Based on computer simulation and experimental verification: mining and characterizing novel antimicrobial peptides from soil microbiome

• Published in: Food chemistry 2025-03, Vol.467, p.142275, Article 142275
• Main Authors: Xu, Chunming, Han, Aiping, Tian, Yuan, Sun, Shiguang
• Format: Article
• Language: English
• Subjects: antimicrobial peptides; antimicrobial properties; Bioactive peptides; computer simulation; Escherichia coli; Food bio-preservatives; food chemistry; food safety; High throughput; Klebsiella pneumoniae; Machine learning; metagenomics; molecular dynamics; prediction; Prediction models; shelf life; soil; soil microorganisms; Staphylococcus aureus; traditional foods
• ISSN: 0308-8146; 1873-7072; 1873-7072
• DOI: 10.1016/j.foodchem.2024.142275

Antimicrobial peptides (AMPs) show great promise for enhancing food safety and extending shelf life, but traditional screening methods are complex and costly. To address these issues, we developed a deep learning-based prediction pipeline to identify potential AMPs from soil metagenomic data, achieving high accuracy (92.71 %) and precision (91.29 %). Based on model scoring, surface charge, and Hemopred and ToxinPred screenings, we identified nine candidate peptides. Peptide P4 (GTAWRWHYRARS) showed the best binding affinity to MrkH in molecular docking studies and was validated through molecular dynamics simulations. The chemically synthesized P4 demonstrated significant antimicrobial activity against Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus, indicating its potential as an effective alternative to traditional food antimicrobial agents. This study highlights the effectiveness of our integrated prediction pipeline for discovering new AMPs. •A new method for mining AMPs from soil microbiome data is proposed.•Discovery of nine potential AMPs through integrated approaches of machine learning and molecular docking.•GTAWRWHYRARS is an effective AMP selected through our model and performed well in computer and experimental validation.•Synthesis and validation of AMP-P4 demonstrating inhibition against K. pneumoniae, E. coli, and S. aureus.•The model of this study contributes to the discovery of new antimicrobial peptides.