Structure-Guided Design and Synthesis of Pyridinone-Based Selective Bromodomain and Extra-Terminal Domain (BET)-First Bromodomain (BD1) Inhibitors

The
bromodomain and extra-terminal domain (BET) proteins are epigenetic
readers, regulating transcription via two highly homologous tandem
bromodomains, BD1 and BD2. Clinical development of nonselective pan-BD
BET inhibitors has been challenging, partly due to dose-limiting side
effects such as thrombocytopenia. This has prompted the push for domain-selective
BET inhibitors to achieve a more favorable therapeutic window. We
report a structure-guided drug design campaign that led to the development
of a potent BD1-selective BET inhibitor, 33 (XL-126),
with a Kd of 8.9 nM and 185-fold BD1/BD2
selectivity. The high selectivity was first assayed by SPR, validated
by a secondary time-resolved fluorescence energy transfer assay, and
further corroborated by BROMOscan (∼57–373 fold selectivity).
The cocrystal of 33 with BRD4 BD1 and BD2 demonstrates
the source of selectivity: repulsion with His437 and lost binding
with the leucine clamp. Notably, the BD1 selectivity of BET inhibitor 33 leads to both the preservation of platelets and potent
anti-inflammatory efficacy.