Mining significant substructure pairs for interpreting polypharmacology in drug-target network

PLoS ONE

Volumn 6, Issue 2, 2011, Pages

  Takigawa, Ichigaku ^a,c   Tsuda, Koji ^b,c   Mamitsuka, Hiroshi ^a,c  

^a KYOTO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BETA 2 ADRENERGIC RECEPTOR; CARAZOLOL; G PROTEIN COUPLED RECEPTOR;

ALGORITHM; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CHEMICAL ANALYSIS; CLUSTER ANALYSIS; CONTROLLED STUDY; DATA MINING; DRUG SELECTIVITY; DRUG STRUCTURE; DRUG TARGETING; LIGAND BINDING; MATHEMATICAL ANALYSIS; MOLECULAR INTERACTION; PHARMACODYNAMICS; POLYPHARMACOLOGY; STRUCTURE ACTIVITY RELATION; BIOLOGICAL MODEL; DRUG APPROVAL; DRUG DELIVERY SYSTEM; DRUG INTERACTION; DRUG REPOSITIONING; EVALUATION; GENE REGULATORY NETWORK; HUMAN; METHODOLOGY; MOLECULARLY TARGETED THERAPY; PHYSIOLOGY; POLYPHARMACY; STATISTICAL ANALYSIS; STATISTICS;

ALGORITHMS; CLUSTER ANALYSIS; DATA INTERPRETATION, STATISTICAL; DATA MINING; DRUG APPROVAL; DRUG DELIVERY SYSTEMS; DRUG INTERACTIONS; DRUG REPOSITIONING; GENE REGULATORY NETWORKS; HUMANS; MATCHED-PAIR ANALYSIS; MODELS, BIOLOGICAL; MOLECULAR TARGETED THERAPY; POLYPHARMACY; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 79952031520     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016999     Document Type: Article

References (24)

1. Hopkins A, (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4: 682-690.
2. Apsel B, Blair J, Gonzalez B, Nazif T, Feldman M, et al. (2008) Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases. Nat Chem Biol 4: 691-699.
3. Campillos M, Kuhn M, Gavin A, Jensen L, Bork P, (2008) Drug target identification using side-effect similarity. Science 321: 263-266.
4. Frantz S, (2005) Drug discovery: playing dirty. Nature 437: 942-943.
5. Yildirim M, Goh K, Cusick M, Barabási A, Vidal M, (2007) Drug-target network. Nat Biotechnol 25: 1119-1126.
6. Morphy R, Rankovic Z, (2007) Fragments, network biology and designing multiple ligands. Drug Discov Today 12: 156-160.
7. Paolini G, Shapland R, van Hoorn W, Mason J, Hopkins A, (2006) Global mapping of pharmacological space. Nat Biotechnol 24: 805-815.
8. Metz J T, Hajduk P J, (2010) Rational approaches to targeted polypharmacology: creating and navigating protein-ligand interaction networks. Curr Opin Chem Biol 14: 498-504.
9. Wishart D, Knox C, Guo A, Cheng D, Shrivastava S, et al. (2008) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 36: D901-906.
10. Rovati G, Capra V, Neubig R, (2007) The highly conserved DRY motif of class a g protein-coupled receptors: beyond the ground state. Mol Pharmacol 71: 959-964.
11. Shi L, Javitch J, (2002) The binding site of aminergic G protein-coupled receptors: the transmembrane segments and second extracellular loop. Annu Rev Pharmacol Toxicol 42: 437-467.
12. Wess J, (1997) G-protein-coupled receptors: molecular mechanisms involved in receptor activation and selectivity of G-protein recognition. FASEB J 11: 346-354.
13. Cherezov V, Rosenbaum D, Hanson M, Rasmussen S, Thian F, et al. (2007) High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science 318: 1258-1265.
14. Murray C, Rees D, (2009) The rise of fragment-based drug discovery. Nat Chem 1: 187-192.
15. Aronov A, Murcko M, (2004) Toward a pharmacophore for kinase frequent hitters. J Med Chem 47: 5616-5619.
16. Han J, Cheng H, Dong X, Yan X, (2007) Frequent pattern mining: current status and future directions. Data Mining and Knowledge Discovery 15 (1): 55-86.
17. Cordell H, (2002) Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Hum Mol Genet 11: 2463-2468.
18. Beissbarth T, Speed T, (2004) GOstat: Find statistically overpresented Gene Ontrologies within a group of genes. Bioinformatics 20 (9): 1464-1465.
19. Batagelj V, Mrvar A, (2003) Pajek - Analysis and visualization of large networks. In: Jünger M, Mutzel P, editors. Graph drawing software Berlin Springer pp. 77-103.
20. Fruchterman, TMJ, Reingold, EM, (1991) Graph drawing by force-directed placement. Software - Practice & Experience 21 (11): 1129-1164.
21. Pearson W, (1991) Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11: 635-650.
22. Wang R, Fang X, Lu Y, Wang S, (2004) The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J Med Chem 47: 2977-2980.
23. Russ A, Lampel S, (2005) The druggable genome: an update. Drug Discov Today 10: 1607-1610.
24. Hopkins A, Groom C, (2002) The druggable genome. Nat Rev Drug Discov 1: 727-730.