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Antimicrobial Peptides (Advances in Molecular and Cellular Biology Series)

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Antimicrobial Peptides (Advances in Molecular and Cellular Biology Series) Advances in Molecular and Cellular Microbiology 18 Antimicrobial Peptides Discovery, Design and Novel Therapeutic Strategies Edited by Guangshun Wang, PhD Eppley Institute University of Nebraska Medical Center Omaha, Nebraska, USA Advances in Molecular and Cellular Microbiology Through the application of molecular and cellular microbiology we now recognize the diversity and dominance of microbial life forms that exist in all environments on our planet. These microbes have many important planetary roles, but for humans a major problem is their ability to colonize our tissues and cause disease. The same techniques of molecular and cellular microbiology have been applied to the problems of human and animal infection since the 1990s and have proved to be immensely powerful tools in elucidating how microorganisms cause human pathology. This series has the aim of providing information on the advances that have been made in the application of molecular and cellular microbiology to specifi c organisms and the diseases they cause. The series is edited by researchers active in the application of molecular and cellular microbiology to human disease states. Each volume focuses on a particular aspect of infectious disease and will enable graduate students and researchers to keep up with the rapidly diversifying literature in current microbiological research. Series Editors Professor Brian Henderson University College London Professor Michael Wilson University College London Titles Available from CABI 17. Helicobacter pylori in the 21st Century Edited by Philip Sutt on and Hazel M. Mitchell 18. Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies Edited by Guangshun Wang Titles Forthcoming from CABI Stress Response in Pathogenic Bacteria Edited by Stephen Kidd Lyme Disease: an Evidence-based Approach Edited by John Halperin Tuberculosis: Molecular Techniques in Diagnosis and Treatment Edited by Timothy McHugh Microbial Metabolomics Edited by Silas Villas-Bôas and Katya Ruggiero Earlier titles in the series are available from Cambridge University Press (www.cup.cam.ac.uk). CABI is a trading name of CAB International CABI Head Offi ce CABI North American Offi ce Nosworthy Way 875 Massachusett s Avenue Wallingford 7th Floor Oxfordshire, OX10 8DE Cambridge, MA 02139 UK USA Tel: +44 (0)1491 832111 Tel: +1 617 395 4056 Fax: +44 (0)1491 833508 Fax: +1 617 354 6875 E-mail: [email protected] E-mail: [email protected] Website: www.cabi.org © CAB International 2010. All rights reserved. No part of this publication may be reproduced in any form or by any means, electronically, mechanically, by photocopying, recording or otherwise, without the prior permission of the copyright owners. A catalogue record for this book is available from the British Library, London, UK. Library of Congress Cataloging-in-Publication Data Antimicrobial peptides : discovery, design, and novel therapeutic strategies / edited by Guangshun Wang. p. ; cm. -- (Advances in molecular and cellular microbiology ; 18) Includes bibliographical references and index. ISBN 978-1-84593-657-0 (alk. paper) 1. Peptide antibiotics. I. Wang, Guangshun. II. Series: Advances in molecular and cellular microbiology ; 18. [DNLM: 1. Antimicrobial Cationic Peptides. 2. Anti-Infective Agents. 3. Drug Design. 4. Immunity, Innate. QU 68 A6308 2010] RS431.P37A575 2010 615’.1--dc22 2010016796 ISBN-13: 978 1 84593 657 0 Commissioning editor: Rachel Cutt s Production editor: Tracy Head Typeset by Columns Design Ltd, Reading, UK. Printed and bound in the UK by CPI Antony Rowe, Chippenham. Contents Contributors xi Preface xiii Introduction xv Michael Zasloff Part I: Natural Antimicrobial Peptides: Nomenclature, Classification and Interesting Templates for Peptide Engineering 1 A Database View of Naturally Occurring Antimicrobial Peptides: Nomenclature, Classifi cation and Amino Acid Sequence Analysis 1 Guangshun Wang, Xia Li and Michael Zasloff 1.1 Database Scope and Overview 2 1.2 Nomenclature of Antimicrobial Peptides 3 1.2.1 Peptide-based method 4 1.2.2 Source-based method 4 1.2.3 Source and peptide combined method 4 1.3 Annotation and Classifi cation of Antimicrobial Peptides 5 1.3.1 Source organisms and peptide family classifi cation 5 1.3.2 Classifi cation based on biological activities 8 1.3.3 Classifi cation based on peptide characteristics 9 1.3.4 Peptide-binding targets and mechanisms of action 14 1.4 Amino Acid Sequence Analysis of Antimicrobial Peptides 15 1.5 Concluding Remarks 17 2 Lantibiotic-related Research and the Application Thereof 22 Brian Healy, Jim O’Mahony, Colin Hill, Paul D. Cott er and R. Paul Ross 2.1 Introduction to Bacteriocins 22 2.2 Biosynthesis and Post-translational Modifi cations 23 2.3 Classifi cation 24 2.4 Lantibiotic Subgroups: Biology, Structure and Mode of Action 25 2.4.1 Nisin-like lantibiotics 25 2.4.2 Epidermin-like lantibiotics 26 v vi Contents 2.4.3 Planosporicin- and streptin-like lantibiotics 27 2.4.4 Pep5-like peptides 27 2.4.5 Lacticin 481-like lantibiotics 27 2.4.6 Mersacidin-like lantibiotics 28 2.4.7 LtnA2-like peptides 28 2.4.8 Other type II lantibiotics 28 2.5 Current and Future Use of Lantibiotics for Food Applications 29 2.6 Lantibiotics and Their Medical Applications 30 2.7 Engineering of Lantibiotics 30 2.8 Screening for New Lantibiotics 31 2.9 Concluding Remarks and Perspectives 32 3 Antimicrobial Peptides in Plants 40 Quentin Kaas, Jan-Christoph Westermann, Sónia Troeira Henriques and David J. Craik 3.1 Introduction to Plant Antimicrobial Peptides 40 3.1.1 Lipid-transfer proteins 41 3.1.2 Thionins 43 3.1.3 Plant defensins 44 3.1.4 Chitin-binding peptides 45 3.1.5 Miscellaneous AMPs from plants 48 3.1.6 Non-ribosomal antimicrobial peptides 49 3.2 Cyclotides 49 3.2.1 Diversity of plant cyclotides 49 3.2.2 Detection and isolation of cyclotides 54 3.2.3 Cyclotide biosynthesis 54 3.2.4 Biological activities of cyclotides 56 3.2.5 Cyclotide engineering and mass production 62 3.3 Concluding Remarks and Perspectives 63 Part II: Expanding the Peptide Space: Prediction Methods, Design Strategies and Peptidomimetics 4 Database-aided Prediction and Design of Novel Antimicrobial Peptides 72 Guangshun Wang 4.1 Database-aided Antimicrobial Peptide Prediction 73 4.1.1 Prediction based on mature peptides 73 4.1.2 Prediction based on highly conserved propeptide sequences 75 4.1.3 Prediction based on both propeptides and mature peptides 75 4.1.4 Prediction based on processing enzymes 76 4.1.5 Genomic context-based bacteriocin prediction 76 4.2 Database-aided Peptide Design and Improvement 76 4.2.1 Database screening for HIV inhibitory antimicrobial peptides 76 4.2.2 Sequence shuffl ing is a primitive combinatorial approach 77 4.2.3 The hybrid approach and grammar-based peptide design 78 4.2.4 De novo peptide design 78 4.2.5 Database-aided enhancement of peptide anti-HIV activity 80 4.3 Strategies for Improving Cell Selectivity of AMPs 80 4.4 Strategies for Improving Peptide Stability to Proteases 82 4.5 Concluding Remarks 82 Contents vii 5 Discovery of Novel Antimicrobial Peptides Using Combinatorial Chemistry and High-throughput Screening 87 William C. Wimley 5.1 The Interfacial Activity Model of AMP Activity 87 5.2 Combinatorial Chemistry Methods 88 5.2.1 Overview of library synthesis 88 5.2.2 Non-indexed methods 89 5.2.3 Indexed methods 90 5.3 High-throughput Screening 90 5.3.1 Biological assays 90 5.3.2 Selection of broad-spectrum peptide antibiotics 92 5.3.3 Non-biological assays 94 5.4 Accomplishments 97 5.4.1 Beyond high-throughput screening 97 5.5 Future Directions 98 6 Chemical Mimics with Systemic Effi cacy 100 Amram Mor 6.1 Introduction 100 6.2 De Novo-designed Rigid Peptidomimetics 102 6.2.1 Hairpin-shaped peptides 102 6.2.2 Peptoids 103 6.2.3 Arylamides 103 6.3 Acyl-lysyl Oligomers 104 6.3.1 Design 104 6.3.2 Structure–activity relationships 104 6.3.3 Antibacterial properties 107 6.3.4 Antiparasital properties 109 6.4 Concluding Remarks and Perspectives 110 Part III: Biophysics, Structural Biology and Mechanism of Action of Antimicrobial Peptides 7 Biophysical Analysis of Membrane-targeting Antimicrobial Peptides: Membrane Properties and the Design of Peptides Specifi cally Targeting Gram-negative Bacteria 116 Richard M. Epand and Raquel F. Epand 7.1 Diff erences in Chemical Composition and Molecular Organization of Gram-positive and Gram-negative Bacteria 116 7.2 Role of Bacterial Membrane Lipid Composition in Antimicrobial Sensitivity 118 7.3 Antimicrobial Agents that Target the Outer Membrane of Gram-negative Bacteria 119 7.4 Antimicrobial Agents that Promote Clustering of Anionic Lipids 120 7.4.1 Evidence for lipid clustering 120 7.4.2 Bacterial species specifi city of toxicity 121 7.4.3 Putative mechanism of action 124 7.4.4 Properties of antimicrobial agents that favour clustering 125 7.4.5 Sources of energy to account for clustering and entropy of demixing 125 7.5 Concluding Remarks and Perspectives 125 viii Contents 8 Non-membrane Targets of Antimicrobial Peptides: Novel Therapeutic Opportunities? 128 Ju Hyun Cho and Sun Chang Kim 8.1 Introduction 128 8.2 Buforin II: α-Helical AMP with Single Proline Residue Binding to Nucleic Acids 130 8.3 PR-39 and Indolicidin: Mammalian Proline-rich Peptides Inhibiting Macromolecule Synthesis and Cell Division 131 8.4 Apidaecin, Drosocin and Pyrrhocoricin: Short, Insect Proline-rich Peptides Binding to Heat-shock Protein DnaK 133 8.5 Concluding Remarks and Perspectives 136 9 Structural Studies of Antimicrobial Peptides Provide Insight into Their Mechanisms of Action 141 Guangshun Wang 9.1 Human Defensins and
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