Virtual Screening Targeting LasR and Elastase of Pseudomonas aeruginosa Followed by In Vitro Antibacterial Evaluation

Pseudomonas aeruginosa is a Gram-negative pathogen with a remarkable capacity to acquire multiple resistance mechanisms, severely limiting current therapeutic options. Consequently, the identification of new antimicrobial agents remains a critical priority. In this study, an integrated in silico-guided strategy was applied to identify small molecules with antibacterial potential against P. aeruginosa, targeting the quorum-sensing regulator LasR (PDB ID: 2UV0) and elastase (PDB ID: 1U4G). Pharmacophore modeling was performed for both targets, followed by ligand-based virtual screening, structure-based virtual screening (SBVS), and MM-GBSA (Molecular Mechanics-Generalized Born Surface Area) binding free energy calculations. Top-ranked compounds based on predicted binding affinity were selected for in vitro cytotoxicity and antibacterial evaluation. Antimicrobial activity was assessed against three P. aeruginosa strains: an American Type Culture Collection (ATCC) reference strain, a clinically susceptible isolate, and an extensively drug-resistant (XDR) clinical isolate. SBVS yielded docking scores ranging from −6.96 to −12.256 kcal/mol, with MM-GBSA binding free energies between −18.554 and −88.00 kcal/mol. Minimum inhibitory concentration (MIC) assays revealed that MolPort-001-974-907, MolPort-002-099-073, MolPort-008-336-135, and MolPort-008-339-179 exhibited MIC values of 62.5 µg/mL against the ATCC strain, indicating weak-to-moderate antibacterial activity consistent with early-stage hit compounds. MolPort-008-336-135 showed the most favorable activity against the clinically susceptible isolate, with an MIC of 62.5 µg/mL, while maintaining HepG2 cell viability above 70% at this concentration and an half-maximal inhibitory concentration (IC50) greater than 500 µg/mL. In contrast, all tested compounds displayed MIC values above 62.5 µg/mL against the XDR isolate, reflecting limited efficacy against highly resistant strains. Overall, these results demonstrate the utility of in silico-driven approaches for the identification of antibacterial hit compounds targeting LasR and elastase, while highlighting the need for structure–activity relationship optimization to improve potency, selectivity, and activity against multidrug-resistant P. aeruginosa.