Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets?

Proteins: Structure, Function and Genetics

Volumn 50, Issue 1, 2003, Pages 5-25

  Bissantz, Caterina ^a,b   Bernard, Philippe ^a,c   Hibert, Marcel ^a   Rognan, Didier ^a  

^a CNRS   (France)

^b ETH ZURICH   (Switzerland)

^c UNIVERSITÉ D'ORLÉANS   (France)

Author keywords

Docking; GPCRs; Homology modeling; Scoring; Structure based ligand design

Indexed keywords

DOPAMINE 3 RECEPTOR; G PROTEIN COUPLED RECEPTOR; MUSCARINIC M1 RECEPTOR; RHODOPSIN; UNCLASSIFIED DRUG; VASOPRESSIN V1 RECEPTOR; VASOPRESSIN V1A RECEPTOR;

ARTICLE; CONFORMATIONAL TRANSITION; DATA BASE; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SCORING SYSTEM; SCREENING; SEQUENCE HOMOLOGY; X RAY ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; CATTLE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, FACTUAL; DRUG DELIVERY SYSTEMS; HETEROTRIMERIC GTP-BINDING PROTEINS; HUMANS; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; RECEPTOR, MUSCARINIC M1; RECEPTORS, ADRENERGIC, BETA-2; RECEPTORS, CELL SURFACE; RECEPTORS, DOPAMINE D2; RECEPTORS, DOPAMINE D3; RECEPTORS, MUSCARINIC; RECEPTORS, OPIOID, DELTA; RECEPTORS, VASOPRESSIN; RHODOPSIN; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

BOVINAE; RUMEX;

EID: 0037235663     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10237     Document Type: Article

References (68)

1. Mander T. Beyond uHTS: ridiculously HTS? Drug Discov Today 2000;5:223-225.
2. Walters WP, Stahl MT, Murcko MA. Virtual screening: an overview. Drug Discov Today 1998;3:160-178.
3. Pickett SD, McLay IM, Clark DE. Enhancing the hit-to-lead properties of lead optimization libraries. J Chem Inf Comput Sci 2000;2:263-272.
4. Gohlke H, Klebe G. Statistical potentials and scoring functions applied to protein-ligand binding. Curr Opin Struct Biol 2001;11: 231-235.
5. Mason JS, Hermsmeier MA. Diversity assessment. Curr Opin Chem Biol 1999;3:342-349.
6. Mason JS, Morize I, Menard PR, Cheney DL, Hulme C, Labaudiniere RF. New 4-point pharmacophore method for molecular similarity and diversity applications: overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures. J Med Chem 1999;42:3251-3264.
7. Dixon JS. Evaluation of the CASP2 docking section. Proteins 1997;(Suppl 1):198-204.
8. Tame JRH. Scoring functions: A view from the bench. J Comput-Aided Mol Design 1999;13:99-108.
9. Marhefka CA, Moore BM, Bishop C, Kirkovsky L, Mukherjee A, Dalton JT, Miller DD. Homology modeling using multiple molecular dynamics simulations and docking studies of the human androgen receptor ligand binding domain bound to testosterone and nonsteroidal ligands. J Med Chem 2001;44:1729-1740.
10. Schafferhans A, Klebe G. Docking ligands onto binding site representations derived from proteins built by homology modelling. J Mol Biol 2001;307:407-427.
11. Schneider, G., Böhm, H.J. Virtual screening and fast automated docking methods. Drug Discov. Today 2002;7:64-70.
12. Marchese A, George SR, Kolakowski LF, Lynch KR, O'Dowd BF. Novel GPCRs and their endogenous ligands: expanding the boundaries of physiology and pharmacology. Trends Pharmacol Sci 1999;20:370-375.
13. Hibert MF, Trumpp-Kallmeyer S, Bruinvels A, Hoflack J. Threedimensional models of neurotransmitter G-binding proteincoupled receptors. Mol Pharmacol 1991;40:8-15.
14. Bikker JA, Trumpp-Kallmeyer S, Humblet C. G-Protein coupled receptors: models, mutagenesis, and drug design. J Med Chem 1998;41:2911-2927.
15. Henderson R, Baldwin JM, Ceska TA, Zemlin F, Beckmann E, Downing KH. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol 1990;213: 899-929.
16. Schertler GF, Villa C, Henderson R. Projection structure of rhodopsin. Nature 1993;362:770-772.
17. Baldwin JM, Schertler GF, Unger VM. An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J Mol Biol 1997;272:144-164.
18. Mouillac B, Chini B, Balestre MN, 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: 25771-25777.
19. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Trong IL, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M. Crystal structure of Rhodopsin: a G protein-coupled receptor. Science 2000;289:739-745.
20. Sokoloff P, Schwartz JC. Novel dopamine receptors half a decade later. Trends Pharmacol Sci 1995;16:270-275.
21. Felder CC, Bymaster FP, Ward J, DeLapp N. Therapeutic opportunities for muscarinic receptors in the central nervous system. J Med Chem 2000;43:4333-4353.
22. Hibert M, Hoflack J, Trumpp-Kallmeyer S, Mouillac B, Chini B, Mahe E, Cotte N, Jard S, Manning M, Barberis C. Functional architecture of vasopressin/oxytocin receptors. J Recept Signal Transduct Res 1999;19:589-596.
23. Bissantz C, Folkers G, Rognan D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem 2000;43:4759-4767.
24. Ewing TJA, Kuntz ID. Critical evaluation of search algorithms for automated molecular docking and database screening. J Comput Chem 1997;18:1175-1189.
25. Jones G, Wilett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997;267:727-748.
26. Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996;261:470-489.
27. Muegge I, Martin YC. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem 1999;42:791-804.
28. Eldridge M, Murray CW, Auton TA, Paolini GV, Lee RP. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput-Aided Mol Des 1997;11:425-445.
29. Rognan D, Laumoeller SL, Holm A, Buus S, Tschinke V. Predicting binding affinities of protein ligands from three-dimensional coordinates: application to peptide binding to class I major histocompatibility proteins. J Med Chem 1999;42:4650-4658.
30. Wang R, Liu L, Lai L, Tang Y. SCORE: a new empirical method for estimating the binding affinity of a protein-ligand complex. J Mol Model 1998;4:379-384.
31. Charifson PS, Corkery JJ, Murcko MA, Walters WP. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem 1999;42:5100-5109.
32. MDL Information Systems, Inc., San Leandro, CA 94577.
33. SYBYL 6.62, Tripos Inc., St. Louis, MO 63144.
34. Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity: a rapid access to atomic charges. Tetrahedron 1980;36:3219-3228.
35. Concord 4.0 is part of the SYBYL software distribution (http:// www.tripos.com).
36. Isis/Draw is distributed from MDL Information Systems (http:// www.mdli.com).
37. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
38. Henikoff S, Henikoff J. G. Amino acid substitution matrices from protein blocks Proc Natl Acad Sci USA 1992;89:10915-10919.
39. Strader CD, Dixon RA, Cheung AH, Candelore MR, Blake AD, Sigal IS. Mutations that uncouple the beta-adrenergic receptor from Gs and increase agonist affinity. J Biol Chem 1987;262: 16439-16443.
40. Case DA, Pearlman DA, Caldwell JW, Cheatham III TE, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Ferguson, DM, Radmer RJ, Seibel GL, Singh, UC, Weiner PK, Kollman PA. AMBER 5.0. University of California, San Francisco; 1997.
41. Cornel WD, Cieplak P, Bayly CI, Gould IR, Merz JKM, Ferguson DM, Spellmeyer DM, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J Am Chem Soc 1995;117:5179-5197.
42. Alberts GL, Pregenzer JF, Im WB. Identification of transmembrane regions critical for ligand binding to the human D3 dopamine receptor using various D3/D1 transmembrane chimeras. Mol Pharmacol 1998;54:379-88.
43. Mansour A, Meng F, Meador-Woodruff JH, Taylor LP, Civelli O, Akil H. Site-directed mutagenesis of the human dopamine D2 receptor. Eur J Pharmacol 1992;227:205-214.
44. Lundstrom K, Turpin P, Large C, Robertson G, Thomas P, Lewell XQ. Mapping of dopamine D3 receptor binding site by pharmacological characterization of mutants expressed in CHO cells with the Semliki Forest virus system. J Recept Signal Transduct Res 1998;18:133-150.
45. Cho W, Taylor LP, Mansour A, Akil H. Hydrophobic residues of the D2 dopamine receptor are important for binding and signal transduction. J Neurochem 1995;65:2105-2115.
46. Bourdon H, Trumpp-Kallmeyer S, Schreuder H, Hoflack J, Hibert M, Wermuth CG. Modelling of the binding site of the human m1 muscarinic receptor: Experimental validation and refinement. J Comput-Aided Mol Design 1997;11:317-332.
47. Cotte N, Balestre MN, Aumelas A, Mahe E, Phalipou S, Morin D, Hibert M, Manning M, Durroux T, Barberis C, Mouillac B. Conserved aromatic residues in the transmembrane region VI of the V1a vasopressin receptor differentiate agonist vs. antagonist ligand binding. Eur J Biochem 2000;267:4253-4263.
48. Strader CD, Candelore MR, Hill WS, Sigal IS, Dixon RAF. Identification of two serine residues involved in agonist activation of the β2-adrenergic receptor. J Biol Chem 1989;264:13572-13578.
49. Strader CD, Gaffney T, Sugg EE, Candelore MR, Keys R, Patchett AA, Dixon RAF. Allele-specific activation of genetically engineered receptors. J Biol Chem 1991;266:5-8.
50. Strader CD, Fong TM, Tota MR, Underwood D, Dixon RA. Structure and function of G protein-coupled receptors. Annu Rev Biochem 1994;63:101-132.
51. Wieland K, Zuurmond HM, Krasel C, Ijzerman AP, Lohse MJ. Involvement of Asn-293 in stereospecific agonist recognition and in activation of the β2-adrenergic receptor. Pharmacology 1996;93: 9276-9281.
52. Liapaski G, Ballesteros JA, Papachristou S, Chan WC, Chen X, Javitch JA. The Forgotten Serine. J Biol Chem 2000;275:37779-37788.
53. Valiquette M, Vu HK, Yue SY, Waehlestedt C, Walker P. Involvement of Trp-284, Val-296, and Val-297 of the human δ-opioid receptor in binding of δ-selective ligands. J Biol Chem 1996;271: 18789-18796.
54. Befort K, Tabbara L, Kling D, Maigret B, Kiefer BL. Role of aromatic transmembrane residues of the δ-opioid receptor in ligand recognition. J Biol Chem 1996;271:10161-10168.
55. Pepin M, Yue SY, Roberts E, Wahlestedt C, Walker P. Novel "restoration of function" mutagenesis strategy to identify amino acids of the δ-opioid receptor involved in ligand binding. J Biol Chem 1997;272:9260-9267.
56. Lemmen C, Lengauer T, Klebe G. FlexS: a method for fast flexible ligand superimposition. J Med Chem 1998;41:4502-4520.
57. Schwartz TW. Locating ligand-binding sites in 7 TM receptors by protein engineering. Cur Opin Biotechnol 1994;5:434-444.
58. Gether U, Kobilka BK. G protein-coupled receptors. II. Mechanism of agonist activation. J Biol Chem 1998;273:17979-17982.
59. Hulme EC, Lu ZL, Ward SDC, Allman K, Curtis CA. The conformational switch in 7-transmembrane receptors: the muscarinic receptor paradigm. Eur J Pharmacol 1999;375:247-260.
60. Ghanouni P, Steenhuis JJ, Farrens DL, Kobilka BK. Agonistinduced conformational changes in the G-protein-coupling domain of the β2 adrenergic receptor. Proc Natl Acd Sci USA 2001;98:5997-6002.
61. Plobeck N, Delorme D, Wei Z, Yang H, Zhou F, Schwarz P, Gawell L, Gagnon H, Pelcman B, Schmidt R, Yue SY, Walpole C, Brown W, Zhou E, Labarre M, Payza K, St-Onge S, Kamassah A, Morin P, Projean D, Ducharme J, Roberts E. New Diarylmethylpiperazines as potent and selective nonpeptidic δ opioid receptor agonists with increased in vitro metabolic stability. J Med Chem 2000;43:3878-3894.
62. Liao S, Alfaro Lopez J, Shenderovich MD, Hosohata K, Lin J, Li X, Stropova D, Davis P, Jernigan KA, Porreca F, Yamamura HI, Hruby VJ. De novo design, synthesis, and biological activities of high-affinity and selective non-peptide agonists of the δ-opioid receptor. J Med Chem 1998;41:4767-4776.
63. Portoghese PS. From models to molecules: opioid receptor dimers, bivalent ligands, and selective opioid receptor probes. J Med Chem 2001;44:2259-2269.
64. Farrens DL, Altenbach C, Yang K, Hubell WL, Khorana HG. Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science 1996;274:768-770.
65. Dunham TD, Farrens DL. Conformational changes in Rhodopsin. J Biol Chem 1999;274:1683-1650.
66. 2 adrenergic receptor mapped by site-selective fluorescent labeling. J Biol Chem 2001;276:9279-9290.
67. Paul N, Rognan D. ConsDock: A new program for the consensus analysis of protein-ligand interactions. Proteins 2002;47:521-533.
68. 2 adrenergic receptor. J Biol Chem 2001;276:24433-24436.