Identification of proteomic landscape of drug-binding proteins in live cells by proximity-dependent target ID

  • Cell Chem Biol. 2022 Dec 15;29(12):1739-1753.e6. doi: 10.1016/j.chembiol.2022.10.001.
Chulhwan Kwak  1 ,  Cheolhun Park  1 ,  Minjeong Ko  2 ,  Chun Young Im  3 ,  Heegyum Moon  3 ,  Young-Hoon Park  3 ,  So Young Kim  3 ,  Seungyeon Lee  3 ,  Myeong-Gyun Kang  1 ,  Ho Jeong Kwon  4 ,  Eunmi Hong  5 ,  Jeong Kon Seo  6 ,  Hyun-Woo Rhee  7
Affiliations
  • 1. Department of Chemistry, Seoul National University, Seoul 08826, Korea.
  • 2. Chemical Genomics Leader Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.
  • 3. New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea.
  • 4. Chemical Genomics Leader Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea. Electronic address: [email protected].
  • 5. New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea. Electronic address: [email protected].
  • 6. Graduate School of Semiconductor Materials and Devices Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea; UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea. Electronic address: [email protected].
  • 7. Department of Chemistry, Seoul National University, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea. Electronic address: [email protected].
PMID: 36272407 DOI: 10.1016/j.chembiol.2022.10.001
Abstract

Direct identification of the proteins targeted by small molecules can provide clues for disease diagnosis, prevention, and drug development. Despite concentrated attempts, there are still technical limitations associated with the elucidation of direct interactors. Herein, we report a target-ID system called proximity-based compound-binding protein identification (PROCID), which combines our direct analysis workflow of proximity-labeled proteins (Spot-ID) with the HaloTag system to efficiently identify the dynamic proteomic landscape of drug-binding proteins. We successfully identified well-known dasatinib-binding proteins (ABL1, ABL2) and confirmed the unapproved dasatinib-binding kinases (e.g., Btk and CSK) in a live chronic myeloid leukemia cell line. PROCID also identified the DNA helicase protein SMARCA2 as a dasatinib-binding protein, and the ATPase domain was confirmed to be the binding site of dasatinib using a proximity ligation assay (PLA) and in cellulo biotinylation assay. PROCID thus provides a robust method to identify unknown drug-interacting proteins in live cells that expedites the mode of action of the drug.

Keywords
HaloTag; SAHA; SMARCA2; dasatinib; proximity labeling; target-ID; translocation assay.
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