Conventional small-molecule probes play their roles by perturbing the functions of proteins, including blocking enzyme catalysis or antagonizing receptor signaling.
However, a compound only binds to only one of these domains that may can not fully inactivate the protein. There exist a novel strategy, chemical probes, which direct proteins to the proteolytic degradation machinery of the cell. As a result, they lead to a complete loss of protein expression.
Here, we present a chemical proteomics approach to discover E3 ligases that support targeted protein degradation when engaged by electrophilic PROTACs.
In this article, we will describe a heterobifunctional compound, KB02-SLF. It is a cysteine-directed fragment electrophile to exhibit broad proteomic reactivity. At the same time, it has reversible ligands for protein targets of interest.
KB02-SLF is a PROTAC-based nuclear FKBP12 degrader (molecular glue).
KB02-SLF promotes nuclear FKBP12 degradation by covalently modifying DCAF16 (E3 ligase). Additionally, it can improve the durability of protein degradation in biological systems. SLF binds ubiquitin E3 ligase ligand KB02 via a linker to form KB02-SLF.
In HEK293T cells, KB02-SLF treatment promotes a substantial reduction in nuclear FKBP12 that is sustained across a 4-72 h time frame. Cell imaging studies confirm the selective loss of nuclear-localized FKBP12 in KB02-SLF-treated cells. KB02-SLF promotes the loss of FKBP12-NLS across a concentration of ~0.5-5 µM. But shows varied reductions in activity at higher concentrations. The degradation of FKBP12_NLS induced by KB02-SLF is mediated by DCAF16.
First, DCAF16 exclusively promotes the degradation of nuclear proteins, it avoids cytosolic proteins that engage a bifunctional compound. Second, it provides a ligand-induced protein degradation at low frictional engagement (~10% for KB02-SLF). Lastly, the covalent adduct formed between electrophilic PROTACs and DCAF16 may improve the durability of protein degradation in biological systems.
In conclusion, DCAF16 supports targeted protein degradation when engaged by electrophilic PROTACs. As an E3 ligase subunit, it offers advantages as a neway to the emerging subset of E3 ligases. And it promotes ligand-induced protein degradation.
Reference:
Zhang X, et al. Nat Chem Biol. 2019 Jul;15(7):737-746.