Structure‐based improvement of the binding affinity and recognition specificity of peptide competitors to target pediatric IL‐5R/IL‐5 interaction by gluing halogen bonds at their complex interface

Abstract

Human interleukin‐5 (IL‐5) cytokine mediates the development of eosinophils and is involved in a variety of immune inflammatory responses that play a major role in the pathogenesis of childhood asthma, leukemia, and other pediatric allergic diseases. The immunomodulatory cytokine functions by binding to its cognate cell surface receptor IL‐5R in a sheet‐by‐sheet manner, which can be conformationally mimicked and competitively disrupted by a double‐stranded cyclic AF18748 peptide. In this study, we systematically examined the co‐crystallized complex structure of human IL‐5R with AF18748 peptide and rationally designed a halogen bond to glue at the protein–peptide complex interface by substituting the indole moiety of AF18748 Trp13 residue with a halogen atom (X = F, Cl, Br, or I). High‐level theoretical calculations imparted presence of the halogen bond between the oxygen atom (O) of IL‐5R Glu58 backbone and the halogen atom (X) of AF18748 Trp13 side chain. Experimental assays confirmed that the halogen bond can promote peptide binding moderately or considerably. More importantly, the halogen bond not only enhances peptide affinity to IL‐5R, but also improves peptide selectivity for its cognate IL‐5R over other noncognate IL‐R proteins. As might be expected, the affinity and selectivity conferred by halogen bond increase consistently in the order: H < F < Cl < Br < I. Structural modeling revealed that the halogen bond plus its vicinal π–cation–π stacking co‐define a ringed noncovalent system at the complex interface, which involves a synergistic effect to effectively improve the peptide binding potency and recognition specificity.