Integrated Computational Screening for Quorum Sensing Inhibitors of Pseudomonas aeruginosa: Molecular Docking, Molecular Dynamics Simulations, and DFT Analysis ​​

Antimicrobial resistance in Pseudomonas aeruginosa is a major global health threat and mostly regulated by quorum sensing, virulence, and biofilm formation. Quorum sensing inhibitors have been proposed as anti-virulence agents that do not exert selective pressure like conventional antibiotics. Herein, an integrated in silico approach was used to screen potential phytochemical inhibitors against key quorum sensing proteins of P. aeruginosa : autoinducer synthase LasI (PDB ID: 1RO5) and LuxR-family transcriptional regulator QscR (PDB ID: 6CC0); N-acyl homoserine lactonase AiiA (PDB ID: 7L5F) was taken as a reference QSI control. A library of phytochemicals underwent ADMET profiling followed by molecular docking, molecular dynamics simulations MM/GBSA binding free energy calculations, and DFT analysis. Boeravinone F was identified through molecular docking as the best LasI inhibitor with binding affinity of -8.5 kcal/mol while 4′,7-dihydroxy-3′-methylflavone was found to be the best binder for QscR with affinity − 9.9 kcal/mol; diffusarotenoid also showed good binding toward AiiA. The subsequent 50 ns MD simulations revealed that LasI-Boeravinone F and QscR-4′,7-dihydroxy-3′-methylflavone complexes have very good structural stability, less backbone fluctuation, and relatively compact structure compared to the highly unstable AiiA-diffusarotenoid complex. Strong binding free energies were further confirmed by MM/GBSA calculations for QscR-4′,7-dihydroxy-3′-methylflavone (− 28.44 kcal/mol) and LasI-boeravinone F (− 23.74 kcal/mol). DFT analysis and molecular electrostatic potential revealed optimal electronic properties with reactive sites suitable for hydrogen bonding as well as π–π interactions supporting the observed interactions. Therefore, boeravinone F and 4′,7-dihydroxy-3′-methylflavone were suggested to be potential dual-target quorum sensing inhibitors that can block both signal synthesis and reception pathways in P. aeruginosa which may be experimentally validated based on this strong computational support toward novel anti-virulence therapeutic development.