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

In this work, computer-based molecular dynamics studies of the interaction of the pharmacological pair “vector–receptor” have been carried out to model promising mechanisms and processes of specific drug delivery to the tumor. The purpose of these computational molecular dynamic calculations is to study the interaction processes and determine the spatial positions of the RGD peptide + αβ-integrin receptor system, which is solvated with water. The configuration positions of the RGD-peptide + αβ-integrin system in 100 ns relaxed states were obtained from molecular dynamic modeling. In this case, two RGD peptides were modeled located outside and inside the αβ-integrin receptor. One of the two RGDs is a peptide of the original PDB file localized inside the αβ-integrin 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 αβ-integrin.