In silico-based high-throughput screen for discovery of novel combinations for tuberculosis treatment

Abstract

There are currently 18 drug classes for the treatment of tuberculosis, including those in the development pipeline. An in silico simulation enabled combing the innumerably large search space to derive multidrug combinations. Through the use of ordinary differential equations (ODE), we constructed an in silico kinetic platform in which the major metabolic pathways in Mycobacterium tuberculosis and the mechanisms of the antituberculosis drugs were integrated into a virtual proteome. The optimized model was used to evaluate 816 triplets from the set of 18 drugs. The experimentally derived cumulative fractional inhibitory concentration (∑FIC) value was within twofold of the model prediction. Bacterial enumeration revealed that a significant number of combinations that were synergistic for growth inhibition were also synergistic for bactericidal effect. The in silico-based screen provided new starting points for testing in a mouse model of tuberculosis, in which two novel triplets and five novel quartets were significantly superior to the reference drug triplet of isoniazid, rifampin, and ethambutol (HRE) or the quartet of HRE plus pyrazinamide (HREZ).

FIG 1

Correlation of FIC results from in silico versus in vitro studies. (A) 2-D combination studies; 65 doublets were analyzed. (B). 3-D combination studies; 51 triplets were analyzed. The experimental values were within twofold of the predicted value.

FIG 2

In vivo efficacy of triplets and quartets in a chronic model of tuberculosis in BALB/c mice following aerosol infection. LOQ, limit of quantitation (30 CFU/ml of lung homogenate).

FIG 3

In vitro-in vivo correlation of bactericidal effect of combinations. The maximum ΔLog₁₀ CFU/ml achieved with each drug concentration that was not greater than 0.5 FIC, i.e., 1/2 MIC, in the combination from the in vitro experiment (see Table S4 in the supplemental material) was plotted against the ΔLog₁₀ CFU/lung from the in vivo experiment.