Predicting epitopes for vaccine development using bioinformatics tools

Abstract

Epitope-based DNA vaccine development is one application of bioinformatics or in silico studies, that is, computational methods, including mathematical, chemical, and biological approaches, which are widely used in drug development. Many in silico studies have been conducted to analyze the efficacy, safety, toxicity effects, and interactions of drugs. In the vaccine design process, in silico studies are performed to predict epitopes that could trigger T-cell and B-cell reactions that would produce both cellular and humoral immune responses. Immunoinformatics is the branch of bioinformatics used to study the relationship between immune responses and predicted epitopes. Progress in immunoinformatics has been rapid and has led to the development of a variety of tools that are used for the prediction of epitopes recognized by B cells or T cells as well as the antigenic responses. However, the in silico approach to vaccine design is still relatively new; thus, this review is aimed at increasing understanding of the importance of in silico studies in the design of vaccines and thereby facilitating future research in this field.

Integration: Gospel for immune bioinformatician on epitope-based therapy

“…The evolution of epitope-based vaccines is one of the most promising developments arising from bioinformatics-based research ( 8 ), and the development of bioinformatics has also made pathogen epitope exploration convenient and cost-effective ( 11 ). We put forward a point of view, “Integration”, aiming to improve the accuracy and fit-in the body’s immune response.…”

“…Effective epitopes play a major therapeutic role in synthetic peptide vaccines. Identifying and screening epitopes, however, is usually an endless and complex process ( 8 ). Fortunately, researchers have developed in silico prediction methods that dramatically reduce the burden associated with epitope mapping by minimizing the list of potential epitope candidates for experimental testing ( 9 ).…”

“…However, the accuracy of single prediction analysis is often only 50%-70% ( 12 – 16 ). This is probably because of the inherent defects in computer algorithms based on epitope databases for fitting functions ( 8 , 11 ). In view of above deficiencies, we propose a novel train of thought, “integration”, to augment the breadth and depth of bioinformatics in peptide-based therapeutics.…”

“…Take an example of the depth implication in affinity analysis and molecular docking ( 8 ). Peptide-MHC interactions are crucial in immune functions.…”

“…GalaxyRefine performs repeated structure perturbation and subsequent overall structural relaxation by molecular dynamics simulation ( 48 ). The integration of I-TASSER and GalaxyRefine server allows the molecular structure to be rebuilt and optimized, providing an overall intuitive molecular structure ( 8 , 49 ).…”