An Activity-based Probe Targeting Non-catalytic, Highly Conserved Amino Acid Residues Within Bromodomains

Bromodomain-containing proteins are epigenetic modulators involved in a wide range of cellular processes, from physiological recruitment of transcription factors to pathological disruption of gene regulation and cancer development. Since the druggability of these acetyl-lysine reader domains was established, efforts were made to develop potent and selective inhibitors across the entire family. Here we report the development of a small molecule based approach to covalently modify recombinant and endogenous bromodomain-containing proteins by targeting a conserved lysine and a tyrosine residue in the variable ZA or BC loops. Moreover, the addition of a reporter tag, via copper-catalyzed alkyne azide coupling, to an alkyne handle on the probe allowed in-gel visualization and selective pull-down of the desired bromodomains using both recombinant and endogenous proteins.