Artemisia campestris L. as a promising source of potential antiviral drugs for SARS-CoV-2: Docking and dynamic simulation studies
Aboubakeur Essedik Khelef, Hanine Hadni, Hicham Gouzi, Borhane Samir Grama · Scientific African · 2024
• Artemisia campestris hot aqueous extract used by peoples of South Algeria to combat COVID-19. • Preparation of a library of 69 phytochemicals derived from Artemisia campestris . • These molecules were analyzed by in silico molecular docking against S-RBD protein and Mpro of SARS CoV-2 to select their potential inhibitors. • The ADMET properties and the drug-likeness in silico were used to test the selected compounds. • Molecular dynamics simulations and thermodynamic parameters revealed the formation of stable complexes. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been considered as global public health security threats. Due to its rapid spread, high mortality rate and unavailability of treatment, we need to find a potent drug against SARS-CoV-2. Natural products are useful agents for the discovery of new potential drugs to combat coronavirus. Artemisia campestris , an aromatic plant widely used in traditional medicine, particularly in southern region of Algeria, is recognized for its essential oils and phenolics compounds possessing a wide range of biological activities. This study selected sixty-nine compounds from this plant to determine their binding interactions with the SARS-CoV-2 main protease (M pro ) and receptor-binding domain of the spike (S-RBD) protein, by using computational methods. Rutin, isoquercetin, and quercetin-3-O-glucuronide were shown to be the most potent inhibitors for Mpro and S-RBD with docking scores and K i values ranging from -16.06 to -10.67 Kcal/mol and 0.005 to 30.01 nM, respectively. Evaluation of ADMET pharmacokinetic properties and the drug likeness in silico revealed that only 3,5-dicaffeoylquinic acid, 3–4–5-tricaffeoylquinic acid, isorhamnetin-3-O-glucoside, and rubescensin A could be more effective drugs against COVID-19. Molecular dynamics (MD) simulations (100 ns) and MM-GBSA calculations confirmed the stability of ligand-protein complexes via hydrogen bonding interactions with crucial residues. The analysis of structural parameters (RMSD, RMSF, H-bonds, Rg, and SASA) indicates that 3,4,5-tricaffeoylquinic acid and rubescensin A compounds have good stability and significant binding affinity with the Mpro and S-RBD protein. Taken together, our findings confirm that Artemisia campestris as a plausible source of anti-SARS-COV-2 phytochemicals and suggest that may play important role in this activity.