Student Research Committee, Babol University of Medical Sciences, Babol, Iran; USERN Office, Babol University of Medical Sciences, Babol, Iran.
Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
Infect Genet Evol. 2022 Aug;102:105290. doi: 10.1016/j.meegid.2022.105290. Epub 2022 May 12.
Recent studies have established the role of bacteria including Streptococcus pneumoniae, Helicobacter pylori, Chlamydia pneumonia, Mycobacterium tuberculosis, and Porphyromonas gingivalis in the development of atherosclerosis. These bacteria contribute to plaque formation via promoting Th1 immune responses and speeding up ox-LDL formation. Hence, we employed computational reverse vaccinology (RV) approaches to deviate immune response toward Th2 via engineering a novel immunogenic chimera protein. Prominent atherogenic antigens from related bacteria were identified. Then, machine learning-based servers were employed for predicting CTL and HTL epitopes. We selected epitopes from a wide variety of HLAs. Then, a chimeric protein sequence containing TAT peptide, adjuvant, IL-10 inducer, and linker-separated epitopes was designed. The conformational structure of the vaccine was built via multiple-template homology modelling using MODELLER. The initial structure was refined and validated by Ramachandran plot. The vaccine was also docked with TLR4. After that, molecular dynamics (MD) simulation of the docked vaccine-TLR4 was conducted. Finally, the immune simulation of the vaccine was conducted via the C-ImmSim server. A chimera protein with 629 amino acids was built and, classified as a non-allergenic probable antigen. An improved ERRAT score of 80.95 for the refined structure verified its stability. Additionally, validation via the Ramachandran plot showed 98.09% of the residues were located in the most favorable and permitted regions. MD simulations showed the vaccine-TLR4 complex reached a stable conformation. Also, RMS fluctuations analysis revealed no sign of protein denaturation or unfolding. Finally, immune response simulations indicated a promising response by innate and adaptive immunity. In summary, we built an immunogenic vaccine against atherosclerosis and demonstrated its favorable properties via advanced Immunoinformatics analyses. This study may pave the path for combat against atherosclerosis.
最近的研究已经确定了包括肺炎链球菌、幽门螺杆菌、肺炎衣原体、结核分枝杆菌和牙龈卟啉单胞菌在内的细菌在动脉粥样硬化发展中的作用。这些细菌通过促进 Th1 免疫反应和加速 ox-LDL 的形成来促进斑块的形成。因此，我们采用计算性反向疫苗学（RV）方法，通过构建一种新型免疫原性嵌合蛋白来使免疫反应偏向 Th2。从相关细菌中鉴定出主要的动脉粥样硬化抗原。然后，使用基于机器学习的服务器预测 CTL 和 HTL 表位。我们从多种 HLA 中选择表位。然后，设计了一种包含 TAT 肽、佐剂、IL-10 诱导剂和链接分隔表位的嵌合蛋白序列。使用 MODELLER 通过多模板同源建模构建疫苗的构象结构。使用 Ramachandran 图对初始结构进行了细化和验证。还对接 TLR4 进行了疫苗。之后，对接疫苗-TLR4 进行了分子动力学（MD）模拟。最后，通过 C-ImmSim 服务器对疫苗进行免疫模拟。构建了一种含有 629 个氨基酸的嵌合蛋白，被归类为非变应原性可能抗原。经过改进的 ERRAT 评分 80.95 验证了其稳定性。此外，通过 Ramachandran 图验证显示 98.09%的残基位于最有利和允许的区域。MD 模拟表明疫苗-TLR4 复合物达到了稳定的构象。此外，RMS 波动分析显示没有蛋白质变性或展开的迹象。最后，免疫反应模拟表明固有和适应性免疫有很好的反应。总之，我们构建了一种针对动脉粥样硬化的免疫原性疫苗，并通过先进的免疫信息学分析证明了其良好的特性。这项研究可能为对抗动脉粥样硬化铺平道路。
