Lysine-targeting, Covalent Inhibitors of Bromodomain BD1 of BET Proteins in Live Cells and Animals

The bromodomain extra-terminal (BET) family of proteins are valuable therapeutic targets for cancer and other diseases. The adverse events of current pan-BET inhibitors (BETi) make the development of BET BD1- or BD2-selective inhibitors as a fresh avenue to overcome safety challenges. On the basis of various lysine-reactive covalent warheads, herein we report a set of activity-based probes (ABPs; P3-P7) capable of global profiling of ligandable lysines within bromodomains (BRDs) in live cells and animals. Chemoproteomic experiments with P7 which utilizes 2-ethynylbenzaldehyde (EBA) identified 16 endogenous BRDs, thus giving a global landscape of ligandable lysines in BRDs. By further introducing EBA and salicylaldehyde into PLX51107 (a noncovalent BETi), we generated lysine-reactive, irreversible (BDS1-4) and reversible (BDS5-6) BD1 covalent inhibitors. Mass spectrometry and X-ray crystallography confirmed the successful covalent engagement between EBA and K91 near the acetylated lysine (Kac)-binding site of BD1 in BRD4. BDS4 showed 104-fold selectivity for BD1 over BD2 with prolonged anticancer effects. Importantly, BDS4 retained robust activity against fibrosis in cells and animals when compared to RVX-208 (a reported BD2-selective noncovalent inhibitor) which showed only marginal effects. Our work serves as a useful tool to delineate distinct functions of BD1 and BD2 in future studies.