Structure-guided design of SIRT2 inhibitors and development of chemical probes for profiling of bromodomains

Abstract

Protein lysine acetylation is an important post-translational modification to regulate the cell signaling pathways. There are three types of proteins playing different roles in the regulation and recognition of lysine acetylation. The lysine acetyl transferases (KAT) are the “writer” of lysine acetylation, which could transfer the acetyl group from Ac-CoA to the lysine side chain4. The lysine deacetylases (KDACs) are the “eraser” of lysine acetylation, which has the opposite function of KAT5. These two classes of proteins regulate the level of lysine acetylation. Meanwhile, there is a third type of protein domain named “ bromodomain” to bind and recognize the acetylated lysine as the “reader” of lysine acetylation. Sirtuin is the class III KDACs, which have vitals roles in transcription regulation and metabolic regulation. Currently, the biological functions of sirtuins still lack comprehensive understanding. Development of selective inhibitors that target sirtuin specifically will be a powerful tool to investigate the functions of each sirtuin. In previous study, SIRT1,2,3 were identified as decrotonylases, binding the Kcr peptide through a π-π stacking. In chapter 2, I developed a series of selective SIRT2 inhibitors based on this distinct π-π stacking. Several potent peptide-based inhibitors were obtained and the inhibition activities were tested in vitro and in living cells. The selectivity of selective inhibitors was also examined. Bromodomain is a small epigenetic reader, which can recognize the acetylated lysine residues in histone and other proteins. The bromodomain-containing proteins play crucial roles in the transcription regulation. In addition, more and more evidence suggest that bromodomain-containing proteins are involved in the development of various diseases. The development of small molecule inhibitors targeting bromodomain-containing proteins is therefore providing new treatment strategy against diseases. In recent years, a lot of bromodomain inhibitors have been reported. A general and quantitative method to evaluate their inhibitory activities in living cells is still lacking. In order to overcome this knowledge gap, I designed and synthesized a chemical probe named “photo-bs” (chapter 3). “Photo-bs” was validated having the ability to capture bromodomains at different levels and can be used as a “Tool” to determine the activity and selectivity for bromodomain inhibitors (chapter 4).