New Binding Sites, New Opportunities for GPCR Drug Discovery.

Many central biological events rely on protein-ligand interactions. The identification and characterization of protein-binding sites for ligands are crucial for the understanding of functions of both endogenous ligands and synthetic drug molecules. G protein-coupled receptors (GPCRs) typically detect extracellular signal molecules on the cell surface and transfer these chemical signals across the membrane, inducing downstream cellular responses via G proteins or β-arrestin. GPCRs mediate many central physiological processes, making them important targets for modern drug discovery. Here, we focus on the most recent breakthroughs in finding new binding sites and binding modes of GPCRs and their potentials for the development of new medicines.

[1]  Nicole J. Yang,et al.  Getting across the cell membrane: an overview for small molecules, peptides, and proteins. , 2015, Methods in molecular biology.

[2]  Naomi R. Latorraca,et al.  Structure of the μ Opioid Receptor-Gi Protein Complex , 2018, Nature.

[3]  S. Filipek,et al.  W246(6.48) opens a gate for a continuous intrinsic water pathway during activation of the adenosine A2A receptor. , 2014, Angewandte Chemie.

[4]  A. Goldman,et al.  G protein-coupled receptors show unusual patterns of intrinsic unfolding. , 2005, Protein engineering, design & selection : PEDS.

[5]  Shuguang Yuan,et al.  Lipid Receptor S1P1 Activation Scheme Concluded from Microsecond All-Atom Molecular Dynamics Simulations , 2013, PLoS Comput. Biol..

[6]  G. Bottegoni,et al.  Structure of the complement C5a receptor bound to the extra-helical antagonist NDT9513727 , 2018, Nature.

[7]  Bryan L Roth,et al.  Discovery of new GPCR ligands to illuminate new biology. , 2017, Nature chemical biology.

[8]  Qi Wu,et al.  COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking , 2018, Nucleic Acids Res..

[9]  A. J. Venkatakrishnan,et al.  Universal allosteric mechanism for Gα activation by GPCRs , 2015, Nature.

[10]  J. Simms,et al.  Lifting the lid on GPCRs: the role of extracellular loops , 2011, British journal of pharmacology.

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

[12]  J. Wess,et al.  Activation and allosteric modulation of a muscarinic acetylcholine receptor , 2013, Nature.

[13]  F. Cordes,et al.  Proline-induced distortions of transmembrane helices. , 2002, Journal of molecular biology.

[14]  A. Kruse,et al.  Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist , 2011, Nature.

[15]  Hugh Rosen,et al.  Crystal Structure of a Lipid G Protein–Coupled Receptor , 2012, Science.

[16]  Richard M. Jackson,et al.  Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites , 2005, Bioinform..

[17]  B. Honig,et al.  On the nature of cavities on protein surfaces: Application to the identification of drug‐binding sites , 2006, Proteins.

[18]  Christofer S Tautermann,et al.  GPCR structures in drug design, emerging opportunities with new structures. , 2014, Bioorganic & medicinal chemistry letters.

[19]  J. García-Nafría,et al.  Cryo-EM structure of the serotonin 5-HT1B receptor coupled to heterotrimeric Go , 2018, Nature.

[20]  Gianni De Fabritiis,et al.  DeepSite: protein‐binding site predictor using 3D‐convolutional neural networks , 2017, Bioinform..

[21]  José Xavier-Neto,et al.  KVFinder: steered identification of protein cavities as a PyMOL plugin , 2014, BMC Bioinformatics.

[22]  Enrico Guarnera,et al.  Allosteric sites: remote control in regulation of protein activity. , 2016, Current opinion in structural biology.

[23]  Shuguang Yuan,et al.  The role of water and sodium ions in the activation of the μ-opioid receptor. , 2013, Angewandte Chemie.

[24]  R. Stevens,et al.  Chemical Diversity in the G Protein-Coupled Receptor Superfamily. , 2018, Trends in pharmacological sciences.

[25]  David Hoksza,et al.  Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features , 2015, Journal of Cheminformatics.

[26]  M. Raida,et al.  NMR structural study of the intracellular loop 3 of the serotonin 5-HT(1A) receptor and its interaction with calmodulin. , 2011, Biochimica et biophysica acta.

[27]  Dahlia R. Weiss,et al.  Structure-based discovery of selective positive allosteric modulators of antagonists for the M2 muscarinic acetylcholine receptor , 2018, Proceedings of the National Academy of Sciences.

[28]  Ruben Abagyan,et al.  Structure of CC Chemokine Receptor 2 with Orthosteric and Allosteric Antagonists , 2016, Nature.

[29]  T. Kawabata Detection of multiscale pockets on protein surfaces using mathematical morphology , 2010, Proteins.

[30]  Gebhard F. X. Schertler,et al.  The 2.1 Å Resolution Structure of Cyanopindolol-Bound β1-Adrenoceptor Identifies an Intramembrane Na+ Ion that Stabilises the Ligand-Free Receptor , 2014, PloS one.

[31]  David E. Gloriam,et al.  Pharmacogenomics of GPCR Drug Targets , 2018, Cell.

[32]  D. Montange,et al.  Impact of ticagrelor on P2Y1 and P2Y12 localization and on cholesterol levels in platelet plasma membrane , 2018, Platelets.

[33]  Arthur Christopoulos,et al.  Crystal structures of the M1 and M4 muscarinic acetylcholine receptors , 2016, Nature.

[34]  H. Brückmann,et al.  Polypharmacology of dopamine receptor ligands , 2016, Progress in Neurobiology.

[35]  Bas Vroling,et al.  GPCRdb: an information system for G protein-coupled receptors , 2015, Nucleic Acids Res..

[36]  S. Hill,et al.  Multiple GPCR conformations and signalling pathways: implications for antagonist affinity estimates , 2007, Trends in pharmacological sciences.

[37]  M. Sturlese,et al.  Exploring Protein-Peptide Recognition Pathways Using a Supervised Molecular Dynamics Approach. , 2017, Structure.

[38]  Sujata Sharma,et al.  Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40 , 2017, Nature Structural &Molecular Biology.

[39]  Naomi R. Latorraca,et al.  Structure of the mu-opioid receptor-Giprotein complex. , 2018 .

[40]  S. Vermeire,et al.  Randomised clinical trial: vercirnon, an oral CCR9 antagonist, vs. placebo as induction therapy in active Crohn's disease , 2015, Alimentary pharmacology & therapeutics.

[41]  K. Lindorff-Larsen,et al.  Role of protein dynamics in transmembrane receptor signalling. , 2018, Current opinion in structural biology.

[42]  Yang Zhang,et al.  Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment , 2013, Bioinform..

[43]  Ruben Abagyan,et al.  Pocketome: an encyclopedia of small-molecule binding sites in 4D , 2011, Nucleic Acids Res..

[44]  Hongbo Zhu,et al.  MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets , 2011, Bioinform..

[45]  Dario Ghersi,et al.  EASYMIFS and SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structures , 2009, Bioinform..

[46]  David Ryan Koes,et al.  PocketQuery: protein–protein interaction inhibitor starting points from protein–protein interaction structure , 2012, Nucleic Acids Res..

[47]  Hualiang Jiang,et al.  Two disparate ligand-binding sites in the human P2Y1 receptor , 2015, Nature.

[48]  Nagasuma Chandra,et al.  PocketDepth: a new depth based algorithm for identification of ligand binding sites in proteins. , 2008, Journal of structural biology.

[49]  George Papadatos,et al.  The ChEMBL database in 2017 , 2016, Nucleic Acids Res..

[50]  Min Liu,et al.  bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming , 2016, Journal of Cheminformatics.

[51]  Naomi R. Latorraca,et al.  Mechanism of intracellular allosteric β2AR antagonist revealed by X-ray crystal structure , 2017, Nature.

[52]  K. Palczewski,et al.  Designing Safer Analgesics via μ-Opioid Receptor Pathways. , 2017, Trends in pharmacological sciences.

[53]  Patrik Johansson,et al.  Structural insight into allosteric modulation of protease-activated receptor 2 , 2017, Nature.

[54]  A. Pioszak,et al.  Structural insights into ligand recognition and selectivity for classes A, B, and C GPCRs. , 2015, European journal of pharmacology.

[55]  Thomas A. Halgren,et al.  Identifying and Characterizing Binding Sites and Assessing Druggability , 2009, J. Chem. Inf. Model..

[56]  Yen-Jen Oyang,et al.  MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm , 2005, Nucleic Acids Res..

[57]  Yu Li,et al.  Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction , 2011, Bioinform..

[58]  Chaok Seok,et al.  GalaxySite: ligand-binding-site prediction by using molecular docking , 2014, Nucleic Acids Res..

[59]  A. T. Nguyen,et al.  New paradigms in adenosine receptor pharmacology: allostery, oligomerization and biased agonism , 2018, British journal of pharmacology.

[60]  S. Rasmussen,et al.  Allosteric coupling from G protein to the agonist binding pocket in GPCRs , 2016, Nature.

[61]  Vadim Cherezov,et al.  Allosteric sodium in class A GPCR signaling. , 2014, Trends in biochemical sciences.

[62]  Guangyu Wu,et al.  A Single Lys Residue on the First Intracellular Loop Modulates the Endoplasmic Reticulum Export and Cell-Surface Expression of α2A-Adrenergic Receptor , 2012, PloS one.

[63]  H Weinstein,et al.  Prokink: a protocol for numerical evaluation of helix distortions by proline. , 2000, Protein engineering.

[64]  David E. Gloriam,et al.  5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology , 2018, Cell.

[65]  J. Cheong,et al.  The N‐terminal region of the dopamine D2 receptor, a rhodopsin‐like GPCR, regulates correct integration into the plasma membrane and endocytic routes , 2012, British journal of pharmacology.

[66]  K. Palczewski,et al.  Exploring a new ligand binding site of G protein-coupled receptors† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc01680a , 2018, Chemical science.

[67]  Kathryn E. Livingston,et al.  Allostery at opioid receptors: modulation with small molecule ligands , 2018, British journal of pharmacology.

[68]  Naomi R. Latorraca,et al.  Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors , 2017, Cell.

[69]  R. Dey,et al.  Regulation, Signaling, and Physiological Functions of G-Proteins. , 2016, Journal of molecular biology.

[70]  Jonathan S. Mason,et al.  Structures of G protein-coupled receptors reveal new opportunities for drug discovery. , 2015, Drug discovery today.

[71]  Charged Extracellular Residues, Conserved throughout a G-protein-coupled Receptor Family, Are Required for Ligand Binding, Receptor Activation, and Cell-surface Expression* , 2006, Journal of Biological Chemistry.

[72]  Stefano Moro,et al.  Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR-Ligand Recognition Pathway in a Nanosecond Time Scale , 2014, J. Chem. Inf. Model..

[73]  Ali Jazayeri,et al.  Intracellular allosteric antagonism of the CCR9 receptor , 2016, Nature.

[74]  Alexander S. Hauser,et al.  GPCRdb in 2018: adding GPCR structure models and ligands , 2017, Nucleic Acids Res..

[75]  Mona Singh,et al.  Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure , 2009, PLoS Comput. Biol..

[76]  Anthony Ivetac,et al.  High-resolution structure of the human GPR40 receptor bound to allosteric agonist TAK-875 , 2014, Nature.

[77]  Bryan L. Roth,et al.  Molecular control of δ-opioid receptor signalling , 2014, Nature.

[78]  A. J. Venkatakrishnan,et al.  Diverse activation pathways in class A GPCRs converge near the G-protein-coupling region , 2016, Nature.

[79]  David E. Gloriam,et al.  Trends in GPCR drug discovery: new agents, targets and indications , 2017, Nature Reviews Drug Discovery.

[80]  A Keith Dunker,et al.  Intrinsically Disordered Proteins Link Alternative Splicing and Post-translational Modifications to Complex Cell Signaling and Regulation. , 2018, Journal of molecular biology.

[81]  Chris de Graaf,et al.  Generic GPCR residue numbers - aligning topology maps while minding the gaps. , 2015, Trends in pharmacological sciences.

[82]  S. Yokoyama,et al.  Na+-mimicking ligands stabilize the inactive state of leukotriene B4 receptor BLT1. , 2018, Nature chemical biology.

[83]  Vadim Cherezov,et al.  Diversity and modularity of G protein-coupled receptor structures. , 2012, Trends in pharmacological sciences.

[84]  Arthur Christopoulos,et al.  Structure of the adenosine-bound human adenosine A1 receptor–Gi complex , 2018, Nature.

[85]  O. Kuybeda,et al.  Cryo-EM structure of human rhodopsin bound to an inhibitory G protein , 2018, Nature.

[86]  Arthur Christopoulos,et al.  Muscarinic acetylcholine receptors: novel opportunities for drug development , 2014, Nature Reviews Drug Discovery.

[87]  Xiliang Zheng,et al.  Pocket-Based Drug Design: Exploring Pocket Space , 2012, The AAPS Journal.

[88]  Tilman Flock,et al.  Structured and disordered facets of the GPCR fold. , 2014, Current opinion in structural biology.

[89]  S. C. Wolff,et al.  Charged residues in the C-terminus of the P2Y1 receptor constitute a basolateral-sorting signal , 2010, Journal of Cell Science.

[90]  Michael J. E. Sternberg,et al.  3DLigandSite: predicting ligand-binding sites using similar structures , 2010, Nucleic Acids Res..

[91]  M. Congreve,et al.  Applying Structure-Based Drug Design Approaches to Allosteric Modulators of GPCRs. , 2017, Trends in pharmacological sciences.

[92]  R. Lewis,et al.  Extracellular Surface Residues of the α1B-Adrenoceptor Critical for G Protein–Coupled Receptor Function , 2015, Molecular Pharmacology.

[93]  Albert C. Pan,et al.  Structure and Dynamics of the M3 Muscarinic Acetylcholine Receptor , 2012, Nature.

[94]  R. Stevens,et al.  The Molecular Mechanism of P2Y1 Receptor Activation , 2016, Angewandte Chemie.