title: Immunoinformatics analysis and in silico designing of a novel multi-epitope peptide vaccine against Staphylococcus aureus.
abstract: Staphylococcus aureus is a pathogen that causes a variety of infections in humans. Methicillin-resistant S. aureus, which is an antibiotic-resistant form, is responsible for nosocomial staphylococcal infections, whose frequency is increasing in healthy people. Thereby, the development of novel techniques is required to overcome this bacterial infection. In this context, the use of vaccines to control infections is an appropriate alternative. In this study, immunoinformatics analysis is used on three antigenic determinants as vaccine candidates, and a novel multi-epitope vaccine is designed to induce cellular, humoral, and innate immune responses against S. aureus. Alpha-enolase, clumping factor A, and iron surface determinant B were selected as the protective antigens; and phenol-soluble modulin alpha 4was applied as the adjuvant. Epitopes identification was done for each antigen using various immunoinformatics servers. Moreover, the tertiary structure of our protein vaccine was predicted and validated. Subsequently, the best-modeled protein structure was used for the refinement process. There fined model was then applied for docking studies with Toll-like receptor 2 (TLR2).In the next step, molecular dynamics (MD) simulation was used to evaluate the stability of vaccine molecule and TLR2-vaccine complex. The high ranked epitopes were selected from the mentioned antigens. The selected epitopes and the adjuvant were fused together by proper linkers. Then, the modeled protein structure was selected and validated. Validation results indicated that the initial model needs refinement. After a refinement process, the final model was generated. Finally, the best-docked model of vaccine and TLR2 complex was selected. In this research, we attempted to design an efficient subunit vaccine, which could stimulate humoral and cellular immune responses. Therefore, we expect that our designed vaccine could defeat antibiotic-resistant staphylococcal infections.
authors.affiliation: Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.
authors.forename: Nasim
authors.initials: N
authors.lastname: Hajighahramani
authors.affiliation: Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.
authors.forename: Navid
authors.initials: N
authors.lastname: Nezafat
authors.affiliation: Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.
authors.forename: Mahboobeh
authors.initials: M
authors.lastname: Eslami
authors.affiliation: Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.
authors.forename: Manica
authors.initials: M
authors.lastname: Negahdaripour
authors.affiliation: Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.
authors.forename: Seyyed Soheil
authors.initials: SS
authors.lastname: Rahmatabadi
authors.affiliation: Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran. Electronic address: ghasemiy@sums.ac.ir.
authors.forename: Younes
authors.initials: Y
authors.lastname: Ghasemi
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D019295:Computational Biology; D000939:Epitopes / Q000276:immunology; D006801:Humans; D056004:Molecular Dynamics Simulation; D013203:Staphylococcal Infections / Q000276:immunology / Q000382:microbiology / Q000517:prevention & control*; D013209:Staphylococcal Vaccines / Q000737:chemistry* / Q000276:immunology; D013211:Staphylococcus aureus / Q000276:immunology*; D022223:Vaccines, Subunit / Q000737:chemistry* / Q000276:immunology
chemical_list: D000939:Epitopes; D013209:Staphylococcal Vaccines; D022223:Vaccines, Subunit
keywords: Alpha-enolase; Clumping factor A; Immunoinformatics; Iron surface determinant B; Staphylococcus aureus; Subunit vaccine