1
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Biswas S, Shukla PK. A DFT study on the scavenging activity of curcumin toward methyl and ethyl radicals. MOLECULAR SIMULATION 2023. [DOI: 10.1080/08927022.2023.2178236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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2
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Balasubramaniyam T, Oh KI, Jin HS, Ahn HB, Kim BS, Lee JH. Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides. Int J Mol Sci 2021; 22:9552. [PMID: 34502459 PMCID: PMC8430589 DOI: 10.3390/ijms22179552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.
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Affiliation(s)
- Thananjeyan Balasubramaniyam
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Kwnag-Im Oh
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Ho-Seong Jin
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Hye-Bin Ahn
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Byeong-Seon Kim
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
- Department of Chemistry Education, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Joon-Hwa Lee
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
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3
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Thum MD, Hong D, Zeppuhar AN, Falvey DE. Visible-Light Photocatalytic Oxidation of DMSO for RAFT Polymerization †. Photochem Photobiol 2021; 97:1335-1342. [PMID: 34129686 DOI: 10.1111/php.13468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/13/2021] [Indexed: 11/28/2022]
Abstract
The solvent is an important, yet often forgotten part of a reaction mechanism. Many photochemical polymerizations are carried out using dimethyl sulfoxide (DMSO) as a way to promote the solubility of both the reactants and products, but its reactivity is rarely considered when initiation mechanisms are proposed. Herein, the oxidation of DMSO by an excited-state quinone is used to form initiating radicals resulting in the polymerization of methacrylate monomers, and the polymerization can be controlled with the addition of a chain transfer agent. This process leads to the formation of polymers with narrow molecular weight distribution, and the polymerization is able to be carried out in the presence of oxygen. A visible light absorbing substituted anthraquinone is synthesized, and nanosecond transient absorption spectroscopy is used to monitor the intermediates involved in the initiation mechanism. Photoproduct analysis indicates formation of methyl radicals as a result of DMSO oxidation. Furthermore, we show that the solvent outcompetes the chain transfer agent for interacting with the excited-state anthraquinone. These observations have a broad impact on photoinduced polymerizations performed in DMSO as many photocatalysts are strong oxidants in the excited state and are capable of reacting with the solvent. Therefore, the role of the solvent needs to be more carefully considered when proposing mechanisms for photoinduced polymerizations in DMSO.
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Affiliation(s)
- Matthew D Thum
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD
| | - Donald Hong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD
| | - Andrea N Zeppuhar
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD
| | - Daniel E Falvey
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD
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4
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Ghodke PP, Pradeepkumar PI. Site‐Specific
N
2
‐dG DNA Adducts: Formation, Synthesis, and TLS Polymerase‐Mediated Bypass. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Pratibha P. Ghodke
- Department of Biochemistry Vanderbilt University School of Medicine 638B Robinson Research Building 2200 Pierce Avenue 37323‐0146 Nashville Tennessee United States
- Department of Chemistry Indian Institute of Technology Bombay 400076 Mumbai Powai India
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5
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Yermolina MV, Papadantonakis GA. Electron and radical cation of sulfur-substituted thymine derivatives produced near photoionization threshold can alter and distort double-helix DNA structure. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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6
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Mi X, Kong Y, Zhang J, Pi C, Cui X. Visible-light-promoted sulfonylmethylation of imidazopyridines. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.09.040] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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Wang L, Zhao J, Sun Y, Zhang HY, Zhang Y. A Catalyst-Free Minisci-Type Reaction: the C-H Alkylation of Quinoxalinones with Sodium Alkylsulfinates and Phenyliodine(III) Dicarboxylates. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901266] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Liping Wang
- School of Chemical Engineering and Technology; Hebei Provincial Key Lab of Green Chemical Technology & High Efficient Energy Saving, Tianjin Key Laboratory of Chemical Process Safety; Hebei University of Technology; Guangrong Road No. 8 300130 Tianjin P. R. China
| | - Jiquan Zhao
- School of Chemical Engineering and Technology; Hebei Provincial Key Lab of Green Chemical Technology & High Efficient Energy Saving, Tianjin Key Laboratory of Chemical Process Safety; Hebei University of Technology; Guangrong Road No. 8 300130 Tianjin P. R. China
| | - Yuting Sun
- School of Chemical Engineering and Technology; Hebei Provincial Key Lab of Green Chemical Technology & High Efficient Energy Saving, Tianjin Key Laboratory of Chemical Process Safety; Hebei University of Technology; Guangrong Road No. 8 300130 Tianjin P. R. China
| | - Hong-Yu Zhang
- School of Chemical Engineering and Technology; Hebei Provincial Key Lab of Green Chemical Technology & High Efficient Energy Saving, Tianjin Key Laboratory of Chemical Process Safety; Hebei University of Technology; Guangrong Road No. 8 300130 Tianjin P. R. China
| | - Yuecheng Zhang
- School of Chemical Engineering and Technology; Hebei Provincial Key Lab of Green Chemical Technology & High Efficient Energy Saving, Tianjin Key Laboratory of Chemical Process Safety; Hebei University of Technology; Guangrong Road No. 8 300130 Tianjin P. R. China
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8
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Chen Y. Recent Advances in Methylation: A Guide for Selecting Methylation Reagents. Chemistry 2018; 25:3405-3439. [DOI: 10.1002/chem.201803642] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Yantao Chen
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, IMED Biotech UnitAstraZeneca Gothenburg Sweden
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9
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Lu SC, Li HS, Gong YL, Zhang SP, Zhang JG, Xu S. Combination of PhI(OAc)2 and 2-Nitropropane as the Source of Methyl Radical in Room-Temperature Metal-Free Oxidative Decarboxylation/Cyclization: Construction of 6-Methyl Phenanthridines and 1-Methyl Isoquinolines. J Org Chem 2018; 83:15415-15425. [DOI: 10.1021/acs.joc.8b02701] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Shi-Chao Lu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, and Beijing Key Laboratory of Active Substance Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 2A NanWei Road, Xicheng Distrct, Beijing 100050, PR China
| | - Hong-Shuang Li
- Institute of Pharmacology, School of Pharmaceutical Sciences, Taishan Medical University, 619 Changcheng Road, Taian 271016, PR China
| | - Ya-Ling Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, and Beijing Key Laboratory of Active Substance Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 2A NanWei Road, Xicheng Distrct, Beijing 100050, PR China
| | - Shi-Peng Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, and Beijing Key Laboratory of Active Substance Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 2A NanWei Road, Xicheng Distrct, Beijing 100050, PR China
| | - Ji-Guo Zhang
- Institute of Pharmacology, School of Pharmaceutical Sciences, Taishan Medical University, 619 Changcheng Road, Taian 271016, PR China
| | - Shu Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, and Beijing Key Laboratory of Active Substance Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 2A NanWei Road, Xicheng Distrct, Beijing 100050, PR China
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10
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Biswas S, Shah PK, Shukla PK. Methylation of DNA bases by methyl free radicals: mechanism of formation of C8-methylguanine. Struct Chem 2018. [DOI: 10.1007/s11224-018-1118-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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11
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Garza-Sanchez RA, Patra T, Tlahuext-Aca A, Strieth-Kalthoff F, Glorius F. DMSO as a Switchable Alkylating Agent in Heteroarene C-H Functionalization. Chemistry 2018; 24:10064-10068. [PMID: 29750378 DOI: 10.1002/chem.201802352] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Indexed: 01/24/2023]
Abstract
Herein, we report a novel strategy for the activation of DMSO to act as a versatile alkylating agent in heteroarene C-H functionalization. This direct, simple, and mild switch between methylation/trideuteromethylation and methylthiomethylation of heteroarenes was achieved under reagent-controlled photoredox catalysis conditions. The proposed mechanism is supported by both experimental and computational studies.
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Affiliation(s)
- R Aleyda Garza-Sanchez
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149, Münster, Germany
| | - Tuhin Patra
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149, Münster, Germany
| | - Adrian Tlahuext-Aca
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149, Münster, Germany
| | - Felix Strieth-Kalthoff
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149, Münster, Germany
| | - Frank Glorius
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149, Münster, Germany
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12
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13
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Uvaydov Y, Geacintov NE, Shafirovich V. Generation of guanine-amino acid cross-links by a free radical combination mechanism. Phys Chem Chem Phys 2014; 16:11729-36. [PMID: 24810398 DOI: 10.1039/c4cp00675e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A direct method has been developed for the in vitro synthesis of stable DNA-protein cross-links (DPC's) between guanine and amino acids (lysine and arginine). This method employs the combination of guanine neutral radicals, G(-H)˙, and side-chain C-centered amino acid radicals. The latter were generated indirectly after first causing the selective photoionization of 2-aminopurine (2AP) embedded in the oligonucleotide, 5'-d(CC[2AP]TCGCTACC), by intense nanosecond 308 nm excimer laser pulses. The 2AP radical cation deprotonates rapidly to form the 2AP(-H)˙ neutral radical which, in turn, oxidizes the nearby guanine to form the neutral guanine G(-H)˙ radical, as described previously (Shafirovich et al., J. Phys. Chem. B, 2001, 105, 8431). In parallel, the hydrated electrons, generated by the photoionization of 2AP, are scavenged by nitrous oxide to generate hydroxyl radicals. In the presence of a large excess of the amino acids, the hydroxyl radicals oxidize the latter to produce C-centered amino acid radicals that combine with the G(-H)˙ radicals to form the guanine-amino acid cross-linked oligonucleotide product. Analogous products were generated by photoionizing the free nucleoside, 2',3',5'-tri-O-acetylguanosine, (tri-O-Ac-Guo), using intense nanosecond 266 nm Nd:YAG laser pulse irradiation. The guanine-amino acid cross-links thus produced site-specifically positioned either in oligonucleotides, or in the free nucleoside tri-O-Ac-Guo were isolated by HPLC methods and identified by high resolution LC-TOF/MS and LC-MS/MS methods. The possibility that analogous guanine-amino acid cross-linked products could be formed in vivo using single hit radical generation mechanisms during oxidative stress is discussed.
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Affiliation(s)
- Yuriy Uvaydov
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003-5180, USA.
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14
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Shrivastav N, Fedeles BI, Li D, Delaney JC, Frick LE, Foti JJ, Walker GC, Essigmann JM. A chemical genetics analysis of the roles of bypass polymerase DinB and DNA repair protein AlkB in processing N2-alkylguanine lesions in vivo. PLoS One 2014; 9:e94716. [PMID: 24733044 PMCID: PMC3986394 DOI: 10.1371/journal.pone.0094716] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 03/18/2014] [Indexed: 01/06/2023] Open
Abstract
DinB, the E. coli translesion synthesis polymerase, has been shown to bypass several N2-alkylguanine adducts in vitro, including N2-furfurylguanine, the structural analog of the DNA adduct formed by the antibacterial agent nitrofurazone. Recently, it was demonstrated that the Fe(II)- and α-ketoglutarate-dependent dioxygenase AlkB, a DNA repair enzyme, can dealkylate in vitro a series of N2-alkyguanines, including N2-furfurylguanine. The present study explored, head to head, the in vivo relative contributions of these two DNA maintenance pathways (replicative bypass vs. repair) as they processed a series of structurally varied, biologically relevant N2-alkylguanine lesions: N2-furfurylguanine (FF), 2-tetrahydrofuran-2-yl-methylguanine (HF), 2-methylguanine, and 2-ethylguanine. Each lesion was chemically synthesized and incorporated site-specifically into an M13 bacteriophage genome, which was then replicated in E. coli cells deficient or proficient for DinB and AlkB (4 strains in total). Biochemical tools were employed to analyze the relative replication efficiencies of the phage (a measure of the bypass efficiency of each lesion) and the base composition at the lesion site after replication (a measure of the mutagenesis profile of each lesion). The main findings were: 1) Among the lesions studied, the bulky FF and HF lesions proved to be strong replication blocks when introduced site-specifically on a single-stranded vector in DinB deficient cells. This toxic effect disappeared in the strains expressing physiological levels of DinB. 2) AlkB is known to repair N2-alkylguanine lesions in vitro; however, the presence of AlkB showed no relief from the replication blocks induced by FF and HF in vivo. 3) The mutagenic properties of the entire series of N2-alkyguanines adducts were investigated in vivo for the first time. None of the adducts were mutagenic under the conditions evaluated, regardless of the DinB or AlkB cellular status. Taken together, the data indicated that the cellular pathway to combat bulky N2-alkylguanine DNA adducts was DinB-dependent lesion bypass.
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Affiliation(s)
- Nidhi Shrivastav
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bogdan I. Fedeles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Deyu Li
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - James C. Delaney
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Lauren E. Frick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - James J. Foti
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - John M. Essigmann
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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15
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Gui J, Zhou Q, Pan CM, Yabe Y, Burns AC, Collins MR, Ornelas MA, Ishihara Y, Baran PS. C-H methylation of heteroarenes inspired by radical SAM methyl transferase. J Am Chem Soc 2014; 136:4853-6. [PMID: 24611732 PMCID: PMC3988686 DOI: 10.1021/ja5007838] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
A practical C–H functionalization
method for the methylation
of heteroarenes is presented. Inspiration from Nature’s methylating
agent, S-adenosylmethionine (SAM), allowed for the
design and development of zinc bis(phenylsulfonylmethanesulfinate),
or PSMS. The action of PSMS on a heteroarene generates a (phenylsulfonyl)methylated
intermediate that can be easily separated from unreacted starting
material. This intermediate can then be desulfonylated to the methylated
product or elaborated to a deuteriomethylated product, and can divergently
access medicinally important motifs. This mild, operationally simple
protocol that can be conducted in open air at room temperature is
compatible with sensitive functional groups for the late-stage functionalization
of pharmacologically relevant substrates.
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Affiliation(s)
- Jinghan Gui
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Pattanayak SK, Chowdhuri S. Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation. Mol Phys 2013. [DOI: 10.1080/00268976.2013.783240] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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Rokhlenko Y, Geacintov NE, Shafirovich V. Lifetimes and reaction pathways of guanine radical cations and neutral guanine radicals in an oligonucleotide in aqueous solutions. J Am Chem Soc 2012; 134:4955-62. [PMID: 22329445 DOI: 10.1021/ja212186w] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The exposure of guanine in the oligonucleotide 5'-d(TCGCT) to one-electron oxidants leads initially to the formation of the guanine radical cation G(•+), its deptotonation product G(-H)(•), and, ultimately, various two- and four-electron oxidation products via pathways that depend on the oxidants and reaction conditions. We utilized single or successive multiple laser pulses (308 nm, 1 Hz rate) to generate the oxidants CO(3)(•-) and SO(4)(•-) (via the photolysis of S(2)O(8)(2-) in aqueous solutions in the presence and absence of bicarbonate, respectively) at concentrations/pulse that were ∼20-fold lower than the concentration of 5'-d(TCGCT). Time-resolved absorption spectroscopy measurements following single-pulse excitation show that the G(•+) radical (pK(a) = 3.9) can be observed only at low pH and is hydrated within 3 ms at pH 2.5, thus forming the two-electron oxidation product 8-oxo-7,8-dihydroguanosine (8-oxoG). At neutral pH, and single pulse excitation, the principal reactive intermediate is G(-H)(•), which, at best, reacts only slowly with H(2)O and lives for ∼70 ms in the absence of oxidants/other radicals to form base sequence-dependent intrastrand cross-links via the nucleophilic addition of N3-thymidine to C8-guanine (5'-G*CT* and 5'-T*CG*). Alternatively, G(-H)(•) can be oxidized further by reaction with CO(3)(•-), generating the two-electron oxidation products 8-oxoG (C8 addition) and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih, by C5 addition). The four-electron oxidation products, guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), appear only after a second (or more) laser pulse. The levels of all products, except 8-oxoG, which remains at a low constant value, increase with the number of laser pulses.
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Affiliation(s)
- Yekaterina Rokhlenko
- Chemistry Department, New York University, 31 Washington Place, New York, New York 10003-5180, United States
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18
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Pattanayak SK, Chowdhuri S. Effect of Water on Solvation Structure and Dynamics of Ions in the Peptide Bond Environment: Importance of Hydrogen Bonding and Dynamics of the Solvents. J Phys Chem B 2011; 115:13241-52. [DOI: 10.1021/jp206027e] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 751013, India
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19
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Chatgilialoglu C, D’Angelantonio M, Kciuk G, Bobrowski K. New Insights into the Reaction Paths of Hydroxyl Radicals with 2′-Deoxyguanosine. Chem Res Toxicol 2011; 24:2200-6. [DOI: 10.1021/tx2003245] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Mila D’Angelantonio
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Gabriel Kciuk
- Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland
| | - Krzysztof Bobrowski
- Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland
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20
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Yan F, Fujimori DG. RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift. Proc Natl Acad Sci U S A 2011; 108:3930-4. [PMID: 21368151 PMCID: PMC3054002 DOI: 10.1073/pnas.1017781108] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RlmN and Cfr are Radical SAM enzymes that modify a single adenosine nucleotide--A2503--in 23S ribosomal RNA. This nucleotide is positioned within the peptidyl transferase center of the ribosome, which is a target of numerous antibiotics. An unusual feature of these enzymes is their ability to carry out methylation of amidine carbons of the adenosine substrate. To gain insight into the mechanism of methylation catalyzed by RlmN and Cfr, deuterium labeling experiments were carried out. These experiments demonstrate that the newly introduced methyl group is assembled from an S-adenosyl-L-methionine (SAM)-derived methylene fragment and a hydrogen atom that had migrated from the substrate amidine carbon. Rather than activating the adenosine nucleotide of the substrate by hydrogen atom abstraction from an amidine carbon, the 5'-deoxyadenosyl radical abstracts hydrogen from the second equivalent of SAM to form the SAM-derived radical cation. This species, or its corresponding sulfur ylide, subsequently adds into the substrate, initiating hydride shift and S-adenosylhomocysteine elimination to complete the formation of the methyl group. These findings indicate that rather than acting as methyltransferases, RlmN and Cfr are methyl synthases. Together with the previously described 5'-deoxyadenosyl and 3-amino-3-carboxypropyl radicals, these findings demonstrate that all three carbon atoms attached to the sulfonium center in SAM can serve as precursors to carbon-derived radicals in enzymatic reactions.
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Affiliation(s)
- Feng Yan
- Department of Cellular and Molecular Pharmacology and Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, CA 94158
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology and Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, CA 94158
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Kasai H, Kawai K, Li YS. DNA Methylation at the C-5 Position of Cytosine by a Methyl Radical: A Link between Environmental Agents and Epigenetic Change. Genes Environ 2011. [DOI: 10.3123/jemsge.33.61] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Duncton MAJ. Minisci reactions: Versatile CH-functionalizations for medicinal chemists. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00134e] [Citation(s) in RCA: 426] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Heyda J, Vincent JC, Tobias DJ, Dzubiella J, Jungwirth P. Ion Specificity at the Peptide Bond: Molecular Dynamics Simulations of N-Methylacetamide in Aqueous Salt Solutions. J Phys Chem B 2009; 114:1213-20. [DOI: 10.1021/jp910953w] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Heyda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic, Department of Chemistry, University of California at Irvine, Irvine California 92697-2025, and Department of Physics T37, Technical University Munich, 85748 Garching, Germany
| | - Jordan C. Vincent
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic, Department of Chemistry, University of California at Irvine, Irvine California 92697-2025, and Department of Physics T37, Technical University Munich, 85748 Garching, Germany
| | - Douglas J. Tobias
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic, Department of Chemistry, University of California at Irvine, Irvine California 92697-2025, and Department of Physics T37, Technical University Munich, 85748 Garching, Germany
| | - Joachim Dzubiella
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic, Department of Chemistry, University of California at Irvine, Irvine California 92697-2025, and Department of Physics T37, Technical University Munich, 85748 Garching, Germany
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic, Department of Chemistry, University of California at Irvine, Irvine California 92697-2025, and Department of Physics T37, Technical University Munich, 85748 Garching, Germany
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