Exploring the Inhibitory role of Persicaria hydropiper bioactive compounds against 2KID protein associated with Staphylococcus aureus biofilm formation: Molecular Docking and Pharmacological property analysis

Abstract

The current communication states the role of Persicaria hydropiper (L.) bioactive compounds in the inhibition of Staphylococcus aureus sortase A protein through bioinformatic approaches. The P. hydropiper-derived phytochemicals’ (kaempferol, winterin, isalpinin, quercetin, quercitrin, and confertifolin) 3D structures in .SDF format were retrieved from PubChem and were docked to Staphylococcus aureus sortase A (PDB ID: 2KID) protein, using AutoDock Vina in-built in Chimera. The crystallographic structure of the 2KID protein was obtained from RCSB protein data bank. The pharmacological properties of the phytochemical ligands were determined through Lipinski’s rule of 5, and ADMET analysis and bioavailability score prediction, using Swiss-ADME and pKCSM webservers. All the ligands displayed good affinity to 2KID protein, displaying binding energy ranging from -8.0 kcal/mol (kaempferol)) to -7.1 kcal/mol (confertifolin), compared to a conventional antibiotic, ciprofloxacin (binding energy: -6.7 kcal/mol). The protein-ligand interaction had hydrogen-bonds and different hydrophobic interactions. The phytochemical ligands obeyed Lipinski’s rule of five without any violation, except quercitrin. The bioavailability score for the ligands were 0.55, except quercitrin displaying the score of 0.17. All the ligands showed acceptable ADMET profiles. Hence, P. hydropiper bioactive phytochemicals might be useful in the development of drugs for the treatment against infection caused with biofilm forming Staphylococcus aureus.