Lin, S.; You, Y.; Chen, X.; Lu, G.

The bromodomain and extra-terminal (BET) family proteins are critical epigenetic readers involved in various diseases, making them attractive therapeutic targets. This study elucidates the molecular basis of inhibition by four clinical-stage BET inhibitors (ZEN-3694, INCB054329, PLX51107, and INCB057643) through detailed structural comparison and analysis. Using X-ray crystallography, we determined their complex structures with the second bromodomain of human BRD2 at 1.4-1.5 Angstrom resolution. All inhibitors occupy the conserved acetyl-lysine binding pocket via extensive hydrophobic interactions. This hydrophobic network is further coupled with hydrogen-bond contacts for inhibitor-binding stabilization. A common feature is the formation of at least one hydrogen bond with a conserved residue of N429. Notably, INCB057643 exhibits an enhanced polar network, forming additional hydrogen bonds with residues D377 and N429, which may contribute to its improved pharmacological profile. These structures reveal a shared competitive inhibition mechanism by occluding the acetyl-lysine binding site, providing a rational basis for their transcriptional repression and guiding future inhibitor design.