1
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Androsavich JR. Frameworks for transformational breakthroughs in RNA-based medicines. Nat Rev Drug Discov 2024; 23:421-444. [PMID: 38740953 DOI: 10.1038/s41573-024-00943-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
RNA has sparked a revolution in modern medicine, with the potential to transform the way we treat diseases. Recent regulatory approvals, hundreds of new clinical trials, the emergence of CRISPR gene editing, and the effectiveness of mRNA vaccines in dramatic response to the COVID-19 pandemic have converged to create tremendous momentum and expectation. However, challenges with this relatively new class of drugs persist and require specialized knowledge and expertise to overcome. This Review explores shared strategies for developing RNA drug platforms, including layering technologies, addressing common biases and identifying gaps in understanding. It discusses the potential of RNA-based therapeutics to transform medicine, as well as the challenges associated with improving applicability, efficacy and safety profiles. Insights gained from RNA modalities such as antisense oligonucleotides (ASOs) and small interfering RNAs are used to identify important next steps for mRNA and gene editing technologies.
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Affiliation(s)
- John R Androsavich
- RNA Accelerator, Pfizer Inc, Cambridge, MA, USA.
- Ginkgo Bioworks, Boston, MA, USA.
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2
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Genna V, Reyes-Fraile L, Iglesias-Fernandez J, Orozco M. Nucleic acids in modern molecular therapies: A realm of opportunities for strategic drug design. Curr Opin Struct Biol 2024; 87:102838. [PMID: 38759298 DOI: 10.1016/j.sbi.2024.102838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/10/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
RNA vaccines have made evident to society what was already known by the scientific community: nucleic acids will be the "drugs of the future." By modifying the genome, interfering in transcription or translation, and by introducing new catalysts into the cell or by mimicking antibody effects, nucleic acids can generate therapeutic activities that are not accessible by any other therapeutic agents. There are, however, challenges that need to be solved in the next few years to make nucleic acids usable in a wide range of therapeutic scenarios. This review illustrates how simulation methods can help achieve this goal.
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Affiliation(s)
- Vito Genna
- NBD|Nostrum Biodiscovery, Josep Tarradellas 8-10, Barcelona 08019, Spain. https://twitter.com/_VitoGenna_
| | - Laura Reyes-Fraile
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain; Sixfold Bioscience Ltd, Translational & Innovation Hub, 84 Wood Ln, London W12 0BZ, United Kingdom
| | | | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain; Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain.
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3
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Zhang J, Chen M, Jiang H, Sun H, Ren J, Yang X, Liu S, Wang D, Liu J, Ma D, Guo X, Luo G. Atom-Modified gDNA Enhances Cleavage Activity of TtAgo Enabling Ultra-Sensitive Nucleic Acid Testing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403120. [PMID: 38728591 DOI: 10.1002/advs.202403120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/02/2024] [Indexed: 05/12/2024]
Abstract
The DNA-guided (gDNA) Argonaute from Thermus thermophilus (TtAgo) has little potential for nucleic acid detection and gene editing due to its poor dsDNA cleavage activity at relatively low temperature. Herein, the dsDNA cleavage activity of TtAgo is enhanced by using 2'-fluorine (2'F)-modified gDNA and developes a novel nucleic acid testing strategy. This study finds that the gDNA with 2'F-nucleotides at the 3'-end (2'F-gDNA) can promote the assembly of the TtAgo-guide-target ternary complex significantly by increasing its intermolecular force to target DNA and TtAgo, thereby providing ≈40-fold activity enhancement and decreasing minimum reaction temperature from 65 to 60°C. Based on this outstanding advance, a novel nucleic acid testing strategy is proposed, termed FAST, which is performed by using the 2'F-gDNA/TtAgo for target recognition and combining it with Bst DNA polymerase for nucleic acid amplification. By integrating G-quadruplex and Thioflavin T, the FAST assay achieves one-pot real-time fluorescence analysis with ultra-sensitivity, providing a limit of detection up to 5 copies (20 µL reaction mixture) for miR-21 detection. In summary, an atom-modification-based strategy has been developed for enhancing the cleavage activity of TtAgo efficiently, thereby improving its practicability and establishing a TtAgo-based nucleic acid testing technology with ultra-sensitivity and high-specificity.
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Affiliation(s)
- Jun Zhang
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Miaomiao Chen
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Huan Jiang
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Huifang Sun
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Jianing Ren
- Department of Oncology & Department of Rheumatology and Immunology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Xin Yang
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Shanshan Liu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Cancer Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Jianping Liu
- Department of Oncology & Department of Rheumatology and Immunology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Daiyuan Ma
- Department of Oncology & Department of Rheumatology and Immunology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Guangcheng Luo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
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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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Chernikov IV, Bachkova IK, Sen’kova AV, Meschaninova MI, Savin IA, Vlassov VV, Zenkova MA, Chernolovskaya EL. Cholesterol-Modified Anti-Il6 siRNA Reduces the Severity of Acute Lung Injury in Mice. Cells 2024; 13:767. [PMID: 38727303 PMCID: PMC11083178 DOI: 10.3390/cells13090767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Small interfering RNA (siRNA) holds significant therapeutic potential by silencing target genes through RNA interference. Current clinical applications of siRNA have been primarily limited to liver diseases, while achievements in delivery methods are expanding their applications to various organs, including the lungs. Cholesterol-conjugated siRNA emerges as a promising delivery approach due to its low toxicity and high efficiency. This study focuses on developing a cholesterol-conjugated anti-Il6 siRNA and the evaluation of its potency for the potential treatment of inflammatory diseases using the example of acute lung injury (ALI). The biological activities of different Il6-targeted siRNAs containing chemical modifications were evaluated in J774 cells in vitro. The lead cholesterol-conjugated anti-Il6 siRNA after intranasal instillation demonstrated dose-dependent therapeutic effects in a mouse model of ALI induced by lipopolysaccharide (LPS). The treatment significantly reduced Il6 mRNA levels, inflammatory cell infiltration, and the severity of lung inflammation. IL6 silencing by cholesterol-conjugated siRNA proves to be a promising strategy for treating inflammatory diseases, with potential applications beyond the lungs.
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Affiliation(s)
- Ivan V. Chernikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Irina K. Bachkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, Pirogova Str., 1, 630090 Novosibirsk, Russia
| | - Aleksandra V. Sen’kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Innokenty A. Savin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Valentin V. Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Marina A. Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Elena L. Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
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6
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Hayashi J, Ochi Y, Senpuku K, Wada SI, Wada F, Harada-Shiba M, Urata H. Rational design of prodrug-type apoB-targeted siRNA for nuclease resistance improvement without compromising gene silencing potency. Bioorg Med Chem 2024; 104:117693. [PMID: 38552598 DOI: 10.1016/j.bmc.2024.117693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
Synthetic siRNA molecules without chemical modifications are easily degraded in the body, and 2'-O-modifications are frequently introduced to enhance stability. However, such chemical modifications tend to impact the gene knockdown potency of siRNA negatively. To circumvent this problem, we previously developed a prodrug-type siRNA bearing 2'-O-methyldithiomethyl (MDTM) groups, which can be converted into unmodified siRNA under the reductive environment in cells. In this study, we developed a nuclease-resistant prodrug-type 2'-O-MDTM siRNA for deployment in future animal experiments. To rationally design siRNA modified with a minimal number of 2'-O-MDTM nucleotide residues, we identified the sites susceptible to nuclease digestion and tolerant to 2'-O-methyl (2'-OMe) modification in the antisense strand of apolipoprotein B-targeted siRNA. Subsequently, we optimized the positions where the 2'-OMe and 2'-O-MDTM groups should be incorporated. siRNA bearing the 2'-O-MDTM and 2'-OMe groups at their respective optimized positions exhibited efficient knockdown potency in vitro and enhanced stability in serum.
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Affiliation(s)
- Junsuke Hayashi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
| | - Yosuke Ochi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Kota Senpuku
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Shun-Ichi Wada
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Fumito Wada
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Mariko Harada-Shiba
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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7
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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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8
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Wang J, Tian F, Cao L, Du R, Tong J, Ding X, Yuan Y, Wang C. Macrophage polarization in spinal cord injury repair and the possible role of microRNAs: A review. Heliyon 2023; 9:e22914. [PMID: 38125535 PMCID: PMC10731087 DOI: 10.1016/j.heliyon.2023.e22914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
The prevention, treatment, and rehabilitation of spinal cord injury (SCI) have always posed significant medical challenges. After mechanical injury, disturbances in microcirculation, edema formation, and the generation of free radicals lead to additional damage, impeding effective repair processes and potentially exacerbating further dysfunction. In this context, inflammatory responses, especially the activation of macrophages, play a pivotal role. Different phenotypes of macrophages have distinct effects on inflammation. Activation of classical macrophage cells (M1) promotes inflammation, while activation of alternative macrophage cells (M2) inhibits inflammation. The polarization of macrophages is crucial for disease healing. A non-coding RNA, known as microRNA (miRNA), governs the polarization of macrophages, thereby reducing inflammation following SCI and facilitating functional recovery. This study elucidates the inflammatory response to SCI, focusing on the infiltration of immune cells, specifically macrophages. It examines their phenotype and provides an explanation of their polarization mechanisms. Finally, this paper introduces several well-known miRNAs that contribute to macrophage polarization following SCI, including miR-155, miR-130a, and miR-27 for M1 polarization, as well as miR-22, miR-146a, miR-21, miR-124, miR-223, miR-93, miR-132, and miR-34a for M2 polarization. The emphasis is placed on their potential therapeutic role in SCI by modulating macrophage polarization, as well as the present developments and obstacles of miRNA clinical therapy.
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Affiliation(s)
- Jiawei Wang
- School and Hospital of Stomatology, Shanxi Medical University, Shanxi Taiyuan, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Taiyuan, China
| | - Feng Tian
- School and Hospital of Stomatology, Shanxi Medical University, Shanxi Taiyuan, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Taiyuan, China
| | - Lili Cao
- School and Hospital of Stomatology, Shanxi Medical University, Shanxi Taiyuan, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Taiyuan, China
| | - Ruochen Du
- Experimental Animal Center, Shanxi Medical University, Shanxi Taiyuan, China
| | - Jiahui Tong
- School and Hospital of Stomatology, Shanxi Medical University, Shanxi Taiyuan, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Taiyuan, China
| | - Xueting Ding
- Experimental Animal Center, Shanxi Medical University, Shanxi Taiyuan, China
| | - Yitong Yuan
- Experimental Animal Center, Shanxi Medical University, Shanxi Taiyuan, China
| | - Chunfang Wang
- School and Hospital of Stomatology, Shanxi Medical University, Shanxi Taiyuan, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Taiyuan, China
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9
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Matsuda S, Bala S, Liao JY, Datta D, Mikami A, Woods L, Harp JM, Gilbert JA, Bisbe A, Manoharan RM, Kim M, Theile CS, Guenther DC, Jiang Y, Agarwal S, Maganti R, Schlegel MK, Zlatev I, Charisse K, Rajeev KG, Castoreno A, Maier M, Janas MM, Egli M, Chaput JC, Manoharan M. Shorter Is Better: The α-(l)-Threofuranosyl Nucleic Acid Modification Improves Stability, Potency, Safety, and Ago2 Binding and Mitigates Off-Target Effects of Small Interfering RNAs. J Am Chem Soc 2023; 145:19691-19706. [PMID: 37638886 DOI: 10.1021/jacs.3c04744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Chemical modifications are necessary to ensure the metabolic stability and efficacy of oligonucleotide-based therapeutics. Here, we describe analyses of the α-(l)-threofuranosyl nucleic acid (TNA) modification, which has a shorter 3'-2' internucleotide linkage than the natural DNA and RNA, in the context of small interfering RNAs (siRNAs). The TNA modification enhanced nuclease resistance more than 2'-O-methyl or 2'-fluoro ribose modifications. TNA-containing siRNAs were prepared as triantennary N-acetylgalactosamine conjugates and were tested in cultured cells and mice. With the exceptions of position 2 of the antisense strand and position 11 of the sense strand, the TNA modification did not inhibit the activity of the RNA interference machinery. In a rat toxicology study, TNA placed at position 7 of the antisense strand of the siRNA mitigated off-target effects, likely due to the decrease in the thermodynamic binding affinity relative to the 2'-O-methyl residue. Analysis of the crystal structure of an RNA octamer with a single TNA on each strand showed that the tetrose sugar adopts a C4'-exo pucker. Computational models of siRNA antisense strands containing TNA bound to Argonaute 2 suggest that TNA is well accommodated in the region kinked by the enzyme. The combined data indicate that the TNA nucleotides are promising modifications expected to increase the potency, duration of action, and safety of siRNAs.
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Affiliation(s)
- Shigeo Matsuda
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Saikat Bala
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3958, United States
| | - Jen-Yu Liao
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3958, United States
| | - Dhrubajyoti Datta
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Atsushi Mikami
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Lauren Woods
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Joel M Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232-0146, United States
| | - Jason A Gilbert
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Anna Bisbe
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - MaryBeth Kim
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Christopher S Theile
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Dale C Guenther
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Saket Agarwal
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Rajanikanth Maganti
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Mark K Schlegel
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | | | - Adam Castoreno
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Martin Maier
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Maja M Janas
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232-0146, United States
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3958, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
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10
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Koyasu K, Chandela A, Ueno Y. Non-terminal conjugation of small interfering RNAs with spermine improves duplex binding and serum stability with position-specific incorporation. RSC Adv 2023; 13:25169-25181. [PMID: 37622021 PMCID: PMC10445083 DOI: 10.1039/d3ra04918c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023] Open
Abstract
The conjugation of small interfering RNAs (siRNAs) has been studied using lipid and ligand conjugates for efficient delivery. However, most conjugates have been inserted at the terminal position; very few have been inserted at non-terminal positions. Herein, we synthesized a 4'-C-propyllevulinate-2'-O-methyluridine analog for non-terminal conjugation of spermine into the passenger strand of siRNA. Solid-phase oligonucleotide synthesis using this analog was successful, with the conjugation of one or two spermine molecules. The siRNAs conjugated with spermine displayed improved thermodynamic stability and resistance against nucleases, which depended on the site of conjugation in each case. Circular dichroism spectroscopy revealed that the A-type helical structure of the RNA duplex was not altered by these modifications. However, the gene-silencing activity of conjugated siRNAs was reduced and further decreased when the number of spermine molecules was increased. Hence, this work supplies valuable information and provides scope for the further development of drug-delivery systems through non-terminal conjugation.
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Affiliation(s)
- Keisuke Koyasu
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University Japan +81-58-293-2919 +81-58-293-2919
| | - Akash Chandela
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University Japan
| | - Yoshihito Ueno
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University Japan +81-58-293-2919 +81-58-293-2919
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University Japan
- United Graduate School of Agricultural Science, Gifu University 1-1 Yanagido Gifu 501-1193 Japan
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11
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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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12
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Sato H, Chandela A, Ueno Y. Synthesis and characterization of novel (S)-5'-C-aminopropyl-2'-fluorouridine modified oligonucleotides as therapeutic siRNAs. Bioorg Med Chem 2023; 87:117317. [PMID: 37196425 DOI: 10.1016/j.bmc.2023.117317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023]
Abstract
The lack of stability of natural nucleosides limits their application in small interfering RNA (siRNA)-mediated RNA interference (RNAi). Various chemical modifications have been reported to improve their pharmacokinetic behavior; however, the development of potential candidates is still underway. In this study, we designed and synthesized (S)-5'-C-aminopropyl-2'-fluorouridine (5'-AP-2'-FU) and evaluated the properties of siRNAs containing this analog. A comparative thermodynamic study revealed the enhanced thermal stability of double-stranded RNAs (dsRNAs) containing 5'-AP-2'-FU in a position-specific manner, whereas (S)-5'-C-aminopropyl-2'-O-methyluridine (5'-AP-2'-MoU)-modified dsRNAs exhibited lower melting temperatures. This improved thermal stability of RNA duplexes is attributed to favorable entropy loss, which induces the duplex into an N-type (C3'-endo) conformation and enhances duplex binding in this case. The 5'-AP-2'-FU analog was also suitable for incorporation into the passenger strand to induce gene-silencing activity. Gene knockdown efficacy was comparable to that of unmodified siRNAs, and the best response was observed by introducing 5'-AP-2'-FU near the 3'-terminal end of the passenger strand. In addition, the single-stranded RNAs (ssRNAs) modified with 5'-AP-2'-FU showed strong resistance against decomposition by nucleases when treated with buffer containing bovine serum, which was similar to 5'-AP-2'-MoU.
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Affiliation(s)
- Hitotaka Sato
- United Graduate School of Agricultural Science, Gifu University, Japan
| | - Akash Chandela
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Japan
| | - Yoshihito Ueno
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Japan; Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Japan; United Graduate School of Agricultural Science, Gifu University, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University Institute for Advanced Study, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
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13
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Egli M, Schlegel MK, Manoharan M. Acyclic ( S)-glycol nucleic acid ( S-GNA) modification of siRNAs improves the safety of RNAi therapeutics while maintaining potency. RNA (NEW YORK, N.Y.) 2023; 29:402-414. [PMID: 36725319 PMCID: PMC10019370 DOI: 10.1261/rna.079526.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Glycol nucleic acid (GNA) is an acyclic nucleic acid analog connected via phosphodiester bonds. Crystal structures of RNA-GNA chimeric duplexes indicated that nucleotides of the right-handed (S)-GNA were better accommodated in the right-handed RNA duplex than were the left-handed (R)-isomers. GNA nucleotides adopt a rotated nucleobase orientation within all duplex contexts, pairing with complementary RNA in a reverse Watson-Crick mode, which explains the inabilities of GNA C and G to form strong base pairs with complementary nucleotides. Transposition of the hydrogen bond donor and acceptor pairs using novel (S)-GNA isocytidine and isoguanosine nucleotides resulted in stable base-pairing with the complementary G and C ribonucleotides, respectively. GNA nucleotide or dinucleotide incorporation into an oligonucleotide increased resistance against 3'-exonuclease-mediated degradation. Consistent with the structural observations, small interfering RNAs (siRNAs) modified with (S)-GNA had greater in vitro potencies than identical sequences containing (R)-GNA. (S)-GNA is well tolerated in the seed regions of antisense and sense strands of a GalNAc-conjugated siRNA in vitro. The siRNAs containing a GNA base pair in the seed region had in vivo potency when subcutaneously injected into mice. Importantly, seed pairing destabilization resulting from a single GNA nucleotide at position 7 of the antisense strand mitigated RNAi-mediated off-target effects in a rodent model. Two GNA-modified siRNAs have shown an improved safety profile in humans compared with their non-GNA-modified counterparts, and several additional siRNAs containing the GNA modification are currently in clinical development.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Mark K Schlegel
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, USA
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14
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Hofmeister A, Jahn-Hofmann K, Brunner B, Helms M, Metz-Weidmann C, Krack A, Kurz M, Heubel C, Scheidler S. Small Interfering RNAs Containing Dioxane- and Morpholino-Derived Nucleotide Analogues Show Improved Off-Target Profiles and Chirality-Dependent In Vivo Knock-Down. J Med Chem 2022; 65:13736-13752. [PMID: 36223135 DOI: 10.1021/acs.jmedchem.2c00873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To expand the applicability of recently developed dioxane- and morpholino-based nucleotide analogues, their seed region destabilizing properties in small interfering RNAs (siRNAs) were investigated in order to improve potential off-target profiles. For this purpose, the corresponding adenosine analogues were synthesized in two diastereomeric series as building blocks for the automated oligonucleotide synthesis. The obtained nucleotide precursors were integrated at position 7 of an siRNA antisense strand, targeting transthyretin messenger RNA. Evaluation of the melting temperatures revealed significant differences in the obtained duplex stabilities between the two diastereomeric series, while the influence of the central scaffold was small. All siRNAs containing these novel nucleotide structures showed improved off-target profiles in vitro compared to their parent sequence with the common 2'-OMe-modified adenosine at the same position. In contrast, in vivo potencies were highly dependent on the chirality within the six-membered nucleotide scaffolds and showed high mRNA downregulations for the (2R,6R)-configured diastereomers.
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Affiliation(s)
- Armin Hofmeister
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | | | - Bodo Brunner
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Mike Helms
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | | | - Arne Krack
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Michael Kurz
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Christoph Heubel
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Sabine Scheidler
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
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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: 14] [Impact Index Per Article: 7.0] [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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Lisitskaya L, Shin Y, Agapov A, Olina A, Kropocheva E, Ryazansky S, Aravin AA, Esyunina D, Murakami KS, Kulbachinskiy A. Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity. Nat Commun 2022; 13:4624. [PMID: 35941106 PMCID: PMC9360449 DOI: 10.1038/s41467-022-32079-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 12/26/2022] Open
Abstract
Argonaute proteins are programmable nucleases that have defense and regulatory functions in both eukaryotes and prokaryotes. All known prokaryotic Argonautes (pAgos) characterized so far act on DNA targets. Here, we describe a new class of pAgos that uniquely use DNA guides to process RNA targets. The biochemical and structural analysis of Pseudooceanicola lipolyticus pAgo (PliAgo) reveals an unusual organization of the guide binding pocket that does not rely on divalent cations and the canonical set of contacts for 5'-end interactions. Unconventional interactions of PliAgo with the 5'-phosphate of guide DNA define its new position within pAgo and shift the site of target RNA cleavage in comparison with known Argonautes. The specificity for RNA over DNA is defined by ribonucleotide residues at the cleavage site. The analysed pAgos sense mismatches and modifications in the RNA target. The results broaden our understanding of prokaryotic defense systems and extend the spectrum of programmable nucleases with potential use in RNA technology.
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Affiliation(s)
- Lidiya Lisitskaya
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yeonoh Shin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Aleksei Agapov
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Ekaterina Kropocheva
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Sergei Ryazansky
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia.
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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17
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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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18
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Rozners E. Chemical Modifications of CRISPR RNAs to Improve Gene-Editing Activity and Specificity. J Am Chem Soc 2022; 144:12584-12594. [PMID: 35796760 DOI: 10.1021/jacs.2c02633] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CRISPR (clustered, regularly interspaced, short palindromic repeats) has become a cutting-edge research method and holds great potential to revolutionize biotechnology and medicine. However, like other nucleic acid technologies, CRISPR will greatly benefit from chemical innovation to improve activity and specificity for critical in vivo applications. Chemists have started optimizing various components of the CRISPR system; the present Perspective focuses on chemical modifications of CRISPR RNAs (crRNAs). As with other nucleic acid-based technologies, early efforts focused on well-established sugar and backbone modifications (2'-deoxy, 2'-F, 2'-OMe, and phosphorothioates). Some more significant alterations of crRNAs have been done using bicyclic (locked) riboses and phosphate backbone replacements (phosphonoacetates and amides); however, the range of chemical innovation applied to crRNAs remains limited to modifications that have been successful in RNA interference and antisense technologies. The encouraging results given by these tried-and-true modifications suggest that, going forward, chemists should take a bolder approach─research must aim to investigate what chemistry will have the most impact on maturing CRISPR as therapeutic and other in vivo technologies. With an eye to the future, this Perspective argues that the complexity of CRISPR presents rich unprecedented opportunities for chemists to synergize advances in synthetic methodology and structural biochemistry to rationally optimize crRNA-protein interactions.
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Affiliation(s)
- Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
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19
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Fjelstrup S, Dupont DM, Bus C, Enghild J, Jensen J, Birkenkamp-Demtröder K, Dyrskjøt L, Kjems J. Differential RNA aptamer affinity profiling on plasma as a potential diagnostic tool for bladder cancer. NAR Cancer 2022; 4:zcac025. [PMID: 36004048 PMCID: PMC9394167 DOI: 10.1093/narcan/zcac025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/08/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
The molecular composition of blood is a signature of human health, reflected in the thousands of blood biomarkers known for human diseases. However, establishing robust disease markers is challenging due to the diversity of individual samples. New sequencing methods have simplified biomarker discovery for circulating DNA and RNA while protein profiling is still laborious and costly. To harness the power of high-throughput sequencing to profile the protein content of a biological sample, we developed a method termed APTASHAPE that uses oligonucleotide aptamers to recognize proteins in complex biofluids. We selected a large pool of 2′Fluoro protected RNA sequences to recognize proteins in human plasma and identified a set of 33 cancer-specific aptamers. Differential enrichment of these aptamers after selection against 1 μl of plasma from individual patients allowed us to differentiate between healthy controls and bladder cancer-diagnosed patients (91% accuracy) and between early non-invasive tumors and late stage tumors (83% accuracy). Affinity purification and mass spectrometry of proteins bound to the predictive aptamers showed the main target proteins to be C4b-binding protein, Complement C3, Fibrinogen, Complement factor H and IgG. The APTASHAPE method thus provides a general, automated and highly sensitive platform for discovering potential new disease biomarkers.
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Affiliation(s)
- Søren Fjelstrup
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark
| | - Daniel M Dupont
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark
| | - Claus Bus
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics (MBG), Aarhus University , Aarhus, Denmark
| | - Jørgen B Jensen
- Department of Urology, Aarhus University Hospital , Aarhus N, Denmark
- Department of Clinical medicine, Aarhus University , Aarhus, Denmark
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine, Aarhus University Hospital , Aarhus, Denmark
- Department of Clinical medicine, Aarhus University , Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital , Aarhus, Denmark
- Department of Clinical medicine, Aarhus University , Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark
- Department of Molecular Biology and Genetics (MBG), Aarhus University , Aarhus, Denmark
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20
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Holm A, Hansen SN, Klitgaard H, Kauppinen S. Clinical advances of RNA therapeutics for treatment of neurological and neuromuscular diseases. RNA Biol 2022; 19:594-608. [PMID: 35482908 PMCID: PMC9067473 DOI: 10.1080/15476286.2022.2066334] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
RNA therapeutics comprise a diverse group of oligonucleotide-based drugs such as antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), and short hairpin RNAs (shRNAs) that can be designed to selectively interact with drug targets currently undruggable with small molecule-based drugs or monoclonal antibodies. Furthermore, RNA-based therapeutics have the potential to modulate entire disease pathways, and thereby represent a new modality with unprecedented potential for generating disease-modifying drugs for a wide variety of human diseases, including central nervous system (CNS) disorders. Here, we describe different strategies for delivering RNA drugs to the CNS and review recent advances in clinical development of ASO drugs and siRNA-based therapeutics for the treatment of neurological diseases and neuromuscular disorders. Abbreviations 2’-MOE: 2’-O-(2-methoxyethyl); 2’-O-Me: 2’-O-methyl; 2’-F: 2’-fluoro; AD: Alzheimer's disease; ALS: Amyotrophic lateral sclerosis; ALSFRS-R: Revised Amyotrophic Lateral Sclerosis Functional Rating Scale; ARC: Antibody siRNA Conjugate; AS: Angelman Syndrome; ASGRP: Asialoglycoprotein receptor; ASO: Antisense oligonucleotide; AxD: Alexander Disease; BBB: Blood brain barrier; Bp: Basepair; CNM: Centronuclear myopathies; CNS: Central Nervous System; CPP: Cell-penetrating Peptide; CSF: Cerebrospinal fluid; DMD: Duchenne muscular dystrophy; DNA: Deoxyribonucleic acid; FAP: Familial amyloid polyneuropathy; FALS: Familial amyotrophic lateral sclerosis; FDA: The United States Food and Drug Administration; GalNAc: N-acetylgalactosamine; GoF: Gain of function; hATTR: Hereditary transthyretin amyloidosis; HD: Huntington's disease; HRQOL: health-related quality of life; ICV: Intracerebroventricular; IT: Intrathecal; LNA: Locked nucleic acid; LoF: Loss of function; mRNA: Messenger RNA; MS: Multiple Sclerosis; MSA: Multiple System Atrophy; NBE: New Biological Entity; NCE: New Chemical Entity; NHP: Nonhuman primate; nt: Nucleotide; PD: Parkinson's disease; PNP: Polyneuropathy; PNS: Peripheral nervous system; PS: Phosphorothioate; RISC: RNA-Induced Silencing Complex; RNA: Ribonucleic acid; RNAi: RNA interference; s.c.: Subcutaneous; siRNA: Small interfering RNA; SMA: Spinal muscular atrophy; SMN: Survival motor neuron; TTR: Transthyretin
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Affiliation(s)
- Anja Holm
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, A.C. Meyers Vænge 15, 2450 Copenhagen, Denmark
| | - Stine N Hansen
- Neumirna Therapeutics, A.C. Meyers Vænge 15, 2450 Copenhagen, Denmark
| | - Henrik Klitgaard
- Neumirna Therapeutics, A.C. Meyers Vænge 15, 2450 Copenhagen, Denmark
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, A.C. Meyers Vænge 15, 2450 Copenhagen, Denmark
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21
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Li Y, Du S, Jin H, He J. A combination of the modified catalytic core and conjugation of 3'-inverted deoxythymidine for a more efficient and nuclease-resistant 10-23 DNAzyme. Bioorg Med Chem Lett 2022; 62:128633. [PMID: 35189319 DOI: 10.1016/j.bmcl.2022.128633] [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: 11/29/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/02/2022]
Abstract
10-23 DNAzyme is a catalytic DNA molecule capable of cleaving complementary RNA. Its high cleavage efficiency is being pursued by chemical modifications, for realizing its genetic therapeutics potential. The most efficient and nuclease-resistant DNAzyme was obtained in this study combined two modifications - 7-aminopropyl-8-aza-7-deaza-2'-deoxyadenosine (residue 1) at A9 and 3'-inverted deoxythymidine residue (iT) at 3'-end. Moreover, this combinatorial modification could be a universal approach for designing efficient and enzyme-resistant 10-23 DNAzyme against other RNA targets, and the catalytic core-modification could be further combined with other recognition arm modifications for practical applications as genetic therapeutics and biosensor tools.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Shanshan Du
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Science, Peking University, Beijing 100191, China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
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22
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Pal S, Chandra G, Patel S, Singh S. Fluorinated Nucleosides: Synthesis, Modulation in Conformation and Therapeutic Application. CHEM REC 2022; 22:e202100335. [PMID: 35253973 DOI: 10.1002/tcr.202100335] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/22/2022] [Indexed: 12/17/2022]
Abstract
Over the last twenty years, fluorination on nucleoside has established itself as the most promising tool to use to get biologically active compounds that could sustain the clinical trial by affecting the pharmacodynamics and pharmacokinetic properties. Due to fluorine's inherent unique properties and its judicious introduction into the molecule, makes the corresponding nucleoside metabolically very stable, lipophilic, and opens a new site of intermolecular binding. Fluorination on various nucleosides has been extensively studied as a result, a series of fluorinated nucleosides come up for different therapeutic uses which are either approved by the FDA or under the advanced stage of the clinical trial. Here in this review, we are summarizing the latest development in the chemistry of fluorination on nucleoside that led to varieties of new analogs like carbocyclic, acyclic, and conformationally biased nucleoside and their biological properties, the influence of fluorine on conformation, oligonucleotide stability, and their use in therapeutics.
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Affiliation(s)
- Shantanu Pal
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
| | - Girish Chandra
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Samridhi Patel
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Sakshi Singh
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
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23
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Wang F, Li P, Chu HC, Lo PK. Nucleic Acids and Their Analogues for Biomedical Applications. BIOSENSORS 2022; 12:bios12020093. [PMID: 35200353 PMCID: PMC8869748 DOI: 10.3390/bios12020093] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 05/07/2023]
Abstract
Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.
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Affiliation(s)
- Fei Wang
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pan Li
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Hoi Ching Chu
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
- Correspondence:
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24
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Zhu G, Song P, Wu J, Luo M, Chen Z, Chen T. Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective. Front Bioeng Biotechnol 2022; 9:792489. [PMID: 35071205 PMCID: PMC8777461 DOI: 10.3389/fbioe.2021.792489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.
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Affiliation(s)
- Gan Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jing Wu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minglan Luo
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhipeng Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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25
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Bao Q, Ganbold T, Qiburi Q, Bao M, Han S, Baigude H. AMP functionalized curdlan nanoparticles as a siRNA carrier: Synthesis, characterization and targeted delivery via adenosine A 2B receptor. Int J Biol Macromol 2021; 193:866-873. [PMID: 34743942 DOI: 10.1016/j.ijbiomac.2021.10.138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022]
Abstract
Receptor-mediated endocytosis has been used for tissue targeted delivery of short interfering RNA (siRNA) drugs. Herein, we investigated adenosine receptor (AR) as a candidate for receptor-mediated siRNA internalization. We synthesized adenosine functionalized cationic curdlan derivatives (denote CuAMP polymers). One of these polymers, CuAMP4, efficiently delivered siRNA to breast cancer cells expressing high level of A2B receptor. The internalization of siRNA loaded CuAMP4 by cancer cells was inhibited by free AMP as well as endocytosis inhibitors. Moreover, knockdown of A2BR by siRNA, or pre-treatment of the cells with anti-A2BR antibody, strongly inhibited the cellular uptake of CuAMP4. Our findings confirmed that A2BR can be utilized for cell type specific siRNA delivery, and CuAMP4 NP may be a promising delivery system for cancer cell targeted delivery of therapeutic siRNAs.
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Affiliation(s)
- Qingming Bao
- Inner Mongolia Key Laboratory of Mongolian Medicinal Chemistry, School of Chemistry & Chemical Engineering, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China
| | - Tsogzolmaa Ganbold
- Inner Mongolia Key Laboratory of Mongolian Medicinal Chemistry, School of Chemistry & Chemical Engineering, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China.
| | - Qiburi Qiburi
- Inner Mongolia Key Laboratory of Mongolian Medicinal Chemistry, School of Chemistry & Chemical Engineering, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China
| | - Mingming Bao
- Inner Mongolia Key Laboratory of Mongolian Medicinal Chemistry, School of Chemistry & Chemical Engineering, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China
| | - Shuqin Han
- Inner Mongolia Key Laboratory of Mongolian Medicinal Chemistry, School of Chemistry & Chemical Engineering, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China.
| | - Huricha Baigude
- Inner Mongolia Key Laboratory of Mongolian Medicinal Chemistry, School of Chemistry & Chemical Engineering, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China.
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26
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Valero J, Civit L, Dupont DM, Selnihhin D, Reinert LS, Idorn M, Israels BA, Bednarz AM, Bus C, Asbach B, Peterhoff D, Pedersen FS, Birkedal V, Wagner R, Paludan SR, Kjems J. A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry. Proc Natl Acad Sci U S A 2021; 118:e2112942118. [PMID: 34876524 PMCID: PMC8685691 DOI: 10.1073/pnas.2112942118] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 12/23/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created an urgent need for new technologies to treat COVID-19. Here we report a 2'-fluoro protected RNA aptamer that binds with high affinity to the receptor binding domain (RBD) of SARS-CoV-2 spike protein, thereby preventing its interaction with the host receptor ACE2. A trimerized version of the RNA aptamer matching the three RBDs in each spike complex enhances binding affinity down to the low picomolar range. Binding mode and specificity for the aptamer-spike interaction is supported by biolayer interferometry, single-molecule fluorescence microscopy, and flow-induced dispersion analysis in vitro. Cell culture experiments using virus-like particles and live SARS-CoV-2 show that the aptamer and, to a larger extent, the trimeric aptamer can efficiently block viral infection at low concentration. Finally, the aptamer maintains its high binding affinity to spike from other circulating SARS-CoV-2 strains, suggesting that it could find widespread use for the detection and treatment of SARS-CoV-2 and emerging variants.
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Affiliation(s)
- Julián Valero
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark;
- Centre for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus DK-8000, Denmark
| | - Laia Civit
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
| | - Daniel M Dupont
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
| | - Denis Selnihhin
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Line S Reinert
- Department of Biomedicine, Aarhus University DK-8000 Aarhus, Denmark
| | - Manja Idorn
- Department of Biomedicine, Aarhus University DK-8000 Aarhus, Denmark
| | - Brett A Israels
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, DK-8000, Aarhus, Denmark
| | - Aleksandra M Bednarz
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, DK-8000, Aarhus, Denmark
| | - Claus Bus
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
| | - Benedikt Asbach
- Institute of Medical Microbiology and Hygiene/Molecular Microbiology (Virology), Regensburg University 93053 Regensburg, Germany
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene/Molecular Microbiology (Virology), Regensburg University 93053 Regensburg, Germany
| | - Finn S Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, DK-8000, Aarhus, Denmark
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene/Molecular Microbiology (Virology), Regensburg University 93053 Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg 93053, Germany
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University DK-8000 Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark;
- Centre for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus DK-8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
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27
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Zhu Y, Li Z, Song W, Khan MA, Li H. Conformation Locking of the Pentose Ring in Nucleotide Monophosphate Coordination Polymers via π-π Stacking and Metal-Ion Coordination. Inorg Chem 2021; 61:818-829. [PMID: 34856096 DOI: 10.1021/acs.inorgchem.1c02356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The conformation of the pentose ring in nucleotides is extremely important and a basic problem in biochemistry and pharmaceutical chemistry. In this study, we used a strategy to regulate the conformation of pentose rings of nucleotides via the synergistic effect of metal-ion coordination and π-π stacking. Seven types of coordination complexes were developed and characterized using Fourier transform infrared spectroscopy, elemental analysis, thermogravimetric analysis, powder X-ray diffraction, ultraviolet-visible spectroscopy, 1H nuclear magnetic resonance spectroscopy, electrospray ionization mass spectrometry, and single-crystal X-ray diffraction. On the basis of two conformational parameters obtained from single-crystal structure analysis, i.e., the pseudorotation phase angle and degree of puckering, the exact conformation of the furanose ring in these coordination polymers was unequivocally determined. Crystallographic studies demonstrate that a short bridging ligand (4,4'-bipyridine) is conducive to the formation of a twist form, and long auxiliary ligands [1,2-bis(4-pyridyl)ethene and 4,4'-azopyridine] induce the formation of an envelope conformation. However, the longest auxiliary ligands [1,4-bis(4-pyridyl)-2,3-diaza-1,3-butadiene] cannot limit the flexibility of a nucleotide. Our results demonstrated that the proposed strategy is universal and controllable. Moreover, the chirality of these coordination polymers was examined by combining the explanation of their crystal structures with solid-state circular dichroism spectroscopy measurements.
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Affiliation(s)
- Yanhong Zhu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Zhongkui Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Wenjing Song
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Maroof Ahmad Khan
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Hui Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, P. R. China
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28
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Teng H, Wu Z, Wang Z, Jin Z, Yang Y, Jin Q. Site-directed mutation of purine nucleoside phosphorylase for synthesis of 2'-deoxy-2'-fluoroadenosine. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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Hunter WB, Wintermantel WM. Optimizing Efficient RNAi-Mediated Control of Hemipteran Pests (Psyllids, Leafhoppers, Whitefly): Modified Pyrimidines in dsRNA Triggers. PLANTS 2021; 10:plants10091782. [PMID: 34579315 PMCID: PMC8472347 DOI: 10.3390/plants10091782] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 01/09/2023]
Abstract
The advantages from exogenously applied RNAi biopesticides have yet to be realized in through commercialization due to inconsistent activity of the dsRNA trigger, and the activity level of RNAi suppression. This has prompted research on improving delivery methods for applying exogenous dsRNA into plants and insects for the management of pests and pathogens. Another aspect to improve RNAi activity is the incorporation of modified 2′-F pyrimidine nucleotides into the dsRNA trigger. Modified dsRNA incorporating 32–55% of the 2′-F- nucleotides produced improved RNAi activity that increased insect mortality by 12–35% greater than non-modified dsRNA triggers of the same sequence. These results were repeatable across multiple Hemiptera: the Asian citrus psyllid (Diaphorina citri, Liviidae); whitefly (Bemisia tabaci, Aleyroididae); and the glassy-winged sharpshooter (Homalodisca vitripennis, Cicadellidae). Studies using siRNA with modified 2′-F- pyrimidines in mammalian cells show they improved resistance to degradation from nucleases, plus result in greater RNAi activity, due to increase concentrations and improved binding affinity to the mRNA target. Successful RNAi biopesticides of the future will be able to increase RNAi repeatability in the field, by incorporating modifications of the dsRNA, such as 2′-F- pyrimidines, that will improve delivery after applied to fruit trees or crop plants, with increased activity after ingestion by insects. Costs of RNA modification have decreased significantly over the past few years such that biopesticides can now compete on pricing with commercial chemical products.
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Affiliation(s)
- Wayne Brian Hunter
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture, Agriculture Research Service, Subtropical Insects Res., Fort Pierce, FL 34945, USA
- Correspondence:
| | - William M. Wintermantel
- U.S. Department of Agriculture, Agriculture Research Service, Crop Improvement and Protection Research, Salinas, CA 93905, USA;
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30
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Bibby G, Krasniqi B, Reddy I, Sekar D, Ross K. Capturing the RNA castle: Exploiting MicroRNA inhibition for wound healing. FEBS J 2021; 289:5137-5151. [PMID: 34403569 DOI: 10.1111/febs.16160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/14/2021] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
The growing pipelines of RNA-based therapies herald new opportunities to deliver better patient outcomes for complex disorders such as chronic nonhealing wounds associated with diabetes. Members of the microRNA (miRNA) family of small noncoding RNAs have emerged as targets for diverse elements of cutaneous wound repair, and both miRNA enhancement with mimics or inhibition with antisense oligonucleotides represent tractable approaches for miRNA-directed wound healing. In this review, we focus on miRNA inhibition strategies to stimulate skin repair given advances in chemical modifications to enhance the performance of antisense miRNA (anti-miRs). We first explore miRNAs whose inhibition in keratinocytes promotes keratinocyte migration, an essential part of re-epithelialisation during wound repair. We then focus on miRNAs that can be targeted for inhibition in endothelial cells to promote neovascularisation for wound healing in the context of diabetic mouse models. The picture that emerges is that direct comparisons of different anti-miRNAs modifications are required to establish the most translationally viable options in the chronic wound environment, that direct comparisons of the impact of inhibition of different miRNAs are needed to quantify and rank their relative efficacies in promoting wound repair, and that a standardised human ex vivo model of the diabetic wound is needed to reduce reliance on mouse models that do not necessarily enhance mechanistic understanding of miRNA-targeted wound healing.
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Affiliation(s)
- George Bibby
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - Blerta Krasniqi
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - Izaak Reddy
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - Durairaj Sekar
- Dental Research Cell and Biomedical Research Unit (DRC-BRULAC), Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Science (SIMATS), Saveetha University, Chennai, India
| | - Kehinde Ross
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
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31
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Murray JK, Long J, Liu L, Singh S, Pruitt D, Ollmann M, Swearingen E, Hardy M, Homann O, Wu B, Holder JR, Sham K, Herberich B, Lo MC, Dou H, Shkumatov A, Florio M, Rulifson IC. Identification and Optimization of a Minor Allele-Specific Small Interfering RNA to Prevent PNPLA3 I148M-Driven Nonalcoholic Fatty Liver Disease. Nucleic Acid Ther 2021; 31:324-340. [PMID: 34297902 DOI: 10.1089/nat.2021.0026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human genome wide association studies confirm the association of the rs738409 single nucleotide polymorphism (SNP) in the gene encoding protein patatin like phospholipase domain containing 3 (PNPLA3) with nonalcoholic fatty liver disease (NAFLD); the presence of the resulting mutant PNPLA3 I148M protein is a driver of nonalcoholic steatohepatitis (NASH). While Pnpla3-deficient mice do not display an adverse phenotype, the safety of knocking down endogenous wild type PNPLA3 in humans remains unknown. To expand the scope of a potential targeted NAFLD therapeutic to both homozygous and heterozygous PNPLA3 rs738409 populations, we sought to identify a minor allele-specific small interfering RNA (siRNA). Limiting our search to SNP-spanning triggers, a series of chemically modified siRNA were tested in vitro for activity and selectivity toward PNPLA3 rs738409 mRNA. Conjugation of the siRNA to a triantennary N-acetylgalactosamine (GalNAc) ligand enabled in vivo screening using adeno-associated virus to overexpress human PNPLA3I148M versus human PNPLA3I148I in mouse livers. Structure-activity relationship optimization yielded potent and minor allele-specific compounds that achieved high levels of mRNA and protein knockdown of human PNPLA3I148M but not PNPLA3I148I. Testing of the minor allele-specific siRNA in PNPLA3I148M-expressing mice fed a NASH-inducing diet prevented PNPLA3I148M-driven disease phenotypes, thus demonstrating the potential of a precision medicine approach to treating NAFLD.
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Affiliation(s)
- Justin K Murray
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Jason Long
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Lei Liu
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
| | - Shivani Singh
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
| | - Danielle Pruitt
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
| | - Michael Ollmann
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Elissa Swearingen
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Miki Hardy
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Oliver Homann
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Bin Wu
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Jerry Ryan Holder
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Kelvin Sham
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Brad Herberich
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Mei-Chu Lo
- Therapeutic Discovery, Amgen Research, South San Francisco, California, USA
| | - Hui Dou
- Therapeutic Discovery, Amgen Research, South San Francisco, California, USA
| | - Artem Shkumatov
- Translational Safety and Bioanalytical Sciences, Amgen Research, South San Francisco, California, USA
| | - Monica Florio
- Cardiometabolic Disorders, Amgen Research, Thousand Oaks, California, USA
| | - Ingrid C Rulifson
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
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32
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Mattelaer CA, Mattelaer HP, Rihon J, Froeyen M, Lescrinier E. Efficient and Accurate Potential Energy Surfaces of Puckering in Sugar-Modified Nucleosides. J Chem Theory Comput 2021; 17:3814-3823. [PMID: 34000809 DOI: 10.1021/acs.jctc.1c00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Puckering of the sugar unit in nucleosides and nucleotides is an important structural aspect that directly influences the helical structure of nucleic acids. The preference for specific puckering modes in nucleic acids can be analyzed via in silico conformational analysis, but the large amount of conformations and the accuracy of the analysis leads to an extensive amount of computational time. In this paper, we show that the combination of geometry optimizations with the HF-3c method with single point energies at the RI-MP2 level results in accurate results for the puckering potential energy surface (PES) of DNA and RNA nucleosides while significantly reducing the necessary computational time. Applying this method to a series of known xeno nucleic acids (XNAs) allowed us to rapidly explore the puckering PES of each of the respective nucleosides and to explore the puckering PES of six-membered modified XNA (HNA and β-homo-DNA) for the first time.
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Affiliation(s)
- Charles-Alexandre Mattelaer
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Henri-Philippe Mattelaer
- Campus Drie Eiken, Laboratory of Medicinal Chemistry, UAntwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Jérôme Rihon
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Matheus Froeyen
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Eveline Lescrinier
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
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33
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Cabrero C, Martín-Pintado N, Mazzini S, Gargallo R, Eritja R, Aviñó A, González C. Structural Effects of Incorporation of 2'-Deoxy-2'2'-Difluorodeoxycytidine (Gemcitabine) in A- and B-Form Duplexes. Chemistry 2021; 27:7351-7355. [PMID: 33772916 DOI: 10.1002/chem.202100503] [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: 02/08/2021] [Indexed: 11/06/2022]
Abstract
We report the structural effect of 2'-deoxy-2',2'-difluorocytidine (dFdC) insertions in the DNA strand of a DNA : RNA hybrid duplex and in a self-complementary DNA : DNA duplex. In both cases, the modification slightly destabilizes the duplex and provokes minor local distortions that are more pronounced in the case of the DNA : RNA hybrid. Analysis of the solution structures determined by NMR methods show that dFdC is an adaptable derivative that adopts North type sugar conformation when inserted in pure DNA, or a South sugar conformation in the context of DNA : RNA hybrids. In this latter context, South sugar pucker favors the formation of a 2'F⋅⋅H8 attractive interaction with a neighboring purine, which compensates the destabilizing effect of base pair distortions. These interactions share some features with pseudohydrogen bonds described previously in other nucleic acids structures with fluorine modified sugars.
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Affiliation(s)
- Cristina Cabrero
- Instituto de Química Física Rocasolano, CSIC, Serrano, 119, 28006, Madrid, Spain
| | - Nerea Martín-Pintado
- Instituto de Química Física Rocasolano, CSIC, Serrano, 119, 28006, Madrid, Spain
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Raimundo Gargallo
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1, 08028, Barcelona, Spain.,BIOESTRAN associated unit UB-CSIC, 08028, Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) CIBER-BBN, Jordi, Girona 18-26, 08034, Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) CIBER-BBN, Jordi, Girona 18-26, 08034, Barcelona, Spain
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, Serrano, 119, 28006, Madrid, Spain.,BIOESTRAN associated unit UB-CSIC, 08028, Barcelona, Spain
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Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
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35
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Antisense technology: an overview and prospectus. Nat Rev Drug Discov 2021; 20:427-453. [PMID: 33762737 DOI: 10.1038/s41573-021-00162-z] [Citation(s) in RCA: 274] [Impact Index Per Article: 91.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/13/2022]
Abstract
Antisense technology is now beginning to deliver on its promise to treat diseases by targeting RNA. Nine single-stranded antisense oligonucleotide (ASO) drugs representing four chemical classes, two mechanisms of action and four routes of administration have been approved for commercial use, including the first RNA-targeted drug to be a major commercial success, nusinersen. Although all the approved drugs are for use in patients with rare diseases, many of the ASOs in late- and middle-stage clinical development are intended to treat patients with very common diseases. ASOs in development are showing substantial improvements in potency and performance based on advances in medicinal chemistry, understanding of molecular mechanisms and targeted delivery. Moreover, the ASOs in development include additional mechanisms of action and routes of administration such as aerosol and oral formulations. Here, we describe the key technological advances that have enabled this progress and discuss recent clinical trials that illustrate the impact of these advances on the performance of ASOs in a wide range of therapeutic applications. We also consider strategic issues such as target selection and provide perspectives on the future of the field.
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36
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Akabane-Nakata M, Erande ND, Kumar P, Degaonkar R, Gilbert JA, Qin J, Mendez M, Woods LB, Jiang Y, Janas M, O’Flaherty DK, Zlatev I, Schlegel M, Matsuda S, Egli M, Manoharan M. siRNAs containing 2'-fluorinated Northern-methanocarbacyclic (2'-F-NMC) nucleotides: in vitro and in vivo RNAi activity and inability of mitochondrial polymerases to incorporate 2'-F-NMC NTPs. Nucleic Acids Res 2021; 49:2435-2449. [PMID: 33577685 PMCID: PMC7969009 DOI: 10.1093/nar/gkab050] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/13/2021] [Accepted: 02/07/2021] [Indexed: 02/01/2023] Open
Abstract
We recently reported the synthesis of 2'-fluorinated Northern-methanocarbacyclic (2'-F-NMC) nucleotides, which are based on a bicyclo[3.1.0]hexane scaffold. Here, we analyzed RNAi-mediated gene silencing activity in cell culture and demonstrated that a single incorporation of 2'-F-NMC within the guide or passenger strand of the tri-N-acetylgalactosamine-conjugated siRNA targeting mouse Ttr was generally well tolerated. Exceptions were incorporation of 2'-F-NMC into the guide strand at positions 1 and 2, which resulted in a loss of the in vitro activity. Activity at position 1 was recovered when the guide strand was modified with a 5' phosphate, suggesting that the 2'-F-NMC is a poor substrate for 5' kinases. In mice, the 2'-F-NMC-modified siRNAs had comparable RNAi potencies to the parent siRNA. 2'-F-NMC residues in the guide seed region position 7 and at positions 10, 11 and 12 were well tolerated. Surprisingly, when the 5'-phosphate mimic 5'-(E)-vinylphosphonate was attached to the 2'-F-NMC at the position 1 of the guide strand, activity was considerably reduced. The steric constraints of the bicyclic 2'-F-NMC may impair formation of hydrogen-bonding interactions between the vinylphosphonate and the MID domain of Ago2. Molecular modeling studies explain the position- and conformation-dependent RNAi-mediated gene silencing activity of 2'-F-NMC. Finally, the 5'-triphosphate of 2'-F-NMC is not a substrate for mitochondrial RNA and DNA polymerases, indicating that metabolites should not be toxic.
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Affiliation(s)
| | - Namrata D Erande
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Pawan Kumar
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Rohan Degaonkar
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Jason A Gilbert
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - June Qin
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Martha Mendez
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Lauren Blair Woods
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Maja M Janas
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Derek K O’Flaherty
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Mark K Schlegel
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
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Pourshahian S. THERAPEUTIC OLIGONUCLEOTIDES, IMPURITIES, DEGRADANTS, AND THEIR CHARACTERIZATION BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:75-109. [PMID: 31840864 DOI: 10.1002/mas.21615] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oligonucleotides are an emerging class of drugs that are manufactured by solid-phase synthesis. As a chemical class, they have unique product-related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product-related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas-phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson, South San Francisco, CA, 94080
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38
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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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Crooke ST, Liang XH, Baker BF, Crooke RM. Antisense technology: A review. J Biol Chem 2021; 296:100416. [PMID: 33600796 PMCID: PMC8005817 DOI: 10.1016/j.jbc.2021.100416] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Antisense technology is beginning to deliver on the broad promise of the technology. Ten RNA-targeted drugs including eight single-strand antisense drugs (ASOs) and two double-strand ASOs (siRNAs) have now been approved for commercial use, and the ASOs in phase 2/3 trials are innovative, delivered by multiple routes of administration and focused on both rare and common diseases. In fact, two ASOs are used in cardiovascular outcome studies and several others in very large trials. Interest in the technology continues to grow, and the field has been subject to a significant number of reviews. In this review, we focus on the molecular events that result in the effects observed and use recent clinical results involving several different ASOs to exemplify specific molecular mechanisms and specific issues. We conclude with the prospective on the technology.
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Affiliation(s)
- Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA.
| | - Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Brenda F Baker
- Development Communication, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Rosanne M Crooke
- Antisense Drug Discovery, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
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40
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Hawner M, Ducho C. Cellular Targeting of Oligonucleotides by Conjugation with Small Molecules. Molecules 2020; 25:molecules25245963. [PMID: 33339365 PMCID: PMC7766908 DOI: 10.3390/molecules25245963] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/20/2022] Open
Abstract
Drug candidates derived from oligonucleotides (ON) are receiving increased attention that is supported by the clinical approval of several ON drugs. Such therapeutic ON are designed to alter the expression levels of specific disease-related proteins, e.g., by displaying antigene, antisense, and RNA interference mechanisms. However, the high polarity of the polyanionic ON and their relatively rapid nuclease-mediated cleavage represent two major pharmacokinetic hurdles for their application in vivo. This has led to a range of non-natural modifications of ON structures that are routinely applied in the design of therapeutic ON. The polyanionic architecture of ON often hampers their penetration of target cells or tissues, and ON usually show no inherent specificity for certain cell types. These limitations can be overcome by conjugation of ON with molecular entities mediating cellular 'targeting', i.e., enhanced accumulation at and/or penetration of a specific cell type. In this context, the use of small molecules as targeting units appears particularly attractive and promising. This review provides an overview of advances in the emerging field of cellular targeting of ON via their conjugation with small-molecule targeting structures.
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41
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Hofmeister A, Jahn-Hofmann K, Krack A, Müller A, Kurz M, Scheidler S. Novel Dioxane and Morpholino Nucleotide Analogues: Syntheses and RNA-Hybridization Properties. Chembiochem 2020; 22:1072-1078. [PMID: 33112485 DOI: 10.1002/cbic.202000693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/26/2020] [Indexed: 11/09/2022]
Abstract
A novel class of nucleotide analogues with a dioxane ring as central scaffold has been developed. Synthetic routes in two diastereomeric series were realized, and the final thymidine analogues were synthesized with common functionalities for the automated oligonucleotide synthesis. The chemical space of the initially derived nucleotides was expanded by changing the central dioxane to analogous morpholine derivatives. This opens up the possibility for further derivatization by attaching different substituents at the morpholine nitrogen. The novel nucleotide building blocks were incorporated into double-stranded RNA sequences, and their hybridization properties investigated by melting-temperature analysis. Both scaffolds, dioxanes and morpholines, had an equal impact on double-strand stability, but Tm values differed depending on the chirality in the six-membered ring.
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Affiliation(s)
- Armin Hofmeister
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | | | - Arne Krack
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | - Armin Müller
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | - Michael Kurz
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | - Sabine Scheidler
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
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42
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Mikami A, Erande N, Matsuda S, Kel'in A, Woods LB, Chickering T, Pallan PS, Schlegel MK, Zlatev I, Egli M, Manoharan M. Synthesis, chirality-dependent conformational and biological properties of siRNAs containing 5'-(R)- and 5'-(S)-C-methyl-guanosine. Nucleic Acids Res 2020; 48:10101-10124. [PMID: 32990754 PMCID: PMC7544225 DOI: 10.1093/nar/gkaa750] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/10/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Various chemical modifications have been identified that enhance potency of small interfering RNAs (siRNAs) and that reduce off-target effects, immune stimulation, and toxicities of metabolites of these therapeutic agents. We previously described 5′-C-methyl pyrimidine nucleotides also modified at the 2′ position of the sugar. Here, we describe the synthesis of 2′-position unmodified 5′-(R)- and 5′-(S)-C-methyl guanosine and evaluation of these nucleotides in the context of siRNA. The (R) isomer provided protection from 5′ exonuclease and the (S) isomer provided protection from 3′ exonuclease in the context of a terminally modified oligonucleotide. siRNA potency was maintained when these modifications were incorporated at the tested positions of sense and antisense strands. Moreover, the corresponding 5′ triphosphates were not substrates for mitochondrial DNA polymerase. Models generated based on crystal structures of 5′ and 3′ exonuclease oligonucleotide complexes with 5′-(R)- and 5′-(S)-C-methyl substituents attached to the 5′- and 3′-terminal nucleotides, respectively, provided insight into the origins of the observed protections. Structural properties of 5′-(R)-C-methyl guanosine incorporated into an RNA octamer were analysed by X-ray crystallography, and the structure explains the loss in duplex thermal stability for the (R) isomer compared with the (S) isomer. Finally, the effect of 5′-C-methylation on endoribonuclease activity has been explained.
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Affiliation(s)
- Atsushi Mikami
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA
| | - Namrata Erande
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA
| | - Alexander Kel'in
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA
| | - Lauren Blair Woods
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA
| | - Tyler Chickering
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA
| | - Pradeep S Pallan
- Department of Biochemistry Vanderbilt University, School of Medicine Nashville, TN 37232, USA
| | - Mark K Schlegel
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA
| | - Martin Egli
- Department of Biochemistry Vanderbilt University, School of Medicine Nashville, TN 37232, USA
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA
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43
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Hyjek-Składanowska M, Stasińska AR, Napiórkowska-Gromadzka A, Bartłomiejczak A, Seth PP, Chmielewski MK, Nowotny M. Disulfide bridge cross-linking between protein and the RNA backbone as a tool to study RNase H1. Bioorg Med Chem 2020; 28:115741. [PMID: 32992250 DOI: 10.1016/j.bmc.2020.115741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 10/23/2022]
Abstract
The chemical cross-linking of complexes of proteins with nucleic acids is often used in structural and mechanistic studies of these oftentimes unstable and transient complexes. To date, no method has been reported for the thiol-based conjugation of proteins with an RNA backbone, mainly because of instability of the modified ribonucleic acid that is functionalized at the phosphodiester and its rapid hydrolysis. Here, we report the site-specific synthesis of stable RNA oligonucleotides with a thiol-bearing linker that was attached to the phosphodiester backbone, where the ribonucleotide at the cross-linking site was either replaced with 2'-deoxy- or 2'-fluororibonucleotide. The utility of this approach was validated in cross-linking tests with RNase H1, a model protein for RNA/DNA binding and key effector in DNA-like antisense drug therapy. Furthermore, scale-up cross-linking and purification of the complexes confirmed that the method is useful for obtaining preparations of protein-RNA/DNA complexes with purity and stability that are suitable for further biochemical and structural studies. The present approach broadens the repertoire of disulfide-based cross-linking strategies and is a novel tool for the stabilization of protein-RNA complexes in which the interaction occurs via the RNA backbone. This methodology may be broadly applicable to studies of otherwise unstable or transient complexes of proteins with RNA and RNA/DNA.
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Affiliation(s)
- Malwina Hyjek-Składanowska
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland; Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland
| | - Anna R Stasińska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznań 61-704, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, Poznań 61-612, Poland
| | - Agnieszka Napiórkowska-Gromadzka
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland; Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland
| | - Aneta Bartłomiejczak
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznań 61-704, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, Poznań 61-612, Poland.
| | - Marcin Nowotny
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland; Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland.
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44
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Antisense drug discovery and development technology considered in a pharmacological context. Biochem Pharmacol 2020; 189:114196. [PMID: 32800852 DOI: 10.1016/j.bcp.2020.114196] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
When coined, the term "antisense" included oligonucleotides of any structure, with any chemical modification and designed to work through any post-RNA hybridization mechanism. However, in practice the term "antisense" has been used to describe single stranded oligonucleotides (ss ASOs) designed to hybridize to RNAswhile the term "siRNA" has come to mean double stranded oligonucleotides designed to activate Ago2. However, the two approaches share many common features. The medicinal chemistry developed for ASOs greatly facilitated the development of siRNA technology and remains the chemical basis for both approaches. Many of challenges faced and solutions achieved share many common features. In fact, because ss ASOs can be designed to activate Ago2, the two approaches intersect at this remarkably important protein. There are also meaningful differences. The pharmacokinetic properties are quite different and thus potential routes of delivery differ. ASOs may be designedto use a variety of post-RNA binding mechanismswhile siRNAs depend solely on the robust activity of Ago2. However, siRNAs and ASOs are both used for therapeutic purposes and both must be and can be understood in a pharmacological context. Thus, the goals of this review are to put ASOs in pharmacological context and compare their behavior as pharmacological agents to the those of siRNAs.
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45
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Xiao F, Chen Z, Wei Z, Tian L. Hydrophobic Interaction: A Promising Driving Force for the Biomedical Applications of Nucleic Acids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001048. [PMID: 32832360 PMCID: PMC7435255 DOI: 10.1002/advs.202001048] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/28/2020] [Indexed: 05/13/2023]
Abstract
The comprehensive understanding and proper use of supramolecular interactions have become critical for the development of functional materials, and so is the biomedical application of nucleic acids (NAs). Relatively rare attention has been paid to hydrophobic interaction compared with hydrogen bonding and electrostatic interaction of NAs. However, hydrophobic interaction shows some unique properties, such as high tunability for application interest, minimal effect on NA functionality, and sensitivity to external stimuli. Therefore, the widespread use of hydrophobic interaction has promoted the evolution of NA-based biomaterials in higher-order self-assembly, drug/gene-delivery systems, and stimuli-responsive systems. Herein, the recent progress of NA-based biomaterials whose fabrications or properties are highly determined by hydrophobic interactions is summarized. 1) The hydrophobic interaction of NA itself comes from the accumulation of base-stacking forces, by which the NAs with certain base compositions and chain lengths show properties similar to thermal-responsive polymers. 2) In conjugation with hydrophobic molecules, NA amphiphiles show interesting self-assembly structures with unique properties in many new biosensing and therapeutic strategies. 3) The working-mechanisms of some NA-based complex materials are also dependent on hydrophobic interactions. Moreover, in recent attempts, NA amphiphiles have been applied in organizing macroscopic self-assembly of DNA origami and controlling the cell-cell interactions.
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Affiliation(s)
- Fan Xiao
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
- School of Materials Science and EngineeringHarbin Institute of TechnologyNangang DistrictHarbin150001P. R. China
| | - Zhe Chen
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
- Cancer Centre and Centre of ReproductionDevelopment and AgingFaculty of Health SciencesUniversity of MacauTaipaMacau999078P. R. China
| | - Zixiang Wei
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
- Cancer Centre and Centre of ReproductionDevelopment and AgingFaculty of Health SciencesUniversity of MacauTaipaMacau999078P. R. China
| | - Leilei Tian
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
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46
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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: 15] [Impact Index Per Article: 3.8] [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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47
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Davis SM, Sousa J, Vangjeli L, Hassler MR, Echeverria D, Knox E, Turanov AA, Alterman JF, Khvorova A. 2'-O-Methyl at 20-mer Guide Strand 3' Termini May Negatively Affect Target Silencing Activity of Fully Chemically Modified siRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:266-277. [PMID: 32610253 PMCID: PMC7327867 DOI: 10.1016/j.omtn.2020.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/27/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
Small interfering RNAs (siRNAs) have the potential to treat a broad range of diseases. siRNAs need to be extensively chemically modified to improve their bioavailability, safety, and stability in vivo. However, chemical modifications variably impact target silencing for different siRNA sequences, making the activity of chemically modified siRNA difficult to predict. Here, we systematically evaluated the impact of 3′ terminal modifications (2′-O-methyl versus 2′-fluoro) on guide strands of different length and showed that 3′ terminal 2′-O-methyl modification negatively impacts activity for >60% of siRNA sequences tested but only in the context of 20- and not 19- or 21-nt-long guide strands. These results indicate that sequence, modification pattern, and structure may cooperatively affect target silencing. Interestingly, the introduction of an extra 2′-fluoro modification in the seed region at guide strand position 5, but not 7, may partially compensate for the negative impact of 3′ terminal 2′-O-methyl modification. Molecular modeling analysis suggests that 2′-O-methyl modification may impair guide strand interactions within the PAZ domain of argonaute-2, which may affect target recognition and cleavage, specifically when guide strands are 20-nt long. Our findings emphasize the complex nature of modified RNA-protein interactions and contribute to design principles for chemically modified siRNAs.
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Affiliation(s)
- Sarah M Davis
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lorenc Vangjeli
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Emily Knox
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anton A Turanov
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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48
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Glazier DA, Liao J, Roberts BL, Li X, Yang K, Stevens CM, Tang W. Chemical Synthesis and Biological Application of Modified Oligonucleotides. Bioconjug Chem 2020; 31:1213-1233. [PMID: 32227878 DOI: 10.1021/acs.bioconjchem.0c00060] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA plays a myriad of roles in the body including the coding, decoding, regulation, and expression of genes. RNA oligonucleotides have garnered significant interest as therapeutics via antisense oligonucleotides or small interfering RNA strategies for the treatment of diseases ranging from hyperlipidemia, HCV, and others. Additionally, the recently developed CRISPR-Cas9 mediated gene editing strategy also relies on Cas9-associated RNA strands. However, RNA presents numerous challenges as both a synthetic target and a potential therapeutic. RNA is inherently unstable, difficult to deliver into cells, and potentially immunogenic by itself or upon modification. Despite these challenges, with the help of chemically modified oligonucleotides, multiple RNA-based drugs have been approved by the FDA. The progress is made possible due to the nature of chemically modified oligonucleotides bearing advantages of nuclease stability, stronger binding affinity, and some other unique properties. This review will focus on the chemical synthesis of RNA and its modified versions. How chemical modifications of the ribose units and of the phosphatediester backbone address the inherent issues with using native RNA for biological applications will be discussed along the way.
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Affiliation(s)
- Daniel A Glazier
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Junzhuo Liao
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Brett L Roberts
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xiaolei Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Ka Yang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Christopher M Stevens
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weiping Tang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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49
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Li Q, Chen J, Trajkovski M, Zhou Y, Fan C, Lu K, Tang P, Su X, Plavec J, Xi Z, Zhou C. 4′-Fluorinated RNA: Synthesis, Structure, and Applications as a Sensitive 19F NMR Probe of RNA Structure and Function. J Am Chem Soc 2020; 142:4739-4748. [DOI: 10.1021/jacs.9b13207] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Qiang Li
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jialiang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chaochao Fan
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Kuan Lu
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Pingping Tang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
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50
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Akabane-Nakata M, Kumar P, Erande ND, Matsuda S, Manoharan M. Synthesis of 2'-Fluorinated Northern Methanocarbacyclic (2'-F-NMC) Nucleosides and Their Incorporation Into Oligonucleotides. ACTA ACUST UNITED AC 2020; 80:e103. [PMID: 31985895 DOI: 10.1002/cpnc.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This article describes chemical synthesis of 2'-fluorinated Northern methanocarbacyclic (2'-F-NMC) nucleosides and phosphoramidites, based on a bicyclo[3.1.0]hexane scaffold bearing all four natural nucleobases (U, C, A, and G), and their incorporation into oligonucleotides by solid-supported synthesis. This synthesis starts from commercially available cyclopent-2-en-1-one to obtain the fluorinated carbocyclic pseudosugar intermediate (S.13), which can be converted to the uridine intermediate by condensation with isocyanate, followed by cyclization, and to adenine and guanine precursors by microwave-assisted reactions. All four 2'-F-NMC phosphoramidites are synthesized from S.13 in a convergent approach, and the monomers are used for synthesis of 2'-F-NMC-modified oligonucleotides. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Preparation of fluorinated carbocyclic pseudosugar intermediate Basic Protocol 2: Preparation of 2'-F-NMC uridine and cytidine phosphoramidites Basic Protocol 3: Preparation of 2'-F-NMC adenosine phosphoramidite Basic Protocol 4: Preparation of 2'-F-NMC guanosine phosphoramidite Basic Protocol 5: Synthesis of oligonucleotides containing 2'-F-NMC.
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Affiliation(s)
| | - Pawan Kumar
- Alnylam Pharmaceuticals, Cambridge, Massachusetts
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