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. None of these molecules, however, are selective for one paralogue over the others. In an effort to find better bromodomain inhibitors, we 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 peptides that recognize individual BET-family paralogues in a bivalent manner, achieving paralogue specificities of 1000-fold or more. Most strikingly, NMR relaxation dispersion data demonstrate that one of these peptides achieves its specificity by exploiting differences in conformational dynamics between BET paralogues rather than differences in ground-state structure.
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, but highlight the challenge of achieving such specificity.