Towards precision epitopes based vaccine against Enterococcus faecalis by integrating vaccinomics, reverse vaccinology and biophysics approaches

Abstract

Enterococcus faecalis is a Gram-positive bacterium and recognized as an etiological agent of different nosocomial infections. E. faecalis has developed resistance to several antibiotics. No licensed vaccine is available to prevent E. faecalis infections. A multi-epitopes-based vaccine construct may provide effective vaccine design foundation. In this study, an integrated bioinformatic approach was applied to design of a multi-epitopes-based vaccine construct against E. faecalis. In subtractive proteomics analysis, 10 proteins were prioritized as potential vaccine candidates based on several literature reported vaccine candidacy parameters. In immunoinformatics analysis, only two proteins (glucosaminidase domain-containing protein and serine protease) were found as promising vaccine targets. Both proteins were then subjected to epitopes mapping for screening of broad-spectrum antigenic epitopes. The predicted epitopes were further refined based on immunoinformatics filters and only six epitopes; DTSDHQKNNV, GMKKRKARY, SVFDESMALR, NLNQRIEKR, NVDKKIEEK, and TTTPSTDNSA were found as non-allergic, antigenic, water-soluble, non-toxic and DRB∗0101 good binders. The selected epitopes were fused via GPGPG linkers and additionally linked to an adjuvant molecule through EAAAK linkers to increase the immunogenicity and antigenicity of the vaccine construct. The net interactions energy of the vaccine and receptors was evaluated through molecular docking analysis, which predicted −833.0 kcal/mol and −1001.6 kcal/mol of binding energy for MHC-I and MHC-II, respectively. The values predict effective vaccine construct binding with host immune cell receptors and triggering of innate and adaptive immune responses. The dynamic behavior of the docked complexes was examined using molecular dynamics (MD) simulation technique on a time scale of 500 ns. The MD revealed minimal intermolecular conformational deviations and exposed presentation of the vaccine epitopes for immune cells recognition and processing. For MHC-I-Vaccine complex, the mean RMSD was found as 2.78 Å while MHC–II–Vaccine complex showed a mean RMSD value of 13.17 Å. The C-immune simulation predicted the formation of high titer humoral and cellular immunological responses against the vaccine antigen. The predicted IgG and IgM titer found against the antigen was 600000–650000 counts per milliliter. The interferon-gamma (IFN-γ) was predicted to be stimulated at 430000 ng per milliliter. Simulation trajectories based MMGB/PBSA binding energy was estimated as < −250 kcal/mol for vaccine-MHC complexes, illustrating formation of robust interactions between the vaccine and MHC receptors. The study outcomes predicted the viability of the proposed epitope-based vaccine construct as a promising therapeutic approach for E. faecalis infections prevention, however, experimental confirmation is required.