De novo Designed Peptides Inhibit the Cytokines Binding to their Receptors from Molecular Simulations and in Vitro Experiments

Abstract

Sepsis, blood poisoning, is a systemic inflammatory response syndrome (SIRS) with high incidence and mortality. An overwhelming systemic response brought about by the release of various inflammatory mediators can lead to shock, multiple organ damage and death. Up to date, several therapeutic agents have been tested in clinical trails of sepsis, but the significant survival advantage is still limited. Some proinflammatory cytokines, such as TNF-α released from LPS-activated macrophages, IL-6, and IL-1β, also have much influence on the septic shock and ;multiple organ dysfunction syndrome (MODS).The aim of this study is to design new peptides to inhibit the cytokines, such as TNF-α, IL-6, and IL-1β, binding to reduce their concentrations in the blood of patients with severe sepsis and to interrupt the initial cytokine cascade. The peptides determined from the binding sites of resolved cytokine-receptor complexes structures were firstly re-docked to validate the selected peptide-cytokine binding and peptides property. These peptides were then combined as a de novo peptide with about 20 amino acids to search for more preferable binding affinity. More than 200 ns molecular dynamics simulations were performed to confirm the stability of complexes. The MM/PBSA binding free energies of these peptide-cytokine complexes were also calculated for comparison. The results showed that de novo peptides have better binding affinities than wild type peptides. Surface plasmon resonance (SPR) detection were performed to validate the docking and binding free energy calculations. The results indicated that the de novo peptides are able to capture the cytokines consistent with our predictions. The outcome of the research may be applied to manufacture a cytokines adsorber for treating patients with severe sepsis in the future.