Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein

• Published in: Vaccines (Basel) Vol. 11; no. 2; p. 399
• Main Authors: Umitaibatin, Ramadhita, Harisna, Azza Hanif, Jauhar, Muhammad Miftah, Syaifie, Putri Hawa, Arda, Adzani Gaisani, Nugroho, Dwi Wahyu, Ramadhan, Donny, Mardliyati, Etik, Shalannanda, Wervyan, Anshori, Isa
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01.02.2023; MDPI
• Subjects: Amino acids; Antibodies; Antigenic determinants; antigenic epitope; Antigens; Binding sites; CD4 antigen; CD8 antigen; Coronaviruses; COVID-19; COVID-19 vaccines; Cytotoxicity; Design; Dynamic stability; epitope prediction; Epitopes; Glycoproteins; Health aspects; LR-4; Lymphocytes; Lymphocytes B; Lymphocytes T; Molecular docking; Molecular dynamics; Mutation; Phylogenetics; Population; Proteins; Severe acute respiratory syndrome coronavirus 2; Side effects; Simulation; Spike glycoprotein; Spike protein; TLR-3; Vaccines; Vectors (Biology); Viral diseases; Viral infections; γ-Interferon; Indonesia; epitope prediction; antigenic epitope; TLR-3; spike glycoprotein; LR-4
• ISSN: 2076-393X; 2076-393X
• DOI: 10.3390/vaccines11020399

The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.