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Crystal structures of NUDT15 variants enabled by a potent inhibitor reveal the structural basis for thiopurine sensitivity

DOI: 10.1016/j.jbc.2021.100568 DOI Help

Authors: Daniel Rehling (Stockholm University) , Si Min Zhang (Karolinska Institutet) , Ann-Sofie Jemth (Karolinska Institutet) , Tobias Koolmeister (Karolinska Institutet) , Adam Throup (Karolinska Institutet) , Olov Wallner (Karolinska Institutet) , Emma Scaletti (Stockholm University; Lund University) , Takaya Moriyama (St. Jude Children’s Research Hospital) , Rina Nishii (St. Jude Children’s Research Hospital) , Jonathan Davies (Stockholm University; Lund University) , Matthieu Desroses (Karolinska Institutet) , Sean G. Rudd (Karolinska Institutet) , Martin Scobie (Karolinska Institutet) , Evert Homan (Karolinska Institutet) , Ulrika Warpman Berglund (Karolinska Institutet) , Jun J. Yang (St. Jude Children’s Research Hospital) , Thomas Helleday (Karolinska Institutet; University of Sheffield) , Pal Stenmark (Stockholm University; Lund University)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of Biological Chemistry , VOL 271

State: Published (Approved)
Published: March 2021
Diamond Proposal Number(s): 21625

Open Access Open Access

Abstract: The enzyme NUDT15 efficiently hydrolyses the active metabolites of thiopurine drugs, which are routinely used for treating cancer and inflammatory diseases. Loss-of-function variants in NUDT15 are strongly associated with thiopurine intolerance, such as leukopenia, and pre-emptive NUDT15 genotyping has been clinically implemented to personalize thiopurine dosing. However, understanding the molecular consequences of these variants has been difficult, as no structural information was available for NUDT15 proteins encoded by clinically actionable pharmacogenetic variants due to their inherent instability. Recently, the small molecule NUDT15 inhibitor TH1760 has been shown to sensitize cells to thiopurines, through enhanced accumulation of 6-thio-guanine in DNA. Building upon this, we herein report the development of the potent and specific NUDT15 inhibitor, TH7755. TH7755 demonstrates a greatly improved cellular target engagement and 6-thioguanine potentiation compared to TH1760, while showing no cytotoxicity on its own. This potent inhibitor also stabilized NUDT15, enabling analysis by X-ray crystallography. We have determined high-resolution structures of the clinically relevant NUDT15 variants Arg139Cys, Arg139His, Val18Ile and V18_V19insGlyVal. These structures provide clear insights into the structural basis for the thiopurine intolerance phenotype observed in patients carrying these pharmacogenetic variants. These findings will aid in predicting the effects of new NUDT15 sequence variations yet to be discovered in the clinic.

Diamond Keywords: Leukaemia

Subject Areas: Biology and Bio-materials, Chemistry, Medicine

Instruments: I24-Microfocus Macromolecular Crystallography

Other Facilities: BioMAX at MAXIV

Added On: 28/03/2021 13:11


Discipline Tags:

Non-Communicable Diseases Health & Wellbeing Cancer Biochemistry Chemistry Structural biology Drug Discovery Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX)