Structure-based design of p62-derived peptides that inhibit autophagy-associated readouts and enhance chemotherapy response in breast cancer cells

Abstract

Rational drug design seeks small molecules, aptamers, or peptides to disrupt key cellular targets. Autophagy, crucial in tumor formation, dormancy, and chemotherapy response, especially in breast cancer, requires potent, specific modulators. This study leverages rational peptide design to develop p62-LIR-derived peptides predicted to target the LC3B interaction interface and modulate autophagy-associated readouts, aiming to sensitize BC cells to chemotherapy. The 6–15-mer peptides, based on the LC3 interacting region (LIR) domain of p62, were evaluated in silico for predicted binding to the LC3B LIR-docking region. Two peptides, LIR-P1 (DDWTHLSRPMKWKK) and LIR-P2 (VHSADRDWTHLSKEV), were selected based on their HADDOCK scores and synthesized for studies in MCF-7 and TNBC MDA-MB 231 cells. At a non-toxic concentration (200 μg/ml), both peptides effectively blocked autophagic flux in BC cells, as shown by western blot analysis of LC3B and p62 protein turnover. Fluorescence microscopy showed that LIR-P2 exhibited higher cellular uptake than LIR-P1, while functional assays were consistent with inhibition of autophagic flux. The combination of LIR-P2 and 5-FU synergistically increased chemotherapy cytotoxicity in MCF-7 and MDA-MB 231 cells, showing LIR-P2's potential to enhance treatment, especially in unresponsive TNBC. These findings support further investigation of p62-derived peptides as candidate modulators of autophagy and chemotherapy response in breast cancer cells.