Zika Virus Surveillance, Vaccinology, and Anti-Zika Drug Discovery: Computer-Assisted Strategies to Combat the Menace

Subhash C. Basak, Ph.D. (Editor)
Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, USA

Apurba K. Bhattacharjee, Ph.D. (Editor)
Department of Microbiology and Immunology, Biomedical Graduate Research Organization (BGRO), School of Medicine, Georgetown University, Washington, DC, USA

Ashesh Nandy, Ph.D. (Editor)
Centre for Interdisciplinary Research and Education, Kolkata, India

Series: Virology Research Progress
BISAC: MED103000

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The bubonic plague, smallpox, HIV/AIDS, malaria, and influenza are some of the worst epidemics/pandemics that afflicted human beings from antiquity to modern times, killing millions of people. The mosquito-borne human-infecting viruses, rotavirus, and the seasonal influenza regularly affect lives across continents in the millions. Currently, we are facing various disease-inducing organisms of the Flavivirus family – the Yellow fever virus (YFV), West Nile virus (WNV), Japanese encephalitis virus (JEV), Tick-borne encephalitis virus (TBEV), Dengue virus (DENV) and Zika virus (ZIKV).

Zika virus was first isolated from a febrile rhesus monkey in the Zika forest of Uganda in 1947. It drew our heightened attention following the large number of microcephaly in newborn babies in Latin America in 2015. On 1 February 2016, WHO declared that the association of Zika infection with clusters of microcephaly and other neurological disorders constituted a Public Health Emergency of International Concern. Although the severity and number of ZIKV afflicted cases have gone down lately, the public health community worldwide is keeping a watchful eye on it.

ZIKV is an enveloped virus with a positive-sense RNA genome that translates into a single polypeptide, which then gets cleaved into three structural and seven nonstructural viral proteins. As compared to the earlier centuries, we have an expanding repertoire of diverse and fast acting technologies available at our hand to manage and mitigate emerging diseases. Completion of the Human Genome Project has given rise to sequencing methods which can quickly determine the genetic sequence of an alarming pathogen. Following Moore’s law, the power of computers, essential for data analysis and visualization, has grown substantially with time. The combination of genomic data of pathogens, computational modeling methods, and data driven methodologies can lead to a “generic approach” of surveillance, mitigation, vaccine design as well as new drug discovery for emerging pathogens. The four pillars of this may consist of:

a) Epidemiological approaches for the characterization of carriers of next possible emerging pathogens;
b) Fast computational sequence comparison methods for the characterization of emerging pathogens to understand how novel or severe they could be;
c) Once the sequences of the pathogen have been determined, computer-aided vaccine design (CAVD) methods can be used to suggest a set of probable vaccine candidates for quick synthesis and testing in the laboratory; and
d) Computer-assisted design of novel therapeutics and their laboratory testing as well as repurposing of already existing FDA-approved drugs.

A combination of different classes of methods – in vivo, in vitro and in silico – will be needed to tackle suddenly emerging viruses like the Zika virus. As in many other fields of biomedical research, high throughput and low cost in silico technologies may provide the first line of defense against such emerging pathogens providing decision support systems for the judicious applications of medium throughput in vitro methods and low throughput as well as costly in vivo techniques.

An emerging trend in many scientific disciplines is a strong tendency of being transformed into some form of information science. The editors of this book sincerely hope that the four-pronged computer-assisted approach described in this book will help in managing and mitigating emerging infectious diseases like Zika.

(Imprint: Nova Medicine and Health)

Preface

Chapter 1. Zika Virus: An Introduction
(Subhash C. Basak, PhD, Apurba Bhattacharjee, PhD, and Ashesh Nandy, PhD, Department of Chemistry and Biochemistry, University of Minnesota Duluth, MN, US, and others)

Chapter 2. Discovery of Anti-Zika Drugs Using in Silico Pharmacophore Modeling
(Apurba K. Bhattacharjee, PhD, Biomedical Graduate Research Organization, Department of Microbiology and Immunology, School of Medicine, Georgetown University, Washington, DC, US)

Chapter 3. Zika Virus: The Quest for Vaccines
(Proyasha Roy, Ashesh Nandy and Subhash C. Basak, Centre for Interdisciplinary Research and Education, Kolkata, India, and others)

Chapter 4. Quantitative Nucleic Acid Sequence Comparison Methods in the Characterization and Surveillance of Emerging Pathogens: A Study of Flavivirus Strains Including the Zika Virus
(Subhash C. Basak, PhD, Marjan Vracko, PhD, and Ashesh Nandy, PhD, Department of Chemistry and Biochemistry, University of Minnesota Duluth, MN, US, and others)

Chapter 5. Data-Driven Strategies to Model and Mitigate the Threat of Zika
(Subhabrata Majumdar, University of Florida Informatics Institute, Gainesville, FL, US)

Index

"The book of Basak et al. treats, at a high level of competence, the Zika virus problems, basic biology, surveillance, vaccine design, and anti-Zika drug discovery, with a computer-aided strategy. Simple to follow, yet complex, this endeavor presents an information content about one of the top current health topics: Zika virus. The topic is genteelly covered by 5 chapters, starting from chapter 1 with a brief and concise up-to-date discussion on Zika, and continued in chapters 2 to 5 with in silico discovery of anti-Zika drugs, designing vaccines, genetic approach for Zika treatment, and finally, data mining and OMICs approaches, respectively. This work is a valuable tool for those working in the field, both for experienced and novice ones. It offers a point-by-point guidance to the real word problems. In silico methods, used to identify issues in Zika drug and vaccine design, are presented in a clear, concise, easy to follow, and organized manner. Major strategies in a drug design project are covered. The book proposes a complex strategy for the Zika menace through effective anti-Zika drugs and vaccines, designed computationally. Work flows are set out to ease work and save time. Lastly, this edition should stay on lab shelves close to the scientists." - Mircea Diudea, PhD, Professor of Chemistry, Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj, Romania

This book represents a beautiful initiative led by Drs. Basak, Bhattacharjee, and Nandy to combat neglected diseases transmitted by mosquitoes, particularly those carrying the Zika virus. The multidisciplinary approach, namely consisting of epidemiology, pathogenesis, and computer-aided design of both new vaccines and new drugs, including repurposing of drugs from those already approved by the FDA for their potential ready access to patients must be emphasized. I am sure it will achieve a great success." - Jorge Galvez, PhD, Professor of Physical Chemistry, University of Valencia, Valencia, Spain

"In recent years, Zika virus has become a global emerging pathogen of international concern to the public health community. The book “Zika Virus Surveillance, Vaccinology, and Anti-Zika Drug Discovery: Computer-Assisted Strategies to Combat the Menace” brings together up-to-date results of research on data-driven and computer-assisted strategies of surveillance, vaccinology, and drug discovery for Zika. If you were once puzzled by relative problems, this book may provide you with a miraculous key." - Chun Li, PhD, Professor of Mathematics, Bohai University, Jinzhou, PR China

"Zika virus is the leading global health concern due to its rapid spread and close relationship with microcephaly in recent years. This book brings together four levels of in silico-approaches in treating Zika virus together. I totally believe that these comprehensive overviews would make a great contribution in the field, especially to help the study of translational medicine of Zika virus." - Guang Hu, PhD, Associate Professor of Systems Biology, Soochow University, Suzhou, PR, China

"Although the basic biology of the virus and surveillance of Zika viral diseases are already known and described in a few books (one published in 2018 by Elsevier), the computer-assisted and data-driven strategies of this book on: a) quantitative modelling of the spread of the disease from past outbreaks, b) vaccine design for Zika, c) anti-Zika drug discovery, and d) mathematical/statistical comparison of emerging strains with the existing ones, have not been covered by anyone till date. Thus, this is a new and timely compilation of information and ideas on Zika virus by the trios, as editors." - Dr. Debprasad Chattopadhyay, Scientist G & Director, Indian Council of Medical Research (ICMR)-National Institute of Traditional Medicine, Nehru Nagar, Belagavi, India

"Aedes aegypti is the principal vector of severe diseases including Zika. With global climate change and development of intercontinental exchanges, the risk of outbreaks is rapidly growing, making mosquito control an important concern. Professor Apurba Bhattacharjee is a recognized expert in mosquito control, and has proposed in various key publications a pioneering approach for repellent study. From a preliminary study of the relation between the structural characteristics of active amides and their protection time, he investigated the molecular stereoelectronic similarity between DEET and the juvenile hormone. This book proposes a cutting edge presentation of such research, with particular emphasis on methodology, acquired results and future developments. No doubt it will constitute an important milestone for researchers involved in vector borne diseases." - Jean Pierre Doucet, Chemistry Department, University Paris Diderot, Paris, France

“This books offers a panoramic view of the Zika virus from different perspectives: modelling the spread of the disease, identification of vulnerable geographical areas, studies of the disease mechanism through virus genomics, description of computational models that could help to devise therapeutic compounds, different strategies for vaccine development and estimation of animal reservoirs for intervention in the virus life cycle. Therefore, the book is an important source of information on the virus that can be taken as the starting point for future research on the area.” - Guillermo Restrepo, Dr. rer. Nat., Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany

Keywords: Zika virus, Flavivirus, Surveillance of emerging viruses, Viral sequence comparison, Peptide vaccine, Computer-assisted drug design (CADD), Pharmacophore, SIR (Susceptible-Infectious-Recovered) model, Anti-Zika drug, Machine learning, Statistical model, Quantitative Structure Activity Relationship (QSAR), Computer-assisted strategies

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