Crystal structures of DCAF1-PROTAC-WDR5 ternary complexes provide insight into DCAF1 substrate specificity

Abstract

Proteolysis-targeting chimeras (PROTACs) have been explored for the degradation of drug targets, particularly undruggable proteins, for more than two decades. They have been employed by various groups successfully, however only a handful of E3 ligase substrate receptors such as CRBN, VHL, MDM2, and IAP have been efficiently used. Downregulation and mutation of these receptors would reduce the effectiveness of PROTACs, thus necessitating the addition of new substrate receptors and E3 ligases to the repertoire to avoid resistance. We recently developed potent ligands for DCAF1, a substrate receptor of EDVP and CUL4 E3 ligases with diverse substrate specificity. Here, we focused on DCAF1 toward the development of PROTACs for WDR5, a drug target in various cancers. We report three DCAF1-based PROTACs with endogenous and exogenous WDR5 degradation effects and solved the first high-resolution crystal structures of DCAF1-PROTAC-WDR5 ternary complexes. The structures reveal detailed insights into the interaction of DCAF1 with various WDR5-PROTACs, including the finding that PROTACs can compress like a spring to similar effective lengths to keep DCAF1 and WDR5 within interaction distance of each other. Furthermore, specific DCAF1 loops play a significant role in providing surface plasticity needed to interact with different PROTAC-WDR5 complexes, reflecting the mechanism by which DCAF1 functions as a substrate receptor for E3 ligases with diverse sets of substrates.