GPCRs are highly versatile transmembrane sensors and have high therapeutic relevance. Because of the complexities associated with surrounding bilayer and buried binding pockets in the protein, free energy based computational approaches have had limited success with sampling affinity changes for GPCR ligands. We apply two precomputed ensemble-based free energy approaches that effectively sample and efficiently estimate relative affinity changes across such transmembrane systems: Single-Step Free Energy Perturbation (SSFEP) and Site Identification by Ligand Competitive Saturation (SILCS). SSFEP repeatedly reuses pre-computed ensemble of conformations of a parent ligand in explicit solvent and in the protein+bilayer environments to evaluate ΔΔG between the parent and modified ligands. This allows for rapid evaluation of ΔΔG for a library of small functional group substitutions to a parent ligand. In SILCS, the protein+bilayer system is subjected to hybrid Grand-Canonical Monte-Carlo/Molecular Dynamics (GCMC/MD) simulations in the presence of multiple organic solutes that represent different types of functional groups. Affinity patterns of these functional groups, called FragMaps, obtained from the GCMC/MD simulations are then used to rapidly evaluate and rank-order ligands in the GPCR pockets using Ligand Grid Free Energy (LGFE) scoring. Both SSFEP and SILCS correctly predicted direction of affinity changes and rank-ordered known ligands of the b2-adrenergic (b2AR) GPCR simulated in a bilayer composed of 90% palmitoyl oleoyl phosphatidyl choline (POPC) and 10% cholesterol. For instance, SSFEP correctly predicted the increase in favorability as dopamine was transformed to epinephrine, norepinephrine and their derivatives. SILCS simulations correctly characterized the differences in functional group requirements across active and inactive states of the b2AR. Differences in the functional group requirements could be used to distinguish agonists, partial-agonists, antagonists and inverse agonists. Additionally, LGFE scoring could be used to identify growth vectors during optimization of dopamine. Thus, SILCS and SSFEP are attractive strategies that can lead drug-design process for challenging targets such as GPCRs.

Rapid estimation of relative binding affinities of G-protein coupled receptor (GPCR) ligands using precomputed ensembles based free energy approaches

256th National Meeting (2018)

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