Differential Antibacterial Activity of Pomegranate Peel Polyphenols Against Gram-Positive and Gram-Negative Bacteria: In Vitro and In Silico Analysis

This study systematically evaluates the antibacterial activity of pomegranate peel extract (PoPEx) and its major polyphenolic constituents against Gram-positive (S. aureus) and Gram-negative (E. coli) bacteria, revealing the relationship between molecular size and membrane permeability. Through LC–MS analysis, in vitro antibacterial testing, molecular docking, and porin channel transport simulations, the research provides an in-depth structure-activity relationship analysis of polyphenols, supporting their potential development as natural antimicrobial agents.

 

Literature Overview
This study, published in the journal Antibiotics, reviews and summarizes the antibacterial activity of pomegranate peel extract (PoPEx) and its primary polyphenolic components against six strains of Staphylococcus aureus (S. aureus) and five strains of Escherichia coli (E. coli). By integrating experimental and computational approaches, the research investigates the structure-activity relationship of pomegranate polyphenols, highlighting differences in their permeability and binding capacity across bacterial strains, offering novel insights for the development of natural antimicrobial agents.

Background Knowledge
Pomegranate (Punica granatum L.) has been widely used in traditional medicine for antimicrobial, anti-inflammatory, and antioxidant applications. Its peel contains abundant polyphenols, including punicalagin, punicalin, ellagic acid, and gallic acid. These polyphenols demonstrate stronger antibacterial activity against Gram-positive bacteria (e.g., S. aureus) compared to Gram-negative bacteria (e.g., E. coli), where the outer membrane's porin channels restrict polyphenol penetration. This study further elucidates the underlying mechanisms through molecular docking analysis and porin channel transport simulations, showing that large-molecule-weight polyphenols (e.g., punicalagin) exhibit strong binding affinity but limited membrane permeability, while smaller molecules (e.g., gallic acid) demonstrate enhanced permeability and antibacterial efficacy. The findings emphasize the interplay between polyphenol structure and activity, providing experimental and computational foundations for optimizing natural products as antimicrobial agents.

 

 

Research Methods and Experiments
The study employed LC–MS to characterize the chemical composition of pomegranate peel extract. Minimum inhibitory concentrations (MICs) against six S. aureus strains and five E. coli strains were determined using broth microdilution assays. Molecular docking was performed with AutoDock Vina to predict polyphenol binding affinity to bacterial targets (e.g., PBP2a, PBP3, MurA, FtsZ). Membrane permeability was assessed using porin channel transport simulations with Caver Web software.

Key Conclusions and Perspectives

• PoPEx exhibits MIC ranges of 15.62–500.00 µg/mL against Gram-positive bacteria (S. aureus) and 125.00–500.00 µg/mL against Gram-negative bacteria (E. coli), indicating greater susceptibility of Gram-positive strains to polyphenols.
• Punicalagin shows the lowest MIC against S. aureus (15.62 µg/mL), while gallic acid demonstrates the lowest MIC against E. coli (125 µg/mL), suggesting distinct antibacterial mechanisms for different polyphenol-bacteria combinations.
• Molecular docking reveals that punicalagin and punicalin exhibit high binding energy to bacterial targets (e.g., PBP2a, MurA, FtsZ), whereas smaller polyphenols like gallic acid show weaker binding but enhanced membrane permeability.
• Porin channel transport simulations indicate that large polyphenols (punicalagin, punicalin) cannot traverse the OmpF porin channel in E. coli, while smaller ones (gallic acid, ellagic acid) do, explaining the reduced sensitivity of Gram-negative bacteria to polyphenols.
• The study establishes that polyphenol antibacterial activity depends not only on target binding but also on molecular weight and membrane permeability, providing a computational model for structure-activity relationship optimization in natural products.

Research Significance and Prospects
This work offers a computational framework for structure-activity relationships in plant-derived antimicrobial agents, supporting further optimization of pomegranate peel polyphenols. Future studies may explore chemical modifications or nanocarrier delivery systems to enhance polyphenol permeability in Gram-negative bacteria. Additionally, in vivo antibacterial activity, pharmacokinetics, and safety profiles require investigation to advance clinical translation of these compounds as novel antimicrobial agents.

 

 

Conclusion
This study demonstrates that the antibacterial activity of pomegranate peel polyphenols is governed by a balance between molecular weight, membrane permeability, and target binding affinity. Large polyphenols (e.g., punicalagin) exhibit strong binding but limited penetration through porin channels in Gram-negative bacteria, while smaller polyphenols (e.g., gallic acid) achieve superior permeability and efficacy in E. coli. These findings establish a structure-activity relationship model for natural polyphenols and provide theoretical and experimental foundations for developing plant-derived antimicrobial agents. Future optimizations through chemical modifications or delivery systems could enhance antibacterial spectrum and bioavailability, broadening their application potential.

 

Relja Suručić, Maja Travar, Tatjana Kundaković Vasović, Miloš P Stojiljković, and Ranko Škrbić. In Vitro and In Silico Analysis of Differential Antibacterial Activity of Pomegranate Polyphenols Against Gram-Positive and Gram-Negative Bacteria. Antibiotics.