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Modification of Purine and Pyrimidine Nucleosides by Direct C-H Bond Activation

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Modification of Purine and Pyrimidine Nucleosides by Direct C-H Bond Activation molecules Nucleoside Modifications Edited by Mahesh K. Lakshman and Fumi Nagatsugi Printed Edition of the Special Issue Published in Molecules www.mdpi.com/journal/molecules Nucleoside Modifications Special Issue Editors Mahesh K. Lakshman Fumi Nagatsugi Guest Editors Mahesh K. Lakshman Fumi Nagatsugi The City College and Tohoku University The City University of New York Japan USA Editorial Office MDPI AG St. Alban-Anlage 66 Basel, Switzerland This edition is a reprint of the Special Issue published online in the open access journal Molecules (ISSN 1420-3049) from 2014–2016 (available at: http://www.mdpi.com/journal/molecules/special_issues/Nucleoside_Modifications). For citation purposes, cite each article independently as indicated on the article page online and as indicated below: Author 1; Author 2; Author 3 etc. Article title. Journal Name. Year. Article number/page range. ISBN 978-3-03842-354-6 (Pbk) ISBN 978-3-03842-355-3 (PDF) Articles in this volume are Open Access and distributed under the Creative Commons Attribution license (CC BY), which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book taken as a whole is © 2017 MDPI, Basel, Switzerland, distributed under the terms and conditions of the Creative Commons by Attribution (CC BY-NC-ND) license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Table of Contents About the Guest Editors ............................................................................................................................ v Preface to “Nucleoside Modifications” ................................................................................................... vii Yong Liang and Stanislaw F. Wnuk Modification of Purine and Pyrimidine Nucleosides by Direct C-H Bond Activation Reprinted from: Molecules 2015, 20(3), 4874–4901; doi: 10.3390/molecules20034874 http://www.mdpi.com/1420-3049/20/3/4874 ........................................................................................... 1 Kevin H. Shaughnessy Palladium-Catalyzed Modification of Unprotected Nucleosides, Nucleotides, and Oligonucleotides Reprinted from: Molecules 2015, 20(5), 9419–9454; doi: 10.3390/molecules20059419 http://www.mdpi.com/1420-3049/20/5/9419 ........................................................................................... 25 Oleg Golubev, Tuomas Lönnberg and Harri Lönnberg Formation of Mixed-Ligand Complexes of Pd2+ with Nucleoside 5'-Monophosphates and Some Metal-Ion-Binding Nucleoside Surrogates Reprinted from: Molecules 2014, 19(10), 16976–16986; doi: 10.3390/molecules191016976 http://www.mdpi.com/1420-3049/19/10/16976 ....................................................................................... 58 Sarah C. Zimmermann, Elizaveta O'Neill, Godwin U. Ebiloma, Lynsey J. M. Wallace, Harry P. De Koning and Katherine L. Seley-Radtke Design and Synthesis of a Series of Truncated Neplanocin Fleximers Reprinted from: Molecules 2014, 19(12), 21200–21214; doi: 10.3390/molecules191221200 http://www.mdpi.com/1420-3049/19/12/21200 ....................................................................................... 67 Yasufumi Fuchi, Hideto Obayashi and Shigeki Sasaki Development of New 1,3-Diazaphenoxazine Derivatives (ThioG-Grasp) to Covalently Capture 8-Thioguanosine Reprinted from: Molecules 2015, 20(1), 1078–1087; doi: 10.3390/molecules20011078 http://www.mdpi.com/1420-3049/20/1/1078 ........................................................................................... 79 Akkaladevi Venkatesham, Dhuldeo Kachare, Guy Schepers, Jef Rozenski, Mathy Froeyen and Arthur Van Aerschot Hybridisation Potential of 1',3'-Di-O-methylaltropyranoside Nucleic Acids Reprinted from: Molecules 2015, 20(3), 4020–4041; doi: 10.3390/molecules20034020 http://www.mdpi.com/1420-3049/20/3/4020 ........................................................................................... 87 Kiet Tran, Michelle R. Arkin and Peter A. Beal Tethering in RNA: An RNA-Binding Fragment Discovery Tool Reprinted from: Molecules 2015, 20(3), 4148–4161; doi: 10.3390/molecules20034148 http://www.mdpi.com/1420-3049/20/3/4148 ........................................................................................... 105 Yuichi Yoshimura, Satoshi Kobayashi, Hitomi Kaneko, Takeshi Suzuki and Tomozumi Imamichi Construction of an Isonucleoside on a 2,6-Dioxobicyclo[3.2.0]-heptane Skeleton Reprinted from: Molecules 2015, 20(3), 4623–4634; doi: 10.3390/molecules20034623 http://www.mdpi.com/1420-3049/20/3/4623 ........................................................................................... 117 iii Takuya Akisawa, Yuki Ishizawa and Fumi Nagatsugi Synthesis of Peptide Nucleic Acids Containing a Crosslinking Agent and Evaluation of Their Reactivities Reprinted from: Molecules 2015, 20(3), 4708–4719; doi: 10.3390/molecules20034708 http://www.mdpi.com/1420-3049/20/3/4708 ........................................................................................... 127 Salvatore V. Giofrè, Roberto Romeo, Caterina Carnovale, Raffaella Mancuso, Santa Cirmi, Michele Navarra, Adriana Garozzo and Maria A. Chiacchio Synthesis and Biological Properties of 5-(1H-1,2,3-Triazol-4-yl)isoxazolidines: A New Class of C-Nucleosides Reprinted from: Molecules 2015, 20(4), 5260–5275; doi: 10.3390/molecules20045260 http://www.mdpi.com/1420-3049/20/4/5260 ........................................................................................... 138 Kaustav Chakraborty, Swagata Dasgupta and Tanmaya Pathak Carboxylated Acyclonucleosides: Synthesis and RNase A Inhibition Reprinted from: Molecules 2015, 20(4), 5924–5941; doi: 10.3390/molecules20045924 http://www.mdpi.com/1420-3049/20/4/5924 ........................................................................................... 151 Jolanta Brzezinska and Wojciech T. Markiewicz Non-Nucleosidic Analogues of Polyaminonucleosides and Their Influence on Thermodynamic Properties of Derived Oligonucleotides Reprinted from: Molecules 2015, 20(7), 12652–12669; doi: 10.3390/molecules200712652 http://www.mdpi.com/1420-3049/20/7/12652 ......................................................................................... 166 Sakilam Satishkumar, Prasanna K. Vuram, Siva Subrahmanyam Relangi, Venkateshwarlu Gurram, Hong Zhou, Robert J. Kreitman, Michelle M. Martínez Montemayor, Lijia Yang, Muralidharan Kaliyaperumal, Somesh Sharma, Narender Pottabathini and Mahesh K. Lakshman Cladribine Analogues via O6-(Benzotriazolyl) Derivatives of Guanine Nucleosides Reprinted from: Molecules 2015, 20(10), 18437–18463; doi: 10.3390/molecules201018437 http://www.mdpi.com/1420-3049/20/10/18437 ....................................................................................... 181 Alicja Stachelska-Wierzchowska, Jacek Wierzchowski, Agnieszka Bzowska and Beata Wielgus-Kutrowska Site-Selective Ribosylation of Fluorescent Nucleobase Analogs Using Purine-Nucleoside Phosphorylase as a Catalyst: Effects of Point Mutations Reprinted from: Molecules 2016, 21(1), 44; doi: 10.3390/molecules21010044 http://www.mdpi.com/1420-3049/21/1/44 ............................................................................................... 203 iv About the Guest Editors Mahesh Lakshman obtained the B.Sc. and M.Sc. degrees from the University of Bombay (Mumbai), and MS and Ph.D. degrees from The University of Oklahoma. He completed postdoctoral work at the National Institutes of Health (NIDDK) developing the first total chemical synthesis approaches to site-specific DNA modification with stereochemically-defined polycyclic aromatic hydrocarbon metabolite adducts. After serving for a short while in industry, he returned to academia, joining the University of North Dakota and then relocating to The City College of New York (The City University of New York system). In addition to an active research program, funded by both the National Science Foundation and the National Institutes of Health, he has held several administrative positions such as Executive Officer for The City University of New York Ph.D. Program in Chemistry and as a Vice Chair of the Department of Chemistry and Biochemistry at The City College of New York. Professor Lakshman was recently inducted as a Fellow of Royal Society of Chemistry (UK). Fumi Nagatsugi joined the Faculty of Pharmaceutical Sciences at Kyushu University as a research assistant in 1989. She received her PhD from the university in 1996 and performed postdoctoral research at the National Institutes of Aging (NIA) in 2001–2002. She was promoted to associate professor at Kyushu University in 2003. She moved to Tohoku University in 2006 as a professor. Her research interests are chemical biology and nucleic acid chemistry. v Preface to “Nucleoside Modifications” Nucleosides are the fundamental components of genetic material, and are present in all living organisms, and in viruses. By virtue of their ubiquity, they are highly important biomolecules. Nucleosides consist of a heterocyclic aglycone and a sugar unit. For several decades, the natural nucleoside structures have inspired the development of chemical and biochemical modifications, leading to new nucleoside-like entities via aglycone as well as saccharide modifications. As a result, modified nucleosides and nucleoside analogues have widespread utilities in biochemistry, biology, as pharmaceutical agents and as biological probes. There is a constant need for access to novel
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