‘In silico’ repurposing new inhibitors of EGFR and VEGFR-2 kinases via biophysical mechanisms

Abstract

Epidermal growth factor receptor (EGFR) controls cell growth, death, and proliferation through a variety of signaling mechanisms. The expression of vascular endothelial growth factor receptor-2 (VEGFR-2) by endothelial cells from malignant tissues triggers a series of signaling pathways that lead to tumor angiogenesis and increase cancer cell survival, proliferation, migration, and vascular permeability. The aim is to find novel inhibitors for EGFR and VEGFR-2 kinases by molecular docking drug-likeness models, pharmacokinetic, interaction analysis, and molecular dynamic simulation. Over 482 ligands were tested against the kinases, there are about 20 compounds that had the best docking scores for the 2 kinases but only compound 2C inhibited them with the highest score values by binding to active sites pocket established through molecular docking study. Secondly, the drug-likeness score of 2C was very good compared to the other compounds. The pharmacokinetics, physicochemical properties, and toxicity of 2C were much better than sorafenib and erlotinib as references. Analysis of interaction showed a strong interaction between 2C and active sites of EGFR and VEGFR-2 kinases illustrated by calculation of halogen bonds, π-Cation Interactions, Hydrogen Bonds, and Hydrophobic Interactions. Finally, the molecular dynamic simulation was also used to assess the stability of the EGFR and VEGFR-2 kinases-2C complexes. The complexes’ stability was validated by RMSD, R_g, RMSF, SASA, and several hydrogen bonds analysis. 2C was shown to interact stably with pocket residues after MD simulation. Compound 2C may be a promising way to slow the signaling cascade of proteins that are significant contributors to the spread of cancer.

Communicated by Ramaswamy H. Sarma

Keywords:

• Drug discovery
• protein
• molecular docking
• molecular dynamic simulation
• eGFR
• VEGFR-2
• kinases

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Our manuscript was not applied to human beings and thus requires no ethical approval.

Authors contributions

M.H.I. designed research, performed research, contributed analytic tools, analyzed data, and reviewed the paper. I.M. helped in designing the research, carried out the experiments, analyzed data, and wrote the paper. I.K. helped in designing the research, supervised the experiments, analyzed data, and reviewed the paper.

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All data are available and attached.

Additional information

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The authors didn’t receive any support or funds to conduct this paper.