Rational design and development of selective BRD7 bromodomain inhibitors and their activity in prostate cancer

Bromodomain-containing proteins are readers of acetylated lysine and play important roles in cancer.1,2 Bromodomain-containing protein 7 (BRD7) has been implicated in multiple malignancies; however, there are no selective chemical probes to study its function in disease.3–13 Using crystal structures of BRD7 and BRD9 bromodomains (BDs) bound to BRD9-selective ligands, we identified a hydrophobic region unique to BRD7. We synthesized a series of ligands designed to occupy this binding region and identified two BRD7-selective inhibitors, 1-78 and 2-77, which show high affinity for the BRD7 BD and selectivity over the BRD9 BD using thermal shift assays and competitive fluorescence polarization. Our binding mode analyses indicate that these ligands occupy the hydrophobic region in BRD7 and maintain key interactions with the Asn and Tyr residues critical for acetyllysine binding. Finally, we validated the utility and selectivity of the compounds in cell-based models of prostate cancer. We then performed gene expression profiling analysis using data obtained from RNA-seq of LNCaP cells with or without drug treatment. Overall design: Comparative gene expression profiling analysis of RNA-seq data for LNCaP cells with or without drug treatment (1µM 2-77, 10 µM ENZA, 0.2 µM ACBI, 2 µM BD98, 10 µM PB16 or DMSO) for 72 hours