1
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Zengin Kurt B, Dhara D, El-Sagheer AH, Brown T. Synthesis and Properties of Oligonucleotides Containing LNA-Sulfamate and Sulfamide Backbone Linkages. Org Lett 2024; 26:4137-4141. [PMID: 38717429 PMCID: PMC11110047 DOI: 10.1021/acs.orglett.4c01232] [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: 04/11/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Oligonucleotides hold great promise as therapeutic agents but poor bioavailability limits their utility. Hence, new analogues with improved cell uptake are urgently needed. Here, we report the synthesis and physical study of reduced-charge oligonucleotides containing artificial LNA-sulfamate and sulfamide linkages combined with 2'-O-methyl sugars and phosphorothioate backbones. These oligonucleotides have high affinity for RNA and excellent nuclease resistance.
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Affiliation(s)
- Belma Zengin Kurt
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Bezmialem Vakif University, 34093 Istanbul, Turkey
| | - Debashis Dhara
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
| | - Afaf H. El-Sagheer
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.
| | - Tom Brown
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
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2
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Genedy HH, Humbert P, Laoulaou B, Le Moal B, Fusellier M, Passirani C, Le Visage C, Guicheux J, Lepeltier É, Clouet J. MicroRNA-targeting nanomedicines for the treatment of intervertebral disc degeneration. Adv Drug Deliv Rev 2024; 207:115214. [PMID: 38395361 DOI: 10.1016/j.addr.2024.115214] [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: 12/13/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
Low back pain stands as a pervasive global health concern, afflicting almost 80% of adults at some point in their lives with nearly 40% attributable to intervertebral disc degeneration (IVDD). As only symptomatic relief can be offered to patients there is a dire need for innovative treatments.Given the accumulating evidence that multiple microRNAs (miRs) are dysregulated during IVDD, they could have a huge potential against this debilitating condition. The way miRs can profoundly modulate signaling pathways and influence several cellular processes at once is particularly exciting to tackle this multifaceted disorder. However, miR delivery encounters extracellular and intracellular biological barriers. A promising technology to address this challenge is the vectorization of miRs within nanoparticles, providing both protection and enhancing their uptake within the scarce target cells of the degenerated IVD. This comprehensive review presents the diverse spectrum of miRs' connection with IVDD and demonstrates their therapeutic potential when vectorized in nanomedicines.
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Affiliation(s)
- Hussein H Genedy
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France; Univ Angers, INSERM, CNRS, MINT, SFR ICAT, F-49000 Angers, France
| | - Paul Humbert
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France
| | - Bilel Laoulaou
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France; Univ Angers, INSERM, CNRS, MINT, SFR ICAT, F-49000 Angers, France
| | - Brian Le Moal
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France; Univ Angers, INSERM, CNRS, MINT, SFR ICAT, F-49000 Angers, France
| | - Marion Fusellier
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France; Department of Diagnostic Imaging, CRIP, ONIRIS, College of Veterinary Medicine, Food Science and Engineering, Nantes F-44307, France
| | | | - Catherine Le Visage
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France
| | - Jérôme Guicheux
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France
| | - Élise Lepeltier
- Univ Angers, INSERM, CNRS, MINT, SFR ICAT, F-49000 Angers, France; Institut Universitaire de France (IUF), France.
| | - Johann Clouet
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France
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3
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Liu Y, Huang H, Zheng Y, Wang C, Chen W, Huang W, Lin L, Wei H, Wang J, Lin M. Development of a POCT detection platform based on a locked nucleic acid-enhanced ARMS-RPA-GoldMag lateral flow assay. J Pharm Biomed Anal 2023; 235:115632. [PMID: 37573622 DOI: 10.1016/j.jpba.2023.115632] [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: 06/05/2023] [Revised: 07/16/2023] [Accepted: 08/04/2023] [Indexed: 08/15/2023]
Abstract
In this study, a novel genotyping point-of-care testing (POCT) rapid detection device, the locked nucleic acid (LNA)-amplification refractory mutation system (ARMS)-recombinase polymerase amplification (RPA)-GoldMag lateral flow assay (LFA) platform, was provided by mining and synthesis based on prior technology. Research methods based on system-integrated innovation and knowledge-integrated generation have become a new trend in technology development. Here, we exploit the combination of LNA-coupled ARMS-RPA and gold nanoparticle probe technology for detection signal amplification, thus pioneering a new tool for accurate, rapid, and cost-effective genotyping. We also performed SNP typing detection and clinical validation of this new assay platform using common glucose-6-phosphate dehydrogenase (G6PD) gene single nucleotide polymorphism (SNP) loci, and the results demonstrated the high sensitivity, specificity, stability, accuracy and feasibility of the LNA-ARMS-RPA-GoldMag lateral flow assay platform. It is hoped that this new technology will make a significant contribution to the field of POCT rapid diagnosis and aim to expand the application space, reflecting its clinical application value and development prospects.
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Affiliation(s)
- Yaqun Liu
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, People's Republic of China
| | - Huiying Huang
- Shool of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, People's Republic of China
| | - Yuzhong Zheng
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, People's Republic of China
| | - Chunfang Wang
- Shool of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, People's Republic of China
| | - Wencheng Chen
- Shool of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, People's Republic of China
| | - Weiyi Huang
- Shool of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, People's Republic of China
| | - Liyun Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, People's Republic of China
| | - Huagui Wei
- Shool of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, People's Republic of China
| | - Junli Wang
- Shool of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, People's Republic of China.
| | - Min Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, People's Republic of China; Shool of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, People's Republic of China.
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4
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An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides. Nat Commun 2022; 13:4036. [PMID: 35821218 PMCID: PMC9276774 DOI: 10.1038/s41467-022-31636-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotides that target mRNA have great promise as therapeutic agents for life-threatening conditions but suffer from poor bioavailability, hence high cost. As currently untreatable diseases come within the reach of oligonucleotide therapies, new analogues are urgently needed to address this. With this in mind we describe reduced-charge oligonucleotides containing artificial LNA-amide linkages with improved gymnotic cell uptake, RNA affinity, stability and potency. To construct such oligonucleotides, five LNA-amide monomers (A, T, C, 5mC and G), where the 3′-OH is replaced by an ethanoic acid group, are synthesised in good yield and used in solid-phase oligonucleotide synthesis to form amide linkages with high efficiency. The artificial backbone causes minimal structural deviation to the DNA:RNA duplex. These studies indicate that splice-switching oligonucleotides containing LNA-amide linkages and phosphorothioates display improved activity relative to oligonucleotides lacking amides, highlighting the therapeutic potential of this technology. Oligonucleotides targeting mRNA are promising therapeutic agents but suffer from poor bioavailability. Here, the authors develop reduced-charge oligonucleotides with artificial LNA-amide linkages with improved cell uptake and minimal structural deviation to the DNA:RNA duplex.
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5
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Kusaka S, Yamamoto K, Shinohara M, Minato Y, Ichikawa S. Design, synthesis and conformation-activity relationship analysis of LNA/BNA-type 5'-O-aminoribosyluridine as MraY inhibitors. Bioorg Med Chem 2022; 65:116744. [PMID: 35500521 DOI: 10.1016/j.bmc.2022.116744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 11/02/2022]
Abstract
It is important to understand and control the biologically active conformation in medicinal chemistry. Muraymycins and caprazamycins, which are strong inhibitors of MraY, are promising antibacterial agents with a novel mode of action. Focusing on a sugar puckering and a dihedral angle ϕ of the uridine moiety of these natural products, LNA/BNA-type 5'-O-aminoribosyluridine analogues, whose puckering of the ribose moiety are completely restricted to the N-type, were designed and synthesized as simplified MraY inhibitors. Their conformation-activity relationship was further investigated in details. The conformation-activity relationship analysis investigated in this study could be a general guideline for simplification and rational drug design of MraY inhibitory nucleoside natural products.
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Affiliation(s)
- Shintaro Kusaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Motoko Shinohara
- Department of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yusuke Minato
- Department of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
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6
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Chan KY, Kinghorn AB, Hollenstein M, Tanner JA. Chemical modifications for a next generation of nucleic acid aptamers. Chembiochem 2022; 23:e202200006. [PMID: 35416400 DOI: 10.1002/cbic.202200006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/11/2022] [Indexed: 11/08/2022]
Abstract
In the past three decades, in vitro systematic evolution of ligands by exponential enrichment (SELEX) has yielded many aptamers for translational applications in both research and clinical settings. Despite their promise as an alternative to antibodies, the low success rate of SELEX (~ 30%) has been a major bottleneck that hampers the further development of aptamers. One hurdle is the lack of chemical diversity in nucleic acids. To address this, the aptamer chemical repertoire has been extended by introducing exotic chemical groups, which provide novel binding functionalities. This review will focus on how modified aptamers can be selected and evolved, with illustration of some successful examples. In particular, unique chemistries are exemplified. Various strategies of incorporating modified building blocks into the standard SELEX protocol are highlighted, with a comparison of the differences between pre-SELEX and post-SELEX modifications. Nucleic acid aptamers with extended functionality evolved from non-natural chemistries will open up new vistas for function and application of nucleic acids.
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Affiliation(s)
- Kwing Yeung Chan
- The University of Hong Kong, School of Biomedical Sciences, HONG KONG
| | | | | | - Julian Alexander Tanner
- The University of Hong Kong, School of Biomedical Sciences, 3/F Laboratory Block, 21 Sassoon Road, 000000, Pokfulam, HONG KONG
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7
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Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. SN- and NS-puckered sugar conformers are precursors of the (6-4) photoproduct in thymine dinucleotide. Org Biomol Chem 2022; 20:2300-2307. [PMID: 35253821 DOI: 10.1039/d2ob00044j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Some amount of furanose in a southern conformation, possibly in both, but certainly in one of the two adjacent nucleotides of a dipyrimidine site, is necessary for (6-4) photoproduct formation in oligonucleotides. To explore the necessity, role, and most favorable location of each South sugar conformer in the formation of the (6-4) adduct in the thymine dinucleotide TpT, the photochemical behavior of two synthetic analogues, in which the South sugar conformation is prohibited for one of their two sugars, has been examined. Herein, we experimentally demonstrate that the presence of one sugar presenting some amount of South puckering, at any of the extremities, is sufficient to trigger (6-4) adduct formation. Nonetheless, the photochemical behavior of the dinucleotide with a South-puckered conformation at the 5'-end, mimics more closely that of TpT. In addition, using the 5' North 3' South-dilocked dinucleotide, we demonstrate that the flexibility of the South pucker at the 3'-end has little influence on the (6-4) adduct formation.
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Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Clément Denhez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
- MaSCA, P3M, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
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8
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Shanmugasundaram M, Senthilvelan A, Kore AR. Chemical Synthesis of a Locked Nucleic Acid-Substituted Dinucleotide Cap Analog. Curr Protoc 2021; 1:e22. [PMID: 33484497 DOI: 10.1002/cpz1.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
This article describes a reliable and efficient method for synthesis of the dinucleotide cap analog m7(LNA) G[5']ppp[5']G containing a locked nucleic acid moiety. The required LNA intermediate for the final coupling reaction, m7(LNA) GDP, is prepared in six steps starting from 5'-DMTr-N-DMF LNA guanosine. The overall reaction involves removal of DMTr and DMF groups, 5' monophosphorylation, imidazolide formation, diphosphorylation, and regioselective m7 methylation. The final coupling reaction of m7(LNA) GDP with ImGMP in the presence of zinc chloride as a catalyst affords m7(LNA) G[5']ppp[5']G in 59% yield. © 2021 Wiley Periodicals LLC. Basic Protocol: Synthesis of an LNA-substituted dinucleotide cap analog Support Protocol: Preparation of the tris(tributylammonium) phosphate linker.
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas
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9
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Maeda R, Saito-Tarashima N, Wakamatsu H, Natori Y, Minakawa N, Yoshimura Y. Synthesis and Properties of 4'-ThioLNA/BNA. Org Lett 2021; 23:4062-4066. [PMID: 33938754 DOI: 10.1021/acs.orglett.1c01306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To develop a new nucleoside analogue applicable to oligonucleotide therapeutics, we designed a 4'-thio analogue of an LNA/BNA monomer. Synthesis of 4'-hydroxymethyl-4'-thioribonucleoside was achieved by a tandem ring-contraction-aldol reaction of a 5-thiopyranose derivative and the subsequent Pummerer-type thioglycosylation reaction of the corresponding sulfoxide. Treatment of 4'-hydroxymethyl-4'-thiopyrimidine nucleosides with diphenyl carbonate in the presence of catalytic NaHCO3 gave the desired 4'-thioLNA/BNA monomers, which were introduced into oligonucleotides.
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Affiliation(s)
- Rion Maeda
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
| | - Noriko Saito-Tarashima
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Hideaki Wakamatsu
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
| | - Yoshihiro Natori
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Yuichi Yoshimura
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
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10
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Kiesman WF, McPherson AK, Diorazio LJ, Van den Bergh L, Smith PD, Northall JM, Fettes A, Wang T, Mehlmann M, Raza S, Held G. Perspectives on the Designation of Oligonucleotide Starting Materials. Nucleic Acid Ther 2021; 31:93-113. [PMID: 33534646 PMCID: PMC7997719 DOI: 10.1089/nat.2020.0909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The designation of starting materials (SMs) for pharmaceuticals has been a topic of great interest and debate since the first ICH quality guidance was published. The increase in the number and variety of commercialized oligonucleotides (antisense oligonucleotides—ASOs, small interfering RNAs—siRNAs, etc.) in recent years has reignited dialogue on this topic because of the unique complexity of the monomeric nucleotides and other contributory materials used to manufacture oligonucleotides. The SM working group in the European Pharma Oligonucleotide Consortium (EPOC) was formed to help establish simple, risk-based criteria to guide the justification of oligonucleotide SMs. This article provides a description of the common types of SMs, classes of SM impurities, and control strategies that will be helpful to maintain manufacturing consistency.
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Affiliation(s)
- William F Kiesman
- Antisense Oligonucleotide Development and Manufacturing, Biogen, Inc., Cambridge, Massachusetts, USA
| | - Andrew K McPherson
- Process Organic Chemistry, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Louis J Diorazio
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | | | - Peter D Smith
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, United Kingdom
| | - John M Northall
- Chemical Development, Product Development and Supply, GlaxoSmithKline, Stevenage, United Kingdom
| | - Alec Fettes
- Pharmaceutical Division, Small Molecule Technical Development, Department of Process Chemistry and Catalysis, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Tiejun Wang
- Global Regulatory Affairs, CMC & Devices, Sanofi, Bridgewater, New Jersey, USA
| | - Martin Mehlmann
- External Technical Oversight Analytics, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Syed Raza
- Amidite Manufacturing and Process Development, Thermo Fisher Scientific, Milwaukee, Wisconsin, USA
| | - Gary Held
- Amidite Quality Control and Analytical Development, Thermo Fisher Scientific, Milwaukee, Wisconsin, USA
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11
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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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12
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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: 43] [Impact Index Per Article: 10.8] [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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13
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Nikam RR, Gore KR. A mild and convenient approach for selective acetonide cleavage involved in carbohydrate synthesis using PPA-SiO2. J Carbohydr Chem 2020. [DOI: 10.1080/07328303.2019.1708374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Rahul R. Nikam
- Department of Chemistry, University of Mumbai, Mumbai, India
| | - Kiran R. Gore
- Department of Chemistry, University of Mumbai, Mumbai, India
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
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14
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Thorpe C, Epple S, Woods B, El-Sagheer AH, Brown T. Synthesis and biophysical properties of carbamate-locked nucleic acid (LNA) oligonucleotides with potential antisense applications. Org Biomol Chem 2019; 17:5341-5348. [PMID: 31099373 PMCID: PMC6686644 DOI: 10.1039/c9ob00691e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/09/2019] [Indexed: 12/13/2022]
Abstract
Antisense oligonucleotides (ASOs) are becoming important drugs for hard to treat diseases. Modifications to their DNA backbones are essential to inhibit degradation in vivo, but they can reduce binding affinity to RNA targets. To address this problem we have combined the enzymatic resistance of carbamate (CBM) DNA backbone analogues with the thermodynamic stability conferred by locked nucleic acid sugars (LNA). Using a dinucleotide phosphoramidite strategy and automated solid phase synthesis, we have synthesised a set of oligonucleotides modified with multiple LNA-CBM units. The LNA sugars restore binding affinity to RNA targets, and in this respect LNA position with respect to the CBM linkage is important. Oligonucleotides containing carbamate flanked on its 5'and 3'-sides by LNA form stable duplexes with RNA and unstable duplexes with DNA, which is desirable for antisense applications. Carbamate-LNA modified oligonucleotides also show increased stability in the presence of snake venom and foetal bovine serum compared to LNA or CBM backbones alone.
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Affiliation(s)
- Cameron Thorpe
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
| | - Sven Epple
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
| | - Benjamin Woods
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
| | - Afaf H. El-Sagheer
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
- Chemistry Branch
, Department of Science and Mathematics
, Faculty of Petroleum and Mining Engineering
, Suez University
,
Suez 43721
, Egypt
| | - Tom Brown
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
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15
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Vejlegaard K, Wegeberg C, McKee V, Wengel J. Novel conformationally constrained 2'-C-methylribonucleosides: synthesis and incorporation into oligonucleotides. Org Biomol Chem 2019; 16:1312-1321. [PMID: 29392247 DOI: 10.1039/c7ob02663c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Synthesis of two novel conformationally constrained bicyclic ribonucleoside phosphoramidites bearing a 2'-C-methyl substituent has been accomplished. These phosphoramidites were used to incorporate the corresponding 2'-C-methyl nucleotides into oligonucleotides and to study their effects on duplex thermal stability. Whereas the C2'-O4'-linked LNA-type derivative induced severe destabilization of duplexes formed with complementary DNA and RNA, the C3'-O4'-linked derivative induced RNA-selective hybridization with increased affinity relative to that of the unmodified DNA-based probe.
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Affiliation(s)
- Kim Vejlegaard
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark. jwe@sdu
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16
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Kumar P, Truong L, Baker YR, El-Sagheer AH, Brown T. Synthesis, Affinity for Complementary RNA and DNA, and Enzymatic Stability of Triazole-Linked Locked Nucleic Acids (t-LNAs). ACS OMEGA 2018; 3:6976-6987. [PMID: 29978149 PMCID: PMC6028152 DOI: 10.1021/acsomega.8b01086] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 05/30/2018] [Indexed: 06/08/2023]
Abstract
Dinucleoside phosphoramidites containing a triazole internucleotide linkage flanked by locked nucleic acid (LNA) were synthesized and incorporated into oligonucleotides (ONs). ONs bearing both LNA and triazole at multiple sites were obtained and their biophysical properties including enzymatic stability and binding affinity for RNA and DNA targets were studied. t-LNAs with four incorporations of a dinucleoside monomer having LNA on either side of the triazole linkage bind to their RNA target with significantly higher affinity and greater specificity than unmodified oligonucleotides, and are remarkably stable to nuclease degradation. A similar but reduced effect on enzymatic stability and binding affinity was noted for LNA only on the 3'-side of the triazole linkage. Thus, by combining unnatural triazole linkages and LNA in one unit (t-LNA), we produced a promising class of ONs with reduced anionic charge and potential for antisense applications.
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Affiliation(s)
- Pawan Kumar
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Lynda Truong
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Ysobel Ruth Baker
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Afaf Helmy El-Sagheer
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
- Chemistry
Branch, Department of Science and Mathematics, Faculty of Petroleum
and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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17
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Islam MA, Fujisaka A, Mori S, Ito KR, Yamaguchi T, Obika S. Synthesis and biophysical properties of 5'-thio-2',4'-BNA/LNA oligonucleotide. Bioorg Med Chem 2018; 26:3634-3638. [PMID: 29886084 DOI: 10.1016/j.bmc.2018.05.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 10/16/2022]
Abstract
Phosphorothioate modification of oligonucleotides is one of the most promising chemical modifications in nucleic acid therapeutics. Structurally similar 5'-thio or phosphorothiolate-modified nucleotides, in which the 5'-bridging oxygen atom is replaced with a sulfur atom, are attracting attention and gaining importance in oligonucleotide-based research. In our present study, we synthesized 5'-thio-2',4'-BNA/LNA monomers bearing thymine or 5-methylcytosine nucleobase. The 5'-thio-2',4'-BNA/LNA monomers were successfully incorporated into target oligonucleotides, and their nuclease stability and binding affinity with complementary strands were evaluated.
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Affiliation(s)
- Md Ariful Islam
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali 3814, Bangladesh
| | - Aki Fujisaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Faculty of Pharmacy, Osaka Ohtani University, Nishikiori-Kita 3-11-1, Tondabayashi, Osaka 584-8540, Japan
| | - Shohei Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kosuke Ramon Ito
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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18
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Kishimoto Y, Fujii A, Nakagawa O, Nagata T, Yokota T, Hari Y, Obika S. Synthesis and thermal stabilities of oligonucleotides containing 2'-O,4'-C-methylene bridged nucleic acid with a phenoxazine base. Org Biomol Chem 2018; 15:8145-8152. [PMID: 28920119 DOI: 10.1039/c7ob01874f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We designed and synthesized a novel artificial 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA/LNA) with a phenoxazine nucleobase and named this compound BNAP. Oligodeoxynucleotide (ODN) containing BNAP showed higher binding affinities toward complementary DNA and RNA as compared to ODNs bearing 2',4'-BNA/LNA with 5-methylcytosine or 2'-deoxyribonucleoside with phenoxazine. Thermodynamic analysis revealed that BNAP exhibits properties associated with the phenoxazine moiety in DNA/DNA duplexes and characteristics associated with the 2',4'-BNA/LNA moiety in DNA/RNA duplexes.
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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19
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Jastrzębska K, Maciaszek A, Dolot R, Bujacz G, Guga P. Thermal stability and conformation of antiparallel duplexes formed by P-stereodefined phosphorothioate DNA/LNA chimeric oligomers with DNA and RNA matrices. Org Biomol Chem 2016; 13:10032-40. [PMID: 26293357 DOI: 10.1039/c5ob01474c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
3'-O-(2-Thio-4,4-pentamethylene-1,3,2-oxathiaphospholane) derivatives of LNA-type nucleosides (LNA-OTPs, 2a-d; B' = Thy, Ade(Bz), Cyt(Bz), Gua(dmf), respectively) were synthesized and separated into pure P-diastereomers. X-ray analysis allowed for assignment of the absolute configuration of the phosphorus atom in the detritylated, fast-eluting diastereomer 2a. The diastereomerically pure LNA-OTP monomers were used in solid phase synthesis of P-stereodefined chimeric PS-(DNA/LNA) 11-mers containing 2-3 LNA units. Formally, among the phosphorothioate oligomers the biggest enhancement in thermal stability of Watson-Crick paired duplexes was found for [SP-PS]-(DNA/LNA)/RNA duplexes (on average 8.2 °C per LNA nucleotide), followed by [RP-PS]-(DNA/LNA)/RNA (6.3 °C), [RP-PS]-(DNA/LNA)/DNA (3.8 °C) and [SP-PS]-(DNA/LNA)/DNA (2.4 °C per LNA nucleotide). However, detailed analysis of the thermal dissociation data showed that the thermal stability of (PS-LNA)-containing duplexes does not depend on the spatial orientation of the sulfur atoms. This conclusion received support from CD measurements.
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Affiliation(s)
- Katarzyna Jastrzębska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Łódź, Poland.
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20
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Vibhute AM, Konieczny V, Taylor CW, Sureshan KM. Triazolophostins: a library of novel and potent agonists of IP3 receptors. Org Biomol Chem 2016; 13:6698-710. [PMID: 25869535 PMCID: PMC4533600 DOI: 10.1039/c5ob00440c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IP3R initiate most cellular Ca2+ signaling. AdA is the most potent agonist of IP3R. The structural complexity of AdA makes synthesis of its analogs cumbersome. We report an easy method for generating a library of potent triazole-based analogs of AdA, triazolophostins, which are the most potent AdA analogs devoid of a nucleobase.
IP3 receptors are channels that mediate the release of Ca2+ from the intracellular stores of cells stimulated by hormones or neurotransmitters. Adenophostin A (AdA) is the most potent agonist of IP3 receptors, with the β-anomeric adenine contributing to the increased potency. The potency of AdA and its stability towards the enzymes that degrade IP3 have aroused interest in AdA analogs for biological studies. The complex structure of AdA poses problems that have necessitated optimization of synthetic conditions for each analog. Such lengthy one-at-a-time syntheses limit access to AdA analogs. We have addressed this problem by synthesizing a library of triazole-based AdA analogs, triazolophostins, by employing click chemistry. An advanced intermediate having all the necessary phosphates and a β-azide at the anomeric position was reacted with various alkynes under Cu(i) catalysis to yield triazoles, which upon deprotection gave triazolophostins. All eleven triazolophostins synthesized are more potent than IP3 and some are equipotent with AdA in functional analyses of IP3 receptors. We show that a triazole ring can replace adenine without compromising the potency of AdA and provide facile routes to novel AdA analogs.
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Affiliation(s)
- Amol M Vibhute
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala-695016, India.
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21
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Sharma VK, Singh SK, Bohra K, L CSR, Khatri V, Olsen CE, Prasad AK. Design and synthesis of LNA-based mercaptoacetamido-linked nucleoside dimers. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 32:256-72. [PMID: 23581718 DOI: 10.1080/15257770.2013.783218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Three LNA-based mercaptoacetamido-linked nonionic nucleoside dimers TL-S-T, T-S-TL, and TL-S-TL have been synthesized by HOBT and HBTU catalyzed condensation of silyl-protected 2-S-(thymidin-5 '-yl)mercaptoacetic acid or 2-S-(2 '-O,4 '-C-methylenethymidin-5 '-yl)mercaptoacetic acid with 3 '-amino-3 '-deoxy-5 '-O-DMT-2 '-O,4 '-C-methylenethymidine or with 3 '-amino-3 '-deoxy-5 '-O-DMT-β-thymidine followed by desilylation of the protected dimers. The 3 '-O-phosphoramidite derivative of one of the nucleoside dimers was successfully prepared by condensation with [P(-Cl)(-OCH2CH2CN)-N(iPr)2}] in DCM in the presence of N,N-diisopropylethylamine (DIPEA), which is a building block for the preparation of mercaptoacetamido-linked oligonucleotides of therapeutic applications.
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Affiliation(s)
- Vivek K Sharma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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22
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Kosbar TR, Sofan MA, Waly MA, Pedersen EB. Anti-parallel triplexes: Synthesis of 8-aza-7-deazaadenine nucleosides with a 3-aminopropynyl side-chain and its corresponding LNA analog. Bioorg Med Chem 2015; 23:2458-69. [PMID: 25868748 DOI: 10.1016/j.bmc.2015.03.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/13/2015] [Accepted: 03/19/2015] [Indexed: 10/23/2022]
Abstract
The phosphoramidites of DNA monomers of 7-(3-aminopropyn-1-yl)-8-aza-7-deazaadenine (Y) and 7-(3-aminopropyn-1-yl)-8-aza-7-deazaadenine LNA (Z) are synthesized, and the thermal stability at pH 7.2 and 8.2 of anti-parallel triplexes modified with these two monomers is determined. When, the anti-parallel TFO strand was modified with Y with one or two insertions at the end of the TFO strand, the thermal stability was increased 1.2°C and 3°C at pH 7.2, respectively, whereas one insertion in the middle of the TFO strand decreased the thermal stability 1.4°C compared to the wild type oligonucleotide. In order to be sure that the 3-aminopropyn-1-yl chain was contributing to the stability of the triplex, the nucleobase X without the aminopropynyl group was inserted in the same positions. In all cases the thermal stability was lower than the corresponding oligonucleotides carrying the 3-aminopropyn-1-yl chain, especially at the end of the TFO strand. On the other hand, the thermal stability of the anti-parallel triplex was dramatically decreased when the TFO strand was modified with the LNA monomer analog Z in the middle of the TFO strand (ΔTm=-9.1°C). Also the thermal stability decreased about 6.1°C when the TFO strand was modified with Z and the Watson-Crick strand with adenine-LNA (A(L)). The molecular modeling results showed that, in case of nucleobases Y and Z a hydrogen bond (1.69 and 1.72Ǻ, respectively) was formed between the protonated 3-aminopropyn-1-yl chain and one of the phosphate groups in Watson-Crick strand. Also, it was shown that the nucleobase Y made a good stacking and binding with the other nucleobases in the TFO and Watson-Crick duplex, respectively. In contrast, the nucleobase Z with LNA moiety was forced to twist out of plane of Watson-Crick base pair which is weakening the stacking interactions with the TFO nucleobases and the binding with the duplex part.
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Affiliation(s)
- Tamer R Kosbar
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; Department of Chemistry, Faculty of Science, Damietta University, 34517 New Damietta, Damietta, Egypt
| | - Mamdouh A Sofan
- Department of Chemistry, Faculty of Science, Damietta University, 34517 New Damietta, Damietta, Egypt
| | - Mohamed A Waly
- Department of Chemistry, Faculty of Science, Damietta University, 34517 New Damietta, Damietta, Egypt
| | - Erik B Pedersen
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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23
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Sharma VK, Rungta P, Maikhuri VK, Prasad AK. An astute synthesis of locked nucleic acid monomers. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40508-015-0028-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Novel attributes of Locked Nucleic Acid (LNA) makes it preferable over most of the other classes of modified nucleic acid analogues and therefore, it has been extensively explored in different synthetic oligonucleotide based therapeutics. In addition to five oligonucleotides of this class undergoing clinical trials, a healthy pipeline in pre-clinical studies validates the tenacity of LNA. Due to the increasing demand, an efficient biocatalytic methodology has recently been devised for the convergent synthesis of LNA monomers via selective enzymatic monoacetylation of diastereotopic hydroxymethyl functions of 3-O-benzyl-4-C-hydroxymethyl-1,2-O-isopropylidene-α-D-ribofuranose. This commentary article provides an insight into the different synthetic strategies followed for the synthesis of LNA monomers and their triumphs in clinical biotechnology.
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24
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Šála M, Dejmek M, Procházková E, Hřebabecký H, Rybáček J, Dračínský M, Novák P, Rosenbergová Š, Fukal J, Sychrovský V, Rosenberg I, Nencka R. Synthesis of locked cyclohexene and cyclohexane nucleic acids (LCeNA and LCNA) with modified adenosine units. Org Biomol Chem 2015; 13:2703-15. [DOI: 10.1039/c4ob02193b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We designed novel conformationally locked cyclohexene nucleic acid and studied their properties.
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25
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Sharma VK, Sharma RK, Singh SK. Antisense oligonucleotides: modifications and clinical trials. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00184b] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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26
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Gao J, Luo X, Li Y, Gao R, Chen H, Ji D. Synthesis and biological evaluation of 2-oxo-pyrazine-3-carboxamide-yl nucleoside analogues and their epimers as inhibitors of influenza A viruses. Chem Biol Drug Des 2014; 85:245-52. [PMID: 24954298 DOI: 10.1111/cbdd.12382] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/22/2014] [Accepted: 06/12/2014] [Indexed: 12/24/2022]
Abstract
Novel 2-oxo-pyrazine-3-carboxamide-yl nucleoside analogues and their epimers were designed, synthesized and evaluated for their activities against influenza A viruses H1N1 and H3N2 in Madin-Darby canine kidney cells. All the compounds showed low cytotoxicities in these anti-influenza tests. One of the epimers, 4-[(1S, 3R, 4R, 7R)-7-hydroxy-1-(hydroxymethyl)-2,5-dioxabicyclo[2.2.1]heptan-3-yl]-3-oxo-3,4-dihydropyrazine-2-carboxamide 8a, with high antiviral activities (IC50 = 7.41, 5.63 μm for H3N2 and H1N1, respectively) and remarkable low cytotoxicity (TC50 > 200 μm), has great potential for further development as a novel anti-influenza A agent. Molecular docking of compound 8a with RNA-dependent RNA polymerase was performed to understand the binding mode between these inhibitors and the active site of RdRp and to rationalize some SARs.
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Affiliation(s)
- Jingjing Gao
- School of Chemistry and Chemical Engineering, Shanghai JiaoTong University, Shanghai, 200240, China
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27
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Kaura M, Kumar P, Hrdlicka PJ. Synthesis, hybridization characteristics, and fluorescence properties of oligonucleotides modified with nucleobase-functionalized locked nucleic acid adenosine and cytidine monomers. J Org Chem 2014; 79:6256-68. [PMID: 24933409 DOI: 10.1021/jo500994c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Conformationally restricted nucleotides such as locked nucleic acid (LNA) are very popular as affinity-, specificity-, and stability-enhancing modifications in oligonucleotide chemistry to produce probes for nucleic acid targeting applications in molecular biology, biotechnology, and medicinal chemistry. Considerable efforts have been devoted in recent years to optimize the biophysical properties of LNA through additional modification of the sugar skeleton. We recently introduced C5-functionalization of LNA uridines as an alternative and synthetically more straightforward approach to improve the biophysical properties of LNA. In the present work, we set out to test the generality of this concept by studying the characteristics of oligonucleotides modified with four different C5-functionalized LNA cytidine and C8-functionalized LNA adenosine monomers. The results strongly suggest that C5-functionalization of LNA pyrimidines is indeed a viable approach for improving the binding affinity, target specificity, and/or enzymatic stability of LNA-modified ONs, whereas C8-functionalization of LNA adenosines is detrimental to binding affinity and specificity. These insights will impact the future design of conformationally restricted nucleotides for nucleic acid targeting applications.
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Affiliation(s)
- Mamta Kaura
- Department of Chemistry, University of Idaho , Moscow, Idaho 83844-2343, United States
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28
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Sharma VK, Kumar M, Olsen CE, Prasad AK. Chemoenzymatic Convergent Synthesis of 2′-O,4′-C-Methyleneribonucleosides. J Org Chem 2014; 79:6336-41. [DOI: 10.1021/jo5008338] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Vivek K Sharma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi , Delhi 110 007, India
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29
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Kumar P, Baral B, Anderson BA, Guenther DC, Østergaard ME, Sharma PK, Hrdlicka PJ. C5-alkynyl-functionalized α-L-LNA: synthesis, thermal denaturation experiments and enzymatic stability. J Org Chem 2014; 79:5062-73. [PMID: 24797769 PMCID: PMC4049248 DOI: 10.1021/jo5006153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Indexed: 12/23/2022]
Abstract
Major efforts are currently being devoted to improving the binding affinity, target specificity, and enzymatic stability of oligonucleotides used for nucleic acid targeting applications in molecular biology, biotechnology, and medicinal chemistry. One of the most popular strategies toward this end has been to introduce additional modifications to the sugar ring of affinity-inducing conformationally restricted nucleotide building blocks such as locked nucleic acid (LNA). In the preceding article in this issue, we introduced a different strategy toward this end, i.e., C5-functionalization of LNA uridines. In the present article, we extend this strategy to α-L-LNA: i.e., one of the most interesting diastereomers of LNA. α-L-LNA uridine monomers that are conjugated to small C5-alkynyl substituents induce significant improvements in target affinity, binding specificity, and enzymatic stability relative to conventional α-L-LNA. The results from the back-to-back articles therefore suggest that C5-functionalization of pyrimidines is a general and synthetically straightforward approach to modulate biophysical properties of oligonucleotides modified with LNA or other conformationally restricted monomers.
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Affiliation(s)
- Pawan Kumar
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Bharat Baral
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Brooke A. Anderson
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Dale C. Guenther
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Michael E. Østergaard
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Pawan K. Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Patrick J. Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
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30
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Synthesis of 2′-O,4′-C-alkylene-bridged ribonucleosides and their evaluation as inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett 2014; 24:2699-702. [DOI: 10.1016/j.bmcl.2014.04.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 12/22/2022]
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31
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Condon D, Yildirim I, Kennedy SD, Mort BC, Kierzek R, Turner DH. Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU). J Phys Chem B 2014; 118:1216-28. [PMID: 24377321 PMCID: PMC3917691 DOI: 10.1021/jp408909t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/27/2013] [Indexed: 01/09/2023]
Abstract
Locked Nucleic Acids (LNAs) are RNA analogues with an O2'-C4' methylene bridge which locks the sugar into a C3'-endo conformation. This enhances hybridization to DNA and RNA, making LNAs useful in microarrays and potential therapeutics. Here, the LNA, L(CAAU), provides a simplified benchmark for testing the ability of molecular dynamics (MD) to approximate nucleic acid properties. LNA χ torsions and partial charges were parametrized to create AMBER parm99_LNA. The revisions were tested by comparing MD predictions with AMBER parm99 and parm99_LNA against a 200 ms NOESY NMR spectrum of L(CAAU). NMR indicates an A-Form equilibrium ensemble. In 3000 ns simulations starting with an A-form structure, parm99_LNA and parm99 provide 66% and 35% agreement, respectively, with NMR NOE volumes and (3)J-couplings. In simulations of L(CAAU) starting with all χ torsions in a syn conformation, only parm99_LNA is able to repair the structure. This implies methods for parametrizing force fields for nucleic acid mimics can reasonably approximate key interactions and that parm99_LNA will improve reliability of MD studies for systems with LNA. A method for approximating χ population distribution on the basis of base to sugar NOEs is also introduced.
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Affiliation(s)
- David
E. Condon
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Ilyas Yildirim
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Scott D. Kennedy
- Department
of Biochemistry and Biophysics, Univeristy
of Rochester, Rochester, New York 14642, United
States
| | - Brendan C. Mort
- University of Rochester
Center for Integrated Research Computing, Rochester, New York 14627, United States
| | - Ryszard Kierzek
- Institute
of Bioorganic Chemistry, Polish Academy
of Sciences, 61-704 Poznan, Poland
| | - Douglas H. Turner
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
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32
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Vidyasagar A, Pathigoolla A, Sureshan KM. Chemoselective alcoholysis/acetolysis of trans-ketals over cis-ketals and its application in the total synthesis of the cellular second messenger, d-myo-inositol-1,4,5-trisphosphate. Org Biomol Chem 2013; 11:5443-53. [DOI: 10.1039/c3ob40789f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Adiyala Vidyasagar
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, India
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33
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Madsen AS, Jørgensen AS, Jensen TB, Wengel J. Large scale synthesis of 2'-amino-LNA thymine and 5-methylcytosine nucleosides. J Org Chem 2012; 77:10718-28. [PMID: 23145501 DOI: 10.1021/jo302036h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thymine intermediate 17 has been synthesized on a multigram scale (50 g, 70 mmol) from starting sugar 1 in 15 steps in an overall yield of 73%, with only 5 purification steps. The key thymine intermediate 18 was obtained from 17 in a single step in 96% yield, whereas the key 5-methylcytosine intermediate 20 was obtained from 17 in 2 steps in 58% yield. This highly efficient large scale route necessitates only 2 and 3 novel steps to obtain N2'-functionalized thymine and 5-methylcytosine amino-LNA phosphoramidites from these key intermediates, respectively.
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Affiliation(s)
- Andreas Stahl Madsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
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34
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Catrina IE, Marras SAE, Bratu DP. Tiny molecular beacons: LNA/2'-O-methyl RNA chimeric probes for imaging dynamic mRNA processes in living cells. ACS Chem Biol 2012; 7:1586-95. [PMID: 22738327 DOI: 10.1021/cb300178a] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
New approaches for imaging dynamic processes involving RNAs in living cells are continuously being developed and optimized. The use of molecular beacons synthesized from 2'-O-methylribonucleotides (which are resistant to cellular nucleases) is an established approach for visualizing native mRNAs in real time. In order to spatially and temporally resolve dynamic steps involving RNA in cells, molecular beacons need to efficiently hybridize to their RNA targets. To expand the repertoire of target sites accessible to molecular beacons, we decreased the length of their probe sequences and altered their backbone by the inclusion of LNA (locked nucleic acid) nucleotides. We named these new LNA/2'-O-methyl RNA chimera oligonucleotides "tiny molecular beacons". We analyzed these tiny molecular beacons and found that the incorporation of just a few LNA nucleotides enables these shorter probes to stably anneal to more structured regions of the RNA than is possible with conventional molecular beacons. The ease of synthesis of tiny molecular beacons and the flexibility to couple them to a large variety of fluorophores and quenchers render them optimal for the detection of less abundant and/or highly structured RNAs. To determine their efficiency to detect endogenous mRNAs in live specimens, we designed tiny molecular beacons that were specific for oskar mRNA and microinjected them into living Drosophila melanogaster oocytes. We then imaged the live oocytes via spinning disk confocal microscopy. The results demonstrate that tiny molecular beacons hybridize to target mRNA at faster rates than classically designed molecular beacons and are able to access previously inaccessible target regions.
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Affiliation(s)
- Irina E. Catrina
- Biological Sciences Department,
Hunter College, City University of New York, New York, New York 10065, United States
| | - Salvatore A. E. Marras
- Public Health Research Institute,
Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, New
Jersey 07103, United States
| | - Diana P. Bratu
- Biological Sciences Department,
Hunter College, City University of New York, New York, New York 10065, United States
- Program in Molecular, Cellular,
and Developmental Biology, and Program in Biochemistry, The Graduate
Center, City University of New York, New
York, New York 10016, United States
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35
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Martínez-Montero S, Fernández S, Sanghvi YS, Gotor V, Ferrero M. CAL-B-Catalyzed Acylation of Nucleosides and Role of the Sugar Conformation: An Improved Understanding of the Enzyme-Substrate Recognition. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200609] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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36
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Dixit SS, Upadhayaya RS, Chattopadhyaya J. New parasite inhibitors encompassing novel conformationally-locked 5′-acyl sulfamoyl adenosines. Org Biomol Chem 2012; 10:6121-9. [DOI: 10.1039/c2ob25879j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Nicolaou KC, Ellery SP, Rivas F, Saye K, Rogers E, Workinger TJ, Schallenberger M, Tawatao R, Montero A, Hessell A, Romesberg F, Carson D, Burton D. Synthesis and biological evaluation of 2',4'- and 3',4'-bridged nucleoside analogues. Bioorg Med Chem 2011; 19:5648-69. [PMID: 21840722 PMCID: PMC3348725 DOI: 10.1016/j.bmc.2011.07.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/12/2011] [Accepted: 07/13/2011] [Indexed: 10/18/2022]
Abstract
Most nucleosides in solution typically exist in equilibrium between two major sugar pucker forms, N-type and S-type, but bridged nucleosides can be locked into one of these conformations depending on their specific structure. While many groups have researched these bridged nucleosides for the purpose of determining their binding affinity for antisense applications, we opted to look into the potential for biological activity within these conformationally-locked structures. A small library of 2',4'- and 3',4'-bridged nucleoside analogues was synthesized, including a novel 3',4'-carbocyclic bridged system. The synthesized compounds were tested for antibacterial, antitumor, and antiviral activities, leading to the identification of nucleosides possessing such biological activities. To the best of our knowledge, these biologically active compounds represent the first example of 2',4'-bridged nucleosides to demonstrate such properties. The most potent compound, nucleoside 33, exhibited significant antiviral activity against pseudoviruses SF162 (IC(50)=7.0 μM) and HxB2 (IC(50)=2.4 μM). These findings render bridged nucleosides as credible leads for drug discovery in the anti-HIV area of research.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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38
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Kumar P, Østergaard ME, Hrdlicka PJ. Preparation of C5-functionalized locked nucleic acids (LNAs). CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2011; Chapter 4:Unit 4.43. [PMID: 21400703 DOI: 10.1002/0471142700.nc0443s44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Relative to conventional locked nucleic acids (LNAs), C5-functionalized LNAs with small entities at the C5-position display markedly higher (1) duplex thermostability with complementary single-stranded DNA/RNA targets, (2) target specificity, and (3) 3'-exonuclease stability. C5-Functionalized LNAs carrying a polarity-sensitive fluorophore enable sensitive and efficient discrimination of single nucleotide polymorphisms (SNPs) under non-stringent conditions. This unit describes protocols for chemical synthesis of an LNA uridine diol and corresponding C5-functionalized LNA uridine phosphoramidites. A procedure for incorporation of C5-functionalized LNA uridine phosphoramidites into oligodeoxyribonucleotides by automated DNA synthesis is also described.
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39
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Doessing H, Vester B. Locked and unlocked nucleosides in functional nucleic acids. Molecules 2011; 16:4511-26. [PMID: 21629180 PMCID: PMC6264650 DOI: 10.3390/molecules16064511] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 05/19/2011] [Accepted: 05/25/2011] [Indexed: 12/28/2022] Open
Abstract
Nucleic acids are able to adopt a plethora of structures, many of which are of interest in therapeutics, bio- or nanotechnology. However, structural and biochemical stability is a major concern which has been addressed by incorporating a range of modifications and nucleoside derivatives. This review summarizes the use of locked nucleic acid (LNA) and un-locked nucleic acid (UNA) monomers in functional nucleic acids such as aptamers, ribozymes, and DNAzymes.
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Affiliation(s)
| | - Birte Vester
- Nucleic Acid Center, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark; E-Mail: (H.D.)
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40
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Campbell MA, Wengel J. Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals. Chem Soc Rev 2011; 40:5680-9. [PMID: 21556437 DOI: 10.1039/c1cs15048k] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Oligonucleotide chemistry has been developed greatly over the past three decades, with many advances in increasing nuclease resistance, enhancing duplex stability and assisting with cellular uptake. Locked nucleic acid (LNA) is a structurally rigid modification that increases the binding affinity of a modified-oligonucleotide. In contrast, unlocked nucleic acid (UNA) is a highly flexible modification, which can be used to modulate duplex characteristics. In this tutorial review, we will compare the synthetic routes to both of these modifications, contrast the structural features, examine the hybridization properties of LNA and UNA modified duplexes, and discuss how they have been applied within biotechnology and drug research. LNA has found widespread use in antisense oligonucleotide technology, where it can stabilize interactions with target RNA and protect from cellular nucleases. The newly emerging field of siRNAs has made use of LNA and, recently, also UNA. These modifications are able to increase double-stranded RNA stability in serum and decrease off-target effects seen with conventional siRNAs. LNA and UNA are also emerging as versatile modifications for aptamers. Their application to known aptamer structures has opened up the possibility of future selection of LNA-modified aptamers. Each of these oligonucleotide technologies has the potential to become a new type of therapy to treat a wide variety of diseases, and LNA and UNA will no doubt play a part in future developments of therapeutic and diagnostic oligonucleotides.
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Affiliation(s)
- Meghan A Campbell
- Nucleic Acid Center, Institute for Physics and Chemistry, University of Southern Denmark, Odense, Denmark
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41
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Upadhayaya R, Deshpande SG, Li Q, Kardile RA, Sayyed AY, Kshirsagar EK, Salunke RV, Dixit SS, Zhou C, Földesi A, Chattopadhyaya J. Carba-LNA-5MeC/A/G/T modified oligos show nucleobase-specific modulation of 3'-exonuclease activity, thermodynamic stability, RNA selectivity, and RNase H elicitation: synthesis and biochemistry. J Org Chem 2011; 76:4408-31. [PMID: 21500818 DOI: 10.1021/jo200073q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Using the intramolecular 5-exo-5-hexenyl radical as a key cyclization step, we previously reported an unambiguous synthesis of carba-LNA thymine (cLNA-T), which we subsequently incorporated in antisense oligonucleotides (AON) and investigated their biochemical properties [J. Am. Chem. Soc.2007, 129 (26), 8362-8379]. These cLNA-T incorporated oligos showed specific RNA affinity of +3.5-5 °C/modification for AON:RNA heteroduplexes, which is comparable to what is found for those of LNAs (Locked Nucleic Acids). These modified oligos however showed significantly enhanced nuclease stability (ca. 100 times more) in the blood serum compared to those of the LNA modified counterparts without compromising any RNase H recruitment capability. We herein report the synthesis of 5-methylcytosine-1-yl ((Me)C), 9-adeninyl (A), and 9-guaninyl (G) derivatives of cLNA and their oligonucleotides and report their biochemical properties as potential RNA-directed inhibitors. In a series of isosequential carba-LNA modified AONs, we herein show that all the cLNA modified AONs are found to be RNA-selective, but the magnitude of RNA-selectivity of 7'-R-Me-cLNA-G (cLNA-G) (ΔT(m) = 2.9 °C/modification) and intractable isomeric mixtures of 7'-(S/R)-Me-cLNA-T (cLNA-T, ΔT(m) = 2.2 °C/modification) was found to be better than diastereomeric mixtures of 7'-(S/R)-Me-cLNA-(Me)C with trace of cENA-(Me)C (cLNA-(Me)C, ΔT(m) = 1.8 °C/modification) and 7'-R-Me-cLNA-A (cLNA-A, ΔT(m) = 0.9 °C/modification). cLNA-(Me)C modified AONs however exhibited the best nuclease stability, which is 4-, 7-, and 20-fold better, respectively, than cLNA-T, cLNA-A, and cLNA-G modified counterparts, which in turn was more than 100 times stable than that of the native. When the modification sites are appropriately chosen in the AONs, the cLNA-A, -G, and -(Me)C modified sites in the AON:RNA hybrids can be easily recognized by RNase H, and the RNA strand of the hybrid is degraded in a specific manner, which is important for the design of oligos for therapeutic purposes. The cLNA-(Me)C modified AON/RNA, however, has been found to be degraded 4 times faster than cLNA-A and G modified counterparts. By appropriately choosing the carba-LNA modification sites in AON strands, the digestion of AON:RNA can be either totally repressed or be limited to cleavage at specific sites or at a single site only (similar to that of catalytic RNAzyme or DNAzyme). Considering all physico- and biochemical aspects of cLNA modified oligos, the work suggests that the cLNA modified antisense oligos have the potential of being a promising therapeutic candidate due to their (i) higher nucleobase-specific RNA affinity and RNA selectivity, (ii) greatly improved nuclease stability, and (iii) efficient RNase H recruitment capability, which can induce target RNA cleavage in a very specific manner at multiple or at a single site, in a designed manner.
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Affiliation(s)
- RamShankar Upadhayaya
- Institute of Molecular Medicine, International Biotech Park, Tal Mulshi, Hinjewadi, Pune, India
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42
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Dutta S, Bhaduri N, Rastogi N, Chandel SG, Vandavasi JK, Upadhayaya RS, Chattopadhyaya J. Carba-LNA modified siRNAs targeting HIV-1 TAR region downregulate HIV-1 replication successfully with enhanced potency. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00225a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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43
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Versteeg K, Zwilling D, Wang H, Church KM. Synthesis, structure, and sugar dynamics of a 2′-spiroisoxazolidine thymidine analog. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.08.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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44
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Ito KR, Kodama T, Tomizu M, Negoro Y, Orita A, Osaki T, Hosoki N, Tanaka T, Imanishi T, Obika S. Double-stranded DNA-templated cleavage of oligonucleotides containing a P3'->N5' linkage triggered by triplex formation: the effects of chemical modifications and remarkable enhancement in reactivity. Nucleic Acids Res 2010; 38:7332-42. [PMID: 20615902 PMCID: PMC2978371 DOI: 10.1093/nar/gkq600] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We recently reported double-stranded DNA-templated cleavage of oligonucleotides as a sequence-specific DNA-detecting method. In this method, triplex-forming oligonucleotides (TFOs) modified with 5′-amino-2′,4′-BNA were used as a DNA-detecting probe. This modification introduced a P3′→N5′ linkage (P–N linkage) in the backbone of the TFO, which was quickly cleaved under acidic conditions when it formed a triplex. The prompt fission of the P–N linkage was assumed to be driven by a conformational strain placed on the linkage upon triplex formation. Therefore, chemical modifications around the P–N linkage should change the reactivity by altering the microenvironment. We synthesized 5′-aminomethyl type nucleic acids, and incorporated them into TFOs instead of 5′-amino-2′,4′-BNA to investigate the effect of 5′-elongation. In addition, 2′,4′-BNA/LNA or 2′,5′-linked DNA were introduced at the 3′- and/or 5′-neighboring residues of 5′-amino-2′,4′-BNA to reveal neighboring residual effects. We evaluated the triplex stability and reaction properties of these TFOs, and found out that chemical modifications around the P–N linkage greatly affected their reaction properties. Notably, 2′,5′-linked DNA at the 3′ position flanking 5′-amino-2′,4′-BNA brought significantly higher reactivity, and we succeeded in indicating that a TFO with this modification is promising as a DNA analysis tool.
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Affiliation(s)
- Kosuke Ramon Ito
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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45
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Seth PP, Vasquez G, Allerson CA, Berdeja A, Gaus H, Kinberger GA, Prakash TP, Migawa MT, Bhat B, Swayze EE. Synthesis and biophysical evaluation of 2',4'-constrained 2'O-methoxyethyl and 2',4'-constrained 2'O-ethyl nucleic acid analogues. J Org Chem 2010; 75:1569-81. [PMID: 20136157 DOI: 10.1021/jo902560f] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We have recently shown that combining the structural elements of 2'O-methoxyethyl (MOE) and locked nucleic acid (LNA) nucleosides yielded a series of nucleoside modifications (cMOE, 2',4'-constrained MOE; cEt, 2',4'-constrained ethyl) that display improved potency over MOE and an improved therapeutic index relative to that of LNA antisense oligonucleotides. In this report we present details regarding the synthesis of the cMOE and cEt nucleoside phosphoramidites and the biophysical evaluation of oligonucleotides containing these nucleoside modifications. The synthesis of the cMOE and cEt nucleoside phosphoramidites was efficiently accomplished starting from inexpensive commercially available diacetone allofuranose. The synthesis features the use of a seldom used 2-naphthylmethyl protecting group that provides crystalline intermediates during the synthesis and can be cleanly deprotected under mild conditions. The synthesis was greatly facilitated by the crystallinity of a key mono-TBDPS-protected diol intermediate. In the case of the cEt nucleosides, the introduction of the methyl group in either configuration was accomplished in a stereoselective manner. Ring closure of the 2'-hydroxyl group onto a secondary mesylate leaving group with clean inversion of stereochemistry was achieved under surprisingly mild conditions. For the S-cEt modification, the synthesis of all four (thymine, 5-methylcytosine, adenine, and guanine) nucleobase-modified phosphoramidites was accomplished on a multigram scale. Biophysical evaluation of the cMOE- and cEt-containing oligonucleotides revealed that they possess hybridization and mismatch discrimination attributes similar to those of LNA but greatly improved resistance to exonuclease digestion.
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Affiliation(s)
- Punit P Seth
- Department of Medicinal Chemistry, Isis Pharmaceuticals, 1896 Rutherford Road, Carlsbad, California 92008, USA.
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46
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Obika S, Imanishi T, Kawada Y, Baba T, Fujisaka A. Bridged Nucleic Acids: Development, Synthesis and Properties. HETEROCYCLES 2010. [DOI: 10.3987/rev-10-667] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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47
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Kumar S, Sharma PK, Stein PC, Nielsen P. Synthesis of the 3′-C-Hydroxymethyl-Branched Locked Nucleic Acid Thymidine Monomer. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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48
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Santhosh Kumar T, Kumar P, Sharma PK, Hrdlicka PJ. Optimized synthesis of LNA uracil nucleosides. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.09.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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49
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Wu QP, Zhou MX, Xi XD, Song D, Wang Y, Liu HX, Li YZ, Zhang QS. A facile one-pot procedure for the transformation of acetonides into diacetates catalyzed with Bi(OTf)3·xH2O. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.02.163] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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50
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Mathé C, Périgaud C. Recent Approaches in the Synthesis of Conformationally Restricted Nucleoside Analogues. European J Org Chem 2008. [DOI: 10.1002/ejoc.200700946] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Christophe Mathé
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS – UM 1 – UM 2, Université Montpellier 2, Case Courrier 1705, Place E. Bataillon, 34095 Montpelliercedex 05, France, Fax: +33‐4‐67042029
| | - Christian Périgaud
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS – UM 1 – UM 2, Université Montpellier 2, Case Courrier 1705, Place E. Bataillon, 34095 Montpelliercedex 05, France, Fax: +33‐4‐67042029
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