Small and colorful stones make beautiful mosaics: Fragment-based chemogenomics

Drug Discovery Today

Volumn 18, Issue 7-8, 2013, Pages 323-330

  De Graaf, Chris ^a   Vischer, Henry F ^a   De Kloe, Gerdien E ^a   Kooistra, Albert J ^a   Nijmeijer, Saskia ^a   Kuijer, Martien ^a   Verheij, Mark H P ^a   England, Paul J ^b   Van Muijlwijk Koezen, Jacqueline E ^a   Leurs, Rob ^a   De Esch, Iwan J P ^a,b  

^a AMSTERDAM INSTITUTE FOR MOLECULES   (Netherlands)

^b ST JOHN S COLLEGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC AMP DEPENDENT PROTEIN KINASE; G PROTEIN COUPLED RECEPTOR; SEROTONIN 3 RECEPTOR;

ARTICLE; BINDING AFFINITY; CROSS REACTION; CRYSTAL STRUCTURE; GENOMICS; MOSAICISM; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING;

BINDING SITES; CYCLIC AMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNITS; DRUG DISCOVERY; HEK293 CELLS; HUMANS; LIGANDS; PHARMACEUTICAL PREPARATIONS; PROTEIN BINDING; RECEPTORS, G-PROTEIN-COUPLED; RECEPTORS, SEROTONIN, 5-HT3; SMALL MOLECULE LIBRARIES;

EID: 84875710113     PISSN: 13596446     EISSN: 18785832     Source Type: Journal    
DOI: 10.1016/j.drudis.2012.12.003     Document Type: Short Survey

References (64)

1. G.E. de Kloe Transforming fragments into candidates: small becomes big in medicinal chemistry Drug Discov. Today 14 2009 630 646
2. C.W. Murray Experiences in fragment-based drug discovery Trends Pharmacol. Sci. 33 2012 224 232
3. S.M. Boyd, and G.E.D. Kloe Fragment library design: efficiently hunting drugs in chemical space Drug Discov. Today: Technol. 7 2010 E173 E180
4. D.A. Erlanson, and S.K. Hansen Making drugs on proteins: site-directed ligand discovery for fragment-based lead assembly Curr. Opin. Chem. Biol. 8 2004 399 406 (Pubitemid 38993733)
5. M. Congreve Recent developments in fragment-based drug discovery J. Med. Chem. 51 2008 3661 3680 (Pubitemid 351956496)
6. K. Loving Computational approaches for fragment-based and de novo design Curr. Top. Med. Chem. 10 2010 14 32
7. M.M. Hann Molecular complexity and its impact on the probability of finding leads for drug discovery J. Chem. Inform. Comput. Sci. 41 2001 856 864
8. A. Schuffenhauer Library design for fragment based screening Curr. Top. Med. Chem. 5 2005 751 762 (Pubitemid 41179715)
9. K. Bondensgaard Recognition of privileged structures by G-protein coupled receptors J. Med. Chem. 47 2004 888 899 (Pubitemid 38176791)
10. R. Morphy, and Z. Rankovic Fragments, network biology and designing multiple ligands Drug Discov. Today 12 2007 156 160 (Pubitemid 46176667)
11. J. Klekota, and F.P. Roth Chemical substructures that enrich for biological activity Bioinformatics 24 2008 2518 2525
12. D.G. Teotico Docking for fragment inhibitors of AmpC beta-lactamase Proc. Natl. Acad. Sci. U.S.A. 106 2009 7455 7460
13. G. Gao Identification of selective enzyme inhibitors by fragment library screening J. Biomol. Screen. 15 2010 1042 1050
14. I.J. Chen, and R. Hubbard Lessons for fragment library design: analysis of output from multiple screening campaigns J. Comput. Aided Mol. Des. 23 2009 603 620
15. S. Barelier Ligand specificity in fragment-based drug design J. Med. Chem. 53 2010 5256 5266
16. P.D. Leeson, and B. Springthorpe The influence of drug-like concepts on decision-making in medicinal chemistry Nat. Rev. Drug Discov. 6 2007 881 890 (Pubitemid 350042396)
17. D. Rognan Chemogenomic approaches to rational drug design Br. J. Pharmacol. 152 2007 38 52 (Pubitemid 47339898)
18. A.J. Thompson An efficient and information-rich biochemical method design for fragment library screening on ion channels Biotechniques 49 2010 822 829
19. C. de Graaf Crystal structure-based virtual screening for fragment-like ligands of the human histamine H(1) receptor J. Med. Chem. 54 2011 8195 8206
20. M.P. Sanders A prospective cross-screening study on G-protein-coupled receptors: lessons learned in virtual compound library design J. Med. Chem. 55 2012 5311 5325
21. F. Sirci Virtual fragment screening: discovery of histamine H(3) receptor ligands using ligand-based and protein-based molecular fingerprints J. Chem. Inform. Model. 52 2012 3308 3324
22. V. Cherezov High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor Science 318 2007 1258 1265 (Pubitemid 350172884)
23. T. Shimamura Structure of the human histamine H1 receptor complex with doxepin Nature 475 2011 65 70
24. M.H. Verheij Fragment library screening reveals remarkable similarities between the G protein-coupled receptor histamine H and the ion channel serotonin 5-HTA Bioorg. Med. Chem. Lett. 21 2011 5460 5464
25. M.H. Verheij Design, synthesis, and structure-activity relationships of highly potent 5-HT(3) receptor ligands J. Med. Chem. 55 2012 8603 8614
26. H.D. Lim Molecular determinants of ligand binding to H4R species variants Mol. Pharmacol. 77 2010 734 743
27. E.P. Istyastono 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. 54 2011 8136 8147
28. S. Schultes Mapping histamine H4 receptor-ligand binding modes MedChemComm 4 2012 193 204
29. W. Smith Tali and tesserea were two distinct types of dice used in Roman board games. The Romans called the six sided marked dice tesserae, but they also had a type of dice with only four marked faces called tali. A tessera (plural: tesserae) is an individual tile, usually formed in the shape of a cube used in creating a mosaic A Dictionary of Greek and Roman Antiquities 1875 John Murray p. 1112-1113
30. M. Congreve A rule of three for fragment-based lead discovery? Drug Discov. Today 8 2003 876 877 (Pubitemid 37194496)
31. T.I. Oprea Property distribution of drug-related chemical databases J. Comput. Aided Mol. Des. 14 2000 251 264 (Pubitemid 30175944)
32. J. Xu A new approach to finding natural chemical structure classes J. Med. Chem. 45 2002 5311 5320 (Pubitemid 35429170)
33. G. Siegal Integration of fragment screening and library design Drug Discov. Today 12 2007 1032 1039 (Pubitemid 350180558)
34. H.J. Verheij Leadlikeness and structural diversity of synthetic screening libraries Mol. Divers. 10 2006 377 388 (Pubitemid 44546689)
35. ChEMBL. http://www.ebi.ac.uk/chembl/
36. M. Wijtmans Histamine H3 receptor ligands with a 3-cyclobutoxy motif: a novel and versatile constraint of the classical 3-propoxy linker MedChemComm 1 2010 84 86
37. A.L. Hopkins Ligand efficiency: a useful metric for lead selection Drug Discov. Today 9 2004 430 431 (Pubitemid 38510559)
38. Molecular Operating Environment (MOE) 2011 Chemical Computing Group Inc.
39. D. Rogers, and M. Hahn Extended-connectivity fingerprints J. Chem. Inform. Model 50 2010 742 754
40. M. Wawer, and J. Bajorath Similarity-potency trees: a method to search for SAR information in compound data sets and derive SAR rules J. Chem. Inform. Model. 50 2010 1395 1409
41. E. van der Horst Substructure mining of GPCR ligands reveals activity-class specific functional groups in an unbiased manner J. Chem. Inform. Model. 49 2009 348 360
42. S. Celanire Keynote review: histamine H3 receptor antagonists reach out for the clinic Drug Discov. Today 10 2005 1613 1627 (Pubitemid 41817610)
43. R.A. Smits Major advances in the development of histamine H4 receptor ligands Drug Discov. Today 14 2009 745 753
44. E.P. Istyastono Molecular determinants of selective agonist and antagonist binding to the histamine H4 receptor Curr. Top. Med. Chem. 11 2011 661 679
45. A. Jongejan Delineation of agonist binding to the human histamine H4 receptor using mutational analysis, homology modeling, and ab initio calculations J. Chem. Inform. Model. 48 2008 1455 1463
46. K. Ohta Site-directed mutagenesis of the histamine H1 receptor: roles of aspartic acid107, asparagine198 and threonine194 Biochem. Biophys. Res. Commun. 203 1994 1096 1101
47. M. Bruysters Mutational analysis of the histamine H1-receptor binding pocket of histaprodifens Eur. J. Pharmacol. 487 2004 55 63 (Pubitemid 38368981)
48. R. Leurs Site-directed mutagenesis of the histamine H1-receptor reveals a selective interaction of asparagine207 with subclasses of H1-receptor agonists Biochem. Biophys. Res. Commun. 201 1994 295 301
49. K. Wieland Mutational analysis of the antagonist-binding site of the histamine H(1) receptor J. Biol. Chem. 274 1999 29994 30000
50. N. Shin Molecular modeling and site-specific mutagenesis of the histamine-binding site of the histamine H4 receptor Mol. Pharmacol. 62 2002 38 47 (Pubitemid 34680514)
51. L. Shi, and J.A. Javitch The binding site of aminergic G protein-coupled receptors: the transmembrane segments and second extracellular loop Annu. Rev. Pharmacol. Toxicol. 42 2002 437 467 (Pubitemid 34162546)
52. J.S. Surgand A chemogenomic analysis of the transmembrane binding cavity of human G-protein-coupled receptors Proteins 62 2006 509 538
53. D.L. Beene Cation-pi interactions in ligand recognition by serotonergic (5-HT3A) and nicotinic acetylcholine receptors: the anomalous binding properties of nicotine Biochemistry 41 2002 10262 10269 (Pubitemid 34856451)
54. K.L. Price, and S.C. Lummis The role of tyrosine residues in the extracellular domain of the 5-hydroxytryptamine3 receptor J. Biol. Chem. 279 2004 23294 23301 (Pubitemid 38685638)
55. K.L. Price A hydrogen bond in loop A is critical for the binding and function of the 5-HT3 receptor Biochemistry 47 2008 6370 6377 (Pubitemid 351874228)
56. A.K. Ghose Knowledge based prediction of ligand binding modes and rational inhibitor design for kinase drug discovery J. Med. Chem. 51 2008 5149 5171
57. Y. Yang Investigation of the relationship between topology and selectivity for druglike molecules J. Med. Chem. 53 2010 7709 7714
58. A.L. Hopkins Can we rationally design promiscuous drugs? Curr. Opin. Struct. Biol. 16 2006 127 136 (Pubitemid 43221881)
59. D. Stumpfe, and J. Bajorath Exploring activity cliffs in medicinal chemistry J. Med. Chem. 55 2012 2932 2942
60. C. de Graaf, and D. Rognan Customizing G protein-coupled receptor models for structure-based virtual screening Curr. Pharm. Des. 15 2009 4026 4048
61. I. Kufareva Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment Structure 19 2011 1108 1126
62. O. Korb Empirical scoring functions for advanced protein-ligand docking with plants J. Chem. Inform. Model. 49 2009 84 96
63. G. Marcou, and D. Rognan Optimizing fragment and scaffold docking by use of molecular interaction fingerprints J. Chem. Inform. Model. 47 2007 195 207 (Pubitemid 46237537)
64. Pipeline Pilot v6.1, SciTegic Inc. http://www.accelrys.com/products/ scitegic