Development of a chemical probe against NUDT15

• Published in: Nature chemical biology Vol. 16; no. 10; pp. 1120 - 1128
• Main Authors: Zhang, Si Min, Desroses, Matthieu, Hagenkort, Anna, Valerie, Nicholas C. K., Rehling, Daniel, Carter, Megan, Wallner, Olov, Koolmeister, Tobias, Throup, Adam, Jemth, Ann-Sofie, Almlöf, Ingrid, Loseva, Olga, Lundbäck, Thomas, Axelsson, Hanna, Regmi, Shruti, Sarno, Antonio, Krämer, Andreas, Pudelko, Linda, Bräutigam, Lars, Rasti, Azita, Göttmann, Mona, Wiita, Elisée, Kutzner, Juliane, Schaller, Torsten, Kalderén, Christina, Cázares-Körner, Armando, Page, Brent D. G., Krimpenfort, Rosa, Eshtad, Saeed, Altun, Mikael, Rudd, Sean G., Knapp, Stefan, Scobie, Martin, Homan, Evert J., Berglund, Ulrika Warpman, Stenmark, Pål, Helleday, Thomas
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.10.2020; Nature Publishing Group
• Subjects: 631/337/1644; 631/67; 631/92/556; 631/92/613; Binding Sites; Biochemical Engineering; Biochemistry; Biochemistry and Molecular Biology; Biokemi och molekylärbiologi; Biologi; Biological Sciences; Biology; Bioorganic Chemistry; Biophysics; Cell Biology; Cell Line; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Drug Design; Drug Development; Enzymes; Escherichia coli; Health services; Humans; Hydrolase; Inflammatory diseases; Inorganic Pyrophosphatase - antagonists & inhibitors; Inorganic Pyrophosphatase - genetics; Inorganic Pyrophosphatase - metabolism; Laboratories; Lead compounds; Leukemia; Medical research; Medicin och hälsovetenskap; Metabolism; Metabolites; Models, Molecular; Natural Sciences; Naturvetenskap; Nucleic acids; Nucleotides; Physiology; Protein Binding; Protein Conformation; Pyrophosphatases - antagonists & inhibitors; Pyrophosphatases - chemistry; Pyrophosphatases - genetics; Pyrophosphatases - metabolism; Structure-Activity Relationship; Thioguanine; Toxicity
• ISSN: 1552-4450; 1552-4469; 1552-4469
• DOI: 10.1038/s41589-020-0592-z

The NUDIX hydrolase NUDT15 was originally implicated in sanitizing oxidized nucleotides, but was later shown to hydrolyze the active thiopurine metabolites, 6-thio-(d)GTP, thereby dictating the clinical response of this standard-of-care treatment for leukemia and inflammatory diseases. Nonetheless, its physiological roles remain elusive. Here, we sought to develop small-molecule NUDT15 inhibitors to elucidate its biological functions and potentially to improve NUDT15-dependent chemotherapeutics. Lead compound TH1760 demonstrated low-nanomolar biochemical potency through direct and specific binding into the NUDT15 catalytic pocket and engaged cellular NUDT15 in the low-micromolar range. We also employed thiopurine potentiation as a proxy functional readout and demonstrated that TH1760 sensitized cells to 6-thioguanine through enhanced accumulation of 6-thio-(d)GTP in nucleic acids. A biochemically validated, inactive structural analog, TH7285, confirmed that increased thiopurine toxicity takes place via direct NUDT15 inhibition. In conclusion, TH1760 represents the first chemical probe for interrogating NUDT15 biology and potential therapeutic avenues. TH1760 is a first-in-class, potent, selective and cell-active inhibitor against human NUDT15, which sensitizes cells to 6-thioguanine treatment. TH1760 represents a valuable tool for deciphering the enigmatic functions of NUDT15.