Khandelwal Nitesh Kumar, Gupta Meghna, Gomez James E, Barkho Sulyman, Guan Ziqiang, Eng Ashley Y, Kawate Tomohiko, Balasubramani Sree Ganesh, Sali Andrej, Hung Deborah T, Stroud Robert M
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA.
Nat Commun. 2025 Apr 1;16(1):3139. doi: 10.1038/s41467-025-58133-6.
A broad chemical genetic screen in Mycobacterium tuberculosis (Mtb) identified compounds (BRD-8000.3 and BRD-9327) that inhibit the essential efflux pump EfpA. To understand the mechanisms of inhibition, we determined the structures of EfpA with these inhibitors bound at 2.7-3.4 Å resolution. Our structures reveal different mechanisms of inhibition by the two inhibitors. BRD-8000.3 binds in a tunnel contacting the lipid bilayer and extending toward the central cavity to displace the fatty acid chain of a lipid molecule bound in the apo structure, suggesting its blocking of an access route for a natural lipidic substrate. Meanwhile, BRD-9327 binds in the outer vestibule without complete blockade of the substrate path to the outside, suggesting its possible inhibition of the movement necessary for alternate access of the transporter. Our results show EfpA as a potential lipid transporter, explain the basis of the synergy of these inhibitors and their potential for combination anti-tuberculosis therapy.
在结核分枝杆菌（Mtb）中进行的一项广泛的化学遗传学筛选鉴定出了抑制必需外排泵EfpA的化合物（BRD - 8000.3和BRD - 9327）。为了解抑制机制，我们确定了与这些抑制剂结合的EfpA的结构，分辨率为2.7 - 3.4Å。我们的结构揭示了这两种抑制剂不同的抑制机制。BRD - 8000.3结合在一个与脂质双层接触并向中央腔延伸的通道中，取代了apo结构中结合的脂质分子的脂肪酸链，这表明它阻断了天然脂质底物的进入途径。同时，BRD - 9327结合在外前庭，并未完全阻断底物通向外部的路径，这表明它可能抑制了转运体交替进入所需的运动。我们的结果表明EfpA是一种潜在的脂质转运体，解释了这些抑制剂协同作用的基础及其在联合抗结核治疗中的潜力。
