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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Autores principales:	Ari Hardianto, Muhammad Yusuf, Ika Wiani Hidayat, Safri Ishmayana, Ukun Mochammad Syukur Soedjanaatmadja
Formato:	article
Lenguaje:	EN
Publicado:	Department of Chemistry, Universitas Gadjah Mada 2021
Materias:	antivirals mpro nigella sativa seeds secondary metabolites virtual screening Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/ab0c707fd36d41abbf540901768fe062
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spelling	oai:doaj.org-article:ab0c707fd36d41abbf540901768fe0622021-12-02T18:02:38ZExploring the Potency of <i>Nigella sativa</i> Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations1411-94202460-157810.22146/ijc.65951https://doaj.org/article/ab0c707fd36d41abbf540901768fe0622021-08-01T00:00:00Zhttps://jurnal.ugm.ac.id/ijc/article/view/65951https://doaj.org/toc/1411-9420https://doaj.org/toc/2460-1578Coronavirus 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.Ari HardiantoMuhammad YusufIka Wiani HidayatSafri IshmayanaUkun Mochammad Syukur SoedjanaatmadjaDepartment of Chemistry, Universitas Gadjah Madaarticleantiviralsmpronigella sativa seedssecondary metabolitesvirtual screeningChemistryQD1-999ENIndonesian Journal of Chemistry, Vol 21, Iss 5, Pp 1252-1262 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	antivirals mpro nigella sativa seeds secondary metabolites virtual screening Chemistry QD1-999
spellingShingle	antivirals mpro nigella sativa seeds secondary metabolites virtual screening Chemistry QD1-999 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
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.
format	article
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
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_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_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_sort	exploring the potency of <i>nigella sativa</i> seed in inhibiting sars-cov-2 main protease using molecular docking and molecular dynamics simulations
publisher	Department of Chemistry, Universitas Gadjah Mada
publishDate	2021
url	https://doaj.org/article/ab0c707fd36d41abbf540901768fe062
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Exploring the Potency of <i>Nigella sativa</i> Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations

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