In Vitro and In Silico Analysis of Differential Antibacterial Activity of Pomegranate Polyphenols Against Gram-Positive and Gram-Negative Bacteria
Background/Objectives: This study investigates the antimicrobial properties of pomegranate peel extract (PoPEx) and its major polyphenolic constituents against Gram-positive and Gram-negative bacteria, employing six clinical isolates of Staphylococcus aureus and five isolates of Escherichia coli. The study further aims to elucidate mechanisms of action through molecular docking and transport studies. Methods: Chemical composition was analyzed using liquid chromatography–mass spectrometry (LC–MS). Antimicrobial activity was determined by the broth microdilution method. Molecular docking was performed with the AutoDock Vina algorithm, and transport studies through porin channels were carried out using Caver software. Results: PoPEx showed stronger activity against Gram-positive (MICs 15.62–500.00 μg/mL) than Gram-negative bacteria (MICs 125.00–500.00 μg/mL). Punicalagin was most active against S. aureus, while gallic acid was most effective against E. coli. Docking revealed high affinities of punicalagin and punicalin, whereas transport studies highlighted the advantage of smaller phenolics like gallic acid in crossing porins. Conclusions: Larger tannins exhibited strong target binding but limited porin permeability, reducing efficacy in Gram-negative bacteria. These findings provide insights into structure–activity relationships of pomegranate polyphenols and support their potential as natural antimicrobial agents.