Enrichment Factor Analyses on G-Protein Coupled Receptors with Known Crystal Structure

G-protein coupled receptors (GPCRs) are highly relevant drug targets. Four GPCRs with known crystal structure were analyzed with docking (AutoDock4) and postdocking (MM-PBSA) in order to evaluate the ability to recognize known antagonists from a larger database of molecular decoys and to predict correct binding modes. Moreover, implications on multitarget drug screening are put forward. The results suggest that these methods may be of interest to the growing field of GPCR structure-based virtual screening.

[1]  Giulio Rastelli,et al.  Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations. , 2012, European journal of medicinal chemistry.

[2]  Brian K Shoichet,et al.  Structure-based drug screening for G-protein-coupled receptors. , 2012, Trends in pharmacological sciences.

[3]  A. Leslie,et al.  Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation , 2011, Nature.

[4]  Ben M. Webb,et al.  ModBase, a database of annotated comparative protein structure models and associated resources , 2013, Nucleic Acids Res..

[5]  András Fiser,et al.  ModLoop: automated modeling of loops in protein structures , 2003, Bioinform..

[6]  Helgi B. Schiöth,et al.  Structural diversity of G protein-coupled receptors and significance for drug discovery , 2008, Nature Reviews Drug Discovery.

[7]  Giulio Rastelli,et al.  Advances and applications of binding affinity prediction methods in drug discovery. , 2012, Biotechnology advances.

[8]  U. Hacksell,et al.  Intrinsic Efficacy of Antipsychotics at Human D2, D3, and D4 Dopamine Receptors: Identification of the Clozapine Metabolite N-Desmethylclozapine as a D2/D3 Partial Agonist , 2005, Journal of Pharmacology and Experimental Therapeutics.

[9]  R. Gur,et al.  Mesolimbic dopamine D3 receptors and use of antipsychotics in patients with schizophrenia. A postmortem study. , 1997, Archives of general psychiatry.

[10]  Matthew P. Repasky,et al.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.

[11]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .

[12]  Satoshi Niijima,et al.  GLIDA: GPCR—ligand database for chemical genomics drug discovery—database and tools update , 2007, Nucleic Acids Res..

[13]  R. Stevens,et al.  The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist , 2008, Science.

[14]  G. Degliesposti,et al.  Binding Estimation after Refinement, a New Automated Procedure for the Refinement and Rescoring of Docked Ligands in Virtual Screening , 2009, Chemical biology & drug design.

[15]  M. Maggiolini,et al.  G protein-coupled receptors: novel targets for drug discovery in cancer , 2010, Nature Reviews Drug Discovery.

[16]  Ian T. Crosby,et al.  Homology Modeling and Docking Evaluation of Aminergic G Protein-Coupled Receptors , 2010, J. Chem. Inf. Model..

[17]  Giulio Rastelli,et al.  Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA , 2009, J. Comput. Chem..

[18]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..

[19]  Jonathan A. Javitch,et al.  Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist , 2010, Science.

[20]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[21]  Hege S. Beard,et al.  Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. , 2004, Journal of medicinal chemistry.

[22]  A. Sali,et al.  Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.

[23]  David S. Goodsell,et al.  A semiempirical free energy force field with charge‐based desolvation , 2007, J. Comput. Chem..

[24]  Ruben Abagyan,et al.  Structure of the human histamine H1 receptor complex with doxepin , 2011, Nature.

[25]  Ruben Abagyan,et al.  The GPCR Network: a large-scale collaboration to determine human GPCR structure and function , 2012, Nature Reviews Drug Discovery.

[26]  S. Stahl Selective Histamine H1 Antagonism: Novel Hypnotic and Pharmacologic Actions Challenge Classical Notions of Antihistamines , 2008, CNS Spectrums.

[27]  R. Stevens,et al.  Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions , 2012, Science.

[28]  Ajay N. Jain Bias, reporting, and sharing: computational evaluations of docking methods , 2008, J. Comput. Aided Mol. Des..

[29]  A. IJzerman,et al.  The crystallographic structure of the human adenosine A2A receptor in a high-affinity antagonist-bound state: implications for GPCR drug screening and design. , 2010, Current opinion in structural biology.

[30]  R. Stevens,et al.  High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. , 2007, Science.