Molecular design and virtual docking of oligopeptides for binding and elimination interleukin-6 from blood plasma

Abstract

Binding of interleukin-6 (IL-6) is the perspective target for the anti-inflammatory therapy in many pathological conditions (sepsis, autoimmune pathology, allergic diseases). The aim of this work was to develop and study the binding IL-6 oligopeptides. To achieve the goal, were set and successfully solved the following tasks: studying three-dimensional models of molecular structures of IL-6 incombination with the R-IL-6 and gp130, prediction and virtual synthesis low molecular weight oligopeptides; evaluating the free energy of IL-6 binding for identity the most effective oligopeptide; studying the changing the concentration of IL-6 inthe model solution after contact with experimental oligopeptides. In the article presents the binding IL-6 energy of 62 peptides, designed using the PyMol. Energy was calculated in the Chimera program using the AutodockVina application. There are also presented results of in vitro experiments interacting 7 sextapeptides, 2 tetrapeptides, and 3 tripeptides with recombinant IL-6. The effectiveness of the peptides was calculated by reducing the concentration of cytokine in solution as a percentage of the initial concentration.The free binding energy has shown that the efficiency of binding increases with an increase in the total number of amino acids and, in particular, of aromatic amino acids in the oligopeptide. Correlation analysis showed that the molecular modeling method is not absolutely effective for predicting the structure of an oligopeptide, however, it can be used as one of the preliminary steps for analyzing the interaction between molecules and studying the optimal interaction points. Two oligopeptides were identified as the most promising for further synthesis as the ligands for binding and evaluating IL-6 inhuman blood plasma.