2D-QSAR modeling and two-fold classification of 1,2,4-triazole derivatives for antitubercular potency against the dormant stage of Mycobacterium tuberculosis

Abstract

The dormant or latent form of Mycobacterium tuberculosis (MTB) is not killed by the conventional antitubercular drugs. The treatment of latent TB is essential to reduce the period of treatment as well as incidences of drug resistance. In this background, we have made an attempt to develop the quantitative structure-activity relationship models (QSAR: regression and classification based) against the dormant form of MTB and later used the developed classifier models (linear discriminant analysis (LDA) and random forest (RF)) for the two-fold classifications. The logic of applying this concept of two-fold classification for the MTB modeling is to increase the confidence of correct classification. The 2D-QSAR modeling suggested the contribution of burden eigen, edge adjacency, van der Waals (vdW) surface area, topological charge, and pharmacophoric indices in predicting the antitubercular activity against the dormant MTB. The prediction qualities of the training and test sets were found to be moderate and good, according to the mean absolute error (MAE)-based criteria's. The LDA and RF models unveiled the importance of burden eigen, edge adjacency, Geary autocorrelation, and drug-like indices as discriminating features to differentiate the antitubercular compounds into higher and lower active groups. The LDA model showed the classification accuracies of 85.14% and 87.10% for the training and test sets, while the RF model exhibited the accuracies of 100.00% and 80.65% for both the sets. The descriptors selected in the final models are only two-dimensional (2D), which are easy to compute and does not require computationally expensive steps of structure conversion, optimization, and energy minimization mandatorily needed before the computation of 3D descriptors. These models could be used for identifying and selection of higher active compounds against the dormant form of the MTB.

Keywords: Classification models; Dormant TB; Linear discriminant analysis (LDA); Mycobacterium tuberculosis (MTB); Nonlinear modeling; QSAR; Random forest (RF).