1
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Xiang L, Hu T, Xue H, Pan W, Xie Y, Shen J. Synthesis and evaluation of NHC derivatives and 4'-fluorouridine prodrugs. Org Biomol Chem 2023; 21:2754-2767. [PMID: 36917467 DOI: 10.1039/d3ob00268c] [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: 03/06/2023]
Abstract
β-D-N4-Hydroxycytidine (NHC) derivatives with structural modifications at the C4', O4' or C6 position and 4'-fluorouridine prodrugs were synthesized and evaluated for their antiviral activities against respiratory syncytial virus (RSV) or influenza virus (IFV) in vitro. The NHC derivatives were found inactive, but 4'-fluorouridine and its prodrugs had potent anti-RSV and anti-IFV activities. 4'-Fluorouridine was proved to be a nucleoside with poor stability, but the tri-ester prodrugs exhibited enhanced stability, especially tri-isobutyrate ester 1a. This prodrug also showed excellent oral pharmacokinetic properties in rats, with potential to be an oral antiviral candidate.
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Affiliation(s)
- Li Xiang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Tianwen Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Haitao Xue
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wenfang Pan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yuanchao Xie
- Lingang Laboratory, Shanghai 200031, P. R. China.
| | - Jingshan Shen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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2
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Wojnowska M, Feng X, Chen Y, Deng H, O'Hagan D. Identification of Genes Essential for Fluorination and Sulfamylation within the Nucleocidin Gene Clusters of Streptomyces calvus and Streptomyces virens. Chembiochem 2023; 24:e202200684. [PMID: 36548247 PMCID: PMC10946740 DOI: 10.1002/cbic.202200684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022]
Abstract
The gene cluster in Streptomyces calvus associated with the biosynthesis of the fluoro- and sulfamyl-metabolite nucleocidin was interrogated by systematic gene knockouts. Out of the 26 gene deletions, most did not affect fluorometabolite production, nine abolished sulfamylation but not fluorination, and three precluded fluorination, but had no effect on sulfamylation. In addition to nucI, nucG, nucJ, nucK, nucL, nucN, nucO, nucQ and nucP, we identified two genes (nucW, nucA), belonging to a phosphoadenosine phosphosulfate (PAPS) gene cluster, as required for sulfamyl assembly. Three genes (orf(-3), orf2 and orf3) were found to be essential for fluorination, although the activities of their protein products are unknown. These genes as well as nucK, nucN, nucO and nucPNP, whose knockouts produced results differing from those described in a recent report, were also deleted in Streptomyces virens - with confirmatory outcomes. This genetic profile should inform biochemistry aimed at uncovering the enzymology behind nucleocidin biosynthesis.
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Affiliation(s)
- Marta Wojnowska
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Xuan Feng
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Yawen Chen
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Hai Deng
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - David O'Hagan
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
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3
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Lowe PT, O'Hagan D. 4'-Fluoro-nucleosides and nucleotides: from nucleocidin to an emerging class of therapeutics. Chem Soc Rev 2023; 52:248-276. [PMID: 36472161 DOI: 10.1039/d2cs00762b] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The history and development of 4'-fluoro-nucleosides is discussed in this review. This is a class of nucleosides which have their origin in the discovery of the rare fluorine containing natural product nucleocidin. Nucleocidin contains a fluorine atom located at the 4'-position of its ribose ring. From its early isolation as an unexpected natural product, to its total synthesis and bioactivity assessment, nucleocidin has played a role in inspiring the exploration of 4'-fluoro-nucleosides as a privileged motif for nucleoside-based therapeutics.
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Affiliation(s)
- Phillip T Lowe
- School of Chemistry and Biomedical Sciences Research Centre, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.
| | - David O'Hagan
- School of Chemistry and Biomedical Sciences Research Centre, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.
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4
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Adamantane-Substituted Purine Nucleosides: Synthesis, Host-Guest Complexes with β-Cyclodextrin and Biological Activity. Int J Mol Sci 2022; 23:ijms232315143. [PMID: 36499470 PMCID: PMC9739181 DOI: 10.3390/ijms232315143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022] Open
Abstract
Purine nucleosides represent an interesting group of nitrogen heterocycles, showing a wide range of biological effects. In this study, we designed and synthesized a series of 6,9-disubstituted and 2,6,9-trisubstituted purine ribonucleosides via consecutive nucleophilic aromatic substitution, glycosylation, and deprotection of the ribofuranose unit. We prepared eight new purine nucleosides bearing unique adamantylated aromatic amines at position 6. Additionally, the ability of the synthesized purine nucleosides to form stable host-guest complexes with β-cyclodextrin (β-CD) was confirmed using nuclear magnetic resonance (NMR) and mass spectrometry (ESI-MS) experiments. The in vitro antiproliferative activity of purine nucleosides and their equimolar mixtures with β-CD was tested against two types of human tumor cell line. Six adamantane-based purine nucleosides showed an antiproliferative activity in the micromolar range. Moreover, their effect was only slightly suppressed by the presence of β-CD, which was probably due to the competitive binding of the corresponding purine nucleoside inside the β-CD cavity.
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5
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Grosse S, Tahri A, Raboisson P, Houpis Y, Stoops B, Jacoby E, Neefs JM, Van Loock M, Goethals O, Geluykens P, Bonfanti JF, Jonckers THM. From Oxetane to Thietane: Extending the Antiviral Spectrum of 2′-Spirocyclic Uridines by Substituting Oxygen with Sulfur. ACS Med Chem Lett 2022; 13:1879-1884. [DOI: 10.1021/acsmedchemlett.2c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Sandrine Grosse
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Abdellah Tahri
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pierre Raboisson
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Yannis Houpis
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Bart Stoops
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Edgar Jacoby
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Jean-Marc Neefs
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marnix Van Loock
- Janssen Global Public Health, R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Olivia Goethals
- Janssen Global Public Health, R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Peggy Geluykens
- Charles River, Discovery, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Tim H. M. Jonckers
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
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6
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Shet H, Sahu R, Sanghvi YS, Kapdi AR. Strategies for the Synthesis of Fluorinated Nucleosides, Nucleotides and Oligonucleotides. CHEM REC 2022; 22:e202200066. [PMID: 35638251 DOI: 10.1002/tcr.202200066] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/11/2022] [Indexed: 11/09/2022]
Abstract
Fluorinated nucleosides and oligonucleotides are of specific interest as probes for studying nucleic acids interaction, structures, biological transformations, and its biomedical applications. Among various modifications of oligonucleotides, fluorination of preformed nucleoside and/or nucleotides have recently gained attention owing to the unique properties of fluorine atoms imparting medicinal properties with respect to the small size, electronegativity, lipophilicity, and ability for stereochemical control. This review deals with synthetic protocols for selective fluorination either at sugar or base moiety in a preformed nucleosides, nucleotides and nucleic acids using specific fluorinating reagents.
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Affiliation(s)
- Harshita Shet
- Department of Chemistry, Institute of Chemical Technology -, Indian Oil Odisha Campus, IIT Kharagpur Extension Centre, Mouza Samantpuri, Bhubaneswar, Odisha-751013, India.,Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh road, Matunga, Mumbai-400019, India
| | - Rajesh Sahu
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh road, Matunga, Mumbai-400019, India
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802, Crystal Ridge, Encinitas, CA92024-6615, California, USA
| | - Anant R Kapdi
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh road, Matunga, Mumbai-400019, India
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7
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Pasternak A, Bechthold A, Zechel DL. Identification of genes essential for sulfamate and fluorine incorporation during nucleocidin biosynthesis. Chembiochem 2022; 23:e202200140. [PMID: 35544615 DOI: 10.1002/cbic.202200140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/05/2022] [Indexed: 11/07/2022]
Abstract
Nucleocidin is an adenosine derivative containing 4'-fluoro and 5'-O-sulfamoyl substituents. In this study, nucleocidin biosynthesis is examined in two newly discovered producers, Streptomyces virens B-24331 and Streptomyces aureorectus B-24301, which produce nucleocidin and related derivatives at titres 30-fold greater than S. calvus . This enabled the identification of two new O -acetylated nucleocidin derivatives, and a potential glycosyl- O-acetyltransferase. Disruption of nucJ , nucG , and nucI , within S. virens B-24331, specifying a radical SAM / Fe-S dependent enzyme, sulfatase, and arylsulfatase, respectively, led to loss of 5'-O-sulfamoyl biosynthesis, but not fluoronucleoside production. Disruption of nucN , nucK , and nucO specifying an amidinotransferase, and two sulfotransferases respectively, led to loss of fluoronucleoside production. Identification of S. virens B-24331 as a genetically tractable and high producing strain sets the stage for understanding nucleocidin biosynthesis and highlights the utility of using 16S-RNA sequences to identify alternative producers of valuable compounds in the absence of genome sequence data.
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Affiliation(s)
- Aleksandra Pasternak
- Queen's University Faculty of Arts and Science, Chemistry, 90 Bader Lane, Chernoff Hall, K7L 3N6, Kingston, CANADA
| | - Andreas Bechthold
- Albert-Ludwigs-Universität Freiburg Fakultät für Chemie Pharmazie und Geowissenschaften: Albert-Ludwigs-Universitat Freiburg Fakultat fur Chemie und Pharmazie, Pharmaceutical Biology and Biotechnology, Stefan-Meier-Str. 19, 79104, Freiburg i. Br., GERMANY
| | - David L Zechel
- Queen's University, Department of Chemsitry, Chernoff Hall, K7L 3N6, Kingston, CANADA
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8
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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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9
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Chen Y, Zhang Q, Feng X, Wojnowska M, O'Hagan D. Streptomyces aureorectus DSM 41692 and Streptomyces virens DSM 41465 are producers of the antibiotic nucleocidin and 4'-fluoroadenosine is identified as a co-product. Org Biomol Chem 2021; 19:10081-10084. [PMID: 34779476 DOI: 10.1039/d1ob01898a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genome homology and the presence of a putative biosynthetic gene cluster identified Streptomyces aureorectus DSM 41692 and Streptomyces virens DSM 41465 as candidate producers of the antibiotic nucleocidin 1. Indeed when these bacterial strains were cultured in a medium supplemented with fluoride (4 mM) they each produced nucleocidin 1 and the previously identified 4'-fluoro-3'-O-β-glucosylated adenosine 2 and its sulfamylated derivative 3. In both of these cases 4'-fluoroadenosine 9 is also identified as a natural product although it has never been observed during fermentations of Streptomyces calvus, the original source of nucleocidin 1. The identity of 4'-fluoroadenosine 9 was confirmed by a total synthesis as well as by its in vitro enzymatic conversion to metabolite 2 using the glucosyl transferase enzyme, NucGT.
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Affiliation(s)
- Yawen Chen
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - Qingzhi Zhang
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - Xuan Feng
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - Marta Wojnowska
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - David O'Hagan
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
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10
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Zhou Y, Lu K, Li Q, Fan C, Zhou C. C4'-Fluorinated Oligodeoxynucleotides: Synthesis, Stability, Structural Studies. Chemistry 2021; 27:14738-14746. [PMID: 34432342 DOI: 10.1002/chem.202102561] [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: 07/14/2021] [Indexed: 11/06/2022]
Abstract
Fluoro-substitution on the ribose moiety (e. g., 2'-F-deoxyribonucleotide) represents a popular way to modulate the ribose conformation and, hence, the structure and function of nucleic acids. In the present study, we synthesized 4'-F-deoxythymidine (4'-F T) and introduced it to oligodeoxyribonucleotides (ODNs). Though scission of the glycosylic bond of 4'-F T followed by strand cleavage occurred to some extent under alkaline conditions, the 4'-F T-modified ODNs were rather stable in neutral buffers. NMR studies showed that like 2'-F-deoxyribonucleoside, 4'-F T exists predominantly in the North conformation not only in the nucleoside form but also in the context of ODN strands. Circular dichroism spectroscopy, thermal denaturing and RNase H1 footprinting studies of 4'-F T-modified ODN/cDNA and ODN/cRNA duplexes indicated that the North conformation tendency of 4'-F T is maintained in the duplexes, leading to a local structural perturbation. Collectively, 4'-F-deoxyribonucleotide structurally resembles the 2'-F-deoxyribonucleotide but imparts less structural perturbation to the duplex than the latter.
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Affiliation(s)
- Yifei Zhou
- 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
| | - Qiang Li
- 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
| | - 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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11
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Chen P, Wang P, Long Q, Ding H, Cheng G, Li T, Li M. Synthesis of Reverse Glycosyl Fluorides and Rare Glycosyl Fluorides Enabled by Radical Decarboxylative Fluorination of Uronic Acids. Org Lett 2020; 22:9325-9330. [PMID: 33226829 DOI: 10.1021/acs.orglett.0c03514] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An efficient protocol for synthesizing reverse glycosyl fluorides is described, relying on silver-promoted decarboxylative fluorination of structurally diverse pentofuran- and hexopyranuronic acids under the mild reaction conditions. The potential applications of the reaction are further demonstrated by converting readily available d-uronic acid derivatives into uncommon d-/l-glycosyl fluorides through a C1-to-C5 switch strategy. The reaction mechanism is corroborated by 5-exo-trig radical cyclization of allyl α-d-C-glucopyranuronic acid triggered by decarboxylative fluorination.
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Affiliation(s)
- Pengwei Chen
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Hainan Key Laboratory for Research and Development of Natural Products from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Peng Wang
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Qing Long
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Han Ding
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Guoqiang Cheng
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Tiantian Li
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Ming Li
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China.,Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
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12
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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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13
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Feng X, Bello D, Lowe PT, Clark J, O'Hagan D. Two 3'- O-β-glucosylated nucleoside fluorometabolites related to nucleocidin in Streptomyces calvus. Chem Sci 2019; 10:9501-9505. [PMID: 32110306 PMCID: PMC7017864 DOI: 10.1039/c9sc03374b] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/19/2019] [Indexed: 12/13/2022] Open
Abstract
The antibiotic nucleocidin is a product of the soil bacterium Streptomyces calvus T-3018. It is among the very rare fluorine containing natural products but is distinct from the other fluorometabolites in that it is not biosynthesised from 5'-fluorodeoxyadenosine via the fluorinase. It seems to have a unique enzymatic fluorination process. We disclose here the structures of two 4'-fluoro-3'-O-β-glucosylated metabolites (F-Mets I and II) which appear and then disappear before nucleocidin production in batch cultures of S. calvus. Full genome sequencing of S. calvus T-3018 and an analysis of the putative biosynthetic gene cluster for nucleocidin identified UDP-glucose dependent glucosyl transferase (nucGT) and glucosidase (nucGS) genes within the cluster. We demonstrate that these genes express enzymes that have the capacity to attach and remove glucose from the 3'-O-position of adenosine analogues. In the case of F-Met II, deglucosylation with the NucGS glucosidase generates nucleocidin suggesting a role in its biosynthesis. Gene knockouts of nucGT abolished nucelocidin production.
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Affiliation(s)
- Xuan Feng
- School of Chemistry , University of St Andrews , North Haugh, St Andrews , Fife , KY16 9ST , UK .
| | - Davide Bello
- School of Chemistry , University of St Andrews , North Haugh, St Andrews , Fife , KY16 9ST , UK .
| | - Phillip T Lowe
- School of Chemistry , University of St Andrews , North Haugh, St Andrews , Fife , KY16 9ST , UK .
| | - Joshua Clark
- School of Chemistry , University of St Andrews , North Haugh, St Andrews , Fife , KY16 9ST , UK .
| | - David O'Hagan
- School of Chemistry , University of St Andrews , North Haugh, St Andrews , Fife , KY16 9ST , UK .
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14
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Malek-Adamian E, Guenther DC, Matsuda S, Martínez-Montero S, Zlatev I, Harp J, Burai Patrascu M, Foster DJ, Fakhoury J, Perkins L, Moitessier N, Manoharan RM, Taneja N, Bisbe A, Charisse K, Maier M, Rajeev KG, Egli M, Manoharan M, Damha MJ. 4'-C-Methoxy-2'-deoxy-2'-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing. J Am Chem Soc 2017; 139:14542-14555. [PMID: 28937776 DOI: 10.1021/jacs.7b07582] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We designed novel 4'-modified 2'-deoxy-2'-fluorouridine (2'-F U) analogues with the aim to improve nuclease resistance and potency of therapeutic siRNAs by introducing 4'-C-methoxy (4'-OMe) as the alpha (C4'α) or beta (C4'β) epimers. The C4'α epimer was synthesized by a stereoselective route in six steps; however, both α and β epimers could be obtained by a nonstereoselective approach starting from 2'-F U. 1H NMR analysis and computational investigation of the α-epimer revealed that the 4'-OMe imparts a conformational bias toward the North-East sugar pucker, due to intramolecular hydrogen bonding and hyperconjugation effects. The α-epimer generally conceded similar thermal stability as unmodified nucleotides, whereas the β-epimer led to significant destabilization. Both 4'-OMe epimers conferred increased nuclease resistance, which can be explained by the close proximity between 4'-OMe substituent and the vicinal 5'- and 3'-phosphate group, as seen in the X-ray crystal structure of modified RNA. siRNAs containing several C4'α-epimer monomers in the sense or antisense strands triggered RNAi-mediated gene silencing with efficiencies comparable to that of 2'-F U.
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Affiliation(s)
- Elise Malek-Adamian
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Dale C Guenther
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Saúl Martínez-Montero
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Ivan Zlatev
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Joel Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Mihai Burai Patrascu
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Donald J Foster
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Johans Fakhoury
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Lydia Perkins
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Nicolas Moitessier
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Nate Taneja
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Anna Bisbe
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin Maier
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Masad J Damha
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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15
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Banda DM, Nuñez NN, Burnside MA, Bradshaw KM, David SS. Repair of 8-oxoG:A mismatches by the MUTYH glycosylase: Mechanism, metals and medicine. Free Radic Biol Med 2017; 107:202-215. [PMID: 28087410 PMCID: PMC5457711 DOI: 10.1016/j.freeradbiomed.2017.01.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/01/2017] [Accepted: 01/04/2017] [Indexed: 12/12/2022]
Abstract
Reactive oxygen and nitrogen species (RONS) may infringe on the passing of pristine genetic information by inducing DNA inter- and intra-strand crosslinks, protein-DNA crosslinks, and chemical alterations to the sugar or base moieties of DNA. 8-Oxo-7,8-dihydroguanine (8-oxoG) is one of the most prevalent DNA lesions formed by RONS and is repaired through the base excision repair (BER) pathway involving the DNA repair glycosylases OGG1 and MUTYH in eukaryotes. MUTYH removes adenine (A) from 8-oxoG:A mispairs, thus mitigating the potential of G:C to T:A transversion mutations from occurring in the genome. The paramount role of MUTYH in guarding the genome is well established in the etiology of a colorectal cancer predisposition syndrome involving variants of MUTYH, referred to as MUTYH-associated polyposis (MAP). In this review, we highlight recent advances in understanding how MUTYH structure and related function participate in the manifestation of human disease such as MAP. Here we focus on the importance of MUTYH's metal cofactor sites, including a recently discovered "Zinc linchpin" motif, as well as updates to the catalytic mechanism. Finally, we touch on the insight gleaned from studies with MAP-associated MUTYH variants and recent advances in understanding the multifaceted roles of MUTYH in the cell, both in the prevention of mutagenesis and tumorigenesis.
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Affiliation(s)
- Douglas M Banda
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Nicole N Nuñez
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Michael A Burnside
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Katie M Bradshaw
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Sheila S David
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States.
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Saikia I, Borah AJ, Phukan P. Use of Bromine and Bromo-Organic Compounds in Organic Synthesis. Chem Rev 2016; 116:6837-7042. [PMID: 27199233 DOI: 10.1021/acs.chemrev.5b00400] [Citation(s) in RCA: 283] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bromination is one of the most important transformations in organic synthesis and can be carried out using bromine and many other bromo compounds. Use of molecular bromine in organic synthesis is well-known. However, due to the hazardous nature of bromine, enormous growth has been witnessed in the past several decades for the development of solid bromine carriers. This review outlines the use of bromine and different bromo-organic compounds in organic synthesis. The applications of bromine, a total of 107 bromo-organic compounds, 11 other brominating agents, and a few natural bromine sources were incorporated. The scope of these reagents for various organic transformations such as bromination, cohalogenation, oxidation, cyclization, ring-opening reactions, substitution, rearrangement, hydrolysis, catalysis, etc. has been described briefly to highlight important aspects of the bromo-organic compounds in organic synthesis.
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Affiliation(s)
| | - Arun Jyoti Borah
- Department of Chemistry, Gauahti University , Guwahati-781014, Assam, India
| | - Prodeep Phukan
- Department of Chemistry, Gauahti University , Guwahati-781014, Assam, India
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17
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Zhu XM, Hackl S, Thaker MN, Kalan L, Weber C, Urgast DS, Krupp EM, Brewer A, Vanner S, Szawiola A, Yim G, Feldmann J, Bechthold A, Wright GD, Zechel DL. Biosynthesis of the Fluorinated Natural Product Nucleocidin inStreptomyces calvusIs Dependent on thebldA-Specified Leu-tRNAUUAMolecule. Chembiochem 2015; 16:2498-506. [DOI: 10.1002/cbic.201500402] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Xi Ming Zhu
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Stefanie Hackl
- Department of Pharmaceutical Biology and Biotechnology; Institute of Pharmaceutical Sciences; Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 19 79104 Freiburg Germany
| | - Maulik N. Thaker
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Lindsay Kalan
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Claudia Weber
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Dagmar S. Urgast
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Eva M. Krupp
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Alyssa Brewer
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Stephanie Vanner
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Anjuli Szawiola
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Grace Yim
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Jörg Feldmann
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology; Institute of Pharmaceutical Sciences; Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 19 79104 Freiburg Germany
| | - Gerard D. Wright
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - David L. Zechel
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
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18
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Martínez-Montero S, Deleavey GF, Martín-Pintado N, Fakhoury JF, González C, Damha MJ. Locked 2'-Deoxy-2',4'-Difluororibo Modified Nucleic Acids: Thermal Stability, Structural Studies, and siRNA Activity. ACS Chem Biol 2015; 10:2016-23. [PMID: 26053215 DOI: 10.1021/acschembio.5b00218] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
2'-Deoxy-2',4'-difluorouridine (2',4'-diF-rU) was readily incorporated into DNA and RNA oligonucleotides via standard solid phase synthesis protocols. NMR and thermal denaturation (Tm) data of duplexes was consistent with the 2',4'-diF-rU nucleotides adopting a rigid North (RNA-like) sugar conformation, as previously observed for the nucleoside monomer. The impact of this modification on Tm is neutral when incorporated within RNA:RNA duplexes, mildly destabilizing when located in the RNA strand of a DNA:RNA duplex, and highly destabilizing when inserted in the DNA strand of DNA:RNA and DNA:DNA duplexes. Molecular dynamics calculations suggest that the destabilization effect in DNA:DNA and DNA:RNA duplexes is the result of structural distortions created by A/B junctions within the helical structures. Quantum mechanics calculations suggest that the "neutral" effect imparted to A-form duplexes is caused by alterations in charge distribution that compensate the stabilizing effect expected for a pure North-puckered furanose sugar. 2',4'-diF-RNA modified siRNAs were able to trigger RNA interference with excellent efficiency. Of note, incorporation of a few 2',4'-diF-rU residues in the middle of the guide (antisense) strand afforded siRNAs that were more potent than the corresponding siRNAs containing LNA and 2'-F-ANA modifications, and as active as the 2'-F-RNA modified siRNAs.
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Affiliation(s)
- Saúl Martínez-Montero
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Glen F. Deleavey
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Nerea Martín-Pintado
- Instituto de Química Física Rocasolano, CSIC, C/. Serrano 119, 28006 Madrid, Spain
| | - Johans F. Fakhoury
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, C/. Serrano 119, 28006 Madrid, Spain
| | - Masad J. Damha
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
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Sakakibara N, Igarashi J, Takata M, Konishi R, Suzue N, Kato Y, Maruyama T, Tsukamoto I. Design, Synthesis, and Evaluation of Novel 2-Halogenated or Aminated Carbocyclic Oxetanocin a Analogs as Potential Angiogenic Agents. HETEROCYCLES 2015. [DOI: 10.3987/com-15-13293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Martínez-Montero S, Deleavey GF, Kulkarni A, Martín-Pintado N, Lindovska P, Thomson M, González C, Götte M, Damha MJ. Rigid 2',4'-difluororibonucleosides: synthesis, conformational analysis, and incorporation into nascent RNA by HCV polymerase. J Org Chem 2014; 79:5627-35. [PMID: 24873952 DOI: 10.1021/jo500794v] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report on the synthesis and conformational properties of 2'-deoxy-2',4'-difluorouridine (2',4'-diF-rU) and cytidine (2',4'-diF-rC) nucleosides. NMR analysis and quantum mechanical calculations show that the strong stereoelectronic effects induced by the two fluorines essentially "lock" the conformation of the sugar in the North region of the pseudorotational cycle. Our studies also demonstrate that NS5B HCV RNA polymerase was able to accommodate 2',4'-diF-rU 5'-triphosphate (2',4'-diF-rUTP) and to link the monophosphate to the RNA primer strand. 2',4'-diF-rUTP inhibited RNA synthesis in dinucleotide-primed reactions, although with relatively high half-maximal inhibitory concentrations (IC50 > 50 μM). 2',4'-diF-rU/C represents rare examples of "locked" ribonucleoside mimics that lack a bicyclic ring structure.
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Affiliation(s)
- Saúl Martínez-Montero
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC Canada H3A 0B8
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Betson M, Allanson N, Wainwright P. A review of methods to synthesise 4′-substituted nucleosides. Org Biomol Chem 2014; 12:9291-306. [DOI: 10.1039/c4ob01449a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modified nucleosides have received a great deal of attention from the scientific community, either for use as therapeutic agents, diagnostic tools, or as molecular probes.
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