Molecular Dynamics Modeling of Pharmacological Vector-Receptor Pairs for Specific Drug Delivery to the Tumor: Atomic/Molecular Mechanisms of RGD Peptide Embedding in the Integrin αvβ3 Receptor

Abstract

Computer-based molecular dynamics studies of the interaction of the pharmacological pair “vector–receptor” have been carried out to simulate promising mechanisms and processes of specific drug delivery to the tumor. The purpose of computational calculations is the description of interaction processes and the determination of the spatial positions of the RGD peptide + integrin α_vβ₃ receptor system, solvated with water. The configuration positions of the RGD peptide + integrin α_vβ₃ system in 100 ns relaxed states were obtained from molecular dynamics modeling. Two RGD peptides located outside and inside the integrin α_vβ₃ receptor were modeled. One of them is a peptide of the original PDB file localized inside the integrin α_vβ₃ receptor. The other RGD peptide is located outside the receptor in its initial position, freely diffuses throughout the entire area of the modeling cell, and naturally comes into contact and binds to integrin α_vβ₃.