Coarse-grained molecular dynamics-guided immunoinformatics to explain the binder and non-binder classification of Cytotoxic T-cell epitope for SARS-CoV-2 peptide-based vaccine discovery.

Autor: Yusuf M; Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia.; Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia., Destiarani W; Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia., Widayat W; Faculty of Pharmacy, Pharmaceutical Biology Science, Universitas Mulawarman, Samarinda, East Kalimantan, Indonesia., Yosua Y; Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia., Gumilar G; Research Center for Electronics, National Research and Innovation Agency Republic of Indonesia (BRIN), Bandung, West Java, Indonesia., Tanudireja AS; Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia., Rohmatulloh FG; Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia., Maulana FA; Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia., Baroroh U; Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia.; Department of Biotechnology, Indonesian School of Pharmacy, Bandung, West Java, Indonesia., Hardianto A; Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia., Maharani R; Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia., Nurainy N; Department of Research and Development, PT Bio Farma, Bandung, West Java, Indonesia., Wijayadikusumah AR; Department of Research and Development, PT Bio Farma, Bandung, West Java, Indonesia., Ristandi RB; West Java Provincial Reference Laboratory, Bandung, West Java, Indonesia., Atmosukarto IIC; Lipotek Pty Ltd. The John Curtin School of Medical Research, The Australian National University, Canberra, Australia., Subroto T; Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia.; Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2023 Oct 05; Vol. 18 (10), pp. e0292156. Date of Electronic Publication: 2023 Oct 05 (Print Publication: 2023).
DOI: 10.1371/journal.pone.0292156
Abstrakt: Epitope-based peptide vaccine can elicit T-cell immunity against SARS-CoV-2 to clear the infection. However, finding the best epitope from the whole antigen is challenging. A peptide screening using immunoinformatics usually starts from MHC-binding peptide, immunogenicity, cross-reactivity with the human proteome, to toxicity analysis. This pipeline classified the peptides into three categories, i.e., strong-, weak-, and non-binder, without incorporating the structural aspect. For this reason, the molecular detail that discriminates the binders from non-binder is interesting to be investigated. In this study, five CTL epitopes against HLA-A*02:01 were identified from the coarse-grained molecular dynamics-guided immunoinformatics screening. The strong binder showed distinctive activities from the non-binder in terms of structural and energetic properties. Furthermore, the second residue from the nonameric peptide was most important in the interaction with HLA-A*02:01. By understanding the nature of MHC-peptide interaction, we hoped to improve the chance of finding the best epitope for a peptide vaccine candidate.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2023 Yusuf et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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