Phytochemical Analysis, Antioxidant, and Antimicrobial Activities of Ducrosia flabellifolia: A Combined Experimental and Computational Approaches

Abstract

Ducrosia flabellifolia Boiss. is a rare desert plant known to be a promising source of bioactive compounds. In this paper, we report for the first time the phytochemical composition and biological activities of D. flabellifolia hydroalcoholic extract by using liquid chromatography-electrospray tandem mass spectrometry (ESI-MS/MS) technique. The results obtained showed the richness of the tested extract in phenols, tannins, and flavonoids. Twenty-three phytoconstituents were identified, represented mainly by chlorogenic acid, followed by ferulic acid, caffeic acid, and sinapic acid. The tested hydroalcoholic extract was able to inhibit the growth of all tested bacteria and yeast on agar Petri dishes at 3 mg/disc with mean growth inhibition zone ranging from 8.00 ± 0.00 mm for Enterococcus cloacae (E. cloacae) to 36.33 ± 0.58 mm for Staphylococcus epidermidis. Minimal inhibitory concentration ranged from 12.5 mg/mL to 200 mg/mL and the hydroalcoholic extract from D. flabellifolia exhibited a bacteriostatic and fungistatic character. In addition, D. flabellifolia hydroalcoholic extract possessed a good ability to scavenge different free radicals as compared to standard molecules. Molecular docking studies on the identified phyto-compounds in bacterial, fungal, and human peroxiredoxin 5 receptors were performed to corroborate the in vitro results, which revealed good binding profiles on the examined protein targets. A standard atomistic 100 ns dynamic simulation investigation was used to further evaluate the interaction stability of the promising phytocompounds, and the results showed conformational stability in the binding cavity. The obtained results highlighted the medicinal use of D. flabellifolia as source of bioactive compounds, as antioxidant, antibacterial, and antifungal agent.

Keywords: Ducrosia flabellifolia; antimicrobial; antioxidant; chemical composition; dynamic simulation; molecular docking.

Figure 1

D. flabellifolia Boiss. plant species collected from the Hail region.

Figure 2

Chemical structure of the main compounds identified by ESI-MS/MS technique in the hydroalcoholic extract from D. flabellifolia aerial parts. Numbers are the same as listed in Table 1.

Figure 3

Mean diameters of bacterial and fungal growth inhibition zones (mGIZ ± mm) obtained with different concentrations of D. flabellifolia hydro-methanolic extract as compared to standard drugs. *: Ampicillin for bacteria and amphotericin B for Candida strains.

Figure 4

Two- and three-dimensional residual interactions network of luteolin 7-glucoside against the active site of S. aureus IIA topoisomerase (PDB ID: 2XCT).

Figure 5

Two- and three-dimensional residual interactions network of (−)-epicatechin in human peroxiredoxin 5 protein (PDB ID: 1HD2).

Figure 6

Two- and three-dimensional residual interactions network of hyperoside against the active site of C. albicans Sap1 (PDB ID: 2QZW).

Figure 7

Two- and three-dimensional residual interactions network of hyperoside against the active site of TyrRS protein (PDB ID: 1JIJ).

Figure 8

MD simulation analysis of hyperoside in complex with S. aureus tyrosyl-tRNA synthetases (TyrRS) (PDB ID: 1JIJ): (A) time dependent RMSD (protein Cα atoms RMSD is shown in teal blue color while the RMSDs of hyperoside with respect to protein are shown in brown color); (B) protein Cα atoms RMSF; (C) 2D diagram of ligand interactions that occurred more than 30.0% of the simulation time; and (D) protein–ligand contact analysis of throughout the simulation.