Inducible Degradation of Oncogenic Nucleolin Using an Aptamer-Based PROTAC

J Med Chem. 2023 Jan 26;66(2):1339-1348. doi: 10.1021/acs.jmedchem.2c01557. Epub 2023 Jan 6.

Abstract

While proteolysis-targeting chimeras (PROTACs) are showing promise for targeting previously undruggable molecules, their application has been limited by difficulties in identifying suitable ligands and undesired on-target toxicity. Aptamers can virtually recognize any protein through their unique and switchable conformations. Here, by exploiting aptamers as targeting warheads, we developed a novel strategy for inducible degradation of undruggable proteins. As a proof of concept, we chose oncogenic nucleolin (NCL) as the target and generated a series of NCL degraders, and demonstrated that dNCL#T1 induced NCL degradation in a ubiquitin-proteasome-dependent manner, thereby inhibiting NCL-mediated breast cancer cell proliferation. To reduce on-target toxicity, we further developed a light-controllable PROTAC, opto-dNCL#T1, by introducing a photolabile complementary oligonucleotide to hybridize with dNCL#T1. UVA irradiation liberated dNCL#T1 from caged opto-dNCL#T1, leading to dNCL#T1 activation and NCL degradation. These results indicate that aptamer-based PROTACs are a viable alternative approach to degrade proteins of interest in a highly tunable manner.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Nucleolin
  • Phosphoproteins* / metabolism
  • Proteasome Endopeptidase Complex* / metabolism
  • Proteolysis
  • RNA-Binding Proteins / metabolism
  • Ubiquitin-Protein Ligases / metabolism

Substances

  • Proteasome Endopeptidase Complex
  • Phosphoproteins
  • RNA-Binding Proteins
  • Ubiquitin-Protein Ligases