Molecular Docking and Dynamics Analysis of COVID-19 Main Protease Interactions with Alkaloids from Hyoscyamus Niger and Datura Stramonium

SARS-CoV-2 is the largest pandemic in the modern world and the etiological agent of COVID-19. Up to now, many efforts have been made to achieve the right drugs and vaccines against the new Coronavirus. Virtual screening methods are highly effective because they are cost-effective and efficient, making them widely utilized in the development of new herbal medicines. This research utilized molecular docking and dynamics studies to identify potential compounds derived from the plants Hyoscyamus niger and Datura stramonium. Alkaloids, a significant group of fundamental compounds found in herbal medicines, have garnered substantial attention due to their diverse pharmacological and medicinal properties. A comprehensive examination of 73 alkaloid molecules was undertaken due to their potential therapeutic properties, encompassing anti-inflammatory, antioxidant, anti-asthma, anti-viral, anti-microbial, and anti-cancer effects. This was based on the notion that these compounds could potentially be effective in treating the new coronavirus. Thus, out of seventy-three compounds five (Hyoscyamine, Moupinamide, Littorina, 7-Hydroxyhyoscyamine, 3-tigloyloxy-6-isobutyryloxy-7-hydroxytropane) with the lowest binding energies (-7, -6.8, -6.4, -6.2, and -6.1Kcal/mol, respectively) were selected for docking study. In addition, atomistic molecular dynamics simulations were conducted to investigate the dynamic behaviour of Mpro: ligand complexes. The alkaloid moupinamide showed promising activity in inhibiting the main protease (Mpro). The ability of the alkaloid moupinamide to obstruct the primary protease (Mpro) of the novel coronavirus has to be confirmed by additional investigation. Studies conducted in vivo, in vitro, and in clinical trials are necessary to support this assertion. Datura stramonium and Hyoscyamus niger, are medicinal plants that belong to the Solanaceae family. Alkaloids are part of the chemical defense in plants that contain low molecular weight nitrogen. Coronavirus disease (COVID-19) is an infectious disease caused by the SARS-CoV-2 virus. Molecular docking is used to predict how a protein will fit with small molecules. Molecular dynamics simulations show how each atom in a protein or other molecular system moves over time.