Computational Modeling and Characterization of Peptides Derived from Nanobody Complementary-Determining Region 2...

This study assessed the suitability of the complementarity-determining region 2 (CDR2) of the nanobody (Nb) as a template for the derivation of nanobody-derived peptides (NDPs) targeting active-state β₂-adrenergic receptor (β₂AR) conformation. Sequences of conformationally selective Nbs favoring the agonist-occupied β₂AR were initially analyzed by the informational spectrum method (ISM). The derived NDPs in complex with β₂AR were subjected to protein-peptide docking, molecular dynamics (MD) simulations, and metadynamics-based free-energy binding calculations. Computational analyses identified a 25-amino-acid-long CDR2-NDP of Nb71, designated P4, which exhibited the following binding free-energy for the formation of the β₂AR:P4 complex (ΔG = -6.8 ± 0.8 kcal/mol or a Ki = 16.5 μM at 310 K) and mapped the β₂AR:P4 amino acid interaction network. In vitro characterization showed that P4 (i) can cross the plasma membrane, (ii) reduces the maximum isoproterenol-induced cAMP level by approximately 40% and the isoproterenol potency by up to 20-fold at micromolar concentration, (iii) has a very low affinity to interact with unstimulated β₂AR in the cAMP assay, and (iv) cannot reduce the efficacy and potency of the isoproterenol-mediated β₂AR/β-arrestin-2 interaction in the BRET²-based recruitment assay. In summary, the CDR2-NDP, P4, binds preferentially to agonist-activated β₂AR and disrupts Gαs-mediated signaling.