2. Academic Validation
  3. Target proteins profiling of irreversible kinase inhibitor pelitinib and discovery of degradation of PRDX4 by label free chemoproteomics

Target proteins profiling of irreversible kinase inhibitor pelitinib and discovery of degradation of PRDX4 by label free chemoproteomics

  • J Pharm Biomed Anal. 2023 Apr 18;230:115398. doi: 10.1016/j.jpba.2023.115398.
Jing Li 1,  Mengmeng Zheng 2,  Yao Xu 2,  Xin Yang 1,  Jingwu Kang 3
Affiliations

Affiliations

  • 1 State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China.
  • 2 State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China.
  • 3 State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China. Electronic address: [email protected].
PMID: 37084663 DOI: 10.1016/j.jpba.2023.115398
Abstract

Cell-based methods for profiling the kinase inhibitor selectivity are badly needed, especially for the irreversible kinase inhibitors. Here we reported a chemoproteomics approach for profiling the target proteins of irreversible kinase inhibitor with label free quantitative proteomics by using iodoacetamide alkyne as a chemical probe. In total 41 proteins were identified in high confidence (fold change 3.5, p value < 0.05) including PRDX4, STAT3, E2 conjugating enzymes UBE2L3, UBE2K, UBE2N, UBE2V1 and UBE2Z as well as E3 ligase TRIM 25. We validated the interaction between pelitinib and PRDX4 with a cell-based assay, and discovered that pelitinib can induce the degradation of PRDX4. The discovery was confirmed by biochemical assay, cellular thermal shift assay and miRNA knockdown experiment. Our data suggested that pelitinib can be a covalent molecular glue inducing the degradation of PRDX4. In addition, our work demonstrated that identification of the interactions between ligand and ubiquitylation associated proteins by chemoproteomics profiling can be used as a new strategy for identifying molecular glue degraders.

Keywords

Chemoproteomics; Drug target identification; Molecular glue degraders; Pelitinib; Peroxiredoxin 4.

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