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Pospíšil Š, Panattoni A, Gracias F, Sýkorová V, Hausnerová VV, Vítovská D, Šanderová H, Krásný L, Hocek M. Epigenetic Pyrimidine Nucleotides in Competition with Natural dNTPs as Substrates for Diverse DNA Polymerases. ACS Chem Biol 2022; 17:2781-2788. [PMID: 35679536 PMCID: PMC9594043 DOI: 10.1021/acschembio.2c00342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Five 2'-deoxyribonucleoside triphosphates (dNTPs) derived from epigenetic pyrimidines (5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, 5-hydroxymethyluracil, and 5-formyluracil) were prepared and systematically studied as substrates for nine DNA polymerases in competition with natural dNTPs by primer extension experiments. The incorporation of these substrates was evaluated by a restriction endonucleases cleavage-based assay and by a kinetic study of single nucleotide extension. All of the modified pyrimidine dNTPs were good substrates for the studied DNA polymerases that incorporated a significant percentage of the modified nucleotides into DNA even in the presence of natural nucleotides. 5-Methylcytosine dNTP was an even better substrate for most polymerases than natural dCTP. On the other hand, 5-hydroxymethyl-2'-deoxyuridine triphosphate was not the best substrate for SPO1 DNA polymerase, which naturally synthesizes 5hmU-rich genomes of the SPO1 bacteriophage. The results shed light onto the possibility of gene silencing through recycling and random incorporation of epigenetic nucleotides and into the replication of modified bacteriophage genomes.
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Affiliation(s)
- Šimon Pospíšil
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic,Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Alessandro Panattoni
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Filip Gracias
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Viola Vaňková Hausnerová
- Lab.
of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Dragana Vítovská
- Lab.
of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Hana Šanderová
- Lab.
of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Libor Krásný
- Lab.
of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic,Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic,E-mail:
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Lamiable-Oulaidi F, Harijan RK, Shaffer KJ, Crump DR, Sun Y, Du Q, Gulab SA, Khan AA, Luxenburger A, Woolhouse AD, Sidoli S, Tyler PC, Schramm VL. Synthesis and Characterization of Transition-State Analogue Inhibitors against Human DNA Methyltransferase 1. J Med Chem 2022; 65:5462-5494. [PMID: 35324190 DOI: 10.1021/acs.jmedchem.1c01869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hypermethylation of CpG regions by human DNA methyltransferase 1 (DNMT1) silences tumor-suppression genes, and inhibition of DNMT1 can reactivate silenced genes. The 5-azacytidines are approved inhibitors of DNMT1, but their mutagenic mechanism limits their utility. A synthon approach from the analogues of S-adenosylhomocysteine, methionine, and deoxycytidine recapitulated the chemical features of the DNMT1 transition state in the synthesis of 16 chemically stable transition-state mimics. Inhibitors causing both full and partial inhibition of purified DNMT1 were characterized. The inhibitors show modest selectivity for DNMT1 versus DNMT3b. Active-site docking predicts inhibitor interactions with S-adenosyl-l-methionine and deoxycytidine regions of the catalytic site, validated by direct binding analysis. Inhibitor action with purified DNMT1 is not reflected in cultured cells. A partial inhibitor activated cellular DNA methylation, and a full inhibitor had no effect on cellular DNA methylation. These compounds provide chemical access to a new family of noncovalent DNMT chemical scaffolds for use in DNA methyltransferases.
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Affiliation(s)
- Farah Lamiable-Oulaidi
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Rajesh K Harijan
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Karl J Shaffer
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Douglas R Crump
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Yan Sun
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Quan Du
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Shivali A Gulab
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Ashna A Khan
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Andreas Luxenburger
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Anthony D Woolhouse
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Simone Sidoli
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Peter C Tyler
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Vern L Schramm
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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An Improved Approach for Practical Synthesis of 5-Hydroxymethyl-2′-deoxycytidine (5hmdC) Phosphoramidite and Triphosphate. Molecules 2022; 27:molecules27030749. [PMID: 35164012 PMCID: PMC8839764 DOI: 10.3390/molecules27030749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/16/2022] Open
Abstract
5-Hydroxymethyl-2′-deoxycytidine (5hmdC) phosphoramidite and triphosphate are important building blocks in 5hmdC-containing DNA synthesis for epigenetic studies. However, efficient and practical methods for the synthesis of these compounds are still limited. The current research provides an intensively improved synthetic method that enables the preparation of commercially available cyanoethyl-protected 5hmdC phosphoramidite with an overall yield of 39% on 5 g scale. On the basis of facile and efficient accesses to cyanoethyl protected-5hmdU and 5hmdC intermediates, two efficient synthetic routes for 5hmdC triphosphate were also developed.
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Chen WJ, Han SB, Xie ZB, Huang HS, Jiang DH, Gong SS, Sun Q. Efficient Synthesis of UDP-Furanoses via 4,5-Dicyanoimidazole(DCI)-Promoted Coupling of Furanosyl-1-Phosphates with Uridine Phosphoropiperidate. Molecules 2019; 24:molecules24040655. [PMID: 30781738 PMCID: PMC6412210 DOI: 10.3390/molecules24040655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 11/16/2022] Open
Abstract
A P(V)-N activation method based on nucleoside phosphoropiperidate/DCI system has been developed for improved synthesis of diverse UDP-furanoses. The reaction conditions including temperature, amount of activator, and reaction time were optimized to alleviate the degradation of UDP-furanoses to cyclic phosphates. In addition, an efficient and facile phosphoramidite route was employed for the preparation of furanosyl-1-phosphates.
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Affiliation(s)
- Wei-Jie Chen
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605 Fenglin Avenue, Nanchang 330013, China.
| | - Shuai-Bo Han
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605 Fenglin Avenue, Nanchang 330013, China.
| | - Zhen-Biao Xie
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605 Fenglin Avenue, Nanchang 330013, China.
| | - Hua-Shan Huang
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605 Fenglin Avenue, Nanchang 330013, China.
| | - Duo-Hua Jiang
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605 Fenglin Avenue, Nanchang 330013, China.
| | - Shan-Shan Gong
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605 Fenglin Avenue, Nanchang 330013, China.
| | - Qi Sun
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605 Fenglin Avenue, Nanchang 330013, China.
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Zheng XA, Huang HS, Kong R, Chen WJ, Gong SS, Sun Q. An efficient PyAOP-based C4-amination method for direct access of oxidized 5MedC derivatives. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.10.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Mondal D, Koehn EM, Yao J, Wiemer DF, Kohen A. Chemo-enzymatic synthesis of the exocyclic olefin isomer of thymidine monophosphate. Bioorg Med Chem 2018; 26:2365-2371. [PMID: 29606487 DOI: 10.1016/j.bmc.2018.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 03/15/2018] [Accepted: 03/21/2018] [Indexed: 12/19/2022]
Abstract
Exocyclic olefin variants of thymidylate (dTMP) recently have been proposed as reaction intermediates for the thymidyl biosynthesis enzymes found in many pathogenic organisms, yet synthetic reports on these materials are lacking. Here we report two strategies to prepare the exocyclic olefin isomer of dTMP, which is a putative reaction intermediate in pathogenic thymidylate biosynthesis and a novel nucleotide analog. Our most effective strategy involves preserving the existing glyosidic bond of thymidine and manipulating the base to generate the exocyclic methylene moiety. We also report a successful enzymatic deoxyribosylation of a non-aromatic nucleobase isomer of thymine, which provides an additional strategy to access nucleotide analogs with disrupted ring conjugation or with reduced heterocyclic bases. The strategies reported here are straightforward and extendable towards the synthesis of various pyrimidine nucleotide analogs, which could lead to compounds of value in studies of enzyme reaction mechanisms or serve as templates for rational drug design.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - Eric M Koehn
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - Jiajun Yao
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - David F Wiemer
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States.
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
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7
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Tanpure AA, Balasubramanian S. Synthesis and Multiple Incorporations of 2'-O-Methyl-5-hydroxymethylcytidine, 5-Hydroxymethylcytidine and 5-Formylcytidine Monomers into RNA Oligonucleotides. Chembiochem 2017; 18:2236-2241. [PMID: 28901692 PMCID: PMC5779611 DOI: 10.1002/cbic.201700492] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Indexed: 01/09/2023]
Abstract
The synthesis of 2'-O-methyl-5-hydroxymethylcytidine (hm5 Cm), 5-hydroxymethylcytidine (hm5 C) and 5-formylcytidine (f5 C) phosphoramidite monomers has been developed. Optimisation of mild post-synthetic deprotection conditions enabled the synthesis of RNA containing all four naturally occurring cytosine modifications (hm5 Cm, hm5 C, f5 C plus 5-methylcytosine). Given the considerable interest in RNA modifications and epitranscriptomics, the availability of synthetic monomers and RNAs containing these modifications will be valuable for elucidating their biological function(s).
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Affiliation(s)
- Arun A. Tanpure
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Shankar Balasubramanian
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research (UK)Cambridge InstituteLi Ka Shing Centre University of CambridgeRobinson WayCambridgeCB2 0REUK
- School of Clinical MedicineUniversity of CambridgeCambridgeCB2 0SPUK
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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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Gong SS, Sun J, You YH, Chen JZ, Liu GD, Sun Q. Efficient Synthesis of 5-Carboxy-2'-Deoxypyrimidine Nucleoside 5'-Triphosphates. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:295-304. [PMID: 27104859 DOI: 10.1080/15257770.2016.1154971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
An efficient P(V)-N activation method for the synthesis of 5-carboxy-2'-deoxyuridine and 5-carboxy-2'-deoxycytidine triphosphates directly from the corresponding phosphoropiperidate precursors has been developed.
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Affiliation(s)
- Shan-Shan Gong
- a Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University , Nanchang , Jiangxi , PR China
| | - Jian Sun
- a Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University , Nanchang , Jiangxi , PR China
| | - Yue-Hai You
- a Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University , Nanchang , Jiangxi , PR China
| | - Ji-Zong Chen
- a Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University , Nanchang , Jiangxi , PR China
| | - Guo-Dong Liu
- a Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University , Nanchang , Jiangxi , PR China
| | - Qi Sun
- a Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University , Nanchang , Jiangxi , PR China
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Sun Q, Sun J, Gong SS, Wang CJ, Wang XC. Synthesis of nucleoside tetraphosphates and dinucleoside pentaphosphates from nucleoside phosphoropiperidates via the activation of P(V)N bond. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2014.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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