Molecular Simulation Studies On Characteristics Of Functional Peptide-dendrimer Conjugates

Functional short peptides play a key role in biological signal transduction,regulating biological functions and protein-protein interactions,while some of functional short peptides derived from protein exhibit low biological activity at their free state,that limit their biomedical applications to a great extent.To raise biological activity of these peptides,carriers were often used in studies,and among them zwitterionic polyamide-amine dendrimer of generation 5(PAM(G5))has been proved to be an effective carrier for functional short peptides.A functional short peptide,Arginine-glycine-aspartate(RGD),can be conjugated on the surface of PAM(G5)through the combination of chemical bonds and hydrogen bonds method to reach a superior configuration and higher biological affinity with integrin αvβ3,and further improve the anti-cancer effect of the functional short peptide.However,the conjugate based on PAM(G5)hold a relatively low drug loading capacity.In order to reach a higher drug loading capacity,we examined a feasible method,that is to reduce the generation of the PAM.The key to the realization of this method is whether the conjugate can maintain the good mass transfer characteristics,conformation,and binding affinity with integrin while reducing the generation of the PAM.Therefore,in this study,the representative functional peptide RGD was conjugated on the surface of zwitterionic PAM carrier of different generations through the conjugating method above,and the mass transfer characteristics,structures and affinity of the conjugates have also been studied by molecular simulations.The main contents and conclusions are as follows:1.Selection of carrier’s generation:Reducing generation of the carrier will not have a negative impact on the diffusion performance of PAM-CRGDS conjugates according to the self-diffusion coefficient.Meanwhile,the RGD peptide conjugated to the surface of the PAM(G3,G4,or G5)carrier has a superior structure and high stability similar to the standard c(RGDfV)ligand,even when the length of peptide changes.It is related to the relatively small structural fluctuations of PAM(G3,G4,or G5)themselves,which can provide stable loading conditions for functional short peptides.Therefore,based on the mass transfer performance and conformational analysis,PAM(G3,G4,or G5)are more suitable choices for loading RGD peptides.2.Developing a docking method of macromolecular ligand and protein:A docking method based on matrix transformation is proposed to realize the docking of integrin αvβ3 and the selected PAM(G3,G4 or G5)-CRGDS conjugates.This method can realize the general docking process of macromolecular ligands and proteins when the binding sites are known.The docking process is relatively accurate and can save a lot of computing resources.3.Studies on characteristic of the conjugates:Under different ion concentrations,RGD peptide on the PAM(G3,G4 or G5)-CRGDS conjugate maintains good structure when binding with integrin αvβ3,and the fluctuation of RGD peptide and the surrounding PAM carrier groups is relatively low,which indicated that the ion concentration has a low impact on the structure of PAM(G3,G4 or G5)-CRGDS conjugates.Meanwhile,by using Molecular Mechanics/PoissonBoltzmann Surface Area(MM/PBSA)method to calculate the binding free energy,it was found that PAM(G3,G4 or G5)-CRGDS conjugates all have strong binding with integrin αvβ3.Therefore,the generation of PAM carriers can be reduced to 3-4 to increase the drug loading capacity of the PAM-CRGDS conjugate.