Druggability Analysis and Structural Classification of Bromodomain Acetyl-lysine Binding Sites

• Published in: Journal of medicinal chemistry 2012-09, Vol.55 (17), p.7346-7359
• Main Authors: Vidler, Lewis R, Brown, Nathan, Knapp, Stefan, Hoelder, Swen
• Format: Article
• Language: English
• Subjects: Binding Sites; Lysine - analogs & derivatives; Lysine - chemistry; Models, Molecular; Molecular Structure; Proteins - chemistry
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm300346w

Bromodomains are readers of the epigenetic code that specifically bind acetyl-lysine containing recognition sites on proteins. Recently the BET family of bromodomains has been demonstrated to be druggable through the discovery of potent inhibitors, sparking an interest in protein–protein interaction inhibitors that directly target gene transcription. Here, we assess the druggability of diverse members of the bromodomain family using SiteMap and show that there are significant differences in predicted druggability. Furthermore, we trace these differences in druggability back to unique amino acid signatures in the bromodomain acetyl-lysine binding sites. These signatures were then used to generate a new classification of the bromodomain family, visualized as a classification tree. This represents the first analysis of this type for the bromodomain family and can prove useful in the discovery of inhibitors, particularly for anticipating screening hit rates, identifying inhibitors that can be explored for lead hopping approaches, and selecting proteins for selectivity screening.