Molecular modeling and rational design of disulfide‐stapled self‐inhibitory peptides to target IL‐17A/IL‐17RA interaction

Abstract Interleukin‐17A (IL‐17A) is a pro‐inflammatory cytokine implicated in diverse autoimmune and inflammatory disorders such as psoriasis and Kawasaki disease. Mature IL‐17A is a homodimer that binds to the extracellular type‐III fibronectin D1:D2‐dual domain of its cognate IL‐17 receptor A (IL‐17RA). In this study, we systematically examined the structural basis, thermodynamics property, and dynamics behavior of IL‐17RA/IL‐17A interaction and computationally identified two continuous hotspot regions separately from different monomers of IL‐17A homodimer that contribute significantly to the interaction, namely I ‐shaped and U ‐shaped segments, thus rendered as a peptide‐mediated protein–protein interaction (PmPPI). Self‐inhibitory peptides (SIPs) are derived from the two segments to disrupt IL‐17RA/IL‐17A interaction by competitively rebinding to the IL‐17A‐binding pocket on IL‐17RA surface, which, however, only have a weak affinity and low specificity for IL‐17RA due to lack of the context support of intact IL‐17A protein, thus exhibiting a large flexibility and intrinsic disorder when splitting from the protein context and incurring a considerable entropy penalty when rebinding to IL‐17RA. The U ‐shaped segment is further extended, mutated and stapled by a disulfide bridge across its two strands to obtain a number of double‐stranded cyclic SIPs, which are partially ordered and conformationally similar to their native status at IL‐17RA/IL‐17A complex interface. Experimental fluorescence polarization assays substantiate that the stapling can moderately or considerably improve the binding affinity of U ‐shaped segment‐derived peptides by 2–5‐fold. In addition, computational structural modeling also reveals that the stapled peptides can bind in a similar mode with the native crystal conformation of U ‐shaped segment in IL‐17RA pocket, where the disulfide bridge is out of the pocket for avoiding intervene of the peptide binding.