Elucidation of novel compounds and epitope-based peptide vaccine design against C30 endopeptidase regions of SARS-CoV-2 using immunoinformatics approaches.

Autor:	Marriam S; Department of Microbiology and Molecular Genetics, Faculty of Life Sciences, University of Okara, Okara, Pakistan., Afghan MS; Department of Ear, Nose, and Throat (ENT), District Headquarter (DHQ) Teaching Hospital Faisalabad, Faisalabad, Punjab, Pakistan., Nadeem M; Department of Ear, Nose, and Throat (ENT), District Headquarter (DHQ) Teaching Hospital Faisalabad, Faisalabad, Punjab, Pakistan., Sajid M; Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, Pakistan., Ahsan M; Institute of Environmental and Agricultural Sciences, University of Okara, Okara, Pakistan., Basit A; Department of Microbiology, University of Jhang, Jhang, Pakistan., Wajid M; Department of Zoology, Faculty of Life Sciences, University of Okara, Okara, Pakistan., Sabri S; Department of Microbiology and Molecular Genetics, Faculty of Life Sciences, University of Okara, Okara, Pakistan., Sajid M; Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, Pakistan., Zafar I; Department of Bioinformatics and Computational Biology, Virtual University, Punjab, Pakistan., Rashid S; Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia., Sehgal SA; Department of Bioinformatics, Faculty of Life Sciences, University of Okara, Okara, Pakistan.; Department of Bioinformatics, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan., Alkhalifah DHM; Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia., Hozzein WN; Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt., Chen KT; Department of Occupational Medicine, Tainan Municipal Hospital (managed by ShowChwan Medical Care Corporation), Tainan, Taiwan.; Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan., Sharma R; Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India.
Jazyk:	angličtina
Zdroj:	Frontiers in cellular and infection microbiology [Front Cell Infect Microbiol] 2023 May 24; Vol. 13, pp. 1134802. Date of Electronic Publication: 2023 May 24 (Print Publication: 2023).
DOI:	10.3389/fcimb.2023.1134802
Abstrakt:	There has been progressive improvement in immunoinformatics approaches for epitope-based peptide design. Computational-based immune-informatics approaches were applied to identify the epitopes of SARS-CoV-2 to develop vaccines. The accessibility of the SARS-CoV-2 protein surface was analyzed, and hexa-peptide sequences (KTPKYK) were observed having a maximum score of 8.254, located between amino acids 97 and 102, whereas the FSVLAC at amino acids 112 to 117 showed the lowest score of 0.114. The surface flexibility of the target protein ranged from 0.864 to 1.099 having amino acid ranges of 159 to 165 and 118 to 124, respectively, harboring the FCYMHHM and YNGSPSG hepta-peptide sequences. The surface flexibility was predicted, and a 0.864 score was observed from amino acids 159 to 165 with the hepta-peptide (FCYMHHM) sequence. Moreover, the highest score of 1.099 was observed between amino acids 118 and 124 against YNGSPSG. B-cell epitopes and cytotoxic T-lymphocyte (CTL) epitopes were also identified against SARS-CoV-2. In molecular docking analyses, -0.54 to -26.21 kcal/mol global energy was observed against the selected CTL epitopes, exhibiting binding solid energies of -3.33 to -26.36 kcal/mol. Based on optimization, eight epitopes (SEDMLNPNY, GSVGFNIDY, LLEDEFTPF, DYDCVSFCY, GTDLEGNFY, QTFSVLACY, TVNVLAWLY, and TANPKTPKY) showed reliable findings. The study calculated the associated HLA alleles with MHC-I and MHC-II and found that MHC-I epitopes had higher population coverage (0.9019% and 0.5639%) than MHC-II epitopes, which ranged from 58.49% to 34.71% in Italy and China, respectively. The CTL epitopes were docked with antigenic sites and analyzed with MHC-I HLA protein. In addition, virtual screening was conducted using the ZINC database library, which contained 3,447 compounds. The 10 top-ranked scrutinized molecules (ZINC222731806, ZINC077293241, ZINC014880001, ZINC003830427, ZINC030731133, ZINC003932831, ZINC003816514, ZINC004245650, ZINC000057255, and ZINC011592639) exhibited the least binding energy (-8.8 to -7.5 kcal/mol). The molecular dynamics (MD) and immune simulation data suggest that these epitopes could be used to design an effective SARS-CoV-2 vaccine in the form of a peptide-based vaccine. Our identified CTL epitopes have the potential to inhibit SARS-CoV-2 replication. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2023 Marriam, Afghan, Nadeem, Sajid, Ahsan, Basit, Wajid, Sabri, Sajid, Zafar, Rashid, Sehgal, Alkhalifah, Hozzein, Chen and Sharma.)
Databáze:	MEDLINE
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