Modeling G protein-coupled receptors in complex with biased agonists

Trends in Pharmacological Sciences

Volumn 35, Issue 6, 2014, Pages 277-283

  Costanzi, Stefano ^a  

^a AMERICAN UNIVERSITY   (United States)

Author keywords

flexible docking; global conformational changes; local conformational changes; molecular dynamics; normal mode analysis; virtual screening

Indexed keywords

G PROTEIN COUPLED RECEPTOR;

ALLOSTERISM; ARTICLE; BINDING AFFINITY; CRYSTAL STRUCTURE; DRUG DEVELOPMENT; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN STABILITY; SIGNAL TRANSDUCTION; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

FLEXIBLE DOCKING; GLOBAL CONFORMATIONAL CHANGES; LOCAL CONFORMATIONAL CHANGES; MOLECULAR DYNAMICS; NORMAL MODE ANALYSIS; VIRTUAL SCREENING;

ADRENERGIC BETA-2 RECEPTOR AGONISTS; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; RECEPTORS, ADRENERGIC, BETA-2; RECEPTORS, G-PROTEIN-COUPLED; SIGNAL TRANSDUCTION; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84901794498     PISSN: 01656147     EISSN: 18733735     Source Type: Journal    
DOI: 10.1016/j.tips.2014.04.004     Document Type: Review

References (74)

1. K. Pierce et al. Seven-transmembrane receptors Nat. Rev. Mol. Cell Biol. 3 2002 639 650 (Pubitemid 34987785)
2. E. Reiter et al. Molecular mechanism of β-arrestin-biased agonism at seven-transmembrane receptors Annu. Rev. Pharmacol. Toxicol. 52 2012 179 197
3. S. Rajagopal et al. Quantifying ligand bias at 7-transmembrane receptors Mol. Pharmacol. 80 2011 367 377
4. J.D. Urban et al. Functional selectivity and classical concepts of quantitative pharmacology J. Pharmacol. Exp. Ther. 320 2007 1 13 (Pubitemid 46025713)
5. 2-adrenergic receptor J. Biol. Chem. 283 2008 5669 5676
6. i switching Cell. Signal. 16 2004 1397 1403 (Pubitemid 39277504)
7. R. Lefkowitz, and S. Shenoy Transduction of receptor signals by β-arrestins Science 308 2005 512 517
8. J.W. Wisler et al. A unique mechanism of β-blocker action: carvedilol stimulates β-arrestin signaling Proc. Natl. Acad. Sci. U.S.A. 104 2007 16657 16662 (Pubitemid 350211072)
9. 2-adrenergic receptor Nat. Chem. Biol. 7 2011 692 700
10. D. Gesty-Palmer et al. Distinct β-arrestin- and G protein-dependent pathways for parathyroid hormone receptor-stimulated ERK1/2 activation J. Biol. Chem. 281 2006 10856 10864 (Pubitemid 43855508)
11. R.W. Walters et al. β-arrestin1 mediates nicotinic acid-induced flushing, but not its antilipolytic effect, in mice J. Clin. Invest. 119 2009 1312 1321
12. M.M. Monasky et al. The β-arrestin-biased ligand TRV120023 inhibits angiotensin II-induced cardiac hypertrophy while preserving enhanced myofilament response to calcium Am. J. Physiol. Heart Circ. Physiol. 305 2013 H856 H866
13. J.D. Violin et al. GPCR biased ligands as novel heart failure therapeutics Trends Cardiovasc. Med. 23 2013 242 249
14. G. Boerrigter et al. TRV120027, a novel β-arrestin biased ligand at the angiotensin II type I receptor, unloads the heart and maintains renal function when added to furosemide in experimental heart failure Circ. Heart Fail. 5 2012 627 634
15. K.S. Kim et al. β-arrestin-biased AT1R stimulation promotes cell survival during acute cardiac injury Am. J. Physiol. Heart Circ. Physiol. 303 2012 H1001 H1010
16. G. Boerrigter et al. Cardiorenal actions of TRV120027, a novel β-arrestin-biased ligand at the angiotensin II type I receptor, in healthy and heart failure canines: a novel therapeutic strategy for acute heart failure Circ. Heart Fail. 4 2011 770 778
17. S.M. DeWire, and J.D. Violin Biased ligands for better cardiovascular drugs: dissecting G-protein-coupled receptor pharmacology Circ. Res. 109 2011 205 216
18. A.K. Shukla et al. Distinct conformational changes in β-arrestin report biased agonism at seven-transmembrane receptors Proc. Natl. Acad. Sci. U.S.A. 105 2008 9988 9993
19. L. Zhou et al. Development of functionally selective, small molecule agonists at kappa opioid receptors J. Biol. Chem. 288 2013 36703 36716
20. K.L. White et al. Identification of novel functionally selective kappa opioid receptor scaffolds Mol. Pharmacol. 85 2013 83 90
21. X.T. Chen et al. Structure-activity relationships and discovery of a G protein biased mu opioid receptor ligand, [(3-methoxythiophen-2-yl)methyl]({2- [(9R)-9-(pyridin-2-yl)-6-oxaspiro-[4.5]decan-9-yl]ethyl})amine (TRV130), for the treatment of acute severe pain J. Med. Chem. 56 2013 8019 8031
22. J.R. Lane et al. Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors Mol. Pharmacol. 84 2013 794 807
23. K. Palczewski, and T. Orban From atomic structures to neuronal functions of G protein-coupled receptors Annu. Rev. Neurosci. 36 2013 139 164
24. s protein complex Nature 477 2011 549 555
25. 2-adrenergic receptor establish a barcode that encodes differential functions of β-arrestin Sci. Signal. 4 2011 ra51
26. 2-adrenergic receptor activation Cell 152 2013 532 542
27. B. Kobilka G protein coupled receptor structure and activation Biochim. Biophys. Acta 1768 2007 794 807 (Pubitemid 46452546)
28. B.K. Kobilka, and X. Deupi Conformational complexity of G-protein-coupled receptors Trends Pharmacol. Sci. 28 2007 397 406 (Pubitemid 47087966)
29. 2-adrenoceptor Nat. Chem. Biol. 2 2006 417 422 (Pubitemid 44114919)
30. T. Warne, and C.G. Tate The importance of interactions with helix 5 in determining the efficacy of β-adrenoceptor ligands Biochem. Soc. Trans. 41 2013 159 165
31. R.C. Stevens et al. The GPCR Network: a large-scale collaboration to determine human GPCR structure and function Nat. Rev. Drug Discov. 12 2013 25 34
32. V. Katritch et al. Structure-function of the G protein-coupled receptor superfamily Annu. Rev. Pharmacol. Toxicol. 53 2013 531 556
33. A.J. Venkatakrishnan et al. Molecular signatures of G-protein-coupled receptors Nature 494 2013 185 194
34. C.G. Tate, and G.F. Schertler Engineering G protein-coupled receptors to facilitate their structure determination Curr. Opin. Struct. Biol. 19 2009 386 395
35. A.C. Kruse et al. Applications of molecular replacement to G protein-coupled receptors Acta Crystallogr. D: Biol. Crystallogr. 69 2013 2287 2292
36. J. Steyaert, and B.K. Kobilka Nanobody stabilization of G protein-coupled receptor conformational states Curr. Opin. Struct. Biol. 21 2011 567 572
37. 1- adrenoceptor bound to the biased agonists bucindolol and carvedilol Structure 20 2012 841 849
38. D. Wacker et al. Structural features for functional selectivity at serotonin receptors Science 340 2013 615 619
39. 19F-NMR Science 335 2012 1106 1110
40. 2 adrenergic receptor with accelerated molecular dynamics Biochemistry 52 2013 5593 5603
41. I.A. Balabin et al. Coarse-grained modeling of allosteric regulation in protein receptors Proc. Natl. Acad. Sci. U.S.A. 106 2009 14253 14258
42. D. Provasi et al. Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques PLoS Comput. Biol. 7 2011 e1002193
43. 2- adrenergic receptor Proc. Natl. Acad. Sci. U.S.A. 108 2011 18684 18689
44. R.O. Dror et al. Pathway and mechanism of drug binding to G-protein-coupled receptors Proc. Natl. Acad. Sci. U.S.A. 108 2011 13118 13123
45. 2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes J. Mol. Recognit. 22 2009 307 318
46. 2-adrenergic receptor J. Mol. Graph. Model. 29 2011 809 817
47. S. Vilar et al. Docking-based virtual screening for ligands of G protein-coupled receptors: not only crystal structures but also in silico models J. Mol. Graph. Model. 29 2011 614 623
48. C.N. Cavasotto Normal mode-based approaches in receptor ensemble docking Methods Mol. Biol. 819 2012 157 168
49. C.N. Cavasotto, and R.A. Abagyan Protein flexibility in ligand docking and virtual screening to protein kinases J. Mol. Biol. 337 2004 209 225 (Pubitemid 38270258)
50. C.N. Cavasotto et al. Representing receptor flexibility in ligand docking through relevant normal modes J. Am. Chem. Soc. 127 2005 9632 9640 (Pubitemid 40934775)
51. M. Rueda et al. Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes J. Chem. Inf. Model. 49 2009 716 725
52. 2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators J. Comput. Aided Mol. Des. 23 2009 273 288
53. S.S. Phatak et al. Ligand-steered modeling and docking: a benchmarking study in class A G-protein-coupled receptors J. Chem. Inf. Model. 50 2010 2119 2128
54. V. Katritch, and R. Abagyan GPCR agonist binding revealed by modeling and crystallography Trends Pharmacol. Sci. 32 2011 637 643
55. M. Rueda et al. ALiBERO: evolving a team of complementary pocket conformations rather than a single leader J. Chem. Inf. Model. 52 2012 2705 2714
56. V. Katritch et al. Ligand-guided receptor optimization Methods Mol. Biol. 857 2012 189 205
57. 2 adrenergic receptor: insight into G-protein-coupled receptor activation Biophys. J. 94 2008 2027 2042
58. S. Bhattacharya, and N. Vaidehi Computational mapping of the conformational transitions in agonist selective pathways of a G-protein coupled receptor J. Am. Chem. Soc. 132 2010 5205 5214
59. S. Bhattacharya, and N. Vaidehi LITiCon: a discrete conformational sampling computational method for mapping various functionally selective conformational states of transmembrane helical proteins Methods Mol. Biol. 914 2012 167 178
60. G. Bottegoni et al. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE) J. Comput. Aided Mol. Des. 22 2008 311 325
61. R.O. Dror et al. Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs Nature 503 2013 295 299
62. 2 adrenergic receptor: implications of inactive and activated state structures J. Comput. Chem. 33 2012 561 572
63. 2-agonist therapy in lung disease Am. J. Respir. Crit. Care Med. 187 2013 690 696
64. J.A. Johnson, and S.B. Liggett Cardiovascular pharmacogenomics of adrenergic receptor signaling: clinical implications and future directions Clin. Pharmacol. Ther. 89 2011 366 378
65. 2 adrenoceptor Nature 469 2011 175 180
66. 2 adrenergic G protein coupled receptor ACS Chem. Biol. 8 2013 1018 1026
67. 2-adrenergic receptor ligands Proc. Natl. Acad. Sci. U.S.A. 106 2009 6843 6848
68. K.A. Jacobson, and S. Costanzi New insights for drug design from the X-ray crystallographic structures of G-protein-coupled receptors Mol. Pharmacol. 82 2012 361 371
69. W. Sherman et al. Novel procedure for modeling ligand/receptor induced fit effects J. Med. Chem. 49 2006 534 553 (Pubitemid 43157487)
70. T.H. Kim et al. The role of ligands on the equilibria between functional states of a G protein-coupled receptor J. Am. Chem. Soc. 135 2013 9465 9474
71. M. Bokoch et al. Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor Nature 463 2010 108 112
72. 19F NMR spectroscopy Angew. Chem. Int. Ed. Engl. 52 2013 10762 10765
73. 2-Adrenergic receptor solutions for structural biology analyzed with microscale NMR diffusion measurements Angew. Chem. Int. Ed. Engl. 52 2013 331 335
74. A.K. Shukla et al. Structure of active β-arrestin-1 bound to a G-protein-coupled receptor phosphopeptide Nature 497 2013 137 141