메뉴 건너뛰기




Volumn 54, Issue 5, 2014, Pages 1391-1400

Computational method to identify druggable binding sites that target protein-protein interactions

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; DRUG INTERACTIONS; LIGANDS; MOLECULES;

EID: 84901596602     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400750x     Document Type: Article
Times cited : (22)

References (63)
  • 1
    • 37249004920 scopus 로고    scopus 로고
    • Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
    • Wells, J. A.; McClendon, C. L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces Nature 2007, 450, 1001-1009
    • (2007) Nature , vol.450 , pp. 1001-1009
    • Wells, J.A.1    McClendon, C.L.2
  • 2
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte, L.; Chothia, C.; Janin, J. The atomic structure of protein-protein recognition sites J. Mol. Biol. 1999, 285, 2177-2198
    • (1999) J. Mol. Biol. , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 4
    • 77955517509 scopus 로고    scopus 로고
    • Druggable pockets and binding site centric chemical space: A paradigm shift in drug discovery
    • Perot, S.; Sperandio, O.; Miteva, M. A.; Camproux, A. C.; Villoutreix, B. O. Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery Drug Discovery Today 2010, 15, 656-667
    • (2010) Drug Discovery Today , vol.15 , pp. 656-667
    • Perot, S.1    Sperandio, O.2    Miteva, M.A.3    Camproux, A.C.4    Villoutreix, B.O.5
  • 5
    • 67649841614 scopus 로고    scopus 로고
    • The road less traveled: Modulating signal transduction enzymes by inhibiting their protein-protein interactions
    • Arkin, M. R.; Whitty, A. The road less traveled: modulating signal transduction enzymes by inhibiting their protein-protein interactions Curr. Opin. Chem. Biol. 2009, 13, 284-290
    • (2009) Curr. Opin. Chem. Biol. , vol.13 , pp. 284-290
    • Arkin, M.R.1    Whitty, A.2
  • 6
    • 33645887230 scopus 로고    scopus 로고
    • Critical review of the role of HTS in drug discovery
    • Macarron, R. Critical review of the role of HTS in drug discovery Drug Discovery Today 2006, 11, 277-279
    • (2006) Drug Discovery Today , vol.11 , pp. 277-279
    • Macarron, R.1
  • 7
    • 33646567148 scopus 로고    scopus 로고
    • Between a rock and a hard place?
    • Whitty, A.; Kumaravel, G. Between a rock and a hard place? Nat. Chem. Biol. 2006, 2, 112-118
    • (2006) Nat. Chem. Biol. , vol.2 , pp. 112-118
    • Whitty, A.1    Kumaravel, G.2
  • 8
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson, T.; Wells, J. A. A hot spot of binding energy in a hormone-receptor interface Science 1995, 267, 383-386
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 9
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme, T.; Baker, D. A simple physical model for binding energy hot spots in protein-protein complexes Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 14116-14121
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 10
    • 0029935202 scopus 로고    scopus 로고
    • The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria
    • Peters, K. P.; Fauck, J.; Frommel, C. The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria J. Mol. Biol. 1996, 256, 201-213
    • (1996) J. Mol. Biol. , vol.256 , pp. 201-213
    • Peters, K.P.1    Fauck, J.2    Frommel, C.3
  • 11
    • 37249062102 scopus 로고    scopus 로고
    • Binding response: A descriptor for selecting ligand binding site on protein surfaces
    • Zhong, S.; MacKerell, A. D., Jr. Binding response: a descriptor for selecting ligand binding site on protein surfaces J. Chem. Inf. Model. 2007, 47, 2303-2315
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 2303-2315
    • Zhong, S.1    Mackerell Jr., A.D.2
  • 12
    • 0041989751 scopus 로고    scopus 로고
    • CASTp: Computed Atlas of Surface Topography of proteins
    • Binkowski, T. A.; Naghibzadeh, S.; Liang, J. CASTp: Computed Atlas of Surface Topography of proteins Nucleic Acids Res. 2003, 31, 3352-3355
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3352-3355
    • Binkowski, T.A.1    Naghibzadeh, S.2    Liang, J.3
  • 13
    • 67649422714 scopus 로고    scopus 로고
    • Fpocket: An open source platform for ligand pocket detection
    • Le Guilloux, V.; Schmidtke, P.; Tuffery, P. Fpocket: an open source platform for ligand pocket detection BMC Bioinf. 2009, 10, 168
    • (2009) BMC Bioinf. , vol.10 , pp. 168
    • Le Guilloux, V.1    Schmidtke, P.2    Tuffery, P.3
  • 14
    • 80054037270 scopus 로고    scopus 로고
    • Beyond structural genomics: Computational approaches for the identification of ligand binding sites in protein structures
    • Ghersi, D.; Sanchez, R. Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures J. Struct. Funct. Genomics 2011, 12, 109-117
    • (2011) J. Struct. Funct. Genomics , vol.12 , pp. 109-117
    • Ghersi, D.1    Sanchez, R.2
  • 15
    • 79953060278 scopus 로고    scopus 로고
    • Context-based identification of protein-protein interfaces and ″hot-spot″ residues
    • Geppert, T.; Hoy, B.; Wessler, S.; Schneider, G. Context-based identification of protein-protein interfaces and ″hot-spot″ residues Chem. Biol. 2011, 18, 344-353
    • (2011) Chem. Biol. , vol.18 , pp. 344-353
    • Geppert, T.1    Hoy, B.2    Wessler, S.3    Schneider, G.4
  • 16
    • 34250831648 scopus 로고    scopus 로고
    • Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites
    • Kawabata, T.; Go, N. Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites Proteins: Struct., Funct., Bioinf. 2007, 68, 516-29
    • (2007) Proteins: Struct., Funct., Bioinf. , vol.68 , pp. 516-529
    • Kawabata, T.1    Go, N.2
  • 18
    • 77951214658 scopus 로고    scopus 로고
    • McVol - A program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm
    • Till, M. S.; Ullmann, G. M. McVol-a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm J. Mol. Graphics Modell. 2010, 16, 419-429
    • (2010) J. Mol. Graphics Modell. , vol.16 , pp. 419-429
    • Till, M.S.1    Ullmann, G.M.2
  • 19
    • 33847142225 scopus 로고    scopus 로고
    • CAVER: A new tool to explore routes from protein clefts, pockets and cavities
    • Petrek, M.; Otyepka, M.; Banas, P.; Kosinova, P.; Koca, J.; Damborsky, J. CAVER: a new tool to explore routes from protein clefts, pockets and cavities BMC Bioinf. 2006, 7, 316
    • (2006) BMC Bioinf. , vol.7 , pp. 316
    • Petrek, M.1    Otyepka, M.2    Banas, P.3    Kosinova, P.4    Koca, J.5    Damborsky, J.6
  • 20
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • Brady, G. P., Jr.; Stouten, P. F. Fast prediction and visualization of protein binding pockets with PASS J. Comput.-Aided Mol. Des. 2000, 14, 383-401
    • (2000) J. Comput.-Aided Mol. Des. , vol.14 , pp. 383-401
    • Brady Jr., G.P.1    Stouten, P.F.2
  • 21
    • 33947420470 scopus 로고    scopus 로고
    • New method for fast and accurate binding-site identification and analysis
    • Halgren, T. New method for fast and accurate binding-site identification and analysis Chem. Biol. Drug Des. 2007, 69, 146-148
    • (2007) Chem. Biol. Drug Des. , vol.69 , pp. 146-148
    • Halgren, T.1
  • 22
    • 65249117514 scopus 로고    scopus 로고
    • Identifying and characterizing binding sites and assessing druggability
    • Halgren, T. A. Identifying and characterizing binding sites and assessing druggability J. Chem. Inf. Model. 2009, 49, 377-389
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 377-389
    • Halgren, T.A.1
  • 23
    • 65449159794 scopus 로고    scopus 로고
    • Binding site detection and druggability index from first principles
    • Seco, J.; Luque, F. J.; Barril, X. Binding site detection and druggability index from first principles J. Med. Chem. 2009, 52, 2363-2371
    • (2009) J. Med. Chem. , vol.52 , pp. 2363-2371
    • Seco, J.1    Luque, F.J.2    Barril, X.3
  • 24
    • 21044444449 scopus 로고    scopus 로고
    • Pocketome via comprehensive identification and classification of ligand binding envelopes
    • An, J.; Totrov, M.; Abagyan, R. Pocketome via comprehensive identification and classification of ligand binding envelopes Mol. Cell. Proteomics 2005, 4, 752-761
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 752-761
    • An, J.1    Totrov, M.2    Abagyan, R.3
  • 25
    • 59449090758 scopus 로고    scopus 로고
    • Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites
    • Ghersi, D.; Sanchez, R. Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites Proteins: Struct., Funct., Bioinf. 2009, 74, 417-424
    • (2009) Proteins: Struct., Funct., Bioinf. , vol.74 , pp. 417-424
    • Ghersi, D.1    Sanchez, R.2
  • 26
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites
    • Laurie, A. T. R.; Jackson, R. M. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21, 1908-1916.
    • Bioinformatics , vol.21 , pp. 1908-1916
    • Laurie, A.T.R.1    Jackson, R.M.2
  • 27
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 1985, 28, 849-857
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 29
    • 0030979125 scopus 로고    scopus 로고
    • Automatic identification and representation of protein binding sites for molecular docking
    • Ruppert, J.; Welch, W.; Jain, A. N. Automatic identification and representation of protein binding sites for molecular docking Protein Sci. 1997, 6, 524-533
    • (1997) Protein Sci. , vol.6 , pp. 524-533
    • Ruppert, J.1    Welch, W.2    Jain, A.N.3
  • 30
    • 23144462493 scopus 로고    scopus 로고
    • MEDock: A web server for efficient prediction of ligand binding sites based on a novel optimization algorithm
    • Chang, D. T.; Oyang, Y. J.; Lin, J. H. MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm Nucleic Acids Res. 2005, 33, W233-238
    • (2005) Nucleic Acids Res. , vol.33 , pp. 233-238
    • Chang, D.T.1    Oyang, Y.J.2    Lin, J.H.3
  • 31
    • 77956308900 scopus 로고    scopus 로고
    • Binding-site assessment by virtual fragment screening
    • Huang, N.; Jacobson, M. P. Binding-site assessment by virtual fragment screening PLoS One 2010, 5, e10109
    • (2010) PLoS One , vol.5 , pp. 10109
    • Huang, N.1    Jacobson, M.P.2
  • 32
    • 33750029942 scopus 로고    scopus 로고
    • LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation
    • Huang, B.; Schroeder, M. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation BMC Struct. Biol. 2006, 6, 19
    • (2006) BMC Struct. Biol. , vol.6 , pp. 19
    • Huang, B.1    Schroeder, M.2
  • 33
    • 33646757492 scopus 로고    scopus 로고
    • On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites
    • Nayal, M.; Honig, B. On the nature of cavities on protein surfaces: application to the identification of drug-binding sites Proteins: Struct., Funct., Bioinf. 2006, 63, 892-906
    • (2006) Proteins: Struct., Funct., Bioinf. , vol.63 , pp. 892-906
    • Nayal, M.1    Honig, B.2
  • 34
    • 33749336161 scopus 로고    scopus 로고
    • Localization of binding sites in protein structures by optimization of a composite scoring function
    • Rossi, A.; Marti-Renom, M. A.; Sali, A. Localization of binding sites in protein structures by optimization of a composite scoring function Protein Sci. 2006, 15, 2366-2380
    • (2006) Protein Sci. , vol.15 , pp. 2366-2380
    • Rossi, A.1    Marti-Renom, M.A.2    Sali, A.3
  • 35
    • 84863661333 scopus 로고    scopus 로고
    • Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
    • Bakan, A.; Nevins, N.; Lakdawala, A. S.; Bahar, I. Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules J. Chem. Theory Comput. 2012, 8, 2435-2447
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2435-2447
    • Bakan, A.1    Nevins, N.2    Lakdawala, A.S.3    Bahar, I.4
  • 37
    • 1642310340 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
    • Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening J. Med. Chem. 2004, 47, 1750-1759
    • (2004) J. Med. Chem. , vol.47 , pp. 1750-1759
    • Halgren, T.A.1    Murphy, R.B.2    Friesner, R.A.3    Beard, H.S.4    Frye, L.L.5    Pollard, W.T.6    Banks, J.L.7
  • 38
    • 77956303799 scopus 로고    scopus 로고
    • Molecular dynamics simulation with weak coupling to heat and material baths
    • Eslami, H.; Mojahedi, F.; Moghadasi, J. Molecular dynamics simulation with weak coupling to heat and material baths J. Chem. Phys. 2010, 133, 084105
    • (2010) J. Chem. Phys. , vol.133 , pp. 084105
    • Eslami, H.1    Mojahedi, F.2    Moghadasi, J.3
  • 39
    • 84901615160 scopus 로고    scopus 로고
    • The AxPyMOL Molecular Graphics Plugin for Microsoft PowerPoint, Version 1.0; Schrödinger, LLC.
    • The AxPyMOL Molecular Graphics Plugin for Microsoft PowerPoint, Version 1.0; Schrödinger, LLC: 2010.
    • (2010)
  • 40
    • 84901630718 scopus 로고    scopus 로고
    • The PyMOL Molecular Graphics System, Version 1.3r1; Schrödinger, LLC.
    • The PyMOL Molecular Graphics System, Version 1.3r1; Schrödinger, LLC: 2010.
    • (2010)
  • 43
    • 84901645920 scopus 로고    scopus 로고
    • Maestro, 9.2; Schrödinger, LLC: New York, NY.
    • Maestro, 9.2; Schrödinger, LLC: New York, NY, 2011.
    • (2011)
  • 44
    • 84901615159 scopus 로고    scopus 로고
    • Suite 2012: LigPrep, 2.5; Schrödinger, LLC: New York, NY.
    • Suite 2012: LigPrep, 2.5; Schrödinger, LLC: New York, NY, 2012.
    • (2012)
  • 45
    • 77955709186 scopus 로고    scopus 로고
    • Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution
    • Greenwood, J. R.; Calkins, D.; Sullivan, A. P.; Shelley, J. C. Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution J. Comput.-Aided Mol. Des. 2010, 24, 591-604
    • (2010) J. Comput.-Aided Mol. Des. , vol.24 , pp. 591-604
    • Greenwood, J.R.1    Calkins, D.2    Sullivan, A.P.3    Shelley, J.C.4
  • 46
    • 84880529288 scopus 로고    scopus 로고
    • Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments
    • Sastry, G. M.; Adzhigirey, M.; Day, T.; Annabhimoju, R.; Sherman, W. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments J. Comput.-Aided Mol. Des. 2013, 27, 221-234
    • (2013) J. Comput.-Aided Mol. Des. , vol.27 , pp. 221-234
    • Sastry, G.M.1    Adzhigirey, M.2    Day, T.3    Annabhimoju, R.4    Sherman, W.5
  • 47
    • 44049086134 scopus 로고    scopus 로고
    • Ligand-stabilized conformational states of human beta(2) adrenergic receptor: Insight into G-protein-coupled receptor activation
    • Bhattacharya, S.; Hall, S. E.; Li, H.; Vaidehi, N. Ligand-stabilized conformational states of human beta(2) adrenergic receptor: insight into G-protein-coupled receptor activation Biophys. J. 2008, 94, 2027-2042
    • (2008) Biophys. J. , vol.94 , pp. 2027-2042
    • Bhattacharya, S.1    Hall, S.E.2    Li, H.3    Vaidehi, N.4
  • 48
    • 84901645919 scopus 로고    scopus 로고
    • Suite 2012: Glide, 5.8; Schrödinger, LLC: New York, NY.
    • Suite 2012: Glide, 5.8; Schrödinger, LLC: New York, NY, 2012.
    • (2012)
  • 51
    • 33745597909 scopus 로고    scopus 로고
    • Predicting protein interaction sites: Binding hot-spots in protein-protein and protein-ligand interfaces
    • Burgoyne, N. J.; Jackson, R. M. Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces Bioinformatics 2006, 22, 1335-1342
    • (2006) Bioinformatics , vol.22 , pp. 1335-1342
    • Burgoyne, N.J.1    Jackson, R.M.2
  • 52
    • 58849145512 scopus 로고    scopus 로고
    • Predicting druggable binding sites at the protein-protein interface
    • Fuller, J. C.; Burgoyne, N. J.; Jackson, R. M. Predicting druggable binding sites at the protein-protein interface Drug Discovery Today 2009, 14, 155-161
    • (2009) Drug Discovery Today , vol.14 , pp. 155-161
    • Fuller, J.C.1    Burgoyne, N.J.2    Jackson, R.M.3
  • 53
    • 0033548664 scopus 로고    scopus 로고
    • Structural response to mutation at a protein-protein interface
    • Vaughan, C. K.; Buckle, A. M.; Fersht, A. R. Structural response to mutation at a protein-protein interface J. Mol. Biol. 1999, 286, 1487-1506
    • (1999) J. Mol. Biol. , vol.286 , pp. 1487-1506
    • Vaughan, C.K.1    Buckle, A.M.2    Fersht, A.R.3
  • 58
    • 0032582542 scopus 로고    scopus 로고
    • Mapping the intercellular adhesion molecule-1 and -2 binding site on the inserted domain of leukocyte function-associated antigen-1
    • Edwards, C. P.; Fisher, K. L.; Presta, L. G.; Bodary, S. C. Mapping the intercellular adhesion molecule-1 and -2 binding site on the inserted domain of leukocyte function-associated antigen-1 J. Biol. Chem. 1998, 273, 28937-28944
    • (1998) J. Biol. Chem. , vol.273 , pp. 28937-28944
    • Edwards, C.P.1    Fisher, K.L.2    Presta, L.G.3    Bodary, S.C.4
  • 59
    • 0029059578 scopus 로고
    • A binding interface on the i domain of lymphocyte function-associated antigen-1 (LFA-1) required for specific interaction with intercellular adhesion molecule 1 (ICAM-1)
    • Huang, C.; Springer, T. A. A binding interface on the I domain of lymphocyte function-associated antigen-1 (LFA-1) required for specific interaction with intercellular adhesion molecule 1 (ICAM-1) J. Biol. Chem. 1995, 270, 19008-19016
    • (1995) J. Biol. Chem. , vol.270 , pp. 19008-19016
    • Huang, C.1    Springer, T.A.2
  • 60
    • 33644878621 scopus 로고    scopus 로고
    • PINT: Protein-protein Interactions Thermodynamic Database
    • Kumar, M. D.; Gromiha, M. M. PINT: Protein-protein Interactions Thermodynamic Database Nucleic Acids Res. 2006, 34, D195-198
    • (2006) Nucleic Acids Res. , vol.34 , pp. 195-198
    • Kumar, M.D.1    Gromiha, M.M.2
  • 61
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan, A. A.; Thorn, K. S. Anatomy of hot spots in protein interfaces J. Mol. Biol. 1998, 280, 1-9
    • (1998) J. Mol. Biol. , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 62
    • 70350776501 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the conformational changes in signal transducers and activators of transcription, Stat1 and Stat3
    • Lin, J.; Buettner, R.; Yuan, Y. C.; Yip, R.; Horne, D.; Jove, R.; Vaidehi, N. Molecular dynamics simulations of the conformational changes in signal transducers and activators of transcription, Stat1 and Stat3 J. Mol. Graphics Modell. 2009, 28, 347-356
    • (2009) J. Mol. Graphics Modell. , vol.28 , pp. 347-356
    • Lin, J.1    Buettner, R.2    Yuan, Y.C.3    Yip, R.4    Horne, D.5    Jove, R.6    Vaidehi, N.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.