Exploring the Potency of <i>Nigella sativa</i> Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations
Coronavirus disease (COVID-19) is a pandemic burdening the global economy. It is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Black cumin (Nigella sativa) seed may contain antivirals for the disease since it was reported to inhibit the human immunodeficiency virus (HIV) an...
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| Format: | Article |
| Language: | English |
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Department of Chemistry, Universitas Gadjah Mada
2021-08-01
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| Series: | Indonesian Journal of Chemistry |
| Subjects: | |
| Online Access: | https://jurnal.ugm.ac.id/ijc/article/view/65951 |
| _version_ | 1818991145658613760 |
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| author | Ari Hardianto Muhammad Yusuf Ika Wiani Hidayat Safri Ishmayana Ukun Mochammad Syukur Soedjanaatmadja |
| author_facet | Ari Hardianto Muhammad Yusuf Ika Wiani Hidayat Safri Ishmayana Ukun Mochammad Syukur Soedjanaatmadja |
| author_sort | Ari Hardianto |
| collection | DOAJ |
| description | Coronavirus disease (COVID-19) is a pandemic burdening the global economy. It is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Black cumin (Nigella sativa) seed may contain antivirals for the disease since it was reported to inhibit the human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Main protease (Mpro) is a vital protein for viral replication and a promising target for COVID-19 drug development. Hence, in this study, we intended to uncover the potency of N. sativa seed as the natural source of inhibitors for SARS-CoV-2 Mpro. We collected secondary metabolites in N. sativa seed through a literature search and employed Lipinski’s rule of five as the initial filter. Subsequently, virtual screening campaigns using a molecular docking method were performed, with N3 inhibitor and leupeptin as reference ligands. The top hits were analyzed further using a molecular dynamics simulation approach. Molecular dynamics simulations showed that binding affinities of nigellamine A2 and A3 to Mpro are comparable to that of leupeptin, with median values of -43.9 and -36.2 kcal mol–1, respectively. Ultimately, this study provides scientific information regarding N. sativa seeds’ potency against COVID-19 and helps direct further wet experiments. |
| first_indexed | 2024-12-20T20:05:37Z |
| format | Article |
| id | doaj.art-ab0c707fd36d41abbf540901768fe062 |
| institution | Directory Open Access Journal |
| issn | 1411-9420 2460-1578 |
| language | English |
| last_indexed | 2024-12-20T20:05:37Z |
| publishDate | 2021-08-01 |
| publisher | Department of Chemistry, Universitas Gadjah Mada |
| record_format | Article |
| series | Indonesian Journal of Chemistry |
| spelling | doaj.art-ab0c707fd36d41abbf540901768fe0622022-12-21T19:27:56ZengDepartment of Chemistry, Universitas Gadjah MadaIndonesian Journal of Chemistry1411-94202460-15782021-08-012151252126210.22146/ijc.6595130481Exploring the Potency of <i>Nigella sativa</i> Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics SimulationsAri Hardianto0Muhammad Yusuf1Ika Wiani Hidayat2Safri Ishmayana3Ukun Mochammad Syukur Soedjanaatmadja4Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang km 21, Jatinangor 45363, West Java, IndonesiaDepartment of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang km 21, Jatinangor 45363, West Java, IndonesiaDepartment of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang km 21, Jatinangor 45363, West Java, IndonesiaDepartment of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang km 21, Jatinangor 45363, West Java, IndonesiaDepartment of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang km 21, Jatinangor 45363, West Java, IndonesiaCoronavirus disease (COVID-19) is a pandemic burdening the global economy. It is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Black cumin (Nigella sativa) seed may contain antivirals for the disease since it was reported to inhibit the human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Main protease (Mpro) is a vital protein for viral replication and a promising target for COVID-19 drug development. Hence, in this study, we intended to uncover the potency of N. sativa seed as the natural source of inhibitors for SARS-CoV-2 Mpro. We collected secondary metabolites in N. sativa seed through a literature search and employed Lipinski’s rule of five as the initial filter. Subsequently, virtual screening campaigns using a molecular docking method were performed, with N3 inhibitor and leupeptin as reference ligands. The top hits were analyzed further using a molecular dynamics simulation approach. Molecular dynamics simulations showed that binding affinities of nigellamine A2 and A3 to Mpro are comparable to that of leupeptin, with median values of -43.9 and -36.2 kcal mol–1, respectively. Ultimately, this study provides scientific information regarding N. sativa seeds’ potency against COVID-19 and helps direct further wet experiments.https://jurnal.ugm.ac.id/ijc/article/view/65951antiviralsmpronigella sativa seedssecondary metabolitesvirtual screening |
| spellingShingle | Ari Hardianto Muhammad Yusuf Ika Wiani Hidayat Safri Ishmayana Ukun Mochammad Syukur Soedjanaatmadja Exploring the Potency of <i>Nigella sativa</i> Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations Indonesian Journal of Chemistry antivirals mpro nigella sativa seeds secondary metabolites virtual screening |
| title | Exploring the Potency of <i>Nigella sativa</i> Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations |
| title_full | Exploring the Potency of <i>Nigella sativa</i> Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations |
| title_fullStr | Exploring the Potency of <i>Nigella sativa</i> Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations |
| title_full_unstemmed | Exploring the Potency of <i>Nigella sativa</i> Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations |
| title_short | Exploring the Potency of <i>Nigella sativa</i> Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations |
| title_sort | exploring the potency of i nigella sativa i seed in inhibiting sars cov 2 main protease using molecular docking and molecular dynamics simulations |
| topic | antivirals mpro nigella sativa seeds secondary metabolites virtual screening |
| url | https://jurnal.ugm.ac.id/ijc/article/view/65951 |
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