Histone deacetylase inhibitor assay based on fluorescence resonance energy transfer

Histone deacetylases (HDACs) are important enzymes for the transcriptional regulation of gene expression in eukaryotic cells. Furthermore, in recent years HDACs occupied a major position as key targets for chemotherapeutic intervention in malignant diseases. However, progress in the development of these new chemotherapeutics is largely dependent on the existence of bioassays well-suited to inhibitor screening. Herein, we present the first nonisotopic competition binding assay for HDACs. The assay principle has been demonstrated using the well-established HDAC homolog FB188 histone deacetylase-like amidohydrolase from Bordetella/Alcaligenes species FB188. The assay is based on a new fluorescent HDAC inhibitor that shows fluorescence resonance energy transfer with tryptophans upon binding to the enzyme. In a competition situation with other HDAC inhibitors the displacement of the fluorescent inhibitor is accompanied by a decrease of fluorescence resonance energy transfer. The assay is well suited to kinetic studies of inhibitor binding and to HDAC inhibitor identification, e.g., in the context of high-throughput inhibitor screening in drug discovery.