Research Teams The Chemical Biology Core Facility collects many natural compounds and stores them in the RIKEN Natural Product Depository (NPDepo) that was constructed recently.
A good chemical library should contain many compounds with various useful biological activities, therefore our team will validate the activity of the compounds in NPDepo by actual screening of the library through various assay systems.
For this purpose, we will develop high throughput screening systems using chemical array and liquid handling robots to screen the large library.
Besides developing new screening systems to identify compounds with novel biological activities, our team also conducts basic research to study the mechanisms behind the biological activities of the compounds.
【Researchers' theme】
Small molecule inhibitors of cell cycle regulatory proteins
 N. WATANABE, Ph.D. |
 We are studying the regulation of cell cycle regulatory proteins, especially proteins that regulate mitosis. A complex of mitotic cyclin and cyclin dependent kinase (CDK) is the main regulator of mitosis and there are several proteins that regulate the activity of the complex. One such protein we have focused on is Wee1, a protein kinase that inactivates cyclin/CDK until cells become ready for mitosis. Upon the onset of mitosis, Wee1 is inactivated both by protein phosphorylation and degradation. As shown in the figure, we have recently identified a protein kinase cascade that induces the degradation of human somatic type Wee1 (Wee1A) through protein ubiquitination and proteasome dependent manner. We also study an HIV-1 encoded protein, Vpr, that also inhibits the entry of mitosis. Vpr is important in AIDS pathogenesis, therefore we would like to know its mode of action. Using the knowledge about the action of these cell cycle regulatory proteins, we are currently focusing on the isolation of small molecule inhibitors of them. We recently established a screening system for the inhibitors of phosphorylation dependent protein-protein interaction such as polo box domain (PBD) dependent binding that is important for the Wee1 degradation upon the onset of mitosis. We also made a screening system for Vpr inhibitors using budding yeast, Saccharomyces cerevisiae, and isolated inhibitors of Vpr. |
Stress meets development in p38 MAP kinase
 T. SUDO, Ph.D. |
We are exposed to various stresses, ranging from drastic environmental changes to long-lasting unseen moderate stimuli, resulting in acute or chronic diseases and more seriously leading to be fatal. p38 MAP kinase has been shown to play important roles in stress responses including inflammatory response, apoptosis and differentiation. We have been studying the physiological roles of p38, through the establishment and the analysis of p38 KO mouse, and also by elucidation of the function of the specific interaction of p38 with p62/SQSTM1 under cytokine induced signaling, to regulate stress signaling. In the course of the study, we found molecular mechanisms that would be possible targets for drug discovery and we developed a bio microplate reader "HiTS" in collaboration with Scinics Corp. to facilitate a new screening method. We will continue our challenges to develop the ways to prevent, to diagnose and to cure the diseases caused by p38 mal-functioning. |
Application of chemical biology to higher plants.
T. ITO, Ph.D. |
 Discovery of novel genes involved in plant productivity is one of the objectives for plant science. To this end, we have been studying pollen maturation process and environmental stress response in higher plants by use of a model organism, Arabidopsis thaliana. Male sterile trait is applicable to agriculture such as hybrid seed production. To produce engineered male sterile plants, elucidation of pollen maturation process is essential. We showed that Arabidopsis MALE STERILITY1 (MS1) functions as a key transcription factor and regulates many downstream genes necessary for pollen maturation. We are (1) investigating these downstream gene functions, and (2) searching for bioprobes interacting with MS1 and the downstream proteins. There is a steady increase in farmland inappropriate for cultivation because of drought and high salinity. To elucidate the response mechanism against environmental stresses such as drought and salinity, we focus on abscisic acid (ABA), so called “a stress phytohormone”. To isolate bioprobes affecting ABA biosynthetic/signal transduction pathway, we are (3) searching for bioprobes which inhibit or activate ABA functions. |
Proteomics-based analysis of the effect of small molecules.
 M. MUROI, Ph.D. |
 New biologically active small molecules have been isolated from microbial metabolites by the cell-based assay system in our laboratory. However, identification of molecular targets of the new compounds is usually difficult and a time-consuming process. Proteomics was therefore applied to predict the targets of such active small molecules. Depending on the targets of the small molecules, profiles of expression level and modification of proteins within the cells will be altered. Using 2-Dimensional Fluorescence Differential Gel Electrophoresis (2D-DIGE), proteome expression profiles have been obtained from the cells treated with the authentic small molecules and based on the expression profiles we analyze the newly isolated compounds. |
Chemical array-based screening of bioprobes
 Y. KONDOH, Ph.D. |
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In chemical genetics, the technology for high-throughput screening of a bioprobe regulating a protein function is very important. The identification of small-molecule bioprobes for a protein of interest can facilitate not only the functional analysis of the protein but also the development of clinical drugs. We have developed chemical array "NPDepoArray" for ultra-high throughput screening of bioprobes. The chemical array contains 2-3 thousands of small molecules immobilized with a unique photo-cross-linking approach in a functional-group-independent manner. Chemical array-based screens have enabled the discovery of small molecules that bind target proteins of interest.
By the present, 15,000 of small molecules; natural products, its derivatives, drugs, etc, were microarrayed as chemical array series “NPDepoArray” and new stored small molecules are also microarrayed. We are now searching bioprobes for a variety of proteins associated with human diseases by using chemical array.Screening for new bioprobes and the analysis of its mechanism of action
 M. KAWATANI, Ph.D. |
We are studying the development of new bioactive small-molecule compounds that regulate growth and differentiation of mammalian cells. We obtain unique bioactive compounds from the chemical library of RIKEN NPDepo by cell- or enzyme-based screening, elucidate their molecular targets and mechanisms of action, and verify the effectiveness as a therapeutic agent using a disease-model animal. Our current work is focused on the following subjects;  1) Screening for small molecules that disrupt osteoclast function and the analysis of its mechanism of action.2) Analysis of the mechanism of action of antiproliferative compounds GUT-70 and BNS-22. 3) Screening for differentiation-inducing small molecules of human leukemia HL-60 cells and the analysis of its mechanism of action. 4) High-content screening based on cellular phenotype. 5) Screening of aminoacyl-tRNA synthetase inhibitors. |
Discovery of bioprobes by the chemical array-based approach
 T.KAWAMURA, Ph.D. |
Obtainment of unique bioprobes, small molecules which can modulate the functions of biomolecules, is required for chemical biology. To obtain bioprobes, we constructed a new type of chemical array which enabled us to perform high-throughput screening for candidate bioprobes. However, additional validation studies, to investigate whether the candidates obtained through chemical array screening can modulate the functions of the target proteins in vitro and in intact cells, are required to obtain bioprobes. This study aims to discover new bioprobes especially modulating the functions of cancer-related proteins, and investigate the functions of the proteins. In addition, we attempt to establish a new method to discover bioprobes modulating cancer-related proteins using the chemical array-based approach. |
