Discovery of potential natural therapeutics targeting cell wall biosynthesis in multidrug-resistant Enterococcus faecalis: a computational perspective

Abstract

Background: Identifying therapeutic inhibitors of crucial enzymes involved in the peptidoglycan biosynthesis pathway is pivotal for developing new treatments against multidrug-resistant Enterococcus faecalis V583. MurM, an essential enzyme in this pathway, plays a significant role in the bacterium's cell wall synthesis, making it an attractive druggable target for novel antimicrobial strategies. This study explored the potential of natural compounds as inhibitors of MurM, aiming to discover promising drug candidates that could serve as the foundation for future therapeutic development.

Methods: The three-dimensional structure of MurM was predicted, optimized, and its binding pocket was analyzed by comparing it with related structures. Over 4,70,000 natural compounds from the COCONUT database were subjected to virtual high-throughput screening (vHTS). The top lead candidates were selected based on their Lipinski's profile, ADME profile, toxicity profile, estimated binding free energy (ΔG) and estimated inhibition constant (Ki). Interaction pattern analysis was used to evaluate the non-covalent interactions between the inhibitors and key residues in MurM's binding pocket. Molecular dynamics simulations were performed over 300 ns to assess the structural stability and impact of these inhibitors on MurM's enzyme.

Results: Three lead compounds-CNP0056520, CNP0126952, and CNP0248480-were identified and prioritized with estimated ΔG ranging from - 9.35 to -7.9 kcal/mol. Molecular dynamics simulations revealed minimal impact on MurM's overall structure and dynamics, with the candidate inhibitors forming stable protein-ligand complexes. These interactions were supported by several non-covalent interactions between the candidate inhibitors and key residues within MurM's binding pocket.

Conclusion: These findings suggest that the identified natural product candidates could serve as promising inhibitors of MurM, potentially leading to novel therapeutics targeting cell wall biosynthesis in multidrug-resistant E. faecalis.

Keywords: Enterococcus faecalis; Molecular dynamics and antibiotic resistance; MurM; Natural compounds; Virtual screening.

Fig. 1

Three-dimensional structure of MurM with colors representing different domains of the MurM protein

Fig. 2

Three-dimensional structure of MurM highlighting the potential active site residues identified through structural comparison technique with related proteins

Fig. 3

Workflow outlining the systematic process to identify and prioritize natural lead candidates against MurM using the COCONUT database

Fig. 4

Molecular docking orientation of prioritized lead candidates and control molecule towards the substrate binding site of MurM

Fig. 5

Electrostatic surface potential map analysis of prioritized lead candidates and control molecule towards substrate binding cleft of MurM

Fig. 6

Two-dimensional schematic ligand interactions depicting prioritized lead candidates and control molecule binding to MurM

Fig. 7

Root mean square deviation (RMSD), Radius of Gyration (Rg), Hydrogen Bonds, and Solvent Accessible Surface Area (SASA) analyses for MurM and its ligand-bound complexes (Color codes: Black–MurM, Red–Control, Green–MurM_CNP0056520 complex, Blue–MurM_CNP0126952, Yellow–MurM_CNP0248480)

Fig. 8

Root mean square fluctuation (RMSF) analysis of MurM and its complexes (Color codes: Black–MurM, Red–Control, Green–MurM_CNP0056520 complex, Blue–MurM_CNP0126952, Yellow–MurM_CNP0248480)

Fig. 9

Essential dynamics analysis of MurM and its complexes (Color codes: Black–MurM, Red-Control, Green- MurM_CNP0056520 complex, Blue-MurM_CNP0126952, Yellow-MurM_ CNP0248480)