Structural mechanism study of KRpep2d anti-cancer peptide interaction with wild type and mutant KRAS using molecular dynamic simulation

Abstract

Background: Cancer is one of the major health concerns worldwide, and there is an ongoing effort to find novel treatment approaches. RAS Proteins play a pivotal role in the proliferation pathways, and their mutations can lead to persistent RAS activation and cancerous cells. In this regard, KRpep2d is an anticancer peptide against KRAS(G12D) mutant, but its exact mechanism of action is unknown. Objective: In this study, the molecular mechanism of KRpep2d on the inhibition of mutant KRAS via the MD simulation method is investigated. Methods: MD simulations of KRAS variants in the free and complex form with KRpep2d were carried out via "GROMACS" software. Supplementary analyses were performed after the simulation of each system. The distance variations of residues in different simulation systems, were conducted to define conformational changes. Moreover, the affinities of KRpep2d and the nucleotide to KRAS were measured by the "Umbrella Sampling" method. Also, residue interactions and β2-strand length of KRAS variants were calculated by "LigPlot plus" software and DSSP plugin of "GROMACS" software, respectively. System snapshots were represented by "CHIMERA UCSF" software. Results: It was shown that KRpep2d binding to the KRAS(G12D) makes the GTP move from the P-loop location. On the other hand, KRpep2d reduces the size of the effector binding region (β2-strand) of KRAS mutants. It was also observed that KRpep2d decreases and increases the Switch II and Switch I flexibility, respectively, in KRAS(G12D). All these results were exclusive for KRAS(G12D). Additionally, the parameters of β2-strand length and the affinity of KRpep2d were combined to measure relative activity. The acquired relative activity was the minimum for KRAS(G12D). Conclusion: KRpep2d shows anticancer activity on KRAS(G12D) by expelling the nucleotide from its location and reducing the β2-strand as the effector binding region of KRAS.