpha 1 antitrypsin deficiency.Areas covered: This article illuminates the mechanism of action of, and drug delivery approaches for therapeutic oligonucleotides such as antisense oligonucleotides (ASOs), short interfering RNAs (siRNAs), and MicroRNAs (miRs). We reveal why the liver is the ideal organ for therapeutic oligonucleotides, discuss its unique architecture, and shed light on those susceptible molecular targets that can be modulated. We also examine preclinical and clinical data on the utility of oligonucleotides in silencing the expression of genes responsible for metabolic liver diseases.Expert opinion: The liver has numerous susceptible molecular therapeutic targets; hence, metabolic liver diseases can be treated effectively by modulating these targets via novel therapeutic oligonucleotides. Undoubtedly, these exciting developments integrate well with precision medicine progress. Specific therapeutic oligonucleotides can be designed based on the exact underlying molecular mechanism of the disease. So, there is a justification for furthering the development of therapeutic oligonucleotides for metabolic liver diseases. Safety concerns such as immunogenicity and off-target effects will however require careful monitoring.
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Affiliation(s)
- Naim Alkhouri
- Department of Hepatology, Arizona Liver Health, Chandler, AZ, USA
| | - Samer Gawrieh
- Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, IN, USA
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Fumoto S, Yamamoto T, Okami K, Maemura Y, Terada C, Yamayoshi A, Nishida K. Understanding In Vivo Fate of Nucleic Acid and Gene Medicines for the Rational Design of Drugs. Pharmaceutics 2021; 13:159. [PMID: 33530309 PMCID: PMC7911509 DOI: 10.3390/pharmaceutics13020159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid and genetic medicines are increasingly being developed, owing to their potential to treat a variety of intractable diseases. A comprehensive understanding of the in vivo fate of these agents is vital for the rational design, discovery, and fast and straightforward development of the drugs. In case of intravascular administration of nucleic acids and genetic medicines, interaction with blood components, especially plasma proteins, is unavoidable. However, on the flip side, such interaction can be utilized wisely to manipulate the pharmacokinetics of the agents. In other words, plasma protein binding can help in suppressing the elimination of nucleic acids from the blood stream and deliver naked oligonucleotides and gene carriers into target cells. To control the distribution of these agents in the body, the ligand conjugation method is widely applied. It is also important to understand intracellular localization. In this context, endocytosis pathway, endosomal escape, and nuclear transport should be considered and discussed. Encapsulated nucleic acids and genes must be dissociated from the carriers to exert their activity. In this review, we summarize the in vivo fate of nucleic acid and gene medicines and provide guidelines for the rational design of drugs.
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Affiliation(s)
- Shintaro Fumoto
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan; (T.Y.); (K.O.); (Y.M.); (C.T.); (A.Y.); (K.N.)
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46
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Liver-targeted polymeric prodrugs of 8-aminoquinolines for malaria radical cure. J Control Release 2020; 331:213-227. [PMID: 33378692 DOI: 10.1016/j.jconrel.2020.12.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022]
Abstract
Primaquine and tafenoquine are the two 8-aminoquinoline (8-AQ) antimalarial drugs approved for malarial radical cure - the elimination of liver stage hypnozoites after infection with Plasmodium vivax. A single oral dose of tafenoquine leads to high efficacy against intra-hepatocyte hypnozoites after efficient first pass liver uptake and metabolism. Unfortunately, both drugs cause hemolytic anemia in G6PD-deficient humans. This toxicity prevents their mass administration without G6PD testing given the approximately 400 million G6PD deficient people across malarial endemic regions of the world. We hypothesized that liver-targeted delivery of 8-AQ prodrugs could maximize liver exposure and minimize erythrocyte exposure to increase their therapeutic window. Primaquine and tafenoquine were first synthesized as prodrug vinyl monomers with self-immolative hydrolytic linkers or cathepsin-cleavable valine-citrulline peptide linkers. RAFT polymerization was exploited to copolymerize these prodrug monomers with hepatocyte-targeting GalNAc monomers. Pharmacokinetic studies of released drugs after intravenous administration showed that the liver-to-plasma AUC ratios could be significantly improved, compared to parent drug administered orally. Single doses of the liver-targeted, enzyme-cleavable tafenoquine polymer were found to be as efficacious as an equivalent dose of the oral parent drug in the P. berghei causal prophylaxis model. They also elicited significantly milder hemotoxicity in the humanized NOD/SCID mouse model engrafted with red blood cells from G6PD deficient donors. The clinical application is envisioned as a single subcutaneous administration, and the lead tafenoquine polymer also showed excellent bioavailability and liver-to-blood ratios exceeding the IV administered polymer. The liver-targeted tafenoquine polymers warrant further development as a single-dose therapeutic via the subcutaneous route with the potential for broader patient administration without a requirement for G6PD diagnosis.
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Zhao Y, Goto M, Vaziri ND, Khazaeli M, Liu H, Farahanchi N, Khanifar E, Farzaneh T, Haslett PA, Moradi H, Soundarapandian MM. RNA Interference Targeting Liver Angiopoietin-Like Protein 3 Protects from Nephrotic Syndrome in a Rat Model Via Amelioration of Pathologic Hypertriglyceridemia. J Pharmacol Exp Ther 2020; 376:428-435. [PMID: 33443084 DOI: 10.1124/jpet.120.000257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/04/2020] [Indexed: 11/22/2022] Open
Abstract
Nephrotic syndrome (NS) is associated with metabolic perturbances including profound dyslipidemia characterized by hypercholesterolemia and hypertriglyceridemia. A major underlying mechanism of hypertriglyceridemia in NS is lipoprotein lipase (LPL) deficiency and dysfunction. There is emerging evidence that elevated angiopoietin-like protein 3 (ANGPTL3), an LPL inhibitor that is primarily expressed and secreted by hepatocytes, may be in part responsible for these findings. Furthermore, there is evidence pointing to the contribution of ANGPTL3 to the pathogenesis of proteinuria in NS. Therefore, we hypothesized that inhibition of hepatic ANGPTL3 by RNA interference will ameliorate dyslipidemia and other symptoms of NS and pave the way for a new therapeutic strategy. To this end, we used a subcutaneously delivered, GalNAc (N-Acetylgalactosamine)-conjugated small interfering RNA (siRNA) to selectively target and suppress liver Angptl3 in rats with puromycin-induced NS, which exhibits clinical features of NS including proteinuria, hypoalbuminemia, hyperlipidemia, and renal histologic abnormalities. The study demonstrated that siRNA-mediated knockdown of the liver Angptl3 relieved its inhibitory effect on LPL and significantly reduced hypertriglyceridemia in nephrotic rats. This was accompanied by diminished proteinuria and hypoalbuminemia, which are the hallmarks of NS, and significant attenuation of renal tissue inflammation and oxidative stress. Taken together, this study confirmed the hypothesis that suppression of Angptl3 is protective in NS and points to the possibility that the use of RNA interference to suppress hepatic Angptl3 can serve as a novel therapeutic strategy for NS. SIGNIFICANCE STATEMENT: The current standard of care for mitigating nephrotic dyslipidemia in nephrotic syndrome is statins therapy. However, the efficacy of statins and its safety in the context of impaired kidney function is not well established. Here, we present an alternate therapeutic approach by using siRNA targeting Angptl3 expressed in hepatocytes. As the liver is the major source of circulating Angptl3, siRNA treatment reduced the profound hypertriglyceridemia in a rat model of nephrotic syndrome and was also effective in improving kidney and cardiac function.
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Affiliation(s)
- Yitong Zhao
- Division of Nephrology and Hypertension, University of California, Irvine, California (Y.Z., M.G., N.D.V., M.K., H.L., N.F., H.M.); Long Beach Memorial Pathology Group, Long Beach, California (E.K.); Department of Pathology and Laboratory Medicine, University of California, Irvine, California (T.F.); Tibor Rubin VA Medical Center, Department of Medicine, Nephrology Section, Long Beach, California (H.M.); and Alnylam Pharmaceuticals Inc, Cambridge, Massachusetts (P.A.H., M.M.S.)
| | - Masaki Goto
- Division of Nephrology and Hypertension, University of California, Irvine, California (Y.Z., M.G., N.D.V., M.K., H.L., N.F., H.M.); Long Beach Memorial Pathology Group, Long Beach, California (E.K.); Department of Pathology and Laboratory Medicine, University of California, Irvine, California (T.F.); Tibor Rubin VA Medical Center, Department of Medicine, Nephrology Section, Long Beach, California (H.M.); and Alnylam Pharmaceuticals Inc, Cambridge, Massachusetts (P.A.H., M.M.S.)
| | - Nosratola D Vaziri
- Division of Nephrology and Hypertension, University of California, Irvine, California (Y.Z., M.G., N.D.V., M.K., H.L., N.F., H.M.); Long Beach Memorial Pathology Group, Long Beach, California (E.K.); Department of Pathology and Laboratory Medicine, University of California, Irvine, California (T.F.); Tibor Rubin VA Medical Center, Department of Medicine, Nephrology Section, Long Beach, California (H.M.); and Alnylam Pharmaceuticals Inc, Cambridge, Massachusetts (P.A.H., M.M.S.)
| | - Mahyar Khazaeli
- Division of Nephrology and Hypertension, University of California, Irvine, California (Y.Z., M.G., N.D.V., M.K., H.L., N.F., H.M.); Long Beach Memorial Pathology Group, Long Beach, California (E.K.); Department of Pathology and Laboratory Medicine, University of California, Irvine, California (T.F.); Tibor Rubin VA Medical Center, Department of Medicine, Nephrology Section, Long Beach, California (H.M.); and Alnylam Pharmaceuticals Inc, Cambridge, Massachusetts (P.A.H., M.M.S.)
| | - Han Liu
- Division of Nephrology and Hypertension, University of California, Irvine, California (Y.Z., M.G., N.D.V., M.K., H.L., N.F., H.M.); Long Beach Memorial Pathology Group, Long Beach, California (E.K.); Department of Pathology and Laboratory Medicine, University of California, Irvine, California (T.F.); Tibor Rubin VA Medical Center, Department of Medicine, Nephrology Section, Long Beach, California (H.M.); and Alnylam Pharmaceuticals Inc, Cambridge, Massachusetts (P.A.H., M.M.S.)
| | - Nazli Farahanchi
- Division of Nephrology and Hypertension, University of California, Irvine, California (Y.Z., M.G., N.D.V., M.K., H.L., N.F., H.M.); Long Beach Memorial Pathology Group, Long Beach, California (E.K.); Department of Pathology and Laboratory Medicine, University of California, Irvine, California (T.F.); Tibor Rubin VA Medical Center, Department of Medicine, Nephrology Section, Long Beach, California (H.M.); and Alnylam Pharmaceuticals Inc, Cambridge, Massachusetts (P.A.H., M.M.S.)
| | - Elham Khanifar
- Division of Nephrology and Hypertension, University of California, Irvine, California (Y.Z., M.G., N.D.V., M.K., H.L., N.F., H.M.); Long Beach Memorial Pathology Group, Long Beach, California (E.K.); Department of Pathology and Laboratory Medicine, University of California, Irvine, California (T.F.); Tibor Rubin VA Medical Center, Department of Medicine, Nephrology Section, Long Beach, California (H.M.); and Alnylam Pharmaceuticals Inc, Cambridge, Massachusetts (P.A.H., M.M.S.)
| | - Ted Farzaneh
- Division of Nephrology and Hypertension, University of California, Irvine, California (Y.Z., M.G., N.D.V., M.K., H.L., N.F., H.M.); Long Beach Memorial Pathology Group, Long Beach, California (E.K.); Department of Pathology and Laboratory Medicine, University of California, Irvine, California (T.F.); Tibor Rubin VA Medical Center, Department of Medicine, Nephrology Section, Long Beach, California (H.M.); and Alnylam Pharmaceuticals Inc, Cambridge, Massachusetts (P.A.H., M.M.S.)
| | - Patrick A Haslett
- Division of Nephrology and Hypertension, University of California, Irvine, California (Y.Z., M.G., N.D.V., M.K., H.L., N.F., H.M.); Long Beach Memorial Pathology Group, Long Beach, California (E.K.); Department of Pathology and Laboratory Medicine, University of California, Irvine, California (T.F.); Tibor Rubin VA Medical Center, Department of Medicine, Nephrology Section, Long Beach, California (H.M.); and Alnylam Pharmaceuticals Inc, Cambridge, Massachusetts (P.A.H., M.M.S.)
| | - Hamid Moradi
- Division of Nephrology and Hypertension, University of California, Irvine, California (Y.Z., M.G., N.D.V., M.K., H.L., N.F., H.M.); Long Beach Memorial Pathology Group, Long Beach, California (E.K.); Department of Pathology and Laboratory Medicine, University of California, Irvine, California (T.F.); Tibor Rubin VA Medical Center, Department of Medicine, Nephrology Section, Long Beach, California (H.M.); and Alnylam Pharmaceuticals Inc, Cambridge, Massachusetts (P.A.H., M.M.S.)
| | - Mangala M Soundarapandian
- Division of Nephrology and Hypertension, University of California, Irvine, California (Y.Z., M.G., N.D.V., M.K., H.L., N.F., H.M.); Long Beach Memorial Pathology Group, Long Beach, California (E.K.); Department of Pathology and Laboratory Medicine, University of California, Irvine, California (T.F.); Tibor Rubin VA Medical Center, Department of Medicine, Nephrology Section, Long Beach, California (H.M.); and Alnylam Pharmaceuticals Inc, Cambridge, Massachusetts (P.A.H., M.M.S.)
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Petrov RA, Mefedova SR, Yamansarov EY, Maklakova SY, Grishin DA, Lopatukhina EV, Burenina OY, Lopukhov AV, Kovalev SV, Timchenko YV, Ondar EE, Ivanenkov YA, Evteev SA, Vaneev AN, Timoshenko RV, Klyachko NL, Erofeev AS, Gorelkin PV, Beloglazkina EK, Majouga AG. New Small-Molecule Glycoconjugates of Docetaxel and GalNAc for Targeted Delivery to Hepatocellular Carcinoma. Mol Pharm 2020; 18:461-468. [PMID: 33264010 DOI: 10.1021/acs.molpharmaceut.0c00980] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, we have developed covalent and low molecular weight docetaxel delivery systems based on conjugation with N-acetyl-d-galactosamine and studied their properties related to hepatocellular carcinoma cells. The resulting glycoconjugates have an excellent affinity to the asialoglycoprotein receptor (ASGPR) in the nanomolar range of concentrations and a high cytotoxicity level comparable to docetaxel. Likewise, we observed the 21-75-fold increase in water solubility in comparison with parent docetaxel and prodrug lability to intracellular conditions with half-life values from 25.5 to 42 h. We also found that the trivalent conjugate possessed selective toxicity against hepatoma cells vs control cell lines (20-35 times). The absence of such selectivity in the case of monovalent conjugates indicates the effect of ligand valency. Specific ASGPR-mediated cellular uptake of conjugates was proved in vitro using fluorescent-labeled analogues. In addition, we showed an enhanced generation of reactive oxygen species in the HepG2 cells, which could be inhibited by the natural ligand of ASGPR. Overall, the obtained results highlight the potential of ASGPR-directed cytostatic taxane drugs for selective therapy of hepatocellular carcinoma.
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Affiliation(s)
- Rostislav A Petrov
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation.,Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) of the Ufa Federal Research Centre, Oktyabrya Prospekt 71, Ufa 450054, Russian Federation
| | - Sofiia R Mefedova
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation
| | - Emil Yu Yamansarov
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation.,National University of Science and Technology MISIS, 9 Leninskiy pr., Moscow 119049, Russian Federation
| | - Svetlana Yu Maklakova
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation.,National University of Science and Technology MISIS, 9 Leninskiy pr., Moscow 119049, Russian Federation
| | - Dmitrii A Grishin
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation
| | - Elena V Lopatukhina
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation
| | - Olga Y Burenina
- Skolkovo Institute of Science and Technology, 3 Nobel str., Skolkovo 143026, Russian Federation
| | - Anton V Lopukhov
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation
| | - Sergey V Kovalev
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation
| | - Yury V Timchenko
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation
| | - Evgenia E Ondar
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation
| | - Yan A Ivanenkov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) of the Ufa Federal Research Centre, Oktyabrya Prospekt 71, Ufa 450054, Russian Federation.,Moscow Institute of Physics and Technology (State University), 9 Institutskiy Lane, Dolgoprudny City, Moscow 141700, Russian Federation
| | - Sergei A Evteev
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation
| | - Alexander N Vaneev
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation.,National University of Science and Technology MISIS, 9 Leninskiy pr., Moscow 119049, Russian Federation
| | - Roman V Timoshenko
- National University of Science and Technology MISIS, 9 Leninskiy pr., Moscow 119049, Russian Federation
| | - Natalia L Klyachko
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation.,Skolkovo Institute of Science and Technology, 3 Nobel str., Skolkovo 143026, Russian Federation
| | - Alexander S Erofeev
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation.,National University of Science and Technology MISIS, 9 Leninskiy pr., Moscow 119049, Russian Federation
| | - Petr V Gorelkin
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation.,National University of Science and Technology MISIS, 9 Leninskiy pr., Moscow 119049, Russian Federation
| | - Elena K Beloglazkina
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation
| | - Alexander G Majouga
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory, Building 1/3, GSP-1, Moscow 119991, Russian Federation.,National University of Science and Technology MISIS, 9 Leninskiy pr., Moscow 119049, Russian Federation.,Dmitry Mendeleev University of Chemical Technology of Russia, Miusskaya sq. 9, Moscow 125047, Russian Federation
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Salim L, Desaulniers JP. To Conjugate or to Package? A Look at Targeted siRNA Delivery Through Folate Receptors. Nucleic Acid Ther 2020; 31:21-38. [PMID: 33121373 DOI: 10.1089/nat.2020.0893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
RNA interference (RNAi) applications have evolved from experimental tools to study gene function to the development of a novel class of gene-silencing therapeutics. Despite decades of research, it was not until August 2018 that the US FDA approved the first-ever RNAi drug, marking a new era for RNAi therapeutics. Although there are many limitations associated with the inherent structure of RNA, delivery to target cells and tissues remains the most challenging. RNAs are unable to diffuse across cellular membranes due to their large size and polyanionic backbone and, therefore, require a delivery vector. RNAi molecules can be conjugated to a targeting ligand or packaged into a delivery vehicle. Alnylam has used both strategies in their FDA-approved formulations to achieve efficient delivery to the liver. To harness the full potential of RNAi therapeutics, however, we must be able to target additional cells and tissues. One promising target is the folate receptor α, which is overexpressed in a variety of tumors despite having limited expression and distribution in normal tissues. Folate can be conjugated directly to the RNAi molecule or used to functionalize delivery vehicles. In this review, we compare both delivery strategies and discuss the current state of research in the area of folate-mediated delivery of RNAi molecules.
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Affiliation(s)
- Lidya Salim
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Canada
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50
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Hagiwara K, Honma M, Harumoto T, Harada K, Sawada T, Yamamoto J, Shinohara F. Development of Prodrug Type Circular siRNA for In Vivo Knockdown by Systemic Administration. Nucleic Acid Ther 2020; 30:346-364. [PMID: 33016851 DOI: 10.1089/nat.2020.0894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
siRNAs are being developed as a novel therapeutic modality; however, problems impeding their application in extrahepatic tissues persist, including inadequate stability in biological environments and inefficient drug delivery system to target tissues. Thus, technological improvements that enable robust silencing of target messenger RNA (mRNA) in extrahepatic tissues are necessary. We developed prodrug type covalently closed siRNA (circular siRNA) as a novel nucleic acid agent to knockdown target genes in extrahepatic tissues by systemic administration without drug delivery components. Circular siRNA, which is chemically synthesizable, can assume optimal structures for efficient knockdown using its cleavable linker; namely, circular and linear structure in extracellular and intracellular environment, respectively. In this study, we investigated circular siRNA physicochemical properties, knockdown mechanism, and characteristics in vitro, as well as pharmacokinetics, accumulation, knockdown activity, and safety in vivo. Our circular siRNA exhibited higher stability against serum and exonucleases, increased cellular uptake, and stronger knockdown activity without transfection reagent in vitro than linear siRNA. Furthermore, after systemic administration to mice, circular siRNA showed prolonged circulation and improved knockdown activity in the liver, kidney, and muscle, without causing adverse effects. Circular siRNA may represent an additional platform for RNAi therapeutics, providing alternate solutions for disease treatment.
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Affiliation(s)
- Kenji Hagiwara
- Nucleic Acid Medicine Research Laboratories and Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Masakazu Honma
- Nucleic Acid Medicine Research Laboratories and Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Toshimasa Harumoto
- Nucleic Acid Medicine Research Laboratories and Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Kenji Harada
- Management Office, Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Takashi Sawada
- Nucleic Acid Medicine Research Laboratories and Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Junichiro Yamamoto
- Nucleic Acid Medicine Research Laboratories and Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Fumikazu Shinohara
- Management Office, Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
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