Hijacking the cellular protein degradation system offers unique opportunities for drug discovery, as exemplified by proteolysis targeting chimeras. Despite their great promise for medical chemistry, it has so far not been possible to reprogram the bacterial degradation machinery to interfere with microbial infections. In the recent years, we developed small-molecule degraders, so-called BacPROTACs, that bind to the substrate receptor of the ClpC:ClpP protease, priming neo-substrates for degradation. In addition to their targeting function, BacPROTACs activate ClpC, transforming the resting unfoldase into its functional state. Drug susceptibility and degradation assays performed in mycobacteria demonstrate in vivo activity of BacPROTACs, allowing selective targeting of endogenous proteins via fusion to an established degron.
In parallel, we characterized the mechanism of the antibiotics cyclomarin A and ecumicin, targeting the ClpC:ClpP system. Our studies revealed two small Clp proteins as scavenger proteins that buffer the amount of antibiotics. To overcome this protection system, we developed a BacPROTAC that induces degradation of ClpC together with its caretaker. The dual Clp degrader, built from linked cyclomarin A heads, was highly efficient in killing pathogenic Mycobacterium tuberculosis, being >100-fold more potent than the parent antibiotic. In sum, our data reveal Clp scavenger proteins as important components of the bacterial stress response and highlight the potential of BacPROTACs as future antibiotics.