Interactions mechanism of commonly used drugs for the treatment of Covid-19
In this study conformation analysis of seven drugs commonly used in the treatment of COVID-19 was performed. The most stable conformers of the drug molecules were used as initial data for docking analysis. Using the Cavityplus program, the probable most active binding sites of both apo and holo form...
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| Veröffentlicht in: | Bulletin of the Chemical Society of Ethiopia 2020-09, Vol.34 (3), p.613-623 |
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| creator | Celik, Sefa Demirag, A. Demet Ozel, Aysen E Akyuz, Sevim |
| description | In this study conformation analysis of seven drugs commonly used in the treatment of COVID-19 was performed. The most stable conformers of the drug molecules were used as initial data for docking analysis. Using the Cavityplus program, the probable most active binding sites of both apo and holo forms of COVID-19 main protease enzyme (Mpro) and spike glycoprotein of SARSCoV-2 receptors were determined. The interaction mechanisms of the 7 FDA approved drugs (arbidol, colchicine, dexamethasone, favipiravir, galidesivir, hydroxychloroquine, remdesivir) were examined using the AutoDock Vina program. The six of the seven drugs were found to be more stable in binding to apo form of COVID-19 Mpro and spike glycoprotein. Moreover, a set of molecular mechanics (MM) Poisson-Boltzmann (PB) surface area (SA) calculations on the investigated drugs-protein systems were performed and the estimated binding free energy of remdesivir and the apo form of Mpro system was found to be the best. The interaction results of FDA drugs with the apo form of COVID-19 Mpro and spike glycoprotein can play an important role for the treatment of COVID-19.
KEY WORDS: COVID-19, Drugs, Molecular modelling, Conformational analysis, Molecular docking
Bull. Chem. Soc. Ethiop. 2020, 34(3), 613-623.
DOI: https://dx.doi.org/10.4314/bcse.v34i3.16 |
| doi_str_mv | 10.4314/bcse.v34i3.16 |
| format | Article |
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KEY WORDS: COVID-19, Drugs, Molecular modelling, Conformational analysis, Molecular docking
Bull. Chem. Soc. Ethiop. 2020, 34(3), 613-623.
DOI: https://dx.doi.org/10.4314/bcse.v34i3.16</description><identifier>ISSN: 1011-3924</identifier><identifier>EISSN: 1726-801X</identifier><identifier>DOI: 10.4314/bcse.v34i3.16</identifier><language>eng</language><publisher>Chemical Society of Ethiopia</publisher><subject>Amino acids ; Analysis ; Colchicine ; Conformational analysis ; Dexamethasone ; Drug approval ; Drug interactions ; Drugs ; Hydroxychloroquine ; Proteases</subject><ispartof>Bulletin of the Chemical Society of Ethiopia, 2020-09, Vol.34 (3), p.613-623</ispartof><rights>COPYRIGHT 2020 Chemical Society of Ethiopia</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c343t-9b57fecddcbe9381bc8c9c3a611bdf3012667a9643077d2591f7a3bdbdcf887b3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,778,782,27913,27914</link.rule.ids></links><search><creatorcontrib>Celik, Sefa</creatorcontrib><creatorcontrib>Demirag, A. Demet</creatorcontrib><creatorcontrib>Ozel, Aysen E</creatorcontrib><creatorcontrib>Akyuz, Sevim</creatorcontrib><title>Interactions mechanism of commonly used drugs for the treatment of Covid-19</title><title>Bulletin of the Chemical Society of Ethiopia</title><description>In this study conformation analysis of seven drugs commonly used in the treatment of COVID-19 was performed. The most stable conformers of the drug molecules were used as initial data for docking analysis. Using the Cavityplus program, the probable most active binding sites of both apo and holo forms of COVID-19 main protease enzyme (Mpro) and spike glycoprotein of SARSCoV-2 receptors were determined. The interaction mechanisms of the 7 FDA approved drugs (arbidol, colchicine, dexamethasone, favipiravir, galidesivir, hydroxychloroquine, remdesivir) were examined using the AutoDock Vina program. The six of the seven drugs were found to be more stable in binding to apo form of COVID-19 Mpro and spike glycoprotein. Moreover, a set of molecular mechanics (MM) Poisson-Boltzmann (PB) surface area (SA) calculations on the investigated drugs-protein systems were performed and the estimated binding free energy of remdesivir and the apo form of Mpro system was found to be the best. The interaction results of FDA drugs with the apo form of COVID-19 Mpro and spike glycoprotein can play an important role for the treatment of COVID-19.
KEY WORDS: COVID-19, Drugs, Molecular modelling, Conformational analysis, Molecular docking
Bull. Chem. Soc. Ethiop. 2020, 34(3), 613-623.
DOI: https://dx.doi.org/10.4314/bcse.v34i3.16</description><subject>Amino acids</subject><subject>Analysis</subject><subject>Colchicine</subject><subject>Conformational analysis</subject><subject>Dexamethasone</subject><subject>Drug approval</subject><subject>Drug interactions</subject><subject>Drugs</subject><subject>Hydroxychloroquine</subject><subject>Proteases</subject><issn>1011-3924</issn><issn>1726-801X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNptkE1LAzEQhoMoWKtH7wHPWzOb3WRzLMWPYsGLgreQzzbSbGSTFvrv3VovgsxhhuF5B-ZB6BbIrKHQ3GuT3WxPm0BnwM7QBHjNqo7Ax_k4E4CKirq5RFc5fxJSE8rbCXpZ9sUNypSQ-oyjMxvVhxxx8tikGFO_PeBddhbbYbfO2KcBl43DZXCqRNeXI7hI-2ArENfowqttdje_fYreHx_eFs_V6vVpuZivKkMbWiqhW-6dsdZoJ2gH2nRGGKoYgLaeEqgZ40qwhhLObd0K8FxRbbU1vuu4plN0d7q7VlsnQ-9TGT-IIRs5Zy00jNFajNTsH2os62IwqXc-jPs_geoUMEPKeXBefg0hquEggcijYHkULH8ES2D0G9DFbyI</recordid><startdate>20200901</startdate><enddate>20200901</enddate><creator>Celik, Sefa</creator><creator>Demirag, A. Demet</creator><creator>Ozel, Aysen E</creator><creator>Akyuz, Sevim</creator><general>Chemical Society of Ethiopia</general><scope>AAYXX</scope><scope>CITATION</scope></search><sort><creationdate>20200901</creationdate><title>Interactions mechanism of commonly used drugs for the treatment of Covid-19</title><author>Celik, Sefa ; Demirag, A. Demet ; Ozel, Aysen E ; Akyuz, Sevim</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c343t-9b57fecddcbe9381bc8c9c3a611bdf3012667a9643077d2591f7a3bdbdcf887b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Amino acids</topic><topic>Analysis</topic><topic>Colchicine</topic><topic>Conformational analysis</topic><topic>Dexamethasone</topic><topic>Drug approval</topic><topic>Drug interactions</topic><topic>Drugs</topic><topic>Hydroxychloroquine</topic><topic>Proteases</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Celik, Sefa</creatorcontrib><creatorcontrib>Demirag, A. Demet</creatorcontrib><creatorcontrib>Ozel, Aysen E</creatorcontrib><creatorcontrib>Akyuz, Sevim</creatorcontrib><collection>CrossRef</collection><jtitle>Bulletin of the Chemical Society of Ethiopia</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Celik, Sefa</au><au>Demirag, A. Demet</au><au>Ozel, Aysen E</au><au>Akyuz, Sevim</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Interactions mechanism of commonly used drugs for the treatment of Covid-19</atitle><jtitle>Bulletin of the Chemical Society of Ethiopia</jtitle><date>2020-09-01</date><risdate>2020</risdate><volume>34</volume><issue>3</issue><spage>613</spage><epage>623</epage><pages>613-623</pages><issn>1011-3924</issn><eissn>1726-801X</eissn><abstract>In this study conformation analysis of seven drugs commonly used in the treatment of COVID-19 was performed. The most stable conformers of the drug molecules were used as initial data for docking analysis. Using the Cavityplus program, the probable most active binding sites of both apo and holo forms of COVID-19 main protease enzyme (Mpro) and spike glycoprotein of SARSCoV-2 receptors were determined. The interaction mechanisms of the 7 FDA approved drugs (arbidol, colchicine, dexamethasone, favipiravir, galidesivir, hydroxychloroquine, remdesivir) were examined using the AutoDock Vina program. The six of the seven drugs were found to be more stable in binding to apo form of COVID-19 Mpro and spike glycoprotein. Moreover, a set of molecular mechanics (MM) Poisson-Boltzmann (PB) surface area (SA) calculations on the investigated drugs-protein systems were performed and the estimated binding free energy of remdesivir and the apo form of Mpro system was found to be the best. The interaction results of FDA drugs with the apo form of COVID-19 Mpro and spike glycoprotein can play an important role for the treatment of COVID-19.
KEY WORDS: COVID-19, Drugs, Molecular modelling, Conformational analysis, Molecular docking
Bull. Chem. Soc. Ethiop. 2020, 34(3), 613-623.
DOI: https://dx.doi.org/10.4314/bcse.v34i3.16</abstract><pub>Chemical Society of Ethiopia</pub><doi>10.4314/bcse.v34i3.16</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Bulletin of the Chemical Society of Ethiopia, 2020-09, Vol.34 (3), p.613-623 |
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| language | eng |
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| source | Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; African Journals Online (Open Access); Free Full-Text Journals in Chemistry |
| subjects | Amino acids Analysis Colchicine Conformational analysis Dexamethasone Drug approval Drug interactions Drugs Hydroxychloroquine Proteases |
| title | Interactions mechanism of commonly used drugs for the treatment of Covid-19 |
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