Computational Design of Myristoylated Cell-Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector-Binding Membrane Interface

A number of small inhibitors have been developed in recent years to target the cancer-driving protein, K-Ras. In this study, we propose and design a novel way of targeting oncogenic K-Ras4B.G12D with myristoylated cell-penetrating peptides which become membrane-anchored and lock the protein into an inactive state. In all atom molecular dynamics simulations, such peptides associate with K-Ras4B exclusively at the effector-binding region, which, in turn, is expected to hinder the binding of downstream effector proteins (e.g., C-Raf). The myristoylated R9 (Arg(9)) peptide locks K-Ras4B.G12D into orientations that are unfavorable for effector binding. After breaking the cyclic structure and myristoylation, a cell-penetrating peptide cyclorasin 9A5, which was designed for targeting the Ras/Raf interface, is also found to be effective in targeting the Ras/membrane interface. The myristoylated peptides likely have high cell permeability because of their mixed cationic/hydrophobic character at the N-terminus, while simultaneously the subsequent multiple charges help to maintain a close association of the peptide with the K-Ras4B.G12D effector-binding lobe. Targeting protein-membrane interfaces is starting to attract attention very recently, thanks to our understanding of the signaling mechanism of an increased number of peripheral membrane proteins. The strategy used in this study has potential applications in the design of drugs against K-Ras4B-driven cancers. It also provides insights into the general principles of targeting protein-membrane interfaces.