An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands

A generally applicable metadynamics
scheme for predicting the free
energy profile of ligand binding to G-protein-coupled receptors (GPCRs)
is described. A common and effective collective variable (CV) has
been defined using the ideally placed and highly conserved Trp6.48
as a reference point for ligand–GPCR distance measurement and
the common orientation of GPCRs in the cell membrane. Using this single
CV together with well-tempered multiple-walker metadynamics with a
funnel-like boundary allows an efficient exploration of the entire
ligand binding path from the extracellular medium to the orthosteric
binding site, including vestibule and intermediate sites. The protocol
can be used with X-ray structures or high-quality homology models
(based on a high-quality template and after thorough refinement) for
the receptor and is universally applicable to agonists, antagonists,
and partial and reverse agonists. The root-mean-square error (RMSE)
in predicted binding free energies for 12 diverse ligands in five
receptors (a total of 23 data points) is surprisingly small (less
than 1 kcal mol–1). The RMSEs for simulations that
use receptor X-ray structures and homology models are very similar.