Computational Chemistry
NAKAYOSHI Tomoki
Starting year 2025
Meijyo University
Faculty of Pharmacy
Assistant Professor
Research fields
Research Interests
Quantum Chemical Calculation
Molecular Modeling
Drug-Metabolizing Enzyme
Professional Memberships
The Pharmaceutical Society of Japan
The Biophysical Society of Japan
Protein Science Society of Japan
The Japanese Biochemical Society
The D-Amino Acid Research Society
Main research topics
I have analyzed the structures and functions of the biological proteins using molecular simulations. Various enzymes are involved in the metabolism of biological materials and pharmaceutical compounds. When administering drugs, it is required to control the blood concentration of drugs to archive the desired drug effects. However, the individual differences in genes encoding the drug-metabolizing enzymes can cause a significant increase or decrease in enzymatic activities, and the analysis of genetic polymorphisms of the drug-metabolizing enzymes is considered important in personalized medicine. In addition, several enzymes in vivo catalyze the production of harmful metabolites, and the inhibition of such enzymes can contribute to the prevention and treatment of diseases triggered by harmful metabolites. I have theoretically analyzed the molecular recognition mechanisms of drug-metabolizing enzymes, the effects of changes of amino acid sequences of drug-metabolizing enzymes on their three dimensional structures and molecular recognition mechanisms, and the binding modes of inhibitors to enzymes using computational methods, such as docking simulations, molecular dynamics simulations, and quantum chemical calculations.
Representative papers
T. Nakayoshi, Koichi Kato, Eiji Kurimoto, Akifumi Oda, “Virtual alanine scan of the main protease active site in severe acute respiratory syndrome coronavirus 2”, Int. J. Mol. Sci., 22: 9837, 2021.
Koichi Kato†, T. Nakayoshi†, Rika Nokura, Hiroki Hosono, Masahiro Hiratsuka, Yoshinobu Ishikawa, Eiji Kurimoto and Akifumi Oda, “Deciphering structural alterations associated with activity reductions of genetic polymorphisms in cytochrome P450 2A6 using molecular dynamics simulations”, Int. J. Mol. Sci., 22: 10119, 2021. (†: equal contribution)
Research URL
Researchmap Tomoki Nakayoshi – My portal – researchmap
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