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.

中文翻译：

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抗原性细胞外蛋白的减法蛋白质组学分析和设计针对金黄色葡萄球菌的多表位疫苗

金黄色葡萄球菌是一种多用途的革兰氏阳性细菌，可作为无症状的定植菌存在，可引起多种皮肤、软组织和医院感染。一种针对多重耐药性金黄色葡萄球菌的疫苗，因此，是迫切需要的。减法蛋白质组学和反向疫苗学是设计基于多表位的疫苗的新兴技术。7290 个蛋白质组（敏感和抗性菌株）、五个有效的非人类同源疫苗靶点的分析 [(UNIPORT ID Q2FZL3 (Stahopain B), Q2G2R8 (Stahopain A), Q2FWP0 (uncharacterized leukocidin-like protein 1), Q2G1S6 (uncharacterized protein 1),和 Q2FWV3（葡萄激酶，推定）]。这些蛋白质在肠道微生物组中不存在，这进一步增强了这些蛋白质在疫苗设计中的重要性。这五种毒力相关蛋白质主要在宿主吞噬细胞的侵袭机制中起作用在这五种蛋白质中鉴定了 MHC I、MHC II 和 B 细胞表位。最终的表位由不同的在线服务器检查，以筛选适合基于多表位的疫苗设计的表位。入围的抗原性和非过敏性相关表位与接头结合，以设计多表位疫苗偶联物的 30 种变体 (VSA1-VSA30)。确定了所有 30 种疫苗构建体的抗原性和过敏性，发现 VSA30 具有最高的抗原性和最低的过敏性，因此被选中进行进一步研究。因此，VSA30 与不同的 HLA 等位基因变体对接，并通过分子动力学模拟 (MDS) 进一步分析了最佳对接复合体 (VSA30-1SYS)。MDS 结果证实了 VSA30 与 MHC（HLA 等位基因变体）的相互作用。因此，最终的疫苗构建体被计算机克隆到 pET28a 载体中，以便在异源系统中进行适当的表达。因此，设计的疫苗构建体 VSA-30 可以开发为合适的疫苗来靶向金黄色葡萄球菌感染。VSA-30 仍需要实验验证以确保抗原性和免疫原性。