Identification of SARS-CoV-2 RNA-dependent RNA polymerase inhibitors from the major phytochemicals of Nigella sativa: An in silico approach

Abstract

The coronavirus disease 2019 (COVID-19), which emerged in December 2019, continues to be a serious health concern worldwide. There is an urgent need to develop effective drugs and vaccines to control the spread of this disease. In the current study, the main phytochemical compounds of Nigella sativa were screened for their binding affinity for the active site of the RNA-dependent RNA polymerase (RdRp) enzyme of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The binding affinity was investigated using molecular docking methods, and the interaction of phytochemicals with the RdRp active site was analyzed and visualized using suitable software. Out of the nine phytochemicals of N. sativa screened in this study, a significant docking score was observed for four compounds, namely α-hederin, dithymoquinone, nigellicine, and nigellidine. Based on the findings of our study, we report that α-hederin, which was found to possess the lowest binding energy (–8.6 kcal/mol) and hence the best binding affinity, is the best inhibitor of RdRp of SARS-CoV-2, among all the compounds screened here. Our results prove that the top four potential phytochemical molecules of N. sativa , especially α-hederin, could be considered for ongoing drug development strategies against SARS-CoV-2. However, further in vitro and in vivo testing are required to confirm the findings of this study.

The importance of molecular structure and functionalization of oxo-graphene sheets for gene silencing

“…The initial siRNA structure (sequence: UGC-GCU-ACG-AUC-GACGAU-G) was obtained using the nucleic acid builder (NAB) included in AMBER18 [24], with RNA.OL3 forcefield [25,26]. PEI starting structure was built using Discovery Studio Visualizer [27], with protonation state assigned based on recent NMR studies [28] for neutral pH and assigned uniformly.…”

The Effect of Black Cumin (Nigella Sativa) on Breastfeeding Mothers

“…Black cumin increases the amount of breast milk due to the combination of lipid elements and the structure of hormones (Mehlsen et al, 2022). Furthermore, the content of polyphenols in black cumin, which is also discovered in katuk leaves, plays a significant role in increasing prolactin levels (Mir et al, 2022). Black cumin administration was examined in mice, with increases in milk production by 31.1% and 37.6% compared to the control group that was not provided with black cumin (Walsh et al, 2019).…”

Investigation of the Anti-TB Potential of Selected Phytochemicals of Nigella Sativa using Molecular Docking Approach

“…In addition, these enzymes represent some emerging drug-targets against which no confirmed drug is presently available [15][16][17]. Although several in silico studies have reported the possible inhibitory potential of various N. sativa phytochemicals against SARS-Cov-2 [26][27][28][29][30][31][32], the anti-mycobacterial potential of N. sativa constituents has been reported in a few studies only [12][13][14]. In this preliminary study, the nine prominent phytochemical compounds of N. sativa were selected and their inhibitory potential against the three selected mycobacterial enzymes was investigated through in silico molecular docking.…”