Development of a Lysine-Reactive Targeted Covalent Inhibitor for the P300/CBP-Associated Factor Bromodomain Through Structure-Based Design

Epigenetics is defined by changes in heritable phenotypes that do not involve a change in DNA sequence. P300/CBP-associated factor (PCAF) is an important epigenetic regulatory protein that can alter chromatin through a histone acetyltransferase domain, while also serving as an epigenetic reader through a C-terminal bromodomain. PCAF promotes the transcription of the HIV-1 genome and is implicated in the development of glioblastoma. The currently reported PCAF inhibitors are non-covalent and require high concentration to maintain target occupancy. Here, we explore a new approach using covalent inhibition. Starting with a lead scaffold (BZ1), test-molecules were rationally designed for selectively targeting PCAF by installing lysine-reactive groups onto the lead scaffold to enable covalent bond formation with the nonconserved lysine residue in the PCAF bromodomain. The inhibition, selectivity, and kinetic properties (k_inact/K_I) of these molecules were evaluated using intact protein mass spectrometry, while biophysical and cellular data were employed to verify the covalent mechanism and in-cell target engagement. After optimization, we developed the first PCAF covalent inhibitor, 10, which labeled PCAF covalently in vitro and engages PCAF in cells. The covalent inhibitor, 10, represents a useful starting point for future inhibitor optimization and heterobifunctional molecule development.