메뉴 건너뛰기




Volumn 8, Issue 5, 2009, Pages 2575-2585

Use of ligand based models for protein domains to predict novel molecular targets and applications to triage affinity chromatography data

Author keywords

Cheminformatics; Chemogenomics; Chemoproteomics; Extrapolation; Gefitinib; In silico; Iressa; Kinases; Protein domains; Pulldown; Resistance; Selectivity; Target prediction

Indexed keywords

DOPAMINE RECEPTOR; SEROTONIN RECEPTOR;

EID: 66749165862     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900107z     Document Type: Article
Times cited : (19)

References (48)
  • 1
    • 4143107932 scopus 로고    scopus 로고
    • Cyclooxygenase isozymes: The biology of prostaglandin synthesis and inhibition
    • Simmons, D. L.; Botting, R. M.; Hla, T. Cyclooxygenase isozymes: The biology of prostaglandin synthesis and inhibition. Pharmacol. Rev . 2004, 56 , 387-437.
    • (2004) Pharmacol. Rev , vol.56 , pp. 387-437
    • Simmons, D.L.1    Botting, R.M.2    Hla, T.3
  • 2
    • 19744365702 scopus 로고    scopus 로고
    • A small molecule-kinase interaction map for clinical kinase inhibitors
    • Fabian, M. A.; Biggs, W. H.; Treiber, D. K.; Atteridge, C. E. A small molecule-kinase interaction map for clinical kinase inhibitors. Nat. Biotechnol . 2005, 23 , 329-336.
    • (2005) Nat. Biotechnol , vol.23 , pp. 329-336
    • Fabian, M.A.1    Biggs, W.H.2    Treiber, D.K.3    Atteridge, C.E.4
  • 3
    • 34948875686 scopus 로고    scopus 로고
    • Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors
    • Bantscheff, M.; Eberhard, D.; Abraham, Y.; Bastuck, S. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol . 2007, 25 , 1035-1044.
    • (2007) Nat. Biotechnol , vol.25 , pp. 1035-1044
    • Bantscheff, M.1    Eberhard, D.2    Abraham, Y.3    Bastuck, S.4
  • 4
    • 3242802116 scopus 로고    scopus 로고
    • Promiscuous anticancer drugs that hit multiple targets may thwart resistance
    • Hampton, T. "Promiscuous" anticancer drugs that hit multiple targets may thwart resistance. JAMA 2004, 292 , 419-422.
    • (2004) JAMA , vol.292 , pp. 419-422
    • Hampton, T.1
  • 5
    • 40049100210 scopus 로고    scopus 로고
    • Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure
    • Bender, A.; Scheiber, J.; Glick, M.; Davies, J. W. Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure. ChemMedChem 2007, 2 , 861-873.
    • (2007) ChemMedChem , vol.2 , pp. 861-873
    • Bender, A.1    Scheiber, J.2    Glick, M.3    Davies, J.W.4
  • 6
    • 35248817286 scopus 로고    scopus 로고
    • Modeling promiscuity based on in vitro safety pharmacology profiling data
    • Azzaoui, K.; Hamon, J.; Faller, B.; Whitebread, S. Modeling promiscuity based on in vitro safety pharmacology profiling data. ChemMedChem 2007, 2 , 874-880.
    • (2007) ChemMedChem , vol.2 , pp. 874-880
    • Azzaoui, K.1    Hamon, J.2    Faller, B.3    Whitebread, S.4
  • 7
    • 33846518797 scopus 로고    scopus 로고
    • In silico target fishing: Predicting biological targets from chemical structure
    • Jenkins, J. L.; Bender, A.; Davies, J. W. In silico target fishing: Predicting biological targets from chemical structure. Drug Discovery Today: Technol . 2007, 3 , 413-421.
    • (2007) Drug Discovery Today: Technol , vol.3 , pp. 413-421
    • Jenkins, J.L.1    Bender, A.2    Davies, J.W.3
  • 8
    • 0035342428 scopus 로고    scopus 로고
    • Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule
    • Chen, Y. Z.; Zhi, D. G. Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins 2001, 43 , 217-226.
    • (2001) Proteins , vol.43 , pp. 217-226
    • Chen, Y.Z.1    Zhi, D.G.2
  • 9
    • 20444369842 scopus 로고    scopus 로고
    • Rapid computational identification of the targets of protein kinase inhibitors
    • Rockey, W. M.; Elcock, A. H. Rapid computational identification of the targets of protein kinase inhibitors. J. Med. Chem . 2005, 48 , 4138-4152.
    • (2005) J. Med. Chem , vol.48 , pp. 4138-4152
    • Rockey, W.M.1    Elcock, A.H.2
  • 10
    • 1542286205 scopus 로고    scopus 로고
    • Recovering the true targets of specific ligands by virtual screening of the Protein Data Bank
    • Paul, N.; Kellenberger, E.; Bret, G.; Muller, P.; Rognan, D. Recovering the true targets of specific ligands by virtual screening of the Protein Data Bank. Proteins 2004, 54 , 671-680.
    • (2004) Proteins , vol.54 , pp. 671-680
    • Paul, N.1    Kellenberger, E.2    Bret, G.3    Muller, P.4    Rognan, D.5
  • 11
    • 33749260698 scopus 로고    scopus 로고
    • A Critical Assessment of Docking Programs and Scoring Functions
    • Warren, G. L.; Andrews, C. W.; Capelli, A.-M.; Clarke, B. A Critical Assessment of Docking Programs and Scoring Functions. J. Med. Chem . 2006, 49 , 5912-5931.
    • (2006) J. Med. Chem , vol.49 , pp. 5912-5931
    • Warren, G.L.1    Andrews, C.W.2    Capelli, A.-M.3    Clarke, B.4
  • 12
    • 33646730764 scopus 로고    scopus 로고
    • Robust ligand-based modeling of the biological targets of known drugs
    • Cleves, A. E.; Jain, A. N. Robust ligand-based modeling of the biological targets of known drugs. J. Med. Chem . 2006, 49 , 2921-2938.
    • (2006) J. Med. Chem , vol.49 , pp. 2921-2938
    • Cleves, A.E.1    Jain, A.N.2
  • 13
    • 33745391215 scopus 로고    scopus 로고
    • Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases
    • Nidhi; Glick, M.; Davies, J. W.; Jenkins, J. L. Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases. J. Chem. Inf. Model . 2006, 46 , 1124-1133.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 1124-1133
    • Nidhi1    Glick, M.2    Davies, J.W.3    Jenkins, J.L.4
  • 14
    • 38349114038 scopus 로고    scopus 로고
    • Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor
    • Faulon, J. L.; Misra, M.; Martin, S.; Sale, K.; Sapra, R. Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor. Bioinformatics 2008, 24 , 225-233.
    • (2008) Bioinformatics , vol.24 , pp. 225-233
    • Faulon, J.L.1    Misra, M.2    Martin, S.3    Sale, K.4    Sapra, R.5
  • 15
    • 33644963750 scopus 로고    scopus 로고
    • Circular fingerprints: Flexible molecular descriptors with applications from physical chemistry to ADME
    • Glen, R. C.; Bender, A.; Arnby, C. H.; Carlsson, L. Circular fingerprints: Flexible molecular descriptors with applications from physical chemistry to ADME. IDrugs 2006, 9 , 199-204.
    • (2006) IDrugs , vol.9 , pp. 199-204
    • Glen, R.C.1    Bender, A.2    Arnby, C.H.3    Carlsson, L.4
  • 16
    • 0038579386 scopus 로고    scopus 로고
    • The signature molecular descriptor. 1. Using extended valence sequences in QSAR and QSPR studies
    • Faulon, J. L.; Visco, D. P., Jr.; Pophale, R. S. The signature molecular descriptor. 1. Using extended valence sequences in QSAR and QSPR studies. J. Chem. Inf. Comput. Sci . 2003, 43 , 707-720.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 707-720
    • Faulon, J.L.1    Visco Jr., D.P.2    Pophale, R.S.3
  • 17
    • 34547697192 scopus 로고    scopus 로고
    • Understanding false positives in reporter gene assays: In silico chemogenomics approaches to prioritize cell-based HTS data
    • Crisman, T. J.; Parker, C. N.; Jenkins, J. L.; Scheiber, J. Understanding false positives in reporter gene assays: in silico chemogenomics approaches to prioritize cell-based HTS data. J. Chem Inf. Model . 2007, 47 , 1319-1327.
    • (2007) J. Chem Inf. Model , vol.47 , pp. 1319-1327
    • Crisman, T.J.1    Parker, C.N.2    Jenkins, J.L.3    Scheiber, J.4
  • 18
    • 33750994920 scopus 로고    scopus 로고
    • Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors
    • Nettles, J. H.; Jenkins, J. L.; Bender, A.; Deng, Z. Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors. J. Med. Chem . 2006, 49 , 6802-6810.
    • (2006) J. Med. Chem , vol.49 , pp. 6802-6810
    • Nettles, J.H.1    Jenkins, J.L.2    Bender, A.3    Deng, Z.4
  • 19
    • 36048992504 scopus 로고    scopus 로고
    • Chemogenomic data analysis: Prediction of small-molecule targets and the advent of biological fingerprint
    • Bender, A.; Young, D. W.; Jenkins, J. L.; Serrano, M. Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprint. Comb. Chem. High Throughput Screening 2007, 10 , 719-731.
    • (2007) Comb. Chem. High Throughput Screening , vol.10 , pp. 719-731
    • Bender, A.1    Young, D.W.2    Jenkins, J.L.3    Serrano, M.4
  • 20
    • 33750049960 scopus 로고    scopus 로고
    • Generalized modeling of enzyme-ligand interactions using proteoch- emometrics and local protein substructures
    • Strombergsson, H.; Kryshtafovych, A.; Prusis, P.; Fidelis, K. Generalized modeling of enzyme-ligand interactions using proteoch- emometrics and local protein substructures. Proteins 2006, 65 , 568-579.
    • (2006) Proteins , vol.65 , pp. 568-579
    • Strombergsson, H.1    Kryshtafovych, A.2    Prusis, P.3    Fidelis, K.4
  • 21
    • 33645023990 scopus 로고    scopus 로고
    • Rough set-based proteochemometrics modeling of G-protein-coupled receptor-ligand interactions
    • Strombergsson, H.; Prusis, P.; Midelfart, H.; Lapinsh, M. Rough set-based proteochemometrics modeling of G-protein-coupled receptor-ligand interactions. Proteins 2006, 63 , 24-34.
    • (2006) Proteins , vol.63 , pp. 24-34
    • Strombergsson, H.1    Prusis, P.2    Midelfart, H.3    Lapinsh, M.4
  • 23
    • 84868969870 scopus 로고    scopus 로고
    • WOrld of Molecular BioAcTivity WOMBAT, available from Sunset Molecular Discovery LLC
    • WOrld of Molecular BioAcTivity (WOMBAT), available from Sunset Molecular Discovery LLC, http://www.sunsetmolecular.com/.
  • 24
    • 0035166973 scopus 로고    scopus 로고
    • The InterPro database, an integrated documentation resource for protein families, domains and functional sites
    • Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res . 2001, 29 , 37-40.
    • (2001) Nucleic Acids Res , vol.29 , pp. 37-40
    • Apweiler, R.1    Attwood, T.K.2    Bairoch, A.3    Bateman, A.4
  • 27
    • 33745714489 scopus 로고    scopus 로고
    • Specific affinity extraction method for small molecule-binding proteins
    • Mano, N.; Sato, K.; Goto, J. Specific affinity extraction method for small molecule-binding proteins. Anal. Chem . 2006, 78 , 4668-4675.
    • (2006) Anal. Chem , vol.78 , pp. 4668-4675
    • Mano, N.1    Sato, K.2    Goto, J.3
  • 28
    • 13344275782 scopus 로고    scopus 로고
    • Fishing for targets: Novel approaches using small molecule baits
    • Szardenings, K.; Li, B.; Ma, L.; Wu, M. Fishing for targets: novel approaches using small molecule baits. Drug Discovery Today: Technol . 2004, 1 , 9-15.
    • (2004) Drug Discovery Today: Technol , vol.1 , pp. 9-15
    • Szardenings, K.1    Li, B.2    Ma, L.3    Wu, M.4
  • 29
    • 0842274205 scopus 로고    scopus 로고
    • Rediscovering the sweet spot in drug discovery
    • Brown, D.; Superti-Furga, G. Rediscovering the sweet spot in drug discovery. Drug Discovery Today 2003, 8 , 1067-1077.
    • (2003) Drug Discovery Today , vol.8 , pp. 1067-1077
    • Brown, D.1    Superti-Furga, G.2
  • 30
    • 0038371369 scopus 로고    scopus 로고
    • Quantitative chemical proteomics for identifying candidate drug targets
    • Oda, Y.; Owa, T.; Sato, T.; Boucher, B. Quantitative chemical proteomics for identifying candidate drug targets. Anal. Chem . 2003, 75 , 2159-2165.
    • (2003) Anal. Chem , vol.75 , pp. 2159-2165
    • Oda, Y.1    Owa, T.2    Sato, T.3    Boucher, B.4
  • 32
    • 0034086397 scopus 로고    scopus 로고
    • Intracellular targets of cyclin-dependent kinase inhibitors: Identification by affinity chromatography using immobilised inhibitors
    • Knockaert, M.; Gray, N.; Damiens, E.; Chang, Y. T. Intracellular targets of cyclin-dependent kinase inhibitors: identification by affinity chromatography using immobilised inhibitors. Chem. Biol . 2000, 7 , 411-422.
    • (2000) Chem. Biol , vol.7 , pp. 411-422
    • Knockaert, M.1    Gray, N.2    Damiens, E.3    Chang, Y.T.4
  • 33
    • 34447556014 scopus 로고    scopus 로고
    • Chemical proteomics for drug discovery based on compound-immobilized affinity chromatography
    • Katayama, H.; Oda, Y. Chemical proteomics for drug discovery based on compound-immobilized affinity chromatography. J. Chro- matogr., B 2007, 855 , 21-27.
    • (2007) J. Chro- matogr., B , vol.855 , pp. 21-27
    • Katayama, H.1    Oda, Y.2
  • 34
    • 2442486588 scopus 로고    scopus 로고
    • Design and synthesis of novel hydrophilic spacers for the reduction of nonspecific binding proteins on affinity resins
    • Shiyama, T.; Furuya, M.; Yamazaki, A.; Terada, T.; Tanaka, A. Design and synthesis of novel hydrophilic spacers for the reduction of nonspecific binding proteins on affinity resins. Bioorg. Med. Chem . 2004, 12 , 2831-2841.
    • (2004) Bioorg. Med. Chem , vol.12 , pp. 2831-2841
    • Shiyama, T.1    Furuya, M.2    Yamazaki, A.3    Terada, T.4    Tanaka, A.5
  • 35
    • 46249125518 scopus 로고    scopus 로고
    • A Bayesian estimator of protein-protein association probabilities
    • Gilmore, J. M.; Auberry, D. L.; Sharp, J. L.; White, A. M. A Bayesian estimator of protein-protein association probabilities. Bioinfor- matics 2008, 24 , 1554-1555.
    • (2008) Bioinfor- matics , vol.24 , pp. 1554-1555
    • Gilmore, J.M.1    Auberry, D.L.2    Sharp, J.L.3    White, A.M.4
  • 36
    • 66749107704 scopus 로고    scopus 로고
    • PipelinePilot 5.1, available from Scitegic. http://www.scitegic.com/.
    • PipelinePilot 5.1, available from Scitegic. http://www.scitegic.com/.
  • 37
    • 84868969871 scopus 로고    scopus 로고
    • SRS Sequence Retrieval System
    • SRS (Sequence Retrieval System), http://srs6.ebi.ac.uk.
  • 38
    • 0001677717 scopus 로고
    • Controlling the false discovery rate-a practical and powerful approach to multiple testing
    • Benjamini, Y.; Hochberg, Y. Controlling the false discovery rate-a practical and powerful approach to multiple testing. J. R. Stat. Soc., Ser. B 1995, 57 , 289-300.
    • (1995) J. R. Stat. Soc., Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 39
    • 3543002852 scopus 로고    scopus 로고
    • Ligand selectivity and competition between enzymes in silico
    • Macchiarulo, A.; Nobeli, I.; Thornton, J. M. Ligand selectivity and competition between enzymes in silico. Nat. Biotechnol . 2004, 22 , 1039-1045.
    • (2004) Nat. Biotechnol , vol.22 , pp. 1039-1045
    • Macchiarulo, A.1    Nobeli, I.2    Thornton, J.M.3
  • 40
    • 3142781225 scopus 로고    scopus 로고
    • Small-molecule inhibitors of protein- protein interactions: Progressing towards the dream
    • Arkin, M. R.; Wells, J. A. Small-molecule inhibitors of protein- protein interactions: progressing towards the dream. Nat. Rev. Drug Discovery 2004, 3 , 301-317.
    • (2004) Nat. Rev. Drug Discovery , vol.3 , pp. 301-317
    • Arkin, M.R.1    Wells, J.A.2
  • 43
    • 0033574530 scopus 로고    scopus 로고
    • Identification of NSF as a beta-arrestin1-binding protein. Implications for beta2-adrenergic receptor regulation
    • McDonald, P. H.; Cote, N. L.; Lin, F. T.; Premont, R. T. Identification of NSF as a beta-arrestin1-binding protein. Implications for beta2-adrenergic receptor regulation. J. Biol. Chem . 1999, 274 , 10677-10680.
    • (1999) J. Biol. Chem , vol.274 , pp. 10677-10680
    • McDonald, P.H.1    Cote, N.L.2    Lin, F.T.3    Premont, R.T.4
  • 44
    • 33749652386 scopus 로고    scopus 로고
    • Emerging roles of beta-arrestins
    • Buchanan, F. G.; DuBois, R. N. Emerging roles of beta-arrestins. Cell Cycle 2006, 5 , 2060-2063.
    • (2006) Cell Cycle , vol.5 , pp. 2060-2063
    • Buchanan, F.G.1    DuBois, R.N.2
  • 45
    • 0037147145 scopus 로고    scopus 로고
    • Beta-arrestin2 is criticallyinvolved in CXCR4-mediated chemotaxis, and this is mediated by its enhancement of p38 MAPK activation
    • Sun, Y.; Cheng, Z.; Ma, L.; Pei, G. Beta-arrestin2 is criticallyinvolved in CXCR4-mediated chemotaxis, and this is mediated by its enhancement of p38 MAPK activation. J. Biol. Chem . 2002, 277 , 49212-49219.
    • (2002) J. Biol. Chem , vol.277 , pp. 49212-49219
    • Sun, Y.1    Cheng, Z.2    Ma, L.3    Pei, G.4
  • 46
    • 31944452649 scopus 로고    scopus 로고
    • Role of betaarrestin 1 in the metastatic progression of colorectal cancer
    • Buchanan, F. G.; Gorden, D. L.; Matta, P.; Shi, Q. Role of betaarrestin 1 in the metastatic progression of colorectal cancer. Proc. Natl. Acad. Sci. U.S.A . 2006, 103 , 1492-1497.
    • (2006) Proc. Natl. Acad. Sci. U.S.A , vol.103 , pp. 1492-1497
    • Buchanan, F.G.1    Gorden, D.L.2    Matta, P.3    Shi, Q.4
  • 47
    • 20144389530 scopus 로고    scopus 로고
    • Multi- drug transporter ABCG2 prevents tumor cell death induced by the epidermal growth factor receptor inhibitor Iressa (ZD1839, Gefitinib)
    • Elkind, N. B.; Szentpetery, Z.; Apati, A.; Ozvegy-Laczka, C. Multi- drug transporter ABCG2 prevents tumor cell death induced by the epidermal growth factor receptor inhibitor Iressa (ZD1839, Gefitinib). Cancer Res . 2005, 65 , 1770-1777.
    • (2005) Cancer Res , vol.65 , pp. 1770-1777
    • Elkind, N.B.1    Szentpetery, Z.2    Apati, A.3    Ozvegy-Laczka, C.4
  • 48
    • 34548240764 scopus 로고    scopus 로고
    • Association of variant ABCG2 and the pharmacokinetics of epidermal growth factor receptor tyrosine kinase inhibitors in cancer patients
    • Li, J.; Cusatis, G.; Brahmer, J.; Sparreboom, A. Association of variant ABCG2 and the pharmacokinetics of epidermal growth factor receptor tyrosine kinase inhibitors in cancer patients. Cancer Biol. Ther . 2007, 6 , 432-438.
    • (2007) Cancer Biol. Ther , vol.6 , pp. 432-438
    • Li, J.1    Cusatis, G.2    Brahmer, J.3    Sparreboom, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.