Global analysis of small molecule binding to related protein targets

PLoS Computational Biology

Volumn 8, Issue 1, 2012, Pages

  Kruger, Felix A ^a   Overington, John P ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULES;

DATA INFORMATIONS; GENERAL MODEL; GLOBAL ANALYSIS; HOMOLOGY INFORMATION; LARGE-SCALE ANALYSIS; ORTHOLOGS; PARALOGS; PROTEIN TARGETS; SMALL-MOLECULE BINDINGS; SPECIES SPECIFICS;

RATS;

PROTEIN; LIGAND;

ARTICLE; BINDING AFFINITY; BINDING AND RELATED PHENOMENA; CONTROLLED STUDY; DRUG BINDING; DRUG DEVELOPMENT; ORTHOLOGY; PARALOGY; PREDICTION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN TARGETING; SEQUENCE HOMOLOGY; SMALL MOLECULE BINDING; SPECIES DIFFERENCE; STATISTICAL ANALYSIS; ANIMAL; BINDING SITE; CHEMISTRY; FACTUAL DATABASE; HUMAN; METABOLISM; RAT;

RATTUS;

ANIMALS; BINDING SITES; DATABASES, FACTUAL; DRUG DISCOVERY; HUMANS; LIGANDS; PROTEINS; RATS;

EID: 84857477790     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002333     Document Type: Article

References (51)

1. George CF, (1980) Clinical pharmacology. Drug development. Br Med J 281: 1397-1399.
2. McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, et al. (2010) Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc Natl Acad Sci U S A 107: 6544-6549.
3. Kimura M, (1981) Possibility of extensive neutral evolution under stabilizing selection with special reference to nonrandom usage of synonymous codons. Proc Natl Acad Sci U S A 78: 5773-5777.
4. Hopkins AL, Groom CR, (2002) The druggable genome. Nat Rev Drug Discov 1: 727-730.
5. Overington JP, Al-Lazikani B, Hopkins AL, (2006) How many drug targets are there? Nat Rev Drug Discov 5: 993-996.
6. Caron PR, Mullican MD, Mashal RD, Wilson KP, Su MS, et al. (2001) Chemogenomic approaches to drug discovery. Curr Opin Chem Biol 5: 464-470.
7. Surgand JS, Rodrigo J, Kellenberger E, Rognan D, (2006) A chemogenomic analysis of the transmembrane binding cavity of human G-protein-coupled receptors. Proteins 62: 509-538.
8. Gloriam DE, Foord SM, Blaney FE, Garland SL, (2009) Definition of the G protein-coupled receptor transmembrane bundle binding pocket and calculation of receptor similarities for drug design. J Med Chem 52: 4429-4442.
9. van der Horst E, Peironcely JE, Ijzerman AP, Beukers MW, Lane JR, et al. (2010) A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. BMC Bioinf 11: 316.
10. Fabian MA, Biggs WH, Treiber DK, Atteridge CE, Azimioara MD, et al. (2005) A small moleculekinase interaction map for clinical kinase inhibitors. Nat Biotechnol 23: 329-336.
11. Karaman MW, Herrgard S, Treiber DK, Gallant P, Atteridge CE, et al. (2008) A quantitative analysis of kinase inhibitor selectivity. Nat Biotechnol 26: 127-132.
12. Metz JT, Johnson EF, Soni NB, Merta PJ, Kie L, et al. (2011) Navigating the kinome. Nat Chem Biol 7: 200-202.
13. Brooijmans N, Chang YW, Mobilio D, Denny RA, Humblet C, (2010) An enriched structural kinase database to enable kinome-wide structure-based analyses and drug discovery. Protein Sci 19: 763-774.
14. Ekroos M, Sjögren T, (2006) Structural basis for ligand promiscuity in cytochrome P450 3A4. Proc Natl Acad Sci U S A 103: 13682-13687.
15. Tanramluk D, Schreyer A, Pitt WR, Blundell TL, (2009) On the origins of enzyme inhibitor selectivity and promiscuity: a case study of protein kinase binding to staurosporine. Chem Biol Drug Des 74: 16-24.
16. Overington J, (2009) ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr. J Comput Aided Mol Des 23: 195-198.
17. Taylor KR, Gledhill RJ, Essex JW, Frey JG, Harris SW, et al. (2006) Bringing Chemical Data onto the Semantic Web. J Chem Inf Mod 46: 939-952.
18. Arens Y, Chee CY, Hsu CN, Knoblock CA, (1993) Retrieving and integrating data from multiple information sources. Int J Intell Coop I 2: 127-158.
19. Halevy A, Rajaraman A, Ordille J, (2006) Data integration: the teenage years. pp. 9-16 Proceedings of the 32nd international conference on Very large data bases. VLDB Endowment, VLDB '06 URL http://dl.acm.org/citation.cfm?id=1182635.1164130.
20. Sujansky W, (2001) Heterogeneous Database Integration in Biomedicine. J Biomed Inf 34: 285-298.
21. Cozzi J, Fraichard A, Thiam K, (2008) Use of genetically modified rat models for translational medicine. Drug Discov Today 13: 488-494.
22. Bellis LJ, Akhtar R, Al-Lazikani B, Atkinson F, Bento AP, et al. (2011) ChEMBL 10. Available: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl10/. Accessed 29 November 2011.
23. Gleeson MP, Hersey A, Montanari D, Overington J, (2011) Probing the links between in vitro potency, ADMET and physicochemical parameters. Nat Rev Drug Discov 10: 197-208.
24. Stephens MS, (1986) Tests for the uniform distribution. In: D'Agostino RB, Stephens MS, editors. Goodness-of-Fit Techniques New York and Basel Marcel Dekker pp. 331-366.
25. Nersesian DL, Black LA, Miller TR, Vortherms TA, Esbenshade TA, et al. (2008) In vitro SAR of pyrrolidine-containing histamine H3 receptor antagonists: trends across multiple chemical series. Bioorg Med Chem Lett 18: 355-359.
26. Black LA, Nersesian DL, Sharma P, Ku YY, Bennani YL, et al. (2007) 4-[6-(2- Aminoethyl)naphthalen-2-yl]benzonitriles are potent histamine H3 receptor antagonists with high CNS penetration. Bioorg Med Chem Lett 17: 1443-1446.
27. Esbenshade TA, (2004) Pharmacological Properties of ABT-239 [4-(2--benzofuran-5- yl)benzonitrile]: I. Potent and Selective Histamine H3 Receptor Antagonist with Drug-Like Properties. J Pharmacol Exp Ther 313: 165-175.
28. Ireland-Denny L, Parihar AS, Miller TR, Kang CH, Krueger KM, et al. (2001) Species-related pharmacological heterogeneity of histamine H(3) receptors. Eur J Pharmacol 433: 141-150.
29. Ligneau X, Morisset S, Tardivel-Lacombe J, Gbahou F, Ganellin CR, et al. (2000) Distinct pharmacology of rat and human histamine H(3) receptors: role of two amino acids in the third transmembrane domain. Br J Pharmacol 131: 1247-1250.
30. Lovenberg TW, Pyati J, Chang H, Wilson SJ, Erlander MG, (2000) Cloning of rat histamine H(3) receptor reveals distinct species pharmacological profiles. J Pharmacol Exp Ther 293: 771-778.
31. Koonin E, (2005) Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39: 309-338.
32. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, et al. (2008) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 19: 327-335.
33. Fitch WM, (1970) Distinguishing Homologous from Analogous Proteins. Syst Zool 19: 99-113.
34. Tatusov RL, (1997) A Genomic Perspective on Protein Families. Science 278: 631-637.
35. Fox J, Weisberg S, (2011) An R Companion to Applied Regression. 2nd edition Thousand Oaks CA Sage URL http://socserv.socsci.mcmaster.ca/jfox/Books/Companion.
36. Bowie JU, Reidhaar-Olson JF, Lim WA, Sauer RT, (1990) Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science 247: 1306-1310.
37. Vieth M, Sutherland JJ, Robertson DH, Campbell RM, (2005) Kinomics: characterizing the therapeutically validated kinase space. Drug Discov Today 10: 839-846.
38. Shamovsky I, Connolly S, David L, Ivanova S, Nordén B, et al. (2008) Overcoming Undesirable hERG Potency of Chemokine Receptor Antagonists Using Baseline Lipophilicity Relationships. J Med Chem 51: 1162-1178.
39. Davis AM, Teague SJ, (1999) Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis. Angewandt Chem Internatl Ed 38: 736-749.
40. Zhi L, Tegley CM, Marschke KB, Jones TK, (1999) Switching androgen receptor antagonists to agonists by modifying C-ring substituents on piperidino-3,2-quinolinone. Bioorg Med Chem Lett 9: 1009-1012.
41. Hopkins A, (2004) Ligand efficiency: a useful metric for lead selection. Drug Discov Today 9: 430-431.
42. Hann MM, Leach AR, Harper G, (2001) Molecular Complexity and Its Impact on the Probability of Finding Leads for Drug Discovery. J Chem Inf Mod 41: 856-864.
43. Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, et al. (2009) Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci 18: 1306-1315.
44. van der Horst E, Peironcely JE, van Westen GJP, van den Hoven OO, Galloway WRJD, et al. (2011) Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space. Cur Top Med Chem 11: 1964-1977.
45. Wichard JD, ter Laak A, Krause G, Heinrich N, Kühne R, et al. (2011) Chemogenomic Analysis of G-Protein Coupled Receptors and Their Ligands Deciphers Locks and Keys Governing Diverse Aspects of Signalling. PloS One 6: e16811.
46. Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2009) The Pfam protein families database. Nucleic Acids Res 38: D211-D222.
47. Bateman A, Punta M, Coggill P, Eberhardt R, Tate J, (2011) Pfam version 24. Available: ftp://ftp.sanger.ac.uk/pub/databases/Pfam/releases/Pfam24.0/. Accessed 29 November 2011.
48. Davies M, Al-Lazikani B, Bento AP, Gaulton A, Hersey A, et al. (2011) Kinase SARfari. Available: http://www.ebi.ac.uk/chembl/sarfari/kinasesarfari. Accessed 29 November 2011.
49. R Development Core Team (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org. ISBN 3-900051-07-0.
50. Vidal D, Thormann M, Pons M, (2005) LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities. J Chem Inf Mod 45: 386-393.
51. OpenEye (2010) OEChem: version 1.7.4. OpenEye Scientific Software Inc.Sante Fe. Available: www.eyesopen.com. Accessed 29 November 2011.