Structure-based design of anti-mycobacterial drug leads that target the mycolic acid transporter MmpL3.

New anti-tubercular agents are urgently needed to address the emerging threat of drug resistance to human tuberculosis. Here, we have used structure-assisted methods to develop compounds that target mycobacterial membrane protein large 3 (MmpL3). MmpL3 is essential for the transport of mycolic acids, an important cell-wall component of mycobacteria. We prepared compounds that potently inhibit the growth of Mycobacterium tuberculosis (Mtb) and other mycobacteria in cell culture. The cryoelectron microscopy (cryo-EM) structure of mycobacterial MmpL3 in complex with one of these compounds (ST004) was determined using lipid nanodiscs at an overall resolution of 3.36 Å. The structure reveals the binding mode of ST004 to MmpL3, with the S4 and S5 subsites of the inhibitor-binding pocket in the proton translocation channel playing vital roles. These data are a promising starting point for the development of anti-tuberculosis drugs that target MmpL3. [Display omitted] • Compounds with antibacterial activity that target MmpL3 are reported • Compound ST004 potently inhibits the growth of Mtb as well as other mycobacteria • Cryo-EM structure of MmpL3 in complex with ST004 is determined in lipid nanodiscs • The scaffolds at the S4 and S5 subsites are important for the efficacy of the compounds MmpL3 is an important target for TB drug discovery. Hu et al. report the structure-based development of potent compounds that target MmpL3. These data are a promising starting point for the development of anti-mycobacterial drugs targeting MmpL3. [ABSTRACT FROM AUTHOR]