3D-QSAR and molecular docking studies of 1,3,4-oxadiazoles containing substituted phenoxy fragment as inhibitors of enoyl-acyl carrier protein reductase from Escherichia coli

Abstract

The antibacterial target, enoyl-acyl carrier protein (ACP) reductase, is a homotetrameric enzyme that catalyzes the last reductive step of fatty acid biosynthesis. In the present paper, Surflex docking and 3D-QSAR studies viz., CoMFA and topomer CoMFA have been carried out on a series (53 compounds) of enoyl ACP reductase inhibitors. An alignment rule for the compounds was defined using the database in SYBYL-X 2.0 package (Tripos Inc., St. Louis, USA, 2012). Models were validated using a data set obtained by dividing the data set into training set and test set. From the CoMFA, topomer CoMFA models, steric and electrostatic maps were generated to analyze the structural features of the datasets to indicate that data are well fitted with high predictive ability and inhibitory potency. The best predictions were obtained with CoMFA model (q ² = 0.403, $r^{ 2}_{\text{pred}} = 0. 8 3 2$) and topomer CoMFA model (q ² = 0.540, $r^{ 2}_{\text{pred}} = 0. 8 9 9$). These models and Surflex-docking studies revealed that the ether linkage, hydroxyl group, and 1,3,4-oxadiazole were significant for binding to the receptor, and some essential features were identified to deduce some interesting SARs. Comparisons of results obtained from both the methods have helped in the understanding of specific activity of some compounds.

Graphical Abstract

Molecular modeling studies of 1,3,4-oxadiazoles containing substituted phenoxy fragments as enoyl ACP reductase inhibitors Database alignment for enoyl ACP reductase inhibitors.