Shan Gao, Fangyu Wu, Yifan Zhang, Sarah M Batt, Chuancun Wei, Zeyu Wang, Xiuna Yang, Katherine A Abrahams, Klaus Fütterer, Xinliang Liu, Ping Wang, Gurdyal S Besra, Zihe Rao, Lu Zhang
Pretomanid and delamanid are prodrugs, whose active derivatives have been reported to target decaprenylphosphoribose-2'-reductase, DprE2, while quabodepistat is a noncovalent inhibitor of decaprenylphosphoribose-2'-oxidase, DprE1. Both enzymes are involved in Mycobacterium tuberculosis cell wall synthesis, but the mechanism of the DprE1-DprE2 epimerase complex and its inhibition by these compounds remain unclear. We report cryo-EM structures of the M. tuberculosis DprE1-DprE2 complex bound with either substrate or quabodepistat in DprE1, and with either activated pretomanid or delamanid in DprE2, respectively. DprE1-DprE2 assembles as a membrane-associated tetramer of a DprE2 dimer flanked on each side by a DprE1 subunit. Both pretomanid and delamanid bind to DprE2 in an NADH-adduct form and within a conserved binding pocket that extends from the NADH-binding site to the substrate-binding site. Quabodepistat binds to DprE1 with a unique mode. Our data reveal the mode of action of these drugs, allowing rational design of new derivatives for improved tuberculosis treatments.