Molecular Docking and Ligand-Binding Analysis of Amidine Derivatives Targeting Pseudomonas aeruginosa and Escherichia coli Bacterial Strains: An In Silico Approach

Authors:
Publisher website
Google Scholar
Abstract
Gram-negative bacteria represent a formidable challenge due to their exhibition of elevated resistance to various antibiotics. This study delves into the crisis posed by antimicrobial resistance (AMR), focusing on the alarming rise of bacteria (Gram-negative), such as Escherichia coli (E. coli) and Pseudomonas aeruginosa (P. aeruginosa), notorious for their severe infections. By examining the binding interaction with antibiotics (ampicillin, ciprofloxacin, trimethoprim, pentamidine, furamidine, and oligoamidine) and bacterial protein targets, the study utilized molecular docking and ligand-binding analysis. The result reveals different LibDock scores with the bacterial strain. Higher scores indicate stronger binding. Pentamidine exhibited the highest scores with all bacterial strains. CDOCKER energy due to interaction was computed to analyze the molecules binding with the bacteria, and pentamidine stood with higher CDOCKER value, indicating strong binding affinity. The work also assessed the antibiotics likeness using the rule of Lipinski’s five (RO5), and several antibiotics conform to the criteria. Molecular dynamics simulations were conducted to estimate compound stabilities, revealing stable conformations. The results revealed a stable potential energy (PE) profile for 5V7A Chain B. The RMSD profiles exhibited deviations within certain time intervals, indicating potential conformational changes in the antibiotics.
Funding Information
  • Deputyship for Research & Innovation, Ministry of Education in Saudi Arabia (IFP-IMSIU-2023083)

This publication has 28 references indexed in Scilit: