Research Summary

Selected Publications

• 1. 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.
• 2. 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.
• 3. 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.
• 4. 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.
• 5. 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.
• 6. 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.
• 7. 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.
• 8. 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.
• 9. 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.
• 10. 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.

Related Links

Lab Members

Contact Information