The use of databases, data mining and immunoinformatics in vaccinology: where are we?

ABSTRACT

Introduction: Vaccinology has evolved from a sub-discipline focussed on simplistic vaccine development based on antibody-mediated protection to a separate discipline involving epidemiology, host and pathogen biology, immunology, genomics, proteomics, structure biology, protein engineering, chemical biology, and delivery systems. Data mining in combination with bioinformatics has provided a scaffold linking all these disciplines to the design of vaccines and vaccine adjuvants.

Areas covered: This review provides background knowledge on immunological aspects which have been exploited with informatics for the in silico analysis of immune responses and the design of vaccine antigens. Furthermore, the article presents various databases and bioinformatics tools, and discusses B and T cell epitope predictions, antigen design, adjuvant research and systems immunology, highlighting some important examples, and challenges for the future.

Expert opinion: Informatics and data mining have not only reduced the time required for experimental immunology, but also contributed to the identification and design of novel vaccine candidates and the determination of biomarkers and pathways of vaccine response. However, more experimental data is required for benchmarking immunoinformatic tools. Nevertheless, developments in immunoinformatics and reverse vaccinology, which are nascent fields, are likely to hasten vaccine discovery, although the path to regulatory approval is likely to remain a necessary impediment.

KEYWORDS:

• Adjuvant
• antigen
• data mining
• immunoinformatics
• structural biology
• systems immunology
• vaccine design

Article Highlights

• Data mining has contributed greatly to the identification of vaccine targets

• Databases have considerable utility in determining biomarkers and pathways of immune responses to antigens

• Informatics combined with structural biology has significant potential for future vaccine design

• Prediction of T cell targets (mostly sequential epitopes) has been easier than prediction of B cell targets (mostly conformational epitopes)

• Adjuvant discovery is another area where immunoinformatics could influence vaccine development

This box summarizes key points contained in the article.

Declaration of Interest

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties. Peer reviewers on this manuscript have no relevant financial or other relationships to disclose

Additional information

Funding

This work was supported in part through grants from the Department of Biotechnology (BT/PR11245/ADV/90/165/2014), Government of India, to NR Hegde, the Centre Franco-Indien pour la Promotion de la Recherche Avancee (CEFIPRA-4803-1) to J Bayry, and the Council of Scientific and Industrial Research (CSC0205), Government of India, to HMS Kumar.