Joint Research Promotion Program (JRPP) in Wako
The Advanced Technology Platform in Wako RIKEN‑CSRS integrates cutting‑edge instruments and technologies in chemical biology and has facilitated a wide range of collaborative research. We will continue to enhance the collaborative‑research framework and expand collaborations both within CSRS and with external partners.
Contact
For inquiries or applications regarding joint research, please contact CSRScollabo [at] ml.riken.jp.
We will follow up with details to schedule an online meeting.
Summary of usage and publication in JRPP
List of joint research partners ／ List of published papers
Biomolecular Characterization Unit
Outline
Our unit provides high quality structural characterization methods to the field of biological science, aiming to further understand the mechanism and action of biological molecules. We manage specialized and technical instruments including protein chemical analyses, mass spectrometry. Our challenge to research, develop and fine-tune novel characterization methods for biological molecules, is an endless yet rewarding process.
Proteins and supermolecules
- Quantitative proteomic analysis (Dohmae)
- Post‑translational modification analysis (Dohmae)
- Compound binding site analysis (Dohmae)
- Mass spectrometric analysis of RNA and RNA therapeutics (Nakayama)
- Amino acid analysis and absolute quantification of proteins (Dohmae)
- Molecular‑weight determination of compounds and polymers by MALDI‑TOF MS (including high‑resolution mass spectrometry (Dohmae)
- Analysis and fractionation by reverse‑phase, gel‑filtration, and other chromatographic method (Dohmae)
Chemicals and small molecules
- Proteome-wide evaluation of protein thermal stability modulation induced by small‑molecule binding [2DE-CETSA] (Muroi)
Molecular Structure Characterization Unit
Outline
We develop new methods and technologies of NMR and MS analyses for structural elucidation and characterization of novel organic compounds that are found or synthesized in chemistry and related scientific fields such as chemical biology, metabolomics research, and several organic synthetic studies. We provide diverse research support activity for characterization of organic molecules through maintenance and operation of MS, NMR, and CD facilities for all RIKEN researchers. Our research supporting activities include training on open access machines, technical assistance, data acquisition, and spectral data analysis and interpretation. We collaborate with many research groups, and continue to improve our capability and methodology for organic molecular characterization and structural determination.
Chemicals and small molecules
- Qualitative and quantitative analysis of organic compounds by mass spectrometry (Nogawa, Imai)
- NMR measurement and analysis (Koshino, Nakamura, Okushita)
- Measurement and analysis of circular dichroism spectra and optical rotation
- Measurement and analysis of UV-vis-NIR, IR, and fluorescence spectra (Muranaka)
- Measurement of cyclic voltammograms (Muranaka)
- Molecular structure analysis based on quantum chemical calculations (Muranaka)
Molecular Bioregulation Research Team
Outline
Although increasing global food supply is the critical issue for sustainable society, crop yields are growing too slowly to meet the expected food demand. We are rather facing many problems such as climate change, which will make it challenging to produce enough food. Our team aims at solving these issues by chemical biology approach. We search key genes for stable food production through forward and reverse chemical genetics. The compounds obtained from chemical screening will be structurally optimized through chemical synthesis and applied to regulate physiological functions of plants. Our goal is to go beyond the limitation of current plant science and agriculture by combining synthetic chemistry and plant biology, and to explore new field of sustainable resource science.
Chemicals and small molecules
- Provision of plant physiological regulators (Hagihara)
- Evaluation of compound bioactivity on plants (Nakamura)
Chemical Resource Development Research Unit
Outline
A chemical library is an indispensable tool to promote research on the regulation of cell functions and drug-discovery under the strategy of chemical biology. To ensure the utilization and application of the chemical library, we promote research supports for chemical biology and resource science by providing chemical compounds, their information, and structure-activity relationship analysis. Moreover, we are enriching the chemical library by cooperating with Natural Product Biosynthesis Research Unit.
Chemicals and small molecules
- Provision of HTS libraries (Hirano)
- Provision of efficient libraries for compound screening (Hirano)
- Authentic library
- Pilot library
- Target Library (bacterial growth, cell morphology, cell proliferation, enzyme inhibition anti-fungal action, kinase inhibition, anti-parasite, effects on plants, protein-protein interaction, antiviral activity)
- Search for hit compound information [published literature, novelty, and availability] (Hirano)
- Analog search and provision of hit compounds (Hirano)
[This includes searching for specified structures outside the NPDepo library, comparing multiple compound groups, and identifying duplicate compounds.] - Structural classification by clustering multiple hit compound groups (Hirano)
Chemical Biology and Biosynthesis Research Team
Outline
Our laboratory aims to contribute to solving social issues such as the decrease and depletion of natural resources and to advance environmental resource science research through research on chemical biology and biosynthesis, including research on new useful natural products using biosynthetic methods. We analyze the biosynthesis pathway of bioactive substances and construct substance production systems in microbial hosts. We create non-natural compounds by modifying biosynthetic pathways and enzyme functions in the production system. We also analyze the mechanism of action of the bioactive compounds and obtain new knowledge in chemical biology.
Chemicals and small molecules
- Chemoenzymatic synthesis and provision of coenzyme‑related molecules (Awakawa)
Molecular Ligand Target Research Team
Outline
Bioactive molecular ligands with unique physiological effects must have specific cellular targets. Target identification is critical for elucidating the mechanism of action of molecular ligands and for drug discovery. However, drug target identification has been extremely difficult, because the interactions between molecular ligands and their targets are not uniform. Our team aims to develop innovative techniques for target identification based on the global analysis of yeast chemical-genetic and genetic interactions, leading to quick and accurate elucidation of ligand-target interactions.
High-throughput screening
- Target identification of compounds using yeast genetic interactions (Yashiroda)
Chemicals and small molecules
- Provision of HTS libraries (Hirano)
- Provision of efficient libraries for compound screening (Hirano)
- Authentic library
- Pilot library
- Target Library (bacterial growth, cell morphology, cell proliferation, enzyme inhibition anti-fungal action, kinase inhibition, anti-parasite, effects on plants, protein-protein interaction, antiviral activity)
- Search for hit compound information [published literature, novelty, and availability] (Hirano)
- Analog search and provision of hit compounds (Hirano)
[This includes searching for specified structures outside the NPDepo library, comparing multiple compound groups, and identifying duplicate compounds.] - Structural classification by clustering multiple hit compound groups (Hirano)
- Proteome-wide evaluation of protein thermal stability modulation induced by small‑molecule binding [2DE-CETSA] (Muroi)
- Preparation of compound beads for target identification (Kawatani)
- Provision of plant physiological regulators (Hagihara)
- Evaluation of compound bioactivity on plants (Nakamura)
- Qualitative and quantitative analysis of organic compounds by mass spectrometry (Nogawa, Imai)
(High-resolution ion mobility analysis; direct ionization of solid samples using desorption electrospray ionization with imaging mass spectrometry; separation by supercritical fluid chromatography; and mass spectrometric analysis of polymer components using pyrolysis GC–MS) - NMR measurement and analysis (Koshino, Nakamura, Okushita)
(Structural analysis of general organic compounds by NMR; specialized measurements using solution NMR; quantitative analysis by solution NMR; and measurement, structural analysis, and physicochemical characterization of chemical substances including polymers by solid-state NMR.) - Measurement and analysis of circular dichroism spectra and optical rotation
- Measurement and analysis of UV-vis-NIR, IR, and fluorescence spectra (Muranaka)
- Measurement of cyclic voltammograms (Muranaka)
- Molecular structure analysis based on quantum chemical calculations (Muranaka)
- Chemoenzymatic synthesis and provision of coenzyme‑related molecules (Awakawa)
High-throughput screening
- Target identification of compounds by shRNA and CRISPR screening in human cultured cells (Matsumoto)
- Development of high-throughput screening and high-content screening systems (Idei)
- Target identification of compounds using yeast genetic interactions (Yashiroda)
- High-throughput screening of protein-binding small molecules using chemical arrays (Kawatani)
Proteins and supermolecules
- Quantitative proteomic analysis (Dohmae)
- Post‑translational modification analysis (Dohmae)
- Compound binding site analysis (Dohmae)
- Mass spectrometric analysis of RNA and RNA therapeutics (Nakayama)
- Amino acid analysis and absolute quantification of proteins (Dohmae)
- Molecular‑weight determination of compounds and polymers by MALDI‑TOF MS (including high‑resolution mass spectrometry (Dohmae)
- Analysis and fractionation by reverse‑phase, gel‑filtration, and other chromatographic method (Dohmae)
Molecular interactions
- Measurement of binding affinity in biomolecular interactions by microscale thermophoresis (MST) (Matsuoka)
- Kinetic analysis of biomolecular interactions by surface plasmon resonance (SPR) (Matsuoka)
- Thermodynamic analysis of biomolecular interactions by isothermal titration calorimetry (ITC) (Matsuoka)
- Evaluation of protein stability by differential scanning fluorimetry (nanoDSF) (Matsuoka)
Person in charge
- Yoko Yashiroda (Molecular Ligand Target Research Team)
- Shinya Hagihara (Molecular Bioregulation Research Team)
- Sakuya Nakamura (Molecular Bioregulation Research Team)
- Hiroyuki Hirano (Chemical Resource Development Research Unit)
- Takayoshi Awakawa (Chemical Biology and Biosynthesis Research Team)
- Akiko Idei (Drug Discovery Seeds Development Unit)
- Ken Matsumoto (Drug Discovery Seeds Development Unit)
- Makoto Kawatani（Drug Discovery Seeds Development Unit / Chemical Resource Development Research Unit)
- Seiji Matsuoka (Drug Discovery Seeds Development Unit)
- Hiroyuki Koshino (Molecular Structure Characterization Unit)
- Atsuya Muranaka (Molecular Structure Characterization Unit)
- Toshihiko Nogawa (Molecular Structure Characterization Unit)
- Keiko Okushita (Molecular Structure Characterization Unit)
- Takashi Nakamura (Molecular Structure Characterization Unit)
- Eiyu Imai (Molecular Structure Characterization Unit)
- Naoshi Dohmae (Biomolecular Characterization Unit)
- Makoto Muroi (Biomolecular Characterization Unit / Chemical Resource Development Research Unit)
Hiroshi Nakayama (Biomolecular Characterization Unit)
