Study of Virtual Molecular Docking of Avocados Compounds against Pseudomonas aeruginosa (5N5H) by Carbapenemase using DOCK 6 Algorithm

Abstract

Antimicrobial resistance from bacteria is a global health problem that can cause death, and the cause is the emergence of carbapenem resistance Pseudomonas aeruginosa through VIM (Verona integron-encode metallo-β-lactamase), which causes the carbapenem class of antibiotics not to work properly. This species is a gram-negative bacteria which is the main cause of nosocomial pneumonia infection. This study aims to determine in silico inhibitory activity of 50 compounds obtained from avocado ( Persea Americana Mill) on VIM, preventing carbapenem antibiotic resistance. The molecular docking process was carried out to test carbapenem's antibiotic resistance control activity by 50 compounds. Docking using DOCK 6 software with a flexible and rigid method, Molecular docking on a protein with PDB ID 5N5H, The target protein was prepared using the Chimera application. Visualization of ligand-protein interactions was carried out with PyMOL and PLIP. The results of the native ligand grid score obtained by each method are -63.013 kcal/mol (Flexible) and -64.032 kcal/mol (Rigid). The best test ligands in the flexible method are 44257090, 14282775 and 44257819, and the grid score are -77.474, -75.274 and -73.219 kcal/mol. The best test ligands in the rigid method are 5280637, 14282775 and 5490064; the grid score is -62.191, -61.714, and -60.453 kcal/mol. The results of the test ligands can provide a better grid score than native ligands, namely in the flexible method. However, the rigid method of grid score results is no better than the native ligand. A good result is that the test ligand grid score is smaller than native ligands, so it has less energy to bind to the active site.