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Hasegawa S, Inagaki M, Kato S, Li Z, Kimura Y, Abe H. Synthesis of nucleoside oligophosphates by electrophilic activation of phosphorothioate. Org Biomol Chem 2023; 21:3997-4001. [PMID: 37186249 DOI: 10.1039/d2ob02260e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We herein report a new synthetic method for nucleoside oligophosphates based on electrophilic activation of 5'-phosphorothioate nucleotides. The treatment of phosphorothioate with 2,4-dinitrochlorobenzene (DNCB) efficiently afforded the key activated species, electrophilic thioester nucleotides (EPT-Ns), which were coupled with various phosphate reagents to afford the target nucleoside oligophosphates, including an mRNA cap analog.
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Affiliation(s)
| | | | - Shunichi Kato
- Graduate School of Science, Nagoya University, Japan.
| | - Zhenmin Li
- Graduate School of Science, Nagoya University, Japan.
| | | | - Hiroshi Abe
- Graduate School of Science, Nagoya University, Japan.
- CREST, Japan Science and Technology Agency, Japan
- Institute for Glyco-core Research (iGCORE), Japan
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2
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Kuznetsova VE, Shershov VE, Guseinov TO, Miftakhov RA, Solyev PN, Novikov RA, Levashova AI, Zasedatelev AS, Lapa SA, Chudinov AV. Synthesis of Cy5-Labelled C5-Alkynyl-modified cytidine triphosphates via Sonogashira coupling for DNA labelling. Bioorg Chem 2023; 131:106315. [PMID: 36528924 DOI: 10.1016/j.bioorg.2022.106315] [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: 10/04/2022] [Revised: 11/15/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
New applications of palladium-catalyzed Sonogashira-type cross-coupling reaction between C5-halogenated 2'-deoxycytidine-5'-monophosphate and novel cyanine dyes with a terminal alkyne group have been developed. The present methodology allows to synthesize of fluorescently labeled C5-nucleoside triphosphates with different acetylene linkers between the fluorophore and pyrimidine base in good to excellent yields under mild reaction conditions. Modified 2'-deoxycytidine-5'-triphosphates were shown to be good substrates for DNA polymerases and were incorporated into the DNA by polymerase chain reaction.
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Affiliation(s)
- Viktoriya E Kuznetsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Valeriy E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Teimur O Guseinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Rinat A Miftakhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Pavel N Solyev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Roman A Novikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna I Levashova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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3
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Synthesis of Mixed Dinucleotides by Mechanochemistry. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103229. [PMID: 35630705 PMCID: PMC9147584 DOI: 10.3390/molecules27103229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/17/2022]
Abstract
We report the synthesis of vitamin B1, B2, and B3 derived nucleotides and dinucleotides generated either through mechanochemical or solution phase chemistry. Under the explored conditions, adenosine and thiamine proved to be particularly amenable to milling conditions. Following optimization of the chemistry related to the formation pyrophosphate bonds, mixed dinucleotides of adenine and thiamine (vitamin B1), riboflavin (vitamin B2), nicotinamide riboside and 3-carboxamide 4-pyridone riboside (both vitamin B3 derivatives) were generated in good yields. Furthermore, we report an efficient synthesis of the MW+4 isotopologue of NAD+ for which deuterium incorporation is present on either side of the dinucleotidic linkage, poised for isotopic tracing experiments by mass spectrometry. Many of these mixed species are novel and present unexplored possibilities to simultaneously enhance or modulate cofactor transporters and enzymes of independent biosynthetic pathways.
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4
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Wang L, Lowary TL. Synthesis of structurally-defined polymeric glycosylated phosphoprenols as potential lipopolysaccharide biosynthetic probes. Chem Sci 2021; 12:12192-12200. [PMID: 34667585 PMCID: PMC8457389 DOI: 10.1039/d1sc03852d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/13/2021] [Indexed: 11/24/2022] Open
Abstract
The biosynthesis of lipopolysaccharide (LPS), a key immunomodulatory molecule produced by gram-negative bacteria, has been a topic of long-term interest. To date, the chemical probes used as tools to study LPS biosynthetic pathways have consisted primarily of small fragments of the larger structure (e.g., the O-chain repeating unit). While such compounds have helped to provide significant insight into many aspects of LPS assembly, understanding other aspects will require larger, more complex probes. For example, the molecular interactions between polymeric LPS biosynthetic intermediates and the proteins that transfer them across the inner and outer membrane remain largely unknown. We describe the synthesis of two lipid-linked polysaccharides, containing 11 and 27 monosaccharide residues, that are related to LPS O-chain biosynthesis in Escherichia coli O9a. This work has led not only to multi-milligram quantities of two biosynthetic probes, but also provided insights into challenges that must be overcome in the chemical synthesis of structurally-defined polysaccharides. The synthesis of lipid-linked polysaccharides containing 11 and 27 monosaccharides via a ‘frame-shift’ strategy is described. The work provides biosynthetic probes and highlights challenges in synthesizing structurally-defined polymeric glycans.![]()
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Affiliation(s)
- Lei Wang
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada .,Institute of Biological Chemistry, Academia Sinica Academia Road, Section 2, #128, Nangang Taipei 11529 Taiwan.,Institute of Biochemical Sciences, National Taiwan University Section 4, #1, Roosevelt Road. Taipei 10617 Taiwan
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5
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Rachwalak M, Rozniewska M, Golebiewska J, Jakubowski T, Sobkowski M, Romanowska J. A practical synthesis of nucleoside 5′-diphosphates from nucleoside 5′- H-phosphonate monoesters. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1814817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Marta Rachwalak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | | | - Justyna Golebiewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Tomasz Jakubowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Michal Sobkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Joanna Romanowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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6
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Mikkola S. Nucleotide Sugars in Chemistry and Biology. Molecules 2020; 25:E5755. [PMID: 33291296 PMCID: PMC7729866 DOI: 10.3390/molecules25235755] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleotide sugars have essential roles in every living creature. They are the building blocks of the biosynthesis of carbohydrates and their conjugates. They are involved in processes that are targets for drug development, and their analogs are potential inhibitors of these processes. Drug development requires efficient methods for the synthesis of oligosaccharides and nucleotide sugar building blocks as well as of modified structures as potential inhibitors. It requires also understanding the details of biological and chemical processes as well as the reactivity and reactions under different conditions. This article addresses all these issues by giving a broad overview on nucleotide sugars in biological and chemical reactions. As the background for the topic, glycosylation reactions in mammalian and bacterial cells are briefly discussed. In the following sections, structures and biosynthetic routes for nucleotide sugars, as well as the mechanisms of action of nucleotide sugar-utilizing enzymes, are discussed. Chemical topics include the reactivity and chemical synthesis methods. Finally, the enzymatic in vitro synthesis of nucleotide sugars and the utilization of enzyme cascades in the synthesis of nucleotide sugars and oligosaccharides are briefly discussed.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, 20014 Turku, Finland
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7
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Green approaches for the synthesis of nucleotides, their conjugates and analogues. PHOSPHORUS SULFUR 2020. [DOI: 10.1080/10426507.2020.1804164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Appy L, Chardet C, Peyrottes S, Roy B. Synthetic Strategies for Dinucleotides Synthesis. Molecules 2019; 24:molecules24234334. [PMID: 31783537 PMCID: PMC6930578 DOI: 10.3390/molecules24234334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Dinucleoside 5′,5′-polyphosphates (DNPs) are endogenous substances that play important intra- and extracellular roles in various biological processes, such as cell proliferation, regulation of enzymes, neurotransmission, platelet disaggregation and modulation of vascular tone. Various methodologies have been developed over the past fifty years to access these compounds, involving enzymatic processes or chemical procedures based either on P(III) or P(V) chemistry. Both solution-phase and solid-support strategies have been developed and are reported here. Recently, green chemistry approaches have emerged, offering attracting alternatives. This review outlines the main synthetic pathways for the preparation of dinucleoside 5′,5′-polyphosphates, focusing on pharmacologically relevant compounds, and highlighting recent advances.
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Depaix A, Peyrottes S, Roy B. One-pot synthesis of nucleotides in water medium. PHOSPHORUS SULFUR 2019. [DOI: 10.1080/10426507.2018.1541239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Anaïs Depaix
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM , Montpellier Cedex 5 , France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM , Montpellier Cedex 5 , France
| | - Béatrice Roy
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM , Montpellier Cedex 5 , France
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10
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Appy L, Depaix A, Bantreil X, Lamaty F, Peyrottes S, Roy B. Straightforward Ball-Milling Access to Dinucleoside 5',5'-Polyphosphates via Phosphorimidazolide Intermediates. Chemistry 2019; 25:2477-2481. [PMID: 30549335 DOI: 10.1002/chem.201805924] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 11/08/2022]
Abstract
A solvent-assisted mechanochemical approach to access symmetrical and mixed dinucleoside 5,5'-polyphosphates is reported. Under ball-milling conditions, nucleoside 5'-monophosphates were quantitatively activated using 1,1'-carbonyldiimidazole, forming their phosphorimidazolide derivatives. The addition of a nucleoside 5'-mono-, di- or triphosphate directly led to the formation of the corresponding dinucleotides. Benefits of the reported one-pot method include the use of unprotected nucleotides in their sodium or acid form, activation by the eco-friendly 1,1'-carbonyldiimidazole, non-dry conditions, short reaction time, high conversion rates, and easy setup and purification. This work offers new perspectives for the synthesis of nucleotide conjugates and analogues, combining the phosphorimidazolide approach and milling conditions.
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Affiliation(s)
- Lucie Appy
- Nucleosides & Phosphorylated Effectors, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1705, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Anaïs Depaix
- Nucleosides & Phosphorylated Effectors, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1705, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Xavier Bantreil
- Green Chemistry and Enabling Technologies, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1703, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Frédéric Lamaty
- Green Chemistry and Enabling Technologies, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1703, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Nucleosides & Phosphorylated Effectors, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1705, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Béatrice Roy
- Nucleosides & Phosphorylated Effectors, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1705, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
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11
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Ahmadipour S, Miller GJ. Recent advances in the chemical synthesis of sugar-nucleotides. Carbohydr Res 2017; 451:95-109. [PMID: 28923409 DOI: 10.1016/j.carres.2017.08.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Sanaz Ahmadipour
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK
| | - Gavin J Miller
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK.
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12
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Synthesis, crystal structure, spectroscopic studies and magnetic behavior of a new diphosphonate-bridged dinuclear copper(II) complex. Polyhedron 2017. [DOI: 10.1016/j.poly.2017.05.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Depaix A, Peyrottes S, Roy B. Water-Medium Synthesis of Nucleoside 5'-Polyphosphates. ACTA ACUST UNITED AC 2017. [PMID: 28628206 DOI: 10.1002/cpnc.30] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This unit describes a one-pot, two step synthesis of ribonucleoside 5'-di- and 5'-triphosphates, as well as their purification. The first step of the synthesis involves the activation of an unprotected ribonucleoside 5'-monophosphate with 2-chloro-1,3-dimethylimidazolinium hexafluorophosphate and imidazole, in a mixture of water/acetonitrile. The resulting phosphorimidazolate intermediate is then treated with inorganic phosphate or pyrophosphate to afford the corresponding nucleoside 5'-di- or 5'-triphosphates. The attractive features of this strategy include the absence of protecting groups on the starting material and convenient set up (i.e., use of water, non-dry solvents and reagents, commercially available sodium salts). © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM, Campus Triolet, Montpellier, France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM, Campus Triolet, Montpellier, France
| | - Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM, Campus Triolet, Montpellier, France
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14
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Depaix A, Peyrottes S, Roy B. One-Pot Synthesis of Nucleotides and Conjugates in Aqueous Medium. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
| | - Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
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15
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Abstract
Focusing on the recent literature (since 2000), this review outlines the main synthetic approaches for the preparation of 5'-mono-, 5'-di-, and 5'-triphosphorylated nucleosides, also known as nucleotides, as well as several derivatives, namely, cyclic nucleotides and dinucleotides, dinucleoside 5',5'-polyphosphates, sugar nucleotides, and nucleolipids. Endogenous nucleotides and their analogues can be obtained enzymatically, which is often restricted to natural substrates, or chemically. In chemical synthesis, protected or unprotected nucleosides can be used as the starting material, depending on the nature of the reagents selected from P(III) or P(V) species. Both solution-phase and solid-support syntheses have been developed and are reported here. Although a considerable amount of research has been conducted in this field, further work is required because chemists are still faced with the challenge of developing a universal methodology that is compatible with a large variety of nucleoside analogues.
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Affiliation(s)
- Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Christian Périgaud
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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16
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Drenichev MS, Mikhailov SN. Poly(ADP-ribose): From chemical synthesis to drug design. Bioorg Med Chem Lett 2016; 26:3395-403. [PMID: 27318540 DOI: 10.1016/j.bmcl.2016.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/02/2016] [Accepted: 06/04/2016] [Indexed: 12/17/2022]
Abstract
Poly(ADP-ribose) (PAR) is an important biopolymer, which is involved in various life processes such as DNA repair and replication, modulation of chromatin structure, transcription, cell differentiation, and in pathogenesis of various diseases such as cancer, diabetes, ischemia and inflammations. PAR is the most electronegative biopolymer and this property is essential for its binding with a wide range of proteins. Understanding of PAR functions in cell on molecular level requires chemical synthesis of regular PAR oligomers. Recently developed methodologies for chemical synthesis of PAR oligomers, will facilitate the study of various cellular processes, involving PAR.
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Affiliation(s)
- Mikhail S Drenichev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russian Federation
| | - Sergey N Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russian Federation.
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17
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Xu Z, Ramsay Shaw B. Synthesis, Hydrolysis, and Protonation-Promoted Intramolecular Reductive Breakdown of Potential NRTIs: Stavudine α-P-Borano-γ-P-N-L-tryptophanyltriphosphates. Molecules 2015; 20:18808-26. [PMID: 26501247 PMCID: PMC6332514 DOI: 10.3390/molecules201018808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 09/15/2015] [Accepted: 09/21/2015] [Indexed: 11/16/2022] Open
Abstract
Phosphorus-modified prodrugs of dideoxynucleoside triphosphates (ddNTPs) have shown promise as pronucleotide strategies for improving antiviral activity compared to their parent dideoxynucleosides. Borane modified NTPs offer a promising choice as nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs). However, the availability of α-P-borano-γ-P-substituted NTP analogs remains limited due to challenges with synthesis and purification. Here, we report the chemical synthesis and stability of a new potential class of NRTI prodrugs: stavudine (d4T) 5′-α-P-borano-γ-P-N-l-tryptophanyltriphosphates. One-pot synthesis of these compounds was achieved via a modified cyclic trimetaphosphate approach. Pure Rp and Sp diastereomers were obtained after HPLC separation. Based on LC-MS analysis, we report degradation pathways, half-lives (5–36 days) and mechanisms arising from structural differences to generate the corresponding borano tri- and di-phosphates, and H-phosphonate, via several parallel routes in buffer at physiologically relevant pH and temperature. Here, the major hydrolysis products, d4T α-P-boranotriphosphate Rp and Sp isomers, were isolated by HPLC and identified with spectral data. We first propose that one of the major degradation products, d4T H-phosphonate, is generated from the d4T pronucleotides via a protonation-promoted intramolecular reduction followed by a second step nucleophilic attack. This report could provide valuable information for pronucleotide-based drug design in terms of selective release of target nucleotides.
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Affiliation(s)
- Zhihong Xu
- Shaw Department of Chemistry, Duke University, Durham, NC 27708, USA.
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18
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Novel concept of enzyme selective nicotinamide adenine dinucleotide (NAD)-modified inhibitors based on enzyme taxonomy from the diphosphate conformation of NAD. Bioorg Med Chem Lett 2015; 25:5133-6. [PMID: 26463132 DOI: 10.1016/j.bmcl.2015.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 09/29/2015] [Accepted: 10/03/2015] [Indexed: 11/23/2022]
Abstract
The dihedral angle θ of the diphosphate part of NAD(P) were investigated to distinguish the differences in the binding-conformation of NAD(P) to enzymes and to create an enzyme taxonomy. Furthermore, new inhibitors with fixed dihedral angles showed that enzymes could recognize the differences in the dihedral angle θ. We suggest the taxonomy and the dihedral angle θ are important values for chemists to consider when designing inhibitors and drugs that target enzymes.
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