Structural investigation of pathogenic variants in dihydropyrimidinase using molecular dynamics simulations

Koichi Kato, Tomoki Nakayoshi, Ayuka Nagura, Eiji Hishinuma, Masahiro Hiratsuka, Eiji Kurimoto, Akifumi Oda

研究成果: Article査読

1 被引用数 (Scopus)


Dihydropyrimidinase (DHP) is an enzyme that catabolizes the degradation of pyrimidine and fluoropyrimidine drugs such as 5-fluorouracil. DHP deficiency triggers various clinical symptoms and increases the risk of fluoropyrimidine drug toxicity. Various pathogenic variants of DHP cause DHP deficiency, and their catalytic activities have been well studied. However, the three-dimensional structures of DHP variants have not been clarified. In this study, we investigated the effects of mutations on DHP structures using the molecular dynamics simulations. Simulations of the wild type and 10 variants were performed and compared. In the T68R, D81G, G278D, and L337P variants, the flexibilities of structures related to the interaction for oligomer formation increased in comparison with those of the wild type. W117R, T343A, and R412 M mutations affected the structures of stereochemistry gate loops or the substrate-binding pocket. The three-dimensional structures of W360R and G435R variants were suggested to collapse. On the other hand, only slight structural changes were observed in the R181W variant, whose experimentally observed activity was similar to that of the wild type. The computational results are expected to clarify the relationship between clinical mutations and structural effects of drug-metabolizing enzymes.

ジャーナルJournal of Molecular Graphics and Modelling
出版ステータスPublished - 2022 12月

ASJC Scopus subject areas

  • 分光学
  • 物理化学および理論化学
  • コンピュータ グラフィックスおよびコンピュータ支援設計
  • 材料化学


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