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Volumn 49, Issue 2, 2009, Pages 377-389

Identifying and characterizing binding sites and assessing druggability

Author keywords

[No Author keywords available]

Indexed keywords

LIGANDS;

EID: 65249117514     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci800324m     Document Type: Article
Times cited : (1277)

References (36)
  • 1
    • 0027053611 scopus 로고
    • A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
    • Levitt, D.; Banaszak, L. POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graphics 1992, 10, 229-243.
    • (1992) J. Mol. Graphics , vol.10 , pp. 229-243
    • Levitt, D.1    Banaszak2    POCKET, L.3
  • 2
    • 0028881975 scopus 로고
    • SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • Laskowski, R. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graphics 1995, 13, 323-330.
    • (1995) J. Mol. Graphics , vol.13 , pp. 323-330
    • Laskowski, R.1
  • 3
    • 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
  • 4
    • 0031370977 scopus 로고    scopus 로고
    • LIGSITE: Automatic and efficient detection of potential small-molecule binding sites in proteins
    • Hendlich, M.; Rippmann, F.; Barnickel, G. LIGSITE: automatic and efficient detection of potential small-molecule binding sites in proteins. J. Mol. Graphics Modell. 1997, 15, 359-363.
    • (1997) J. Mol. Graphics Modell , vol.15 , pp. 359-363
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 5
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • Liang, J.; Edelsbrunner, H.; Woodward, C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 1998, 7, 1884-1897.
    • (1998) Protein Sci , vol.7 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 6
    • 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
  • 7
    • 0041989751 scopus 로고    scopus 로고
    • CASTp: Computed atlas of surface topography of proteins
    • Blinkowski, T.; 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
    • Blinkowski, T.1    Naghibzadeh, S.2    Liang, J.3
  • 8
    • 33750029942 scopus 로고    scopus 로고
    • CSC: Predicting ligand binding sites using the Connolly surface and degree of conservation
    • accessed June 11, 2007
    • CSC: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol [Online] 2006, 6. http://www.biomedcentral.com/1472-6807/ 6/ 19 (accessed June 11, 2007).
    • (2006) BMC Struct. Biol [Online] , vol.6
    • Huang, B.1    Schroeder, M.2
  • 9
    • 21044444449 scopus 로고    scopus 로고
    • Comprehensive identification and classification of ligand-binding envelopes
    • An, J.; Totrov, M.; Abagyan, R. 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
  • 10
    • 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 2006, 63, 892-906.
    • (2006) Proteins , vol.63 , pp. 892-906
    • Nayal, M.1    Honig, B.2
  • 11
    • 0037007068 scopus 로고    scopus 로고
    • Computational mapping identifies the binding sites of organic solvents on proteins
    • Dennis, S.; Kortvelyesi, T.; Vajda, S. Computational mapping identifies the binding sites of organic solvents on proteins. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 4290-4295.
    • (2002) Proc. Natl. Acad. Sci. U.S.A , vol.99 , pp. 4290-4295
    • Dennis, S.1    Kortvelyesi, T.2    Vajda, S.3
  • 13
    • 0030979125 scopus 로고    scopus 로고
    • Automatic identification and representation of protein binding sites for molecular docking
    • Ruppert, J.; Welch, W.; Jain, A. 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.3
  • 14
    • 0035970295 scopus 로고    scopus 로고
    • SuperStar: Improved knowledge-based interaction fields for protein binding sites
    • Verdonk, M. L.; Cole, J. C.; Watson, P.; Gillet, V.; Willett, P. SuperStar: improved knowledge-based interaction fields for protein binding sites. J. Mol. Biol. 2001, 307, 841-859, 2001.
    • (2001) J. Mol. Biol , vol.2001 , Issue.307 , pp. 841-859
    • Verdonk, M.L.1    Cole, J.C.2    Watson, P.3    Gillet, V.4    Willett, P.5
  • 15
    • 0000416633 scopus 로고    scopus 로고
    • Simple method for locating possible ligand binding sites on protein surfaces
    • Bliznyuk, A.; Gready, J. Simple method for locating possible ligand binding sites on protein surfaces. J. Comput. Chem. 1999, 9, 983-988.
    • (1999) J. Comput. Chem , vol.9 , pp. 983-988
    • Bliznyuk, A.1    Gready, J.2
  • 17
    • 33845806987 scopus 로고    scopus 로고
    • Structure-based identification of small molecule binding sites using a free-energy model
    • Coleman, R. G.; Salzberg, A.; Cheng, A. C. Structure-based identification of small molecule binding sites using a free-energy model. J. Chem. Inf. Model. 2006, 46, 2631-2637.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 2631-2637
    • Coleman, R.G.1    Salzberg, A.2    Cheng, A.C.3
  • 18
    • 11144245309 scopus 로고    scopus 로고
    • A computational method for the analysis and prediction of protein:phosphopeptide-binding sites
    • Joughin, B. A.; Tidor, B.; Yaffe, M. B. A computational method for the analysis and prediction of protein:phosphopeptide-binding sites. Protein Sci. 2005, 14, 131-139.
    • (2005) Protein Sci , vol.14 , pp. 131-139
    • Joughin, B.A.1    Tidor, B.2    Yaffe, M.B.3
  • 19
    • 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
  • 21
    • 84868925273 scopus 로고    scopus 로고
    • SiteMap, version 2.2 2008 update release, Schrödinger, LLC: Portland, OR, 2008. Maestro, version 8.5; Schrödinger, LLC: Portland, OR, 2008. QikProp, version 2.5; Schrödinger, LLC: Portland, OR, 2006. OPLS-2001; Schrödinger, LLC: Portland, OR, 2008
    • SiteMap, version 2.2 (2008 update release); Schrödinger, LLC: Portland, OR, 2008. Maestro, version 8.5; Schrödinger, LLC: Portland, OR, 2008. QikProp, version 2.5; Schrödinger, LLC: Portland, OR, 2006. OPLS-2001; Schrödinger, LLC: Portland, OR, 2008.
  • 22
    • 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
  • 23
    • 20444422149 scopus 로고    scopus 로고
    • Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. The PDBbind database: methodologies and updates. J. Med. Chem. 2005, 48, 4111-4119. PDBbind database, version 2004; University of Michigan: Ann Arbor, MI, 2005.
    • Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. The PDBbind database: methodologies and updates. J. Med. Chem. 2005, 48, 4111-4119. PDBbind database, version 2004; University of Michigan: Ann Arbor, MI, 2005.
  • 24
    • 65249168366 scopus 로고    scopus 로고
    • Wermuth, C. G. The Practice of Medicinal Chemistry, 2nd ed.; Academic Press: London, U.K. and San Diego, CA, 2003.
    • Wermuth, C. G. The Practice of Medicinal Chemistry, 2nd ed.; Academic Press: London, U.K. and San Diego, CA, 2003.
  • 25
    • 24944536065 scopus 로고    scopus 로고
    • Roehrig, S.; Straub, A.; Pohlman, J.; Lampe, T.; Pernerstorfer, J.; Schlemmer, K. H.; Reinemer, P.; Perzborn, E. Discovery of the novel antithrombotic agent 5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]- 1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide (BAY 59-7939): an oral, direct factor Xa inhibitor. J. Med. Chem. 2005, 48, 5900-5908. The crystallographic structure has been solved but does not appear to have been deposited. However, a factor Xa structure with a similar group in the S1 pocket has been deposited as PDB refcode lnfw.
    • Roehrig, S.; Straub, A.; Pohlman, J.; Lampe, T.; Pernerstorfer, J.; Schlemmer, K. H.; Reinemer, P.; Perzborn, E. Discovery of the novel antithrombotic agent 5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]- 1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide (BAY 59-7939): an oral, direct factor Xa inhibitor. J. Med. Chem. 2005, 48, 5900-5908. The crystallographic structure has been solved but does not appear to have been deposited. However, a factor Xa structure with a similar group in the S1 pocket has been deposited as PDB refcode lnfw.
  • 26
    • 35848929515 scopus 로고    scopus 로고
    • Pinto, D. J. P.; Orwat, M. J.; Koch, S.; Rossi, K. A.; Alexander, R. S.; Smallwood, A.; Wong, P. C.; Rendina, A. R.; Luettgen, J. M.; Knabb, R. M.; He, K.; Xin, B.; Wexler, R. R.; Lam, P. Y. Discovery of l-(4-Methoxyphenyl)-7-oxo-6- (4-(2-oxopiperidin-l-yl)phenyl)-4,5,6,7-tet-rahydro-lH-pyrazolo[3,4-c] pyridine-3-carboxamide (Apixaban, BMS-562247), a highly potent, selective, efficacious, and orally bioavailable inhibitor of blood coagulation factor Xa. J. Med. Chem. 2007, 50, 5339-5356. The crystallographic structure is deposited as PDB refcode 2pl6.
    • Pinto, D. J. P.; Orwat, M. J.; Koch, S.; Rossi, K. A.; Alexander, R. S.; Smallwood, A.; Wong, P. C.; Rendina, A. R.; Luettgen, J. M.; Knabb, R. M.; He, K.; Xin, B.; Wexler, R. R.; Lam, P. Y. Discovery of l-(4-Methoxyphenyl)-7-oxo-6- (4-(2-oxopiperidin-l-yl)phenyl)-4,5,6,7-tet-rahydro-lH-pyrazolo[3,4-c] pyridine-3-carboxamide (Apixaban, BMS-562247), a highly potent, selective, efficacious, and orally bioavailable inhibitor of blood coagulation factor Xa. J. Med. Chem. 2007, 50, 5339-5356. The crystallographic structure is deposited as PDB refcode 2pl6.
  • 27
    • 42449113368 scopus 로고    scopus 로고
    • Karlsberg. http://agknapp.chemie.fu-berlin.de/karlsberg (accessed Aug 23, 2008). Kieseritzky, G.; Knapp, E. W. Optimizing pKa computation in proteins with pH adapted conformations. Proteins: Struct., Funct, Bioinf. 2008, 71, 1335-1348.
    • Karlsberg. http://agknapp.chemie.fu-berlin.de/karlsberg (accessed Aug 23, 2008). Kieseritzky, G.; Knapp, E. W. Optimizing pKa computation in proteins with pH adapted conformations. Proteins: Struct., Funct, Bioinf. 2008, 71, 1335-1348.
  • 28
    • 0037434510 scopus 로고    scopus 로고
    • Burgey, C. S, Robinson, K. A, Lyle, T. A, Sanderson, P. E, Lewis, S. D, Lucas, B. J, Krueger, J. A, Singh, R, Miller-Stein, C, White, R. B, Wong, B, Lyle, E. A, Williams, P. D, Coburn, C. A, Dorsey, B. D, Barrow, J. C, Stranieri, M. T, Holahan, M. A, Sitko, G. R, Cook, J. J, McMasters, D. R, McDonough, C. M, Sanders, W. M, Wallace, A. A, Clayton, F. C, Bohn, D, Leonard, Y. M, Detwiler, T. J, Jr, Lynch, J. J, Jr, Yan, Y, Chen, Z, Kuo, L, Gardell, S. J, Shafer, J. A, Vacca, J. P. Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines. J. Med. Chem. 2003, 46, 461-473. Crystallographic structures are deposited as PDB refcodes lmu6, lmu8, and lmue
    • Burgey, C. S.; Robinson, K. A.; Lyle, T. A.; Sanderson, P. E.; Lewis, S. D.; Lucas, B. J.; Krueger, J. A.; Singh, R.; Miller-Stein, C.; White, R. B.; Wong, B.; Lyle, E. A.; Williams, P. D.; Coburn, C. A.; Dorsey, B. D.; Barrow, J. C.; Stranieri, M. T.; Holahan, M. A.; Sitko, G. R.; Cook, J. J.; McMasters, D. R.; McDonough, C. M.; Sanders, W. M.; Wallace, A. A.; Clayton, F. C.; Bohn, D.; Leonard, Y. M.; Detwiler, T. J., Jr.; Lynch, J. J., Jr.; Yan, Y.; Chen, Z.; Kuo, L.; Gardell, S. J.; Shafer, J. A.; Vacca, J. P. Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines. J. Med. Chem. 2003, 46, 461-473. Crystallographic structures are deposited as PDB refcodes lmu6, lmu8, and lmue.
  • 29
    • 0025925104 scopus 로고
    • Design and synthesis of P2-Pl′-linked macrocyclic human renin inhibitors
    • Weber, A.; Halgren, T. A. Design and synthesis of P2-Pl′-linked macrocyclic human renin inhibitors. J. Med. Chem. 1991, 34, 2692-2701.
    • (1991) J. Med. Chem , vol.34 , pp. 2692-2701
    • Weber, A.1    Halgren, T.A.2
  • 30
    • 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
  • 32
    • 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
  • 34
    • 0031024171 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 Delivery Rev. 1997, 23, 3-25.
    • (1997) Adv. Drug Delivery Rev , vol.23 , pp. 3-25
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 35
    • 0035438391 scopus 로고    scopus 로고
    • Is there a difference between leads and drugs? A historical perspective
    • Oprea, T. I.; Davis, A. M.; Teague, S. J.; Leeson, P. D. Is there a difference between leads and drugs? A historical perspective. J. Chem. Inf. Model. 2001, 41, 1308-1315.
    • (2001) J. Chem. Inf. Model , vol.41 , pp. 1308-1315
    • Oprea, T.I.1    Davis, A.M.2    Teague, S.J.3    Leeson, P.D.4


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