Mechanism-based Drug Discovery
Several PIs, including Drs. Chung-I Chang, Rita Chen, Shui-Tein Chen, Meng-Chao Ho, Ming-Ting Lee, Po-Huang Liang, Chun-Hung Lin, Inn-Ho Tsai, Ming-Daw Tsai, Andrew Wang, Kuan Wang, and Shih-Hsiung Wu place a special emphasis on mechanism-based drug discovery. These PIs belong to the interest group of “Protein Chemistry and Chemical Biology”. Representing a long-standing tradition of IBC, this group is specialized at producing effective natural products and small molecules or resolving novel protein structures.
Their research is mainly focused on three areas:
- Structure-based drug discovery by resolving protein structures to understand the structure-activity or function relationship that usually affords useful information for designing potent inhibitors;
- Investigate ions of specific natural products and examine their medical effects;
- Development of chemical probes to identify important posttranslational modifications and protein-protein interactions that correspond to great therapeutic potential.
This team has published impressive papers in outstanding journals such as EMBO J, J. Am. Chem Soc, Angew Chem Int. Ed. Cancer Research, Advanced Synthesis & Catalysis, Acta Crystallographica Sec D, J Clinical Investigation. These great results not only demonstrate value for therapeutic interventions in infectious diseases, cancers, Alzheimer’s disease, etc., but also shed light on new mechanistic aspects of important diseases, which has led to great opportunities for further translational research.
The glycobiology development in IBC started in 1995, owing to the vision and effort of the former director Darrel Liu, as a great addition to its traditional strength in protein chemistry. So far four PIs are directly associated with glycobiology research, including Shih-Hsiung Wu, Kay-Hooi Khoo, Chun-Hung Lin and Takashi Angata. Several others are also linked to this field through collaboration, such as Yu-Ling Shih, Andrew Wang, Shang-Te Hsu, Meng-Chao Ho. At the current stage, there are intensive activities going on at IBC and on the Academia Sinica campus as well. Such development requires an incubation period to evolve into the next stage where 1-2 subjects are identified as flagship projects with allocated resources. Two developments are highlighted herein due to their great research promise.
First of all, Dr. Chun-Hung Lin and Dr. Andrew Wang successfully resolved 9 complex structures of L-fucosidase/inhibitor with the Ki values spanning the range from μM to nM. The 106-fold difference in the binding affinity afforded the identification of important factors that contribute to the high inhibition potency, as well as to the dynamic motion of the enzyme–inhibitor interaction transition from low to high binding affinity. The information provides new insight to develop selective inhibitors for human type 2 fucosidase that was discovered to correlate with gastric carcinoma and duodenal ulcer. Having a similar teamwork, several other projects in IBC are able to publish papers in high profile journals (e.g. Proc Natl Acad Sci, EMBO J, Angew Chem Int Ed, Mol Cell, Cancer Res, Circulation Res, J Clin Investigation, and Nat Commun) every year that also offer great translational values.
Furthermore, the research of specific glycans and glycan-binding proteins (such as selectins, galectins and siglecs) is another main focus of IBC’s glycobiology. The research contains multiple components. For instance, Dr. Khoo is working on sulfo- and sialic acid-glycomics to identify essential glycan-structures that are connected to the binding with specific selectin and siglec members. Dr. Angata is interested to study how siglec member(s) play a role in infectious diseases (e.g. chronic obstructive pulmonary disease caused by Haemophilus influenza). The combined efforts of carbohydrate synthesis, x-ray crystallography and NMR spectroscopy (by Dr. Lin, Shang-Te Hsu and others) are examining the structure-activity relationship of specific galectin and siglec members.
Recently there has been encouraging development. Since the development of glycobiology has rapidly advanced under the leadership of President Chi-Huey Wong and there is a critical mass on the campus, Glyco Program in Academia Sinica (GPAS) was recently established to tackle long-standing challenges. In addition to organizing international conferences and inviting heavyweight researchers for a visit, GPAS will build new infrastructures, including the core facilities of Glycan array, Glycan sequencing and Glycan specific antibodies, and Glyco-enzymes/glycan-binding proteins, which not only benefits the researchers on the campus, but also promotes the glycoscience development in the whole country.
Post-Translational Modifications in Physiology and Diseases
There are five research themes at IBC focusing on functional and structural characterizations of protein post-translational modifications (PTMs). We have investigated Cys-based protein tyrosine phosphatases (PTPs) as the foundation and gradually expand our interests to other type of Cys-based enzymes sharing similar biochemical property.
1. Targeting PTPs for intervention in acute coronary artery disease. This project is led by TC Meng in collaboration with KH Khoo. We have shown that multiple PTPs are rapidly activated in heart tissue response to ischemic stress when coronary artery is occluded. This process is mainly Cys-reduction dependent because of lack of oxygen supply to the heart tissue. By using pan-PTP inhibitors to suppress PTP activity, we were able to prevent ischemic injury to the heart. Several PTP inhibitors are currently under examination for their potential of therapeutic intervention.
2. Mass spectrometry-based quantitative proteomics for dissecting multiplexed redox Cys modifications. This project is led by KH Khoo in collaboration with TC Meng. Using recently available iodo-TMT tags in conjunction with high-resolution mass spectrometric analysis, we were able to measure quantitatively various forms of reversible Cys modifications in PTPs and other Cys-based enzymes, such as caspases, in a complicated proteome. This platform, integrated with super SILAC-based analysis, will be used in dissecting redox Cys modifications of signaling contexts and disease conditions in animal tissues and patient samples.
3. Functional characterization of PTPs in regulating Drosophila development. This project is led by GC Chen in collaboration with TC Meng. We have used genetic approaches to illustrate critical roles of individual PTPs involved in various developmental processes using Drosophila as a model organism. Quite a few non-receptor PTPs were already characterized by such approaches. We are now moving forward to study more PTPs, including receptor PTPs, for their roles involved in Drosophila development.
4. Structural study of PTP-substrate complex to elucidate the molecular basis for substrate specificity determined by the phosphatase domain of PTPs. This project is led by AHJ Wang in collaboration with GC Chen and TC Meng. Using PTPN3 as an example, we have already resolved the crystal structure in complex with phosphopeptide of Eps15, and identified a number of critical residues in the phosphatase domain responsible for determining the preference of substrates. By doing so, we are able to explain why a minor sequence variation in phosphatase domains among various PTPs could result in a major difference in substrates specifically.
5. New approaches to tackle structure of protein complexes between PTPs and protein tyrosine kinases (PTKs). This project is led by MC Ho and MD Tsai in collaboration with TC Meng and KH Khoo. It has been extremely difficult to examine the structural insights into a complex between two intact proteins, such as complex formation between a PTP and a PTK, which is mediated by tyrosine phosphorylation-dependent process. With a new approach of intein technique available, we will be able to synthesize a protein with ~100% phosphorylation on one particular Tyr residue responsible for PTP-PKT interaction. A good starting point is the complex between receptor PTP-a and Src. This type of study will open a new avenue for PIs at IBC to explore highly challenging projects in the next generation of structural biology.
The membrane dynamic interest group was organized by associate director Ruey-Hwa Chen in IBC in 2012 in viewing of a growing number of PIs working in this area. Currently, the group consists of 6 PIs, Ruey-Hwa Chen, Guang-Chao Chen, Chi-Kuang Yao, Yung-Shu Kuan, and Wei-Yuan Yang.
Ruey-Hwa Chen, Guang-Chao Chen, and Wei-Yuan Yang started to collaborate on the Academia Sinica Thematic Project in 2010. This project focuses on the functional and mechanistic studies on autophagy, an evolutionarily conserved, intracellular degradation process important for maintaining cell and tissue homeostasis. While Ruey-Hwa Chen and Guang-Chao Chen have focused on the molecular mechanisms of autophagy induction and regulation, Wei-Yuan Yang has developed cutting-edge live cell image technology to monitor autophagy-mediated destruction of damaged organelles.
In addition to autophagy, several members of this group are interested in membrane trafficking. For instance, Guang-Chao Chen has studied the function of tyrosine phosphorylation/dephosphorylation in endocytic trafficking, while Ruey-Hwa Chen has investigated the effects of ubiquitination in secretory pathway. Induction of membrane curvature is an essential element in membrane trafficking. Yu-Ling Shih has integrated biophysics, structural biology and cell biology technologies for studying the mechanism of membrane curvature generation and its impact on bacterial cell division. Two other members of this group have used model organisms to study the impacts of membrane trafficking on development. Chi-Kuang Yao has investigated the roles of exocytosis and endocytosis in synapse transmission and neural development using Drosophila system, whereas Yung-Shu Kuan has studied vesicular trafficking in Zebrafish neurogenesis.