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Chemical Inactivation of the E3 Ubiquitin Ligase Cereblon by Pomalidomide-based Homo-PROTACs
Published on: May 15, 2019
Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival
David M Hoi1, Sabryna Junker2, Lukas Junk3
1Research 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.
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.
Insights
New antitubercular agents, BacPROTACs, target the Clp protease system in Mycobacterium tuberculosis. These agents degrade ClpC1 and ClpC2, showing over 100-fold increased potency against tuberculosis.
Area of Science:
- Microbiology
- Molecular Biology
- Drug Discovery
Background:
- The ClpC1:ClpP1P2 protease is crucial for maintaining protein homeostasis (proteostasis) in mycobacteria.
- Existing antitubercular drugs targeting the Clp protease have limited efficacy.
- Mycobacteria possess stress response factors that may confer resistance.
Purpose of the Study:
- To elucidate the mechanism of action for cyclomarin A and ecumicin, antitubercular antibiotics.
- To investigate the role of newly identified stress response factors, ClpC2 and ClpC3.
- To develop novel therapeutic strategies overcoming bacterial resistance mechanisms.
Main Methods:
- Quantitative proteomics to analyze proteome-wide changes induced by antibiotics.
- Biochemical assays to characterize antibiotic mechanisms and protein interactions.
- Development and testing of a novel bifunctional degrader (BacPROTAC).
Main Results:
- Cyclomarin A and ecumicin induce significant proteome imbalances and upregulate ClpC2 and ClpC3.
- ClpC2 and ClpC3 act as protective factors for the Clp protease against antibiotic stress.
- A novel BacPROTAC targeting both ClpC1 and ClpC2 demonstrated >100-fold enhanced potency against Mycobacterium tuberculosis.
Conclusions:
- Clp scavenger proteins (ClpC2, ClpC3) are vital safeguards of the mycobacterial proteostasis network.
- BacPROTACs represent a promising new class of antibiotics with enhanced efficacy against pathogenic mycobacteria.
- Targeting bacterial resistance mechanisms through protein degradation offers a viable strategy for future drug development.
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