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Quantum life science and bioinformatics(Biology)

Fukuzawa KaoriProfessor

In our laboratory, we aim to understand phenomena invisible in experiments by means of quantum chemistry. After completing graduate school, I worked as a researcher at a science and technology think tank for 14 years, and after working at Nihon University School of Dentistry at Matsudo and Hoshi University, I came to the Graduate School of Pharmaceutical Sciences, Osaka University in April 2022. I have been engaged in the development of methods for quantum chemical calculations of biomolecules and their application to life sciences, and established the FMO Drug Design Consortium in 2014. In addition, I am leading supercomputer drug discovery projects such as "Fugaku" and expanding to structural life science research.

Research theme

Exploration of life science phenomena based on quantum theory

Quantum chemical calculations are expected to elucidate and predict diverse life science phenomena by revealing molecular structures and reactivity based on quantum theory. We are using quantum chemical calculations and molecular dynamics calculations to elucidate molecular recognition and reaction mechanisms by biomolecules such as proteins, nucleic acids, lipids, and chemical compounds, aiming to understand life science phenomena from a molecular theoretical perspective.

Development of drug design technology based on the fragment molecular orbital (FMO) method

The fragment molecular orbital (FMO) method, a theoretical method originated in Japan, is a state-of-the-art method that enables quantum chemical calculations of whole protein molecules. It is expected to be useful for predicting protein-ligand binding, designing new compounds, and designing antibodies, because it can quantitatively evaluate interaction energies of molecular complexes and discuss the nature of the interaction based on their energy components. In order to develop the FMO method as a practical drug design technology, the FMO Drug Discovery Consortium, an industry-academia-government collaboration, is conducting activities.

Research and development integrating computational chemistry and structural biology

Various life science phenomena woven by biomolecules are based on molecular structures, and structural analysis techniques are fundamental to elucidate their functions and develop them into drug discovery. We are developing quantitative structural analysis methods by integrating structural biology and computational chemistry.

Development of data science and FMO-AI using the FMO method

The supercomputer "Fugaku" has made it possible to obtain large amounts of data at high speed. The FMO database (FMODB), which is being developed in collaboration with RIKEN, makes the results of FMO calculations of biomolecules available to the public so that researchers around the world can make use of them. The FMODB will be the information infrastructure for future data-driven drug discovery, and we have already begun to develop it for AI drug discovery.

Representative achievements

K. Takaba, C. Watanabe, A. Tokuhisa, et. al., “Protein–ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy” J. Comput. Chem. (2022).

K. Fukuzawa and S. Tanaka, “Fragment Molecular Orbital Calculations for Biomolecules” Curr. Opin. Struct. Biol, 72, 127-134 (2022).

“Recent Advances of the Fragment Molecular Orbital Method” ed. by Y. Mochizuki, S. Tanaka and K. Fukuzawa, Springer Nature (2021).

K. Fukuzawa, K. Kato, C. Watanabe, et. al., “Special Feature of COVID-19 in FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2 Related Proteins” J. Chem. Info. Model. 61, 4594-4612 (2021).

D. Takaya, C. Watanabe, S. Nagase, et. al., “FMODB: The world's first database of quantum mechanical calculation for biomacromolecules based on the fragment molecular orbital method” J. Chem. Info. Model., 61, 777-794 (2021).

H. Tanaka, T. Takahashi, M. Konishi, et. al., “Self‐Degradable Lipid‐Like Materials Based on “Hydrolysis accelerated by the intra‐Particle Enrichment of Reactant (HyPER)” for Messenger RNA Delivery” Advanced Functional Materials, 1910575 (2020).

S. Iwasaki, W. Iwasaki, M. Takahashi, et. al., “The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA”, Molecular Cell, 73, 1-11 (2018).

S. Tanaka, Y. Mochizuki, Y. Komeiji, Y. Okiyama and K. Fukuzawa, "Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems" Phys. Chem. Chem. Phys., 16, 10310-10344 (2014).

K. Fukuzawa, Y. Mochizuki, S. Tanaka, K. Kitaura, and T. Nakano “Molecular Interactions between Estrogen Receptor and Its Ligand Studied by the Ab Initio Fragment Molecular Orbital Method” J. Phys. Chem. B, 110, 16102-16110 (2006)

K. Fukuzawa, K. Kitaura, M. Uebayasi, et. al., “Ab initio Quantum Mechanical Study of the Binding Energies of Human Estrogen Receptor α with its Ligands: An Application of Fragment Molecular Orbital Method” J. Comp. Chem., 26, 1-10 (2005).