Computational design and experimental validation of peptide inhibitors targeting the p53-COP1 interaction to suppress p53 ubiquitination

Breast cancer, as one of the most prevalent malignant tumors among women, is a leading cause of female mortality. Inhibiting the ubiquitination of p53 protein would be helpful to control the development and progression of breast cancer, as p53 is crucial for regulating cell proliferation, DNA damage repair, and apoptosis. Herein, peptide inhibitors were designed to inhibit the interaction between p53 protein and ubiquitin ligase COP1. Molecular dynamics (MD) simulations with combined Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) calculations were used to explore the molecular interface of the p53 protein. Peptide ligands were then designed to bind the COP1-interacting region of p53, followed by the screening including docking, MD simulations and the experimental validation. QTSWGPEM and QPSGGPYM were obtained and proven to be capable of binding to p53 protein in the enzyme-linked immunosorbent assay (ELISA) and the fluorescence polarization (FP) assay. Effective suppression on p53-COP1 interaction by peptides was confirmed in pull-down assay. Inhibition rates of 75% (QTSWGPEM) and 36% (QPSGGPYM) were obtained in the competitive ELISA. The results demonstrated the effective design of inhibitors using a strategy combining computational design and experimental validation, which would be helpful for the development of therapeutic strategies for breast cancer.