Comparative chemical and antimicrobial evaluation of the essential oils from Callistemon and podocarpus species supported by in-silico molecular simulations against bacterial LacY protease

TL;DR

This study evaluates the antimicrobial properties of essential oils from Callistemon and Podocarpus plants and uses computer simulations to explore their potential against bacterial protease.

Contribution

The study introduces in-silico molecular docking to explain the antibacterial mechanism of essential oils from these plant species.

Findings

Callistemon essential oils are rich in oxygenated monoterpenes with strong antimicrobial activity against E. coli and S. viridans.

Podocarpus essential oils show notable activity against Staphylococcus comparable to antibiotics like ciprofloxacin.

Molecular docking simulations suggest strong binding affinity of essential oil constituents to the LacY protease enzyme.

Abstract

Myrtaceae and Podocarpaceae botanical families include several aromatic species that have been proven to have diverse pharmacological potential, especially antimicrobial effects. Additionally, plants of both families were reported for their benefits in traditional medicine. The current study demonstrated the chemical profile, antimicrobial of four investigated plant species (C. subulatus, C. rigidus, P. gracilior, and P. elongatus) leaves cultivated in the same place in Egypt and propose in-silico modeling for the antibacterial mechanistic action.

The essential oils samples were prepared via hydrodistillation and headspace extraction protocol and GC analysis was conducted to obtain a comparative chemical profile. The antimicrobial activity of the obtained hydrodistillation essential oil samples was screened via agar diffusion, and the MIC was calculated via broth microdilution assays. An in silico molecular docking study was performed to investigate the inhibition of the LacY protease efflux pump.

GC results revealed that the percentage of oxygenated monoterpenes was highest in the oil samples from Callistemon species (60.38 and 82.68%). In contrast, sesquiterpene hydrocarbons constituted the highest percentage of volatile classes in the oil samples from Podocarpus species (57.37 and 43.16%). C. rigidus-EO shows significant inhibitory activity against Gram-negative and Gram-positive pathogens, especially E. coli and S. viridans, with a calculated MIC of 0.878 ml, whereas P. elongatus EO shows notable activity against coagulase-negative Staphylococcus and the activity was comparable to that of the positive control antibiotics used (ciprofloxacin & doxycycline). Ultimately, an in silico molecular docking study on the binding site of the LacY protease enzyme revealed a significant binding affinity of the major docked volatile constituents.

The plant species investigated are considered a vital source of safe antimicrobial volatile constituents that are recommended as bioactive entities for controlling microbial infection topically or systemically. The proposed mechanistic action encourages further modification of the major EOs chemical structure by adding more polar substitutions to improve the binding affinity and produce more active semisynthetic analogues.

The online version contains supplementary material available at 10.1186/s12906-025-04826-w.

Figures