Science 10.1126/science.1249830

Credit: ALESSIO CIULLI

JQ1 and I-BET are chemical probes that inhibit bromo and extra-terminal (BET) proteins, which are transcriptional regulatory proteins that contain bromodomains, 'readers' of acetylated lysines within chromatin. These compounds potently bind bromodomains of BET-family proteins but are pan-selective within the BET family. Baud et al. now report a chemical genetics approach that identifies an orthogonal and more selective BET-bromodomain inhibitor. Sequence alignments and structure-guided analyses identified a conserved leucine residue in BET-bromodomains involved in inhibitor-protein interactions; mutation of this leucine to the smaller alanine (L/A) created a 'hole' that did not interfere with BET protein stability or function but could accommodate an inhibitor with a complementary hydrophobic 'bump'. An ethylated I-BET analog (ET) was designed and synthesized, and crystallographic analysis of an ET–L/A mutant bromodomain complex identified a specific contact between the ethyl group of ET and the mutant alanine residue. Differential scanning fluorimetry and isothermal titration calorimetry measurements revealed that ET is up to 540-fold selective for L/A mutants relative to wild-type bromodomains, including in BET proteins with tandem bromodomains. This selectivity persists in cells and was applied to demonstrate that targeting the first bromodomain of a BET protein is sufficient to displace the protein from chromatin. The new study shows that the bump-and-hole approach offers potential as a tool to enhance our understanding of chromatin biology.