Seq12, Seq12m, and Seq13m, Peptide Analogues of the Spike Glycoprotein Shows Antiviral Properties Against Sars-Cov an in Silico Study Through Molecular Docking, Molecular Dynamics Simulation, and Mm-pb/Gbsa Calculations

dc.authorid Dutta, Kunal/0000-0002-0818-8787
dc.authorid Khalifa, Ibrahim/0000-0002-7648-2961
dc.authorid AL-OBAIDI, ANAS/0000-0002-6089-8188
dc.authorid Shityakov, Sergey/0000-0002-6953-9771
dc.authorid Morozova, Olga/0000-0002-8058-8187
dc.authorid Zhu, Wei/0000-0002-7957-7843
dc.authorwosid Zhu, Wei/AFK-0930-2022
dc.authorwosid Dutta, Kunal/C-5447-2018
dc.authorwosid Khalifa, Ibrahim/H-8916-2019
dc.authorwosid AL-OBAIDI, ANAS/AAU-4056-2020
dc.authorwosid Shityakov, Sergey/H-3322-2019
dc.authorwosid Morozova, Olga/F-6041-2012
dc.contributor.author Dutta, Kunal
dc.contributor.author Elmezayen, Ammar D.
dc.contributor.author Al-Obaidi, Anas
dc.contributor.author Zhu, Wei
dc.contributor.author Morozova, Olga, V
dc.contributor.author Shityakov, Sergey
dc.contributor.author Khalifa, Ibrahim
dc.date.accessioned 2023-10-19T15:11:39Z
dc.date.available 2023-10-19T15:11:39Z
dc.date.issued 2021
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, Russia en_US
dc.description.abstract At 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.sponsorship Council of Scientific and Industrial Research (CSIR); New Delhi, India [09/599(0082)/2019-EMR-I] en_US
dc.description.sponsorship Council 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.citationcount 11
dc.identifier.doi 10.1016/j.molstruc.2021.131113 en_US
dc.identifier.issn 0022-2860
dc.identifier.issn 1872-8014
dc.identifier.pmid 34305174 en_US
dc.identifier.scopus 2-s2.0-85111268327 en_US
dc.identifier.scopusquality Q2
dc.identifier.uri https://doi.org/10.1016/j.molstruc.2021.131113
dc.identifier.uri https://hdl.handle.net/20.500.12469/5149
dc.identifier.volume 1246 en_US
dc.identifier.wos WOS:000702899000012 en_US
dc.khas 20231019-WoS en_US
dc.language.iso en en_US
dc.publisher Elsevier en_US
dc.relation.ispartof Journal of Molecular Structure en_US
dc.relation.publicationcategory Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı en_US
dc.rights info:eu-repo/semantics/openAccess en_US
dc.scopus.citedbyCount 12
dc.subject Web Server
dc.subject Protein
dc.subject Web Server En_Us
dc.subject Prediction
dc.subject Protein En_Us
dc.subject SARS-CoV-2 en_US
dc.subject spike glycoprotein en_US
dc.subject Prediction En_Us
dc.subject antiviral peptide en_US
dc.subject Affinity
dc.subject receptor-binding domain en_US
dc.subject Affinity En_Us
dc.subject mutation en_US
dc.title Seq12, Seq12m, and Seq13m, Peptide Analogues of the Spike Glycoprotein Shows Antiviral Properties Against Sars-Cov an in Silico Study Through Molecular Docking, Molecular Dynamics Simulation, and Mm-pb/Gbsa Calculations en_US
dc.type Article en_US
dc.wos.citedbyCount 13
dspace.entity.type Publication

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