Introduction Of Researches
本實驗室致力於癌症代謝以及致癌基因的研究，著重以胃癌、口腔癌、攝護腺癌為研究題材，利用蛋白質酵素動力學、細胞生物學、以及生物化學分析方法為基礎，配合蛋白質晶體結構進行癌症致病機制以及抑制劑開發，涉足的領域包括表觀遺傳學、細胞能量代謝、遺傳工程、以及蛋白質結構生物學。
Anti-microbial/ anti-cancer agents design
Anti-microbial agents design
Apart from the H. pylori pathogenesis, a combined biochemical/crystallographic strategy has been utilized in the PI’s lab to study important enzymes as well as discovery of inhibitors toward the enzymes of the shikimate pathway. We have developed the structure-based means by Core Site-moiety Maps to interrogate pharmacologically H. pylori shikimate kinase and Mycobacterium tuberculosis shikimate kinase, and identified six potent inhibitors (<8.0 μM). The structure of the inhibitor complex, E114A∙162535, was also determined, which revealed a dramatic shift in the elastic LID region and resulted in conformational locking into a distinctive form.
Figure 4. Framework of the orthSiMMap-based screening method. In Step 1, GEMDOCK was used to generate docked poses for HpSK and MtSK by screening compound libraries (Maybridge and NCI). For each target (HpSK or MtSK), the protein-compound interacting profile was derived from fusing the top ranked 2% (~6,000) compounds. In Step 3, conserved interactions of the target protein and chemical moieties of ligands are identified to deduce the anchors of HpSK and MtSK. The orthSiMMap is constructed based on the conserved features between orthologous target site-moiety maps, which will be used to select candidate compounds for the enzymatic assay. Finally, the model is refined based on the bioassay of candidate compounds.
Anti-cancer agents design
Epigenetic regulation in part involves a dynamic, reversible post-translational modification of histones, which convey inherited information concerning chromatin structure, and dictate the gene expression pattern. Methylation of histone tails has been recently recognized as a key post-translational modification in epigenetics owing to the discovery of histone demethylases. In conjunction with histone methyltransferases (HMTs), these counterpart modifiers work in coordination to maintain a steady global level of methylated histones, mainly at the side chains of lysine (K) and arginine (R) residues of N-terminal unstructured region of histones. Misregulated methylated status of histones from mutational inactivation or abnormal expression of these modifiers has been implicated in oncogenesis.
We are recently interested to investigate lysine demethylases of histones (KDMs), focusing on the regulation of post-translational modifications of histones during the initiation and progression of cancer as well as their link to cancer metabolism. We first target a new histone lysine demethylase KDM8 required for cell cycle progression. Structure-based inhibitor discovery toward KDMs is also underway.
Figure 1. Crystal structure of the catalytic domain of histone lysine demethylase KDM4B. (A) The 2Fo-Fc electron density map of inhibitor PD2 (orange), Ni2+ ion (magenta), and the substrate peptide (cyan), where lysine 9 (K9) is trimethylated. (B) Structure comparison of KDM4A (PDB code: 2OQ6), KDM4B (this study; PDB code: 4LXL), KDM4C (PDB code: 2XML), and KDM4D (PDB code: 4HON). Adapted from Chu et al., J. Med. Chem., 2014.
