Rational Design and Virtual Screening of Antimicrobial Terpene-Based Leads from Marrubium vulgare Essential Oil: Structure-Based Optimization for Food Preservation and Safety Applications

<i>Pseudomonas aeruginosa</i> elastase LasB accelerates refrigerated food spoilage through proteolytic degradation of muscle and milk proteins. While <i>Marrubium vulgare</i> essential oil terpenes exhibit antimicrobial activity, their weak potency and nonspecificity limit direct food preservation applications. This computational study aimed to rationally redesign terpene scaffolds into predicted selective LasB inhibitors. A virtual library of 635 terpene-peptide-phosphinic acid hybrids (expanded to 3940 conformers) was evaluated using consensus molecular docking (Glide/Flare) against LasB (PDB: 3DBK) and three human off-target proteases. Top candidates underwent duplicate 150 ns molecular dynamics simulations with MM/GBSA binding free-energy calculations. Computational screening identified thymol-Leu-Trp-phosphinic acid as the lead candidate with predicted binding affinity of -12.12 kcal/mol, comparable to reference inhibitor phosphoramidon (-11.87 kcal/mol), and predicted selectivity index of +0.12 kcal/mol representing a 2.3 kcal/mol advantage over human proteases. Molecular dynamics simulations indicated exceptional stability (98.7% stable frames, 0.12 Å inter-replica RMSD) with consistent zinc coordination. Structure-activity analysis revealed phosphinic zinc-binding groups (+1.57 kcal/mol), Leu-Trp linkers (+2.47 kcal/mol), and phenolic scaffolds (+1.35 kcal/mol) as predicted optimal structural features. This in silico study provides a computational framework and prioritized candidate set for developing natural product-derived food preservatives. All findings represent computational predictions requiring experimental validation through enzymatic assays, food model studies, and toxicological evaluation.