Design of Drug Efficacy Guided by Free Energy Simulations of the β₂‐Adrenoceptor

Abstract

G-protein-coupled receptors (GPCRs) play important roles in physiological processes and are modulated by drugs that either activate or block signaling. Rational design of the pharmacological efficacy profiles of GPCR ligands could enable the development of more efficient drugs, but is challenging even if highresolution receptor structures are available. We performed molecular dynamics simulations of the β 2 adrenergic receptor in active and inactive conformations to assess if binding free energy calculations can predict differences in ligand efficacy for closely related compounds. Previously identified ligands were successfully classified into groups with comparable efficacy profiles based on the calculated shift in ligand affinity upon activation. A series of ligands were then predicted and synthesized, leading to the discovery of partial agonists with nanomolar potencies and novel scaffolds. Our results demonstrate that free energy simulations enable design of ligand efficacy and the same approach can be applied to other GPCR drug targets.

Is the Functional Response of a Receptor Determined by the Thermodynamics of Ligand Binding?

“…A comparison between simulations with and without these restraints (Figure C) revealed a significant accuracy gain when the restraints were used, confirming the validity of our underlying reasoning. Notably, the restraints ensured that the separation between agonists and antagonists was close to ΔΔ G = 0, an outcome that had not been achieved by similar approaches in previous studies with tight restraints outside the binding pocket. , Overall, our protocol has proven to be effective in accurately separating agonists and antagonists.…”

“…Notably, the restraints ensured that the separation between agonists and antagonists was close to ΔΔG = 0, an outcome that had not been achieved by similar approaches in previous studies with tight restraints outside the binding pocket. 17,18 Overall, our protocol has proven to be effective in accurately separating agonists and antagonists.…”

“…Saleh et al compared the ligand binding free energy calculated via metadynamics on different states of the receptor to explain biased signaling of the β2-adrenoceptor . An analogous version of this thermodynamic model for relative binding free energies has recently been used to design partial agonists for the same target and for the adenosine receptor A2A . Similarly, the docking scores of ligands in distinct conformational states were used as a proxy for the binding free energy to predict the functional responses of various ligands. − The ATOM3D benchmark study proposed the use of structure-based machine learning (ML) models for ligand efficacy prediction (LEP) following the same hypothesis…”

Alchemical Free Energy Calculations on Membrane-Associated Proteins

“…Finally, in a more recent study, the ligand efficacy of closely related β 2 -AR compounds was also explored using RBFE calculations. 115 RBFE calculations have gained increased confidence in driving SBDD for GPCR targets through their successful implementation on supporting the ligand binding elucidation hypothesis and through studies where they retrospectively confirmed previous experimental/computational results. There are successful examples of prospective applications to GPCR SBDD and retrospective studies probing the limits of applicability of RBFE calculation, for example for fragmentbased drug design (FBDD), as described later in this section.…”

Mechanistic insights into G protein association with a G protein-coupled receptor

“…In the present study, with an aim to understand the process of receptor-mediated G-protein activation, we investigate the rst steps of this reaction sequence for the β 2 -adrenoceptor-Gs (β 2 AR-Gs) signaling system, for which there is a wealth of experimental data that can expand further interpretation 5,10,16,22,23,24,25 . The β 2 AR is a family A GPCR that primarily couples to Gs to enhance intracellular cAMP levels 26 , hence regulating important physiological responses such as smooth muscle relaxation and bronchodilation 27 .…”