Subtractive proteomic analysis of antigenic extracellular proteins and design a multi-epitope vaccine against Staphylococcus aureus

Staphylococcus aureus is a versatile Gram's positive bacterium that can reside as an asymptomatic colonizer, which can cause a wide range of skin, soft-tissue, and nosocomial infections. A vaccine against multi-drug resistant S. aureus, therefore, is urgently needed. Subtractive proteomics and reverse vaccinology are newly emerging techniques to design multiepitope-based vaccines. The analysis of 7290 proteomes (sensitive and resistant strains), five potent nonhuman homologous vaccine targets [(UNIPORT ID Q2FZL3 (Staphopain B), Q2G2R8 (Staphopain A), Q2FWP0 (uncharacterized leukocidin-like protein 1), Q2G1S6 (uncharacterized protein), and Q2FWV3 (Staphylokinase, putative)] were selected. These proteins were absent in the gut microbiome, which further enhances the significance of these proteins in vaccine design. These five virulence-associated proteins mainly have a role in the invasion mechanism in the host phagocyte cells. MHC I, MHC II, and B cell epitopes were identified in these five proteins. Finalized epitopes were examined by different online servers to screen suitable epitopes for multi-epitope based vaccine design. Shortlisted antigenic and nonallergenic associated epitopes were joined with linkers to design 30 variants (VSA1-VSA30) of multi-epitope vaccine conjugates. The antigenicity and allergenicity of all the 30 vaccine constructs were identified, and VSA30 was found to have the highest antigenicity and lowest allergenicity, and hence was selected for further study. Accordingly, VSA30 was docked with different HLA allelic variants, and the best-docked complex (VSA30-1SYS) was further analyzed by molecular dynamics simulation (MDS). The MDS result confirms the interaction of VSA30 with MHC (HLA-allelic variant). Thus, the final vaccine construct was in silico cloned in the pET28a vector for suitable expression in a heterologous system. Therefore, the designed vaccine construct VSA-30 can be developed as an appropriate vaccine to target S. aureus infection. VSA-30 still needs experimental validation to assure the antigenic and immunogenic properties.