Direct capture, inhibition and crystal structure of HsaD (Rv3569c) from M. tuberculosis

FEBS J. 2023 Mar;290(6):1563-1582. doi: 10.1111/febs.16645. Epub 2022 Oct 13.


A hallmark of Mycobacterium tuberculosis (M. tb), the aetiologic agent of tuberculosis, is its ability to metabolise host-derived lipids. However, the enzymes and mechanisms underlying such metabolism are still largely unknown. We previously reported that the Cyclophostin & Cyclipostins (CyC) analogues, a new family of potent antimycobacterial molecules, react specifically and covalently with (Ser/Cys)-based enzymes mostly involved in bacterial lipid metabolism. Here, we report the synthesis of new CyC alkyne-containing inhibitors (CyCyne ) and their use for the direct fishing of target proteins in M. tb culture via bio-orthogonal click-chemistry activity-based protein profiling (CC-ABPP). This approach led to the capture and identification of a variety of enzymes, and many of them involved in lipid or steroid metabolisms. One of the captured enzymes, HsaD (Rv3569c), is required for the survival of M. tb within macrophages and is thus a potential therapeutic target. This prompted us to further explore and validate, through a combination of biochemical and structural approaches, the specificity of HsaD inhibition by the CyC analogues. We confirmed that the CyC bind covalently to the catalytic Ser114 residue, leading to a total loss of enzyme activity. These data were supported by the X-ray structures of four HsaD-CyC complexes, obtained at resolutions between 1.6 and 2.6 Å. The identification of mycobacterial enzymes directly captured by the CyCyne probes through CC-ABPP paves the way to better understand and potentially target key players at crucial stages of the bacilli life cycle.

Keywords: Cyclipostins & Cyclophostin; activity-based protein profiling; anti-tuberculous molecules; cholesterol metabolism; inhibition mechanism.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antitubercular Agents* / chemical synthesis
  • Antitubercular Agents* / pharmacology
  • Antitubercular Agents* / therapeutic use
  • Bacterial Proteins* / antagonists & inhibitors
  • Bacterial Proteins* / chemistry
  • Computer Simulation
  • Crystallography, X-Ray
  • Humans
  • Hydrolases* / antagonists & inhibitors
  • Hydrolases* / chemistry
  • Macrophages / microbiology
  • Molecular Docking Simulation*
  • Mycobacterium tuberculosis* / drug effects
  • Mycobacterium tuberculosis* / enzymology
  • Organophosphorus Compounds* / chemistry
  • Tuberculosis / drug therapy


  • Antitubercular Agents
  • HsaD protein, Mycobacterium tuberculosis
  • Bacterial Proteins
  • cyclophostin
  • Organophosphorus Compounds
  • Hydrolases