Dual Aptamers‐Based SETDB1 PROTACs as Effective Anti‐Tumor Strategies for Breast Cancer

ABSTRACT PROteolysis TArgeting Chimeras (PROTACs) have emerged as a promising strategy for drug development targeting oncogenic proteins. Here, we report the development and characterization of dual aptamer‐based PROTACs targeting SET domain bifurcated histone lysine methyltransferase 1 (SETDB1), a key epigenetic regulator implicated in breast cancer progression, drug resistance, and tumor immune evasion. Using the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, we identified a high‐affinity single‐stranded DNA (ssDNA) aptamer against SETDB1. This aptamer was conjugated to the nucleolin‐targeting aptamer AS1411, generating a single‐strand PROTAC (AP‐SETDB1‐S6A) and a partial double‐strand PROTAC (AP‐SETDB1‐D2), both of which exhibit good serum stability. These two PROTACs directly penetrate breast cancer cells and effectively recruit the E3 ligase mouse double minute 2 homolog (MDM2) to SETDB1, inducing proteasome‐dependent degradation of SETDB1. Functional assays demonstrated that both AP‐SETDB1‐S6A and AP‐SETDB1‐D2 significantly inhibit breast cancer cell proliferation and migration, and resensitize drug‐resistant breast cancer cells to tamoxifen. Notably, they further enhance the cytotoxic activity of CD8 + T cells against breast cancer cells and directly target breast cancer cells to suppress tumor growth in vivo. This study establishes dual aptamers‐based PROTACs targeting SETDB1, offering effective therapeutic strategies for breast cancer treatment.