Molecular Docking and Dynamics Simulation Studies of Ginsenosides with SARS-CoV-2 Host and Viral Entry Protein Targets

Abstract

Despite the contemporary advancements in the field of science and medicine, combating the coronavirus disease 2019 (COVID-19) is extremely challenging in many aspects as the virus keeps spreading and mutating rapidly. As there is no effective and conclusive drug therapy to date, it is crucial to explore plant-based natural compounds for their potential to inhibit SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). Recent research highly focuses on screening various phytochemicals to elucidate their anti-viral efficacy. However, very few studies were published investigating the anti-viral efficacy of ginsenosides. Hence, the main aim of this study was to investigate the inhibitory potential of the available 122 ginsenosides from Panax ginseng against SARS-CoV-2-related proteins using a molecular docking and molecular dynamics approach. The major bioactive compounds “ginsenosides” of P. ginseng were docked to six vital SAR-CoV-2 host entry-related proteins such as ACE2, Spike RBD, ACE2 and Spike RBD complex, Spike (pre-fused), Spike (post-fused), and HR domain, with lowest binding energies of −9.5 kcal/mol, −8.1 kcal/mol, −10.4 kcal/mol, −10.4 kcal/mol, −9.3 kcal/mol, and −8.2 kcal/mol, respectively. Almost all the ginsenosides have shown low binding energies and were found to be favourable for efficient docking and resultant inhibition of the viral proteins. However, ACE2 has shown the highest interaction capability. Hence, the top five ginsenosides with the highest binding energy with ACE2 were subjected to MD, post MD analysis, and MM/PBSA calculations. MD simulation results have shown higher stability, flexibility, and mobility of the selected compounds. Additionally, MM-PBSA also affirms the docking results. The results obtained from this study have provided highly potential candidates for developing natural inhibitors against COVID-19.

Diadema setosum Chemical Compounds with GC-MS Analysis as a Triple Inhibitor Antiviral Covid-19

“…In addition, the potential compound has the same inhibitory position as the control compound on each receptor. This similarity illustrates that the potential compounds have the same inhibitory ability to control drugs (Shifeng et al, 2022).…”

In Silico and In Vitro Evaluation of Antiobesogenic and Osteoprotective Effect of Pomegranate Juice Fermented by Tannin Acyl Hydrolase and Lactobacillus vespulae DCY75 via the Wnt/β-Catenin Pathway

“…28 The simulations employed the single-point-charge (SPC) 29 water model and the CHAARM 30 force field. The MD procedure followed our previous study, 31 and a simulation time of 20 ns was chosen. Subsequently, we analyzed the MD trajectories using GROMACS utilities using output data such as RMSD (Root Mean Square Deviation), RMSF (Root Mean Square Fluctuation), R g (Radius of Gyration), and the number of hydrogen bonds.…”

Phytochemicals Against SARS-COV-2 Infection

“…In conclusion, ginsenosides were suggested to be potential natural inhibitors of SARS-CoV-2 related proteins. 7 Wang et al explored the potential mechanisms and efficacy of polydatin against COVID-19 by the combined application of network pharmacology, molecular docking, and an experimental verification approach. They suggested that polydatin may alter the immune, cytokines, and inflammatory responses, as well as SARS-CoV-2 innate immunity evasion and cell-specific immune response.…”

“…In conclusion, ginsenosides were suggested to be potential natural inhibitors of SARS-CoV-2 related proteins. 7…”