Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs

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  • dc.contributor.author Ferruz Capapey, Noelia, 1988-ca
  • dc.contributor.author Doerr, Stefan, 1987-ca
  • dc.contributor.author Vanase Frawley, Michelle A.ca
  • dc.contributor.author Zou, Yaozhongca
  • dc.contributor.author Chen, Xiaominca
  • dc.contributor.author Marr, Eric S.ca
  • dc.contributor.author Nelson, Robin T.ca
  • dc.contributor.author Kormos, Bethany L.ca
  • dc.contributor.author Wager, Travis T.ca
  • dc.contributor.author Hou, Xinjun J.ca
  • dc.contributor.author Villalobos, Anabellaca
  • dc.contributor.author Sciabola, Simoneca
  • dc.contributor.author De Fabritiis, Giannica
  • dc.date.accessioned 2018-05-04T07:43:01Z
  • dc.date.available 2018-05-04T07:43:01Z
  • dc.date.issued 2018
  • dc.description.abstract 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, F6.52. Our study highlights the importance of GPCR dynamics to understand ligand binding and provides new opportunities for drug discovery.
  • dc.description.sponsorship N.F. acknowledges support from Generalitat de Catalunya (FI-Agaur). GDF acknowledges support from MINECO (BIO2014-53095-P) and FEDER. We also thank all the volunteers of GPUGRID who donated GPU computing time to the project.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Ferruz N, Doerr S, Vanase-Frawley MA, Zou Y, Chen X, Marr ES et al. Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs. Sci Rep. 2018 Dec;8(1):897. DOI: 10.1038/s41598-018-19345-7
  • dc.identifier.doi http://dx.doi.org/10.1038/s41598-018-19345-7
  • dc.identifier.issn 2045-2322
  • dc.identifier.uri http://hdl.handle.net/10230/34555
  • dc.language.iso eng
  • dc.publisher Nature Publishing Groupca
  • dc.relation.ispartof Scientific Reports. 2018 Dec;8(1):897
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BIO2014-53095-P
  • dc.rights © The Author(s) 2018. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword G-protein coupled receptors
  • dc.subject.keyword Molecular dynamics
  • dc.subject.keyword Markov state models
  • dc.subject.keyword Dopamine D3 receptor
  • dc.title Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRsca
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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