Identification of Potent Cell Penetrating, Nontoxic Peptides for Inhibiting MDM2–p53 Interactions: Characterization of Anticancer Peptides via Molecular Dynamics Simulations

Inhibiting MDM2–p53 interactions is a crucial therapeutic strategy in cancer treatment, as it can restore the tumor suppressor activity of p53 and inhibit tumor progression. Peptide inhibitors have shown promise in targeting this interaction; however, their optimization for in vivo use often encounters challenges, particularly in cellular uptake. The present study addresses this limitation by identifying cell-penetrating peptides (CPPs) that are predicted to be nontoxic to humans and capable of inhibiting the MDM2–p53 interaction. We utilized a comprehensive CPP database to extract unmodified peptides, focusing on those predicted to be nontoxic. Selected candidates were subjected to molecular docking followed by 500-ns all-atom explicit-solvent molecular dynamics (MD) simulations, performed in triplicates, to evaluate their binding stability and affinity with MDM2. Binding affinity calculations using MM-PBSA, AREA AFFINITY, and PRODIGY revealed that two peptides consistently exhibited stable binding to MDM2 and demonstrated higher affinity compared with the p53 reference fragment. These peptides not only maintained favorable interactions throughout the simulations but also showed strong potential to disrupt MDM2–p53 binding and reactivate p53 function. The findings highlight these peptides as promising nontoxic anticancer agents and provide a strong foundation for the development of peptide-based therapeutics targeting the MDM2–p53 interaction.