Targeting the Undruggable: Design of Potent Bifunctional Degraders for the p53 Oncoprotein

TP53 is the most frequently mutated gene in human cancers. The p53 protein, encoded by the TP53 gene, regulates cell growth and prevents tumor formation. As a transcriptional factor, p53 lacks binding pockets for small molecule compounds, and despite decades of research, no drugs targeting this protein have proven effective. Recently, RNA aptamer-based PROTACs targeting the p53-R175H mutant have been developed. In this research, we utilized in silico simulations to study the protein-PROTAC interactions. First, the secondary and tertiary structures of the aptamer were elucidated. Next, the aptamers were conjugated with E3 ligase binders, forming bifunctional degraders. To understand the binding orientations of the aptamer-based PROTAC to p53, molecular docking simulations were performed using the HDOCK software. Based on the structure of this initial ternary complex, we rationally designed novel aptamer-based PROTACs that can specifically bind to p53 and CRBN, facilitating mutant p53 degradation. One was selected based on the number of interactions it generated with the target protein. This selected PROTAC demonstrated higher binding energy than PROTACs obtained from experimental studies. Additionally, we proposed a novel conformational change of the p53 protein upon DNA complex formation, which has not been previously reported in the literature. Binding to DNA causes p53 to expand significantly, with the DNA interacting with the protein's positive region. This work holds promise for treating a broad range of advanced solid tumors that are challenging to control with conventional therapies.