Determinants of Improved CGRP Peptide Binding Kinetics Revealed by Enhanced Molecular Simulations

Peptides are desirable therapeutics due to their inherent potency, safety, cost-effectiveness and ability to engage large or more complex protein surfaces. Slower kinetics of protein-peptide (un)binding can directly influence their drug efficacy and duration of action, in part by improving plasma stability of the peptide. The CLR:RAMP1 complex and its endogenous agonist peptide CGRP are of particularly high interest because of their central role in migraine pathophysiology. A better understanding of peptide binding mechanisms is needed for the development of next-generation peptide-based drugs with optimized kinetic properties. In this study, we comparatively analyze constructs of native CGRP and “ssCGRP”, an engineered variant with 430-fold longer residence time on the CLR:RAMP1 complex. Using large-scale computational resources and our high-dimensional weighted-ensemble algorithm, we then thoroughly sample and compare unbinding path ensembles for the two peptides. This elucidates the basis of the engineered residence time enhancement for ssCGRP and provides a detailed view of the intra- and intermolecular stabilizing interactions for both peptides in the bound ensemble and along the unbinding transition path. The bias-free nature of the sampling approach in combination with Markov state modeling allows for the calculation of committor values and the first analysis of protein-peptide binding transition state ensembles. Through analysis of the unbinding committor, we find that ssCGRP(27–37) also demonstrates enhanced ligand recapture of intermediate unbinding conformations and samples a more heterogeneous bound-state ensemble that entropically stabilizes the bound basin. This study shows the molecular determinants of peptide residence time at CLR:RAMP1 and provides valuable insight for the design of long-acting peptide therapeutics.