Molecular Modeling of Enoyl Acyl Carrier Protein Reductase Inhibitors for Mycobacterium tuberculosis and their Pharmacokinetic Predictions

Abstract

Tuberculosis (TB) is a deep public health concern worldwide worsened by reported multi drugresistant (MDR) and extensively drug- resistant (XDR) stralins of Mycobacterium tuberculosis, the causative agent of the disease. A new class of thiadiazole inhibitors were reported to inhibit the enoyl-acyl transporter protein reductase (InhA) of Mycobacterium tuberculosis (MTb). We performed here the computer-aided molecular design of novel thiadiazole (TDZ) inhibitors of InhA by in situ modifying the reference crystal structure of (S)-1-(5-((1-(2,6-difluorobenzyl)-1 H-pyrazol-3yl)amino)-1,3,4-thiadiazol-2-yl)-1-(4-methylthiazol-2-yl)ethanol-InhA (PDB code: 4BQP). Thus a training set of 15 hybrids with known inhibition potency \(\left(\mathrm{IC}_{50}^{\exp }\right)\) was selected to establish a onedescriptor quantitative structure-activity relationship (QSAR) model resulting in a linear correlation between the Gibbs free energy (GFE) during the formation of the InhA-TDZ complex and \(\mathrm{IC}_{50}^{\mathrm{exp}}\left(\mathrm{plC} \mathrm{C}_{50} \exp ==-0.29 \mathrm{x} \Delta \Delta \mathrm{G}_{\mathrm{com}}+8.13 ; \mathrm{n}=15 ; \mathrm{R}^2=0.92, \mathrm{R}^2{ }_{\mathrm{xv}}=0.91 ;\right.\) F-test of \(142.6 ; \sigma=0.21 ; \alpha>\) \(\left.95 \% ; R^2-R_{x v}^2=0.01\right)\). The 3D pharmacophore model \((\mathrm{PH} 4)\) generated from the active conformations of TDZs ( \(\mathrm{pIC}_{50}^{\mathrm{exp}}=0.93 \times \mathrm{pIC}_{50}^{\text {pred }}+0.47 ; \mathrm{n}=15 ; \mathrm{R}^2=0.97 ; \mathrm{R}_{\mathrm{xv}}=0.94 ;\) F-test of \(215.45 ; \sigma=0.17 ; \alpha>98 \% ; R^2-R_{x v}^2=0.03\) ) served as a virtual screening tool for new analogs from a virtual library (VL). The combination of molecular modeling and \(\mathrm{PH} 4\) in silico screening of (\(\mathrm{VL}\)) resulted in the identification of novel potent antitubercular agent candidates with favorable pharmacokinetic profiles of which the six best hits predicted inhibitory potencies \(\mathrm{IC}_{50}^{\text {pre }}\) in the sub nanomolar range \((0.1-0.2 \mathrm{nM})\).