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Research
HPC- and AI-driven Drug Development Platform Division
AI-driven Drug Discovery Collaborative Unit
AI-driven Drug Discovery Collaborative Unit
Japanese
Unit Leader Yasushi Okuno
yasushi.okuno[at]riken.jp (Lab location: Yokohama)- Please change [at] to @
- 2021
- Director, HPC- and AI-driven Drug Development Platform Division, Unit Leader, Biomedical Computational Intelligence Unit, Unit Leader, AI-driven Drug Discovery Collaborative Unit, RIKEN R-CCS (-present)
Representative Director, Life Intelligence Consortium (-present) - 2016
- Professor, Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University (-present)
- 2014
- Program-Specific Professor (Endowed Chair), Graduate School of Medicine, Kyoto University
- 2008
- Professor (Endowed Chair), Graduate School of Pharmaceutical Sciences, Kyoto University
- 2006
- Associate Professor, Graduate School of Pharmaceutical Sciences, Kyoto University
- 2003
- Program-Specific Assistant Professor, Graduate School of Pharmaceutical Sciences, Kyoto University
- 2000
- Ph.D. in Pharmaceutical Sciences, Kyoto University
Keyword
- Drug Discovery
- Artificial Intelligence
- Deep Learning
- Supercomputer
- Molecular Simulation
Research summary
- Development of next-generation drug discovery technologies based on AI and Simulation
- Building an HPC/AI-driven research platform for life science
- Application of HPC/AI technologies to drug discovery and genomic medicine through collaborations with DMP RIKEN etc.
Main research results
- Identification of therapeutic drug candidates for new coronavirus using Fugaku
- Elucidation of drug resistance mechanisms and application to genomic medicine using molecular dynamics simulation
- Development of coarse-grained force field by using machine learning method
Representative papers
- Araki M, Matsumoto S, Bekker G.J, Isaka Y, Sagae Y, Kamiya N, Okuno Y:
“Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics”
Nature Communications. 12:2793, 2021.
- Mizuta H, Okada K, Araki M, Adachi J, Takemoto A, Kutkowska J, Maruyama K, Yanagitani N, Oh-hara T, Watanabe K, Tamai K, Friboulet L, Katayama K, Ma B, Sasakura Y, Sagae Y, Kukimoto-Niino M, Shirouzu M, Takagi S, Simizu S, Nishio M, Okuno Y, Fujita N, Katayama R:
"Gilteritinib overcomes lorlatinib resistance in ALK-rearranged cancer"
Nature Communications. 12:1261, 2021.
- Saito Y, Koya J, Araki M, Kogure Y, Shingaki S, Tabata, M, McClure M, Yoshifuji K, Matsumoto S, Isaka Y, Tanaka H, Kanai T, Miyano S, Shiraishi Y, Okuno Y, Kataoka K:
"Landscape and function of multiple mutations within individual oncogenes invasive bladder cancer"
Nature. 582:95-99, 2020.
- Ono F, Chiba S, Isaka Y, Matsumoto S, Ma B, Katayama R, Araki M, Okuno Y:
“Improvement in predicting drug sensitivity changes associated with protein mutations using a molecular dynamics based alchemical mutation method”
Scientific Reports. 2:2161, 2020.
- Kanada R, Tokuhisa A, Tsuda K, Okuno Y, Terayama K:
"Exploring Successful Parameter Region for Coarse-Grained Simulation of Biomolecules by Bayesian Optimization and Active Learning"
Biomolecules, 10 (3) 482, 2020.
- Ikemura S, Yasuda H, Matsumoto S, Kamada M, Hamamoto J, Masuzawa K, Kobayashi K, Manabe T, Arai D, Nakachi I, Kawada I, Ishioka K, Nakamura M, Namkoong H, Naoki K, Ono F, Araki M, Kanada R, Ma B, Hayashi Y, Mimaki S, Yoh K, Kobayashi S, Kohno T, Okuno Y, Goto K, Tsuchihara K, Soejima K:
"Molecular dynamics simulation-guided drug sensitivity prediction for lung cancer with rare EGFR mutations"
Proc. Natl. Acad. Sci. USA. 116 (20):10025-10030, 2019.
- Okada K, Araki M, Sakashita T, Ma B, Kanada R, Yanagitani N, Horiike A, Koike S, Oh-Hara T, Watanabe K, Tamai K, Maemondo M, Nishio M, Ishikawa T, Okuno Y, Fujita N, Katayama R:
“Prediction of ALK mutations mediating ALK-TKIs resistance and drug re-purposing to overcome the resistance”
EBioMedicine, 41, 105-119, 2019.
- Nakaoku T, Kohno T, Araki M, Niho S, Chauhan R, Knowles PP, Tsuchihara K, Matsumoto S, Shimada Y, Mimaki S, Ishii G, Ichikawa H, Nagatoishi S, Tsumoto K, Okuno Y, Yoh K, McDonald NQ, Goto K:
"A secondary RET mutation in the activation loop conferring resistance to vandetanib"
Nature Communications. 9 (1):625, 2018.
- Uchibori K, Inase N, Araki M, Kamada M, Sato S, Okuno Y, Fujita N, Katayama R:
"Brigatinib combined with anti-EGFR antibody overcomes osimertinib resistance in EGFR-mutated non-small-cell lung cancer"
Nature Communications. 8:14768, 2017.
- Kanada R, Terayama K, Tokuhisa A, Matsumoto S, Okuno Y:
“Enhanced Conformational Sampling with an Adaptive Coarse-Grained Elastic Network Model Using Short-Time All-Atom Molecular Dynamics”
Journal of Chemical Theory and Computation. 18(4): 2062–2074, 2022.
