Discovery of a Covalent Inhibitor Selectively Targeting the Autophosphorylation Site of c-Src Kinase

  • ACS Chem Biol. 2024 Apr 19;19(4):999-1010. doi: 10.1021/acschembio.4c00048.
Huimin Zhang  1  2 ,  Dounan Xu  1  2  3 ,  Hongchan Huang  4  5 ,  Hao Jiang  2 ,  Linghao Hu  1 ,  Liping Liu  2  5 ,  Ge Sun  2  5 ,  Jing Gao  2  5 ,  Yuanqing Li  2  5  6 ,  Cuicui Xia  7 ,  Shijie Chen  2  5 ,  Hu Zhou  2  5 ,  Xiangqian Kong  4  5 ,  Mingliang Wang  1  2 ,  Cheng Luo  1  2  5  6
Affiliations
  • 1. Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China.
  • 2. State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
  • 3. Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China.
  • 4. Center for Chemical Biology and Drug Discovery, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
  • 5. University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China.
  • 6. School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.
  • 7. Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230026, China.
PMID: 38513196 DOI: 10.1021/acschembio.4c00048
Abstract

Nonreceptor tyrosine kinase c-Src plays a crucial role in cell signaling and contributes to tumor progression. However, the development of selective c-Src inhibitors turns out to be challenging. In our previous study, we performed posttranslational modification-inspired drug design (PTMI-DD) to provide a plausible way for designing selective kinase inhibitors. In this study, after identifying a unique pocket comprising a less conserved cysteine and an autophosphorylation site in c-Src as well as a promiscuous covalent inhibitor, chemical optimization was performed to obtain (R)-LW-Srci-8 with nearly 75-fold improved potency (IC50 = 35.83 ± 7.21 nM). Crystallographic studies revealed the critical C-F···C═O interactions that may contribute to tight binding. The kinact and Ki values validated the improved binding affinity and decreased warhead reactivity of (R)-LW-Srci-8 for c-Src. Notably, in vitro tyrosine kinase profiling and cellular activity-based protein profiling (ABPP) cooperatively indicated a specific inhibition of c-Src by (R)-LW-Srci-8. Intriguingly, (R)-LW-Srci-8 preferentially binds to inactive c-Src with unphosphorylated Y419 both in vitro and in cells, subsequently disrupting the autophosphorylation. Collectively, our study demonstrated the feasibility of developing selective kinase inhibitors by cotargeting a nucleophilic residue and a posttranslational modification site and providing a chemical probe for c-Src functional studies.

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