A high-throughput screen against pantothenate synthetase (PanC) identifies 3-biphenyl-4-cyanopyrrole-2-carboxylic acids as a new class of inhibitor with activity against Mycobacterium tuberculosis

Abstract

The enzyme pantothenate synthetase, PanC, is an attractive drug target in Mycobacterium tuberculosis. It is essential for the in vitro growth of M. tuberculosis and for survival of the bacteria in the mouse model of infection. PanC is absent from mammals. We developed an enzyme-based assay to identify inhibitors of PanC, optimized it for high-throughput screening, and tested a large and diverse library of compounds for activity. Two compounds belonging to the same chemical class of 3-biphenyl-4- cyanopyrrole-2-carboxylic acids had activity against the purified recombinant protein, and also inhibited growth of live M. tuberculosis in manner consistent with PanC inhibition. Thus we have identified a new class of PanC inhibitors with whole cell activity that can be further developed.

Figure 1. Single-time point fluorescence assay for PanC.

A) Reaction schematic. Upper panel shows the reaction catalyzed by PanC and the enzyme cascade that is initiated by the reaction product AMP resulting in βNADH oxidation. Lower panel shows the final βNADH dependent fluorescence generating reaction that is coupled to the PanC-initiated enzyme cascade. B) Low-throughput assay: kinetic reaction monitoring the rate of βNADH oxidation. C) High-throughput assay: fluorescent resorufin signal generated by residual βNADH following the PanC initiated enzyme cascade. D) Fluorescence generated with varied βNADH in solution using the same conditions as in (B).

Figure 2. Design and implementation of HTS campaign.

A) Plate layout for 320-array with four sets of controls (n = 16 for each) in columns 1, 2, 23, and 24. B) Results from Blank Plate Validation using DMSO alone in all 320 assay wells.

Figure 3. Screening results.

A) Activity of compounds from LISSP4 (grey) and Diversity (black) libraries shown as percent inhibition against PanC_MTB. B) Concentration response curves (CRCs) for two representative hits and nafronyl oxalate. C) Structures of compound 1 and 2.

Figure 4. Biochemical characterization of Class 1 compounds.

Michaelis-Menten plots with varied concentrations of pantoate and A) compound 1 and B) compound 2. Graphpad Prism was used to fit the data to nonlinear regressions.

Figure 5. Activity against whole-cell M. tuberculosis.

Wild-type MTB (RvS; black circles), PanC conditional knockdown (PanC-TetON; white circles), and the knockdown supplemented with pantothenate (PanC-TetON+supplement; x) were grown in the presence of varied concentrations of A) compound 1 or B) compound 2. Results are the average and standard deviation of triplicates. The MIC₅₀ was determined by plotting %inhibition against compound concentration and fitting to a non-linear curve with Graphpad Prism™.