Allosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination

Abstract

Recent crystallographic study revealed the involvement of allosteric site in active site inhibition of penicillin binding protein (PBP2a), where one molecule of Ceftaroline (Cef) binds to the allosteric site of PBP2a and paved way for the other molecule (Cef) to bind at the active site. Though Cef has the potency to inhibit the PBP2a, its adverse side effects are of major concern. Previous studies have reported the antibacterial property of Quercetin derivatives, a group of natural compounds. Hence, the present study aims to evaluate the effect of Quercetin 3-o-rutinoside (Rut) in allosteric site-mediated active site inhibition of PBP2a. The molecular docking studies between allosteric site and ligands (Rut, Que, and Cef) revealed a better binding efficiency (G-score) of Rut (−7.790318) and Cef (−6.194946) with respect to Que (−5.079284). Molecular dynamic (MD) simulation studies showed significant changes at the active site in the presence of ligands (Rut and Cef) at allosteric site. Four different combinations of Rut and Cef were docked and their G-scores ranged between −6.320 and −8.623. MD studies revealed the stability of the key residue (Ser403) with Rut being at both sites, compared to other complexes. Morphological analysis through electron microscopy confirmed that combination of Rut and Cefixime was able to disturb the bacterial cell membrane in a similar fashion to that of Rut and Cefixime alone. The results of this study indicate that the affinity of Rut at both sites were equally good, with further validations Rut could be considered as an alternative for inhibiting MRSA growth.

Keywords:

• MRSA
• PBP2a
• Quercetin 3-o-rutinoside
• molecular docking
• simulation
• SEM and TEM

Acknowledgments

The authors thank Centre for Bioinformatics, Pondicherry University, for providing necessary computational facility; CIF, Pondicherry University for SEM analysis; Sophisticated Analytical Instrumentation Facility, AIIMS for TEM analysis; Pondicherry Institute of Medical Science for providing MRSA standard strain.