Chemoproteomic discovery of a covalent allosteric inhibitor of WRN helicase.


Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
24 Apr 2024
Historique:
received: 19 10 2023
accepted: 14 03 2024
medline: 25 4 2024
pubmed: 25 4 2024
entrez: 24 4 2024
Statut: aheadofprint

Résumé

WRN helicase is a promising target for treatment of cancers with microsatellite instability (MSI) due to its essential role in resolving deleterious non-canonical DNA structures that accumulate in cells with faulty mismatch repair mechanisms

Identifiants

pubmed: 38658751
doi: 10.1038/s41586-024-07318-y
pii: 10.1038/s41586-024-07318-y
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

© 2024. The Author(s), under exclusive licence to Springer Nature Limited.

Références

Behan, F. M. et al. Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. Nature 568, 511–516 (2019).
doi: 10.1038/s41586-019-1103-9 pubmed: 30971826
Chan, E. M. et al. WRN helicase is a synthetic lethal target in microsatellite unstable cancers. Nature 568, 551–556 (2019).
doi: 10.1038/s41586-019-1102-x pubmed: 30971823 pmcid: 6580861
Kategaya, L., Perumal, S. K., Hager, J. H. & Belmont, L. D. Werner syndrome helicase is required for the survival of cancer cells with microsatellite instability. iScience 13, 488–497 (2019).
doi: 10.1016/j.isci.2019.02.006 pubmed: 30898619 pmcid: 6441948
Lieb, S. et al. Werner syndrome helicase is a selective vulnerability of microsatellite instability-high tumor cells. eLife 8, e43333 (2019).
doi: 10.7554/eLife.43333 pubmed: 30910006 pmcid: 6435321
van Wietmarschen, N. et al. Repeat expansions confer WRN dependence in microsatellite-unstable cancers. Nature 586, 292–298 (2020).
doi: 10.1038/s41586-020-2769-8 pubmed: 32999459 pmcid: 8916167
Kawakami, H., Zaanan, A. & Sinicrope, F. A. Microsatellite instability testing and its role in the management of colorectal cancer. Curr. Treat. Options Oncol. 16, 30 (2015).
doi: 10.1007/s11864-015-0348-2 pubmed: 26031544 pmcid: 4594190
Hause, R. J., Pritchard, C. C., Shendure, J. & Salipante, S. J. Classification and characterization of microsatellite instability across 18 cancer types. Nat. Med. 22, 1342–1350 (2016).
doi: 10.1038/nm.4191 pubmed: 27694933
Bonneville, R. et al. Landscape of microsatellite instability across 39 cancer types. JCO Precis. Oncol. 2017, PO.17.00073 (2017).
pubmed: 29850653
Andre, T. et al. Pembrolizumab in microsatellite-instability-high advanced colorectal cancer. N. Engl. J. Med. 383, 2207–2218 (2020).
doi: 10.1056/NEJMoa2017699 pubmed: 33264544
Lenz, H. J. et al. First-line nivolumab plus low-dose ipilimumab for microsatellite instability-Hhigh/mismatch repair-deficient metastatic colorectal cancer: the Phase II CheckMate 142 Study. J. Clin. Oncol. 40, 161–170 (2022).
doi: 10.1200/JCO.21.01015 pubmed: 34637336
Shan, J., Han, D., Shen, C., Lei, Q. & Zhang, Y. Mechanism and strategies of immunotherapy resistance in colorectal cancer. Front. Immunol. 13, 1016646 (2022).
doi: 10.3389/fimmu.2022.1016646 pubmed: 36238278 pmcid: 9550896
Wang, R. et al. Intrinsic resistance and efficacy of immunotherapy in microsatellite instability-high colorectal cancer: a systematic review and meta-analysis. Biomol. Biomed. 23, 198–208 (2023).
doi: 10.17305/bjbms.2022.8286 pubmed: 36408953 pmcid: 10113953
Fuca, G. et al. Ascites and resistance to immune checkpoint inhibition in dMMR/MSI-H metastatic colorectal and gastric cancers. J. Immunother. Cancer 10, e004001 (2022).
doi: 10.1136/jitc-2021-004001 pubmed: 35110358 pmcid: 8811606
Sui, Q. et al. Inflammation promotes resistance to immune checkpoint inhibitors in high microsatellite instability colorectal cancer. Nat. Commun. 13, 7316 (2022).
doi: 10.1038/s41467-022-35096-6 pubmed: 36443332 pmcid: 9705377
Huang, S. et al. The premature ageing syndrome protein, WRN, is a 3’->5’ exonuclease. Nat. Genet. 20, 114–116 (1998).
doi: 10.1038/2410 pubmed: 9771700 pmcid: 4940158
Gray, M. D. et al. The Werner syndrome protein is a DNA helicase. Nat. Genet. 17, 100–103 (1997).
doi: 10.1038/ng0997-100 pubmed: 9288107
Zong, D. et al. Comprehensive mapping of cell fates in microsatellite unstable cancer cells support dual targeting of WRN and ATR. Genes Dev. 37, 913–928 (2023).
Backus, K. M. et al. Proteome-wide covalent ligand discovery in native biological systems. Nature 534, 570–574 (2016).
doi: 10.1038/nature18002 pubmed: 27309814 pmcid: 4919207
Weerapana, E. et al. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature 468, 790–795 (2010).
doi: 10.1038/nature09472 pubmed: 21085121 pmcid: 3058684
Parker, M. J. et al. Identification of 2-sulfonyl/sulfonamide pyrimidines as covalent inhibitors of WRN using a multiplexed high-throughput screening assay. Biochemistry 62, 2147–2160 (2023).
doi: 10.1021/acs.biochem.2c00599 pubmed: 37403936
Hansen, R. et al. The reactivity-driven biochemical mechanism of covalent KRASG12C inhibitors. Nat. Struct. Mol. Biol. 25, 454–462 (2018).
doi: 10.1038/s41594-018-0061-5 pubmed: 29760531
Rudolph, M. G. & Klostermeier, D. When core competence is not enough: functional interplay of the DEAD-box helicase core with ancillary domains and auxiliary factors in RNA binding and unwinding. Biol. Chem. 396, 849–865 (2015).
doi: 10.1515/hsz-2014-0277 pubmed: 25720120
Cancer Dependency Map Portal (RRID:SCR_017655). DepMap Portal https://depmap.org/portal/ (2019).
Bird, J. L. et al. Recapitulation of Werner syndrome sensitivity to camptothecin by limited knockdown of the WRN helicase/exonuclease. Biogerontology 13, 49–62 (2012).
doi: 10.1007/s10522-011-9341-8 pubmed: 21786128
Soto-Gamez, A., Quax, W. J. & Demaria, M. Regulation of survival networks in senescent cells: from mechanisms to interventions. J. Mol. Biol. 431, 2629–2643 (2019).
doi: 10.1016/j.jmb.2019.05.036 pubmed: 31153901
Kang, K., Lee, S. B., Yoo, J. H. & Nho, C. W. Flow cytometric fluorescence pulse width analysis of etoposide-induced nuclear enlargement in HCT116 cells. Biotechnol. Lett. 32, 1045–1052 (2010).
doi: 10.1007/s10529-010-0277-x pubmed: 20429026 pmcid: 2903698
Skog, S. & Tribukait, B. Cell size following irradiation in relation to cell cycle. Acta Radiol. Oncol. 25, 269–273 (1986).
doi: 10.3109/02841868609136417 pubmed: 3030055
Rogakou, E. P., Pilch, D. R., Orr, A. H., Ivanova, V. S. & Bonner, W. M. DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J. Biol. Chem. 273, 5858–5868 (1998).
doi: 10.1074/jbc.273.10.5858 pubmed: 9488723
Liu, Y. et al. Patient-derived xenograft models in cancer therapy: technologies and applications. Signal Transduct. Target. Ther. 8, 160 (2023).
doi: 10.1038/s41392-023-01419-2 pubmed: 37045827 pmcid: 10097874
Overman, M. J. Overview of the management of primary colon cancer. uptodate https://www.uptodate.com/contents/overview-of-the-management-of-primary-colon-cancer (2024).
Picco, G. et al. Werner helicase is a synthetic-lethal vulnerability in mismatch repair-deficient colorectal cancer refractory to targeted therapies, chemotherapy, and immunotherapy. Cancer Discov. 11, 1923–1937 (2021).
doi: 10.1158/2159-8290.CD-20-1508 pubmed: 33837064
Study of HRO761 Alone or in Combination in Cancer Patients With Specific DNA Alterations Called Microsatellite Instability or Mismatch Repair Deficiency (US National Library of Medicine, 2023): https://classic.clinicaltrials.gov/show/NCT05838768 .
Bordas, V. et al. Triazolo-pyrimidine analogues for treating diseases connected to the inhibiton of Werner syndrome RECQ helicase (WRN). International Patent WO 2022/249060 (2022).
A Study to Evaluate the Safety, Pharmacokinetics, and Anti-tumor Activity of RO7589831 in Participants with Advanced Solid Tumors (US National Library of Medicine, 2023); https://classic.clinicaltrials.gov/show/NCT06004245 .
Newman, J. A. et al. Crystal structure of the Bloom’s syndrome helicase indicates a role for the HRDC domain in conformational changes. Nucleic Acids Res. 43, 5221–5235 (2015).
doi: 10.1093/nar/gkv373 pubmed: 25901030 pmcid: 4446433
Schwanhäusser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337–342 (2011).
Sommers, J. A. et al. A high-throughput screen to identify novel small molecule inhibitors of the Werner Syndrome Helicase-Nuclease (WRN). PLoS One 14, e0210525 (2019).
doi: 10.1371/journal.pone.0210525 pubmed: 30625228 pmcid: 6326523
Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543–d552 (2022).
doi: 10.1093/nar/gkab1038 pubmed: 34723319
Diederichs, K. & Karplus, P. A. Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat. Struct. Biol. 4, 269–275 (1997).
doi: 10.1038/nsb0497-269 pubmed: 9095194
Karplus, P. A. & Diederichs, K. Linking crystallographic model and data quality. Science 336, 1030–1033 (2012).
doi: 10.1126/science.1218231 pubmed: 22628654 pmcid: 3457925

Auteurs

Kristen A Baltgalvis (KA)

Vividion Therapeutics, San Diego, CA, USA.

Kelsey N Lamb (KN)

Vividion Therapeutics, San Diego, CA, USA.

Kent T Symons (KT)

Vividion Therapeutics, San Diego, CA, USA.

Chu-Chiao Wu (CC)

Vividion Therapeutics, San Diego, CA, USA.

Melissa A Hoffman (MA)

Vividion Therapeutics, San Diego, CA, USA.

Aaron N Snead (AN)

Vividion Therapeutics, San Diego, CA, USA.

Xiaodan Song (X)

Vividion Therapeutics, San Diego, CA, USA.

Thomas Glaza (T)

Vividion Therapeutics, San Diego, CA, USA.

Shota Kikuchi (S)

Vividion Therapeutics, San Diego, CA, USA.

Jason C Green (JC)

Vividion Therapeutics, San Diego, CA, USA.

Donald C Rogness (DC)

Vividion Therapeutics, San Diego, CA, USA.

Betty Lam (B)

Vividion Therapeutics, San Diego, CA, USA.

Maria E Rodriguez-Aguirre (ME)

Vividion Therapeutics, San Diego, CA, USA.

David R Woody (DR)

Vividion Therapeutics, San Diego, CA, USA.

Christie L Eissler (CL)

Vividion Therapeutics, San Diego, CA, USA.

Socorro Rodiles (S)

Vividion Therapeutics, San Diego, CA, USA.

Seth M Negron (SM)

Vividion Therapeutics, San Diego, CA, USA.

Steffen M Bernard (SM)

Vividion Therapeutics, San Diego, CA, USA.

Eileen Tran (E)

Vividion Therapeutics, San Diego, CA, USA.

Jonathan Pollock (J)

Vividion Therapeutics, San Diego, CA, USA.

Ali Tabatabaei (A)

Vividion Therapeutics, San Diego, CA, USA.

Victor Contreras (V)

Vividion Therapeutics, San Diego, CA, USA.

Heather N Williams (HN)

Vividion Therapeutics, San Diego, CA, USA.

Martha K Pastuszka (MK)

Vividion Therapeutics, San Diego, CA, USA.

John J Sigler (JJ)

Vividion Therapeutics, San Diego, CA, USA.

Piergiorgio Pettazzoni (P)

Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland.

Markus G Rudolph (MG)

Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland.

Moritz Classen (M)

Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland.

Doris Brugger (D)

Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland.

Christopher Claiborne (C)

Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland.

Jean-Marc Plancher (JM)

Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland.

Isabel Cuartas (I)

Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain.

Joan Seoane (J)

Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain.

Laurence E Burgess (LE)

Vividion Therapeutics, San Diego, CA, USA.

Robert T Abraham (RT)

Vividion Therapeutics, San Diego, CA, USA.
Odyssey Therapeutics, San Diego, CA, USA.

David S Weinstein (DS)

Vividion Therapeutics, San Diego, CA, USA.

Gabriel M Simon (GM)

Vividion Therapeutics, San Diego, CA, USA.

Matthew P Patricelli (MP)

Vividion Therapeutics, San Diego, CA, USA. mattp@vividion.com.

Todd M Kinsella (TM)

Vividion Therapeutics, San Diego, CA, USA. tkinsella71c@gmail.com.

Classifications MeSH