Solanki Vandana, Tiwari Monalisa, Tiwari Vishvanath
Department of Biochemistry, Central University of Rajasthan, Ajmer, Rajasthan, India.
PeerJ. 2021 Mar 23;9:e11126. doi: 10.7717/peerj.11126. eCollection 2021.
The rapid Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV2) outbreak caused severe pandemic infection worldwide. The high mortality and morbidity rate of SARS CoV2 is due to the unavailability of vaccination and mutation in this virus. The present article aims to design a potential vaccine construct VTC3 targeting the non-mutational region of structural and non-structural proteins of SARS CoV2.
In this study, vaccines were designed using subtractive proteomics and reverse vaccinology. To target the virus adhesion and evasion, 10 different structural and non-structural proteins have been selected. Shortlisted proteins have been screened for B cell, T cell and IFN gamma interacting epitopes. 3D structure of vaccine construct was modeled and evaluated for its physicochemical properties, immunogenicity, allergenicity, toxicity and antigenicity. The finalized construct was implemented for docking and molecular dynamics simulation (MDS) with different toll-like receptors (TLRs) and human leukocyte antigen (HLA). The binding energy and dissociation construct of the vaccine with HLA and TLR was also calculated. Mutational sensitivity profiling of the designed vaccine was performed, and mutations were reconfirmed from the experimental database. Antibody production, clonal selection, antigen processing, immune response and memory generation in host cells after injection of the vaccine was also monitored using immune simulation.
Subtractive proteomics identified seven (structural and non-structural) proteins of this virus that have a role in cell adhesion and infection. The different epitopes were predicted, and only extracellular epitopes were selected that do not have similarity and cross-reactivity with the host cell. Finalized epitopes of all proteins with minimum allergenicity and toxicity were joined using linkers to designed different vaccine constructs. Docking different constructs with different TLRs and HLA demonstrated a stable and reliable binding affinity of VTC3 with the TLRs and HLAs. MDS analysis further confirms the interaction of VTC3 with HLA and TLR1/2 complex. The VTC3 has a favorable binding affinity and dissociation constant with HLA and TLR. The VTC3 does not have similarities with the human microbiome, and most of the interacting residues of VTC3 do not have mutations. The immune simulation result showed that VTC3 induces a strong immune response. The present study designs a multiepitope vaccine targeting the non-mutational region of structural and non-structural proteins of the SARS CoV2 using an immunoinformatic approach, which needs to be experimentally validated.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的迅速爆发在全球范围内引发了严重的大流行感染。SARS-CoV-2的高死亡率和发病率归因于疫苗的不可用以及该病毒的突变。本文旨在设计一种针对SARS-CoV-2结构蛋白和非结构蛋白非突变区域的潜在疫苗构建体VTC3。
在本研究中，使用减法蛋白质组学和反向疫苗学设计疫苗。为了靶向病毒的粘附和逃避，选择了10种不同的结构蛋白和非结构蛋白。对入围的蛋白质进行B细胞、T细胞和干扰素γ相互作用表位的筛选。对疫苗构建体的三维结构进行建模，并评估其物理化学性质、免疫原性、致敏性、毒性和抗原性。对最终确定的构建体进行与不同Toll样受体（TLR）和人类白细胞抗原（HLA）的对接和分子动力学模拟（MDS）。还计算了疫苗与HLA和TLR的结合能和解离常数。对设计的疫苗进行突变敏感性分析，并从实验数据库中重新确认突变。注射疫苗后，还使用免疫模拟监测宿主细胞中的抗体产生、克隆选择、抗原加工、免疫反应和记忆生成。
减法蛋白质组学鉴定出该病毒的七种（结构和非结构）蛋白，它们在细胞粘附和感染中起作用。预测了不同的表位，仅选择与宿主细胞无相似性和交叉反应性的细胞外表位。使用接头连接所有具有最低致敏性和毒性的蛋白质的最终确定表位，以设计不同的疫苗构建体。将不同的构建体与不同的TLR和HLA对接，证明VTC3与TLR和HLA具有稳定可靠的结合亲和力。MDS分析进一步证实了VTC3与HLA和TLR1/2复合物的相互作用。VTC3与HLA和TLR具有良好的结合亲和力和解离常数。VTC3与人类微生物群无相似性，且VTC3的大多数相互作用残基没有突变。免疫模拟结果表明，VTC3可诱导强烈的免疫反应。本研究使用免疫信息学方法设计了一种针对SARS-CoV-2结构蛋白和非结构蛋白非突变区域的多表位疫苗，该疫苗需要进行实验验证。
