Identification of natural inhibitors against Acinetobacter baumanniid-alanine-d-alanine ligase enzyme: A multi-spectrum in silico approach

Abstract

d-Alanine-d-alanine ligase (Ddl), an enzyme that catalyzes the d-ala-d-ala dipeptide formation in UDPMurNAc pentapeptide, is a part of peptidoglycan biosynthesis machinery. Inhibition of enzyme leads to bacterial growth arrest making it a viable and attractive target for screening of potent antibacterial drugs. Combination of virtual screening, molecular docking, in silico pharmacokinetics, molecular dynamics (MD) simulation, and binding free energy calculations based on Molecular Mechanics Generalized Born and Surface Area (MMGBSA) and WaterSwap were applied in the current framework for the detailed analysis of potent natural inhibitors against Ddl enzyme. Comparative molecular docking supported with computational druglikeness revealed compound-331 (6-(4-((3-methoxyphenylsulfonamido) methyl) phenyl)-2-methylnicotinamide) as the best docked inhibitor. The inhibitor has Genetic Optimization for Ligand Docking (GOLD) fitness score of 84.2 and AutoDock Vina binding energy of −7.2 kcal/mol. The inhibitor exhibited to have a better druglikeness by adhering to Lipinski rule of five, Ghose rule, Veber filter, Egan filter, and Muegge filter in contrast to d-cycloserine, which violates Ghose and Muegge rule. MD simulation unravels that in complex over the course of 100-ns, the enzyme remained highly stable with mean Root Mean Square Deviation (RMSD) of 1.4 Å when compared to an undocked structure having RMSD of 1.6 Å. Root Mean Square Fluctuation (RMSF) predicted stable behaviour of the active site residues in both undocked and docked system with average RMSD values of 1.2 Å and 0.7 Å, respectively. Radial Distribution Function (RDF) and Axial Frequency Distribution (AFD) demonstrated Lys176 and Trp177 as critical residues of enzyme for binding, anchoring and bridging strong hydrogen and hydrophobic contacts between enzyme and the inhibitor. The estimated MMGBSA based binding free energy for the complex is −47.36 kcal/mol, signifying its stable nature. WaterSwap further indicated a worthy agreement on the affinity of inhibitor towards enzyme active pocket. This newly discovered natural inhibitor might serve a parent structure for the development of more potent derivatives with encouraging biological activity.