Structural Basis for BD1-Preferring 2,4-Disubstituted Pyrimidine BRDT Inhibitors

The first bromodomain
of the BET protein BRDT (BRDT-BD1) possesses
a unique Arg54 residue at the terminus of the ZA channel, absent in
other BET family members. We explored this structural uniqueness with
23 analogs of the BET/kinase inhibitor SG3–179, each bearing an amino acid side chain to enable potential interactions
between the positively charged arginine group and the negatively charged
carboxylate groups. In an AlphaScreen assay, serine analog 13 showed 35-fold selectivity for BRDT-T over BRD4-T. The BRDT-BD1
cocrystal structure with glutamic acid analog 14 showed
no interaction with Arg54, suggesting that the observed preference
may be related to differences in the structured water molecules. Compound 13 displayed exceptional in vitro metabolic stability but
had limited cellular permeability in MDCK-MDR1 cells. Compounds 13 and 14 are among the best BRDT-BD1-preferring
inhibitors reported to date and demonstrate a significant step toward
identifying highly selective BRDT inhibitors for male contraception.