Computational Study on the Inhibitory Effect of Natural Compounds against the SARS-CoV-2 Proteins
COVID-19 is more virulent and challenging to human life. In India, the Ministry of AYUSH recommended some strategies through Siddha, homeopathy, and other methods to effectively manage COVID-19 (Guidelines for AYUSH Clinical Studies in COVID-19, 2020). Kabasura Kudineer and homeopathy medicines are...
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| Format: | Article |
| Language: | English |
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Wiley
2022-01-01
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| Series: | Bioinorganic Chemistry and Applications |
| Online Access: | http://dx.doi.org/10.1155/2022/8635054 |
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| author | John Marshal Jayaraj Muralidharan Jothimani Chella Perumal Palanisamy Olli T. Pentikäinen Mehboobali Pannipara Abdullah G. Al-Sehemi Karthikeyan Muthusamy Krishnasamy Gopinath |
| author_facet | John Marshal Jayaraj Muralidharan Jothimani Chella Perumal Palanisamy Olli T. Pentikäinen Mehboobali Pannipara Abdullah G. Al-Sehemi Karthikeyan Muthusamy Krishnasamy Gopinath |
| author_sort | John Marshal Jayaraj |
| collection | DOAJ |
| description | COVID-19 is more virulent and challenging to human life. In India, the Ministry of AYUSH recommended some strategies through Siddha, homeopathy, and other methods to effectively manage COVID-19 (Guidelines for AYUSH Clinical Studies in COVID-19, 2020). Kabasura Kudineer and homeopathy medicines are in use for the prevention and treatment of COVID-19 infection; however, the mechanism of action is less explored. This study aims to understand the antagonist activity of natural compounds found in Kabasura Kudineer and homeopathy medicines against the SARS-CoV-2 using computational methods. Potential compounds were screened against NSP-12, NSP-13, NSP-14, NSP-15, main protease, and spike proteins. Structure-based virtual screening results shows that, out of 14,682 Kabasura Kudineer compounds, the 250395, 129677029, 44259583, 44259584, and 88583189 compounds and, out of 3,112 homeopathy compounds, the 3802778, 320361, 5315832, 14590080, and 74029795 compounds have good scoring function against the SARS-CoV-2 structural and nonstructural proteins. As a result of docking, homeopathy compounds have a docking score ranging from −5.636 to 13.631 kcal/mol, while Kabasura Kudineer compounds have a docking score varying from −8.290 to −13.759 kcal/mol. It has been found that the selected compounds bind well to the active site of SARS-CoV-2 proteins and form hydrogen bonds. The molecular dynamics simulation study shows that the selected compounds have maintained stable conformation in the simulation period and interact with the target. This study supports the antagonist activity of natural compounds from Kabasura Kudineer and homeopathy against SARS-CoV-2’s structural and nonstructural proteins. |
| format | Article |
| id | doaj-art-ca353293518c4e87bceffef27e67304d |
| institution | OA Journals |
| issn | 1687-479X |
| language | English |
| publishDate | 2022-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Bioinorganic Chemistry and Applications |
| spelling | doaj-art-ca353293518c4e87bceffef27e67304d2025-08-20T02:19:37ZengWileyBioinorganic Chemistry and Applications1687-479X2022-01-01202210.1155/2022/8635054Computational Study on the Inhibitory Effect of Natural Compounds against the SARS-CoV-2 ProteinsJohn Marshal Jayaraj0Muralidharan Jothimani1Chella Perumal Palanisamy2Olli T. Pentikäinen3Mehboobali Pannipara4Abdullah G. Al-Sehemi5Karthikeyan Muthusamy6Krishnasamy Gopinath7Pharmacogenomics and CADD LabPharmacogenomics and CADD LabState Key Laboratory of Biobased Materials and Green Paper MakingFaculty of MedicineResearch Centre for Advanced Materials ScienceDepartment of ChemistryPharmacogenomics and CADD LabFaculty of MedicineCOVID-19 is more virulent and challenging to human life. In India, the Ministry of AYUSH recommended some strategies through Siddha, homeopathy, and other methods to effectively manage COVID-19 (Guidelines for AYUSH Clinical Studies in COVID-19, 2020). Kabasura Kudineer and homeopathy medicines are in use for the prevention and treatment of COVID-19 infection; however, the mechanism of action is less explored. This study aims to understand the antagonist activity of natural compounds found in Kabasura Kudineer and homeopathy medicines against the SARS-CoV-2 using computational methods. Potential compounds were screened against NSP-12, NSP-13, NSP-14, NSP-15, main protease, and spike proteins. Structure-based virtual screening results shows that, out of 14,682 Kabasura Kudineer compounds, the 250395, 129677029, 44259583, 44259584, and 88583189 compounds and, out of 3,112 homeopathy compounds, the 3802778, 320361, 5315832, 14590080, and 74029795 compounds have good scoring function against the SARS-CoV-2 structural and nonstructural proteins. As a result of docking, homeopathy compounds have a docking score ranging from −5.636 to 13.631 kcal/mol, while Kabasura Kudineer compounds have a docking score varying from −8.290 to −13.759 kcal/mol. It has been found that the selected compounds bind well to the active site of SARS-CoV-2 proteins and form hydrogen bonds. The molecular dynamics simulation study shows that the selected compounds have maintained stable conformation in the simulation period and interact with the target. This study supports the antagonist activity of natural compounds from Kabasura Kudineer and homeopathy against SARS-CoV-2’s structural and nonstructural proteins.http://dx.doi.org/10.1155/2022/8635054 |
| spellingShingle | John Marshal Jayaraj Muralidharan Jothimani Chella Perumal Palanisamy Olli T. Pentikäinen Mehboobali Pannipara Abdullah G. Al-Sehemi Karthikeyan Muthusamy Krishnasamy Gopinath Computational Study on the Inhibitory Effect of Natural Compounds against the SARS-CoV-2 Proteins Bioinorganic Chemistry and Applications |
| title | Computational Study on the Inhibitory Effect of Natural Compounds against the SARS-CoV-2 Proteins |
| title_full | Computational Study on the Inhibitory Effect of Natural Compounds against the SARS-CoV-2 Proteins |
| title_fullStr | Computational Study on the Inhibitory Effect of Natural Compounds against the SARS-CoV-2 Proteins |
| title_full_unstemmed | Computational Study on the Inhibitory Effect of Natural Compounds against the SARS-CoV-2 Proteins |
| title_short | Computational Study on the Inhibitory Effect of Natural Compounds against the SARS-CoV-2 Proteins |
| title_sort | computational study on the inhibitory effect of natural compounds against the sars cov 2 proteins |
| url | http://dx.doi.org/10.1155/2022/8635054 |
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