Irvan Faizal, Darrian Chandra, Tarwadi, Sabar Pambudi, Astutiati Nurhasanah, Rizky Priambodo, Muhammad Yusuf
The emergence of new variants of SARS-CoV-2, including Alpha, Beta, Gamma, Delta, Omicron variants, and XBB sub-variants, contributes to the number of coronavirus cases worldwide. SARS-CoV-2 is a positive RNA virus with a genome of 29.9 kb that encodes four structural proteins: spike glycoprotein (S), envelope glycoprotein (E), membrane glycoprotein (M), and nucleocapsid glycoprotein (N). These proteins are vital for viral activity, with the S protein facilitating attachment and membrane fusion through the receptor-binding domain (RBD) located in the S1 subunit. The RBD recognizes and binds to the human angiotensin-converting enzyme 2 (ACE-2) protein. An immunoinformatic-aided design of a peptide-based multiepitope vaccine candidate targeting the RBD glycoprotein is constructed from the SARS-CoV-2 sequence data base from various regions of Indonesia (Jakarta, West Java, and Bali). The results show that the RBD region of with accession ID EPI_ISL_15982641 from West Java had the highest antigenicity of 0.5904. This isolate is non-toxic and non-allergenic and shows a total of 18 LBL epitopes, 72 CTL epitopes, and 98 HTL epitopes. The epitope that has the best overall binding affinity was GCHNKCAY for MHC-I and GGCVFSYVGCHNKCAYWV for MHC-II which show a binding affinity of -13.6 and -15.5 (kcal/mol), respectively. Therefore, this study aims to design an epitope vaccine candidate based on samples from Indonesia that has good characteristics and may have the potential to stimulate an immune response against SARS-CoV-2. © 2024 the author(s), published by De Gruyter, Berlin/Boston.
Research Centre for Vaccine and Drugs, National Research and Innovation Agency-Republic of Indonesia, Kawasan Puspiptek Serpong, Indonesia; Department of Biotechnology, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, BSD Campus, Tangerang, 15345, Indonesia; Department of Biology, Universitas Negeri Jakarta, Jl. Rawamangun Muka, Indonesia; Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, 40133, Indonesia; Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
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