Investigation of complex of lysine dendrimer of 2nd generation with molecules of therapeutic KED peptide by computer simulation

Abstract

Lysine dendrimers could be used in many biomedical applications. For example these dendrimers could be used for delivery of short regulatory peptides consisting of several aminoacid residues. We investigated earlier interactions between lysine dendrigraft of 2nd generation and molecules of KED peptide. In present paper we study interaction of lysine dendrimer and molecules of KED peptide. The system containing one dendrimer of 2nd generation and 8 molecules of KED in water with explicit account of counterions was studied by computer simulation. The method of molecular dynamics was used for this goal. We obtained that formation of complex consisting of the dendrimer and all peptide molecules occurs during initial time (t < 40 ns) of simulation. The size, anisotropy of shape and radial density profile of stable complex (after t > 40ns) were studied also. We have shown that formation of complex occurs due to electrostatic interaction between oppositely charged dendrimer. At the same time other interactions, for example hydrogen bonds, also give their contribution to this process. Stable dendrimer-peptide complex has size close to 1,5nm and small shape anisotropy. Density of dendrimer atoms is highest in the centre of complex while density of peptides atoms has maximum at radial distance r=1nm. It total we have shown that lysine dendrimers is suitable carrier for molecules of KED peptide.

Theoretical–experimental prediction of the selectivity between polyamidoamine dendrimers and bioactive peptides derived from amaranth seeds

“…The interactions of these oligopeptides can benefit from the various protons that can be exchanged in the structure and thus lead to better interaction energies, as has been described in previous studies. 47 In previously reported theoretical-experimental studies with dendrimers of different natures, it was shown that the interaction with some peptides is stronger in the periphery, 63,64 given the large number of functional groups that give rise to a stable complex. 64 This opens a wide range of possibilities for using a PAMAM dendrimer as a base with high affinity towards different amino acids for the separation of peptides encrypted in a protein hydrolysate.…”