Evaluation of phytochemicals from Coccinia grandis leaves as potential inhibitors of penicillin-binding protein 5 (PBP5) of Escherichia coli: an in silico study

Abstract

This study aimed to investigate the antimicrobial activity of phytochemicals of Coccinia grandis leaves against Penicillin-binding protein 5 (PBP 5) of Escherichia coli (E. coli) using site-specific molecular docking. Penicillin-binding protein 5 (PBP 5) of E. coli is involved in cell wall synthesis. The main constituent of the bacterial cell wall is Peptidoglycan. PBP 5 enzyme performs a DD-carboxypeptidase reaction on the bacterial Peptidoglycan. The active site of PBP 5 contains a specific serine residue, which acts like a hook to grab a unit of the Peptidoglycan chain during the enzymatic reaction. Near the active site, two lysine residues (Lys47 and Lys213) play a critical role in proton-transfer events during acylation and deacylation events. PBP 5 is inactivated by β-lactam antibiotics such as penicillin. Inactivation happens when the antibiotic forms a covalent bond with a serine residue in PBP 5, creating a stable complex that prevents enzymatic activity. When PBP 5 binds to the antibiotic, it is dormant in an acylation state, thus, disrupting the cell wall synthesis, resulting in cell death. The phytochemicals of Coccinia grandis leaves, and the structure of the active site of the PBP5 were identified through a literature survey. The structures of selected molecules were obtained from the PubChem database. The energy-minimization of ligands was performed using Avogadro software version 1.2.0. The crystal structure of E. coli PBP 5, in complex with a peptide-mimetic penicillin (PDB ID- 3BEB), was obtained from the Protein Data Bank. The protein was prepared using Autodock tool version 1.5.7. Then, sitespecific molecular docking was performed using Autodock version 4.2.6. In this study, Penicillin was selected as the reference molecule. Lupeol (-7.72 kcal/mol) and Beta-sitosterol (-8.21 kcal/mol) show higher binding affinity to PBP 5 of E. coli than the Penicillin (-7.20 kcal/mol). Both Beta-sitosterol (0.953 µM) and Lupeol (2.19 µM) show lower inhibition constant than Penicillin (5.32 µM), indicating higher potency than Penicillin. Both Lupeol and Beta-sitosterol fulfill Lipinski’s and Veber’s rules. When considering the H-bonding interactions, two hydrogen bonds can be seen between Penicillin and the protein (Ser87 & Asn112). Between PBP5 and Lupeol one H-bonding interaction (Ser44), PBP5 and Beta-sitosterol one H-bonding interaction (Asn112) can be seen. These two molecules may act as potential inhibitors for Penicillin-binding protein 5 (PBP 5) of E. coli. Future studies should focus on the structural optimization of Lupeol and Beta-sitosterol to enhance their binding affinity and inhibitory potency against PBP5 of E. coli, potentially leading to novel antibiotic therapies.