Reverse Vaccinology

Concept, Methods and Advancement

1st Edition - July 6, 2024
Imprint: Academic Press
Editors: Jayashankar Das, Sushma Dave, Siomar de Castro Soares, Sandeep Tiwari
Language: English
Paperback ISBN:
9 7 8 - 0 - 4 4 3 - 1 3 3 9 5 - 4
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 1 3 3 9 6 - 1

Reverse Vaccinology: Concept, Methods, and Advancement presents the development strategy of new vaccines through genome sequencing bioinformatics analysis. This book promis… Read more

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Reverse Vaccinology: Concept, Methods, and Advancement presents the development strategy of new vaccines through genome sequencing bioinformatics analysis. This book promises to revolutionize vaccine development, especially for pathogens to which the classical applications of Pasteur’s principles have failed, and it is explained in detail in this book.

This book is split into three sections: the first, Concept, brings the basis of reverse vaccinology, vaccine antigen discovery, and subunit vaccine; the second, Tools and Methods, describes immunoinformatic, proteomics for epitope-vaccine design, databases, network analysis, machine learning, and NGS-driven antigen screening technology; and the last one, Disease Case Study, discusses real-world examples in the development of new vaccines for diverse diseases.

It is a valuable resource for bioinformaticians, researchers, students, and members of the biomedical and medical fields who want to learn more about a new and agile process for the development of new vaccines.

Cover image
Title page
Table of Contents
Copyright
List of contributors
About the editors
Preface
Section 1: Concept
Chapter 1. Fundamentals of reverse vaccinology: history and advantages over the discovery of conventional vaccine candidates
Abstract
1.1 Immune system
1.2 Classical vaccinology
1.3 Omics and reverse vaccinology
1.4 Conclusion
References
Chapter 2. Vaccine antigen discovery: a breakthrough in genomic era
Abstract
2.1 Introduction
2.2 Conventional vaccines to biotechnological vaccines
2.3 Antigen discovery by reverse vaccinology
2.4 Conclusion
References
Chapter 3. Development of subunit vaccine: A step forward toward cost-effective technology of vaccine candidate discovery
Abstract
3.1 Introduction
3.2 Importance of subunit vaccines in vaccine discovery
3.3 Advantages of subunit vaccines over conventional treatments
3.4 Methods for discovering antigenic determinants
3.5 Development and testing of subunit vaccines
3.6 Potential benefits of subunit vaccines
3.7 Conclusion
References
Section 2: Tools and Methods
Chapter 4. Machine learning approach for vaccine development-fundamentals
Abstract
4.1 Introduction
4.2 Classification of machine learning algorithms
4.3 Clustering
4.4 Dimensionality reduction
4.5 Regression
4.6 Classification
4.7 Conclusion
References
Chapter 5. Immunoinformatics: an interdisciplinary technique for designing and engineering vaccine antigen
Abstract
5.1 Introduction
5.2 Development of a multiepitope vaccine
5.3 Evaluation of antigenic, allergenic, immunogenicity, and toxicity
5.4 Population coverage analysis
5.5 Molecular docking
5.6 Molecular dynamic prediction
5.7 Construction of the peptide vaccine
5.8 Future challenges and conclusion
References
Chapter 6. Proteomics for epitope-based vaccine design
Abstract
6.1 Introduction
6.2 Western blotting and two-dimensional gel electrophoresis
6.3 Enzyme-linked immunosorbent assay
6.4 Phage display
6.5 Immunoprecipitation and epitope extraction
6.6 Mass spectrometry in proteomics
6.7 Proteomics workflows
6.8 Posttranslational modifications
6.9 Proteogenomics
6.10 Conclusion
References
Chapter 7. Databases and web server for conducting reverse vaccinology
Abstract
7.1 Introduction
7.2 Online tools and web servers
7.3 Databases for reverse vaccinology
7.4 In silico case study: reverse vaccinology on Mycoplasma genitalium
7.5 Conclusions
References
Chapter 8. Bacterial dynamics and network analysis for antigen screening
Abstract
8.1 Background
8.2 Systematic biology and network analysis
8.3 Genome annotation
8.4 Pangenomic tools
8.5 Gene transfer analysis tools
8.6 Conclusion
References
Chapter 9. Tools and platform for allergenicity prediction
Abstract
9.1 Introduction
9.2 Databases and tools for allergens/allergenicity prediction
9.3 Case studies
9.4 Conclusion
Ethics declarations
Financial interests
Conflicts of interest
References
Chapter 10. Screening of potential vaccine candidates through machine learning approach
Abstract
10.1 Introduction to machine learning
10.2 Training of a machine learning model
10.3 Machine learning approaches
10.4 Performance measures
10.5 Applications of machine learning in reverse vaccinology
10.6 Conclusion and prospects
References
Chapter 11. Reverse vaccinology 2.0: computational resources for B-cell epitope prediction
Abstract
11.1 Introduction
11.2 Prediction of linear (continuous) B-cell epitopes
11.3 Prediction of conformational (discontinuous) B-cell epitopes
11.4 Case studies
11.5 Conclusion
Abbreviations
Funding
Data availability statement
Declaration of competing interest
References
Chapter 12. Structural vaccinology approaches to enhance efficacy, stability, and delivery of protective antigens
Abstracts
12.1 Introduction
12.2 Challenges in structure-based design of improved viral antigens
12.3 Phosphorylcholine
12.4 Malondialdehyde
12.5 Natural antibodies
12.6 Hepatitis C virus
12.7 Respiratory syncytial virus
12.8 Influenza virus
12.9 Dengue virus
12.10 Masking of nonneutralizing epitopes
12.11 Improvement of vaccine thermostability
12.12 Structural vaccinology pitfalls
12.13 Conclusion
References
Chapter 13. Next-gen sequencing-driven antigen screening technology in vaccine development
Abstract
13.1 Introduction
13.2 Next-generation sequencing—a platform for screening the antigens
13.3 Artificial intelligence and machine learning—in silico–derived vaccines
13.4 Next-generation sequencing revolution in collective high-performance computing systems
13.5 Reverse vaccinology approach against antibiotic-resistant bacteria
13.6 Conclusion
References
Section 3: Disease Case Study
Chapter 14. Bioinformatics approach to design peptide vaccines for viruses
Abstract
14.1 Introduction
14.2 Foot-and-mouth disease context
14.3 Foot-and-mouth disease vaccines over the years
14.4 Reverse vaccinology applied to foot-and-mouth disease
14.5 Advances in computational vaccine development against foot-and-mouth disease virus
14.6 Adopting different strategies in reverse vaccinology against foot-and-mouth disease
14.7 Challenges and perspectives
14.8 Conclusion
References
Chapter 15. Confirmation of candidates identified by reverse vaccinology in animal models or other immunogenicity assays
Abstract
15.1 Introduction
15.2 Stages of vaccine development
15.3 In vivo tests
15.4 In vitro tests
15.5 Conclusions and perspectives
References
Chapter 16. Clinical trials of vaccines incorporating antigens identified from a reverse vaccinology approach
Abstract
16.1 Introduction
16.2 Reverse vaccinology
16.3 Clinical trials
16.4 New approaches
16.5 Conclusion
References
Chapter 17. Developing meningococcal and bacterial vaccines using reverse vaccinology Review on the development of the meningococcal and bacterial vaccines (Streptococcus and Staphylococcus) using reverse vaccinology
Abstract
17.1 Meningococcal diseases
17.2 Bacteremic pneumonia
17.3 Staphylococcus aureus infections
References
Index

Jayashankar Das

Dr. Das received his PhD in biotechnology and served as a Scientist at the IBSD, DBT, Government of India. He is the Founder and CEO of Valnizen which deals with regulatory documents and healthcare compliances and support services to African and southeast Asian countries. He has served as a Joint Director of the Gujarat State Biotechnology Mission, DST, and Joint Director to Gujarat Biotechnology Research Centre, DST, both from the Government of Gujarat. He has served as a Director of the Savli Technology and Business Incubator, DST, Government of Gujarat, India. He was actively involved in the development and implementation of various policies and action plans like biotechnology policy, innovation policy, interpole disaster management policy, start-up policy for many universities and governments. His research team is involved in addressing societal challenges via cutting-edge research, namely, the development of molecular diagnostics for infectious diseases, the development of universal vaccine candidate for emerging diseases, the development of miRNA-based targeted therapeutics, and artificial intelligence in healthcare applications.

Affiliations and expertise

Director of Research, Valnizen Healthcare Pvt Ltd, India

Sushma Dave

Dr. Sushma Dave received a master of science and PhD in analytical, electrochemistry, and environmental chemistry from the Biosensor Lab in the Chemistry Department of Jai Narayan Vyas University, Jodhpur. She is involved continuously in the field of higher education teaching pure, applied chemistry, cheminformatics, nanotechnology, electrochemistry, biology, solid waste management, wastewater treatment, and environmental chemistry to students of engineering and basic sciences. She also served as a Research Associate in the Soil Biochemistry and Microbiology Division, CAZRI, Jodhpur. She has published and presented over 50 papers in international and national journals, conferences and participated in various workshops and training programs. Her areas of interest are electrochemistry, biosensors environmental science, nanotechnology, biochemistry, cheminformatics, immunoinformatics, and drug repurposing.

Affiliations and expertise

Associate Professor, Department of Applied Sciences, JIET, India

Siomar de Castro Soares

Dr. Soares obtained his MSc and PhD in genetics from the Federal University of Minas Gerais with 1-year experience in the Center for Biotechnology (CeBiTec) of Universität Bielefeld. He obtained a second PhD and postdoc research in bioinformatics. He was a Senior Bioinformatics’ Researcher at the Official Laboratory of the Ministry of Fisheries. Dr. Soares is currently Secretary of the Southeast Regional of the Brazilian Society of Genetics (2017–present), Substitute Coordinator of the Bachelor’s in Biomedicine of UFTM (2017–present), Director of the Department for the Development of Research and Technological Innovation of UFTM (2019–present), and Affiliate Member of the Brazilian Academy of Sciences (2018–present). His areas of expertise are molecular genetics, genomic sequencing, and microbial comparative genomics, mainly focused on pan-genomics, the role of pathogenicity islands and virulence factors in genome plasticity, phylogenomics, molecular epidemiology, reverse vaccinology, and software development (Perl and Java languages).

Affiliations and expertise

Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil

Sandeep Tiwari

Dr. Tiwari obtained his BSc from Deen Dayal Upadhyaya Gorakhpur University, MSc in bioinformatics from Devi Ahilya University, and PhD in bioinformatics from the Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Brazil. He is a Guest Associate Editorial Board of Frontier in Genetics and frequently serves as an external reviewer for PeerJ and Frontiers. His main areas of expertise are molecular genetics, genomic sequencing, and comparative genomics of microorganisms, with a focus on pan-genomics, genomic plasticity in the identification of pathogenicity islands and virulence factors for drug discovery, phylogenomic, molecular epidemiology, reverse vaccinology, and immunoinformatic.

Affiliations and expertise

Visiting Adjunct Professor, Department of Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil; Department of Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil

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Reverse Vaccinology

Concept, Methods and Advancement

Purchase options

World Book Day Celebration!

Institutional subscription on ScienceDirect

Jayashankar Das

Sushma Dave

Siomar de Castro Soares

Sandeep Tiwari

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