Computational protocol: Repurposing metformin as a quorum sensing inhibitor in Pseudomonas aeruginosa

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Protocol publication

[…] To determine the molecular interaction of metformin with the LasR, rhlR receptors, docking study was performed. The crystal structure of P. aeruginosa LasR ligand binding domain was obtained from Protein Data Bank (PDB ID: 2UV0), while the rhlr receptor model (ID: P54292.1) was achieved from protein model portal28. The interaction of metformin, the natural ligand, 3-oxo-dodecanoylhomoserine lactone and the classical quorum sensing inhibitor C30 furanone into the receptor active site was investigated using Molegro Virtual Docker (MVD Version 6.0). Metformin was drawn into Marvin Sketch V5.11.5.29, and, for docking, and the most energetically favored conformer was saved in the file format of (*.mol2). The optimal geometry of the ligand was determined during the docking process and the E monomer was selected for analysis. Water was discarded, cavities were determined and the search area was set to be 9 Å from the center of the active site. Iterative simplex algorithm was selected to perform docking process with 10 runs per ligand, 200 population size, 1000 max iteration and 5 poses for each ligand. MolDock docking engine employing docking template and the optimized ligands was executed. Finally, the top returned poses were selected for analysis. Similarly, docking metformin and the autoinducer, butanoyl homoserine lactone (C4-HSL), into the active site of the rhlr receptor model was performed. […]

Pipeline specifications

Software tools MVD, Marvin
Databases PMP
Applications Drug design, Protein interaction analysis
Organisms Pseudomonas aeruginosa, Bacteria, Pseudomonas aeruginosa PAO1, Chromobacterium violaceum
Chemicals Hydrogen, Metformin