Structure-based design of potent and selective inhibitors targeting RIPK3 for eliminating on-target toxicity in vitro PMID: 40341069

ADC Targets in Oncology

2026-04-10

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

Nat Commun. 2025 May 8;16(1):4288. doi: 10.1038/s41467-025-59432-8.

Haixia Su ^# ¹ ² , Guofeng Chen ^# ³ , Hang Xie ^# ⁴ , Wanchen Li ^# ⁵ , Muya Xiong ³ , Jian He ⁶ ⁷ , Hangchen Hu ⁶ , Wenfeng Zhao ⁶ , Qiang Shao ⁶ ⁷ , Minjun Li ⁸ , Qiang Zhao ⁹ ¹⁰ ¹¹ , Yechun Xu ¹² ¹³ ¹⁴

Affiliations

1. State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, 201203, China. [email protected].
2. University of Chinese Academy of Sciences, Beijing, 100049, China. [email protected].
3. School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
4. School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
5. Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, 315100, China.
6. State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, 201203, China.
7. University of Chinese Academy of Sciences, Beijing, 100049, China.
8. Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China.
9. State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, 201203, China. [email protected].
10. University of Chinese Academy of Sciences, Beijing, 100049, China. [email protected].
11. School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China. [email protected].
12. State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, 201203, China. [email protected].
13. University of Chinese Academy of Sciences, Beijing, 100049, China. [email protected].
14. School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China. [email protected].
# Contributed equally.

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 I^1/2 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.