In-silico design of peptide inhibitors of K-Ras target in cancer disease

Abstract

Cancer is a leading cause of death, over one million individuals analyzed, and around 500,000 deaths happen due to cancer every year alone in the United States. The Ras is a significant protein in the signaling transduction pathways and has a leading role in cell proliferation. Above 30% of all human tumors arises due to the mutations in genes that encode a Ras protein that operate signaling cascades necessary for malignant transformation, tumor angiogenesis, and metastasis. The Ras gene family comprised of 36 total genes in human. The N-Ras, K-Ras, and H-Ras are accounted for to assume noticeable function in human cancer. The mutation in K-Ras protein is most commonly found in tumors. K-Ras is the most crucial driver in lung and pancreatic cancers. Among the mutations of N-Ras, H-Ras, and K-Ras, the mutant K-Ras is the most prevalent target for the development of Lungs, colon, and pancreatic cancers. The study aimed to develop the peptide inhibitors of the K-Ras G12D. The crystal structure of the mutant K-Ras/R11.1.6 G12D complex was retrieved from the protein databank. The protein R11.1.6 directly blocks interaction with Raf and diminishes signaling through the Raf-MEK-ERK signaling pathway. Here, in this study, we designed novel peptides from the truncated reference peptide (R11.1.6) through residue scan methodology. The top ten designed peptides (based on binding free energies) were subjected to molecular dynamics simulations using AMBER to evaluate stability. Our results indicate that the top ten selected peptides have strong interactions with K-Ras than the reference peptide (R11.1.6) and have the potency to prevent the binding of Raf and K-Ras.

Communicated by Ramaswamy H. Sarma

Keywords:

• Cancer
• K-Ras protein
• per-mutations
• molecular dynamics simulation

Disclosure statement

The authors declare no competing financial interests.

Authors contribution

AW Conceived and designed the experiments; MG performed Molecular Dynamics simulation study and analysis wrote the initial draft of the paper; AUR plots all the analyzed data and refines the manuscript. AW, MS, and MA reviewed and approved the manuscript.

Additional information

Funding

This work was supported by the Higher Education Commission of Pakistan for the financial support under the National Research Program for Universities; detail of Project No. 20.3479.