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

In this work, computer-based molecular dynamics studies of the interaction of the pharmacological pair “VECTOR-RECEPTOR” were conducted in order to model promising mechanisms and processes of delivering a specific drug to a tumor. The purpose of these computational MD calculations is to study the interaction processes and determine the spatial position of the RGD-peptide + αvβ3-integrin receptor system, which is solvated with water. The configuration positions of the RGD-peptide + αvβ3-integrin system in relaxed states with duration of 100 ns were obtained as a result of MD modeling. In this case, two RGD peptides were modeled, located outside and inside the αvβ3-integrin receptor. One of the two RGDs is a peptide from the original PDB file localized inside the αvβ3-integrin receptor. Another RGD peptide is located outside the receptor in its initial position, freely diffuses over the entire area of the modeling cell and naturally comes into contact and binds to αvβ3-integrin. This fact may be of great importance from the point of view of “pharmacological” perspectives, mechanisms of specificity and binding of RGD peptides to the αvβ3 integrin receptor, predicting the functional aspects of the interaction processes of the pharmacological pair “VECTOR-RECEPTOR” (RGD peptide + αvβ3 integrin receptor) for the purposes of specific drug delivery to the tumor.