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Structure-based design of potent and selective inhibitors targeting RIPK3 for eliminating on-target toxicity in vitro

Author

Listed:
  • Haixia Su

    (University of Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Guofeng Chen

    (University of Chinese Academy of Sciences)

  • Hang Xie

    (Nanjing University of Chinese Medicine)

  • Wanchen Li

    (University of Nottingham Ningbo China)

  • Muya Xiong

    (University of Chinese Academy of Sciences)

  • Jian He

    (University of Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Hangchen Hu

    (University of Chinese Academy of Sciences)

  • Wenfeng Zhao

    (University of Chinese Academy of Sciences)

  • Qiang Shao

    (University of Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Minjun Li

    (Chinese Academy of Sciences)

  • Qiang Zhao

    (University of Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    Nanjing University of Chinese Medicine)

  • Yechun Xu

    (University of Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

Abstract

The essential role of RIPK3 in necroptosis makes its inhibition a promising therapeutic strategy. However, the development of RIPK3 inhibitors has been hampered by on-target apoptosis and limited kinase selectivity. Inspired by the R69H mutation, which prevents on-target apoptosis by disrupting RIPK3 dimerization, we design LK-series inhibitors that effectively inhibit RIPK3 in biochemical assays and block TNF-α-induced necroptosis in both mouse L929 and human HT29 cells without inducing apoptosis. The representative compound, LK01003, shows high selectivity across a panel of 379 kinases. Our structural studies reveal that LK compounds act as Type I1/2 inhibitors, engaging a unique hydrophobic site and stabilizing an inactive conformation of RIPK3. Moreover, several type II inhibitors are also revealed to maintain RIPK3 in the inactive conformation and do not induce on-target apoptosis. These findings suggest a promising strategy for rational design of safe and selective inhibitors by locking the inactive conformation of RIPK3.

Suggested Citation

  • Haixia Su & Guofeng Chen & Hang Xie & Wanchen Li & Muya Xiong & Jian He & Hangchen Hu & Wenfeng Zhao & Qiang Shao & Minjun Li & Qiang Zhao & Yechun Xu, 2025. "Structure-based design of potent and selective inhibitors targeting RIPK3 for eliminating on-target toxicity in vitro," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59432-8
    DOI: 10.1038/s41467-025-59432-8
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    References listed on IDEAS

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    1. William J. Kaiser & Jason W. Upton & Alyssa B. Long & Devon Livingston-Rosanoff & Lisa P. Daley-Bauer & Razqallah Hakem & Tamara Caspary & Edward S. Mocarski, 2011. "RIP3 mediates the embryonic lethality of caspase-8-deficient mice," Nature, Nature, vol. 471(7338), pages 368-372, March.
    2. Ruicong Wang & Hongda Li & Jianfeng Wu & Zhi-Yu Cai & Baizhou Li & Hengxiao Ni & Xingfeng Qiu & Hui Chen & Wei Liu & Zhang-Hua Yang & Min Liu & Jin Hu & Yaoji Liang & Ping Lan & Jiahuai Han & Wei Mo, 2020. "Gut stem cell necroptosis by genome instability triggers bowel inflammation," Nature, Nature, vol. 580(7803), pages 386-390, April.
    3. Avishekh Gautam & David F. Boyd & Sameer Nikhar & Ting Zhang & Ioannis Siokas & Lee-Ann Velde & Jessica Gaevert & Victoria Meliopoulos & Bikash Thapa & Diego A. Rodriguez & Kathy Q. Cai & Chaoran Yin , 2024. "Necroptosis blockade prevents lung injury in severe influenza," Nature, Nature, vol. 628(8009), pages 835-843, April.
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