The Impact of D614G Mutation of SARS-COV-2 on the Efficacy of Anti-viral Drugs: A Comparative Molecular Docking and Molecular Dynamics Study
D614G is one of the most reported mutations in the spike protein of SARS-COV-2 that has altered some crucial characteristics of coronaviruses, such as rate of infection and binding affinities. The binding affinity of different antiviral drugs was evaluated using rigid molecular docking. The reliabil...
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| Veröffentlicht in: | Current microbiology 2022-08, Vol.79 (8), p.241-241, Article 241 |
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| creator | Poustforoosh, Alireza Hashemipour, Hassan Tüzün, Burak Azadpour, Mahdiyeh Faramarz, Sanaz Pardakhty, Abbas Mehrabani, Mehrnaz Nematollahi, Mohammad Hadi |
| description | D614G is one of the most reported mutations in the spike protein of SARS-COV-2 that has altered some crucial characteristics of coronaviruses, such as rate of infection and binding affinities. The binding affinity of different antiviral drugs was evaluated using rigid molecular docking. The reliability of the docking results was evaluated with the induced-fit docking method, and a better understanding of the drug-protein interactions was performed using molecular dynamics simulation. The results show that the D614G variant could change the binding affinity of antiviral drugs and spike protein remarkably. Although Cytarabine showed an appropriate interaction with the wild spike protein, Ribavirin and PMEG diphosphate exhibited a significant binding affinity to the mutated spike protein. The parameters of the ADME/T analysis showed that these drugs are suitable for further in-vitro and in-vivo investigation. D614G alteration affected the binding affinity of the RBD and its receptor on the cell surface. |
| doi_str_mv | 10.1007/s00284-022-02921-6 |
| format | Article |
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D614G alteration affected the binding affinity of the RBD and its receptor on the cell surface.</description><identifier>ISSN: 0343-8651</identifier><identifier>EISSN: 1432-0991</identifier><identifier>DOI: 10.1007/s00284-022-02921-6</identifier><identifier>PMID: 35792936</identifier><language>eng</language><publisher>New York: Springer US</publisher><subject>Affinity ; Antiviral agents ; Binding ; Biomedical and Life Sciences ; Biotechnology ; Cell surface ; Coronaviruses ; COVID-19 ; Cytarabine ; Drug development ; Life Sciences ; Medical research ; Microbiology ; Molecular docking ; Molecular dynamics ; Mutation ; Protein interaction ; Proteins ; Reliability analysis ; Ribavirin ; Severe acute respiratory syndrome coronavirus 2 ; Spike protein ; Viral diseases ; Viruses</subject><ispartof>Current microbiology, 2022-08, Vol.79 (8), p.241-241, Article 241</ispartof><rights>The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2022</rights><rights>The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2022.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c447t-d1bb3e072c8bd58609e957c5680c05f8c3401861e23daf650407edc4d9c68b833</citedby><cites>FETCH-LOGICAL-c447t-d1bb3e072c8bd58609e957c5680c05f8c3401861e23daf650407edc4d9c68b833</cites><orcidid>0000-0002-9529-4077</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00284-022-02921-6$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00284-022-02921-6$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,780,784,885,27924,27925,41488,42557,51319</link.rule.ids></links><search><creatorcontrib>Poustforoosh, Alireza</creatorcontrib><creatorcontrib>Hashemipour, Hassan</creatorcontrib><creatorcontrib>Tüzün, Burak</creatorcontrib><creatorcontrib>Azadpour, Mahdiyeh</creatorcontrib><creatorcontrib>Faramarz, Sanaz</creatorcontrib><creatorcontrib>Pardakhty, Abbas</creatorcontrib><creatorcontrib>Mehrabani, Mehrnaz</creatorcontrib><creatorcontrib>Nematollahi, Mohammad Hadi</creatorcontrib><title>The Impact of D614G Mutation of SARS-COV-2 on the Efficacy of Anti-viral Drugs: A Comparative Molecular Docking and Molecular Dynamics Study</title><title>Current microbiology</title><addtitle>Curr Microbiol</addtitle><description>D614G is one of the most reported mutations in the spike protein of SARS-COV-2 that has altered some crucial characteristics of coronaviruses, such as rate of infection and binding affinities. The binding affinity of different antiviral drugs was evaluated using rigid molecular docking. The reliability of the docking results was evaluated with the induced-fit docking method, and a better understanding of the drug-protein interactions was performed using molecular dynamics simulation. The results show that the D614G variant could change the binding affinity of antiviral drugs and spike protein remarkably. Although Cytarabine showed an appropriate interaction with the wild spike protein, Ribavirin and PMEG diphosphate exhibited a significant binding affinity to the mutated spike protein. The parameters of the ADME/T analysis showed that these drugs are suitable for further in-vitro and in-vivo investigation. D614G alteration affected the binding affinity of the RBD and its receptor on the cell surface.</description><subject>Affinity</subject><subject>Antiviral agents</subject><subject>Binding</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Cell surface</subject><subject>Coronaviruses</subject><subject>COVID-19</subject><subject>Cytarabine</subject><subject>Drug development</subject><subject>Life Sciences</subject><subject>Medical research</subject><subject>Microbiology</subject><subject>Molecular docking</subject><subject>Molecular dynamics</subject><subject>Mutation</subject><subject>Protein interaction</subject><subject>Proteins</subject><subject>Reliability analysis</subject><subject>Ribavirin</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Spike protein</subject><subject>Viral 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| ispartof | Current microbiology, 2022-08, Vol.79 (8), p.241-241, Article 241 |
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| subjects | Affinity Antiviral agents Binding Biomedical and Life Sciences Biotechnology Cell surface Coronaviruses COVID-19 Cytarabine Drug development Life Sciences Medical research Microbiology Molecular docking Molecular dynamics Mutation Protein interaction Proteins Reliability analysis Ribavirin Severe acute respiratory syndrome coronavirus 2 Spike protein Viral diseases Viruses |
| title | The Impact of D614G Mutation of SARS-COV-2 on the Efficacy of Anti-viral Drugs: A Comparative Molecular Docking and Molecular Dynamics Study |
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