Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 6 February 2019 doi:10.20944/preprints201902.0064.v1 Peer-reviewed version available at Molecules 2019, 24, 1196; doi:10.3390/molecules24071196 Article A Complete Assessment of Dopamine Receptor- Ligand Interactions through Computational Methods Beatriz Bueschbell 1, Carlos A. V. Barreto 2, António J. Preto 2, Anke C. Schiedel 1 and Irina S. Moreira 2,3,* 1 PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, D-53121 Bonn, Germany;
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[email protected] 2 Center for Neuroscience and Cell Biology, UC- Biotech Parque Tecnológico de Cantanhede, Núcleo 04, Lote B, 3060- 197 Cantanhede, Portugal;
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[email protected] 3 Institute for Interdisciplinary Research, University of Coimbra *Correspondence:
[email protected]; Tel.: +351 231 249 730 Abstract Background: Selectively targeting dopamine receptors has been a persistent challenge in the last years for the development of new treatments to combat the large variety of diseases evolving these receptors. Although, several drugs have been successfully brought to market, the subtype-specific binding mode on a molecular basis has not been fully elucidated. Methods: Homology modeling and molecular dynamics were applied to construct robust conformational models of all dopamine receptor subtypes (D1-like and D2- like receptors). Fifteen structurally diverse ligands were docked to these models. Contacts at the binding pocket were fully described in order to reveal new structural findings responsible for DR sub-type specificity. Results: We showed that the number of conformations for a receptor:ligand complex was associated to unspecific interactions > 2.5 Å and hydrophobic contacts, while the decoys binding energy was influenced by specific electrostatic interactions.