Modeling Membrane Protein–Ligand Binding Interactions: The Human Purinergic Platelet Receptor

Abstract

Membrane proteins, due to their roles as cell receptors and signaling mediators, make prime candidates for drug targets. The computational analysis of protein-ligand binding affinities has been widely employed as a tool in rational drug design efforts. Although efficient implicit solvent-based methods for modeling globular protein-ligand binding have been around for many years, the extension of such methods to membrane protein-ligand binding is still in its infancy. In this study, we extended the widely used Amber/MMPBSA method to model membrane protein-ligand systems, and we used it to analyze protein-ligand binding for the human purinergic platelet receptor (P2Y12R), a prominent drug target in the inhibition of platelet aggregation for the prevention of myocardial infarction and stroke. The binding affinities, computed by the Amber/MMPBSA method using standard parameters, correlate well with experiment. A detailed investigation of these parameters was conducted to assess their impact on the accuracy of the method. These analyses show the importance of properly treating the non-polar solvation interactions and the electrostatic polarization in the binding of nucleotide agonists and non-nucleotide antagonists to P2Y12R. Based on the crystal structures and the experimental conditions in the binding assay, we further hypothesized that the nucleotide agonists lose their bound magnesium ion upon binding to P2Y12R, and our computational study supports this hypothesis. Ultimately, this work illustrates the value of computational analysis in the interpretation of experimental binding reactions.

A Continuum Poisson–Boltzmann Model for Membrane Channel Proteins

“…Our previous studies have shown that a high protein dielectric constant best reproduces experimental results in MMPBSA calculations when charged ligands/active sites present in globular proteins 118, 124 . A similar conclusion can also be drawn in the tested membrane protein: when the “default” protein dielectric value of 4 is used, the correlation is reduced from 0.79 to 0.75 with INP=1.…”

“…The water relative dielectric constant was set at 80.0. The membrane dielectric constant was set to be 7.0 124 . And the protein dielectric constant was set to be 20.0 due to the presence of charged ligand molecules 118, 124 .…”

Recent Developments and Applications of the MMPBSA Method

“…To improve the convergence rate for use in biomolecular applications, the Incomplete Cholesky preconditioning method and the geometric multigrid method were both extended to incorporate periodicity (Botello-Smith and Luo, 2015 ). Applications to protein-ligand binding utilizing the newly developed membrane MMPBSA method were also reported (Greene et al, 2016 ; Xiao et al, 2017 ).…”

Robustness and Efficiency of Poisson–Boltzmann Modeling on Graphics Processing Units

“…All CUDA PBE solvers were implemented in both single and double precisions in the PBSA program 45,46,78,79,[149][150][151][152][153][154][155][156][157][158][159][160][161] of the Amber/AmberTools 18 packages. 162,163 The double precision was implemented for the robustness analysis only, and the single precision was used throughout the study unless otherwise specified.…”