Al-Megrin Wafa Abdullah I, Karkashan Alaa, Alnuqaydan Abdullah M, Aba Alkhayl Faris F, Alrumaihi Faris, Almatroudi Ahmad, Allemailem Khaled S
Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
Department of Biology, College of Sciences, University of Jeddah, Jeddah 21959, Saudi Arabia.
Vaccines (Basel). 2022 Jun 1;10(6):886. doi: 10.3390/vaccines10060886.
(EC) is a significant emerging pathogen that is occasionally associated with lung infection, surgical site infection, urinary infection, sepsis, and outbreaks in neonatal intensive care units. In light of the fact that there is currently no approved vaccine or therapeutic option for the treatment of EC, the current study was developed to concentrate on applications based on modern computational approaches to design a multi-epitope-based peptide vaccine (MEBEPV) expressing the antigenic determinants prioritized from the EC genome. Integrated computational analyses identified two potential protein targets (phosphoporin protein-PhoE and putative outer-membrane porin protein) for further exploration on the basis of pangenome subtractive proteomics and immunoinformatic in-depth examination of the core proteomes. Then, a multi-epitope peptide vaccine was designed, which comprised shortlisted epitopes that were capable of eliciting both innate and adaptive immunity, as well as the cholera toxin's B-subunit, which was used as an adjuvant in the vaccine formulation. To ensure maximum expression, the vaccine's 3D structure was developed and the loop was refined, improving the stability by disulfide engineering, and the physicochemical characteristics of the recombinant vaccine sequence were found to be ideal for both in vitro and in vivo experimentation. Blind docking was then used for the prediction of the MEBEPV predominant blinding mode with MHCI, MHCII, and TLR3 innate immune receptors, with lowest global energy of -18.64 kJ/mol, -48.25 kJ/mol, and -5.20 kJ/mol for MHC-I, MHC-II, and TLR-4, respectively, with docked complexes considered for simulation. In MD and MMGBSA investigations, the docked models of MEBEPV-TLR3, MEBEPV-MHCI, and MEBEPV-MHCII were found to be stable during the course of the simulation. MM-GBSA analysis calculated -122.17 total net binding free energies for the TLR3-vaccine complex, -125.4 for the MHC I-vaccine complex, and -187.94 for the MHC II-vaccine complex. Next, MM-PBSA analysis calculated -115.63 binding free energy for the TLR3-vaccine complex, -118.19 for the MHC I-vaccine complex, and -184.61 for the MHC II-vaccine complex. When the vaccine was tested in silico, researchers discovered that it was capable of inducing both types of immune responses (cell mediated and humoral) at the same time. Even though the suggested MEBEPV has the potential to be a powerful contender against -associated illnesses, further testing in the laboratory will be required before it can be declared safe and immunogenic.
肠球菌（EC）是一种重要的新兴病原体，偶尔与肺部感染、手术部位感染、泌尿系统感染、败血症以及新生儿重症监护病房的疫情爆发有关。鉴于目前尚无批准用于治疗EC的疫苗或治疗方案，本研究旨在专注于基于现代计算方法的应用，以设计一种表达从EC基因组中优先选择的抗原决定簇的多表位肽疫苗（MEBEPV）。综合计算分析基于全基因组减法蛋白质组学和核心蛋白质组的免疫信息学深入研究，确定了两个潜在的蛋白质靶点（磷酸转运蛋白PhoE和假定的外膜孔蛋白）以供进一步探索。然后，设计了一种多表位肽疫苗，其包含能够引发先天免疫和适应性免疫的入围表位，以及霍乱毒素的B亚基，其在疫苗配方中用作佐剂。为确保最大表达，构建了疫苗的三维结构并优化了环区，通过二硫键工程提高了稳定性，发现重组疫苗序列的物理化学特性对于体外和体内实验都是理想的。然后使用盲对接预测MEBEPV与MHC I、MHC II和TLR3先天免疫受体的主要结合模式，MHC-I、MHC-II和TLR-4的最低全局能量分别为-18.64 kJ/mol、-48.25 kJ/mol和-5.20 kJ/mol，对接复合物用于模拟。在分子动力学（MD）和MMGBSA研究中，发现MEBEPV-TLR3、MEBEPV-MHC I和MEBEPV-MHC II的对接模型在模拟过程中是稳定的。MM-GBSA分析计算出TLR3-疫苗复合物的总净结合自由能为-122.17，MHC I-疫苗复合物为-125.4，MHC II-疫苗复合物为-187.94。接下来，MM-PBSA分析计算出TLR3-疫苗复合物的结合自由能为-115.63，MHC I-疫苗复合物为-118.19，MHC II-疫苗复合物为-184.61。当在计算机上对疫苗进行测试时，研究人员发现它能够同时诱导两种类型的免疫反应（细胞介导和体液免疫）。尽管所建议的MEBEPV有可能成为对抗相关疾病的有力竞争者，但在宣布其安全且具有免疫原性之前，还需要在实验室进行进一步测试。
