Table Of Content

Antibiotics Current Innovations and Future Trends Edited by Sergio Sánchez and Arnold L. Demain Caister Academic Press Antibiotics Current Innovations and Future Trends Edited by Sergio Sánchez Departamento de Biología Molecular y Biotecnología Instituto de Investigaciones Biomédicas Universidad Nacional Autónoma de México México, DF México and Arnold L. Demain Research Institute for Scientists Emeriti (RISE) Drew University Madison, NJ USA Caister Academic Press Copyright © 2015 Caister Academic Press Norfolk, UK www.caister.com British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN: 978-1-908230-54-6 (hardback) ISBN: 978-1-908230-55-3 (ebook) Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or publisher. The author and publisher do not assume responsibility for the validity of any products or procedures mentioned or described in this book or for the consequences of their use. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the publisher. No claim to original U.S. Government works. Cover design adapted from Figures 2.1, 2.2, 2.3 and 2.4 Contents iii Contributors v Current Books of Interest x Preface xi Contents What is an Antibiotic? 1 Introduction 1 The etymology of the word antibiotic 3 Disinfectants and related compounds 4 Chemotherapeutic agents, magic bullets and selective toxicity 5 The long shadow of Selman Waksman and synthetic antibiotics 8 Antibiotic resistance and the emergence of ‘antibacterial’ as a synonym for ‘antibiotic’ 9 Selective toxicity, lexicography and the evolving definition of antibiotic 11 Why worry about definitions? 13 Summary 14 Main Applications of Antibiotics 19 Introduction 19 Antibiotics for treatment of infectious diseases 19 Further discussion 34 Conclusion and future perspectives 36 Microorganisms Producing Antibiotics 49 The antibiotic producers and antibiotic functions 49 The numbers of antibiotic-producing microbes 54 Chemical diversity 58 Biodiversity 59 The way ahead 61 Contributors v Epilogue 63 Preface xi The Need for New Antibiotics 65 The antibiotic crisis 65 Antibiotic resistance 66 1 What is an Antibiotic? 1 Emergence of new diseases 70 Lack of new drugs 70 Joan Wennstrom Bennett Why drug discovery has dropped 71 Lack of new antibiotics 73 Natural products versus synthetics as drugs 73 2 Main Applications of Antibiotics 19 Possible solutions to the problem 74 Biao Ren, Pei Huang, Jingyu Zhang, Wenni He, Jianying Han, Xueting Liu Tackling Antibiotic Resistance 83 and Lixin Zhang Introduction 83 Preparation of new vaccines against resistant bacterial strains 84 Search for new antibiotics 85 3 Microorganisms Producing Antibiotics 49 Newly approved antibiotics and antibiotics in the pipeline 85 Search for new antibiotics from non-traditional or less traditional sources 86 János Bérdy Microbial genome sequences – search for genes specifying biosynthesis of antibiotics 87 Forgotten antibiotics to be revitalized 89 New 4 The Need for New Antibiotics 65 antibiotic targets 90 Discussion and conclusions 91 Arnold L. Demain and Sergio Sánchez Eradication of Dormant Pathogens 95 Persisters and infectious disease 95 5 Tackling Antibiotic Resistance 83 Mechanisms of persister formation 97 Persister eradication 100 Jaroslav Spizek and Vladimir Havlicek Toxicity of Antibacterial Drugs 109 Class effects 109 6 Eradication of Dormant Pathogens 95 Has genomics been misleading? 110 Collateral damage 111 Kim Lewis, Brian Conlon and Michael LaFleur What is ‘safe enough’? 111 Into the future: prophylaxis and precision medicine 111 7 Toxicity of Antibacterial Drugs 109 Conclusions 112 Overuse of Antibiotics: Non-medical Applications 113 Steven J. Projan Introduction 113 Antibiotic resistance – evolution and drivers 116 8 Overuse of Antibiotics: Non-medical Applications 113 Problem: overuse of antibiotics in agriculture 121 Overuse of antibiotics leads to environmental contamination 132 Nelson Kardos Antibiotic overuse in international travel and trade 140 Conclusion 143 9 Antibiotics for Emerging and Re-emerging Diseases 147 Antibiotics for Emerging and Re-emerging Diseases 147 Introduction 147 Kazuro Shiomi and Satoshi Ōmura Antiparasitic antibiotics 148 Antiviral antibiotics 160 Anti-pathogenic E. coli antibiotics 163 10 Endophytes as a Potential Source of New Antibiotics 175 Conclusions 165 Silvia Guzmán-Trampe, Karol Rodríguez-Peña, Allan Espinosa-Gómez, Endophytes as a Potential Source of New Antibiotics 175 Introduction 175 Rosa E. Sánchez-Fernández, Martha L. Macías-Rubalcava, Endophyte definition 176 Luis B. Flores-Cotera and Sergio Sánchez Distribution in the plant 176 Biological properties 177 Pharmaceutical importance of endophytes 178 11 Antibiotics from Microorganisms from Hot Springs/Geysers 205 Girish B. Mahajan iv | Contents 12 New Sources of Antibiotics: Caves 213 Naowarat Cheeptham and Cesareo Saiz-Jimenez 13 Animal Venoms as Natural Sources of Antimicrobials 229 Ramar Perumal Samy, Seetharama Satyanarayanajois, Octavio L. Franco, Bradley G. Stiles and Ponnampalam Gopalakrishnakone 14 New Targets for Antibacterial Compounds 249 Lynn L. Silver 15 Novel Antimicrobial and Other Bioactive Metabolites Obtained from Silent Gene Clusters 275 Juan F. Martín and Paloma Liras 16 Combinatorial Biosynthesis for Antibiotic Discovery 293 Sung Ryeol Park and Yeo Joon Yoon 17 Lantibiotics and Other Antibacterial Peptides 321 Margherita Sosio and Stefano Donadio 18 Antiviral Compounds of Natural Origin 331 Patricia Veiga-Crespo, Miquel Viñas and Tomás G. Villa 19 New Compounds with Antibacterial Activity 345 Patricia Veiga-Crespo, Angeles Sánchez-Pérez, Daniel Piso and Tomás G. Villa 20 Use of Antibiotic Core Structures to Generate New and Useful Macrolide Antibiotics 375 Prabhavathi Fernandes 21 Antibiotics in the Pipeline 395 Hyunjun Park and Michael Thomas Index 417 Contributors Joan Wennstrom Bennett Stefano Donadio Department of Plant Biology and Pathology Naicons Srl Rutgers University Milan New Brunswick, NJ Italy USA [email protected] [email protected] Allan Espinosa-Gómez János Bérdy Departamento de Biología Molecular y Biotecnología H-1124 Budapest Instituto de Investigaciones Biomédicas Thoman I. u. 6 Universidad Nacional Autónoma de México Hungary México D.F. México [email protected] [email protected] Naowarat Cheeptham Department of Biological Sciences Prabhavathi Fernandes Faculty of Science Cempra Inc. Thompson Rivers University Chapel Hill, NC Kamloops, BC USA Canada [email protected] [email protected] Luis B. Flores-Cotera Brian Conlon Departamento de Biotecnología Department of Biology Centro de Investigación y de Estudios Avanzados Northeastern University Instituto Politécnico Nacional Boston, MA México D.F. USA México [email protected] [email protected] Arnold L. Demain Octavio L. Franco Research Institute for Scientists Emeriti (RISE) Universidade Católica de Brasília Drew University Centro de Análises Proteômicas e Bioquímicas Madison, NJ Pós-Graduação em Ciências Genômicas e USA Biotecnologia UCB Brasília-DF [email protected] Brazil [email protected] vi | Contributors Ponnampalam Gopalakrishnakone Pei Huang Department of Anatomy Chinese Academy of Sciences Key Laboratory of Yong Loo Lin School of Medicine Pathogenic Microbiology and Immunology National University Health System (NUHS) Institute of Microbiology National University of Singapore Chinese Academy of Sciences; and Singapore University of Chinese Academy of Sciences Beijing [email protected] China Silvia Guzmán-Trampe [email protected] Departamento de Biología Molecular y Biotecnología Instituto de Investigaciones Biomédicas Nelson Kardos Universidad Nacional Autónoma de México International Technology Development Corporation México D.F. Coatesville, PA México USA [email protected] [email protected] Jianying Han Michael LaFleur Chinese Academy of Sciences Key Laboratory of Arietis Corporation Pathogenic Microbiology and Immunology Boston, MA Institute of Microbiology USA Chinese Academy of Sciences; and [email protected] University of Chinese Academy of Sciences Beijing Kim Lewis China Department of Biology [email protected] Northeastern University Boston, MA Vladimir Havlicek USA Institute of Microbiology [email protected] Academy of Sciences of the Czech Republic Prague Paloma Liras Czech Republic Microbiology Section [email protected] Departament of Molecular Biology Faculty of Biological and Environmental Sciences Wenni He University of León Chinese Academy of Sciences Key Laboratory of León Pathogenic Microbiology and Immunology Spain Institute of Microbiology [email protected] Chinese Academy of Sciences Beijing Xueting Liu China Chinese Academy of Sciences Key Laboratory of [email protected] Pathogenic Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences Beijing China [email protected] Contributors | vii Martha L. Macías-Rubalcava Karol Rodríguez-Peña Departamento de Productos Naturales Departamento de Biología Molecular y Biotecnología Instituto de Química Instituto de Investigaciones Biomédicas Universidad Nacional Autónoma de México Universidad Nacional Autónoma de México México D.F. México D.F. México México [email protected] [email protected] Girish B. Mahajan Daniel Piso Piramal Enterprises Limited Control Division Mumbai European Spallation Source (ESS) Maharashtra Sweden India [email protected] [email protected] Steven J. Projan Juan F. Martín Infectious Diseases and Vaccines Innovative Medicines Microbiology Section Unit Departament of Molecular Biology MedImmune Faculty of Biological and Environmental Sciences Gaithersburg, MD University of León USA León [email protected] Spain [email protected] Biao Ren Chinese Academy of Sciences Key Laboratory of Satoshi Ōmura Pathogenic Microbiology and Immunology Graduate School of Infection Control Sciences and Institute of Microbiology Kitasato Institute for Life Sciences Chinese Academy of Sciences; and Kitasato University University of Chinese Academy of Sciences Shirokane Beijing Tokyo China Japan [email protected] [email protected] Cesareo Saiz-Jimenez Hyunjun Park Instituto de Recursos Naturales y Agrobiologia Department of Bacteriology IRNAS-CSIC University of Wisconsin Sevilla Madison, WI Spain USA [email protected] [email protected] Ramar Perumal Samy Sung Ryeol Park Departments of Anatomy, Microbiology and Life Sciences Institute Orthopaedic Surgery University of Michigan Yong Loo Lin School of Medicine Ann Arbor, MI National University Health System (NUHS) USA National University of Singapore Singapore [email protected] [email protected] viii | Contributors Sergio Sánchez Margherita Sosio Departamento de Biología Molecular y Biotecnología Naicons Srl Instituto de Investigaciones Biomédicas Milan Universidad Nacional Autónoma de México Italy México D.F. [email protected] México [email protected] Jaroslav Spizek Institute of Microbiology Rosa E. Sánchez-Fernández Academy of Sciences of the Czech Republic Departamento de Productos Naturales Prague Instituto de Química Czech Republic Universidad Nacional Autónoma de México [email protected] México D.F. México Bradley G. Stiles [email protected] Integrated Toxicology Division US Army Medical Research Institute of Infectious Angeles Sánchez-Pérez Diseases Discipline of Physiology and Bosch Institute Fort Detrick, MD; and School of Medical Sciences Department of Biology University of Sydney Wilson College Australia Chambersburg, PA USA [email protected] [email protected] Seetharama Satyanarayanajois Department of Basic Pharmaceutical Sciences Michael Thomas School of Pharmacy Department of Bacteriology University of Louisiana at Monroe University of Wisconsin Monroe, LA Madison, WI USA USA [email protected] [email protected] Kazuro Shiomi Patricia Veiga-Crespo Graduate School of Infection Control Sciences and Department of Microbiology Kitasato Institute for Life Sciences Faculty of Pharmacy; and Kitasato University School of Biotechnology Shirokane University of Santiago de Compostela Tokyo Spain Japan [email protected] [email protected] Tomás G. Villa Lynn L. Silver Department of Microbiology LL Silver Consulting, LLC Faculty of Pharmacy; and Springfield, NJ School of Biotechnology USA University of Santiago de Compostela Spain [email protected] [email protected] Contributors | ix Miquel Viñas Jingyu Zhang Department of Pathology and Experimental Chinese Academy of Sciences Key Laboratory of Therapeutics, IDIBELL Pathogenic Microbiology and Immunology Schools of Medicine and Dentistry Institute of Microbiology University of Barcelona Chinese Academy of Sciences Spain Beijing China [email protected] [email protected] Yeo Joon Yoon Department of Chemistry and Nano Sciences Lixin Zhang Ewha Womans University Chinese Academy of Sciences Key Laboratory of Seoul Pathogenic Microbiology and Immunology Republic of Korea Institute of Microbiology Chinese Academy of Sciences; and [email protected] University of Chinese Academy of Sciences Beijing China [email protected]