Improved Phenoxyalkylbenzimidazoles with Activity against Mycobacterium tuberculosis Appear to Target QcrB

Abstract

The phenoxy alkyl benzimidazoles (PABs) have good antitubercular activity. We expanded our structure–activity relationship studies to determine the core components of PABs required for activity. The most potent compounds had minimum inhibitory concentrations against Mycobacterium tuberculosis in the low nanomolar range with very little cytotoxicity against eukaryotic cells as well as activity against intracellular bacteria. We isolated resistant mutants against PAB compounds, which had mutations in either Rv1339, of unknown function, or qcrB, a component of the cytochrome bc1 oxidase of the electron transport chain. QcrB mutant strains were resistant to all PAB compounds, whereas Rv1339 mutant strains were only resistant to a subset, suggesting that QcrB is the target. The discovery of the target for PAB compounds will allow for the improved design of novel compounds to target intracellular M. tuberculosis.

Oxidative Phosphorylation—an Update on a New, Essential Target Space for Drug Discovery in Mycobacterium tuberculosis

“…The Qp site of the Cyt-bcc-aa3 complex is particularly susceptible to chemical inhibition, as evident from the multitude of structurally diverse and distinct compounds detailed above. It has been consistently observed across several of the studies that characteristic consequences of cytochrome bcc inhibition include a general depletion of intracellular bacterial ATP levels, an upregulation of Cyt-bd oxidase, and an increase in OCR and bacterial respiration due to Cyt-bd [12,76,77,[128][129][130]134,135,155,158]. This compensation by the alternate terminal oxidase leads to an incomplete respiratory shutdown in M. tb, resulting in the bacteriostatic nature of cytochrome bcc inhibitors alone.…”

“…The phenoxyalkylbenzimidazole (PAB) series, with an excellent growth-inhibitory potency and low cytotoxicity, is another promising QcrB inhibitor [130,153]. The lead compound, 54, demonstrated good efficacy against intracellular M. tb.…”

“…Resistant mutants to PAB isolated in M. tb revealed mutations in qcrB and rv1339, a gene of unknown function. Through additional cross-resistance studies, QcrB was implicated as the main target [130]. The mutations identified in QcrB were A179P, M342T, W312C, and W312G, residues of the Qp binding site.…”

“…However, this antagonistic effect disappeared within three weeks, with PAB-BDQ combinations becoming highly bactericidal [195]. The specificity of the PAB series needs to be further studied since it kills nutrient-starved M. tb while remaining bacteriostatic against replicating mycobacteria, a property not shared with other specific Cyt-bcc inhibitors [130,153]. A MenA inhibitor, NM-4, was synergistic even at low doses together with sub-bactericidal concentrations of BDQ, CFZ, and the QcrB inhibitor ND-10885 [196], causing enhanced and efficient killing of M. tb in a time-kill curve assay [117].…”

Intracellular and in vivo evaluation of imidazo[2,1-b]thiazole-5-carboxamide anti-tuberculosis compounds

“…The IPAs, including Q203 (1, Fig 1), target the electron transport chain, specifically at QcrB, a component of the terminal cytochrome oxidase [16,17]. Various scaffolds have emerged that target QcrB (Fig 1) [ [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31], two classes, imidazo[2,1-b]thiazole-5-carboxamides (ITAs) (2) [26][27][28] and pyrazolo [1,5-a] pyridine-3-carboxamides (3) [28][29][30][31], bear the greatest structural homology and potency relative to the IPAs (Fig 1). We have disclosed the impressive in vitro properties of various ITAs, including low nanomolar potency against replicating and drug-resistant Mtb strains and low cyctotoxicity [26,27], as exemplified by ND-11543 (2).…”