Mutations in rv0678 Confer Low-Level Resistance to Benzothiazinone DprE1 Inhibitors in Mycobacterium tuberculosis

Tuberculosis (TB) is the leading cause of death from any bacterial infection, causing 1.5 million deaths worldwide each year. Due to the emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) there have been significant efforts aimed at developing novel drugs to treat TB. One promising drug target in Mtb is the arabinogalactan biosynthetic enzyme DprE1, and there have been over a dozen unique chemical scaffolds identified which inhibit the activity of this protein. Among the most promising lead compounds are the benzothiazinones BTZ043 and PBTZ169, both of which are currently in or have completed phase IIa clinical trials. Due to the potential clinical utility of these drugs, we sought to identify potential synergistic interactions and new mechanisms of resistance using a genome-scale CRISPRi chemical-genetic screen with PBTZ169. We found that knockdown of rv0678, the negative regulator of the mmpS5/L5 drug efflux pump, confers resistance to PBTZ169. Mutations in rv0678 are the most common form of resistance to bedaquiline and there is already abundant evidence of these mutations emerging in bedaquiline-treated patients. We confirmed that rv0678 mutations from clinical isolates confer low level cross-resistance to BTZ043 and PBTZ169. While it is yet unclear whether rv0678 mutations would render benzothiazinones ineffective in treating TB, these results highlight the importance of monitoring for clinically prevalent rv0678 mutations during ongoing BTZ043 and PBTZ169 clinical trials.

Automated summary

Tuberculosis is a fatal bacterial infection, causing 1.5 million deaths globally each year. Drug-resistant strains of Mycobacterium tuberculosis (Mtb) have emerged, leading to efforts in developing novel drugs. The arabinogalactan biosynthetic enzyme DprE1 in Mtb is a promising drug target, with over a dozen inhibitory compounds identified. Among them, BTZ043 and PBTZ169 have shown promise and are in clinical trials. A study using CRISPRi chemical-genetic screen with PBTZ169 identified rv0678 as a negative regulator of the mmpS5/L5 drug efflux pump, which confers resistance to PBTZ169. Mutations in rv0678 are associated with resistance to another drug, bedaquiline. These results highlight the importance of monitoring for rv0678 mutations in ongoing clinical trials of BTZ043 and PBTZ169.