Crystal structure of the Mycobacterium tuberculosis VirS regulator reveals its interaction with the lead compound SMARt751

Tuberculosis (TB) persists as one of the world's deadliest infectious diseases, claiming the lives of 1.6 million people in 2021 (World Health Organization, 2022). It is noteworthy that TB stands as one of the oldest infectious diseases to afflict humanity, a fact substantiated by numerous paleopathology studies (Donoghue, 2016, Buzic and Giuffra, 2020). Over the past few decades, the public health challenge posed by TB has markedly escalated due to the emergence and dissemination of strains resistant to both first-line and second-line drugs (World Health Organization, 2022). Consequently, there is an imperative need for sustained research efforts aimed at the development of new antitubercular agents and therapies.

Ethionamide (ETO) is one of the antibiotics recommended by the World Health Organization for the treatment of drug-resistant TB. Functioning as a prodrug, ETO requires bioactivation to unleash its antibacterial potential. The active form, of the antibiotic is an ETO-NAD adduct that targets the InhA protein (Banerjee et al., 1994), resulting in a potent inhibition of mycolic acid biosynthesis, the major membrane component of Mycobacterium tuberculosis (Mtb) (Wang et al., 2007, Vale et al., 2013). The mycobacterial Baeyer-Villiger monooxygenase (BVMO) EthA was the first enzyme identified as a biological activator of the prodrug ETO. The regulation of its gene expression is controlled by the transcriptional repressor EthR (Baulard et al., 2000, Engohang-Ndong et al., 2004). Various small synthetic molecules have thus been developed to thwart the binding of EthR to DNA, thereby releasing EthA production and forcing bacteria to produce the ETO-NAD active form in greater quantity (Willand et al., 2009, Tanina et al., 2019, Willand et al., 2019). Notably, the co-administration of ethionamide and the EthR ligand BDM41906 has been assessed both in vitro and in vivo, revealing the ability of this ligand to boost the antibacterial activity of ETO against Mtb (Costa-Gouveia et al., 2017, Villemagne et al., 2020).

A second pathway involved in the bioactivation of ETO has been recently unveiled (Grant et al., 2016). MymA, the pivotal enzyme of this pathway, is encoded within an operon composed of 7 genes (Rv3083-Rv3089), collectively known as the mymA operon. This operon is under the control of the AraC-like regulator VirS (Rv3082c) (Singh et al., 2003).

Concurrently, our recent drug design campaign has identified a chemical series of compounds targeting VirS (Flipo et al., 2022). The lead compound, named SMARt751, exhibits a remarkable potency to enhance the efficacy of ETO, both in vitro and in mouse models of acute and chronic TB (Flipo et al., 2022). In addition, SMARt751 has demonstrated the ability to overcome acquired resistances to ETO in clinical strains that bear mutations in ethA.

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