Simulation Study of Stapled Alpha-Helical P53 Peptide Analogs:probing the Relationship between Structural Stability and Biological Potency

Abstract

Reactivation of the p53 cell apoptosis pathway through inhibition of the p53-hDM2 interaction is known to be a viable approach to suppressing tumor growth in many human cancers and stabilization of the helical structure of p53 analogs via a hydrocarbon cross-link (staple) has been found to lead to increased potency and inhibition of protein-protein binding. However, details of the structure and dynamic stability of the stapled peptides and their relationship to the nature and location of hydrocarbon linker are not well understood. Here, we use extensive molecular dynamics simulations to study a series of stapled α−helical peptides over a range of temperatures in solution. The peptides are found to exhibit substantial variations in predicted helicities that are in good agreement with the experimental values. In addition, we find significant variation in local structural flexibility of the peptides with the position of the linker, which appears to be more closely related to the observed differences in activity than the absolute helical stability. These simulations provide new insights into the design of α−helical stapled peptides and could aid in the development of potent inhibitors of protein interfaces.