Molecular Docking, Dynamics Simulations, ADMET, and DFT Calculations: Combined In Silico Approach to Screen Natural Inhibitors of 3CL and PL Proteases of SARS-CoV-2
Considering natural compounds for the antiviral effect is another opportunity for exploring novel drug candidates for severe acute respiratory syndrome coronavirus 2. The selected natural compounds were interacted using a molecular docking approach. The 3D structures of the main protease and papain-...
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| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2024-01-01
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| Series: | Cellular Microbiology |
| Online Access: | http://dx.doi.org/10.1155/2024/6647757 |
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| author | Sugumar Mohanasundaram Porkodi Karthikeyan Venkatesan Sampath M. Anbazhagan Sundramurthy Venkatesa Prabhu Jamal M. Khaled Muthu Thiruvengadam |
| author_facet | Sugumar Mohanasundaram Porkodi Karthikeyan Venkatesan Sampath M. Anbazhagan Sundramurthy Venkatesa Prabhu Jamal M. Khaled Muthu Thiruvengadam |
| author_sort | Sugumar Mohanasundaram |
| collection | DOAJ |
| description | Considering natural compounds for the antiviral effect is another opportunity for exploring novel drug candidates for severe acute respiratory syndrome coronavirus 2. The selected natural compounds were interacted using a molecular docking approach. The 3D structures of the main protease and papain-like protease were used for the virtual screening to detect the potent inhibitor against SARS-CoV-2. The top-scored compounds were further analyzed for absorption, digestion, metabolism, excretion, and toxicity properties and density functional theory analysis. Our results indicated that glycyrrhizin exhibited better docking scores of -9.5 kcal/mol with main protease and -9.7 kcal/mol with papain-like protease. Next to glycyrrhizin, rutin showed a better docking score of -9.1 kcal/mol and -9.2 kcal/mol with 3-chymotrypsin-like and papain-like proteases. Violaxanthin and naringin occupied the subsequent position in the docking score table with 3CL and PL proteases, respectively. In addition, the crucial properties like drug likeliness and pharmacokinetics of the compounds were determined. There is no significant toxicity identified. |
| format | Article |
| id | doaj-art-443662de5a8d4898b87654488f078f39 |
| institution | Kabale University |
| issn | 1462-5822 |
| language | English |
| publishDate | 2024-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Cellular Microbiology |
| spelling | doaj-art-443662de5a8d4898b87654488f078f392025-02-03T05:57:03ZengWileyCellular Microbiology1462-58222024-01-01202410.1155/2024/6647757Molecular Docking, Dynamics Simulations, ADMET, and DFT Calculations: Combined In Silico Approach to Screen Natural Inhibitors of 3CL and PL Proteases of SARS-CoV-2Sugumar Mohanasundaram0Porkodi Karthikeyan1Venkatesan Sampath2M. Anbazhagan3Sundramurthy Venkatesa Prabhu4Jamal M. Khaled5Muthu Thiruvengadam6Department of Biochemistry and Crop PhysiologyDepartment of BiochemistryDepartment of BiochemistryDepartment of Environmental ScienceCentre for Food NanotechnologyDepartment of Botany and MicrobiologyDepartment of Crop ScienceConsidering natural compounds for the antiviral effect is another opportunity for exploring novel drug candidates for severe acute respiratory syndrome coronavirus 2. The selected natural compounds were interacted using a molecular docking approach. The 3D structures of the main protease and papain-like protease were used for the virtual screening to detect the potent inhibitor against SARS-CoV-2. The top-scored compounds were further analyzed for absorption, digestion, metabolism, excretion, and toxicity properties and density functional theory analysis. Our results indicated that glycyrrhizin exhibited better docking scores of -9.5 kcal/mol with main protease and -9.7 kcal/mol with papain-like protease. Next to glycyrrhizin, rutin showed a better docking score of -9.1 kcal/mol and -9.2 kcal/mol with 3-chymotrypsin-like and papain-like proteases. Violaxanthin and naringin occupied the subsequent position in the docking score table with 3CL and PL proteases, respectively. In addition, the crucial properties like drug likeliness and pharmacokinetics of the compounds were determined. There is no significant toxicity identified.http://dx.doi.org/10.1155/2024/6647757 |
| spellingShingle | Sugumar Mohanasundaram Porkodi Karthikeyan Venkatesan Sampath M. Anbazhagan Sundramurthy Venkatesa Prabhu Jamal M. Khaled Muthu Thiruvengadam Molecular Docking, Dynamics Simulations, ADMET, and DFT Calculations: Combined In Silico Approach to Screen Natural Inhibitors of 3CL and PL Proteases of SARS-CoV-2 Cellular Microbiology |
| title | Molecular Docking, Dynamics Simulations, ADMET, and DFT Calculations: Combined In Silico Approach to Screen Natural Inhibitors of 3CL and PL Proteases of SARS-CoV-2 |
| title_full | Molecular Docking, Dynamics Simulations, ADMET, and DFT Calculations: Combined In Silico Approach to Screen Natural Inhibitors of 3CL and PL Proteases of SARS-CoV-2 |
| title_fullStr | Molecular Docking, Dynamics Simulations, ADMET, and DFT Calculations: Combined In Silico Approach to Screen Natural Inhibitors of 3CL and PL Proteases of SARS-CoV-2 |
| title_full_unstemmed | Molecular Docking, Dynamics Simulations, ADMET, and DFT Calculations: Combined In Silico Approach to Screen Natural Inhibitors of 3CL and PL Proteases of SARS-CoV-2 |
| title_short | Molecular Docking, Dynamics Simulations, ADMET, and DFT Calculations: Combined In Silico Approach to Screen Natural Inhibitors of 3CL and PL Proteases of SARS-CoV-2 |
| title_sort | molecular docking dynamics simulations admet and dft calculations combined in silico approach to screen natural inhibitors of 3cl and pl proteases of sars cov 2 |
| url | http://dx.doi.org/10.1155/2024/6647757 |
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