In silico antimicrobial potential of some flavonoids from Retama sphaerocarpa: molecular docking studies, pharmacokinetics and toxicity prediction

Flavonoids are one of the largest classes of secondary metabolites that have been shown to be potent antimicrobials against a wide range of pathogenic organisms in vitro. The interest in the antimicrobial properties of flavonoids and their use to treat human diseases has increased with respect to plants that synthesize these compounds as a response to microbial infection. The objective of this study was to evaluate the antimicrobial potential of certain flavonoids from an Algerian medicinal plant. A molecular docking study against DNA Gyrase Topoisomerase II (E. coli, PDB ID: 1Kzn), Penicillin Binding Protein 3(PDB ID: 3Vsl), Cytochrome P450 14 alpha-sterol Demethylase (PDB ID: 1EA1) and N-Myristoyl Transferase (PDB ID: 1Iyl) was performed to assess the antimicrobial effects of the selected compounds. In addition, the parameters of bioavailability, pharmacokinetics and toxicity were estimated. According to computational studies, the highest scores were presented by quercetin-3,7-di-O-glucoside, vicenin-2 and vitexin, indicating a good binding affinity towards the tested targets. The docking score values of quercetin-3,7-di-O-glucoside against 1Kzn, 3Vsl, 1EA1 and 1Iyl were in theorder of -8.110, -10.285, -13.101 and -15.043 Kcal.mol^-1, respectively. Vicenin-2 showed binding affinity toward 1Kzn, 3Vsl, 1EA1 and 1Iyl with scores equal to -7.507, -11.125, -13.465 and -14.094 Kcal.mol^-1, respectively. Finally, the docking scores of vitexin against 1Kzn, 3Vsl, 1EA1 and 1Iyl were -6.950, -7.944, -12.592 and -12.728 Kcal.mol^-1, respectively. The in silico investigation shows that by targeting specific proteins, the best hits have significant anti-antimicrobial activity; however, more studies are required.