BET Bromodomain Inhibitors with One-Step Synthesis Discovered from Virtual Screen

Abstract

Chemical inhibition of epigenetic regulatory proteins BrdT and Brd4 is emerging as a promising therapeutic strategy in contraception, cancer, and heart disease. We report an easily synthesized dihydropyridopyrimidine pan-BET inhibitor scaffold, which was uncovered via a virtual screen followed by testing in a fluorescence anisotropy assay. Dihydropyridopyimidine 3 was subjected to further characterization and is highly selective for the BET family of bromodomains. Structure-activity relationship data and ligand deconstruction highlight the importance of the substitution of the uracil moiety for potency and selectivity. Compound 3 was also cocrystallized with Brd4 for determining the ligand binding pose and rationalizing subsequent structure-activity data. An additional series of dihydropyridopyrimidines was synthesized to exploit the proximity of a channel near the ZA loop of Brd4, leading to compounds with submicromolar affinity and cellular target engagement. Given these findings, novel and easily synthesized inhibitors are being introduced to the growing field of bromodomain inhibitor development.

Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target Validation

“…This method of assay readout is less prone to compound interference compared to other displacement assays,s uch as FP or the AlphaScreen. Label-free methods based on DSF, [32, 47b,d,49] ITC, [32,47b] NMR spectroscopy (water-LOGSY, 19 F-observed, and STD) [50] have also been established to assess binding to bromodomains. These label-free methods do not rely on the availability of previously identified ligands,w hich can be especially useful when studying bromodomains for which an endogenous binding partner is not known, or for which only low affinity ligands have been identified.…”

Targeting Brd4 for cancer therapy: inhibitors and degraders

“…82 William's group disclosed dihydropyridopyrimidine derivative 79 as a novel Brd4 inhibitor, which was facilely generated in a single step from commercially available starting materials. 83 Through a midthroughput screen, a xanthine derivative compound 81 was identified as a Brd4 inhibitor with a K d of 2.1 μM determined by ITC. Despite compound 81 showing weak cellular activity against Jurkat T cells with an EC 50 of 27 μM, impressive selectivity for Brd4(1) (IC 50 = 5.0 μM) over Brd2/3(1) (IC 50 > 50 μM) and BrdT(1) (IC 50 > 100 μM) was observed; more unexpectedly, compound 81 showed no detectable inhibition against the BD2 counterparts of all BET proteins tested.…”

Computer-Aided Drug Design in Epigenetics

“…Among them, crystal structure of compound NSC127133 (compound 61 in Figure 4 ) in complex with BRD2(2) was resolved, which displayed distinct structural features. In 2017, Ayoub et al performed high throughput virtual screen with 6,000,000 compounds in ZINC database using the crystal structure of BRDT(1) (Ayoub et al, 2017 ). A dihydropyridopyrimidine scaffold (compound 62 in Figure 4 ) was identified with highly selectivity for BET family and submicromolar affinity for BRD4(1) and BRDT(1), which could be easily synthesized in one step.…”