2. Academic Validation
  3. Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival

Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival

  • Cell. 2023 Apr 27;S0092-8674(23)00404-X. doi: 10.1016/j.cell.2023.04.009.
David M Hoi 1,  Sabryna Junker 2,  Lukas Junk 3,  Kristin Schwechel 4,  Katharina Fischel 5,  David Podlesainski 6,  Paige M E Hawkins 7,  Lasse van Geelen 4,  Farnusch Kaschani 6,  Julia Leodolter 2,  Francesca Ester Morreale 2,  Stefan Kleine 6,  Somraj Guha 8,  Klaus Rumpel 5,  Volker M Schmiedel 5,  Harald Weinstabl 5,  Anton Meinhart 2,  Richard J Payne 7,  Markus Kaiser 6,  Markus Hartl 9,  Guido Boehmelt 5,  Uli Kazmaier 10,  Rainer Kalscheuer 4,  Tim Clausen 11
Affiliations

Affiliations

  • 1 Research Institute of Molecular Pathology, Vienna BioCenter, 1030 Vienna, Austria; Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria; University of Vienna, Center for Molecular Biology, Department for Biochemistry and Cell Biology, 1030 Vienna, Austria.
  • 2 Research Institute of Molecular Pathology, Vienna BioCenter, 1030 Vienna, Austria.
  • 3 Saarland University, Organic Chemistry I, 66123 Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany. Electronic address: lukas.junk@helmholtz-hips.de.
  • 4 Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Düsseldorf, Germany.
  • 5 Boehringer Ingelheim RCV GmbH & Co KG, 1120 Vienna, Austria.
  • 6 University of Duisburg-Essen, Center of Medical Biotechnology, Faculty of Biology, 45141 Essen, Germany.
  • 7 School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, NSW 2006, Australia.
  • 8 Saarland University, Organic Chemistry I, 66123 Saarbrücken, Germany.
  • 9 Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria; University of Vienna, Center for Molecular Biology, Department for Biochemistry and Cell Biology, 1030 Vienna, Austria.
  • 10 Saarland University, Organic Chemistry I, 66123 Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany.
  • 11 Research Institute of Molecular Pathology, Vienna BioCenter, 1030 Vienna, Austria; Medical University of Vienna, 1030 Vienna, Austria. Electronic address: tim.clausen@imp.ac.at.
PMID: 37137307 DOI: 10.1016/j.cell.2023.04.009
Abstract

The ClpC1:ClpP1P2 Protease is a core component of the proteostasis system in mycobacteria. To improve the efficacy of antitubercular agents targeting the Clp Protease, we characterized the mechanism of the Antibiotics cyclomarin A and ecumicin. Quantitative proteomics revealed that the Antibiotics cause massive proteome imbalances, including upregulation of two unannotated yet conserved stress response factors, ClpC2 and ClpC3. These proteins likely protect the Clp Protease from excessive amounts of misfolded proteins or from cyclomarin A, which we show to mimic damaged proteins. To overcome the Clp security system, we developed a BacPROTAC that induces degradation of ClpC1 together with its ClpC2 caretaker. The dual Clp degrader, built from linked cyclomarin A heads, was highly efficient in killing pathogenic Mycobacterium tuberculosis, with >100-fold increased potency over the parent Antibiotic. Together, our data reveal Clp scavenger proteins as important proteostasis safeguards and highlight the potential of BacPROTACs as future Antibiotics.

Keywords

BacPROTAC; Clp protease; ClpC1; Mycobacterium tuberculosis; antibiotics; cyclomarin A; ecumicin; protein quality control; small-molecule degrader; targeted protein degradation.

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