Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs

• Published in: Scientific reports 2018-01, Vol.8 (1), p.897-10, Article 897
• Main Authors: Ferruz, Noelia, Doerr, Stefan, Vanase-Frawley, Michelle A., Zou, Yaozhong, Chen, Xiaomin, Marr, Eric S., Nelson, Robin T., Kormos, Bethany L., Wager, Travis T., Hou, Xinjun, Villalobos, Anabella, Sciabola, Simone, De Fabritiis, Gianni
• Format: Article
• Language: English
• Subjects: 119/118; 631/154/309/606; 631/92/606; Animals; BASIC BIOLOGICAL SCIENCES; Binding Sites - physiology; Cell Line; Computational chemistry; Crystal structure; Crystallography, X-Ray - methods; Dopamine; Dopamine D3 receptor; Dopamine D3 receptors; Drug development; G protein-coupled receptors; Humanities and Social Sciences; Humans; Ligands; Macromolecules; Markov state models; Molecular Docking Simulation - methods; Molecular dynamics; Molecular Dynamics Simulation; multidisciplinary; Mutagenesis, Site-Directed - methods; Protein Binding - physiology; Protein structure; Receptors, Dopamine D3 - antagonists & inhibitors; Receptors, G-Protein-Coupled - chemistry; Receptors, G-Protein-Coupled - metabolism; Salicylamides - chemistry; Salicylamides - metabolism; Science; Science (multidisciplinary); Sf9 Cells; Site-directed mutagenesis
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-018-19345-7

The recent increase in the number of X-ray crystal structures of G-protein coupled receptors (GPCRs) has been enabling for structure-based drug design (SBDD) efforts. These structures have revealed that GPCRs are highly dynamic macromolecules whose function is dependent on their intrinsic flexibility. Unfortunately, the use of static structures to understand ligand binding can potentially be misleading, especially in systems with an inherently high degree of conformational flexibility. Here, we show that docking a set of dopamine D3 receptor compounds into the existing eticlopride-bound dopamine D3 receptor (D3R) X-ray crystal structure resulted in poses that were not consistent with results obtained from site-directed mutagenesis experiments. We overcame the limitations of static docking by using large-scale high-throughput molecular dynamics (MD) simulations and Markov state models (MSMs) to determine an alternative pose consistent with the mutation data. The new pose maintains critical interactions observed in the D3R/eticlopride X-ray crystal structure and suggests that a cryptic pocket forms due to the shift of a highly conserved residue, F 6.52 . Our study highlights the importance of GPCR dynamics to understand ligand binding and provides new opportunities for drug discovery.