Advances in Experimental Medicine and Biology 1053 Theam Soon Lim Editor Recombinant Antibodies for Infectious Diseases Advances in Experimental Medicine and Biology Volume 1053 Editorial Board: IRUN R. COHEN, The Weizmann Institute of Science, Rehovot, Israel ABEL LAJTHA, N.S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA JOHN D. LAMBRIS, University of Pennsylvania, Philadelphia, PA, USA RODOLFO PAOLETTI, University of Milan, Milan, Italy NIMA REZAEI, Tehran University of Medical Sciences Children’s Medical Center, Children’s Medical Center Hospital, Tehran, Iran More information about this series at http://www.springer.com/series/5584 Theam Soon Lim Editor Recombinant Antibodies for Infectious Diseases Editor Theam Soon Lim Institute for Research in Molecular Medicine Universiti Sains Malaysia Penang, Malaysia ISSN 0065-2598 ISSN 2214-8019 (electronic) Advances in Experimental Medicine and Biology ISBN 978-3-319-72076-0 ISBN 978-3-319-72077-7 (eBook) https://doi.org/10.1007/978-3-319-72077-7 Library of Congress Control Number: 2018931166 © Springer International Publishing AG, part of Springer Nature 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Springer imprint is published by the registered company Springer International Publishing AG part of Springer Nature. The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Preface The fate of antibodies and infectious diseases has been entwined since the early days when Emil von Behring and Shibasaburo Kitasato first witnessed the unique toxin neutralization ability of antibodies in sera from immunized rabbits. The hybridoma technology by Köhler and Milstein in the mid-1970s revolutionized the way antibodies can be applied in the future. Their contri- butions set about the first monospecific antibodies to be generated against a specific target. This brought about major revolutions in the way we carry out basic research, medical diagnostics, and therapeutics. However, the ability to produce murine monospecific antibodies was not the finish article due to major side reactions associated with the use of animal- derived antibodies in humans. The quest for further improvements in the way antibodies were being gen- erated meant there was a need to generate monoclonal antibodies at a more rapid pace with more human-like characteristics. The biotechnology boom at the turn of the century resulted in rapid advancements in recombinant DNA technology, molecular biology, and DNA sequencing technologies. The tech- nological developments allowed the floodgates of genetic information to open making molecular-based technologies accessible to many laboratories around the world. The knowledge, information, and technological advance- ments worked symbiotically to fuel the advancements of complementary technologies. Recombinant antibody technology also benefited from this evo- lution with the improved understanding of genes and mechanisms associated with in vivo antibody production. In the quest to make antibodies more human, researchers sought after new alternative methods to generate recombinant versions of human antibodies. This possibility was only realized with the introduction of phage display technology by George Smith, which allowed the presentation of peptides on the surface of bacteriophages. This allowed for the evolution of the technol- ogy to present antibodies on the surface, which catalyzed the growth of human monoclonal antibody technology. Since then, numerous versions of human antibody formats have been developed with astonishing success. As a result, new antibody libraries have been developed and are now an important tool for monoclonal human antibody development work. The technology has allowed for different antibodies to be developed against many different kinds of targets which was otherwise impossible with conventional approaches. The ability to generate fully human monoclonal antibodies at a rapid pace has shaped the pharmaceutical landscape in recent years. This signaled a turning v vi Preface point for many medical approaches applied at that time and has helped shaped the way modern immunotherapeutics are designed. The ongoing challenges associated with infectious diseases like antibiotic resistance and the cost for drug discovery meant that an alternative treatment was required. This book provides an in-depth introduction to bacteriophage biology as well as its application for antibody phage display. The book also includes examples of different forms of antibody libraries that are used to tackle the issue of infectious diseases. It also provides a comprehensive list of antibody phage display technologies and the application of antibodies against different infectious agents. In addition to that, the book also includes con- cepts of computational-based antibody design, antibody engineering strate- gies, and considerations in the application of antibody-based therapy for infectious diseases. On a personal note, the treatment of infectious disease is a topic close at heart due to the constant threat it poses around Southeast Asia. This is a key focus area for me personally as part of the antibody technology initiative at the Institute for Research in Molecular Medicine (INFORMM), which is the brainchild of the Malaysian Ministry of Higher Education under the Higher Institutions’ Centre of Excellence (HICoE) program together with Universiti Sains Malaysia (USM). It is our aim that this book can provide technical assistance to new start-up laboratories and researchers looking to apply anti- body phage display for infectious diseases. We also hope this book will help spur interest and ideas in the field while at the same time expand research focusing on antibody-based therapy for infectious diseases. I would like to thank the authors whose contributions to this book have allowed it to be a comprehensive guide for antibody phage display in infec- tious diseases. I would also like to thank Prof. Michael Hust for his guidance and advice throughout the preparation of this book. My scientific career would not have been possible without the influence of great mentors like Zoltàn Konthur and Jörn Glökler. On a personal note, I would like to thank Poi Hong, Hayley, Hayden, and my parents for their support while preparing this book and throughout my scientific career. Penang, Malaysia Theam Soon Lim Contents 1 Filamentous Phage: Structure and Biology . . . . . . . . . . . . . . . . 1 Jasna Rakonjac, Marjorie Russel, Sofia Khanum, Sam J. Brooke, and Marina Rajič 2 Antibody Phage Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Hyunbo Shim 3 Naïve Human Antibody Libraries for Infectious Diseases . . . . 35 Soo Khim Chan, Anizah Rahumatullah, Jing Yi Lai, and Theam Soon Lim 4 Immune Human Antibody Libraries for Infectious Diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 Soo Khim Chan and Theam Soon Lim 5 Synthetic Antibodies in Infectious Disease . . . . . . . . . . . . . . . . . 79 Gang Chen, Sachdev S. Sidhu, and Johan Nilvebrant 6 Monoclonal Antibodies and Antibody Like Fragments Derived from Immunised Phage Display Libraries . . . . . . . . . . 99 Obinna Ubah and Soumya Palliyil 7 Anti-bacterial Monoclonal Antibodies . . . . . . . . . . . . . . . . . . . . 119 Eszter Nagy, Gábor Nagy, Christine A. Power, Adriana Badarau, and Valéria Szijártó 8 Anti-parasitic Antibodies from Phage Display . . . . . . . . . . . . . . 155 Luiz R. Goulart, Vanessa da S. Ribeiro, and Julia M. Costa-Cruz 9 Therapeutic Antibodies for Biodefense . . . . . . . . . . . . . . . . . . . . 173 Arnaud Avril 10 Engineering Antibodies for the Treatment of Infectious Diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207 Gaowei Fan and Jinming Li 11 Computer-Aided Antibody Design: An Overview . . . . . . . . . . . 221 Yee Siew Choong, Yie Vern Lee, Jia Xin Soong, Cheh Tat Law, and Yee Ying Lim vii viii Contents 12 Using High-Throughput Sequencing to Characterize the Development of the Antibody Repertoire During Infections: A Case Study of HIV-1 . . . . . . . . . . . . . . . . . . . . . . . 245 Felix Breden and Corey T. Watson 13 Safety and General Considerations for the Use of Antibodies in Infectious Diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265 Adam Seidelin Hey Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295 Contributors Arnaud Avril Département des maladies infectieuses, Unité biothérapies anti-infectieuses et immunité, Institut de Recherche Biomédical des Armées, Brétigny-sur-Orge, France Adriana Badarau Arsanis Biosciences GmbH/Arsanis, Inc, Vienna, Austria Felix Breden Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada Sam J. Brooke Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand Soo Khim Chan Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia Gang Chen Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada Yee Siew Choong Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia Julia M. Costa-Cruz Laboratory of Parasitology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil Gaowei Fan Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China Luiz R. Goulart Laboratory of Nanobiotechnology, Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil Department of Medical Microbiology and Immunology, University of California-Davis, Genome and Biomedical Sciences Facility, Davis, CA, USA Adam Seidelin Hey Novartis Institutes for BioMedical Research, Basel, Switzerland Sofia Khanum Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand ix