Research Group for Nucleic Acid-Targeted Small Molecule Drug Discovery / ISIR / Osaka University

About the Research Group

This website introduces our research activities and members.

Research

We are developing data collection and analysis technologies to identify small molecules that interact with nucleic acids and rapidly apply these findings to drug discovery.

Details of each research topic are provided on separate pages.

• Screening of Small Molecules Binding to RNA
• Construction of RNA–Small Molecule Interaction Database
• Development of Machine Learning-Based Methods for Predicting Small Molecules Binding to Specific RNA Targets
• Development and Evaluation of Small Molecules Binding to Repeat Nucleic Acids

Members and Profiles

• Specially Appointed Professor Kazuhiko Nakatani (Ph.D. in Science)
  • Apr. 1997 Associate Professor, Graduate School of Engineering, Kyoto University
  • Apr. 2005 Professor, Institute of Scientific and Industrial Research, Osaka University
  • Aug. 2015 Director, Institute of Scientific and Industrial Research, Osaka University
  • Aug. 2019 Executive Vice President, Osaka University
  • Mar. 2025 Retirement
  • Apr. 2025 Specially Appointed Professor, ISIR, Osaka University
  • Awards: Chemical Society of Japan Award, Osaka Science Prize, IBM Science Prize, Ichimura Academic Award
  • Contact: nakatani@sanken.osaka-u.ac.jp

• Postdoctoral Researcher Chen Qingwen (Ph.D. in Science)
  • Sep. 2023 Completed Ph.D. in Chemistry, Graduate School of Science, Osaka University
  • Oct. 2023 Researcher, ISIR, Osaka University
  • During Ph.D., studied under Prof. Yasuyuki Matsushita (now Microsoft Research Asia), gaining expertise in information science

Technical Assistant Ayako Sugai
• Responsible for screening using BIAcore 8K+
　　　

• Technical Assistant Kanako Kurisaki
  • Working on data analysis of small molecule–RNA interactions

Recent Publications

• Clustering On Surface Plasmon Resonance Profiles to Improve Hit Assignment of Small Molecules Targeting CAG Repeat DNA, Chen, Q.; Yamada, T.; Murata, A.; Santo, H.; Murakami, E; Matsushita, Y.; Nakatani, K. Advanced Intelligent Discovery, accepted.
• The heterodimer of 2-amino-1,8-naphthyridine and 3-aminoisoquinoline binds to the CTG/CTG triad via hydrogen bonding, Sakurabayashi, S.; Yamada, T.; Nakatani, K. Bioorg. Med. Chem. Lett. 2024, 114, 129985. DOI: 10.1016/j.bmcl.2024.129985.
• Enhancing Binding Affinity to CGG/CGG Triad: Optimizing Naphthyridine Carbamate Dimer Derivatives with Varied Linker Lengths, Nakatani, K.; Shibata, T.; Nakamachi, A. ChemMedChem 2024, accepted. DOI: 10.1002/cmdc.202400351.
• Utility of oligonucleotide in upregulating circular RNA production in a cellular model, Ni, L.; Yamada, T.; Nakatani, K. Sci. Rep. 2024, 14, 8096. DOI: 10.1038/s41598-024-58663-x.
• NMR analysis of N-labeled naphthyridine carbamate dimer (NCD) to contiguous CGG/CGG units in DNA, Yamada, T.; Sakurabayashi, S.; Sugiura, N.; Haneoka, H.; Nakatani, K. Chem. Commun. 2024, 60, 3645-3648. DOI: 10.1039/d4cc00544a.
• Machine learning approach toward generating the focused molecule library targeting CAG repeat DNA, Chen, Q.; Yamada, T.; Murata, A.; Sugai, A.; Matsushita, Y.; Nakatani, K. Digital Discovery 2024, 3, 243-248. DOI: 10.1039/d3dd00160a.
• A new small molecule DoNA binding to CAG repeat RNA, Chen, Q.; Yamada, T.; Miyagawa, K.; Murata, A.; Shoji, M.; Nakatani, K. Bioorg. Med. Chem. 2024, 98, 117580. DOI: 10.1016/j.bmc.2023.117580.

Contact