Cryo-EM structure and resistance landscape of M. tuberculosis MmpL3: An emergent therapeutic target

Abstract

Highlights d Cryo-EM structure of M. tuberculosis MmpL3 determined at 3.0 Å resolution d An LMNG molecule within the periplasmic cavity suggests the TMM export pathway d Comprehensive structural mapping of resistance-conferring MmpL3 variants d Genome-mined MmpL3 mutations indicate minimal preexisting resistance

MmpL3, the trehalose monomycolate transporter, is stable in solution in several detergents and can be reconstituted into peptidiscs

“…MmpL3 inhibitors bind to the transmembrane domains (TM) of MmpL3 and are likely to block the proton relay and thus the TMM transport [14,18,19,21,23,24]. The mechanism of MmpL3-dependent transport of TMM and the mode of action of the inhibitors are still difficult to apprehend, mainly because of the absence of an in vitro transport assay.…”

“…In the studies describing MmpL3 crystal structures, both M. smegmatis [19] and E. coli [17] were used to produce recombinant MmpL3. Furthermore, MmpL3 purification was achieved using n-Dodecyl-ß-d-Maltopyranoside (DDM) for MmpL3Msm and Lauryl Maltose Neopentyl Glycol (LMNG) for MmpL3Mtb [21] as detergents. The present study was undertaken to expand the repertoire of useful detergent(s) to extract, purify and stabilize MmpL3Msm, particularly warranted to further decipher the biological/biochemical function of MmpL3 and for subsequent structural investigations.…”

“…The presence of the C-terminal domain predicted to be flexible and not folded is not conserved in all MmpL3 orthologues and is dispensable for TMM transport [16]. The monomeric state of MmpL3 was further confirmed by the cryo-electron microscopy (Cryo-EM) structure of MmpL3 from Mycobacterium tuberculosis (MmpL3Mtb) [21]. A detailed study combining crystal and Cryo-EM structures of MmpL3Msm and including the cryogenic structure of MmpL3Msm bound to TMM has brought important structural elements with respect to the TMM transport mechanism [22].…”

Molecular insights into Mmpl3 lead to the development of novel indole-2-carboxamides as antitubercular agents

“…A Cryogenic electron microscopy (Cryo-EM) structure of Mycobacterium tuberculosis Mmpl3 (PDB ID ) was reported recently by Adams et al 19 Although the resolution of the structure had an acceptable value of 3 Å, one of the major issues we faced with the structure was defining the binding site space for our molecules of interest. As the reported structure was not in a ligand bound state, the known binding residues were used to define the binding site.…”

Structural Rigidification of N-Aryl-pyrroles into Indoles Active against Intracellular and Drug-Resistant Mycobacteria

“…The N -substituted indoles were docked into a Mtb MmpL3 homology model ,, and their binding poses were compared to those of pyrrole 2 and SQ109 (a comparison of the best-scoring binding poses of both SQ109 and 7j is reported in Figure S1, while the best scoring binding poses of 5f , 7a , 7h , and 7m are reported in Figure S3). The molecular docking study suggested that the introduction of lipophilic aliphatic groups of varying sizes at the N1 position could lead to a better interaction of the compounds with the hydrophobic binding pocket of MmpL3 (Figure ).…”