In Silico Assessment of Thymol as a Natural Plant-derived Antibacterial Candidate against Pseudomonas aeruginosa

Introduction: Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen of relevance to food microbiology, biofilm formation, and antibiotic resistance. The inclusion of carbapenem-resistant P. aeruginosa among high-priority pathogens in the 2024 World Health Organisation Bacterial Priority Pathogens List highlights the need for new antibacterial candidates. This study aims to evaluate thymol against P. aeruginosa using an integrated in silico bioinformatics and cheminformatics approach.

Methods: The in silico workflow first evaluated thymol for physicochemical properties, predicted pharmacokinetic characteristics, and drug-likeness using the Swiss Absorption, Distribution, Metabolism and Excretion web tool (SwissADME). Literature-relevant P. aeruginosa protein targets with resolved structures were selected from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), after which potential binding pockets were identified using the Computed Atlas of Surface Topography of Proteins (CASTp). Docking calculations were performed in triplicate using AutoDock Vina. Binding orientations and interaction patterns were then analysed using the Python Molecular Graphics System (PyMOL), University of California, San Francisco Chimera (UCSF Chimera), and BIOVIA Discovery Studio Visualiser.

Results: Thymol showed a favourable in silico profile, with predicted pharmacokinetic and drug-like properties consistent with Lipinski’s Rule of Five. Triplicate molecular docking indicated plausible interactions with the selected P. aeruginosa targets, supporting the prioritisation of thymol for further experimental investigation. These findings are consistent with existing in vitro evidence reporting antibacterial and anti-biofilm activity of thymol against P. aeruginosa, as well as the activity of thymol-rich essential oils against antibiotic-resistant P. aeruginosa isolates.

Conclusions: This study suggests plausible molecular interactions between thymol and selected P. aeruginosa targets. These findings should be validated experimentally, starting with in vitro antibacterial and antibiofilm assays that include antibiotic-resistant isolates, followed by mechanistic studies and in vivo assessments to evaluate safety and efficacy.