Investigating the binding interactions of arg-gly-asp peptide with integrin αvβ3 and αvβ6: An In Silico study

Integrins found on the surfaces of cancer cells serve a key role in tumor angiogenesis as well as cancer cell metastasis. The RGD (Arg-Gly-Asp) peptide binds as a targeting moiety for integrin receptor-mediated targeted delivery of therapeutics. The interactive study of RGD (Arg-Gly-Asp) peptide with integrin αvβ3 and integrin αvβ6 proteins has been studied using the isolated rigid receptor and flexible ligand concept by using molecular docking calculations at the binding sites of the crystal structure of integrin αvβ3 and integrin αvβ6 proteins. To achieve this, a rigid receptor-flexible ligand docking methodology has been followed to interpret the RGD peptide's binding sites with integrin αvβ3 and integrin αvβ6 proteins. The RGD interaction with αVβ6 mimics the RGD binding mode seen in αVβ3, however, the variations in the integrin-binding pockets can have a significant impact on the ligand-binding ability. The characteristics of the binding pocket, as well as the study of docking poses offered a justification for the recognition of ligand as well as its selectivity. This paper presents the molecular docking study to analyze the ligand recognition and selectivity on basis of their binding performances.