Chemical tools for BAZ2A/B biology: discovery of dual and BAZ2B-selective PROTAC degraders

Bromodomain adjacent to zinc finger 2A and 2B (BAZ2A/B) are regulatory subunits of imitation switch (ISWI) chromatin remodelling complexes. Despite their implication in diverse pathologies, BAZ2A/B remain poorly understood, largely due to the lack of chemical probes capable of discriminating between these homologues or targeting their multiple domains. To address this challenge, we recently disclosed two first-in-class PROTACs: dBAZ2, which degrades both BAZ2A and BAZ2B, and the BAZ2B-selective degrader dBAZ2B. Here, we describe the medicinal chemistry campaign that led to their discovery. In addition, we report here an optimized synthesis of the BAZ2A/B bromodomain (BRD) ligand BAZ2-ICR enabling two different attachment points for linker incorporation and demonstrate that BAZ2A/B degradation is more readily achieved through recruitment of VHL than CRBN. We also identify a third degrader, 8, which employs an alternative linkage vector to BAZ2-ICR compared to dBAZ2 and dBAZ2B, adding to the structural diversity of BAZ2 PROTACs. Cooperativity assays and the BAZ2B-BRD:8:VHL-EloC-EloB co-crystal structure reflect the ability of 8 to degrade both BAZ2A and BAZ2B. In contrast, dBAZ2B achieves selectivity through preferential ternary complex formation with BAZ2B. Finally, we demonstrate the utility of dBAZ2/dBAZ2B as chemical probes: dBAZ2 induces expression of BAZ2A-regulated genes more strongly than dBAZ2B or BAZ2-ICR, and the BAZ2B selectivity of dBAZ2B is maintained across multiple cell lines. Collectively, this work delivers new chemical tools to interrogate BAZ2A/B biology and establishes a platform for developing heterobifunctional molecules targeting these understudied yet disease-relevant proteins.