Molecular design and systematic optimization of a halogen‐bonding system between the asthma interleukin‐5 receptor and its cyclic peptide ligand

Abstract

AbstractHuman interleukin‐5 (IL‐5) functions as an important pro‐inflammatory factor by binding to its specific receptor, IL‐5Rα, which has been implicated in the pathogenesis of asthma. Previously, a disulfide‐bonded cyclic peptide AF17121 obtained from random library screening and sequence variation was found to competitively disrupt the cognate IL‐5Rα/IL‐5 interaction with moderate potency. In this study, the crystal complex of IL‐5Rα with AF17121 was investigated at structural and energetic levels. It is revealed that the side‐chain indole moiety of the AF17121 Trp5 residue is a potential site for a stem putative halogen bond (X‐bond) with IL‐5Rα, which is just located within the key 3EXXR6 motif region recognized specifically by IL‐5Rα. We systematically examined four halogen substitution types at five positions of the indole moiety; QM/MM calculations theoretically unraveled that only halogenations at 5 and 6 positions can form effective X‐bonds with the side‐chain hydroxyl oxygen of the IL‐5Rα Thr21 residue and the backbone carbonyl oxygen of Ala66 residue, respectively. Binding assays observed that I‐substitution at the 5 position and Br‐substitution at the 6 position can result in two potent halogenated peptides, [5I]AF17121 and [6Br]AF17121, which are improved by 1.6‐fold and 3.5‐fold relative to the native AF17121, respectively. 5I/6Br‐double substitution, resulting in [5I/6Br]AF17121, can further enhance the peptide affinity by 7.5‐fold. Structural analysis revealed that the X‐bond stemming from 6Br‐substitution is also involved in an orthogonal interaction system with a H‐bond; they share a common backbone carbonyl oxygen acceptor of IL‐5Rα Ala66 residue and exhibit a significant synergistic effect between them.