Development of the ULK1-Recruiting Chimeras (ULKRECs) to enable proximity-induced and ULK1-dependent degradation of mitochondria

Abstract

Targeted protein degradation (TPD) has opened new opportunities to investigate signalling pathways as a research tool, and as a unique therapeutic strategy using bifunctional chimeric small molecules, with candidate molecules in clinical trials for the treatment of breast cancer and prostate cancer. Most current TPD approaches use the 26S proteasomal machinery via PROteolysis TArgeting Chimeras (PROTACs), however, new emerging strategies using the autophagy system, termed AUtophagy TArgeting Chimeras (AUTACs) expand on the degrader arsenal and repertoire of targets that can be degraded. This includes non-protein molecules such as lipid droplets, organelles, insoluble protein aggregates as well as typical TPD targets, soluble intracellular proteins. AUTACs were proposed to operate by binding the target of interest (TOI) and linking it to an autophagy cargo protein (LC3 or p62), tethering the TOI into forming autophagosomes. In this study, we designed an alternative strategy for AUTACs, reasoning that the local recruitment and activation of ULK1 is sufficient to induce the formation of an autophagosome at the site of recruitment. As a proof of concept, we used an ULK1 agonist linked to a mitochondrial targeting ligand and termed these chimeric molecules ULK1-Recruiting Chimeras (ULKRECs). We show that local activation of ULK1 by ULKRECs at the outer mitochondrial membrane (OMM) induces mitophagy, further enhanced by mitochondrial insult. Using Parkinsons disease (PD) patient-derived fibroblasts, we show the ULKRECs induce mitophagy independently of the PRKN/PINK axis, components required to signal for canonical mitophagy in response to stressors and often dysfunctional in many neurological diseases. We propose that ULKRECs are a novel class of degraders that have potential as unique therapeutics for diseases where dysfunctional mitophagy plays a key role in disease pathology and progression.