title: Chemical Inhibition of Human Thymidylate Kinase and Structural Insights into the Phosphate Binding Loop and Ligand-Induced Degradation.
abstract: Targeting thymidylate kinase (TMPK) that catalyzes the phosphotransfer reaction for formation of dTDP from dTMP is a new strategy for anticancer treatment. This study is to understand the inhibitory mechanism of a previously identified human TMPK (hTMPK) inhibitor YMU1 (1a) by molecular docking, isothermal titration calorimetry, and photoaffinity labeling. The molecular dynamics simulation suggests that 1a prefers binding at the catalytic site of hTMPK, whereas the hTMPK inhibitors that bear pyridino[d]isothiazolone or benzo[d]isothiazolone core structure in lieu of the dimethylpyridine-fused isothiazolone moiety in 1a can have access to both the ATP-binding and catalytic sites. The binding sites of hTMPK inhibitors were validated by photoaffinity labeling and mass spectrometric studies. Taking together, 1a and its analogues stabilize the conformation of ligand-induced degradation (LID) region of hTMPK and block the catalytic site or ATP-binding site, thus attenuating the ATP binding-induced closed conformation that is required for phosphorylation of dTMP.
authors.affiliation: Department of Chemistry, National Taiwan University , Taipei 106, Taiwan.
authors.forename: Yi-Hsuan
authors.initials: YH
authors.lastname: Chen
authors.affiliation: Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University , Taipei 112, Taiwan.
authors.forename: Hua-Yi
authors.initials: HY
authors.lastname: Hsu
authors.affiliation: Department of Chemistry, National Taiwan University , Taipei 106, Taiwan.
authors.forename: Ming-Tyng
authors.initials: MT
authors.lastname: Yeh
authors.affiliation: Graduate Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan.
authors.forename: Chen-Cheng
authors.initials: CC
authors.lastname: Chen
authors.affiliation: Graduate Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan.
authors.forename: Chang-Yu
authors.initials: CY
authors.lastname: Huang
authors.affiliation: Graduate Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan.
authors.forename: Ying-Hsuan
authors.initials: YH
authors.lastname: Chung
authors.affiliation: Graduate Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan.
authors.forename: Zee-Fen
authors.initials: ZF
authors.lastname: Chang
authors.affiliation: Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University , Taipei 100, Taiwan.
authors.forename: Wei-Chen
authors.initials: WC
authors.lastname: Kuo
authors.affiliation: Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University , Taipei 100, Taiwan.
authors.forename: Nei-Li
authors.initials: NL
authors.lastname: Chan
authors.affiliation: Institute of Molecular Biology, Academia Sinica , Taipei 115, Taiwan.
authors.forename: Jui-Hsia
authors.initials: JH
authors.lastname: Weng
authors.affiliation: Institute of Molecular Biology, Academia Sinica , Taipei 115, Taiwan.
authors.forename: Bon-Chu
authors.initials: BC
authors.lastname: Chung
authors.affiliation: Department of Chemistry, National Taiwan University , Taipei 106, Taiwan.|Institute of Chemistry, Academia Sinica , Taipei, 115, Taiwan.
authors.forename: Yu-Ju
authors.initials: YJ
authors.lastname: Chen
authors.affiliation: Department of Chemistry, National Taiwan University , Taipei 106, Taiwan.
authors.forename: Cheng-Bang
authors.initials: CB
authors.lastname: Jian
authors.affiliation: Department of Chemistry, National Taiwan University , Taipei 106, Taiwan.
authors.forename: Ching-Chieh
authors.initials: CC
authors.lastname: Shen
authors.affiliation: Department of Chemistry, National Taiwan University , Taipei 106, Taiwan.
authors.forename: Hwan-Ching
authors.initials: HC
authors.lastname: Tai
authors.affiliation: Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University , Taipei 112, Taiwan.|Institute of Biomedical Informatics, National Yang-Ming University , Taipei 112, Taiwan.
authors.forename: Sheh-Yi
authors.initials: SY
authors.lastname: Sheu
authors.affiliation: Department of Chemistry, National Taiwan University , Taipei 106, Taiwan.|The Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.
authors.forename: Jim-Min
authors.initials: JM
authors.lastname: Fang
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000187:drug effects; D002151:Calorimetry; D002460:Cell Line; D002470:Cell Survival / Q000187:drug effects; D018360:Crystallography, X-Ray; D004305:Dose-Response Relationship, Drug; D006801:Humans; D051379:Mice; D008958:Models, Molecular; D015394:Molecular Structure; D009703:Nucleoside-Phosphate Kinase / Q000037:antagonists & inhibitors* / Q000378:metabolism; D010710:Phosphates / Q000378:metabolism*; D047428:Protein Kinase Inhibitors / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D059748:Proteolysis / Q000187:drug effects*; D013329:Structure-Activity Relationship
chemical_list: D010710:Phosphates; D047428:Protein Kinase Inhibitors; D009703:Nucleoside-Phosphate Kinase; C020093:dTMP kinase