Chemical Inhibition of Human Thymidylate Kinase and Structural Insights into the Phosphate Binding Loop and Ligand-Induced Degradation

• Published in: Journal of medicinal chemistry 2016-11, Vol.59 (21), p.9906-9918
• Main Authors: Chen, Yi-Hsuan, Hsu, Hua-Yi, Yeh, Ming-Tyng, Chen, Chen-Cheng, Huang, Chang-Yu, Chung, Ying-Hsuan, Chang, Zee-Fen, Kuo, Wei-Chen, Chan, Nei-Li, Weng, Jui-Hsia, Chung, Bon-chu, Chen, Yu-Ju, Jian, Cheng-Bang, Shen, Ching-Chieh, Tai, Hwan-Ching, Sheu, Sheh-Yi, Fang, Jim-Min
• Format: Article
• Language: English
• Subjects: Animals; Binding Sites - drug effects; Calorimetry; Cell Line; Cell Survival - drug effects; Crystallography, X-Ray; Dose-Response Relationship, Drug; Humans; Mice; Models, Molecular; Molecular Structure; Nucleoside-Phosphate Kinase - antagonists & inhibitors; Nucleoside-Phosphate Kinase - metabolism; Phosphates - metabolism; Protein Kinase Inhibitors - chemical synthesis; Protein Kinase Inhibitors - chemistry; Protein Kinase Inhibitors - pharmacology; Proteolysis - drug effects; Structure-Activity Relationship
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/acs.jmedchem.6b01280

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.