Immunoinformatics-based design of artificial chimeric proteins as universal vaccine candidates against foot-and-mouth disease virus serotypes A, O, and SAT2

Abstract

Abstract Foot-and-mouth disease virus (FMDV) remains a major constraint to livestock health due to its high mutation rate and serotype diversity. Currently, FMDV vaccines, primarily inactivated whole-virus formulations, have significant limitations, including limited cross-protection, high production costs, and potential biosafety risks. To address the need for broad-spectrum protection, this study aimed to design a universal vaccine candidate by rationally constructing artificial chimeric proteins (ACPs) integrating conserved structural (VP1–VP3) and non-structural (3 A, 3 C) proteins from the predominant Egyptian FMDV serotypes A, O, and SAT 2. Three-dimensional modeling via AlphaFold3 and Swiss-Model confirmed the high structural quality of the constructs, with the ACP2 candidate exhibiting superior stability and reliability metrics (TM-score > 0.95, RMSD < 0.5, and overall quality > 88). Functional annotation revealed three conserved domains critical for virion assembly, receptor interaction, and host immune activation. Immunoinformatics analysis identified a robust antigenic profile for ACP1 and ACP2 proteins, comprising (21 and 36) cytotoxic T-lymphocyte (CTL), (18 and 20) helper T-lymphocyte (THL), and (15 and 19) B-cell epitopes prioritized for conservancy and population coverage. Based on these epitopes, three multiepitope vaccine constructs were assembled and analyzed computationally. Molecular docking demonstrated strong and stable binding affinities between the vaccine constructs and bovine TLR9 and TLR4 receptors (lowest binding energies of − 19.4 and − 16.9 kcal/mol, respectively), supported by stable interactions in 100 ns molecular dynamics simulations. These findings highlight the ACP2 construct as a novel, structurally stable, and highly immunogenic candidate capable of eliciting cross-serotype protection. The study provides a translational blueprint for a universal recombinant FMDV vaccine, warranting immediate in vitro expression and in vivo validation.