Pharmacophore modelling, QSAR study, molecular docking and insilico ADME prediction of 1,2,3-triazole and pyrazolopyridones as DprE1 inhibitor antitubercular agents

Abstract

Tuberculosis (TB) is a chronic lung infected airborne disease caused by Mycobacterium tuberculosis (MTB). The development of resistance towards available antitubercular agents leads to the discovery of new drugs for treatment against these resistant bacteria. Decaprenyl phosphoryl-β-D-Ribose 20-epimerase (DprE1) is a vulnerable target for the design of antitubercular agents which are more acting against multidrug resistant bacterial pathogens. DprE1 is an oxidase involved in the synthesis of arabinogalactan. Inhibition of DprE1 leads to blocking off cell wall synthesis, causing the death of the bacteria. A series of 50 DprE1 inhibitors having activity were subjected to 2D, 3D QSAR, Pharmacophore Modeling, Molecular Docking and in silico ADME studies. Prediction of preliminary Pharmacokinetic and the Drug Likeliness profile was performed for these compounds by in silico ADME study. 2D-QSAR and 3D- QSAR models developed by Partial Least Square associated with the Sphere Exclusion method (PLS-SE) and StepWise variable selection method (SW-kNN MFA) based on k- Nearest Neighbor technique are more significant which have cross-validated squared correlation coefficient (q2), coefficient of determination (r2), Fisher ratio (F) values as 0.7499, 0.8917 and 85.04 and the internal (q2 = 0.8198), external (pred_r2 = 0.6109) model validation correctly predicts activity ~ 81% and ~ 61% for the training and test set, respectively. Pharmacophore model was developed with two aromatic regions (Aro), one aliphatic (Ala) and one hydrogen donor (HDr). Docking studies of the selected inhibitors with the active site of DprE1 enzyme showed hydrogen bond interaction with Gly-116, His-131, Arg-118, Thr-117 and Gln-299 residues present at the active site. The results of the present work provide more useful information and important structural insights for designing DprE1 inhibitors with much more enhanced potency.