Self-Assembled Aptamer-Derived PROTAC Enables Efficient Cellular Internalization for Intracellular Sclerostin Degradation and Triple-Negative Breast Cancer Therapy.

Abstract

Comprising an aptamer for protein of interest (POI) recognition, a linker, and an E3 ligand, aptamer-derived PROTAC enables precise intracellular POI degradation via ubiquitin-proteasome system. Due to hydrophilic polyanionic backbone, their efficacy was fundamentally constrained by inefficient cellular internalization. Here, we engineered a self-assembled aptamer-derived PROTAC (SADP) featuring a dual-hydrophobic module composed of an alkyl linker and a separate fatty acid. The alkyl linker could modulate the spatial arrangement between the aptamer and E3 ligand while also synergize with the fatty acid to drive formation of SADP nanomicelles for cellular internalization enhancement. As a proof of concept, SADP (Apt-F-10-V) was screened and achieved approximately five-fold higher internalization efficiency than conventional aptamer-derived PROTAC, resulting in potent intracellular sclerostin degradation (DC50 = 76.8 nM, Dmax = 82%) in triple-negative breast cancer (TNBC) cells. Mechanistically, Apt-F-10-V could be internalized via clathrin-mediated endocytosis, followed by lysosomal disassembly and escape into the cytoplasm. The liberated monomers could induce a sclerostin/PROTAC/VHL ligase ternary complex for intracellular sclerostin degradation. Importantly, Apt-F-10-V demonstrated tumor accumulation and robust tumor suppression in both TNBC cell-derived and patient-derived xenograft models. This study presents that cooperative micellization of aptamer-derived PROTAC could overcome the cellular internalization barrier, enabling potent intracellular sclerostin degradation and TNBC therapy.