Development of Small Molecules as New Bromodomain Inhibitors for Cancer and Other Diseases

The post-translational modifications of DNA and the chromosomal DNA-packing histone is essential to gene regulations. As the impact of epigenetic marks on gene expression has been recognized, the domains responsible for reading them have become attractive therapeutic targets in cancer. Chemical probes have proven to be an effective method to provide insights into human biology and diseases, in addition to their great potential as therapeutic agents to study the protein-protein interactions. However, the lack of high-quality and selective chemical probes for transcriptional studies presents a great barrier to understand the gene regulation. This dissertation focuses on the discovery and development of chemical probes for cancer and other diseases. Small molecule inhibitors were designed, synthesized and tested for bromodomain and kinase inhibition, and latent HIV-1 activation. Fluorescence-tagged kinase inhibitors were prepared for imaging studies of cancer cells. The project presented in Chapter 1 was to develop BRD4 bromodomain inhibitors. Bromodomain inhibition has been widely studied in gene regulation. Small molecule inhibitors of bromodomains is a promising strategy for drug discovery. Taking advantage of fluorous technologies developed by our lab, fluorous multicomponent reactions were used for the synthesis of a 3,5-dimethylisoxazole compound library for testing on the BRD4 bromodomain. After synthetic design, compound synthesis and biological screening, we identified UMB-32 as the lead compound with 637 nM biochemical potency and 724 nM celluar potency for BRD4. Chapter 2 describes the development of dual bromodomain-kinase inhibitors. Recent studies have shown that the treatment of cancer with bromodomain inhibitors might develop drug resistance over time. The development of novel inhibitors with different mechanisms of action might overcome the resistance issue and provide new therapeutic opportunities. Among the diverse kinase inhibitors, compound BI-2536 is a potent polo-like kinase 1 (PLK1) inhibitor. PLK1 and BRD4 are both implicated as polypharmacological targets in several diseases, like acute myeloid leukemia. Through the structure modification of BI-2536 and biological tests, we discovered UMB160 as an equipotent BRD 4 and PLK 1 dual inhibitor at 28nM and 40nM, respectively. Chapter 3 describes the development of BRD4 inhibitors as activators for latent HIV-1 virus. It has been reported that binding of bromodomain proteins to chromatin may provide an effective way to regulate HIV-1 gene expression and transcription elongation. The BRB4 active compound UMB-32 has bioactivities on latent HIV-1. After lead optimization effort, UMB136 was found more potent than UMB-32 and can be used alone or in combination with other reagents for activation of latent HIV-1. Chapter 4 describes the development of dasatinib- and saracatinib-BODIPY as fluorescent probes for cancer cell studies. Both dasatinib and saracatinib are potent small molecule inhibitors for chemotherapy medication at subnanomolar activities. BODIPY-conjugated dasatinib and saracatinib were synthesized as fluorescent probes for imaging studies of kinase protein localization and abundance. It was found that dasatinib-BODIPY can be used to monitor the intracellular localization of relevant kinase target in live cells, suggesting that this compound could be useful in monitoring intracellular kinase dynamics