Related Experiment Video
Updated: Jul 16, 2026
A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes
Published on: March 25, 2014
Rational design of a multi-epitope vaccine for hand, foot, and mouth disease: an in silico perspective
Sunil Desai1, Sneha Dokhale1, Shine Devarajan2
1Department, of Biotechnology, B. K. Birla College (Empowered Autonomous Status), Kalyan, 421301, Maharashtra India.
Insights
This study designed a novel multiepitope vaccine (V4) against Hand, Foot, and Mouth Disease (HFMD) using reverse vaccinology. The V4 construct shows promise for broad cross-protection against major HFMD-causing enteroviruses.
Area of Science:
- Vaccinology
- Computational Biology
- Immunology
Background:
- Hand, Foot, and Mouth Disease (HFMD) is a significant public health concern, particularly in young children.
- Current treatments are supportive, and existing vaccines are monovalent, necessitating a broadly effective multivalent vaccine.
- HFMD is primarily caused by Coxsackievirus A16 (CV-A16) and Enterovirus 71 (EV-A71).
Purpose of the Study:
- To design a multiepitope vaccine candidate using reverse vaccinology targeting immunogenic regions of CV-A6, CV-A16, and EV-A71.
- To computationally evaluate the structural stability, immunogenicity, and immune response of the designed vaccine construct.
Main Methods:
- Utilized reverse vaccinology principles to identify and select immunogenic epitopes from viral capsid proteins.
- Employed computational tools for sequence analysis, epitope prediction (B-cell, CTL, HTL), structural stability assessment, molecular docking, and molecular dynamics simulations.
- Conducted in silico immune simulations (C-ImmSim) to predict the immune response profile and HLA coverage.
Main Results:
- A multiepitope vaccine construct, V4, was designed with optimal structural stability and strong binding affinity to TLR4.
- Molecular dynamics simulations confirmed the stability of the V4-TLR4 complex.
- In silico immune simulations predicted a robust Th1/Th17 response, significant B-cell activation, and broad global HLA coverage (99.06%).
Conclusions:
- The computationally validated V4 multi-epitope vaccine candidate offers a promising strategy for cross-protective immunity against major HFMD-causing enteroviruses.
- The designed vaccine warrants further experimental validation and preclinical development.
- This approach provides a robust framework for developing next-generation HFMD vaccines.
Abstract:
Hand, Foot, and Mouth Disease (HFMD) presents a serious public health concern, especially in children below five years of age and is predominantly caused by Coxsackievirus A16 (CV-A16) and Enterovirus 71 (EV-A71). Despite the availability of supportive treatments and strain-specific protection offered by existing monovalent vaccines, there is an urgent need for a broadly effective, widely accessible multivalent vaccine. This study implements reverse vaccinology to design a multiepitope vaccine targeting key immunogenic regions of CV-A6, CV-A16 and EV-A71. From 18,278 VP1 capsid protein sequences, redundancy was eliminated using CD-HIT (90% identity threshold), yielding 4,309 non-redundant sequences. Further screening for antigenic potential, non-allergenicity, non-toxicity, resulted in 306 qualified candidates for epitope prediction analysis. Highly immunogenic B-cell (BCPred score > 0.8, specificity > 75%), CTL (MHC-I binding IC50 < 200 nM), and HTL (MHC-II binding IC50 < 200 nM) epitopes were predicted from these sequences and integrated into four chimeric vaccine constructs. Among these the Vaccine 4 (V4) construct exhibited optimal structural stability. Molecular docking of the V4 construct with human Toll-Like Receptor 4 (TLR4) revealed a strong complex with a ClusPro-weighted score of -801.3 kcal/mol. Molecular dynamics simulations over 120 ns showed V4-TLR4 complex stabilization with RMSD values of 0.3-0.4 nm. C-ImmSim immune simulation predicted a predominant Th1/Th17 immune response, characterized by robust B-cell activation with peak IgG1 antibody titres, progressive memory B-cell formation, and effective antigen clearance upon repeated exposure. Epitopes of the designed construct projected a broad global HLA coverage (99.06%), including 92.71% in India. The V4 construct was codon-optimized for expression in E. coli achieving a Codon Adaptation Index (CAI) of 0.95. This computationally validated V4 multi-epitope vaccine candidate offers a promising, cross-protective strategy against major HFMD-causing enteroviruses, providing a robust preclinical framework that warrants subsequent experimental validation.
Supplementary Information:
The online version contains supplementary material available at 10.1007/s40203-026-00695-4.
