In silico Identification of Peptide Deformylase Inhibitors from Escherichia coli using Phytochemical Constituent of Pomegranate Leaves

Abstract

Escherichia coli is a member of the bacterial family of Enterobacteriaceae, is the most prevalent commensal inhabitant of the gastrointestinal tracts of humans and warm-blooded animals, as well as one of the most important pathogens. Peptide Deformylase (PDF) is a well-defined intracellular target for discovery of new antibiotic agents owing to its importance in bacterial protein synthesis. Phytochemicals from pomegranate had demonstrated antimicrobial properties. In this study, we explored phytochemicals from Pomegranate as inhibitors of Peptide Deformylase. A total of 17 compounds were obtained from GC-MS analysis and used for the virtual screening based on physiochemical properties (Lipinski’s rule of five) and molecular docking analysis. Results showed that 12 compounds had good AutoDock binding energies values ranging between -7.03 and -24.34 kcal/mol and thus, where selected for pharmacokinetic and toxicity analyses. Nine (9) compounds (CID_561786, CID_6421507, CID_6421505, CID_87299998, CID_534400, CID_6429040, CID_95337, CID_561668, and CID6428442), with desirable pharmacokinetic properties were selected. Therefore, these compounds are considered as suitable prospective inhibitors of PDF after successful experimental validation.

Keywords: Docking, ADME, Peptide Deformylase, GC-MS, Phytochemicals