메뉴 건너뛰기




Volumn 55, Issue 2, 2015, Pages 251-262

Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints: Interaction cliffs

Author keywords

[No Author keywords available]

Indexed keywords

LANDFORMS; PROTEINS;

EID: 84923342620     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500721x     Document Type: Article
Times cited : (23)

References (73)
  • 1
    • 78649844432 scopus 로고    scopus 로고
    • Activity Landscape Representations for Structure-Activity Relationship Analysis
    • Wassermann, A. M.; Wawer, M.; Bajorath, J. R. Activity Landscape Representations for Structure-Activity Relationship Analysis J. Med. Chem. 2010, 53, 8209-8223
    • (2010) J. Med. Chem. , vol.53 , pp. 8209-8223
    • Wassermann, A.M.1    Wawer, M.2    Bajorath, J.R.3
  • 4
    • 84867818837 scopus 로고    scopus 로고
    • Scanning Structure-Activity Relationships with Structure-Activity Similarity and Related Maps: From Consensus Activity Cliffs to Selectivity Switches
    • Medina-Franco, J. L. Scanning Structure-Activity Relationships with Structure-Activity Similarity and Related Maps: From Consensus Activity Cliffs to Selectivity Switches J. Chem. Inf. Model. 2012, 52, 2485-2493
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2485-2493
    • Medina-Franco, J.L.1
  • 5
    • 84866263978 scopus 로고    scopus 로고
    • Bioactivity landscape modeling: Chemoinformatic characterization of structure-activity relationships of compounds tested across multiple targets
    • Waddell, J.; Medina-Franco, J. L. Bioactivity landscape modeling: Chemoinformatic characterization of structure-activity relationships of compounds tested across multiple targets Bioorg. Med. Chem. 2012, 20, 5443-5452
    • (2012) Bioorg. Med. Chem. , vol.20 , pp. 5443-5452
    • Waddell, J.1    Medina-Franco, J.L.2
  • 8
    • 53549123322 scopus 로고    scopus 로고
    • Structure-Activity Relationship Anatomy by Network-like Similarity Graphs and Local Structure-Activity Relationship Indices
    • Wawer, M.; Peltason, L.; Weskamp, N.; Teckentrup, A.; Bajorath, J. r. Structure-Activity Relationship Anatomy by Network-like Similarity Graphs and Local Structure-Activity Relationship Indices J. Med. Chem. 2008, 51, 6075-6084
    • (2008) J. Med. Chem. , vol.51 , pp. 6075-6084
    • Wawer, M.1    Peltason, L.2    Weskamp, N.3    Teckentrup, A.4    Bajorath, J.R.5
  • 9
    • 84867377213 scopus 로고    scopus 로고
    • Exploring structure-activity data using the landscape paradigm
    • Guha, R. Exploring structure-activity data using the landscape paradigm WIREs Comput. Mol. Sci. 2012, 2, 829-841
    • (2012) WIREs Comput. Mol. Sci. , vol.2 , pp. 829-841
    • Guha, R.1
  • 10
    • 33746931581 scopus 로고    scopus 로고
    • On outliers and activity cliffs - Why QSAR often disappoints
    • Maggiora, G. M. On outliers and activity cliffs-Why QSAR often disappoints J. Chem. Inf. Model. 2006, 46, 1535
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1535
    • Maggiora, G.M.1
  • 11
    • 84876875741 scopus 로고    scopus 로고
    • Activity Cliffs: Facts or Artifacts?
    • Medina-Franco, J. L. Activity Cliffs: Facts or Artifacts? Chem. Biol. Drug Des. 2013, 81, 553-556
    • (2013) Chem. Biol. Drug Des. , vol.81 , pp. 553-556
    • Medina-Franco, J.L.1
  • 13
    • 84881119997 scopus 로고    scopus 로고
    • Activity landscape analysis, CoMFA and CoMSIA studies of pyrazole CB1 antagonists
    • Hernández-Vázquez, E.; Méndez-Lucio, O.; Hernández-Luis, F. Activity landscape analysis, CoMFA and CoMSIA studies of pyrazole CB1 antagonists Med. Chem. Res. 2013, 22, 4133-4145
    • (2013) Med. Chem. Res. , vol.22 , pp. 4133-4145
    • Hernández-Vázquez, E.1    Méndez-Lucio, O.2    Hernández-Luis, F.3
  • 15
    • 80053327464 scopus 로고    scopus 로고
    • Multitarget structure-activity relationships characterized by activity-difference maps and consensus similarity measure
    • Medina-Franco, J. L.; Yongye, A. B.; Pérez-Villanueva, J.; Houghten, R. A.; Martinez-Mayorga, K. Multitarget structure-activity relationships characterized by activity-difference maps and consensus similarity measure J. Chem. Inf. Model. 2011, 51, 2427-2439
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2427-2439
    • Medina-Franco, J.L.1    Yongye, A.B.2    Pérez-Villanueva, J.3    Houghten, R.A.4    Martinez-Mayorga, K.5
  • 16
    • 84870013075 scopus 로고    scopus 로고
    • Design of a Three-Dimensional Multitarget Activity Landscape
    • de la Vega de Leon, A.; Bajorath, J. Design of a Three-Dimensional Multitarget Activity Landscape J. Chem. Inf. Model. 2012, 52, 2876-2883
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2876-2883
    • De La Vega De Leon, A.1    Bajorath, J.2
  • 18
    • 84894248000 scopus 로고    scopus 로고
    • Rationalization of Activity Cliffs of a Sulfonamide Inhibitor of DNA Methyltransferases with Induced-Fit Docking
    • Medina-Franco, J.; Méndez-Lucio, O.; Yoo, J. Rationalization of Activity Cliffs of a Sulfonamide Inhibitor of DNA Methyltransferases with Induced-Fit Docking Int. J. Mol. Sci. 2014, 15, 3253-3261
    • (2014) Int. J. Mol. Sci. , vol.15 , pp. 3253-3261
    • Medina-Franco, J.1    Méndez-Lucio, O.2    Yoo, J.3
  • 20
    • 80052080825 scopus 로고    scopus 로고
    • From Activity Cliffs to Target-Specific Scoring Models and Pharmacophore Hypotheses
    • Seebeck, B.; Wagener, M.; Rarey, M. From Activity Cliffs to Target-Specific Scoring Models and Pharmacophore Hypotheses ChemMedChem. 2011, 6, 1630-1639
    • (2011) ChemMedChem. , vol.6 , pp. 1630-1639
    • Seebeck, B.1    Wagener, M.2    Rarey, M.3
  • 21
    • 84875479590 scopus 로고    scopus 로고
    • Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs
    • Desaphy, J.; Raimbaud, E.; Ducrot, P.; Rognan, D. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model. 2013, 53, 623-637
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 623-637
    • Desaphy, J.1    Raimbaud, E.2    Ducrot, P.3    Rognan, D.4
  • 22
    • 42449152858 scopus 로고    scopus 로고
    • The use of protein-ligand interaction fingerprints in docking
    • Brewerton, S. C. The use of protein-ligand interaction fingerprints in docking Curr. Opin. Drug Discovery Dev. 2008, 11, 356-364
    • (2008) Curr. Opin. Drug Discovery Dev. , vol.11 , pp. 356-364
    • Brewerton, S.C.1
  • 24
    • 82255172411 scopus 로고    scopus 로고
    • Structure-Based Discovery of Allosteric Modulators of Two Related Class B G-Protein-Coupled Receptors
    • de Graaf, C.; Rein, C.; Piwnica, D.; Giordanetto, F.; Rognan, D. Structure-Based Discovery of Allosteric Modulators of Two Related Class B G-Protein-Coupled Receptors ChemMedChem. 2011, 6, 2159-2169
    • (2011) ChemMedChem. , vol.6 , pp. 2159-2169
    • De Graaf, C.1    Rein, C.2    Piwnica, D.3    Giordanetto, F.4    Rognan, D.5
  • 26
    • 84881652938 scopus 로고    scopus 로고
    • A structural chemogenomics analysis of aminergic GPCRs: Lessons for histamine receptor ligand design
    • Kooistra, A. J.; Kuhne, S.; de Esch, I. J. P.; Leurs, R.; de Graaf, C. A structural chemogenomics analysis of aminergic GPCRs: lessons for histamine receptor ligand design Br. J. Pharmacol. 2013, 170, 101-126
    • (2013) Br. J. Pharmacol. , vol.170 , pp. 101-126
    • Kooistra, A.J.1    Kuhne, S.2    De Esch, I.J.P.3    Leurs, R.4    De Graaf, C.5
  • 27
    • 84893065058 scopus 로고    scopus 로고
    • KLIFS: A knowledge-based structural database to navigate kinase-ligand interaction space
    • van Linden, O. P.; Kooistra, A. J.; Leurs, R.; de Esch, I. J.; de Graaf, C. KLIFS: a knowledge-based structural database to navigate kinase-ligand interaction space J. Med. Chem. 2014, 57, 249-77
    • (2014) J. Med. Chem. , vol.57 , pp. 249-277
    • Van Linden, O.P.1    Kooistra, A.J.2    Leurs, R.3    De Esch, I.J.4    De Graaf, C.5
  • 28
    • 84920947777 scopus 로고    scopus 로고
    • Comprehensive Analysis of Three-Dimensional Activity Cliffs Formed by Kinase Inhibitors with Different Binding Modes and Cliff Mapping of Structural Analogs
    • Furtmann, N.; Hu, Y.; Bajorath, J. Comprehensive Analysis of Three-Dimensional Activity Cliffs Formed by Kinase Inhibitors with Different Binding Modes and Cliff Mapping of Structural Analogs J. Med. Chem. 2015, 58, 252-264
    • (2015) J. Med. Chem. , vol.58 , pp. 252-264
    • Furtmann, N.1    Hu, Y.2    Bajorath, J.3
  • 31
    • 84923331194 scopus 로고    scopus 로고
    • MayaChemTools. (accessed Feb.)
    • Sud, M. MayaChemTools. http://www.MayaChemTools.org (accessed Feb. 2013).
    • (2013)
    • Sud, M.1
  • 32
    • 0000992784 scopus 로고    scopus 로고
    • Chemical similarity assessment through multilevel neighborhoods of atoms: Definition and comparison with the other descriptors
    • Filimonov, D.; Poroikov, V.; Borodina, Y.; Gloriozova, T. Chemical similarity assessment through multilevel neighborhoods of atoms: definition and comparison with the other descriptors J. Chem. Inf. Comput. Sci. 1999, 39, 666-670
    • (1999) J. Chem. Inf. Comput. Sci. , vol.39 , pp. 666-670
    • Filimonov, D.1    Poroikov, V.2    Borodina, Y.3    Gloriozova, T.4
  • 33
    • 0029404240 scopus 로고
    • Electrotopological state indices for atom types: A novel combination of electronic, topological, and valence state information
    • Hall, L. H.; Kier, L. B. Electrotopological state indices for atom types: A novel combination of electronic, topological, and valence state information J. Chem. Inf. Comput. Sci. 1995, 35, 1039-1045
    • (1995) J. Chem. Inf. Comput. Sci. , vol.35 , pp. 1039-1045
    • Hall, L.H.1    Kier, L.B.2
  • 34
    • 77952772341 scopus 로고    scopus 로고
    • Extended-connectivity fingerprints
    • Rogers, D.; Hahn, M. Extended-connectivity fingerprints J. Chem. Inf. Model. 2010, 50, 742-754
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 742-754
    • Rogers, D.1    Hahn, M.2
  • 36
    • 33845379303 scopus 로고
    • Atom pairs as molecular features in structure-activity studies: Definition and applications
    • Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. Atom pairs as molecular features in structure-activity studies: definition and applications J. Chem. Inf. Comput. Sci. 1985, 25, 64-73
    • (1985) J. Chem. Inf. Comput. Sci. , vol.25 , pp. 64-73
    • Carhart, R.E.1    Smith, D.H.2    Venkataraghavan, R.3
  • 37
    • 0003076470 scopus 로고
    • Topological torsion: A new molecular descriptor for SAR applications. Comparison with other descriptors
    • Nilakantan, R.; Bauman, N.; Dixon, J. S.; Venkataraghavan, R. Topological torsion: a new molecular descriptor for SAR applications. Comparison with other descriptors J. Chem. Inf. Comput. Sci. 1987, 27, 82-85
    • (1987) J. Chem. Inf. Comput. Sci. , vol.27 , pp. 82-85
    • Nilakantan, R.1    Bauman, N.2    Dixon, J.S.3    Venkataraghavan, R.4
  • 38
    • 84952912906 scopus 로고    scopus 로고
    • Alignment-free pharmacophore patterns - A correlation-vector approach
    • In; Wiley-VCH Verlag GmbH & Co. KGaA
    • Renner, S.; Fechner, U.; Schneider, G. Alignment-free pharmacophore patterns-A correlation-vector approach. In Pharmacophores and Pharmacophore Searches; Wiley-VCH Verlag GmbH & Co. KGaA: 2006; pp 49-79.
    • (2006) Pharmacophores and Pharmacophore Searches , pp. 49-79
    • Renner, S.1    Fechner, U.2    Schneider, G.3
  • 39
    • 33845791138 scopus 로고    scopus 로고
    • Fuzzy tricentric pharmacophore fingerprints. 1. Topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes
    • Bonachéra, F.; Parent, B.; Barbosa, F.; Froloff, N.; Horvath, D. Fuzzy tricentric pharmacophore fingerprints. 1. Topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes J. Chem. Inf. Model. 2006, 46, 2457-2477
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 2457-2477
    • Bonachéra, F.1    Parent, B.2    Barbosa, F.3    Froloff, N.4    Horvath, D.5
  • 40
    • 0001368373 scopus 로고
    • Etude Comparative de la Distribution Florale dans une Portion des Alpes et des Jura
    • Jaccard, P. Etude Comparative de la Distribution Florale dans une Portion des Alpes et des Jura Bull. Soc. Vaudoise Sci. Nat. 1901, 37, 547-579
    • (1901) Bull. Soc. Vaudoise Sci. Nat. , vol.37 , pp. 547-579
    • Jaccard, P.1
  • 42
    • 10344230435 scopus 로고    scopus 로고
    • Molecular similarity: A key technique in molecular informatics
    • Bender, A.; Glen, R. C. Molecular similarity: a key technique in molecular informatics Org. Biomol. Chem. 2004, 2, 3204-3218
    • (2004) Org. Biomol. Chem. , vol.2 , pp. 3204-3218
    • Bender, A.1    Glen, R.C.2
  • 43
    • 84923358970 scopus 로고    scopus 로고
    • version 3.2.0.4; OpenEye Scientific Software, Inc. Santa Fe, NM, U.S.A
    • ROCS, version 3.2.0.4; OpenEye Scientific Software, Inc.: Santa Fe, NM, U.S.A. http://www.eyesopen.com.
    • ROCS
  • 44
    • 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
  • 47
    • 84859270118 scopus 로고    scopus 로고
    • Classification of scaffold-hopping approaches
    • Sun, H. M.; Tawa, G.; Wallqvist, A. Classification of scaffold-hopping approaches Drug Discovery Today 2012, 17, 310-324
    • (2012) Drug Discovery Today , vol.17 , pp. 310-324
    • Sun, H.M.1    Tawa, G.2    Wallqvist, A.3
  • 53
    • 77951689893 scopus 로고    scopus 로고
    • Analysis of Imatinib and Sorafenib Binding to p38α Compared with c-Abl and b-Raf Provides Structural Insights for Understanding the Selectivity of Inhibitors Targeting the DFG-Out Form of Protein Kinases
    • Namboodiri, H. V.; Bukhtiyarova, M.; Ramcharan, J.; Karpusas, M.; Lee, Y.; Springman, E. B. Analysis of Imatinib and Sorafenib Binding to p38α Compared with c-Abl and b-Raf Provides Structural Insights for Understanding the Selectivity of Inhibitors Targeting the DFG-Out Form of Protein Kinases Biochemistry 2010, 49, 3611-3618
    • (2010) Biochemistry , vol.49 , pp. 3611-3618
    • Namboodiri, H.V.1    Bukhtiyarova, M.2    Ramcharan, J.3    Karpusas, M.4    Lee, Y.5    Springman, E.B.6
  • 56
    • 52949141884 scopus 로고    scopus 로고
    • Modulation of kinase-inhibitor interactions by auxiliary protein binding: Crystallography studies on Aurora A interactions with VX-680 and with TPX2
    • Zhao, B.; Smallwood, A.; Yang, J.; Koretke, K.; Nurse, K.; Calamari, A.; Kirkpatrick, R. B.; Lai, Z. Modulation of kinase-inhibitor interactions by auxiliary protein binding: Crystallography studies on Aurora A interactions with VX-680 and with TPX2 Protein Sci. 2008, 17, 1791-1797
    • (2008) Protein Sci. , vol.17 , pp. 1791-1797
    • Zhao, B.1    Smallwood, A.2    Yang, J.3    Koretke, K.4    Nurse, K.5    Calamari, A.6    Kirkpatrick, R.B.7    Lai, Z.8
  • 57
    • 80054943801 scopus 로고    scopus 로고
    • Mutants of protein kinase A that mimic the ATP-binding site of Aurora kinase
    • Pflug, A.; de Oliveira, T. M.; Bossemeyer, D.; Engh, R. A. Mutants of protein kinase A that mimic the ATP-binding site of Aurora kinase Biochem. J. 2011, 440, 85-93
    • (2011) Biochem. J. , vol.440 , pp. 85-93
    • Pflug, A.1    De Oliveira, T.M.2    Bossemeyer, D.3    Engh, R.A.4
  • 62
    • 33846899405 scopus 로고    scopus 로고
    • Molecular Recognition of Protein Kinase Binding Pockets for Design of Potent and Selective Kinase Inhibitors
    • Liao, J. J.-L. Molecular Recognition of Protein Kinase Binding Pockets for Design of Potent and Selective Kinase Inhibitors J. Med. Chem. 2007, 50, 409-424
    • (2007) J. Med. Chem. , vol.50 , pp. 409-424
    • Liao, J.J.-L.1
  • 63
    • 33747872588 scopus 로고    scopus 로고
    • Molecular complexes at a glance: Automated generation of two-dimensional complex diagrams
    • Stierand, K.; Maaß, P. C.; Rarey, M. Molecular complexes at a glance: automated generation of two-dimensional complex diagrams Bioinformatics 2006, 22, 1710-1716
    • (2006) Bioinformatics , vol.22 , pp. 1710-1716
    • Stierand, K.1    Maaß, P.C.2    Rarey, M.3
  • 64
    • 84923347999 scopus 로고    scopus 로고
    • PoseViewWeb 1.97.0. (accessed Feb.)
    • PoseViewWeb 1.97.0. http://poseview.zbh.uni-hamburg.de (accessed Feb. 2014).
    • (2014)
  • 65
    • 34548825448 scopus 로고    scopus 로고
    • Targeting Protein Multiple Conformations: A Structure-Based Strategy for Kinase Drug Design
    • Liao, J. J.-L.; Andrews, R. C. Targeting Protein Multiple Conformations: A Structure-Based Strategy for Kinase Drug Design Curr. Top. Med. Chem. 2007, 7, 1394-1407
    • (2007) Curr. Top. Med. Chem. , vol.7 , pp. 1394-1407
    • Liao, J.J.-L.1    Andrews, R.C.2
  • 66
    • 84880177115 scopus 로고    scopus 로고
    • Type II kinase inhibitors: An opportunity in cancer for rational design
    • Blanc, J.; Geney, R.; Menet, C. Type II kinase inhibitors: an opportunity in cancer for rational design Anticancer Agents Med. Chem. 2013, 13, 731-47
    • (2013) Anticancer Agents Med. Chem. , vol.13 , pp. 731-747
    • Blanc, J.1    Geney, R.2    Menet, C.3
  • 71
    • 67649995940 scopus 로고    scopus 로고
    • Development of a Fluorescent-Tagged Kinase Assay System for the Detection and Characterization of Allosteric Kinase Inhibitors
    • Simard, J. R.; Getlik, M.; Grutter, C.; Pawar, V.; Wulfert, S.; Rabiller, M.; Rauh, D. Development of a Fluorescent-Tagged Kinase Assay System for the Detection and Characterization of Allosteric Kinase Inhibitors J. Am. Chem. Soc. 2009, 131, 13286-13296
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 13286-13296
    • Simard, J.R.1    Getlik, M.2    Grutter, C.3    Pawar, V.4    Wulfert, S.5    Rabiller, M.6    Rauh, D.7
  • 72
    • 42149090634 scopus 로고    scopus 로고
    • Structure-Activity Landscape Index: Identifying and Quantifying Activity Cliffs
    • Guha, R.; Van Drie, J. H. Structure-Activity Landscape Index: Identifying and Quantifying Activity Cliffs J. Chem. Inf. Model. 2008, 48, 646-658
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 646-658
    • Guha, R.1    Van Drie, J.H.2
  • 73
    • 36148989137 scopus 로고    scopus 로고
    • Quantifying the Nature of Structure-Activity Relationships
    • Peltason, L.; Bajorath, J.; Index, S. A. R. Quantifying the Nature of Structure-Activity Relationships J. Med. Chem. 2007, 50, 5571-5578
    • (2007) J. Med. Chem. , vol.50 , pp. 5571-5578
    • Peltason, L.1    Bajorath, J.2    Index, S.A.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.