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

Abstract

For an effective drug, strong binding to the target protein is a prerequisite, but it is not enough. To produce a particular functional response, drugs need to either block the proteins' functions or modulate their activities by changing their conformational equilibrium. The binding free energy of a compound to its target is routinely calculated, but the timescales for the protein conformational changes are prohibitively long to be efficiently modeled via physics-based simulations. Thermodynamic principles suggest that the binding free energies of the ligands with different receptor conformations may infer their efficacy. However, this hypothesis has not been thoroughly validated. We present an actionable protocol and a comprehensive study to show that binding thermodynamics provides a strong predictor of the efficacy of a ligand. We apply the absolute binding free energy perturbation method to ligands bound to active and inactive states of eight G protein-coupled receptors and a nuclear receptor and then compare the resulting binding free energies. We find that carefully designed restraints are often necessary to efficiently model the corresponding conformational ensembles for each state. Our method achieves unprecedented performance in classifying ligands as agonists or antagonists across the various investigated receptors, all of which are important drug targets.

Computational Modeling and Characterization of Peptides Derived from Nanobody Complementary-Determining Region 2 (CDR2) Targeting Active-State Conformation of the β2-Adrenergic Receptor (β2AR)

“…This corroborated the preliminarily determined Kd value of ~15 µM in MST. A recent computational study using the binding free-energy perturbation method reported unprecedented performance in classifying ligands as agonists or antagonists for various receptors, including GPCRs [37]. The estimated affinity of CDR2-NDP P4 was similar to a previously characterized Nb71 CDR3-NDP P3; therefore, the β 2 AR:P3 complex exhibited a −∆G of 7.23 ± 0.04 kcal/mol or a Ki of 7.9 ± 0.5 µM [17].…”

Intracellular pocket conformations determine signaling through the μ opioid receptor

“…The calculated shift in binding affinity was used to successfully classify the compounds as agonists, partial agonists, or antagonists. In another study, a team from the computational chemistry software company Schrödinger performed absolute binding free energy calculations of ligands to active and inactive conformations of 7TMR and nuclear hormone receptor targets 5 . Based on higher predicted binding affinity to the active conformation, 168 of 180 ligands (93%) could be correctly classified as agonists opposed to antagonists.…”

“…Our study provides the first evidence for what could be a scientific law. While recent work has categorized ligands as active or inactive (or partially active) based on binding affinities to two conformations 4,5 , our approach accurately computes signaling efficacy along multiple pathways.…”

Exploring the Activation Mechanism of the GPR183 Receptor

“…Last year, Wang et. al presented a technique for categorizing ligands as agonists or antagonists using the absolute binding free energy perturbation method based on thermodynamic principles, which has been validated on multiple GPCRs . Recently, Milka et.…”

“…al presented a technique for categorizing ligands as agonists or antagonists using the absolute binding free energy perturbation method based on thermodynamic principles, which has been validated on multiple GPCRs. 59 Recently, Milka et. al used protein− peptide docking, molecular dynamic simulations, and metadynamic-based free-energy binding calculations to analyze the specific binding of complementary determinant regions of nanobody to the agonist-activated β2 adrenergic receptor.…”