Structure-Guided Development of Potent Benzoylurea Inhibitors of BCL-XL and BCL-2

The BCL-2 family of proteins (including the prosurvival proteins BCL-2, BCL-X-L, and MCL-1) is an important target for the development of novel anticancer therapeutics. Despite the challenges of targeting protein-protein interaction (PPI) interfaces with small molecules, a number of inhibitors (called BH3 mimetics) have entered the clinic and the BCL-2 inhibitor, ABT-199/venetoclax, is already proving transformative. For BCL-X-L, new validated chemical series are desirable. Here, we outline the crystallography-guided development of a structurally distinct series of BCL-X-L/BCL-2 inhibitors based on a benzoylurea scaffold, originally proposed as alpha-helix mimetics. We describe structure-guided exploration of a cryptic "p5" pocket identified in BCL-X-L. This work yields novel inhibitors with submicromolar binding, with marked selectivity toward BCL-X-L. Extension into the hydrophobic p2 pocket yielded the most potent inhibitor in the series, binding strongly to BCL-X-L and BCL-2 (nanomolar-range half-maximal inhibitory concentration (IC50)) and displaying mechanism-based killing in cells engineered to depend on BCL-X-L for survival.