An in silico vaccinomics strategy to develop multiepitope vaccine using essential hypothetical protein as a target against Brevundimonas subvibrioides: A combined subtractive proteomics and immunoinformatics approach

Abstract

The genus Brevundimonas, responsible for a spectrum of diseases, encompasses opportunistic pathogens against diverse infections, with B. subvibrioides possessing the largest genome size. Presence of Brevundimonas genus has been found in clinical samples of patients with urinary tract infections (UTIs) and mastitis, specifically, B. subvibrioides. However, former treatment methods using antibiotics have rendered the bacteria resistant to the inhibitory effects of chloramphenicol, azithromycin, etc. as well as alternative chemical treatments. Reckoning with the present scenario, vaccination emerges as the safest and most effective treatment strategy to address the global issue of evolving microbial threats. The growing concern of antibiotic resistance necessitates a shift towards vaccination as the primary treatment strategy. For this study, a total of 15 essential hypothetical proteins (EsHPs) were retrieved from the database of essential genes (DEG) for further multi-server functional annotation, physicochemical characterization, and non-homology analysis. The target antigen for our peptide-based vaccine construct was localized in the extracellular space, exhibited virulence factor and non-homology against human host and gut microflora. The final screened candidate was detected to be antigenic, probable non-allergen, soluble, non-toxic with near absence of transmembrane helices. The linear B-cell lymphocyte (LBL), helper T lymphocyte (HTL), and cytotoxic T lymphocyte (CTL) epitopes present on this protein were predicted and further docked with their respective major histocompatibility complex (MHC) molecules to verify their affinities for favourable antigen presentation. The final vaccine construct was built with human beta-defensin 3 (HBD3) as the adjuvant, 2 LBL epitopes, 3 CTL epitopes, 1 HTL epitope, and the required linkers. The designed construct was found to be immune response-inducing and was therefore cloned into a suitable vector to assess the possibility of appropriate expression. The final construct, when docked with Toll-like receptor 4 (TLR4), followed by molecular dynamics (MD) simulation of unbound and bound complexes, demonstrated a strong generation of immunity, whose safety might be experimentally tested in the near future. This was corroborated by stabilizing root-mean-square deviation (RMSD) curves, increasing hydrogen bonds, and decreasing residual mobility.

Keywords: Brevundimonas subvibrioides; Essential hypothetical protein; Extracellular; Innate and adaptive immune response; Multi-epitope vaccine construct.