2. Academic Validation
  3. Structure and inhibition mechanisms of Mycobacterium tuberculosis essential transporter efflux protein A

Structure and inhibition mechanisms of Mycobacterium tuberculosis essential transporter efflux protein A

  • Nat Commun. 2025 Apr 1;16(1):3139. doi: 10.1038/s41467-025-58133-6.
Nitesh Kumar Khandelwal # 1 2,  Meghna Gupta # 1 2,  James E Gomez 3,  Sulyman Barkho 3,  Ziqiang Guan 4,  Ashley Y Eng 3,  Tomohiko Kawate 3,  Sree Ganesh Balasubramani 5,  Andrej Sali 5,  Deborah T Hung 6 7 8,  Robert M Stroud 9
Affiliations

Affiliations

  • 1 Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
  • 2 Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA.
  • 3 Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • 4 Department of Biochemistry, Duke University Medical Center, Durham, NC, USA.
  • 5 Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
  • 6 Broad Institute of MIT and Harvard, Cambridge, MA, USA. hung@molbio.mgh.harvard.edu.
  • 7 Department of Genetics, Harvard Medical School, Boston, MA, USA. hung@molbio.mgh.harvard.edu.
  • 8 Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA. hung@molbio.mgh.harvard.edu.
  • 9 Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA. stroud@msg.ucsf.edu.
  • # Contributed equally.
PMID: 40169593 DOI: 10.1038/s41467-025-58133-6
Abstract

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.

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