Immunoinformatics-driven design and computational analysis of a multiepitope vaccine targeting uropathogenic Escherichia coli

Abstract

Urinary tract infections (UTIs), largely caused by uropathogenic Escherichia coli (UPEC), are increasingly resistant to antibiotics and frequently recur. Using immunoinformatics, we designed a multiepitope peptide vaccine targeting UPEC virulence factors, including iron acquisition systems and adhesins. The construct features 12 cytotoxic T lymphocyte epitopes, six helper T lymphocyte epitopes, and six B-cell epitopes,and isoptimized for high antigenicity, immunogenicity, nontoxic, and low allergenic potential. Molecular docking and 0.4-µs molecular dynamics simulations revealed the molecular mechanism of theinteraction of the vaccine with Toll-like receptor 4 and a favorable binding energy of - 41.83 kcal/mol using an implicit solvation model. These promising in silico results suggest the potential efficacy of the vaccine in preventing UPEC infections and underscore immunoinformatics as a powerful tool for addressing antibiotic-resistant UTI pathogens.

Supplementary information: The online version contains supplementary material available at 10.1007/s40203-024-00288-z.

Keywords: Immunoinformatics; Molecular Dynamics Simulations; Multiepitope Vaccine; Toll-like Receptor 4; Uropathogenic Escherichia coli.

Fig. 1

Illustration of the multiepitope vaccine construct. The epitopes were constructed using amino acids and including adjuvants at both the N- and C-termini connected with the first CTL epitope via an EAAAK linker. The CTL epitopes are linked with AAY linkers, whereas the HTL and B-cell epitopes are linked with GPGPG linkers

Fig. 2

A Visualization of the interaction interface between the multiepitope vaccine construct (top molecule) and the TLR4 receptor (bottom molecule) using the Rosetta protocol, highlighted with a red surface using the ClusPro algorithm. B 3D molecular alignment of the top 10 multiepitope construct-TLR4 complexes predicted with the Rosetta protocol, with the reference structure depicted in green for comparison. C Scatter plot showing the correlation between energy, measured in Rosetta energy units (REUs), and root-mean-square deviation (RMSD), illustrating the stability and energy distribution of the complexes

Fig. 3

RMSD (A), RMSF (B), Rg (C), and the fraction of the dominated intermolecular H-bonds calculated for the TLR4-vaccine complex during 0.4 μs MD simulation (D)

Fig. 4

In silico cloning. Multiple epitope antigens (red) were integrated into the pET28a (+) expression vector between the Eco53kI and EcoRV restriction sites