Discovery of Potential Inhibitors of SARS-CoV-2 (COVID-19) Main Protease (Mpro) from Nigella Sativa (Black Seed) by Molecular Docking Study (Preprint)

Abstract

BACKGROUND Coronavirus disease is an infectious disease caused by a coronavirus. A new human coronavirus (HCoV), which has been labeled SARS-CoV-2, began spreading in December 2019 in Wuhan City, China triggering pneumonia termed as COVID-19. As of now till 3 April 2020; there were 972,640 confirmed cases, 50,325 confirmed deaths and 207 countries, areas or territories with cases around the world. The World Health Organization (WHO) declared this disease a pandemic. At present, there are no specific vaccines or treatments for COVID-19. However, there are many ongoing clinical trials evaluating potential treatments. From the literature of N. sativa, we came to know about its diverse biological activities. It has been observed that it contains a variety of chemical compounds that enables us to perform virtual screening against COVID-19 Mpro with the aid of molecular docking. So here in this present work, we have made an attempt to identify natural potential inhibitors of SARS-COVID-19 Mpro. OBJECTIVE A new human coronavirus (HCoV), triggering pneumonia termed as COVID-19. There is an alarming situation now as this new virus is spreading around the world. At present, there are no specific treatments for COVID-19. Nigella sativa is known as Prophetic Medicine as its use has been mentioned in Prophetic Hadit, as a natural remedy for all the diseases except death. The aim of this research is to provide a potential inhibitor of COVID-19 Mpro. METHODS The molecular docking tool was used to optimize the binding affinities of chemical constituents of N. sativa with SARS-COVID-19 Mpro. RESULTS Many constituents from N. Sativa have shown better binding affinity than reported drugs with SARS-COVID-19 Mpro i.e. alpha-hederin, Stigmasterol glucoside, Nigellidine-4-O-sulfite, Nigellidine, Sterol-3-β-D-glucoside, Dithymoquinone, beta-sitosterol have binding affinities (kcal/mol) -9, -8.1, -8, -7.7, -7.7, -7.4, -7.4, -6.9 and no. of hydrogen bonds formed are 06, 04, 03, 03, 03, 00 and 01 respectively. CONCLUSIONS There is rationale and pre-clinical evidence of effectiveness of N. Sativa that it may be helpful for the treatment of SARS-COVID-19 and can serve as potential natural candidate. However, more studies should be conducted to collect high quality data and scientific evidences of N. Sativa to use it against COVID-19 clinically.