Abstract

PROteolysis TArgeting Chimeras (PROTACs) are bifunctional molecules that induce target protein degradation by engaging the intracellular proteosomes and have attracted great attention for their potential to tackle targets considered undruggable and difficult to modulate with conventional small molecules. However, as for any new technology, new challenges can arise, one of them being the ability to identify and investigate clinical safety risks. Here we explore the use of Cell Painting, an unbiased, multiplexed high-content image-based assay, to identify phenotypic signatures of PROTACs and perform computational prediction of toxicity. In this study, we have tested 341 PROTACs and 149 non-PROTACs compounds (small molecule inhibitors, E3 ligase ligands, reference compounds with know mitotoxicity) directed at more than 15 different targets. Our data suggest that clustering of PROTACs based on phenotypic similarity and the use of phenotypic profiles for mitotoxicity prediction can provide insights on their mechanism of action and safety assessment.