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

Rehling, Daniel ; Zhang, Si Min ; Jemth, Ann-Sofie ; Koolmeister, Tobias ; Throup, Adam ; Wallner, Olov ; Scaletti, Emma LU ; Moriyama, Takaya ; Nishii, Rina and Davies, Jonathan , et al. (2021) In The Journal of biological chemistry 296.
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... (More)

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.

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type
Contribution to journal
publication status
published
subject
in
The Journal of biological chemistry
volume
296
article number
100568
publisher
American Society for Biochemistry and Molecular Biology
external identifiers
  • pmid:33753169
  • scopus:85104572939
ISSN
1083-351X
DOI
10.1016/j.jbc.2021.100568
language
English
LU publication?
yes
id
8780462f-c9d4-451d-aa12-c4aaa707f667
date added to LUP
2021-03-29 07:12:43
date last changed
2024-06-15 08:38:02
@article{8780462f-c9d4-451d-aa12-c4aaa707f667,
  abstract     = {{<p>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.</p>}},
  author       = {{Rehling, Daniel and Zhang, Si Min and Jemth, Ann-Sofie and Koolmeister, Tobias and Throup, Adam and Wallner, Olov and Scaletti, Emma and Moriyama, Takaya and Nishii, Rina and Davies, Jonathan and Desroses, Matthieu and Rudd, Sean G and Scobie, Martin and Homan, Evert and Berglund, Ulrika Warpman and Yang, Jun J and Helleday, Thomas and Stenmark, Pål}},
  issn         = {{1083-351X}},
  language     = {{eng}},
  month        = {{03}},
  publisher    = {{American Society for Biochemistry and Molecular Biology}},
  series       = {{The Journal of biological chemistry}},
  title        = {{Crystal structures of NUDT15 variants enabled by a potent inhibitor reveal the structural basis for thiopurine sensitivity}},
  url          = {{http://dx.doi.org/10.1016/j.jbc.2021.100568}},
  doi          = {{10.1016/j.jbc.2021.100568}},
  volume       = {{296}},
  year         = {{2021}},
}