Immunoinformatic design of chimeric multiepitope vaccine for the prevention of human metapneumovirus (hMPV)

Abstract

Background: Human metapneumovirus (hMPV) is a significant etiological agent of acute respiratory infections in children and immunocompromised individuals. Despite its growing clinical impact, no approved vaccines or targeted antiviral therapies are currently available.

Methods: An immunoinformatic approach was employed to design a chimeric multi-epitope vaccine candidate against hMPV. Conserved and virulence-associated proteins were analyzed to predict highly antigenic B cell, cytotoxic T lymphocyte (CTL), and helper T lymphocyte (HTL) epitopes. The selected epitopes were screened for antigenicity, non-toxicity, non-allergenicity, and lack of homology to human proteins. The final construct included six B cell epitopes, six CTL epitopes, and two HTL epitopes, linked with appropriate adjuvants and Toll-like receptor (TLR) agonists. Structural modeling, molecular docking, and molecular dynamics simulations were conducted to evaluate the stability and receptor binding. Immunogenicity and expression potential were assessed through in silico immune simulation and codon optimization for expression in Escherichia coli.

Results: All selected epitopes showed high antigenicity with no allergenic or toxicity. Structural validation indicated a stable vaccine construct with favorable physicochemical properties. Molecular docking analysis predicted a high binding affinity between the vaccine construct and TLR2/TLR4 receptors. Molecular dynamics (MD) simulations suggested that the docked complexes maintained stable interactions under simulated physiological conditions. In silico immune simulations predicted strong B- and T-cell responses following three doses. Codon adaptation analysis supported the high-level expression in E. coli.

Conclusion: The proposed multi-epitope vaccine demonstrates strong potential against hMPV, as supported by comprehensive computational analyses. Further experimental studies are required to validate its efficacy and safety.

Keywords: HMPV; Immunoinformatic; MD simulation; Molecular Docking; Multi-epitope vaccine.

Fig. 1

World population coverage for combined MHC-I and MHC-II alleles showed that the selected epitopes provide coverage for 99.74% of the global population, with an average hit of 15.98. The bar represents the population coverage for each epitope, whereas the cumulative percentage of population coverage is represented by a line graph (-o-)

Fig. 2

(A) The amino acid sequences of multiepitope vaccine candidate with different elements exhibited by different colors, (B) Structural arrangement of the final vaccine candidate constructed from adjuvant, LBL, CTL, and HTL epitopes separated by linkers; (C) The strand, helix, and coil secondary structures in the amino acid sequences of vaccine candidate are shown in yellow, pink, and grey, respectively

Fig. 3

Validation of the tertiary structure of the multiepitope vaccine candidate. A The 3D model structure of the multiepitope vaccine candidate predicted using AlphaFold3 and refined using GalaxyRefine. B Z-score graphs generated by the ProSA-web server of the refined models of multiepitope vaccine candidate. C The Ramachandran Plots of multiepitope vaccine candidate show the allowed regions (depicted in orange and deep yellow), the generously allowed regions (in light yellow), the outlier regions (in white), and the glycine residues represented as triangles

Fig. 4

Discontinuous B cell epitopes predicted by the ElliPro server. Yellow spheres represent spatially clustered, surface-exposed residues

Fig. 5

Molecular docking between multi-epitope vaccine candidate and TLR2 and TLR4 receptors using ClusPro 2.0. Depiction of the docked conformation of multiepitope vaccine-TLR2/TLR4 and representation of the interactions in complex using PDBsum. The multiepitope vaccine is shown in light pink and the TLR2 and TLR4 are shown in light blue

Fig. 6

MD Simulation Results. A RMSD curve for vaccine-TLRs complexes, B) RMSF curve for vaccine-TLRs complexes, C) Variation in the Radius of Gyration (Rg) of the complexes, D) Solvent-accessible surface area (SASA) of the complexes, E) Changes in the number of hydrogen bonds (H-bonds) in the complexes

Fig. 7

Simulation of the immune response against the vaccine candidate using C-ImmSim server. (A) Immunoglobulin production in response to immunization with the proposed multiepitope vaccine candidate. Specific subclasses are shown in different colors. (B) Levels of cytokines: The main diagram shows the cytokine levels after the multiepitope vaccine candidate injection. The inset plot shows the levels of the white blood cell growth factor IL-2 and the general activation signal of macrophage D. (C) Evolution of B cell populations after three vaccinations of the multiepitope vaccine candidate. (D) Production of B cells after the injection. Active B cells (depicted in purple) showed the highest secretion levels compared to other B cell subtypes. (E) Production of CD4 helper T cells in response to antigen exposure, including active, duplicating, resting, and anergic CD4 helper T cells. (F) Cytotoxic T cells production. The “resting state” indicates that no antigen occurs by cytotoxic T cells, while the “anergic state” indicates T cell tolerance to antigens due to repeated exposure

Fig. 8

In silico cloning of designed multiepitope vaccine construct. The optimized DNA sequence of the designed multiepitope vaccine construct (shown in red) was cloned between the NcoI and XhoI restriction enzyme sites into the expression vector pET-28a (+)