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Volumn 52, Issue 9, 2012, Pages 2410-2421

Structural insights into the molecular basis of the ligand promiscuity

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BINDING SITES; PHYSICOCHEMICAL PROPERTIES; PROTEINS;

EID: 84866638168     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300196g     Document Type: Article
Times cited : (52)

References (52)
  • 1
    • 34548317031 scopus 로고    scopus 로고
    • Chemogenomic approaches to rational drug design
    • Rognan, D. Chemogenomic approaches to rational drug design Br. J. Pharmacol. 2007, 152, 38-52
    • (2007) Br. J. Pharmacol. , vol.152 , pp. 38-52
    • Rognan, D.1
  • 3
    • 79952115164 scopus 로고    scopus 로고
    • Ligand-based approaches to in silico pharmacology
    • Vidal, D.; Garcia-Serna, R.; Mestres, J. Ligand-based approaches to in silico pharmacology Methods Mol. Biol. 2011, 672, 489-502
    • (2011) Methods Mol. Biol. , vol.672 , pp. 489-502
    • Vidal, D.1    Garcia-Serna, R.2    Mestres, J.3
  • 4
    • 47249146126 scopus 로고    scopus 로고
    • Drug Target Identification Using Side-Effect Similarity
    • Campillos, M.; Kuhn, M.; Gavin, A.-C.; Jensen, L. J.; Bork, P. Drug Target Identification Using Side-Effect Similarity Science 2008, 321, 263-266
    • (2008) Science , vol.321 , pp. 263-266
    • Campillos, M.1    Kuhn, M.2    Gavin, A.-C.3    Jensen, L.J.4    Bork, P.5
  • 5
    • 80052090244 scopus 로고    scopus 로고
    • Similar Interactions of Natural Products with Biosynthetic Enzymes and Therapeutic Targets could explain why Nature produces such a Large Proportion of Existing Drugs
    • Kellenberger, E.; Hofmann, A.; Quinn, R. Similar Interactions of Natural Products with Biosynthetic Enzymes and Therapeutic Targets could explain why Nature produces such a Large Proportion of Existing Drugs Nat. Prod. Rep. 2011, 28, 1483-1492
    • (2011) Nat. Prod. Rep. , vol.28 , pp. 1483-1492
    • Kellenberger, E.1    Hofmann, A.2    Quinn, R.3
  • 6
    • 84866682694 scopus 로고    scopus 로고
    • Public Domain Databases for Medicinal Chemistry
    • 10.1021/jm300501t
    • Nicola, G.; Liu, T.; Gilson, M. K. Public Domain Databases for Medicinal Chemistry J. Med. Chem. 2012, 10.1021/jm300501t
    • (2012) J. Med. Chem.
    • Nicola, G.1    Liu, T.2    Gilson, M.K.3
  • 7
    • 79959453191 scopus 로고    scopus 로고
    • BindingDB and ChEMBL: Online compound databases for drug discovery
    • Wassermann, A.; Bajorath, J. BindingDB and ChEMBL: online compound databases for drug discovery Expert. Opin. Drug. Discov. 2011, 6, 683-687
    • (2011) Expert. Opin. Drug. Discov. , vol.6 , pp. 683-687
    • Wassermann, A.1    Bajorath, J.2
  • 9
    • 77957857557 scopus 로고    scopus 로고
    • Binding of protein kinase inhibitors to synapsin i inferred from pair-wise binding site similarity measurements
    • Defranchi, E.; Schalon, C.; Messa, M.; Onofri, F.; Benfenati, F.; Rognan, D. Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements PLoS One 2010, 5, e12214
    • (2010) PLoS One , vol.5 , pp. 12214
    • Defranchi, E.1    Schalon, C.2    Messa, M.3    Onofri, F.4    Benfenati, F.5    Rognan, D.6
  • 11
    • 68249144628 scopus 로고    scopus 로고
    • Drug discovery using chemical systems biology: Repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis
    • Kinnings, S. L.; Liu, N.; Buchmeier, N.; Tonge, P. J.; Xie, L.; Bourne, P. E. Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis PLoS Comput. Biol. 2009, 5, e1000423
    • (2009) PLoS Comput. Biol. , vol.5 , pp. 1000423
    • Kinnings, S.L.1    Liu, N.2    Buchmeier, N.3    Tonge, P.J.4    Xie, L.5    Bourne, P.E.6
  • 15
    • 35748934487 scopus 로고    scopus 로고
    • The influence of drug-like concepts on decision-making in medicinal chemistry
    • Leeson, P. D.; Springthorpe, B. The influence of drug-like concepts on decision-making in medicinal chemistry Nat. Rev. Drug Discov. 2007, 6, 881-890
    • (2007) Nat. Rev. Drug Discov. , vol.6 , pp. 881-890
    • Leeson, P.D.1    Springthorpe, B.2
  • 17
    • 78149236457 scopus 로고    scopus 로고
    • Investigation of the relationship between topology and selectivity for druglike molecules
    • Yang, Y.; Chen, H.; Nilsson, I.; Muresan, S.; Engkvist, O. Investigation of the relationship between topology and selectivity for druglike molecules J. Med. Chem. 2010, 53, 7709-7714
    • (2010) J. Med. Chem. , vol.53 , pp. 7709-7714
    • Yang, Y.1    Chen, H.2    Nilsson, I.3    Muresan, S.4    Engkvist, O.5
  • 18
    • 80052844344 scopus 로고    scopus 로고
    • Getting physical in drug discovery II: The impact of chromatographic hydrophobicity measurements and aromaticity
    • Young, R. J.; Green, D. V. S.; Luscombe, C. N.; Hill, A. P. Getting physical in drug discovery II: the impact of chromatographic hydrophobicity measurements and aromaticity Drug Discovery Today 2011, 16, 822-830
    • (2011) Drug Discovery Today , vol.16 , pp. 822-830
    • Young, R.J.1    Green, D.V.S.2    Luscombe, C.N.3    Hill, A.P.4
  • 19
    • 84857982668 scopus 로고    scopus 로고
    • The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future
    • Berman, H. M.; Kleywegt, G. J.; Nakamura, H.; Markley, J. L. The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future Structure 2012, 20, 391-396
    • (2012) Structure , vol.20 , pp. 391-396
    • Berman, H.M.1    Kleywegt, G.J.2    Nakamura, H.3    Markley, J.L.4
  • 20
    • 79954520873 scopus 로고    scopus 로고
    • Sc-PDB: A database for identifying variations and multiplicity of ″druggable″ binding sites in proteins
    • Meslamani, J.; Rognan, D.; Kellenberger, E. sc-PDB: a database for identifying variations and multiplicity of ″druggable″ binding sites in proteins Bioinformatics 2011, 27, 1324-1326
    • (2011) Bioinformatics , vol.27 , pp. 1324-1326
    • Meslamani, J.1    Rognan, D.2    Kellenberger, E.3
  • 21
    • 45749117025 scopus 로고    scopus 로고
    • Ranking targets in structure-based virtual screening of 3-D protein libraries: Methods and Problems
    • Kellenberger, E.; Foata, N.; Rognan, D. Ranking targets in structure-based virtual screening of 3-D protein libraries: Methods and Problems J. Chem. Inf. Model. 2008, 48, 1014-1025
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1014-1025
    • Kellenberger, E.1    Foata, N.2    Rognan, D.3
  • 22
    • 84860833500 scopus 로고    scopus 로고
    • The UniProt, C. Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • The UniProt, C., Reorganizing the protein space at the Universal Protein Resource (UniProt) Nucleic Acids Res. 2012, 40, D71-D75
    • (2012) Nucleic Acids Res. , vol.40
  • 24
    • 33846933784 scopus 로고    scopus 로고
    • Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
    • Marcou, G.; Rognan, D. Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints J. Chem. Inf. Model. 2006, 47, 195-207
    • (2006) J. Chem. Inf. Model. , vol.47 , pp. 195-207
    • Marcou, G.1    Rognan, D.2
  • 25
    • 0001109246 scopus 로고    scopus 로고
    • A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape
    • 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
    • (1996) J. Comput. Chem. , vol.17 , pp. 1653-1666
    • Grant, J.A.1    Gallardo, M.A.2    Pickup, B.T.3
  • 27
    • 0036518771 scopus 로고    scopus 로고
    • Short EMBOSS User Guide. European Molecular Biology Open Software Suite
    • Mullan, L. J.; Bleasby, A. J. Short EMBOSS User Guide. European Molecular Biology Open Software Suite Brief Bioinform. 2002, 3, 92-94
    • (2002) Brief Bioinform. , vol.3 , pp. 92-94
    • Mullan, L.J.1    Bleasby, A.J.2
  • 28
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost, B. Twilight zone of protein sequence alignments Protein Eng. 1999, 12, 85-94
    • (1999) Protein Eng. , vol.12 , pp. 85-94
    • Rost, B.1
  • 29
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov, I. N.; Bourne, P. E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng. 1998, 11, 739-747
    • (1998) Protein Eng. , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 30
    • 84865516554 scopus 로고    scopus 로고
    • Comparison and prediction of protein-ligand binding sites from pharmacophore-annotated cavity shapes
    • 10.1021/ci300184x
    • Desaphy, J.; Azdimoussa, K.; Kellenberger, E.; Rognan, D. Comparison and prediction of protein-ligand binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model. 2012, 10.1021/ci300184x
    • (2012) J. Chem. Inf. Model.
    • Desaphy, J.1    Azdimoussa, K.2    Kellenberger, E.3    Rognan, D.4
  • 32
    • 75749155406 scopus 로고    scopus 로고
    • Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites
    • Weill, N.; Rognan, D. Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites J. Chem. Inf. Model. 2010, 50, 123-135
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 123-135
    • Weill, N.1    Rognan, D.2
  • 34
    • 31344462177 scopus 로고    scopus 로고
    • Conformational diversity of ligands bound to proteins
    • Stockwell, G. R.; Thornton, J. M. Conformational diversity of ligands bound to proteins J. Mol. Biol. 2006, 356, 928-944
    • (2006) J. Mol. Biol. , vol.356 , pp. 928-944
    • Stockwell, G.R.1    Thornton, J.M.2
  • 35
    • 0035289779 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Deliver. Rev. 2001, 46, 3-26
    • (2001) Adv. Drug Deliver. Rev. , vol.46 , pp. 3-26
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 37
    • 50149091296 scopus 로고    scopus 로고
    • DrugBank and its relevance to pharmacogenomics
    • Wishart, D. S. DrugBank and its relevance to pharmacogenomics Pharmacogenomics 2008, 9, 1155-1162
    • (2008) Pharmacogenomics , vol.9 , pp. 1155-1162
    • Wishart, D.S.1
  • 38
    • 84855290528 scopus 로고    scopus 로고
    • Divergence and Convergence in Enzyme Evolution
    • Galperin, M. Y.; Koonin, E. V. Divergence and Convergence in Enzyme Evolution J. Biol. Chem. 2012, 287, 21-28
    • (2012) J. Biol. Chem. , vol.287 , pp. 21-28
    • Galperin, M.Y.1    Koonin, E.V.2
  • 39
    • 0032527698 scopus 로고    scopus 로고
    • The additivity of substrate fragments in enzyme-ligand binding
    • Stout, T. J.; Sage, C. R.; Stroud, R. M. The additivity of substrate fragments in enzyme-ligand binding Structure 1998, 6, 839-848
    • (1998) Structure , vol.6 , pp. 839-848
    • Stout, T.J.1    Sage, C.R.2    Stroud, R.M.3
  • 40
    • 23944516742 scopus 로고    scopus 로고
    • Structures of Leishmania major Pteridine Reductase Complexes Reveal the Active Site Features Important for Ligand Binding and to Guide Inhibitor Design
    • Schüttelkopf, A. W.; Hardy, L. W.; Beverley, S. M.; Hunter, W. N. Structures of Leishmania major Pteridine Reductase Complexes Reveal the Active Site Features Important for Ligand Binding and to Guide Inhibitor Design J. Mol. Biol. 2005, 352, 105-116
    • (2005) J. Mol. Biol. , vol.352 , pp. 105-116
    • Schüttelkopf, A.W.1    Hardy, L.W.2    Beverley, S.M.3    Hunter, W.N.4
  • 42
    • 0037474479 scopus 로고    scopus 로고
    • Reconstructing the Binding Site of Factor Xa in Trypsin Reveals Ligand-induced Structural Plasticity
    • Reyda, S.; Sohn, C.; Klebe, G.; Rall, K.; Ullmann, D.; Jakubke, H.-D.; Stubbs, M. T. Reconstructing the Binding Site of Factor Xa in Trypsin Reveals Ligand-induced Structural Plasticity J. Mol. Biol. 2003, 325, 963-977
    • (2003) J. Mol. Biol. , vol.325 , pp. 963-977
    • Reyda, S.1    Sohn, C.2    Klebe, G.3    Rall, K.4    Ullmann, D.5    Jakubke, H.-D.6    Stubbs, M.T.7
  • 43
    • 39749162787 scopus 로고    scopus 로고
    • Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: Structure of lck/imatinib complex
    • Jacobs, M. D.; Caron, P. R.; Hare, B. J. Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: Structure of lck/imatinib complex Proteins: Struct., Funct., Bioinf. 2008, 70, 1451-1460
    • (2008) Proteins: Struct., Funct., Bioinf. , vol.70 , pp. 1451-1460
    • Jacobs, M.D.1    Caron, P.R.2    Hare, B.J.3
  • 45
    • 35649019748 scopus 로고    scopus 로고
    • A Single Amino Acid Mutation in Zebrafish (Danio rerio) Liver Bile Acid-binding Protein Can Change the Stoichiometry of Ligand Binding
    • Capaldi, S.; Guariento, M.; Saccomani, G.; Fessas, D.; Perduca, M.; Monaco, H. L. A Single Amino Acid Mutation in Zebrafish (Danio rerio) Liver Bile Acid-binding Protein Can Change the Stoichiometry of Ligand Binding J. Biol. Chem. 2007, 282, 31008-31018
    • (2007) J. Biol. Chem. , vol.282 , pp. 31008-31018
    • Capaldi, S.1    Guariento, M.2    Saccomani, G.3    Fessas, D.4    Perduca, M.5    Monaco, H.L.6
  • 49
    • 33846108633 scopus 로고    scopus 로고
    • BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities
    • Liu, T.; Lin, Y.; Wen, X.; Jorissen, R. N.; Gilson, M. K. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities Nucleic Acids Res. 2007, 35, D198-D201
    • (2007) Nucleic Acids Res. , vol.35
    • Liu, T.1    Lin, Y.2    Wen, X.3    Jorissen, R.N.4    Gilson, M.K.5
  • 50
    • 77951245620 scopus 로고    scopus 로고
    • On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins
    • Kahraman, A.; Morris, R. J.; Laskowski, R. A.; Favia, A. D.; Thornton, J. M. On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins Proteins: Struct., Funct., Bioinf. 2010, 78, 1120-1136
    • (2010) Proteins: Struct., Funct., Bioinf. , vol.78 , pp. 1120-1136
    • Kahraman, A.1    Morris, R.J.2    Laskowski, R.A.3    Favia, A.D.4    Thornton, J.M.5
  • 52
    • 71049126548 scopus 로고    scopus 로고
    • Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success
    • Lovering, F.; Bikker, J.; Humblet, C. Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success J. Med. Chem. 2009, 52, 6752-6756
    • (2009) J. Med. Chem. , vol.52 , pp. 6752-6756
    • Lovering, F.1    Bikker, J.2    Humblet, C.3


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