Quercetin, a secondary metabolite present in methanolic extract of Calendula officinalis, is a potent inhibitor of peptide deformylase, undecaprenyl pyrophosphate synthase and DNA primase enzymes of Staphylococcus aureus: an in vitro and in silico result analysis

Abstract

Plant-based naturally occurring phytochemicals have great inhibitory potential against various pathogenic bacteria, but the mechanism of inhibition and the essential cell molecules to which they bind and inhibit, remain unclear and unexplored so far. In the present study, we examined the effect of secondary metabolites from C officinalis both in vitro and in silico to decrypt the probable pathway of inhibition. In in vitro experiments, Staphylococcus aureus was used to evaluate the antibacterial potential of secondary metabolites present in different organic extracts of C officinalis using agar-well diffusion and XTT-colorimetric methods. In in silico experiments, 4 important C officinalis secondary metabolites viz. Alpha cadinol, Scopoletin, Esculetin and Quercetin were docked against 4 essential enzymes of bacteria like Peptide deformylase, Gamma hemolysins, Undecaprenyl pyrophosphate synthase and DNA primases to assess their antibacterial potential using AutoDock Vina (1.0). The enzyme-ligand interaction of docked complexes was further analyzed by Molecular Dynamics Simulation technique using GROMACS (4.6.6). As per in vitro results, methanolic extract was found to be the most promising extract having highest antibacterial potential, where the 20mg/ml concentration of the extract was found to completely inhibit the bacterial growth, whereas for pure Quercetin the complete inhibition was achieved at 5mg/ml concentration. MIC was observed to be 20 and 5mg/ml with methanolic and pure Quercetin extracts, respectively. Whereas, MBC values were found to be 40 and 5mg/ml for methanolic extract and Quercetin, respectively. As per in silico results, Quercetin was found to be the only secondary metabolite which strongly inhibited three essential enzymes of S aureus like Peptide deformylase, Undecaprenyl pyrophosphate synthase and DNA primases enzymes, which resulted in the inhibition of post-translation, cell-wall biosynthesis and initiation of replication pathways, respectively. As Quercetin was found in methanolic extract of C officinalis, we have successfully demonstrated that C officinalis has great potential to inhibit the growth of S aureus.