Functional characterization of pathway inhibitors for the ubiquitin-proteasome system (UPS) as tool compounds for CRBN and VHL-mediated targeted protein degradation

Abstract

Small molecule degraders such as PROteolysis TArgeting Chimeras (PROTACs) or molecular glues are new modalities for drug development and important tools for target validation. Both modalities recruit an E3 ubiquitin ligase to a protein of interest (POI) either via two independent, but linked ligands (PROTACs) or through binding of a small molecule that alters the E3 binding surface to recruit a neo-substrate (molecular glues). If optimized appropriately, both modalities result in the degradation of the POI. Due to the complexity of the induced multistep degradation process, controls for degrader evaluation are critical and they are commonly used in the literature. However, comparative studies and evaluation of cellular potencies of these control compounds and their appropriate uses have not been published so far. Additionally, the high diversity of mechanisms requires diverse small molecule controls to ensure appropriate inhibition of the investigated system while keeping potential cellular toxicity and unintended effects on cellular pathways as low as possible. Here, we scrutinized a diverse set of ubiquitin pathway inhibitors and evaluated their potency and utility within the CRBN and VHL mediated POI degradation pathway. We used the HiBiT system to measure the levels of target rescue after treatment with control compounds. Additionally, cell health was investigated using a multiplex high content assay. This assay panel allows us to determine non-toxic effective concentrations for control experiments and to perform rescue experiments in the absence of cellular toxicity, which has a profound effect on target degradation by ubiquitin-dependent and -independent pathways.