BacPROTACs mediate targeted protein degradation in bacteria

Abstract

Hijacking the cellular protein degradation system offers unique opportunities for drug discovery, as exemplified by proteolysis targeting chimeras (PROTACs). Despite their superior properties over classical inhibitors, it has so far not been possible to reprogram the bacterial degradation machinery to interfere with microbial infections. Here, we develop 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. The induced higher-order oligomer was visualized by cryo-EM analysis, providing a structural snapshot of activated ClpC unfolding a protein substrate. Finally, degradation assays performed in mycobacteria demonstrate in vivo activity of BacPROTACs, highlighting the potential of the technology to provide next generation antibiotics.

Targeted protein degradation: from small molecules to complex organelles—a Keystone Symposia report

“…bacPROTACs can, therefore, bring novel substrates to ClpCP and induce their degradation. Clausen's group has conducted proof‐of‐principle studies of bacPROTACs in vitro and in vivo 24 . They hope that bacPROTACs may represent a novel, broadly applicable antibiotic strategy.…”

“…Clausen's group has conducted proof-of-principle studies of bacPROTACs in vitro and in vivo. 24 They hope that bacPROTACs may represent a novel, broadly applicable antibiotic strategy.…”

Prospects for Antibacterial Discovery and Development

“…For example, cyclomarin A ( 18 ) activates ATPase activity, leading to cell death by uncontrolled protein degradation, while acyl-depsipeptides such as 19 (ADEPs) achieve the same goal through allosteric activation of ClpP. , While neither is a viable class of lead molecules unto themselves ( 18 depends upon the reactivity of an electrophilic epoxide, whereas naturally occurring 19 has poor aqueous solubility and high clearance), these molecules set the stage for a more expansive approach toward medicinal lead identification against this target family. , A particularly intriguing mode of action might involve borrowing a page from proteolysis-targeting chimeras (PROTACS), bifunctional small molecules that facilitate the degradation of specific proteins in eukaryotes . The Clp protease system could be analogously hijacked through the engineering of chimeric molecules that target proteolysis of specific proteins in bacteria . One example of a target protein is FtsZ, discussed below.…”

Targeted protein degradation at the host–pathogen interface

“…Further developed, this strategy could be used to eliminate certain virulence proteins and lead to the development of novel antibiotics (Morreale et al, 2021).…”

“…PROTAC-mediated degradation of pathogenic proteins and their subsequent presentation on the cell surface via MHC proteins could stimulate a potent immune response leading to specifically enhanced T-cell response against infected cells during overwhelming infections, cell death, and immune-mediated elimination of the pathogen. The demonstrated capability of PROTACs to induce MHC presentation of POIderived peptides (Jensen et al, 2018) Next-generation antibiotics and antiparasitic molecules can be generated through the novel mode of action provided by TPD in pathogens through hijacking the pathogens' own proteasomal machinery, as highlighted by BacPROTACs (Morreale et al, 2021).…”