Targeted Degradation of DNA/RNA Binding Proteins via Covalent Hydrophobic Tagging

Targeted protein degradation (TPD) holds great promise for biological inquiry and therapeutic development. However, it still remains elusive to destruct DNA/RNA binding proteins (DBPs/RBPs) previously deemed undruggable. Herein, we report ligandassisted covalent hydrophobic tagging (LACHT) as a modular strategy for TPD of these difficult-to target proteins. Guided by a noncovalent protein ligand, LACHT leverages a reactive N-acyl-N-alkyl sulfonamide group to covalently label the protein target with a hydrophobic adamantane, which further engages the cellular quality control mechanism to induce proteolytic degradation. Using a small molecule ligand, we demonstrated that LACHT allowed TPD of a DBP, bromodomain-containing protein 4, in human leukemia cells with high efficiency. Mechanistic studies revealed that LACHT-mediated TPD dependent on ligand-directed irreversible tagging and the covalently labeled proteins underwent polyubiquitination before removal through both the proteasome and the lysosome. Furthermore, when an RNA ligand was employed, we showed that LACHT also enabled TPD of an RBP, Lin28a, leading to upregulation of its downstream let-7 miRNA. This study thus provides a generalizable platform to expand the TPD toolbox for biomedical applications.

Automated summary

A new strategy called LACHT has been developed to degrade previously undruggable DNA/RNA binding proteins. This strategy utilizes a noncovalent protein ligand to covalently label the protein target with a reactive N-acyl-N-alkyl sulfonamide group, leading to proteolytic degradation through cellular quality control mechanism. This study provides a generalizable TPD platform for biomedical applications.