Phosphorothioate-Modified DNA Aptamer-Based PROTACs for Targeted Degradation of Estrogen Receptor α

Proteolysis-targeting chimeras (PROTACs) have emerged as a powerful modality for selectively degrading intracellular proteins via the ubiquitin–proteasome system. However, their development is often hindered by the limited availability of high-affinity small-molecule ligands, particularly for challenging targets, such as transcription factors. Aptamerssynthetic oligonucleotides with high affinity and specificityoffer a promising alternative as target-binding modules in the PROTAC design. In this study, we developed DNA aptamer-based PROTACs targeting estrogen receptor α (ERα), incorporating phosphorothioate (PS) backbone modifications to enhance nuclease resistance and cellular uptake. A series of aptamer–PROTACs with varying PS modification patterns were synthesized and conjugated to a cereblon ligand via copper-catalyzed click chemistry. Biophysical analyses demonstrated that PS modifications preserved the aptamer’s secondary structure and binding affinity. Notably, both fully and partially PS-modified constructs exhibited significantly improved nuclease stability and intracellular delivery in MCF-7 cells. Western blot analysis confirmed that these modifications enhanced the ERα degradation activity, with partially modified constructs achieving a favorable balance between potency and specificity. In contrast, scrambled-sequence controls bearing full PS modification showed nonspecific degradation, underscoring the need for judicious PS positioning. Our findings highlight the utility of strategic PS modification for optimizing the pharmacological properties of aptamer-based PROTACs and provide a design framework for developing chemically stabilized nucleic acid degraders capable of targeting previously “undruggable” intracellular proteins.