Virtual fragment screening: Discovery of histamine H3 receptor ligands using ligand-based and protein-based molecular fingerprints

Journal of Chemical Information and Modeling

Volumn 52, Issue 12, 2012, Pages 3308-3324

  Sirci, Francesco ^a   Istyastono, Enade P ^b,c   Vischer, Henry F ^b   Kooistra, Albert J ^b   Nijmeijer, Saskia ^b   Kuijer, Martien ^b   Wijtmans, Maikel ^b   Mannhold, Raimund ^d   Leurs, Rob ^b   De Esch, Iwan J P ^b   De Graaf, Chris ^b  

^a UNIVERSITY OF PERUGIA   (Italy)

^b AMSTERDAM INSTITUTE FOR MOLECULES   (Netherlands)

^c SANATA DHARMA UNIVERSITY   (Indonesia)

^d HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BINDERS; MOLECULES; PROTEINS;

BIOLOGICALLY ACTIVE MOLECULES; FIRST CONSTRUCTIONS; G-PROTEIN COUPLED RECEPTORS; MOLECULAR FINGERPRINT; MOLECULAR INTERACTION FIELDS; PROTEIN FRAGMENTS; RECEPTOR LIGANDS; VIRTUAL SCREENING;

LIGANDS;

HISTAMINE H3 RECEPTOR; LIGAND;

ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER INTERFACE; DISCRIMINANT ANALYSIS; DRUG SCREENING; METABOLISM; METHODOLOGY; MOLECULAR DOCKING; PROTEIN CONFORMATION; PROTEIN DATABASE;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DISCRIMINANT ANALYSIS; DRUG EVALUATION, PRECLINICAL; LIGANDS; MOLECULAR DOCKING SIMULATION; PROTEIN CONFORMATION; RECEPTORS, HISTAMINE H3; USER-COMPUTER INTERFACE;

EID: 84871596792     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci3004094     Document Type: Article

References (108)

1. Verheij, M. H. P.; de Graaf, C.; de Kloe, G. E.; Nijmeijer, S.; Vischer, H. F.; Smits, R. A.; Zuiderveld, O. P.; Hulscher, S.; Silvestri, L.; Thompson, A. J.; van Muijlwijk-Koezen, J. E.; Lummis, S. C. R.; Leurs, R.; de Esch, I. J. P. Fragment library screening reveals remarkable similarities between the G protein-coupled receptor histamine H(4) and the ion channel serotonin 5-HT(3A) Bioorg. Med. Chem. Lett. 2011, 21, 5460-5464
2. Congreve, M.; Carr, R.; Murray, C.; Jhoti, H. A 'rule of three' for fragment-based lead discovery? Drug Discovery Today 2003, 8, 876-7
3. Murray, C. W.; Verdonk, M. L.; Rees, D. C. Experiences in fragment-based drug discovery Trends Pharmacol. Sci. 2012, 33, 224-32
4. de Graaf, C.; Vischer, H. F.; de Kloe, G. E.; Kooistra, A. J.; Nijmeijer, S.; Kuijer, M.; Verheij, M. H. P.; England, P.; van Muijlwijk-Koezen, J. E.; Leurs, R.; de Esch, I. J. P. Small and colourful stones make beautiful mosaics: Fragment-Based Chemogenomics Drug Discovery Today 2012, http://dx.doi.org/10. 1016/j.drudis.2012
5. de Kloe, G. E.; Bailey, D.; Leurs, R.; de Esch, I. J. P. Transforming fragments into candidates: small becomes big in medicinal chemistry Drug Discovery Today 2009, 14, 630-646
6. Schultes, S.; De Graaf, C.; Haaksma, E. J.; De Esch, I. J. P.; Leurs, R.; Kramer, O. Ligand efficiency as a guide in fragment hit selection and optimization Drug Discovery Today: Technol. 2010, 7, 153-162
7. Congreve, M.; Chessari, G.; Tisi, D.; Woodhead, A. J. Recent developments in fragment-based drug discovery J. Med. Chem. 2008, 51, 3661-80
8. Yuriev, E.; Agostino, M.; Ramsland, P. A. Challenges and advances in computational docking: 2009 in review J. Molec. Recog. 2011, 24, 149-164
9. Reymond, J.-L.; van Deursen, R.; Blum, L. C.; Ruddigkeit, L. Chemical space as a source for new drugs MedChemComm 2010, 1, 30-38
10. Moitessier, N.; Englebienne, P.; Lee, D.; Lawandi, J.; Corbeil, C. R. Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go Br. J. Pharmacol. 2008, 153, S7-S26
11. Wijtmans, M.; de Graaf, C.; de Kloe, G.; Istyastono, E. P.; Smit, J.; Lim, H.; Boonnak, R.; Nijmeijer, S.; Smits, R. A.; Jongejan, A.; Zuiderveld, O.; de Esch, I. J. P.; Leurs, R. Triazole Ligands Reveal Distinct Molecular Features That Induce Histamine H(4) Receptor Affinity and Subtly Govern H(4)/H(3) Subtype Selectivity J. Med. Chem. 2011, 54, 1693-1703
12. Loving, K.; Alberts, I.; Sherman, W. Computational Approaches for Fragment-Based and De Novo Design Curr. Top. Med. Chem. 2010, 10, 14-32
13. Marcou, G.; Rognan, D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints J. Chem. Inf. Model. 2007, 47, 195-207
14. Crisman, T. J.; Bender, A.; Milik, M.; Jenkins, J. L.; Scheiber, J.; Sukuru, S. C. K.; Fejzo, J.; Hommel, U.; Davies, J. W.; Glick, M. "Virtual fragment linking": an approach to identify potent binders from low affinity fragment hits J. Med. Chem. 2008, 51, 2481-2491
15. Villar, H. O.; Hansen, M. R. Computational techniques in fragment based drug discovery Curr. Top. Med. Chem. 2007, 7, 1509-1513
16. Chen, Y.; Shoichet, B. K. Molecular docking and ligand specificity in fragment-based inhibitor discovery Nat. Chem. Biol. 2009, 5, 358-364
17. de Graaf, C.; Kooistra, A. J.; Vischer, H. F.; Katritch, V.; Kuijer, M.; Shiroishi, M.; Iwata, S.; Shimamura, T.; Stevens, R. C.; de Esch, I. J. P.; Leurs, R. Crystal Structure-Based Virtual Screening for Fragment-like Ligands of the Human Histamine H(1) Receptor J. Med. Chem. 2011, 54, 8195-8206
18. de Graaf, C.; Rognan, D. Customizing G Protein-Coupled Receptor Models for Structure-Based Virtual Screening Curr. Pharm. Des. 2009, 15, 4026-4048
19. Katritch, V.; Cherezov, V.; Stevens, R. C. Diversity and modularity of G protein-coupled receptor structures Trends Pharma. Sci. 2012, 33, 17-27
20. Verdonk, M. L.; Berdini, V.; Hartshorn, M. J.; Mooij, W. T. M.; Murray, C. W.; Taylor, R. D.; Watson, P. Virtual screening using protein-ligand docking: Avoiding artificial enrichment J. Chem. Inf. Comput. Sci. 2004, 44, 793-806
21. Gleeson, M. P.; Gleeson, D. QM/MM As a Tool in Fragment Based Drug Discovery. A Cross-Docking, Rescoring Study of Kinase Inhibitors J. Chem. Inf. Model. 2009, 49, 1437-1448
22. Verdonk, M. L.; Giangreco, I.; Hall, R. J.; Korb, O.; Mortenson, P. N.; Murray, C. W. Docking Performance of Fragments and Drug like Compounds J. Med. Chem. 2011, 54, 5422-5431
23. Holliday, J. D.; Salim, N.; Whittle, M.; Willett, P. Analysis and display of the size dependence of chemical similarity coefficients J. Chem. Inf. Comput. Sci. 2003, 43, 819-28
24. Flower, D. R. On the properties of bit string-based measures of chemical similarity J. Chem. Inf. Comput. Sci. 1998, 38, 379-386
25. Huang, X.; Lai, J.; Jennings, S. F. Maximum common subgraph: some upper bound and lower bound results BMC Bioinf. 2006, 7
26. de Graaf, C.; Rognan, D. Selective Structure-Based Virtual Screening for Full and Partial Agonists of the beta 2 Adrenergic Receptor J. Med. Chem. 2008, 51, 4978-4985
27. Olah, M.;; Rad, L.;; Ostopovici, L.;; Bora, A.;; Hadaruga, N.;; Hadaruga, D.;; Moldovan, R.;; Fulias, A.;; Mracec, M.;; Oprea, T. I. WOMBAT and WOMBAT-PK: Bioactivity Databases for Lead and Drug Discovery. In Chemical Biology: From Small Molecules to Systems Biology and Drug Design; Wiley-VCH Verlag GmbH: Weinheim, Germany, 2008; pp 1-3.
28. Gaulton, A.; Bellis, L. J.; Bento, A. P.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B.; Overington, J. P. ChEMBL: a large-scale bioactivity database for drug discovery Nucl. Acids Res. 2012, 40 (D1) D1100-D1107
29. Knox, C.; Law, V.; Jewison, T.; Liu, P.; Ly, S.; Frolkis, A.; Pon, A.; Banco, K.; Mak, C.; Neveu, V.; Djoumbou, Y.; Eisner, R.; Guo, A. C.; Wishart, D. S. DrugBank 3.0: a comprehensive resource for 'omics' research on drugs Nucl. Acids Res. 2011, 39 (Database issue) D1035-D1041
30. Chen, X.; Lin, Y.; Gilson, M. K. The binding database: Overview and user's guide Biopolymers 2002, 61 (2) 127-141
31. Nicholls, A. What do we know and when do we know it? J. Comput.-Aided Molec. Des. 2008, 22, 239-255
32. Scior, T.; Bender, A.; Tresadern, G.; Medina-Franco, J. L.; Martínez-Mayorga, K.; Langer, T.; Cuanalo-Contreras, K.; Agrafiotis, D. K. Recognizing Pitfalls in Virtual Screening: A Critical Review J. Chem. Inf. Model. 2012, 52, 867-881
33. Leurs, R.; Bakker, R. A.; Timmerman, H.; de Esch, I. J. The histamine H3 receptor: from gene cloning to H3 receptor drugs. Nat. Rev. Drug. Discov. 2005, 4, 107-120
34. Berlin, M.; Boyce, C. W.; Ruiz, M. d. L. Histamine H(3) Receptor as a Drug Discovery Target J. Med. Chem. 2011, 54, 26-53
35. Celanire, S.; Wijtmans, M.; Talaga, P.; Leurs, R.; de Esch, I. J. P. Histamine H-3 receptor antagonists reach out for the clinic Drug Discovery Today 2005, 10, 1613-1627
36. Baroni, M.; Cruciani, G.; Sciabola, S.; Perruccio, F.; Mason, J. S. A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for ligands and proteins (FLAP): Theory and application J. Chem. Inf. Model. 2007, 47, 279-294
37. Goodford, P. J. A computational procedure for determining energetically favorable binding-sites on biologically important macromolecules J. Med. Chem. 1985, 28, 849-857
38. Brincat, J. P.; Carosati, E.; Sabatini, S.; Manfroni, G.; Fravolini, A.; Raygada, J. L.; Pate, D.; Kaatz, G. W.; Cruciani, G. Discovery of Novel Inhibitors of the NorA Multidrug Transporter of Staphylococcus aureus J. Med. Chem. 2011, 54, 354-365
39. Cross, S.; Baroni, M.; Carosati, E.; Benedetti, P.; Clementi, S. FLAP: GRID Molecular Interaction Fields in Virtual Screening. Validation using the DUD Data Set J. Chem. Inf. Model. 2010, 50, 1442-1450
40. Carosati, E.; Mannhold, R.; Wahl, P.; Hansen, J. B.; Fremming, T.; Zamora, I.; Cianchetta, G.; Baroni, M. Virtual screening for novel openers of pancreatic K-ATP channels J. Med. Chem. 2007, 50, 2117-2126
41. Rogers, D.; Hahn, M. Extended-Connectivity Fingerprints J. Chem. Inf. Model. 2010, 50, 742-754
42. Grant, J. A.; Gallardo, M. A.; Pickup, B. T. A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape J. Comput. Chem. 1996, 17, 1653-1666
43. Korb, O.; Stützle, T.; Exner, T. E. An ant colony optimization approach to flexible protein-ligand docking Swarm Intell. 2007, 1, 115-134
44. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and Validation of a Genetic Algorithm for Flexible Docking J. Mol. Biol. 1997, 267, 727-748
45. Fisher, R. A. The Use of Multiple Measurements in Taxonomic Problems Ann. Eugenics 1936, 7, 179-188
46. McLachlan, G. J. Discriminant Analysis and Statistical Pattern Recognition; Wiley Series in Probability and Statistics; Wiley-Interscience: New York, 2004
47. Sirci, F.; Goracci, L.; Rodríguez, D.; van Muijlwijk-Koezen, J.; Gutiérrez-de-Terán, H.; Mannhold, R. Ligand-, structure- and pharmacophore-based molecular fingerprints: a case study on adenosine A1, A2A, A2B, and A3 receptor antagonists J. Comput.-Aided Molec. Des. 2012, 10.1007/s10822-012-9612-8
48. Gasteiger, J.; Teckentrup, A.; Terfloth, L.; Spycher, S. Neural networks as data mining tools in drug design J. Phys. Org. Chem. 2003, 16, 232-245
49. Milletti, F.; Storchi, L.; Sforna, G.; Cruciani, G. New and original pK(a) prediction method using grid molecular interaction fields J. Chem. Inf. Model. 2007, 47, 2172-2181
50. FILTER, version 2.1.1; OpenEye Scientific Software: Santa Fe, NM, 2011; http://www.eyesopen.com/filter.
51. Sciabola, S.; Stanton, R. V.; Mills, J. E.; Flocco, M. M.; Baroni, M.; Cruciani, G.; Perruccio, F.; Mason, J. S. High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields J. Chem. Inf. Model. 2010, 50, 155-169
52. Ioan, P.; Ciogli, A.; Sirci, F.; Budriesi, R.; Cosimelli, B.; Pierini, M.; Severi, E.; Chiarini, A.; Cruciani, G.; Gasparrini, F.; Spinelli, D.; Carosati, E. Absolute configuration and biological profile of two thiazinooxadiazol-3-ones with L-type calcium channel activity: a study of the structural effects Org. Biomol. Chem. 2012, 10, 8994-9003
53. 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 H(1) receptor complex with doxepin Nature 2011, 475, 65-70
54. Shi, L.; Javitch, J. A. The binding site of aminergic G protein-coupled receptors: The transmembrane segments and second extracellular loop Annu. Rev. Pharmacol. Toxicol. 2002, 42, 437-467
55. Ohta, K.; Hayashi, H.; Mizuguchi, H.; Kagamiyama, H.; Fujimoto, K.; Fukui, H. Site-directed mutagenesis of the histamine H1 receptor-Role of the aspartic acid (107), asparagine (198) and threonine (194) Biochem. Biophys. Res. Commun. 1994, 203, 1096-1101
56. Gantz, I.; Delvalle, J.; Wang, L. D.; Tashiro, T.; Munzert, G.; Guo, Y. J.; Konda, Y.; Yamada, T. Molecular basis for the interaction of histamine with the histamine H2 receptor J. Biol. Chem. 1992, 267, 20840-20843
57. Jongejan, A.; Lim, H. D.; Smits, R. A.; de Esch, I. J. P.; Haaksma, E.; Leurs, R. Delineation of agonist binding to the human histamine H-4 receptor using mutational analysis, homology modeling, and ab initio calculations J. Chem. Inf. Model. 2008, 48, 1455-1463
58. Shin, N.; Coates, E.; Murgolo, N. J.; Morse, K. L.; Bayne, M.; Strader, C. D.; Monsma, F. J. Molecular Modeling and site-specific mutagenesis of the histamine-binding site of the histamine H-4 receptor Mol. Pharmacol. 2002, 62, 38-47
59. Pipeline Pilot, version 6.1.5; Accelrys: San Diego, CA, 2008; http://accelrys.com/products/pipeline-pilot/.
60. Bostrom, J.; Greenwood, J. R.; Gottfries, J. Assessing the performance of OMEGA with respect to retrieving bioactive conformations J. Molec. Graph. Modell. 2003, 21, 449-462
61. ROCS, version 2.3.1; OpenEye Scientific Software: Santa Fe, NM, 2011; http://www.eyesopen.com/rocs.
62. Fulekar, M. H. Bioinformatics: Application in Life and Environmental Sciences; Springer: Dordrecht, The Netherlands, 2009; p 110.
63. Jain, A. N.; Nicholls, A. Recommendations for evaluation of computational methods J. Comput.-Aided Molec. Des. 2008, 22, 133-139
64. Istyastono, E. P.; Nijmeijer, S.; Lim, H. D.; van de Stolpe, A.; Roumen, L.; Kooistra, A. J.; Vischer, H. F.; de Esch, S. J. P.; Leurs, R.; de Graaf, C. Molecular Determinants of Ligand Binding Modes in the Histamine H(4) Receptor: Linking Ligand-Based Three-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR) Models to in Silico Guided Receptor Mutagenesis Studies J. Med. Chem. 2011, 54, 8136-8147
65. Uveges, A. J.; Kowal, D.; Zhang, Y. X.; Spangler, T. B.; Dunlop, J.; Semus, S.; Jones, P. G. The role of transmembrane helix 5 in agonist binding to the human H3 receptor J. Pharmacol. Exp. Ther. 2002, 301, 451-458
66. Case, D. A.; Darden, T. A.; Cheatham, T. E.; Simmerling, C. L.; Wang, L.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Wang, B.; Hayik, S.; Roitberg, A. G.; Seabra, I.; Kolossvai, K. F.; Wong, F.; Paesani, J.; Vanicek, J.; Liu, X.; Wu, S. R.; Brozell, T.; Steinbrecher, H.; Gohlke, Q.; Cai, X.; Ye, J.; Wang, M. J.; Hsieh, G.; Cui, D. R.; Roe, D. H.; Mathews, M. G.; Seetin, C.; Sagui, V.; Babin, T.; Luchko, S.; Gusarov, A.; Kovalenko, P. A.; Kollman. AMBER 11; University of California, San Francisco, 2010.
67. Wang, J.; Wang, W.; Kollman, P. Antechamber, an accessory software package for molecular mechanical calculations J. Comput. Chem. 2005, 25, 1157-1174
68. Urizar, E.; Claeysen, S.; Deupi, X.; Govaerts, C.; Costagliola, S.; Vassart, G.; Pardo, L. An activation switch in the rhodopsin family of G protein-coupled receptors-The thyrotropin receptor J. Biol. Chem. 2005, 280, 17135-17141
69. Jarvis, R. A.; Patrick, E. A. Clustering Using a Similarity Measure Based on Shared Near Neighbors IEEE Trans. Comput. 1973, C-22, 1025-1034
70. Cheng, Y.; Prusoff, W. H. Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50% inhibition (I50) of an enzymatic reaction Biochem. Pharma. 1973, 22, 3099-108
71. Govoni, M.; Lim, H. D.; El-Atmioui, D.; Menge, W.; Timmerman, H.; Bakker, R. A.; Leurs, R.; De Esch, I. J. P. A chemical switch for the modulation of the functional activity of higher homologues of histamine on the human histamine H-3 receptor: Effect of various substitutions at the primary amino function J. Med. Chem. 2006, 49, 2549-2557
72. Tawa, G. J.; Baber, J. C.; Humblet, C. Computation of 3D queries for ROCS based virtual screens J. Comput.-Aided Molec. Des. 2009, 23, 853-868
73. Swann, S. L.; Brown, S. P.; Muchmore, S. W.; Patel, H.; Merta, P.; Locklear, J.; Hajduk, P. J. A Unified, Probabilistic Framework for Structure- and Ligand-Based Virtual Screening J. Med. Chem. 2011, 54, 1223-1232
74. Krueger, D. M.; Evers, A. Comparison of Structure- and Ligand-Based Virtual Screening Protocols Considering Hit List Complementarity and Enrichment Factors ChemMedChem 2010, 5, 148-158
75. Nettles, J. H.; Jenkins, J. L.; Bender, A.; Deng, Z.; Davies, J. W.; Glick, M. Bridging chemical and biological space: "Target fishing" using 2D and 3D molecular descriptors J. Med. Chem. 2006, 49, 6802-6810
76. Yeap, S. K.; Walley, R. J.; Snarey, M.; van Hoorn, W. P.; Mason, J. S. Designing compound subsets: Comparison of random and rational approaches using statistical simulation J. Chem. Inf. Model. 2007, 47, 2149-2158
77. Kogej, T.; Engkvist, O.; Blomberg, N.; Muresan, S. Multifingerprint based similarity searches for targeted class compound selection J. Chem. Inf. Model. 2006, 46, 1201-1213
78. Oellien, F.; Cramer, J.; Beyer, C.; Ihlenfeldt, W.-D.; Selzer, P. M. The impact of tautomer forms on pharmacophore-based virtual screening J. Chem. Inf. Model. 2006, 46, 2342-2354
79. Park, M.-S.; Gao, C.; Stern, H. A. Estimating binding affinities by docking/scoring methods using variable protonation states Proteins-Struct. Funct. Bioinf. 2011, 79, 304-314
80. Greenwood, J. R.; Calkins, D.; Sullivan, A. P.; Shelley, J. C. Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution J. Comput.-Aided Molec. Des. 2010, 24, 591-604
81. Martin, Y. C. Lets not forget tautomers J. Comput.-Aided Molec. Des. 2009, 23, 693-704
82. Milletti, F.; Storchi, L.; Sforna, G.; Cross, S.; Cruciani, G. Tautomer Enumeration and Stability Prediction for Virtual Screening on Large Chemical Databases J. Chem. Inf. Model. 2009, 49, 68-75
83. ten Brink, T.; Exner, T. E. pK(a) based protonation states and microspecies for protein-ligand docking J. Comput.-Aided Molec. Des. 2010, 24, 935-942
84. Milletti, F.; Vulpetti, A. Tautomer Preference in PDB Complexes and its Impact on Structure-Based Drug Discovery J. Chem. Inf. Model. 2010, 50, 1062-1074
85. Polgar, T.; Magyar, C.; Simon, I.; Keserue, G. M. Impact of ligand protonation on virtual screening against ss-secretase (BACEI) J. Chem. Inf. Model. 2007, 47, 2366-2373
86. Kitbunnadaj, R.; Hashimoto, T.; Poli, E.; Zuiderveld, O. P.; Menozzi, A.; Hidaka, R.; de Esch, I. J. P.; Bakker, R. A.; Menge, W.; Yamatodani, A.; Coruzzi, G.; Timmerman, H.; Leurs, R. N-substituted piperidinyl alkyl imidazoles: Discovery of methimepip as a potent and selective histamine H-3 receptor agonist J. Med. Chem. 2005, 48, 2100-2107
87. De Esch, I. J. P.; Mills, J. E. J.; Perkins, T. D. J.; Romeo, G.; Hoffmann, M.; Wieland, K.; Leurs, R.; Menge, W.; Nederkoorn, P. H. J.; Dean, P. M.; Timmerman, H. Development of a pharmacophore model for histamine H-3 receptor antagonists, using the newly developed molecular modeling program SLATE J. Med. Chem. 2001, 44, 1666-1674
88. Mills, J. E. J.; de Esch, I. J. P.; Perkins, T. D. J.; Dean, P. M. SLATE: A method for the superposition of flexible ligands J. Comput.-Aided Molec. Des. 2001, 15, 81-96
89. http://zinc.docking.org/. Accessed April 2011.
90. Irwin, J. J.; Shoichet, B. K. ZINC-A free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 2005, 45, 177-182
91. Oprea, T. I. Property distribution of drug-related chemical databases J. Comput.-Aided Molec. Des. 2000, 14, 251-264
92. Rishton, G. M. Reactive compounds and in vitro false positives in HTS Drug Discovery Today 1997, 2, 382-384
93. Olah, M. M.; Bologa, C. G.; Oprea, T. I. Strategies for compound selection Curr. Drug Discovery Technol. 2004, 1, 211-20
94. Congreve, M.; Carr, R.; Murray, C.; Jhoti, H. A rule of three for fragment-based lead discovery? Drug Discovery Today 2003, 8, 876-877
95. https://www.ebi.ac.uk/chembl/. Accessed April 2011.
96. Wawer, M.; Bajorath, J. Similarity-Potency Trees: A Method to Search for SAR Information in Compound Data Sets and Derive SAR Rules J. Chem. Inf. Model. 2010, 50, 1395-1409
97. Blum, L. C.; van Deursen, R.; Reymond, J.-L. Visualisation and subsets of the chemical universe database GDB-13 for virtual screening J. Comput.-Aided Molec. Des. 2011, 25, 637-647
98. Bender, A.; Jenkins, J. L.; Scheiber, J.; Sukuru, S. C. K.; Glick, M.; Davies, J. W. How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space J. Chem. Inf. Model. 2009, 49, 108-119
99. Duan, J.; Dixon, S. L.; Lowrie, J. F.; Sherman, W. Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods J. Molec. Graph. Modell. 2010, 29, 157-170
100. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J. Protein-ligand docking: Current status and future challenges Proteins-Struct. Funct. Bioinf. 2006, 65, 15-26
101. Lee, J.; Seok, C. A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect Proteins-Struct. Funct. Bioinf. 2008, 70, 1074-1083
102. de Graaf, C.; Rein, C.; Piwnica, D.; Giordanetto, F.; Rognan, D. Structure-based discovery of allosteric modulators of two related class B G-protein-coupled receptors ChemMedChem 2011, 6, 2159-69
103. Istyastono, E. P. Computational Studies of Histamine H4 Receptor-Ligand Interactions. Ph.D. thesis, VU University Amsterdam, Amsterdam, 2012.
104. Rognan, D. Docking Methods for Virtual Screening: Principles and Recent Advances. In Virtual Screening; Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Germany, 2011; pp 153-176.
105. Kim, S.-K.; Fristrup, P.; Abrol, R.; Goddard, W. A. III. Structure-Based Prediction of Subtype Selectivity of Histamine H(3) Receptor Selective Antagonists in Clinical Trials J. Chem. Inf. Model. 2011, 51, 3262-3274
106. Kuhne, S.; Wijtmans, M.; Lim, H. D.; Leurs, R.; de Esch, I. J. P. Several down, a few to go: histamine H(3) receptor ligands making the final push towards the market? Expert Opin. Invest. Drugs 2011, 20, 1629-1648
107. Istyastono, E. P.; de Graaf, C.; de Esch, I. J. P.; Leurs, R. Molecular Determinants of Selective Agonist and Antagonist Binding to the Histamine H(4) Receptor Curr. Top. Med. Chem. 2011, 11, 661-679
108. Lim, H. D.; van Rijn, R. M.; Ling, P.; Bakker, R. A.; Thurmond, R. L.; Leurs, R. Evaluation of histamine H-1-, H-2-, and H-3-receptor ligands at the human histamine H-4 receptor: Identification of 4-methylhistamine as the first potent and selective H-4 receptor agonist J. Pharmacol. Exp. Ther. 2005, 314, 1310-1321