Smiline Girija A S
Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India.
Front Microbiol. 2020 Sep 8;11:2078. doi: 10.3389/fmicb.2020.02078. eCollection 2020.
To predict the novel vaccine peptide candidates against gacS protein involved with the citrate utilization in the two-component system of -associated virulence as an alternative strategy to combat the multi-drug resistant strains using an immuno-informatic approach.
The study is designed as an observational study design with the application of BepiPred, AlgPred, VaxiJen, AntigenPro, SolPro, Expasy ProtParam server, IEDB database, and MHC cluster analytical tools and servers to predict the immuno-dominant B-cell and T-cell epitopes from gacS FASTA sequences retrieved from UNIPROT database. Further peptide interactions with TLR-4 was assessed based on the number of hydrogen bonds.
Nine peptides (20aa) with the highest score of 1 were selected from the 137 epitopes, and five were predicted as antigenic epitopes (E1-E5). E3 was selected as the potent antigen (score: 0.939537) and E1 as the best vaccine candidate (score: 0.9803) under AntigenPro and Vaxijen server, respectively. SolPro predicted all epitopes as soluble peptides. ProtParam predictions showed E3 and E5 as stable proteins with a shelf life of 3.5 and 1.9 h and possessed negative GRAVY values. PsortB server predicted a final localization score of 7.88 for the gacS protein sequence as a cytoplasmic membrane protein. IEDB conservancy analysis showed 100% conserved sequences within the gacS sequence, and class I conservancy yielded positive values for all epitopes. Cluster analysis showed strong interactions, and the protein-peptide interactions with TLR-2 finally detected E5 as the best interacting peptide (H bonds = 14) followed by E3 (H bonds = 12).
The study suggests five antigenic peptides as promiscuous vaccine candidates to target the gacS of using immuno-informatic approach toward the peptide synthesis and analysis. However, the study recommends further experimental validation for immunological response and memory through studies.
利用免疫信息学方法预测针对双组分系统中与柠檬酸盐利用相关的gacS蛋白的新型疫苗肽候选物，作为对抗多重耐药菌株的替代策略。
本研究设计为观察性研究，应用BepiPred、AlgPred、VaxiJen、AntigenPro、SolPro、Expasy ProtParam服务器、IEDB数据库以及MHC聚类分析工具和服务器，从从UNIPROT数据库检索的gacS FASTA序列中预测免疫显性B细胞和T细胞表位。基于氢键数量进一步评估肽与TLR-4的相互作用。
从137个表位中选择了9个得分最高为1的肽（20个氨基酸），其中5个被预测为抗原表位（E1-E5）。在AntigenPro和Vaxijen服务器下，E3分别被选为强效抗原（得分：0.939537），E1被选为最佳疫苗候选物（得分：0.9803）。SolPro预测所有表位均为可溶性肽。ProtParam预测显示E3和E5为稳定蛋白，半衰期分别为3.5小时和1.9小时，且具有负的亲水性值。PsortB服务器预测gacS蛋白序列作为细胞质膜蛋白的最终定位得分为7.88。IEDB保守性分析显示gacS序列内100%保守序列，I类保守性对所有表位均产生正值。聚类分析显示有强相互作用，蛋白质-肽与TLR-2的相互作用最终检测到E5为最佳相互作用肽（氢键=14），其次是E3（氢键=12）。
本研究表明，利用免疫信息学方法进行肽合成和分析，有5种抗原肽作为通用疫苗候选物可靶向的gacS。然而，该研究建议通过进一步研究对免疫反应和记忆进行进一步的实验验证。
