Chemical genomics approach for GPCR-ligand interaction prediction and extraction of ligand binding determinants

Journal of Chemical Information and Modeling

Volumn 53, Issue 6, 2013, Pages 1253-1262

  Shiraishi, Akira ^a   Niijima, Satoshi ^a   Brown, J B ^a   Nakatsui, Masahiko ^a   Okuno, Yasushi ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; PREDICTIVE ANALYTICS; VIRTUAL ADDRESSES;

AMINO ACID PROPERTIES; G PROTEIN COUPLED RECEPTORS; INTERACTION SITE; LIGAND INTERACTIONS; MACHINE LEARNING APPROACHES; SEQUENCE SIMILARITY; STATISTICAL APPROACH; VIRTUAL LIGAND SCREENING;

LIGANDS;

G PROTEIN COUPLED RECEPTOR; LIGAND; PROTEIN BINDING;

ARTIFICIAL INTELLIGENCE; BINDING SITE; BIOLOGICAL MODEL; CHEMISTRY; GENOMICS; HUMAN; METABOLISM; PROCEDURES; ARTICLE; METHODOLOGY; PROTEIN BINDING;

ARTIFICIAL INTELLIGENCE; BINDING SITES; GENOMICS; HUMANS; LIGANDS; MODELS, BIOLOGICAL; PROTEIN BINDING; RECEPTORS, G-PROTEIN-COUPLED;

EID: 84879578484     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300515z     Document Type: Article

References (74)

1. Vroling, B.; Sanders, M.; Baakman, C.; Borrmann, A.; Verhoeven, S.; Klomp, J.; Oliveira, L.; de Vlieg, J.; Vriend, G. GPCRDB: information system for G protein-coupled receptors Nucleic Acids Res. 2011, 39, D309-19
2. Kristiansen, K. Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function Pharmacol. Ther. 2004, 103, 21-80
3. Jacoby, E.; Bouhelal, R.; Gerspacher, M.; Seuwen, K. The 7 TM G-protein-coupled receptor target family ChemMedChem. 2006, 1, 761-82
4. Klabunde, T.; Hessler, G. Drug design strategies for targeting G-protein-coupled receptors ChemBioChem. 2002, 3, 928-44
5. Gether, U. Uncovering molecular mechanisms involved in activation of G protein-coupled receptors Endocr. Rev. 2000, 21, 90-113
6. Attwood, T. K.; Findlay, J. B. Fingerprinting G-protein-coupled receptors Protein Eng. 1994, 7, 195-203
7. Surgand, J. S.; Rodrigo, J.; Kellenberger, E.; Rognan, D. A chemogenomic analysis of the transmembrane binding cavity of human G-protein-coupled receptors Proteins 2006, 62, 509-38
8. Sanders, M. P.; Fleuren, W. W.; Verhoeven, S.; van den Beld, S.; Alkema, W.; de Vlieg, J.; Klomp, J. P. ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs BMC Bioinf. 2011, 12, 332
9. Ye, K.; Lameijer, E. W.; Beukers, M. W.; Ijzerman, A. P. A two-entropies analysis to identify functional positions in the transmembrane region of class A G protein-coupled receptors Proteins 2006, 63, 1018-30
10. Davies, M. N.; Gloriam, D. E.; Secker, A.; Freitas, A. A.; Timmis, J.; Flower, D. R. Present perspectives on the automated classification of the G-protein coupled receptors (GPCRs) at the protein sequence level Curr. Top. Med. Chem. 2011, 11, 1994-2009
11. Mulder, N. J.; Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A.; Binns, D.; Bork, P.; Buillard, V.; Cerutti, L.; Copley, R.; Courcelle, E.; Das, U.; Daugherty, L.; Dibley, M.; Finn, R.; Fleischmann, W.; Gough, J.; Haft, D.; Hulo, N.; Hunter, S.; Kahn, D.; Kanapin, A.; Kejariwal, A.; Labarga, A.; Langendijk-Genevaux, P. S.; Lonsdale, D.; Lopez, R.; Letunic, I.; Madera, M.; Maslen, J.; McAnulla, C.; McDowall, J.; Mistry, J.; Mitchell, A.; Nikolskaya, A. N.; Orchard, S.; Orengo, C.; Petryszak, R.; Selengut, J. D.; Sigrist, C. J.; Thomas, P. D.; Valentin, F.; Wilson, D.; Wu, C. H.; Yeats, C. New developments in the InterPro database Nucleic Acids Res. 2007, 35, D224-8
12. Mouillac, B.; Chini, B.; Balestre, M. N.; Elands, J.; Trumpp-Kallmeyer, S.; Hoflack, J.; Hibert, M.; Jard, S.; Barberis, C. The binding site of neuropeptide vasopressin V1a receptor. Evidence for a major localization within transmembrane regions J. Biol. Chem. 1995, 270, 25771-7
13. An, J.; Totrov, M.; Abagyan, R. Pocketome via comprehensive identification and classification of ligand binding envelopes Mol. Cell Proteomics 2005, 4, 752-61
14. Cavasotto, C. N.; Orry, A. J.; Abagyan, R. A. Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors Proteins 2003, 51, 423-33
15. Frimurer, T. M.; Ulven, T.; Elling, C. E.; Gerlach, L. O.; Kostenis, E.; Högberg, T. A physicogenetic method to assign ligand-binding relationships between 7TM receptors Bioorg. Med. Chem. Lett. 2005, 15, 3707-12
16. Kratochwil, N. A.; Malherbe, P.; Lindemann, L.; Ebeling, M.; Hoener, M. C.; Mühlemann, A.; Porter, R. H.; Stahl, M.; Gerber, P. R. An automated system for the analysis of G protein-coupled receptor transmembrane binding pockets: alignment, receptor-based pharmacophores, and their application J. Chem. Inf. Model. 2005, 45, 1324-36
17. Bywater, R. P. Location and nature of the residues important for ligand recognition in G-protein coupled receptors J. Mol. Recognit. 2005, 18, 60-72
18. Wichard, J. D.; Ter Laak, A.; Krause, G.; Heinrich, N.; Kühne, R.; Kleinau, G. Chemogenomic analysis of G-protein coupled receptors and their ligands deciphers locks and keys governing diverse aspects of signalling PLoS One 2011, 6, e16811
19. Reynolds, K. A.; Katritch, V.; Abagyan, R. Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators J. Comput.-Aided Mol. Des. 2009, 23, 273-88
20. Kenakin, T. Ligand-selective receptor conformations revisited: the promise and the problem Trends. Pharmacol. Sci. 2003, 24, 346-54
21. Kobilka, B. K.; Deupi, X. Conformational complexity of G-protein-coupled receptors Trends. Pharmacol. Sci. 2007, 28, 397-406
22. Schwartz, T. W.; Frimurer, T. M.; Holst, B.; Rosenkilde, M. M.; Elling, C. E. Molecular mechanism of 7TM receptor activation-a global toggle switch model Annu. Rev. Pharmacol. Toxicol. 2006, 46, 481-519
23. Urban, J. D.; Clarke, W. P.; von Zastrow, M.; Nichols, D. E.; Kobilka, B.; Weinstein, H.; Javitch, J. A.; Roth, B. L.; Christopoulos, A.; Sexton, P. M.; Miller, K. J.; Spedding, M.; Mailman, R. B. Functional selectivity and classical concepts of quantitative pharmacology J. Pharmacol. Exp. Ther. 2007, 320, 1-13
24. Palczewski, K.; Kumasaka, T.; Hori, T.; Behnke, C. A.; Motoshima, H.; Fox, B. A.; Le Trong, I.; Teller, D. C.; Okada, T.; Stenkamp, R. E.; Yamamoto, M.; Miyano, M. Crystal structure of rhodopsin: A G protein-coupled receptor Science 2000, 289, 739-45
25. Cherezov, V.; Rosenbaum, D. M.; Hanson, M. A.; Rasmussen, S. G.; Thian, F. S.; Kobilka, T. S.; Choi, H. J.; Kuhn, P.; Weis, W. I.; Kobilka, B. K.; Stevens, R. C. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor Science 2007, 318, 1258-65
26. Jaakola, V. P.; Griffith, M. T.; Hanson, M. A.; Cherezov, V.; Chien, E. Y.; Lane, J. R.; Ijzerman, A. P.; Stevens, R. C. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist Science 2008, 322, 1211-7
27. Hanson, M. A.; Roth, C. B.; Jo, E.; Griffith, M. T.; Scott, F. L.; Reinhart, G.; Desale, H.; Clemons, B.; Cahalan, S. M.; Schuerer, S. C.; Sanna, M. G.; Han, G. W.; Kuhn, P.; Rosen, H.; Stevens, R. C. Crystal structure of a lipid G protein-coupled receptor Science 2012, 335, 851-5
28. Zhang, C.; Srinivasan, Y.; Arlow, D. H.; Fung, J. J.; Palmer, D.; Zheng, Y.; Green, H. F.; Pandey, A.; Dror, R. O.; Shaw, D. E.; Weis, W. I.; Coughlin, S. R.; Kobilka, B. K. High-resolution crystal structure of human protease-activated receptor 1 Nature 2012, 492, 387-92
29. Warne, T.; Serrano-Vega, M. J.; Baker, J. G.; Moukhametzianov, R.; Edwards, P. C.; Henderson, R.; Leslie, A. G.; Tate, C. G.; Schertler, G. F. Structure of a beta1-adrenergic G-protein-coupled receptor Nature 2008, 454, 486-91
30. Haga, K.; Kruse, A. C.; Asada, H.; Yurugi-Kobayashi, T.; Shiroishi, M.; Zhang, C.; Weis, W. I.; Okada, T.; Kobilka, B. K.; Haga, T.; Kobayashi, T. Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist Nature 2012, 482, 547-51
31. Kruse, A. C.; Hu, J.; Pan, A. C.; Arlow, D. H.; Rosenbaum, D. M.; Rosemond, E.; Green, H. F.; Liu, T.; Chae, P. S.; Dror, R. O.; Shaw, D. E.; Weis, W. I.; Wess, J.; Kobilka, B. K. Structure and dynamics of the M3 muscarinic acetylcholine receptor Nature 2012, 482, 552-6
32. Chien, E. Y.; Liu, W.; Zhao, Q.; Katritch, V.; Han, G. W.; Hanson, M. A.; Shi, L.; Newman, A. H.; Javitch, J. A.; Cherezov, V.; Stevens, R. C. Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist Science 2010, 330, 1091-5
33. Shimamura, T.; Shiroishi, M.; Weyand, S.; Tsujimoto, H.; Winter, G.; Katritch, V.; Abagyan, R.; Cherezov, V.; Liu, W.; Han, G. W.; Kobayashi, T.; Stevens, R. C.; Iwata, S. Structure of the human histamine H1 receptor complex with doxepin Nature 2011, 475, 65-70
34. Wu, H.; Wacker, D.; Mileni, M.; Katritch, V.; Han, G. W.; Vardy, E.; Liu, W.; Thompson, A. A.; Huang, X. P.; Carroll, F. I.; Mascarella, S. W.; Westkaemper, R. B.; Mosier, P. D.; Roth, B. L.; Cherezov, V.; Stevens, R. C. Structure of the human κ-opioid receptor in complex with JDTic Nature 2012, 485, 327-32
35. Granier, S.; Manglik, A.; Kruse, A. C.; Kobilka, T. S.; Thian, F. S.; Weis, W. I.; Kobilka, B. K. Structure of the δ-opioid receptor bound to naltrindole Nature 2012, 485, 400-4
36. Manglik, A.; Kruse, A. C.; Kobilka, T. S.; Thian, F. S.; Mathiesen, J. M.; Sunahara, R. K.; Pardo, L.; Weis, W. I.; Kobilka, B. K.; Granier, S. Crystal structure of the μ-opioid receptor bound to a morphinan antagonist Nature 2012, 485, 321-6
37. Thompson, A. A.; Liu, W.; Chun, E.; Katritch, V.; Wu, H.; Vardy, E.; Huang, X. P.; Trapella, C.; Guerrini, R.; Calo, G.; Roth, B. L.; Cherezov, V.; Stevens, R. C. Structure of the nociceptin/orphanin FQ receptor in complex with a peptide mimetic Nature 2012, 485, 395-9
38. White, J. F.; Noinaj, N.; Shibata, Y.; Love, J.; Kloss, B.; Xu, F.; Gvozdenovic-Jeremic, J.; Shah, P.; Shiloach, J.; Tate, C. G.; Grisshammer, R. Structure of the agonist-bound neurotensin receptor Nature 2012, 490, 508-13
39. Gayen, A.; Goswami, S. K.; Mukhopadhyay, C. NMR evidence of GM1-induced conformational change of Substance P using isotropic bicelles Biochim. Biophys. Acta 2011, 1808, 127-39
40. Park, S. H.; Das, B. B.; Casagrande, F.; Tian, Y.; Nothnagel, H. J.; Chu, M.; Kiefer, H.; Maier, K.; De Angelis, A. A.; Marassi, F. M.; Opella, S. J. Structure of the chemokine receptor CXCR1 in phospholipid bilayers Nature 2012, 491, 779-83
41. Wu, B.; Chien, E. Y.; Mol, C. D.; Fenalti, G.; Liu, W.; Katritch, V.; Abagyan, R.; Brooun, A.; Wells, P.; Bi, F. C.; Hamel, D. J.; Kuhn, P.; Handel, T. M.; Cherezov, V.; Stevens, R. C. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists Science 2010, 330, 1066-71
42. Phatak, S. S.; Gatica, E. A.; Cavasotto, C. N. Ligand-steered modeling and docking: A benchmarking study in class A G-protein-coupled receptors J. Chem. Inf. Model. 2010, 50, 2119-28
43. Eckert, H.; Bajorath, J. Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches Drug Discovery Today 2007, 12, 225-33
44. Klabunde, T. Chemogenomic approaches to drug discovery: similar receptors bind similar ligands Br. J. Pharmacol. 2007, 152, 5-7
45. Weill, N.; Rognan, D. Development and validation of a novel protein-ligand fingerprint to mine chemogenomic space: application to G protein-coupled receptors and their ligands J. Chem. Inf. Model. 2009, 49, 1049-62
46. Yabuuchi, H.; Niijima, S.; Takematsu, H.; Ida, T.; Hirokawa, T.; Hara, T.; Ogawa, T.; Minowa, Y.; Tsujimoto, G.; Okuno, Y. Analysis of multiple compound-protein interactions reveals novel bioactive molecules Mol. Syst. Biol. 2011, 7, 472
47. Jacob, L.; Vert, J. P. Protein-ligand interaction prediction: an improved chemogenomics approach Bioinformatics 2008, 24, 2149-56
48. van der Horst, E.; Okuno, Y.; Bender, A.; IJzerman, A. P. Substructure mining of GPCR ligands reveals activity-class specific functional groups in an unbiased manner J. Chem. Inf. Model. 2009, 49, 348-60
49. Wassermann, A. M.; Geppert, H.; Bajorath, J. Ligand prediction for orphan targets using support vector machines and various target-ligand kernels is dominated by nearest neighbor effects J. Chem. Inf. Model. 2009, 49, 2155-2167
50. Schiöth, H. B.; Fredriksson, R. The GRAFS classification system of G-protein coupled receptors in comparative perspective Gen. Comp. Endrocrinol. 2005, 142, 94-101
51. GVK Bio Target inhibitor databases; GVK Biosciences Private Limited: Hyderabad, India, 2007.
52. Shawe-Taylor, J.; Cristianini, N. Kernel Methods for Pattern Analysis; Cambridge University Press: Cambridge, 2004.
53. Rogers, D.; Hahn, M. Extended-connectivity fingerprints J. Chem. Inf. Model. 2010, 50, 742-54
54. DRAGON, version 5.5; Talete srl: Milano, Italy, 2011.
55. Pipeline Pilot, version 6.5.1; Accelrys, Inc.: San Diego, CA, 2007.
56. El-Manzalawy, Y.; Dobbs, D.; Honavar, V. Predicting linear B-cell epitopes using string kernels J. Mol. Recognit. 2008, 21, 243-55
57. Bissantz, C.; Logean, A.; Rognan, D. High-throughput modeling of human G-protein coupled receptors: amino acid sequence alignment, three-dimensional model building, and receptor library screening J. Chem. Inf. Comput. Sci. 2004, 44, 1162-76
58. Saigo, H.; Vert, J. P.; Akutsu, T. Optimizing amino acid substitution matrices with a local alignment kernel BMC Bioinf. 2006, 7, 246
59. Sandberg, M.; Eriksson, L.; Jonsson, J.; Sjöström, M.; Wold, S. New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids J. Med. Chem. 1998, 41, 2481-91
60. Rao, H. B.; Zhu, F.; Yang, G. B.; Li, Z. R.; Chen, Y. Z. Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence Nucleic Acids Res. 2011, 39, W385-90
61. Vapnik, V. N. Statistical Learning Theory; John Wiley & Sons, Inc.: New York, 1998.
62. Chang, C.-C.; Lin, C.-J. LIBSVM: a library for support vector machines ACM Trans. Intell. Systems Technol. 2011, 2, 27
63. Shackelford, G.; Karplus, K. Contact prediction using mutual information and neural nets Proteins 2007, 69 (Suppl 8) 159-64
64. Gatica, E. A.; Cavasotto, C. N. Ligand and decoy sets for docking to G protein-coupled receptors J. Chem. Inf. Model. 2012, 52, 1-6
65. GPCR SARfari, version 2.0; European Bioinformatics Institute: Hinxton, U.K., 2011.
66. Weaver, S.; Gleeson, M. P. The importance of the domain of applicability in QSAR modeling J. Mol. Graphics Modell. 2008, 26, 1315-26
67. Leslie, C. S.; Eskin, E.; Cohen, A.; Weston, J.; Noble, W. S. Mismatch string kernels for discriminative protein classification Bioinformatics 2004, 20, 467-76
68. Hanley, J. A.; McNeil, B. J. The meaning and use of the area under a receiver operating characteristic (ROC) curve Radiology 1982, 143, 29-36
69. Christopoulos, A. Allosteric binding sites on cell-surface receptors: novel targets for drug discovery Nat. Rev. Drug Discovery 2002, 1, 198-210
70. van Koppen, C. J.; Zaman, G. J.; Timmers, C. M.; Kelder, J.; Mosselman, S.; van de Lagemaat, R.; Smit, M. J.; Hanssen, R. G. A signaling-selective, nanomolar potent allosteric low molecular weight agonist for the human luteinizing hormone receptor Naunyn Schmiedebergs Arch. Pharmacol. 2008, 378, 503-14
71. Keiser, M. J.; Setola, V.; Irwin, J. J.; Laggner, C.; Abbas, A. I.; Hufeisen, S. J.; Jensen, N. H.; Kuijer, M. B.; Matos, R. C.; Tran, T. B.; Whaley, R.; Glennon, R. A.; Hert, J.; Thomas, K. L.; Edwards, D. D.; Shoichet, B. K.; Roth, B. L. Predicting new molecular targets for known drugs Nature 2009, 462, 175-81
72. Suryanarayana, S.; Kobilka, B. K. Amino acid substitutions at position 312 in the seventh hydrophobic segment of the beta 2-adrenergic receptor modify ligand-binding specificity Mol. Pharmacol. 1993, 44, 111-4
73. Katritch, V.; Reynolds, K. A.; Cherezov, V.; Hanson, M. A.; Roth, C. B.; Yeager, M.; Abagyan, R. Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes J. Mol. Recognit. 2009, 22, 307-18
74. Ivanov, A. A.; Costanzi, S.; Jacobson, K. A. Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling J. Comput.-Aided Mol. Des. 2006, 20, 417-26