1
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Roussis SG. Formulas of High MW Unknown Compounds from Accurate Mass Differences and Ranking of Best Candidates from First Principles. Anal Chem 2024. [PMID: 38949572 DOI: 10.1021/acs.analchem.4c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The number of possible candidate formulas for high molecular weight unknown compounds (e.g., 7000-8000 Da for common 20-mer oligonucleotides) by high-resolution mass spectrometry is in the order of several hundred thousand even at the highest level of experimental accuracy. In demanding analytical applications involving new chemistries and synthetic routes where little is known about the chemical nature or mechanisms of formation of the unknown compounds (e.g., impurities), the generation of a short list of the most plausible formulas would be highly desirable. Such an approach has been developed in the current work. The concept of mass difference from a reference compound is introduced to simplify the approach and greatly reduce the number of possible formulas. The approach allows for the generation of candidate formulas by both the addition and subtraction of atoms to account for all possible molecular changes from the parent compound. A reduction of 3 orders of magnitude in the number of possible formulas has been achieved by the approach. Ranking of the formulas by the product of the sums of the absolute changes in the total number of all atoms and all heteroatoms in the proposed difference formula successfully ranked the correct formula within the top 10 from a list of 200-250 best candidate formulas. There is a tendency for the impurities to be formed involving the least change in the number of atoms and heteroatoms. ΔfHo and ΔfG'o values can be used as a complementary ranking system of the top candidates. The approach is applicable to unknowns in any other systems of high MW compounds.
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Affiliation(s)
- Stilianos G Roussis
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
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2
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Li Q, Dong M, Chen P. Advances in structural-guided modifications of siRNA. Bioorg Med Chem 2024; 110:117825. [PMID: 38954918 DOI: 10.1016/j.bmc.2024.117825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
To date, the US Food and Drug Administration (FDA) has approved six small interfering RNA (siRNA) drugs: patisiran, givosiran, lumasiran, inclisiran, vutrisiran, and nedosiran, serving as compelling evidence of the promising potential of RNA interference (RNAi) therapeutics. The successful implementation of siRNA therapeutics is improved through a combination of various chemical modifications and diverse delivery approaches. The utilization of chemically modified siRNA at specific sites on either the sense strand (SS) or antisense strand (AS) has the potential to enhance resistance to ribozyme degradation, improve stability and specificity, and prolong the efficacy of drugs. Herein, we provide comprehensive analyses concerning the correlation between chemical modifications and structure-guided siRNA design. Various modifications, such as 2'-modifications, 2',4'-dual modifications, non-canonical sugar modifications, and phosphonate mimics, are crucial for the activity of siRNA. We also emphasize the essential strategies for enhancing overhang stability, improving RISC loading efficacy and strand selection, reducing off-target effects, and discussing the future of targeted delivery.
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Affiliation(s)
- Qiang Li
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China; Research and Development Department, NanoPeptide (Qingdao) Biotechnology Ltd., Qingdao, China.
| | - Mingxin Dong
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China.
| | - Pu Chen
- Research and Development Department, NanoPeptide (Qingdao) Biotechnology Ltd., Qingdao, China; Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.
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3
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Lei L, Harp JM, Chaput JC, Wassarman K, Schlegel MK, Manoharan M, Egli M. Structure and Stability of Ago2 MID-Nucleotide Complexes: All-in-One (Drop) His 6-SUMO Tag Removal, Nucleotide Binding, and Crystal Growth. Curr Protoc 2024; 4:e1088. [PMID: 38923271 DOI: 10.1002/cpz1.1088] [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] [Indexed: 06/28/2024]
Abstract
The middle (MID) domain of eukaryotic Argonaute (Ago) proteins and archaeal and bacterial homologues mediates the interaction with the 5'-terminal nucleotide of miRNA and siRNA guide strands. The MID domain of human Ago2 (hAgo2) is comprised of 139 amino acids with a molecular weight of 15.56 kDa. MID adopts a Rossman-like beta1-alpha1-beta2-alpha2-beta3-alpha3-beta4-alpha4 fold with a nucleotide specificity loop between beta3 and alpha3. Multiple crystal structures of nucleotides bound to hAgo2 MID have been reported, whereby complexes were obtained by soaking ligands into crystals of MID domain alone. This protocol describes a simplified one-step approach to grow well-diffracting crystals of hAgo2 MID-nucleotide complexes by mixing purified His6-SUMO-MID fusion protein, Ulp1 protease, and excess nucleotide in the presence of buffer and precipitant. The crystal structures of MID complexes with UMP, UTP and 2'-3' linked α-L-threofuranosyl thymidine-3'-triphosphate (tTTP) are presented. This article also describes fluorescence-based assays to measure dissociation constants (Kd) of MID-nucleotide interactions for nucleoside 5'-monophosphates and nucleoside 3',5'-bisphosphates. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Crystallization of Ago2 MID-nucleotide complexes Basic Protocol 2: Measurement of dissociation constant Kd between Ago2 MID and nucleotides.
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Affiliation(s)
- Li Lei
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Joel M Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, California
| | | | | | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
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4
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Tang Q, Khvorova A. RNAi-based drug design: considerations and future directions. Nat Rev Drug Discov 2024; 23:341-364. [PMID: 38570694 PMCID: PMC11144061 DOI: 10.1038/s41573-024-00912-9] [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] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
More than 25 years after its discovery, the post-transcriptional gene regulation mechanism termed RNAi is now transforming pharmaceutical development, proved by the recent FDA approval of multiple small interfering RNA (siRNA) drugs that target the liver. Synthetic siRNAs that trigger RNAi have the potential to specifically silence virtually any therapeutic target with unprecedented potency and durability. Bringing this innovative class of medicines to patients, however, has been riddled with substantial challenges, with delivery issues at the forefront. Several classes of siRNA drug are under clinical evaluation, but their utility in treating extrahepatic diseases remains limited, demanding continued innovation. In this Review, we discuss principal considerations and future directions in the design of therapeutic siRNAs, with a particular emphasis on chemistry, the application of informatics, delivery strategies and the importance of careful target selection, which together influence therapeutic success.
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Affiliation(s)
- Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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5
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Xin J, Lu X, Cao J, Wu W, Liu Q, Wang D, Zhou X, Ding D. Fluorinated Organic Polymers for Cancer Drug Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2404645. [PMID: 38678386 DOI: 10.1002/adma.202404645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/22/2024] [Indexed: 04/30/2024]
Abstract
In the realm of cancer therapy, the spotlight is on nanoscale pharmaceutical delivery systems, especially polymer-based nanoparticles, for their enhanced drug dissolution, extended presence in the bloodstream, and precision targeting achieved via surface engineering. Leveraging the amplified permeation and retention phenomenon, these systems concentrate therapeutic agents within tumor tissues. Nonetheless, the hurdles of systemic toxicity, biological barriers, and compatibility with living systems persist. Fluorinated polymers, distinguished by their chemical idiosyncrasies, are poised for extensive biomedical applications, notably in stabilizing drug metabolism, augmenting lipophilicity, and optimizing bioavailability. Material science heralds the advent of fluorinated polymers that, by integrating fluorine atoms, unveil a suite of drug delivery merits: the hydrophobic traits of fluorinated alkyl chains ward off lipid or protein disruption, the carbon-fluorine bond's stability extends the drug's lifecycle in the system, and a lower alkalinity coupled with a diminished ionic charge bolsters the drug's ability to traverse cellular membranes. This comprehensive review delves into the utilization of fluorinated polymers for oncological pharmacotherapy, elucidating their molecular architecture, synthetic pathways, and functional attributes, alongside an exploration of their empirical strengths and the quandaries they encounter in both experimental and clinical settings.
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Affiliation(s)
- Jingrui Xin
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Xue Lu
- Frontiers Science Center for New Organic Matter, Nankai International Advanced Research Institute (Shenzhen, Futian), and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jimin Cao
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, and First Clinical Medical College, Shanxi Medical University, Taiyuan, 030001, China
| | - Weihui Wu
- Frontiers Science Center for New Organic Matter, Nankai International Advanced Research Institute (Shenzhen, Futian), and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Qian Liu
- Department of Urology, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Deping Wang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, and First Clinical Medical College, Shanxi Medical University, Taiyuan, 030001, China
| | - Xin Zhou
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, and First Clinical Medical College, Shanxi Medical University, Taiyuan, 030001, China
| | - Dan Ding
- Frontiers Science Center for New Organic Matter, Nankai International Advanced Research Institute (Shenzhen, Futian), and College of Life Sciences, Nankai University, Tianjin, 300071, China
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6
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Hofman CR, Corey DR. Targeting RNA with synthetic oligonucleotides: Clinical success invites new challenges. Cell Chem Biol 2024; 31:125-138. [PMID: 37804835 PMCID: PMC10841528 DOI: 10.1016/j.chembiol.2023.09.005] [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: 07/05/2023] [Revised: 08/27/2023] [Accepted: 09/15/2023] [Indexed: 10/09/2023]
Abstract
Synthetic antisense oligonucleotides (ASOs) and duplex RNAs (dsRNAs) are an increasingly successful strategy for drug development. After a slow start, the pace of success has accelerated since the approval of Spinraza (nusinersen) in 2016 with several drug approvals. These accomplishments have been achieved even though oligonucleotides are large, negatively charged, and have little resemblance to traditional small-molecule drugs-a remarkable achievement of basic and applied science. The goal of this review is to summarize the foundation underlying recent progress and describe ongoing research programs that may increase the scope and impact of oligonucleotide therapeutics.
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Affiliation(s)
- Cristina R Hofman
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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7
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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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8
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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9
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Khorkova O, Stahl J, Joji A, Volmar CH, Wahlestedt C. Amplifying gene expression with RNA-targeted therapeutics. Nat Rev Drug Discov 2023; 22:539-561. [PMID: 37253858 PMCID: PMC10227815 DOI: 10.1038/s41573-023-00704-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2023] [Indexed: 06/01/2023]
Abstract
Many diseases are caused by insufficient expression of mutated genes and would benefit from increased expression of the corresponding protein. However, in drug development, it has been historically easier to develop drugs with inhibitory or antagonistic effects. Protein replacement and gene therapy can achieve the goal of increased protein expression but have limitations. Recent discoveries of the extensive regulatory networks formed by non-coding RNAs offer alternative targets and strategies to amplify the production of a specific protein. In addition to RNA-targeting small molecules, new nucleic acid-based therapeutic modalities that allow highly specific modulation of RNA-based regulatory networks are being developed. Such approaches can directly target the stability of mRNAs or modulate non-coding RNA-mediated regulation of transcription and translation. This Review highlights emerging RNA-targeted therapeutics for gene activation, focusing on opportunities and challenges for translation to the clinic.
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Affiliation(s)
- Olga Khorkova
- OPKO Health, Miami, FL, USA
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
| | - Jack Stahl
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Aswathy Joji
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Chemistry, University of Miami, Miami, FL, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA.
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA.
- Department of Chemistry, University of Miami, Miami, FL, USA.
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10
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Hariharan VN, Caiazzi J, Miller R, Ferguson C, Sapp E, Fakih H, Tang Q, Yamada N, Furgal R, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho B, Hildebrand S, Echeverria D, Hassler M, Alterman J, DiFiglia M, Aronin N, Khvorova A, Yamada K. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. RESEARCH SQUARE 2023:rs.3.rs-2987323. [PMID: 37398145 PMCID: PMC10312934 DOI: 10.21203/rs.3.rs-2987323/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Metabolic stabilization of therapeutic oligonucleotides requires both sugar and backbone modifications, where phosphorothioate (PS) is the only backbone chemistry used in the clinic. Here, we describe the discovery, synthesis, and characterization of a novel biologically compatible backbone, extended nucleic acid (exNA). Upon exNA precursor scale up, exNA incorporation is fully compatible with common nucleic acid synthetic protocols. The novel backbone is orthogonal to PS and shows profound stabilization against 3'- and 5'-exonucleases. Using small interfering RNAs (siRNAs) as an example, we show exNA is tolerated at most nucleotide positions and profoundly improves in vivo efficacy. A combined exNA-PS backbone enhances siRNA resistance to serum 3'-exonuclease by ~ 32-fold over PS backbone and > 1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure (~ 6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions.
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Affiliation(s)
| | | | | | - Chantal Ferguson
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | - Qi Tang
- University of Massachusetts Chan Medical School
| | | | | | | | | | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | - Bruno Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | | | - Neil Aronin
- University of Massachusetts Worcester Campus
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11
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Yamada K, Hariharan VN, Caiazzi J, Miller R, Furguson C, Sapp E, Fakih H, Tan Q, Yamada N, Furgal RC, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho BM, Hildebrand S, Echeverria D, Hassler MR, Alterman JF, DiFiglia M, Aronin N, Khvorova A. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542506. [PMID: 37292886 PMCID: PMC10245983 DOI: 10.1101/2023.05.26.542506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Metabolic stabilization of therapeutic oligonucleotides requires both sugar and backbone modifications, where phosphorothioate (PS) is the only backbone chemistry used in the clinic. Here, we describe the discovery, synthesis, and characterization of a novel biologically compatible backbone, extended nucleic acid (exNA). Upon exNA precursor scale up, exNA incorporation is fully compatible with common nucleic acid synthetic protocols. The novel backbone is orthogonal to PS and shows profound stabilization against 3'- and 5'-exonucleases. Using small interfering RNAs (siRNAs) as an example, we show exNA is tolerated at most nucleotide positions and profoundly improves in vivo efficacy. A combined exNA-PS backbone enhances siRNA resistance to serum 3'-exonuclease by ~32-fold over PS backbone and >1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure (~6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions.
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Affiliation(s)
- Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Vignesh Narayan Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Chantal Furguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United State
| | - Hassan Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Qi Tan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Nozomi Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Raymond C. Furgal
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Joseph Paquette
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Clemens Lochmann
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Bruno M.D.C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Matthew R. Hassler
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United State
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Molecular Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
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12
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Datta D, Theile CS, Wassarman K, Qin J, Racie T, Schmidt K, Jiang Y, Sigel R, Janas MM, Egli M, Manoharan M. Rational optimization of siRNA to ensure strand bias in the interaction with the RNA-induced silencing complex. Chem Commun (Camb) 2023; 59:6347-6350. [PMID: 37144553 DOI: 10.1039/d3cc01143g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
To ensure specificity of small interfering RNAs (siRNAs), the antisense strand must be selected by the RNA-induced silencing complex (RISC). We have previously demonstrated that a 5'-morpholino-modified nucleotide at the 5'-end of the sense strand inhibits its interaction with RISC ensuring selection of the desired antisense strand. To improve this antagonizing binding property even further, a new set of morpholino-based analogues, Mo2 and Mo3, and a piperidine analogue, Pip, were designed based on the known structure of Argonaute2, the slicer enzyme component of RISC. Sense strands of siRNAs were modified with these new analogues, and the siRNAs were evaluated in vitro and in mice for RNAi activity. Our data demonstrated that Mo2 is the best RISC inhibitor among the modifications tested and that it effectively mitigates sense strand-based off-target activity of siRNA.
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Affiliation(s)
- Dhrubajyoti Datta
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Christopher S Theile
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Kelly Wassarman
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - June Qin
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Tim Racie
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Karyn Schmidt
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Rachel Sigel
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Maja M Janas
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
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13
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Engelbeen S, Pasteuning-Vuhman S, Boertje-van der Meulen J, Parmar R, Charisse K, Sepp-Lorenzino L, Manoharan M, Aartsma-Rus A, van Putten M. Efficient Downregulation of Alk4 in Skeletal Muscle After Systemic Treatment with Conjugated siRNAs in a Mouse Model for Duchenne Muscular Dystrophy. Nucleic Acid Ther 2023; 33:26-34. [PMID: 36269327 PMCID: PMC9940804 DOI: 10.1089/nat.2022.0021] [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] [Indexed: 02/07/2023] Open
Abstract
Downregulation of genes involved in the secondary pathology of Duchenne muscular dystrophy, for example, inflammation, fibrosis, and adiposis, is an interesting approach to ameliorate degeneration of muscle and replacement by fibrotic and adiposis tissue. Small interfering RNAs (siRNAs) are able to downregulate target genes, however, delivery of siRNAs to skeletal muscle still remains a challenge. We investigated delivery of fully chemically modified, cholesterol-conjugated siRNAs targeting Alk4, a nontherapeutic target that is expressed highly in muscle. We observed that a single intravenous or intraperitoneal (IP) injection of 10 mg/kg resulted in significant downregulation of Alk4 mRNA expression in skeletal muscles in both wild-type and mdx mice. Treatment with multiple IP injections of 10 mg/kg led to an overall reduction of Alk4 expression, reaching significance in tibialis anterior (39.7% ± 6.2%), diaphragm (32.7% ± 5.8%), and liver (41.3% ± 29.9%) in mdx mice. Doubling of the siRNA dose did not further increase mRNA silencing in muscles of mdx mice. The chemically modified conjugated siRNAs used in this study are very promising for delivery to both nondystrophic and dystrophic muscles and could have major implications for treatment of muscular dystrophy pathology.
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Affiliation(s)
- Sarah Engelbeen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Rubina Parmar
- Alnalym Pharmaceuticals, Cambridge, Massachusetts, USA
| | | | | | | | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Maaike van Putten
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,Address correspondence to: Maaike van Putten, PhD, Department of Human Genetics, Leiden University Medical Center, Leiden 2300 RC, the Netherlands
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14
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Das G, Harikrishna S, Gore KR. Influence of Sugar Modifications on the Nucleoside Conformation and Oligonucleotide Stability: A Critical Review. CHEM REC 2022; 22:e202200174. [PMID: 36048010 DOI: 10.1002/tcr.202200174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/16/2022] [Indexed: 12/15/2022]
Abstract
Ribofuranose sugar conformation plays an important role in the structure and dynamics of functional nucleic acids such as siRNAs, AONs, aptamers, miRNAs, etc. To improve their therapeutic potential, several chemical modifications have been introduced into the sugar moiety over the years. The stability of the oligonucleotide duplexes as well as the formation of stable and functional protein-oligonucleotide complexes are dictated by the conformation and dynamics of the sugar moiety. In this review, we systematically categorise various ribofuranose sugar modifications employed in DNAs and RNAs so far. We discuss different stereoelectronic effects imparted by different substituents on the sugar ring and how these effects control sugar puckering. Using this data, it would be possible to predict the precise use of chemical modifications and design novel sugar-modified nucleosides for therapeutic oligonucleotides that can improve their physicochemical properties.
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Affiliation(s)
- Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
| | - S Harikrishna
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
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15
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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: 18] [Impact Index Per Article: 9.0] [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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16
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Pereira PA, Serra MES, Serra AC, Coelho JFJ. Application of vinyl polymer-based materials as nucleic acids carriers in cancer therapy. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1820. [PMID: 35637638 DOI: 10.1002/wnan.1820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 04/13/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Nucleic acid-based therapies have changed the paradigm of cancer treatment, where conventional treatment modalities still have several limitations in terms of efficacy and severe side effects. However, these biomolecules have a short half-life in vivo, requiring multiple administrations, resulting in severe suffering, discomfort, and poor patient compliance. In the early days of (nano)biotechnology, these problems caused concern in the medical community, but recently it has been recognized that these challenges can be overcome by developing innovative formulations. This review focuses on the use of vinyl polymer-based materials for the protection and delivery of nucleic acids in cancer. First, an overview of the properties of nucleic acids and their versatility as drugs is provided. Then, key information on the achievements to date, the most effective delivery methods, and the evaluation of functionalization approaches (stimulatory strategies) are critically discussed to highlight the importance of vinyl polymers in the new cancer treatment approaches. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
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Affiliation(s)
- Patrícia Alexandra Pereira
- Department of Chemical Engineering, CEMMPRE, University of Coimbra, Rua Sílvio Lima-Pólo II, Coimbra, Portugal
- IPN, Instituto Pedro Nunes, Associação para a Inovação e Desenvolvimento em Ciência e Tecnologia, Rua Pedro Nunes, Coimbra, Portugal
| | | | - Arménio C Serra
- Department of Chemical Engineering, CEMMPRE, University of Coimbra, Rua Sílvio Lima-Pólo II, Coimbra, Portugal
| | - Jorge F J Coelho
- Department of Chemical Engineering, CEMMPRE, University of Coimbra, Rua Sílvio Lima-Pólo II, Coimbra, Portugal
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17
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Zhang M, Huang Y. siRNA modification and delivery for drug development. Trends Mol Med 2022; 28:892-893. [PMID: 36031544 DOI: 10.1016/j.molmed.2022.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 10/15/2022]
Affiliation(s)
- Mengjie Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China; Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China
| | - Yuanyu Huang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China; Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China; School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China; Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China; Rigerna Therapeutics, Suzhou, Jiangsu 215127, China.
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18
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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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19
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Guenther DC, Mori S, Matsuda S, Gilbert JA, Willoughby JLS, Hyde S, Bisbe A, Jiang Y, Agarwal S, Madaoui M, Janas MM, Charisse K, Maier MA, Egli M, Manoharan M. Role of a "Magic" Methyl: 2'-Deoxy-2'-α-F-2'-β- C-methyl Pyrimidine Nucleotides Modulate RNA Interference Activity through Synergy with 5'-Phosphate Mimics and Mitigation of Off-Target Effects. J Am Chem Soc 2022; 144:14517-14534. [PMID: 35921401 PMCID: PMC9389587 DOI: 10.1021/jacs.2c01679] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Although 2′-deoxy-2′-α-F-2′-β-C-methyl (2′-F/Me) uridine nucleoside derivatives
are a successful class of antiviral drugs, this modification had not
been studied in oligonucleotides. Herein, we demonstrate the facile
synthesis of 2′-F/Me-modified pyrimidine phosphoramidites and
their subsequent incorporation into oligonucleotides. Despite the
C3′-endo preorganization of the parent nucleoside,
a single incorporation into RNA or DNA resulted in significant thermal
destabilization of a duplex due to unfavorable enthalpy, likely resulting
from steric effects. When located at the terminus of an oligonucleotide,
the 2′-F/Me modification imparted more resistance to degradation
than the corresponding 2′-fluoro nucleotides. Small interfering
RNAs (siRNAs) modified at certain positions with 2′-F/Me had
similar or better silencing activity than the parent siRNAs when delivered
via a lipid nanoparticle formulation or as a triantennary N-acetylgalactosamine conjugate in cells and in mice. Modification
in the seed region of the antisense strand at position 6 or 7 resulted
in an activity equivalent to the parent in mice. Additionally, placement
of the antisense strand at position 7 mitigated seed-based off-target
effects in cell-based assays. When the 2′-F/Me modification
was combined with 5′-vinyl phosphonate, both E and Z isomers had silencing activity comparable
to the parent. In combination with other 2′-modifications such
as 2′-O-methyl, the Z isomer
is detrimental to silencing activity. Presumably, the equivalence
of 5′-vinyl phosphonate isomers in the context of 2′-F/Me
is driven by the steric and conformational features of the C-methyl-containing sugar ring. These data indicate that
2′-F/Me nucleotides are promising tools for nucleic acid-based
therapeutic applications to increase potency, duration, and safety.
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Affiliation(s)
- Dale C Guenther
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | - Shohei Mori
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | - Jason A Gilbert
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | | | - Sarah Hyde
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | - Anna Bisbe
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | - Saket Agarwal
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | - Mimouna Madaoui
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | - Maja M Janas
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | - Martin A Maier
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall, Cambridge, Massachusetts 02142, United States
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20
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Schlegel MK, Janas MM, Jiang Y, Barry JD, Davis W, Agarwal S, Berman D, Brown CR, Castoreno A, LeBlanc S, Liebow A, Mayo T, Milstein S, Nguyen T, Shulga-Morskaya S, Hyde S, Schofield S, Szeto J, Woods L, Yilmaz V, Manoharan M, Egli M, Charissé K, Sepp-Lorenzino L, Haslett P, Fitzgerald K, Jadhav V, Maier M. From bench to bedside: Improving the clinical safety of GalNAc-siRNA conjugates using seed-pairing destabilization. Nucleic Acids Res 2022; 50:6656-6670. [PMID: 35736224 PMCID: PMC9262600 DOI: 10.1093/nar/gkac539] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/02/2022] [Accepted: 06/09/2022] [Indexed: 12/24/2022] Open
Abstract
Preclinical mechanistic studies have pointed towards RNA interference-mediated off-target effects as a major driver of hepatotoxicity for GalNAc-siRNA conjugates. Here, we demonstrate that a single glycol nucleic acid or 2'-5'-RNA modification can substantially reduce small interfering RNA (siRNA) seed-mediated binding to off-target transcripts while maintaining on-target activity. In siRNAs with established hepatotoxicity driven by off-target effects, these novel designs with seed-pairing destabilization, termed enhanced stabilization chemistry plus (ESC+), demonstrated a substantially improved therapeutic window in rats. In contrast, siRNAs thermally destabilized to a similar extent by the incorporation of multiple DNA nucleotides in the seed region showed little to no improvement in rat safety suggesting that factors in addition to global thermodynamics play a role in off-target mitigation. We utilized the ESC+ strategy to improve the safety of ALN-HBV, which exhibited dose-dependent, transient and asymptomatic alanine aminotransferase elevations in healthy volunteers. The redesigned ALN-HBV02 (VIR-2218) showed improved specificity with comparable on-target activity and the program was reintroduced into clinical development.
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Affiliation(s)
| | | | | | | | - Wendell Davis
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Saket Agarwal
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Daniel Berman
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - Sarah LeBlanc
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Tara Mayo
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Tuyen Nguyen
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Sarah Hyde
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - John Szeto
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | | | | | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Martin A Maier
- To whom correspondence should be addressed: Tel: +1 617 551 8274; Fax: +1 617 682 4020;
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21
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Shiohama Y, Fujita R, Sonokawa M, Hisano M, Kotake Y, Krstic-Demonacos M, Demonacos C, Kashiwazaki G, Kitayama T, Fujii M. Elimination of Off-Target Effect by Chemical Modification of 5′-End of Small Interfering RNA. Nucleic Acid Ther 2022; 32:438-447. [DOI: 10.1089/nat.2021.0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yasuo Shiohama
- Environmental and Biological Information Group, Tropical Biosphere Research Centre, University of the Ryukyus, Nishihara, Japan
| | - Ryosuke Fujita
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Maika Sonokawa
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Masaaki Hisano
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Yojiro Kotake
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Marija Krstic-Demonacos
- School of Science, Engineering and Environment, University of Salford, Salford, United Kingdom
| | - Constantinos Demonacos
- Division of Pharmacy and Optometry, Faculty of Biology Medicine and Health, School of Health Science, University of Manchester, Manchester, United Kingdom
| | - Gengo Kashiwazaki
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Takashi Kitayama
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Masayuki Fujii
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
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22
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Gangopadhyay S, Gore KR. Advances in siRNA therapeutics and synergistic effect on siRNA activity using emerging dual ribose modifications. RNA Biol 2022; 19:452-467. [PMID: 35352626 PMCID: PMC8973385 DOI: 10.1080/15476286.2022.2052641] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Nucleic acid-based therapeutics that control gene expression have been steadily progressing towards achieving their full clinical potential throughout the last few decades. Rapid progress has been achieved in RNAi-based therapy by optimizing high specificity and gene silencing efficiency using chemically modified siRNAs. Since 2018, four siRNA drugs – patisiran, givosiran, lumasiran, and inclisiran, were approved by the US FDA, providing a testament to the promise of RNAi therapeutics. Despite these promising results, safe and efficient siRNA delivery at the target site remains a major obstacle for efficient siRNA-based therapeutics. In this review, we have outlined the synergistic effects of emerging dual ribose modifications, including 2’,4’- and 2’,5’-modifications, 5’-E/Z-vinylphosphonate, and northern methanocarbacyclic (NMC) modifications that have contributed to drug-like effects in siRNA. These modifications enhance nuclease stability, prolong gene silencing efficiency, improve thermal stability, and exhibit high tissue accumulation. We also highlight the current progress in siRNA clinical trials. This review will help to understand the potential effects of dual ribose modifications and provides alternative ways to use extensive 2’-modifications in siRNA drugs. Moreover, the minimal number of these dual ribose modifications could be sufficient to achieve the desired therapeutic effect. In future, detailed in vivo studies using these dual ribose modifications could help to improve the therapeutic effects of siRNA. Rational design could further open doors for the rapid progress in siRNA therapeutics. ![]() ![]()
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Affiliation(s)
- Sumit Gangopadhyay
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
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23
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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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24
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Schlegel MK, Matsuda S, Brown CR, Harp JM, Barry JD, Berman D, Castoreno A, Schofield S, Szeto J, Manoharan M, Charissé K, Egli M, Maier MA. Overcoming GNA/RNA base-pairing limitations using isonucleotides improves the pharmacodynamic activity of ESC+ GalNAc-siRNAs. Nucleic Acids Res 2021; 49:10851-10867. [PMID: 34648028 PMCID: PMC8565336 DOI: 10.1093/nar/gkab916] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/19/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022] Open
Abstract
We recently reported that RNAi-mediated off-target effects are important drivers of the hepatotoxicity observed for a subset of GalNAc–siRNA conjugates in rodents, and that these findings could be mitigated by seed-pairing destabilization using a single GNA nucleotide placed within the seed region of the guide strand. Here, we report further investigation of the unique and poorly understood GNA/RNA cross-pairing behavior to better inform GNA-containing siRNA design. A reexamination of published GNA homoduplex crystal structures, along with a novel structure containing a single (S)-GNA-A residue in duplex RNA, indicated that GNA nucleotides universally adopt a rotated nucleobase orientation within all duplex contexts. Such an orientation strongly affects GNA-C and GNA-G but not GNA-A or GNA-T pairing in GNA/RNA heteroduplexes. Transposition of the hydrogen-bond donor/acceptor pairs using the novel (S)-GNA-isocytidine and -isoguanosine nucleotides could rescue productive base-pairing with the complementary G or C ribonucleotides, respectively. GalNAc-siRNAs containing these GNA isonucleotides showed an improved in vitro activity, a similar improvement in off-target profile, and maintained in vivo activity and guide strand liver levels more consistent with the parent siRNAs than those modified with isomeric GNA-C or -G, thereby expanding our toolbox for the design of siRNAs with minimized off-target activity.
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Affiliation(s)
| | | | | | - Joel M Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Daniel Berman
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - John Szeto
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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25
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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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Zhou X, Pan Y, Yu L, Wu J, Li Z, Li H, Guan Z, Tang X, Yang Z. Feasibility of cRGD conjugation at 5'-antisense strand of siRNA by phosphodiester linkage extension. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:603-612. [PMID: 34589281 PMCID: PMC8463321 DOI: 10.1016/j.omtn.2021.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022]
Abstract
Small interfering RNAs (siRNAs) are widely studied for their highly specific gene silencing activity. However, obstacles remain to the clinical application of siRNAs. Attaching conjugates to siRNAs can improve their stability and broaden their application, and most functional conjugates of siRNAs locate at the 3'-terminus of the sense or antisense strand. In this work, we found that conjugating a group at the 5'-terminus of the antisense strand via phosphodiester was practicable, especially when the group was a flexible moiety such as an alkyl linker. When conjugating a bulky ligand, such as cRGD, the length of the 5'-phosphodiester linker between the ligand and the 5'-terminus of the antisense strand was the key in terms of RNA interference (RNAi). With a relative longer linker, the conjugates showed potency similar to siRNA. A highly efficient transfection system composed of a neutral cytidinyl lipid (DNCA) and a gemini-like cationic lipid (CLD) was employed to deliver siRNAs or their conjugates. The cRGD conjugates showed superior targeting delivery and antitumor efficacy in vivo and also selective cellular uptake in vitro. This unity of encapsulation and conjugation strategy may provide potential strategies for siRNA-based gene therapy.
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Affiliation(s)
- Xinyang Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- People’s Public Security University of China, Beijing 100038, China
| | - Yufei Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Lijia Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- National Center for Occupational Safety and Health, NHC, Beijing 102308, China
| | - Jing Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zheng Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Huantong Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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Brechin V, Shinohara F, Saito JI, Seitz H, Tomari Y. Mechanistic analysis of the enhanced RNAi activity by 6-mCEPh-purine at the 5' end of the siRNA guide strand. RNA (NEW YORK, N.Y.) 2021; 27:151-162. [PMID: 33177187 PMCID: PMC7812867 DOI: 10.1261/rna.073775.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 10/15/2020] [Indexed: 05/05/2023]
Abstract
A key approach for improving siRNA efficacy is chemical modifications. Through an in silico screening of modifications at the 5'-end nucleobase of the guide strand, an adenine-derived compound called 6-(3-(2-carboxyethyl)phenyl)-purine (6-mCEPh-purine) was identified to improve the RNAi activity in cultured human cells and in vivo mouse models. Nevertheless, it remains unclear how this chemical modification enhances the siRNA potency. Here, we used a series of biochemical approaches to quantitatively evaluate the effect of the 6-mCEPh-purine modification at each step in the assembly of the RNAi effector complex called RISC. We found that the modification improves the formation of mature RISC at least in two different ways, by fixing the loading orientation of siRNA duplexes and increasing the stability of mature RISC after passenger strand ejection. Our data will provide a molecular platform for further development of chemically modified siRNA drugs.
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Affiliation(s)
- Vincent Brechin
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Fumikazu Shinohara
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Jun-Ichi Saito
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Hervé Seitz
- Institut de Génétique Humaine, UMR 9002 CNRS and Université de Montpellier, 34396 Montpellier, France
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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Shinohara F, Oashi T, Harumoto T, Nishikawa T, Takayama Y, Miyagi H, Takahashi Y, Nakajima T, Sawada T, Koda Y, Makino A, Sato A, Hamaguchi K, Suzuki M, Yamamoto J, Tomari Y, Saito JI. siRNA potency enhancement via chemical modifications of nucleotide bases at the 5'-end of the siRNA guide strand. RNA (NEW YORK, N.Y.) 2021; 27:163-173. [PMID: 33177188 PMCID: PMC7812868 DOI: 10.1261/rna.073783.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 11/05/2020] [Indexed: 05/03/2023]
Abstract
Small interfering RNAs (siRNAs) can be utilized not only as functional biological research tools but also as therapeutic agents. For the clinical use of siRNA as drugs, various chemical modifications have been used to improve the activity of siRNA drugs, and further chemical modifications are expected to improve the utility of siRNA therapeutics. As the 5' nucleobase of the guide strand affects the interaction between an siRNA and AGO2 and target cleavage activity, structural optimization of this specific position may be a useful strategy for improving siRNA activity. Here, using the in silico model of the complex between human AGO2 MID domain and nucleoside monophosphates, we screened and synthesized an original adenine-derived analog, 6-(3-(2-carboxyethyl)phenyl)purine (6-mCEPh-purine), that fits better than the natural nucleotide bases into the MID domain of AGO2. Introduction of the 6-mCEPh-purine analog at the 5'-end of the siRNA guide strand significantly enhanced target knockdown activity in both cultured cell lines and in vivo animal models. Our findings can help expand strategies for rationally optimizing siRNA activity via chemical modifications of nucleotide bases.
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Affiliation(s)
- Fumikazu Shinohara
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Taiji Oashi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Toshimasa Harumoto
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Tomoyuki Nishikawa
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yuki Takayama
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Hikaru Miyagi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yuichi Takahashi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Takahiro Nakajima
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Takashi Sawada
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yasuo Koda
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Asana Makino
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Atsuko Sato
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Kaori Hamaguchi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Michihiko Suzuki
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Junichiro Yamamoto
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Jun-Ichi Saito
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
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Varley AJ, Desaulniers JP. Chemical strategies for strand selection in short-interfering RNAs. RSC Adv 2021; 11:2415-2426. [PMID: 35424193 PMCID: PMC8693850 DOI: 10.1039/d0ra07747j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Therapeutic small interfering RNAs (siRNAs) are double stranded RNAs capable of potent and specific gene silencing through activation of the RNA interference (RNAi) pathway. The potential of siRNA drugs has recently been highlighted by the approval of multiple siRNA therapeutics. These successes relied heavily on chemically modified nucleic acids and their impact on stability, delivery, potency, and off-target effects. Despite remarkable progress, clinical trials still face failure due to off-target effects such as off-target gene dysregulation. Each siRNA strand can downregulate numerous gene targets while also contributing towards saturation of the RNAi machinery, leading to the upregulation of miRNA-repressed genes. Eliminating sense strand uptake effectively reduces off-target gene silencing and helps limit the disruption to endogenous regulatory mechanisms. Therefore, our understanding of strand selection has a direct impact on the success of future siRNA therapeutics. In this review, the approaches used to improve strand uptake are discussed and effective methods are summarized.
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Affiliation(s)
- Andrew J Varley
- Faculty of Science, University of Ontario Institute of Technology Oshawa Ontario L1G 0C5 Canada +1 905 721 3304 +1 905 721 8668 (ext. 3621)
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology Oshawa Ontario L1G 0C5 Canada +1 905 721 3304 +1 905 721 8668 (ext. 3621)
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30
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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31
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Brown CR, Gupta S, Qin J, Racie T, He G, Lentini S, Malone R, Yu M, Matsuda S, Shulga-Morskaya S, Nair AV, Theile CS, Schmidt K, Shahraz A, Goel V, Parmar RG, Zlatev I, Schlegel MK, Nair JK, Jayaraman M, Manoharan M, Brown D, Maier MA, Jadhav V. Investigating the pharmacodynamic durability of GalNAc-siRNA conjugates. Nucleic Acids Res 2020; 48:11827-11844. [PMID: 32808038 PMCID: PMC7708070 DOI: 10.1093/nar/gkaa670] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
One hallmark of trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNAs is the remarkable durability of silencing that can persist for months in preclinical species and humans. Here, we investigated the underlying biology supporting this extended duration of pharmacological activity. We found that siRNA accumulation and stability in acidic intracellular compartments is critical for long-term activity. We show that functional siRNA can be liberated from these compartments and loaded into newly generated Argonaute 2 protein complexes weeks after dosing, enabling continuous RNAi activity over time. Identical siRNAs delivered in lipid nanoparticles or as GalNAc conjugates were dose-adjusted to achieve similar knockdown, but only GalNAc–siRNAs supported an extended duration of activity, illustrating the importance of receptor-mediated siRNA trafficking in the process. Taken together, we provide several lines of evidence that acidic intracellular compartments serve as a long-term depot for GalNAc–siRNA conjugates and are the major contributor to the extended duration of activity observed in vivo.
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Affiliation(s)
| | - Swati Gupta
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - June Qin
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Timothy Racie
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Guo He
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Scott Lentini
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Ryan Malone
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Mikyung Yu
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - Anil V Nair
- MGH Program in Membrane Biology, Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Karyn Schmidt
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Azar Shahraz
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Varun Goel
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Ivan Zlatev
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | | | | | - Dennis Brown
- MGH Program in Membrane Biology, Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
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32
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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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33
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Kotikam V, Rozners E. Amide-Modified RNA: Using Protein Backbone to Modulate Function of Short Interfering RNAs. Acc Chem Res 2020; 53:1782-1790. [PMID: 32658452 DOI: 10.1021/acs.accounts.0c00249] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA-based technologies to control gene expression, such as RNA interference (RNAi) and CRISPR-Cas9, have become powerful tools in molecular biology and genomics. The exciting potential that RNAi and CRISPR-Cas9 may also become new therapeutic approaches has reinvigorated interest in chemically modifying RNA to improve its properties for in vivo applications. Chemical modifications can improve enzymatic stability, in vivo delivery, cellular uptake, and sequence specificity as well as minimize off-target activity of short interfering RNAs (siRNAs) and CRISPR associated RNAs. While numerous good solutions for improving stability toward enzymatic degradation have emerged, optimization of the latter functional properties remains challenging. In this Account, we discuss synthesis, structure, and biological activity of novel nonionic analogues of RNA that have the phosphodiester backbone replaced by amide linkages (AM1). Our long-term goal is to use the amide backbone to improve the stability and specificity of siRNAs and other functional RNAs. Our work in this area was motivated by early discoveries that nonionic backbone modifications, including AM1, did not disturb the overall structure or thermal stability of RNA duplexes. We hypothesized that the reduced negative charge and hydrophobic nature of the AM1 backbone modification might be useful in optimizing functional applications through enhanced cellular uptake, and might suppress unwanted off-target effects of siRNAs. NMR and X-ray crystallography studies showed that AM1 was an excellent mimic of phosphodiester linkages in RNA. The local conformational changes caused by the amide linkages were easily accommodated by small adjustments in RNA's conformation. Further, the amide carbonyl group assumed an orientation that is similar to one of the nonbridging P-O bonds, which may enable amide/phosphate mimicry by conserving hydrogen bonding interactions. The crystal structure of a short amide-modified DNA-RNA hybrid in complex with RNase H indicated that the amide N-H could also act as an H-bond donor to stabilize RNA-protein interactions, which is an interaction mode not available to phosphate groups. Functional assays established that amides were well tolerated at internal positions in both strands of siRNAs. Surprisingly, amide modifications in the middle of the guide strand and at the 5'-end of the passenger strand increased RNAi activity compared to unmodified siRNA. Most importantly, an amide linkage between the first and second nucleosides of the passenger strand completely abolished its undesired off-target activity while enhancing the desired RNAi activity. These results suggest that RNAi may tolerate more substantial modifications of siRNAs than the chemistries tried so far. The findings are also important and timely because they demonstrate that amide modifications may reduce off-target activity of siRNAs, which remains an important roadblock for clinical use of RNAi. Taken together, our work suggests that amide linkages have underappreciated potential to optimize the biological and pharmacological properties of RNA. Expanded use of amide linkages in RNA to enhance CRISPR and other technologies requiring chemically stable, functional mimics of noncoding RNAs is expected.
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Affiliation(s)
- Venubabu Kotikam
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
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34
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Weingärtner A, Bethge L, Weiss L, Sternberger M, Lindholm MW. Less Is More: Novel Hepatocyte-Targeted siRNA Conjugates for Treatment of Liver-Related Disorders. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:242-250. [PMID: 32590173 PMCID: PMC7321783 DOI: 10.1016/j.omtn.2020.05.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 03/30/2020] [Accepted: 05/19/2020] [Indexed: 12/14/2022]
Abstract
N-acetyl-galactosamine (GalNAc) conjugation enhances liver specificity for therapeutic oligonucleotides. Here we report on a novel design with improved activity and stability compared with a triantennary design. We applied a versatile monovalent serinol-GalNAc conjugation strategy. First, 1-4 serial serinol-linked GalNAc units were conjugated to terminal positions of small interfering RNA (siRNA) molecules. In primary hepatocytes, 5' antisense GalNAc conjugates were inactive, whereas 3' antisense and 3' or 5' sense conjugates displayed low activity for single GalNAc units, while 2-4 serial GalNAc conjugates were all equally potent. In mice, 5' sense conjugates with 2-4 serial GalNAc units were all as potent as a triantennary GalNAc control (1 mg/kg). Second, increased spacing between two serial 5' sense-conjugated GalNAc units did not affect in vitro activity. Finally, two single GalNAc units were positioned at opposite ends of the sense strand. A single dose (0.3 mg/kg) of this novel conjugate in mice showed a 3-fold reduction of serum target protein level at day 7 and 4-fold lower serum level at day 27, relative to an equimolar dose of a triantennary GalNAc conjugate of the same siRNA. Improved tritosome stability (by liquid chromatography-mass spectrometry [LC-MS] analysis) can at least partially explain the increased activity and duration of action for the novel GalNAc conjugate.
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Affiliation(s)
- Adrien Weingärtner
- Silence Therapeutics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany.
| | - Lucas Bethge
- Silence Therapeutics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Lisa Weiss
- Silence Therapeutics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Maria Sternberger
- Silence Therapeutics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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35
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Varley AJ, Hammill ML, Salim L, Desaulniers JP. Effects of Chemical Modifications on siRNA Strand Selection in Mammalian Cells. Nucleic Acid Ther 2020; 30:229-236. [DOI: 10.1089/nat.2020.0848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Andrew J. Varley
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Canada
| | - Matthew L. Hammill
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Canada
| | - Lidya Salim
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Canada
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Kumar P, Degaonkar R, Guenther DC, Abramov M, Schepers G, Capobianco M, Jiang Y, Harp J, Kaittanis C, Janas MM, Castoreno A, Zlatev I, Schlegel MK, Herdewijn P, Egli M, Manoharan M. Chimeric siRNAs with chemically modified pentofuranose and hexopyranose nucleotides: altritol-nucleotide (ANA) containing GalNAc-siRNA conjugates: in vitro and in vivo RNAi activity and resistance to 5'-exonuclease. Nucleic Acids Res 2020; 48:4028-4040. [PMID: 32170309 PMCID: PMC7192627 DOI: 10.1093/nar/gkaa125] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/15/2020] [Accepted: 03/04/2020] [Indexed: 12/23/2022] Open
Abstract
In this report, we investigated the hexopyranose chemical modification Altriol Nucleic Acid (ANA) within small interfering RNA (siRNA) duplexes that were otherwise fully modified with the 2′-deoxy-2′-fluoro and 2′-O-methyl pentofuranose chemical modifications. The siRNAs were designed to silence the transthyretin (Ttr) gene and were conjugated to a trivalent N-acetylgalactosamine (GalNAc) ligand for targeted delivery to hepatocytes. Sense and antisense strands of the parent duplex were synthesized with single ANA residues at each position on the strand, and the resulting siRNAs were evaluated for their ability to inhibit Ttr mRNA expression in vitro. Although ANA residues were detrimental at the 5′ end of the antisense strand, the siRNAs with ANA at position 6 or 7 in the seed region had activity comparable to the parent. The siRNA with ANA at position 7 in the seed region was active in a mouse model. An Oligonucleotide with ANA at the 5′ end was more stable in the presence of 5′-exonuclease than an oligonucleotide of the same sequence and chemical composition without the ANA modification. Modeling studies provide insight into the origins of regiospecific changes in potency of siRNAs and the increased protection against 5′-exonuclease degradation afforded by the ANA modification.
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Affiliation(s)
- Pawan Kumar
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Rohan Degaonkar
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Dale C Guenther
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Mikhail Abramov
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Marie Capobianco
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Joel Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Maja M Janas
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Adam Castoreno
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Mark K Schlegel
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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Kamiya Y, Takeyama Y, Mizuno T, Satoh F, Asanuma H. Investigation of Strand-Selective Interaction of SNA-Modified siRNA with AGO2-MID. Int J Mol Sci 2020; 21:ijms21155218. [PMID: 32717920 PMCID: PMC7432901 DOI: 10.3390/ijms21155218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/22/2022] Open
Abstract
Small interfering RNA (siRNA) has been recognized as a powerful gene-silencing tool. For therapeutic application, chemical modification is often required to improve the properties of siRNA, including its nuclease resistance, activity, off-target effects, and tissue distribution. Careful siRNA guide strand selection in the RNA-induced silencing complex (RISC) is important to increase the RNA interference (RNAi) activity as well as to reduce off-target effects. The passenger strand-mediated off-target activity was previously reduced and on-target activity was enhanced by substitution with acyclic artificial nucleic acid, namely serinol nucleic acid (SNA). In the present study, the reduction of off-target activity caused by the passenger strand was investigated by modifying siRNAs with SNA. The interactions of SNA-substituted mononucleotides, dinucleotides, and (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO)-labeled double-stranded RNA (dsRNA) with the MID domain of the Argonaute 2 (AGO2) protein, which plays a pivotal role in strand selection by accommodation of the 5’-terminus of siRNA, were comprehensively analyzed. The obtained nuclear magnetic resonance (NMR) data revealed that AGO2-MID selectively bound to the guide strand of siRNA due to the inhibitory effect of the SNA backbone located at the 5’ end of the passenger strand.
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Affiliation(s)
- Yukiko Kamiya
- Correspondence: (Y.K.); (H.A.); Tel.: +81-52-789-2552 (Y.K.); +81-52-789-2488 (H.A.)
| | | | | | | | - Hiroyuki Asanuma
- Correspondence: (Y.K.); (H.A.); Tel.: +81-52-789-2552 (Y.K.); +81-52-789-2488 (H.A.)
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Hu B, Zhong L, Weng Y, Peng L, Huang Y, Zhao Y, Liang XJ. Therapeutic siRNA: state of the art. Signal Transduct Target Ther 2020; 5:101. [PMID: 32561705 PMCID: PMC7305320 DOI: 10.1038/s41392-020-0207-x] [Citation(s) in RCA: 621] [Impact Index Per Article: 155.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/08/2020] [Accepted: 05/03/2020] [Indexed: 02/07/2023] Open
Abstract
RNA interference (RNAi) is an ancient biological mechanism used to defend against external invasion. It theoretically can silence any disease-related genes in a sequence-specific manner, making small interfering RNA (siRNA) a promising therapeutic modality. After a two-decade journey from its discovery, two approvals of siRNA therapeutics, ONPATTRO® (patisiran) and GIVLAARI™ (givosiran), have been achieved by Alnylam Pharmaceuticals. Reviewing the long-term pharmaceutical history of human beings, siRNA therapy currently has set up an extraordinary milestone, as it has already changed and will continue to change the treatment and management of human diseases. It can be administered quarterly, even twice-yearly, to achieve therapeutic effects, which is not the case for small molecules and antibodies. The drug development process was extremely hard, aiming to surmount complex obstacles, such as how to efficiently and safely deliver siRNAs to desired tissues and cells and how to enhance the performance of siRNAs with respect to their activity, stability, specificity and potential off-target effects. In this review, the evolution of siRNA chemical modifications and their biomedical performance are comprehensively reviewed. All clinically explored and commercialized siRNA delivery platforms, including the GalNAc (N-acetylgalactosamine)-siRNA conjugate, and their fundamental design principles are thoroughly discussed. The latest progress in siRNA therapeutic development is also summarized. This review provides a comprehensive view and roadmap for general readers working in the field.
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Affiliation(s)
- Bo Hu
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, 100081, Beijing, People's Republic of China
| | - Liping Zhong
- National Center for International Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Theranostics, Guangxi Medical University, 530021, Guangxi, People's Republic of China
| | - Yuhua Weng
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, 100081, Beijing, People's Republic of China
| | - Ling Peng
- Aix-Marseille University, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Equipe Labellisée Ligue Contre le Cancer, 13288, Marseille, France
| | - Yuanyu Huang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, 100081, Beijing, People's Republic of China.
| | - Yongxiang Zhao
- National Center for International Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Theranostics, Guangxi Medical University, 530021, Guangxi, People's Republic of China.
| | - Xing-Jie Liang
- Chinese Academy of Sciences (CAS), Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 100190, Beijing, People's Republic of China.
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Kumar P, Parmar RG, Brown CR, Willoughby JLS, Foster DJ, Babu IR, Schofield S, Jadhav V, Charisse K, Nair JK, Rajeev KG, Maier MA, Egli M, Manoharan M. 5'-Morpholino modification of the sense strand of an siRNA makes it a more effective passenger. Chem Commun (Camb) 2019; 55:5139-5142. [PMID: 30977478 DOI: 10.1039/c9cc00977a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The 5'-monophosphate group plays an important role in strand selection during gene silencing mediated by small-interfering RNA. We show that blocking of 5' phosphorylation of the sense strand by introducing a 5'-morpholino modification improves antisense strand selection and RNAi activity. The 5'-morpholino modification of the antisense strand triggers complete loss of activity.
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Affiliation(s)
- Pawan Kumar
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, USA.
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Chernikov IV, Vlassov VV, Chernolovskaya EL. Current Development of siRNA Bioconjugates: From Research to the Clinic. Front Pharmacol 2019; 10:444. [PMID: 31105570 PMCID: PMC6498891 DOI: 10.3389/fphar.2019.00444] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
Small interfering RNAs (siRNAs) acting via RNA interference mechanisms are able to recognize a homologous mRNA sequence in the cell and induce its degradation. The main problems in the development of siRNA-based drugs for therapeutic use are the low efficiency of siRNA delivery to target cells and the degradation of siRNAs by nucleases in biological fluids. Various approaches have been proposed to solve the problem of siRNA delivery in vivo (e.g., viruses, cationic lipids, polymers, nanoparticles), but all have limitations for therapeutic use. One of the most promising approaches to solve the problem of siRNA delivery to target cells is bioconjugation; i.e., the covalent connection of siRNAs with biogenic molecules (lipophilic molecules, antibodies, aptamers, ligands, peptides, or polymers). Bioconjugates are "ideal nanoparticles" since they do not need a positive charge to form complexes, are less toxic, and are less effectively recognized by components of the immune system because of their small size. This review is focused on strategies and principles for constructing siRNA bioconjugates for in vivo use.
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Affiliation(s)
- Ivan V Chernikov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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41
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Abstract
Efforts to chemically modify nucleic acids got underway merely a decade after the discovery of the DNA double helix and initially targeted nucleosides and nucleotides. The origins of three analogues that remain staples of modification strategies and figure prominently in FDA-approved nucleic acid therapeutics can be traced to the 1960s: 2'-deoxy-2'-fluoro-RNA (2'-F RNA), 2'- O-methyl-RNA (2'- OMe RNA), and the phosphorothioates (PS-DNA/RNA). Progress in nucleoside phosphoramidite-based solid phase oligonucleotide synthesis has gone hand in hand with the creation of second-generation (e.g., 2'- O-(2-methoxyethyl)-RNA, MOE-RNA) and third-generation (e.g., bicyclic nucleic acids, BNAs) analogues, giving rise to an expanding universe of modified nucleic acids. Thus, beyond site-specifically altered DNAs and RNAs with a modified base, sugar, and/or phosphate backbone moieties, nucleic acid chemists have created a host of conjugated oligonucleotides and artificial genetic polymers (XNAs). The search for oligonucleotides with therapeutic efficacy constitutes a significant driving force for these investigations. However, nanotechnology, diagnostics, synthetic biology and genetics, nucleic acid etiology, and basic research directed at the properties of native and artificial pairing systems have all stimulated the design of ever more diverse modifications. Modification of nucleic acids can affect pairing and chemical stability, conformation and interactions with a flurry of proteins and enzymes that play important roles in uptake, transport or processing of targets. Enhancement of metabolic stability is a central concern in the design of antisense, siRNA and aptamer oligonucleotides for therapeutic applications. In the antisense approach, uniformly modified oligonucleotides or so-called gapmers are used to target a specific RNA. The former may sterically block transcription or direct alternative splicing, whereas the latter feature a central PS window that elicits RNase H-mediated cleavage of the target. The key enzyme in RNA interference (RNAi) is Argonaute 2 (Ago2), a dynamic multidomain enzyme that binds multiple regions of the guide (antisense) and passenger (sense) siRNAs. The complexity of the individual interactions between Ago2 and the siRNA duplex provides significant challenges for chemical modification. Therefore, a uniform (the same modification throughout, e.g., antisense) or nearly uniform (e.g., aptamer) modification strategy is less useful in the pursuit of siRNA therapeutic leads. Instead, unique structural features and protein interactions of 5'-end (guide/Ago2MID domain), seed region, central region (cleavage site/Ago2 PIWI domain), and 3'-terminal nucleotides (guide/Ago2 PAZ domain) demand a more nuanced approach in the design of chemically modified siRNAs for therapeutic use. This Account summarizes current siRNA modification strategies with an emphasis on the regio-specific interactions between oligonucleotide and Ago2 and how these affect the choice of modification and optimization of siRNA efficacy. In addition to standard assays applied to measure the effects of modification on the stability of pairing and resistance against nuclease degradation, structural insights based on crystallographic data for modified RNAs alone and in complex with Ago2 from molecular modeling studies are a valuable guide in the design of siRNA therapeutics. Thus, this comprehensive approach is expected to result in accelerated generation of new siRNA-based therapies against various diseases, now that the first siRNA has obtained approval by the US FDA for treatment of hereditary hATTR amyloidosis.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
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ELTA: Enzymatic Labeling of Terminal ADP-Ribose. Mol Cell 2019; 73:845-856.e5. [PMID: 30712989 DOI: 10.1016/j.molcel.2018.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/22/2018] [Accepted: 12/21/2018] [Indexed: 12/14/2022]
Abstract
ADP-ribosylation refers to the addition of one or more ADP-ribose groups onto proteins. The attached ADP-ribose monomers or polymers, commonly known as poly(ADP-ribose) (PAR), modulate the activities of the modified substrates or their binding affinities to other proteins. However, progress in this area is hindered by a lack of tools to investigate this protein modification. Here, we describe a new method named ELTA (enzymatic labeling of terminal ADP-ribose) for labeling free or protein-conjugated ADP-ribose monomers and polymers at their 2'-OH termini using the enzyme OAS1 and dATP. When coupled with various dATP analogs (e.g., radioactive, fluorescent, affinity tags), ELTA can be used to explore PAR biology with techniques routinely used to investigate DNA or RNA function. We demonstrate that ELTA enables the biophysical measurements of protein binding to PAR of a defined length, detection of PAR length from proteins and cells, and enrichment of sub-femtomole amounts of ADP-ribosylated peptides from cell lysates.
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43
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Synthesis and in vivo anti- or pro-inflammatory activity of new bisphosphonates and vinylphosphonates. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-018-2328-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Dürr E, Doherty W, Lee SY, El‐Sagheer AH, Shivalingam A, McHugh PJ, Brown T, McGouran JF. Squaramide-Based 5'-Phosphate Replacements Bind to the DNA Repair Exonuclease SNM1A. ChemistrySelect 2018; 3:12824-12829. [PMID: 31414040 PMCID: PMC6685075 DOI: 10.1002/slct.201803375] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/19/2018] [Indexed: 12/26/2022]
Abstract
Phosphate groups are often crucial to biological activity and interactions of oligonucleotides, but confer poor membrane permeability. In addition, the group's lability to enzymatic hydrolysis is an obstacle to its use in therapeutics and in biological tools. We present the synthesis of N-oxyamide and squaramide modifications at the 5'-end of oligonucleotides as phosphate replacements and their biological evaluation using the 5'-exonuclease SNM1A. The squaryl diamide modification showed minimal recognition as a 5'-phosphate mimic; however, modest inhibition of SNM1A, postulated to occur through metal coordination at the active site, was observed. Their facile incorporation after solid-phase synthesis and recognition by the exonuclease makes squaryl diamides attractive neutral 5'-phosphate replacements for oligonucleotides. This work is the first example of squaryl diamide modifications at the 5'-terminal position of oligonucleotides and of the potential use of modified oligonucleotides to bind to the metal center of SNM1A.
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Affiliation(s)
- Eva‐Maria Dürr
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
| | - William Doherty
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
| | - Sook Y. Lee
- Department of OncologyWeatherall Institute of Molecular MedicineUniversity of Oxford, John Radcliffe HospitalOxford OX3 9DSUK
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Afaf H. El‐Sagheer
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
- Chemistry Branch, Department of Science and MathematicsFaculty of Petroleum and Mining Engineering, Suez UniversitySuez43721Egypt
| | - Arun Shivalingam
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Peter J. McHugh
- Department of OncologyWeatherall Institute of Molecular MedicineUniversity of Oxford, John Radcliffe HospitalOxford OX3 9DSUK
| | - Tom Brown
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Joanna F. McGouran
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
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45
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Abstract
Small-molecule and protein/antibody drugs mainly act on genome-derived proteins to exert pharmacological effects. RNA based therapies hold the promise to expand the range of druggable targets from proteins to RNAs and the genome, as evidenced by several RNA drugs approved for clinical practice and many others under active trials. While chemo-engineered RNA mimics have found their success in marketed drugs and continue dominating basic research and drug development, these molecules are usually conjugated with extensive and various modifications. This makes them completely different from cellular RNAs transcribed from the genome that usually consist of unmodified ribonucleotides or just contain a few posttranscriptional modifications. The use of synthetic RNA mimics for RNA research and drug development is also in contrast with the ultimate success of protein research and therapy utilizing biologic or recombinant proteins produced and folded in living cells instead of polypeptides or proteins synthesized in vitro. Indeed, efforts have been made recently to develop RNA bioengineering technologies for cost-effective and large-scale production of biologic RNA molecules that may better capture the structures, functions, and safety profiles of natural RNAs. In this article, we provide an overview on RNA therapeutics for the treatment of human diseases via RNA interference mechanisms. By illustrating the structural differences between natural RNAs and chemo-engineered RNA mimics, we focus on discussion of a novel class of bioengineered/biologic RNA agents produced through fermentation and their potential applications to RNA research and drug development.
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA.
| | - Chao Jian
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Allan H Yu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Mei-Juan Tu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
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46
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O'Shea J, Theile CS, Das R, Babu IR, Charisse K, Manoharan M, Maier MA, Zlatev I. An efficient deprotection method for 5′-[O,O-bis(pivaloyloxymethyl)]-(E)-vinylphosphonate containing oligonucleotides. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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47
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Cen B, Wei Y, Huang W, Teng M, He S, Li J, Wang W, He G, Bai X, Liu X, Yuan Y, Pan X, Ji A. An Efficient Bivalent Cyclic RGD-PIK3CB siRNA Conjugate for Specific Targeted Therapy against Glioblastoma In Vitro and In Vivo. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 13:220-232. [PMID: 30312846 PMCID: PMC6178240 DOI: 10.1016/j.omtn.2018.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 01/14/2023]
Abstract
The PI3K-AKT-mTOR-signaling pathway is frequently activated in glioblastoma (GBM). Inhibition of phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta (PIK3CB)/p110β (a PI3K catalytic isoform) by RNAi substantially suppresses GBM growth with less toxicity to normal astrocytes. However, insufficient and non-specific small interfering RNA (siRNA) delivery may limit the efficacy of RNAi-based therapies against GBM. Here we prepared a novel methoxy-modified PIK3CB siRNA molecule (siPIK3CB) that was covalently conjugated to a [cyclo(Arg-Gly-Asp-D-Phe-Lys)-Ahx]2-Glu-PEG-MAL (biRGD) peptide, which selectively binds to integrin αvβ3 receptors. The αvβ3-positive U87MG cell line was selected as a representative for GBM. An orthotopic GBM xenograft model based on luciferase-expressing U87MG was established and validated in vivo to investigate bio-distribution and anti-tumor efficacy of biRGD-siPIK3CB. In vitro, biRGD-siPIK3CB specifically entered and silenced PIK3CB expression in GBM cells in an αvβ3 receptor-dependent manner, thus inhibiting cell cycle progression and migration and enhancing apoptosis. In vivo, intravenously injected biRGD-siPIK3CB substantially slowed GBM growth and prolonged survival by reducing tumor viability with silencing PIK3CB expression. Furthermore, biRGD-siPIK3CB led to mild tubulointerstitial injury in the treatment of GBM without obvious hepatotoxicity, whereas co-infusion of Gelofusine obviously alleviated this injury without compromising anti-tumor efficacy. These findings revealed a great translational potential of biRGD-siPIK3CB conjugate as a novel molecule for GBM therapy.
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Affiliation(s)
- Bohong Cen
- Department of Pharmacy, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, Guangdong, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China; Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, Guangdong, China; Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou 510515, Guangdong, China
| | - Yuanyi Wei
- Department of Pharmacy, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, Guangdong, China
| | - Wen Huang
- Department of Pharmacy, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, Guangdong, China
| | - Muzhou Teng
- Cancer Research Institute, Southern Medical University, Guangzhou 510515, China
| | - Shuai He
- Department of Pharmacy, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, Guangdong, China
| | - Jianlong Li
- Department of Orthopaedic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Wei Wang
- Guangzhou RiboBio Co., Guangzhou 510663, Guangdong, China
| | - Guolin He
- Department of Hepatobiliary Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, Guangdong, China
| | - Xin Bai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China; Department of Orthopaedic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Xiaoxia Liu
- Department of Pharmacy, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, Guangdong, China; Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510275, Guangdong, China
| | - Yawei Yuan
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, Guangdong, China.
| | - Xinghua Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China; Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou 510515, Guangdong, China; Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA.
| | - Aimin Ji
- Department of Pharmacy, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, Guangdong, China; Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, Guangdong, China; Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China.
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48
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Haraszti RA, Miller R, Didiot MC, Biscans A, Alterman JF, Hassler MR, Roux L, Echeverria D, Sapp E, DiFiglia M, Aronin N, Khvorova A. Optimized Cholesterol-siRNA Chemistry Improves Productive Loading onto Extracellular Vesicles. Mol Ther 2018; 26:1973-1982. [PMID: 29937418 DOI: 10.1016/j.ymthe.2018.05.024] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 05/27/2018] [Accepted: 05/30/2018] [Indexed: 01/01/2023] Open
Abstract
Extracellular vesicles are promising delivery vesicles for therapeutic RNAs. Small interfering RNA (siRNA) conjugation to cholesterol enables efficient and reproducible loading of extracellular vesicles with the therapeutic cargo. siRNAs are typically chemically modified to fit an application. However, siRNA chemical modification pattern has not been specifically optimized for extracellular vesicle-mediated delivery. Here we used cholesterol-conjugated, hydrophobically modified asymmetric siRNAs (hsiRNAs) to evaluate the effect of backbone, 5'-phosphate, and linker chemical modifications on productive hsiRNA loading onto extracellular vesicles. hsiRNAs with a combination of 5'-(E)-vinylphosphonate and alternating 2'-fluoro and 2'-O-methyl backbone modifications outperformed previously used partially modified siRNAs in extracellular vesicle-mediated Huntingtin silencing in neurons. Between two commercially available linkers (triethyl glycol [TEG] and 2-aminobutyl-1-3-propanediol [C7]) widely used to attach cholesterol to siRNAs, TEG is preferred compared to C7 for productive exosomal loading. Destabilization of the linker completely abolished silencing activity of loaded extracellular vesicles. The loading of cholesterol-conjugated siRNAs was saturated at ∼3,000 siRNA copies per extracellular vesicle. Overloading impaired the silencing activity of extracellular vesicles. The data reported here provide an optimization scheme for the successful use of hydrophobic modification as a strategy for productive loading of RNA cargo onto extracellular vesicles.
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Affiliation(s)
- Reka Agnes Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marie-Cecile Didiot
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ellen Sapp
- Mass General Institute for Neurodegenerative Disease, Boston, MA, USA
| | - Marian DiFiglia
- Mass General Institute for Neurodegenerative Disease, Boston, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
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Craig K, Abrams M, Amiji M. Recent preclinical and clinical advances in oligonucleotide conjugates. Expert Opin Drug Deliv 2018; 15:629-640. [PMID: 29727206 DOI: 10.1080/17425247.2018.1473375] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Oligonucleotide therapeutics have the potential to change the way disease is treated due to their ability to modulate gene expression of any therapeutic target in a highly specific and potent manner. Unfortunately, this drug class is plagued with inherently poor pharmacological characteristics, which need to be overcome. The development of a chemical modification library for oligonucleotides has addressed many of the initial challenges, but delivery of these payloads across plasma membranes remains difficult. The latest technological advances in oligonucleotide therapeutics utilizes direct conjugation to targeting ligands, which has improved bioavailability and target tissue exposure many-fold. The success of this approach has resulted in numerous clinical programs over the past 5 years. AREAS COVERED We review the literature on oligonucleotide conjugate strategies which have proven effective preclinically and clinically. We summarize the chemical modifications which allow parenteral administration as well as evaluate the efficacy of a multitude of conjugate approaches including lipids, peptides, carbohydrates, and antibodies. EXPERT OPINION The success of future conjugate strategies will likely rely on the effective combination of characteristics from earlier technologies. High-affinity ligand-receptor interactions can be critical to achieving meaningful accumulation in target tissues, but pharmacokinetic modulators which increase the circulating half-life may also be necessary. Synthesis of these approaches has the potential to bring the next breakthrough in oligonucleotide therapeutics.
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Affiliation(s)
- Kevin Craig
- a Department of Pharmaceutical Sciences , School of Pharmacy, Northeastern University , Boston , MA , USA.,b Department of Preclinical Development , Dicerna Pharmaceuticals, Inc , Cambridge , MA , USA
| | - Marc Abrams
- b Department of Preclinical Development , Dicerna Pharmaceuticals, Inc , Cambridge , MA , USA
| | - Mansoor Amiji
- a Department of Pharmaceutical Sciences , School of Pharmacy, Northeastern University , Boston , MA , USA
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50
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Reversal of siRNA-mediated gene silencing in vivo. Nat Biotechnol 2018; 36:509-511. [PMID: 29786096 DOI: 10.1038/nbt.4136] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022]
Abstract
We report rapid, potent reversal of GalNAc-siRNA-mediated RNA interference (RNAi) activity in vivo with short, synthetic, high-affinity oligonucleotides complementary to the siRNA guide strand. We found that 9-mers with five locked nucleic acids (LNAs) have the highest potency across several targets. Our modular, sequence-specific approach, named REVERSIR, may enhance the therapeutic profile of any long-acting GalNAc-siRNA (short interfering RNA) conjugate by enabling control of RNAi pharmacology.
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