Targeting 3CLpro and SARS-CoV-2 RdRp by <i>Amphimedon</i> sp. Metabolites: A Computational Study
Since December 2019, novel coronavirus disease 2019 (COVID-19) pandemic has caused tremendous economic loss and serious health problems worldwide. In this study, we investigated 14 natural compounds isolated from <i>Amphimedon</i> sp. via a molecular docking study, to examine their abili...
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MDPI AG
2021-06-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/26/12/3775 |
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| author | Nourhan Hisham Shady Alaa M. Hayallah Mamdouh F. A. Mohamed Mohammed M. Ghoneim Garri Chilingaryan Mohammad M. Al-Sanea Mostafa A. Fouad Mohamed Salah Kamel Usama Ramadan Abdelmohsen |
| author_facet | Nourhan Hisham Shady Alaa M. Hayallah Mamdouh F. A. Mohamed Mohammed M. Ghoneim Garri Chilingaryan Mohammad M. Al-Sanea Mostafa A. Fouad Mohamed Salah Kamel Usama Ramadan Abdelmohsen |
| author_sort | Nourhan Hisham Shady |
| collection | DOAJ |
| description | Since December 2019, novel coronavirus disease 2019 (COVID-19) pandemic has caused tremendous economic loss and serious health problems worldwide. In this study, we investigated 14 natural compounds isolated from <i>Amphimedon</i> sp. via a molecular docking study, to examine their ability to act as anti-COVID-19 agents. Moreover, the pharmacokinetic properties of the most promising compounds were studied. The docking study showed that virtually screened compounds were effective against the new coronavirus via dual inhibition of SARS-CoV-2 RdRp and the 3CL main protease. In particular, nakinadine B (<b>1</b>), 20-hepacosenoic acid (<b>11</b>) and amphimedoside C (<b>12</b>) were the most promising compounds, as they demonstrated good interactions with the pockets of both enzymes. Based on the analysis of the molecular docking results, compounds <b>1</b> and <b>12</b> were selected for molecular dynamics simulation studies. Our results showed <i>Amphimedon</i> sp. to be a rich source for anti-COVID-19 metabolites. |
| first_indexed | 2024-03-10T10:12:38Z |
| format | Article |
| id | doaj.art-5d225e9dd144456bae2f8b737f0ec072 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T10:12:38Z |
| publishDate | 2021-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-5d225e9dd144456bae2f8b737f0ec0722023-11-22T01:04:36ZengMDPI AGMolecules1420-30492021-06-012612377510.3390/molecules26123775Targeting 3CLpro and SARS-CoV-2 RdRp by <i>Amphimedon</i> sp. Metabolites: A Computational StudyNourhan Hisham Shady0Alaa M. Hayallah1Mamdouh F. A. Mohamed2Mohammed M. Ghoneim3Garri Chilingaryan4Mohammad M. Al-Sanea5Mostafa A. Fouad6Mohamed Salah Kamel7Usama Ramadan Abdelmohsen8Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia City 61111, EgyptDepartment of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, EgyptDepartment of Pharmaceutical Chemistry, Faculty of Pharmacy, Sohag University, Sohag 82524, EgyptDepartment of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi ArabiaInstitute of Molecular Biology of NAS RA, Yerevan 0014, ArmeniaDepartment of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Aljouf 72341, Saudi ArabiaDepartment of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, EgyptDepartment of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia City 61111, EgyptDepartment of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia City 61111, EgyptSince December 2019, novel coronavirus disease 2019 (COVID-19) pandemic has caused tremendous economic loss and serious health problems worldwide. In this study, we investigated 14 natural compounds isolated from <i>Amphimedon</i> sp. via a molecular docking study, to examine their ability to act as anti-COVID-19 agents. Moreover, the pharmacokinetic properties of the most promising compounds were studied. The docking study showed that virtually screened compounds were effective against the new coronavirus via dual inhibition of SARS-CoV-2 RdRp and the 3CL main protease. In particular, nakinadine B (<b>1</b>), 20-hepacosenoic acid (<b>11</b>) and amphimedoside C (<b>12</b>) were the most promising compounds, as they demonstrated good interactions with the pockets of both enzymes. Based on the analysis of the molecular docking results, compounds <b>1</b> and <b>12</b> were selected for molecular dynamics simulation studies. Our results showed <i>Amphimedon</i> sp. to be a rich source for anti-COVID-19 metabolites.https://www.mdpi.com/1420-3049/26/12/3775COVID-19coronavirusmolecular docking<i>Amphimedon</i> sp.sponge |
| spellingShingle | Nourhan Hisham Shady Alaa M. Hayallah Mamdouh F. A. Mohamed Mohammed M. Ghoneim Garri Chilingaryan Mohammad M. Al-Sanea Mostafa A. Fouad Mohamed Salah Kamel Usama Ramadan Abdelmohsen Targeting 3CLpro and SARS-CoV-2 RdRp by <i>Amphimedon</i> sp. Metabolites: A Computational Study Molecules COVID-19 coronavirus molecular docking <i>Amphimedon</i> sp. sponge |
| title | Targeting 3CLpro and SARS-CoV-2 RdRp by <i>Amphimedon</i> sp. Metabolites: A Computational Study |
| title_full | Targeting 3CLpro and SARS-CoV-2 RdRp by <i>Amphimedon</i> sp. Metabolites: A Computational Study |
| title_fullStr | Targeting 3CLpro and SARS-CoV-2 RdRp by <i>Amphimedon</i> sp. Metabolites: A Computational Study |
| title_full_unstemmed | Targeting 3CLpro and SARS-CoV-2 RdRp by <i>Amphimedon</i> sp. Metabolites: A Computational Study |
| title_short | Targeting 3CLpro and SARS-CoV-2 RdRp by <i>Amphimedon</i> sp. Metabolites: A Computational Study |
| title_sort | targeting 3clpro and sars cov 2 rdrp by i amphimedon i sp metabolites a computational study |
| topic | COVID-19 coronavirus molecular docking <i>Amphimedon</i> sp. sponge |
| url | https://www.mdpi.com/1420-3049/26/12/3775 |
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