The bromodomain-containing proteins BRD2, BRD3, BRD4 and BRDT are epigenetic readers that are currently of great interest as therapeutic targets. These proteins recognize short protein sequences that contain acetyllysine residues and small molecules targeting the acetyllysine-binding pocket are currently the subject of numerous clinical trials, mostly focused in the area of cancer. These molecules however mostly do not have particularly high affinities and are not selective for one of these proteins over the others. In an effort to find better bromodomain inhibitors, we have used the RaPID mRNA display approach developed in Hiroaki Suga's laboratory to screen a library of approximately a trillion cyclic peptides. Our biophysical and structural data reveal a subset of peptides that are capable of recognizing a single BET-family paralogue with high specificity – and do so by simultaneously engaging two copies of the bromodomain via distinct surfaces on the protein. Furthermore, relaxation dispersion data indicate that one basis for this selectivity might be the distinct dynamics displayed by the paralogous bromodomains.
Our data suggest that dual targeting peptides might open the door to a completely new class of bromodomain inhibitors that have unprecedented paralogue-level specificity.