Computational Analysis and Rational Design of N-Substituting Perturbation on the Affinity and Specificity of Pediatric Fyn SH3–Peptoid Interaction

Abstract

Human nonreceptor tyrosine kinase (TK) Fyn is implicated in various cellular processes and has been exploited as a sophisticated druggable target of pediatric T-cell lymphoma by blocking its kinase domain with small-molecule inhibitors or disrupting its regulatory SH2 and SH3 domains with peptidic inhibitors. In this study, the proline-heavy 9P1Y-peptide was found as a good binder of Fyn SH3 domain, of which the chemical diversity space was extended by replacing its proline residues with a variety of N-substituted amino acids, since N-substitution can mimic the side-chain location and shape of proline. A systematic single-point N-substituting perturbation profile (SSNPP) for 9P1Y-peptide was created theoretically, from which a systematic combinatorial peptoid library (SCPL) was then generated by introducing favorable N-substituted to different proline residue positions of the peptide. The computational design was further substantiated by fluorescence spectroscopy assays to identify five promising peptoid hits in the SCPL as potential Fyn SH3 binders. In particular, the designed peptoid Ptoid2 exhibited a good affinity to Fyn SH3 domain ([Formula: see text]M) and a moderate selectivity for Fyn over Lyn (3.8-fold), which are improved substantially from the natural 9P1Y-peptide. Molecular mechanism underlying the N-substituting perturbation effect was also examined in detail.