Exploring SARS-COV-2 structural proteins to design a multi-epitope vaccine using immunoinformatics approach: An in silico study

• Published in: Computers in biology and medicine 2021-06, Vol.133, p.104390-104390, Article 104390
• Main Authors: Sanami, Samira, Alizadeh, Morteza, Nosrati, Masoud, Dehkordi, Korosh Ashrafi, Azadegan-Dehkordi, Fatemeh, Tahmasebian, Shahram, Nosrati, Hamed, Arjmand, Mohammad-Hassan, Ghasemi-Dehnoo, Maryam, Rafiei, Ali, Bagheri, Nader
• Format: Article
• Language: English
• Subjects: Algorithms; Allergenicity; Amino acids; Antigenicity; Antigens; Biocompatibility; Bioinformatics; Biomedical materials; China; Cholera; Cholera toxin; Cholera toxin B subunit; Cloning; Cloning vectors; Coronaviruses; COVID-19; COVID-19 Vaccines; CTxB; Cytokines; Cytotoxicity; Disease transmission; Epitope; Epitopes; Epitopes, B-Lymphocyte; Epitopes, T-Lymphocyte; Genomes; Humans; Immune response; In vivo methods and tests; Infections; Lymphocytes; Lymphocytes T; Machine learning; Microorganisms; Molecular Docking Simulation; Molecular dynamics; Molecular weight; Nucleocapsids; Pathogens; Peptides; Proteins; Reverse vaccinology; SARS-COV-2; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Simulation; Structural proteins; Three dimensional models; TLR4 protein; Toll-like receptors; Toxicity; Toxins; Vaccine; Vaccines; Vaccines, Subunit; Viruses; Waterborne diseases
• ISSN: 0010-4825; 1879-0534; 1879-0534
• DOI: 10.1016/j.compbiomed.2021.104390

In December 2019, a new virus called SARS-CoV-2 was reported in China and quickly spread to other parts of the world. The development of SARS-COV-2 vaccines has recently received much attention from numerous researchers. The present study aims to design an effective multi-epitope vaccine against SARS-COV-2 using the reverse vaccinology method. In this regard, structural proteins from SARS-COV-2, including the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins, were selected as target antigens for epitope prediction. A total of five helper T lymphocytes (HTL) and five cytotoxic T lymphocytes (CTL) epitopes were selected after screening the predicted epitopes for antigenicity, allergenicity, and toxicity. Subsequently, the selected HTL and CTL epitopes were fused via flexible linkers. Next, the cholera toxin B-subunit (CTxB) as an adjuvant was linked to the N-terminal of the chimeric structure. The proposed vaccine was analyzed for the properties of physicochemical, antigenicity, and allergenicity. The 3D model of the vaccine construct was predicted and docked with the Toll-like receptor 4 (TLR4). The molecular dynamics (MD) simulation was performed to evaluate the stable interactions between the vaccine construct and TLR4. The immune simulation was also conducted to explore the immune responses induced by the vaccine. Finally, in silico cloning of the vaccine construct into the pET-28 (+) vector was conducted. The results obtained from all bioinformatics analysis stages were satisfactory; however, in vitro and in vivo tests are essential to validate these results. •To design a multi-epitope vaccine against SARS-COV-2, we used a set of bioinformatics approaches.•The vaccine was designed using several epitopes, adjuvant, and appropriate linkers.•The prediction of secondary and 3D models of the vaccine was conducted.•The molecular docking, MD simulation, immune simulation was performed.•Our results indicated that the vaccine could be proposed as vaccine candidate against SARS-COV-2.