Seq12, Seq12m, and Seq13m, peptide analogues of the spike glycoprotein shows antiviral properties against SARS-CoV-2: An in silico study through molecular docking, molecular dynamics simulation, and MM-PB/GBSA calculations

dc.authoridDutta, Kunal/0000-0002-0818-8787
dc.authoridKhalifa, Ibrahim/0000-0002-7648-2961
dc.authoridAL-OBAIDI, ANAS/0000-0002-6089-8188
dc.authoridShityakov, Sergey/0000-0002-6953-9771
dc.authoridMorozova, Olga/0000-0002-8058-8187
dc.authoridZhu, Wei/0000-0002-7957-7843
dc.authorwosidZhu, Wei/AFK-0930-2022
dc.authorwosidDutta, Kunal/C-5447-2018
dc.authorwosidKhalifa, Ibrahim/H-8916-2019
dc.authorwosidAL-OBAIDI, ANAS/AAU-4056-2020
dc.authorwosidShityakov, Sergey/H-3322-2019
dc.authorwosidMorozova, Olga/F-6041-2012
dc.contributor.authorDutta, Kunal
dc.contributor.authorElmezayen, Ammar D.
dc.contributor.authorAl-Obaidi, Anas
dc.contributor.authorZhu, Wei
dc.contributor.authorMorozova, Olga, V
dc.contributor.authorShityakov, Sergey
dc.contributor.authorKhalifa, Ibrahim
dc.date.accessioned2023-10-19T15:11:39Z
dc.date.available2023-10-19T15:11:39Z
dc.date.issued2021
dc.department-temp[Dutta, Kunal] Vidyasagar Univ, Dept Human Physiol, Midnapore 721102, W Bengal, India; [Elmezayen, Ammar D.; Al-Obaidi, Anas] Kadir Has Univ, Fac Engn & Nat Sci, Dept Bioinformat & Genet, TR-34083 Istanbul, Turkey; [Khalifa, Ibrahim] Benha Univ, Fac Agr, Food Technol Dept, Moshtohor 13736, Egypt; [Zhu, Wei] Huazhong Agr Univ, Coll Food Sci & Technol, Key Lab Environm Correlat Food Sci, Minist Educ, Wuhan 430070, Peoples R China; [Morozova, Olga, V] IN Blokhina Nizhny Novgorod Res Inst Epidemiol &, 71 Malaya Yamskaya Str, Nizhnii Novgorod 603950, Russia; [Shityakov, Sergey] ITMO Univ, Infochem Sci Ctr, Lab Chemoinformat, St Petersburg 191002, Russiaen_US
dc.description.abstractAt the very beginning of the new decade, the COVID-19 pandemic has badly hit modern human soci-eties. SARS-CoV-2, the causative agent of COVID-19 acquiring mutations and circulating as new variants. Herein, we have found three new antiviral peptides (AVPs) against the SARS-CoV-2. These AVPs are anal-ogous to the spike glycoprotein of the SARS-CoV-2. Antiviral peptides, i.e., Seq12, Seq12m, and Seq13m, can block the receptor-binding domain (RBD) of the SARS-CoV-2, which is necessary for communicating with the angiotensin-converting enzyme 2 (ACE2). Also, these AVPs sustain their antiviral properties, even after the insertion of 25 mutations in the RBD (Rosetta and FoldX based). Further, Seq12 and Seq12m showed negligible cytotoxicity. Besides, the binding free energies calculated using MM-PB/GBSA method are also in agreement with the molecular docking studies. The molecular interactions between AVPs and the viral membrane protein (M) also showed a favorable interaction suggesting it could inhibit the viral re-packaging process. In conclusion, this study suggests Seq12, Seq12m, and Seq13m could be helpful to fight against SARS-CoV-2. These AVPs could also aid virus diagnostic tools and nasal spray against SARS-CoV-2 in the future. (c) 2021 Elsevier B.V. All rights reserved.en_US
dc.description.sponsorshipCouncil of Scientific and Industrial Research (CSIR); New Delhi, India [09/599(0082)/2019-EMR-I]en_US
dc.description.sponsorshipCouncil of Scientific and Industrial Research (CSIR), Govt. of India, New Delhi, India is sincerely acknowledged by K.D. for Senior Research Fellowship (SRF), sanction letter no. 09/599(0082)/2019-EMR-I.en_US
dc.identifier.citation11
dc.identifier.doi10.1016/j.molstruc.2021.131113en_US
dc.identifier.issn0022-2860
dc.identifier.issn1872-8014
dc.identifier.pmid34305174en_US
dc.identifier.scopus2-s2.0-85111268327en_US
dc.identifier.scopusqualityQ2
dc.identifier.urihttps://doi.org/10.1016/j.molstruc.2021.131113
dc.identifier.urihttps://hdl.handle.net/20.500.12469/5149
dc.identifier.volume1246en_US
dc.identifier.wosWOS:000702899000012en_US
dc.identifier.wosqualityN/A
dc.khas20231019-WoSen_US
dc.language.isoenen_US
dc.publisherElsevieren_US
dc.relation.ispartofJournal of Molecular Structureen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectWeb ServerEn_Us
dc.subjectProteinEn_Us
dc.subjectPredictionEn_Us
dc.subjectAffinityEn_Us
dc.subjectSARS-CoV-2en_US
dc.subjectWeb Server
dc.subjectspike glycoproteinen_US
dc.subjectProtein
dc.subjectantiviral peptideen_US
dc.subjectPrediction
dc.subjectreceptor-binding domainen_US
dc.subjectAffinity
dc.subjectmutationen_US
dc.titleSeq12, Seq12m, and Seq13m, peptide analogues of the spike glycoprotein shows antiviral properties against SARS-CoV-2: An in silico study through molecular docking, molecular dynamics simulation, and MM-PB/GBSA calculationsen_US
dc.typeArticleen_US
dspace.entity.typePublication

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