Molecular Dynamics Study of the Effect of the γ-Abu Insert on the Conformational Behavior of the Glycopeptide Dendrimers Based on the Oligolysine Scaffold in N, N'-dimethylformamide.

Abstract Glycodendrimers bearing Tn (α-D-GalNAc-(1→O)-Ser/Thr), an identified tumor-associated carbohydrate antigen, hold promise in the post-surgery treatment of a variety of tumors such as metastatic breast cancer. We used molecular dynamics (MD) techniques to examine structural differences taking place during synthesis of two classes of tetravalent Multiple Antigen Glycopeptides (MAG) that differ only by the y-Abu insert in the structure of the oligolysine core. Each of the selected intermediates of the synthesis was modeled, subjected to the 2 ns run in N,N'-dimethylformamide (DMF) and geometrically characterized.