Effect of linker on the binding free energy of stapled p53/HDM2 complex

Inactivation of the tumor suppressor p53 resulting from the binding with a negative regulator HDM2 is among the predominant defects in human cancers. p53-mimicking peptides whose conformational and proteolytic stability is enhanced by an all-hydrocarbon staple are being recognized as promising anticancer agents for disrupting the p53–HDM2 binding and reactivating p53. Herein, we conduct a computational modeling and thermodynamic characterization of stapled p53/HDM2 complex via molecular docking, simulations, and binding free energy analysis. The binding thermodynamics analysis is done based on the end-point calculation of the effective binding energy—a sum of the direct peptide–protein interaction energy and the dehydration penalty—and on its decomposition into contributions from specific groups constituting the complex. This allows us to investigate how individual amino acids in the stapled p53 and HDM2 contribute to the binding affinity. We find that not only the epitope residues (F19, W23 and L26), but also the hydrocarbon linker of the stapled p53 impart significant contributions. Our computational approach will be useful in designing new stapled peptides in which the staple location is also optimized to improve the binding affinity.