Deciphering conformational selectivity in the A 2A adenosine G protein-coupled receptor by Free Energy simulations

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Transmembranal G Protein-Coupled Receptors (GPCRs) transduce extracellular chemical signals to the cell, via conformational change from a resting (inactive) to an active (canonically bound to a G-protein) conformation. Receptor activation is normally modulated by extracellular ligand binding, but mutations in the receptor can also shift this equilibrium by stabilizing different conformational states. In this work, we built structure-energetic relationships of receptor activation based on original thermodynamic cycles that represent the conformational equilibrium of the prototypical A 2A adenosine receptor (AR). These cycles were solved with efficient free energy perturbation (FEP) protocols, allowing to distinguish the pharmacological profile of different series of A 2A AR agonists with different efficacies. The modulatory effects of point mutations on the basal activity of the receptor or on ligand efficacies could also be detected. This methodology can guide GPCR ligand design with tailored pharmacological properties, or allow the identification of mutations that modulate receptor activation with potential clinical implications. Author Summary The design of new ligands as chemical modulators of G protein-coupled receptors (GPCRs) has benefited considerably during the last years of advances in both the structural and computational biology disciplines. Within the last, area, the use of free energy calculation methods has arisen as a computational tool to predict ligand affinities to explain structure-affinity relationships and guide lead optimization campaigns. However, our comprehension of the structural determinants of ligands with different pharmacological profile is scarce, and knowledge of the chemical modifications associated with an agonistic or antagonistic profile would be extremely valuable. We herein report an original implementation of the thermodynamic cycles associated with free energy perturbation (FEP) simulations, to mimic the conformational equilibrium between active and inactive GPCRs, and establish a framework to describe pharmacological profiles as a function of the ligands selectivity for a given receptor conformation. The advantage of this method resides into its simplicity of use, and the only consideration of active and inactive conformations of the receptor, with no simulation of the transitions between them. This model can accurately predict the pharmacological profile of series of full and partial agonists as opposed to antagonists of the A 2A adenosine receptor, and moreover, how certain mutations associated with modulation of basal activity can influence this pharmacological profiles, which enables our understanding of such clinically relevant mutations.

Authors 7

1. Willem Jespers corresponding Aachen Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University · Uppsala University

   Affiliation as printed

   Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC)

   Drug Discovery and Safety, Leiden Academic Centre for Drug Research

   Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC), Box 596, SE-75 24, Uppsala, Sweden

   Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 333 CC, Leiden, The Netherlands

2. Laura H. Heitman Aachen Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University · Oncode Institute

   Affiliation as printed

   Drug Discovery and Safety, Leiden Academic Centre for Drug Research

   Oncode Institute

   Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 333 CC, Leiden, The Netherlands

   Oncode Institute, 2333 CC Leiden, Leiden

3. Adriaan P. IJzerman Aachen Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Drug Discovery and Safety, Leiden Academic Centre for Drug Research

   Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 333 CC, Leiden, The Netherlands

4. Eddy Sotelo

   Universidade de Santiago de Compostela · Centro Singular de Investigación en Química Biológica y Materiales Moleculares

   Affiliation as printed

   Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)

   Departamento de Química Orgánica, Facultade de Farmacia. Universidade de Santiago de Compostela

   Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS),

   Departamento de Química Orgánica, Facultade de Farmacia. Universidade de Santiago de Compostela, 15782. Santiago de Compostela, Spain

5. Gerard J. P. van Westen Aachen Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Drug Discovery and Safety, Leiden Academic Centre for Drug Research

   Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 333 CC, Leiden, The Netherlands

6. Johan Åqvist

   Uppsala University

   Affiliation as printed

   Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC)

   Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC), Box 596, SE-75 24, Uppsala, Sweden

7. Hugo Gutiérrez‐de‐Terán corresponding

   Uppsala University · Science for Life Laboratory

   Affiliation as printed

   Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC)

   Science for Life Laboratories

   Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC), Box 596, SE-75 24, Uppsala, Sweden

   Science for Life Laboratories, BMC, Uppsala (Sweden)