Bump-BET · Bump and Hole approach to elucidate function of individual bromodomains of BET proteins

Bump and Hole approach to elucidate function of individual bromodomains of BET proteins

Small molecules can be used to probe the biological function of individual proteins, but achieving high selectivity against structurally similar paralogues remains a challenging task. The Bromo and Extra-Terminal (BET) proteins brd2, brd3, brd4 and brdt play important roles in transcriptional regulation by controlling networks of genes involved in cellular proliferation and cell cycle regulation. Key to the functions of BET proteins is a pair of highly homologous bromodomains (BD) in tandem, which bind to chromatin and recognize histone acetylation on its tail. Misregulation of BET proteins activity has been linked to disease states. Elucidation of the processes controlled by BET proteins would benefit greatly from chemical probes that perturb individual BDs with exquisite control and selectivity. Potent small molecule inhibitors have been developed against BET BD, however their lack of selectivity against individual BD within the family renders these compounds unsuitable to interrogate the function of individual proteins or their individual domains. A “bump-and-hole” approach is employed to untangle the function of each single BD. A mutation is introduced in the BD of interest making a “hole” in the ligand binding pocket while retaining its biological function. On the other hand, a “bump” modification is made to the inhibitor scaffold so that the “bump” is tolerated by the “hole” on the mutant BD which the derivative is selective for the mutant over WT. A discriminative and fine-tuned pair of BD mutant / BET-inhibitor (I-BET) derivative was obtained with the best compound demonstrated >100 fold selectivity towards BD mutant over WT, as measured by isothermal titration calorimetry. At the same time, the researcher pursued a closely related project using a proteolysis targeting chimera (PROTAC) approach to target BET proteins. The researcher contributed to the report of the first-ever PROTAC-induced E3-target ternary complex and led an SAR study to understand E3 ligand selectivity in the context of ternary complex formation. These works provide structural basis for PROTAC-mediated target protein degradation.

Data: CORDIS, © European Union