A proximity biotinylation-based approach to identify protein-E3 ligase interactions induced by PROTACs and molecular glues

Satoshi Yamanaka, Yuto Horiuchi, Saya Matsuoka, Kohki Kido, Kohei Nishino, Mayaka Maeno, Norio Shibata, Hidetaka Kosako and Tatsuya Sawasaki ()
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Satoshi Yamanaka: Ehime University
Yuto Horiuchi: Ehime University
Saya Matsuoka: Ehime University
Kohki Kido: Ehime University
Kohei Nishino: Tokushima University
Mayaka Maeno: Nagoya Institute of Technology
Norio Shibata: Nagoya Institute of Technology
Hidetaka Kosako: Tokushima University
Tatsuya Sawasaki: Ehime University

Nature Communications, 2022, vol. 13, issue 1, 1-17

Abstract: Abstract Proteolysis-targeting chimaeras (PROTACs) as well as molecular glues such as immunomodulatory drugs (IMiDs) and indisulam are drugs that induce interactions between substrate proteins and an E3 ubiquitin ligases for targeted protein degradation. Here, we develop a workflow based on proximity-dependent biotinylation by AirID to identify drug-induced neo-substrates of the E3 ligase cereblon (CRBN). Using AirID-CRBN, we detect IMiD-dependent biotinylation of CRBN neo-substrates in vitro and identify biotinylated peptides of well-known neo-substrates by mass spectrometry with high specificity and selectivity. Additional analyses reveal ZMYM2 and ZMYM2-FGFR1 fusion protein—responsible for the 8p11 syndrome involved in acute myeloid leukaemia—as CRBN neo-substrates. Furthermore, AirID-DCAF15 and AirID-CRBN biotinylate neo-substrates targeted by indisulam and PROTACs, respectively, suggesting that this approach has the potential to serve as a general strategy for characterizing drug-inducible protein–protein interactions in cells.

Date: 2022
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DOI: 10.1038/s41467-021-27818-z

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