{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T05:58:36Z","timestamp":1784786316618,"version":"3.55.0"},"reference-count":54,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2022,3,24]],"date-time":"2022-03-24T00:00:00Z","timestamp":1648080000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Coronaviruses (CoVs) are positive-stranded RNA viruses with short clubs on their edges. CoVs are pathogenic viruses that infect several animals and plant organisms, as well as humans (lethal respiratory dysfunctions). A noval strain of CoV has been reported and named as SARS-CoV-2. Numerous COVID-19 cases were being reported all over the World. COVID-19 and has a high mortality rate. In the present study, immunoinformatics techniques were utilized to predict the antigenic epitopes against 3C like protein. B-cell epitopes and Cytotoxic T-lymphocyte (CTL) were designed computationally against SARS-CoV-2. Multiple Sequence Alignment (MSA) of seven complete strains (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2) was performed to elucidate the binding domain and interacting residues. MHC-I binding epitopes were evaluated by analyzing the binding affinity of the top-ranked peptides having HLA molecule. By utilizing the docked complexes of CTL epitopes with antigenic sites, the binding relationship and affinity of top-ranked predicted peptides with the MHC-I HLA protein were investigated. The molecular docking analyses were conducted on the ZINC database library and twelve compounds having least binding energy were scrutinized. In conclusion, twelve CTL epitopes (GTDLEGNFY, TVNVLAWLY, GSVGFNIDY, SEDMLNPNY, LSQTGIAV, VLDMCASLK, LTQDHVDIL, TTLNDFNLV, CTSEDMLNP, TTITVNVLA, YNGSPSGVY, and SMQNCVLKL) were identified against SARS-CoV-2.<\/jats:p>","DOI":"10.1371\/journal.pone.0264700","type":"journal-article","created":{"date-parts":[[2022,3,24]],"date-time":"2022-03-24T21:34:58Z","timestamp":1648157698000},"page":"e0264700","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":16,"title":["Epitope-based peptide vaccine design and elucidation of novel compounds against 3C like protein of SARS-CoV-2"],"prefix":"10.1371","volume":"17","author":[{"given":"Muhammad","family":"Sajid","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saigha","family":"Marriam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hamid","family":"Mukhtar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Summar","family":"Sohail","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Sajid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3901-5344","authenticated-orcid":true,"given":"Sheikh Arslan","family":"Sehgal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,3,24]]},"reference":[{"issue":"1","key":"pone.0264700.ref001","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1111\/j.1750-3639.2001.tb00384.x","article-title":"Viral induced demyelination","volume":"11","author":"SA Stohlman","year":"2001","journal-title":"Brain pathology"},{"issue":"12","key":"pone.0264700.ref002","doi-asserted-by":"crossref","first-page":"4523","DOI":"10.1128\/JCM.38.12.4523-4526.2000","article-title":"Characterization of a coronavirus isolated from a diarrheic foal","volume":"38","author":"JS Guy","year":"2000","journal-title":"Journal of Clinical Microbiology"},{"issue":"7827","key":"pone.0264700.ref003","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/s41586-020-2577-1","article-title":"Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing","volume":"586","author":"L Riva","year":"2020","journal-title":"Nature"},{"key":"pone.0264700.ref004","first-page":"2021","article-title":"Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening","author":"M Waqas","year":"2021","journal-title":"BioMed research international"},{"key":"pone.0264700.ref005","article-title":"Homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human","author":"W Ji","year":"2020","journal-title":"Journal of medical virology"},{"key":"pone.0264700.ref006","article-title":"et al. 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