Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry

  1. Tiantian Wei
  2. Jue Wang
  3. Ruqi Liang
  4. Wendong Chen
  5. Yilan Chen
  6. Mingzhe Ma
  7. An He
  8. Yifei Du
  9. Wenjing Zhou
  10. Zhiying Zhang
  11. Xin Zeng
  12. Chu Wang
  13. Jin Lu
  14. Xing Guo
  15. Xiao-Wei Chen
  16. Youjun Wang
  17. Dr. Ruijun Tian
  18. Junyu Xiao  Is a corresponding author
  19. Xiaoguang Lei  Is a corresponding author
  1. Peking University, China
  2. Southern University of Science and Technology, China
  3. Beijing Normal University, China
  4. Zhejiang University, China

Abstract

The dual-specificity tyrosine phosphorylation-regulated kinase DYRK2 has emerged as a critical regulator of cellular processes. We took a chemical biology approach to gain further insights into its function. We developed C17, a potent small-molecule DYRK2 inhibitor, through multiple rounds of structure-based optimization guided by several cocrystallized structures. C17 displayed an effect on DYRK2 at a single-digit nanomolar IC50 and showed outstanding selectivity for the human kinome containing 467 other human kinases. Using C17 as a chemical probe, we further performed quantitative phosphoproteomic assays and identified several novel DYRK2 targets, including eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) and stromal interaction molecule 1 (STIM1). DYRK2 phosphorylated 4E-BP1 at multiple sites, and the combined treatment of C17 with AKT and MEK inhibitors showed synergistic 4E-BP1 phosphorylation suppression. The phosphorylation of STIM1 by DYRK2 substantially increased the interaction of STIM1 with the ORAI1 channel, and C17 impeded the store-operated calcium entry process. These studies collectively further expand our understanding of DYRK2 and provide a valuable tool to pinpoint its biological function.

Data availability

The structural coordinates of DYRK2 in complex with compounds 5, 6, 7, 8, 10, 13, 14, 17, 18, 19, and 20 have been deposited in the Protein Data Bank with accession codes 7DH3, 7DG4, 7DH9, 7DHV, 7DHC, 7DHK, 7DHO, 7DJO, 7DL6, 7DHH, and 7DHN, respectively.All the raw mass spectrometry data as well as the identified and significantly regulated phosphosites tables have been deposited in the public proteomics repository MassIVE and are accessible at ftp://massive.ucsd.edu/MSV000087106/.

Article and author information

Author details

  1. Tiantian Wei

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  2. Jue Wang

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  3. Ruqi Liang

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Wendong Chen

    SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
    Competing interests
    The authors declare that no competing interests exist.
  5. Yilan Chen

    Beijing Normal University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Mingzhe Ma

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  7. An He

    SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
    Competing interests
    The authors declare that no competing interests exist.
  8. Yifei Du

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  9. Wenjing Zhou

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  10. Zhiying Zhang

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  11. Xin Zeng

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  12. Chu Wang

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  13. Jin Lu

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  14. Xing Guo

    Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  15. Xiao-Wei Chen

    Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4564-5120
  16. Youjun Wang

    Beijing Normal University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0961-1716
  17. Dr. Ruijun Tian

    SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
    Competing interests
    The authors declare that no competing interests exist.
  18. Junyu Xiao

    Peking University, Beijing, China
    For correspondence
    junyuxiao@pku.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1822-1701
  19. Xiaoguang Lei

    Peking University, Beijing, China
    For correspondence
    xglei@pku.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0380-8035

Funding

National Key Research and Development Plan (2017YFA0505200)

  • Tiantian Wei
  • Jue Wang
  • Ruqi Liang
  • Wendong Chen
  • Yilan Chen
  • Mingzhe Ma
  • An He
  • Yifei Du
  • Wenjing Zhou
  • Zhiying Zhang
  • Xin Zeng
  • Chu Wang
  • Jin Lu
  • Xing Guo
  • Xiao-Wei Chen
  • Youjun Wang
  • Junyu Xiao
  • Xiaoguang Lei

National Natural Science Foundation of China (91853202,21625201,21961142010,21661140001,and 21521003)

  • Tiantian Wei
  • Jue Wang
  • Ruqi Liang
  • Wendong Chen
  • Yilan Chen
  • Mingzhe Ma
  • An He
  • Yifei Du
  • Wenjing Zhou
  • Zhiying Zhang
  • Xin Zeng
  • Chu Wang
  • Jin Lu
  • Xing Guo
  • Xiao-Wei Chen
  • Youjun Wang
  • Junyu Xiao
  • Xiaoguang Lei

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Hening Lin, Cornell University, United States

Version history

  1. Preprint posted: February 12, 2021 (view preprint)
  2. Received: February 8, 2022
  3. Accepted: April 12, 2022
  4. Accepted Manuscript published: April 19, 2022 (version 1)
  5. Accepted Manuscript updated: April 21, 2022 (version 2)
  6. Version of Record published: May 17, 2022 (version 3)

Copyright

© 2022, Wei et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Tiantian Wei
  2. Jue Wang
  3. Ruqi Liang
  4. Wendong Chen
  5. Yilan Chen
  6. Mingzhe Ma
  7. An He
  8. Yifei Du
  9. Wenjing Zhou
  10. Zhiying Zhang
  11. Xin Zeng
  12. Chu Wang
  13. Jin Lu
  14. Xing Guo
  15. Xiao-Wei Chen
  16. Youjun Wang
  17. Dr. Ruijun Tian
  18. Junyu Xiao
  19. Xiaoguang Lei
(2022)
Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry
eLife 11:e77696.
https://doi.org/10.7554/eLife.77696

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