Advancements in Vaccine Development: A Comprehensive Design of a Multi-Epitopic Immunodominant Peptide Vaccine Targeting Kyasanur Forest Disease via Reverse Vaccinology

Abstract

Introduction/Objective: Kyasanur Forest Disease (KFD), caused by the Kyasanur Forest Disease Virus (KFDV), is a tick-borne haemorrhagic fever endemic to South India and spreading to neighbouring states. The formalin-inactivated Chick Embryo Fibroblast (CEF) vaccine currently in use provides only short-term protection, requires repeated inoculations, and has limited coverage. A safe, simple-to-administer vaccine, which includes chills, fever, and headaches, was designed as a multi-epitope peptide vaccine (MEPV) against the immunodominant E protein of KFDV by using cutting-edge immunoinformatic and reverse vaccinology approaches. Methods: Ten KFDV strains (1962-2016) were retrieved from NCBI and screened for antigenicity. The sequence of the E protein of the selected strain was screened for CTL, HTL, and B-cell epitopes using IEDB, NetMHCpan, and ABCPred. Predicted epitopes were evaluated for antigenicity, allergenicity, toxicity, immunogenicity, and conservancy across all the shortlisted strains. Potential epitopes were linked with suitable linkers to form the PKFDVac-I construct. Its physicochemical properties, structure stability, and immunogenic potential were evaluated using Expasy ProtParam, PSIPRED, AlphaFold, molecular docking with TLR-4, molecular dynamics simulation, and C-ImmSim immune simulation. Results: Sixteen epitopes (5 CTL, 3 HTL, 8 B-cell) cleared all screening criteria and were included in PKFDVac-I, a 279-amino-acid construct with a molecular weight of 29.16 kDa. The vaccine demonstrated high antigenicity, non-toxicity, non-allergenicity, solubility, and stability. Docking was found to be good, with a TLR-4 binding affinity of-1150.78 kcal/mol (Piper energy), supported by 387 non-bonding interactions. A 100-ns molecular dynamics simulation confirmed the stability of the complex. Immune simulation also anticipated robust humoral and cellular immunogenicity, higher antibody titers, long-lived persistence of memory cells, and robust IFN-γ induction. Discussion: PKFDVac-I had favorable immunological properties in silico. The design comprises conserved epitopes that are antigenic, safe, and immunogenic to the tested Indian KFDV strains from 1962 to 2016, ensuring lineage representativeness. Molecular docking and simulation reveal a stable interaction between receptors, and immune simulations predict durable adaptive immunity. Conclusion: PKFDVac-I is a proposed multi-epitope peptide vaccine candidate for Kyasanur Forest Disease. The integration of diverse epitopes into a cohesive vaccine prototype demonstrates a promising avenue for custom synthesis and application in immunization strategies. The design represents a significant advancement in the evolution of KFD vaccines and warrants further in vitro and in vivo validation.