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Volumn 53, Issue 6, 2013, Pages 1388-1405

Hydration properties of ligands and drugs in protein binding sites: Tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CONFORMATIONS; CRYSTAL STRUCTURE; EFFICIENCY; HYDRATION; LIGANDS; MOLECULES; PHYSICOCHEMICAL PROPERTIES; STRUCTURAL PROPERTIES;

EID: 84879563426     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci3005786     Document Type: Article
Times cited : (68)

References (111)
  • 1
    • 0003012148 scopus 로고    scopus 로고
    • How water provides the impetus for molecular recognition in aqueous solution
    • Lemieux, R. U. How water provides the impetus for molecular recognition in aqueous solution Acc. Chem. Res. 1996, 29, 373-380
    • (1996) Acc. Chem. Res. , vol.29 , pp. 373-380
    • Lemieux, R.U.1
  • 2
    • 0030471364 scopus 로고    scopus 로고
    • The role of water in sequence-independent ligand binding by an oligopeptide transporter protein
    • Tame, J. R. H.; Sleigh, S. H.; Wilkinson, A. J.; Ladbury, J. E. The role of water in sequence-independent ligand binding by an oligopeptide transporter protein Nat. Struct. Biol. 1996, 3, 998-1001
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 998-1001
    • Tame, J.R.H.1    Sleigh, S.H.2    Wilkinson, A.J.3    Ladbury, J.E.4
  • 3
    • 12344276782 scopus 로고    scopus 로고
    • The effect of water displacement on binding thermodynamics: Concanavalin A
    • Li, Z.; Lazaridis, T. The effect of water displacement on binding thermodynamics: concanavalin A J. Phys. Chem. B 2005, 109, 662-670
    • (2005) J. Phys. Chem. B , vol.109 , pp. 662-670
    • Li, Z.1    Lazaridis, T.2
  • 5
    • 67749099405 scopus 로고    scopus 로고
    • High-energy water sites determine peptide binding affinity and specificity of PDZ domains
    • Beuming, T.; Farid, R.; Sherman, W. High-energy water sites determine peptide binding affinity and specificity of PDZ domains Protein Sci. 2009, 18, 1609-1619
    • (2009) Protein Sci. , vol.18 , pp. 1609-1619
    • Beuming, T.1    Farid, R.2    Sherman, W.3
  • 6
    • 79952161696 scopus 로고    scopus 로고
    • Ligand binding to protein-binding pockets with wet and dry regions
    • Wang, L.; Berne, B. J.; Friesner, R. A. Ligand binding to protein-binding pockets with wet and dry regions Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 1326-1330
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , pp. 1326-1330
    • Wang, L.1    Berne, B.J.2    Friesner, R.A.3
  • 7
    • 77956583186 scopus 로고    scopus 로고
    • How can hydrophobic association be enthalpy driven?
    • Setny, P.; Baron, R.; McCammon, J. A. How can hydrophobic association be enthalpy driven? J. Chem. Theory Comput. 2010, 6, 2866-2871
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 2866-2871
    • Setny, P.1    Baron, R.2    McCammon, J.A.3
  • 8
    • 64049102289 scopus 로고    scopus 로고
    • Binding of small-molecule ligands to proteins: "What you see" is not always "what you get"
    • Mobley, D. L.; Dill, K. A. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get" Structure 2009, 17, 489-498
    • (2009) Structure , vol.17 , pp. 489-498
    • Mobley, D.L.1    Dill, K.A.2
  • 9
    • 33847655150 scopus 로고    scopus 로고
    • Calculation of water molecules in protein binding sites
    • Gilson, M. K.; Zhou, H.-X. Calculation of water molecules in protein binding sites J. Am. Chem. Soc. 2007, 129, 2577-2587
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 2577-2587
    • Gilson, M.K.1    Zhou, H.-X.2
  • 10
    • 3042592839 scopus 로고    scopus 로고
    • Hydration free energies and entropies for water in protein interiors
    • Olano, L. R.; Rick, S. W. Hydration free energies and entropies for water in protein interiors J. Am. Chem. Soc. 2004, 25, 7991-8000
    • (2004) J. Am. Chem. Soc. , vol.25 , pp. 7991-8000
    • Olano, L.R.1    Rick, S.W.2
  • 12
    • 84962336504 scopus 로고    scopus 로고
    • Microwave catalysis through rotationally hot reactive species
    • Bren, U.; Kržan, A.; Mavri, J. Microwave catalysis through rotationally hot reactive species J. Phys. Chem. A. 2008, 112, 166-171
    • (2008) J. Phys. Chem. A. , vol.112 , pp. 166-171
    • Bren, U.1    Kržan, A.2    Mavri, J.3
  • 13
    • 84863970196 scopus 로고    scopus 로고
    • Individual degrees of freedom and the solvation properties of water
    • Bren, U.; Janežič, D. Individual degrees of freedom and the solvation properties of water J. Chem. Phys. 2012, 137, 024108
    • (2012) J. Chem. Phys. , vol.137 , pp. 024108
    • Bren, U.1    Janežič, D.2
  • 14
    • 0742306902 scopus 로고    scopus 로고
    • Thermodynamic dissection of the binding energetics of proline-rich peptides to the Abl-SH3 domain: Implications for rational ligand design
    • Palencia, A.; Cobos, E. S.; Mateo, P. L.; Martinez, J. C.; Luque, I. Thermodynamic dissection of the binding energetics of proline-rich peptides to the Abl-SH3 domain: implications for rational ligand design J. Mol. Biol. 2004, 336, 527-537
    • (2004) J. Mol. Biol. , vol.336 , pp. 527-537
    • Palencia, A.1    Cobos, E.S.2    Mateo, P.L.3    Martinez, J.C.4    Luque, I.5
  • 16
    • 33747880625 scopus 로고    scopus 로고
    • A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: Conformational and hydration patterns
    • Vaiana, A. C.; Westhof, E.; Auffinger, P. A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns Biochimie 2006, 88, 1061-1073
    • (2006) Biochimie , vol.88 , pp. 1061-1073
    • Vaiana, A.C.1    Westhof, E.2    Auffinger, P.3
  • 17
    • 77953631827 scopus 로고    scopus 로고
    • A medicinal chemist's guide to molecular interactions
    • Bissantz, C.; Kuhn, B.; Stahl, M. A medicinal chemist's guide to molecular interactions J. Med. Chem. 2010, 53, 5061-5084
    • (2010) J. Med. Chem. , vol.53 , pp. 5061-5084
    • Bissantz, C.1    Kuhn, B.2    Stahl, M.3
  • 18
    • 80051775090 scopus 로고    scopus 로고
    • Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration
    • Genheden, S.; Mikulskis, P.; Hu, L. H.; Kongsted, J.; Soderhjelm, P.; Ryde, U. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration J. Am. Chem. Soc. 2011, 133, 13081-13092
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 13081-13092
    • Genheden, S.1    Mikulskis, P.2    Hu, L.H.3    Kongsted, J.4    Soderhjelm, P.5    Ryde, U.6
  • 19
    • 79957585828 scopus 로고    scopus 로고
    • Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases
    • Abel, R.; Salam, N. K.; Shelley, J.; Farid, R.; Friesner, R. A.; Sherman, W. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases ChemMedChem 2011, 6, 1049-1066
    • (2011) ChemMedChem , vol.6 , pp. 1049-1066
    • Abel, R.1    Salam, N.K.2    Shelley, J.3    Farid, R.4    Friesner, R.A.5    Sherman, W.6
  • 20
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Conte, L. 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
    • Conte, L.L.1    Chothia, C.2    Janin, J.3
  • 22
    • 84863812540 scopus 로고    scopus 로고
    • Ligand binding stepwise disrupts water network in thrombin: Enthalpic and entropic changes reveal classical hydrophobic effect
    • Biela, A.; Sielaff, F.; Terwesten, F.; Heine, A.; Steinmetzer, T.; Klebe, G. Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect J. Med. Chem. 2012, 55, 6094-6110
    • (2012) J. Med. Chem. , vol.55 , pp. 6094-6110
    • Biela, A.1    Sielaff, F.2    Terwesten, F.3    Heine, A.4    Steinmetzer, T.5    Klebe, G.6
  • 23
    • 84873351927 scopus 로고    scopus 로고
    • Dissecting the hydrophobic effect on the molecular level: The role of water, enthalpy, and entropy in ligand binding to thermolysin
    • Biela, A.; Nasief, N. N.; Betz, M.; Heine, A.; Hangauer, D.; Klebe, G. Dissecting the hydrophobic effect on the molecular level: The role of water, enthalpy, and entropy in ligand binding to thermolysin Angew. Chem., Int. Ed. 2013, 52, 1822-1828
    • (2013) Angew. Chem., Int. Ed. , vol.52 , pp. 1822-1828
    • Biela, A.1    Nasief, N.N.2    Betz, M.3    Heine, A.4    Hangauer, D.5    Klebe, G.6
  • 24
    • 33745199815 scopus 로고    scopus 로고
    • Virtual ligand screening: Strategies, perspectives and limitations
    • Klebe, G. Virtual ligand screening: strategies, perspectives and limitations Drug Discovery Today 2006, 11, 580-594
    • (2006) Drug Discovery Today , vol.11 , pp. 580-594
    • Klebe, G.1
  • 25
    • 34247187356 scopus 로고    scopus 로고
    • Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes
    • Lu, Y.; Wang, R.; Yang, C. -Y.; Wang, S. Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes J. Chem. Inf. Model. 2007, 47, 668-675
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 668-675
    • Lu, Y.1    Wang, R.2    Yang, C.-Y.3    Wang, S.4
  • 26
    • 0141907191 scopus 로고    scopus 로고
    • WaterScore: A novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes
    • García-Sosa, A. T.; Mancera, R. L.; Dean, P. M. WaterScore: A novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes J. Mol. Model 2003, 9, 172-182
    • (2003) J. Mol. Model , vol.9 , pp. 172-182
    • García-Sosa, A.T.1    Mancera, R.L.2    Dean, P.M.3
  • 27
    • 0033615637 scopus 로고    scopus 로고
    • Thermodynamic analyses reveal role of water release in epitope recognition by a monoclonal antibody against the human guanyl cyclase C receptor
    • Swaminathan, C. P.; Nandi, A.; Visweswariah, S. S.; Surolia, A. Thermodynamic analyses reveal role of water release in epitope recognition by a monoclonal antibody against the human guanyl cyclase C receptor J. Biol. Chem. 1999, 274, 31272-31278
    • (1999) J. Biol. Chem. , vol.274 , pp. 31272-31278
    • Swaminathan, C.P.1    Nandi, A.2    Visweswariah, S.S.3    Surolia, A.4
  • 29
    • 0032811591 scopus 로고    scopus 로고
    • Crystallographic and calorimetric analysis of peptide binding to OppA protein
    • Sleigh, S. H.; Seavers, P. R.; Wilkinson, A. J.; Ladbury, J. E.; Tame, J. R. H. Crystallographic and calorimetric analysis of peptide binding to OppA protein J. Mol. Biol. 1999, 291, 393-415
    • (1999) J. Mol. Biol. , vol.291 , pp. 393-415
    • Sleigh, S.H.1    Seavers, P.R.2    Wilkinson, A.J.3    Ladbury, J.E.4    Tame, J.R.H.5
  • 30
    • 33644764283 scopus 로고    scopus 로고
    • The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo design of CDK2 inhibitors
    • García-Sosa, A. T.; Mancera, R. L. The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo design of CDK2 inhibitors J. Mol. Model. 2006, 12, 422-431
    • (2006) J. Mol. Model. , vol.12 , pp. 422-431
    • García-Sosa, A.T.1    Mancera, R.L.2
  • 31
    • 20444381685 scopus 로고    scopus 로고
    • Including tightly-bound water molecules in de novo drug design. Exemplification through the in silico generation of poly(ADP-Ribose) polymerase ligands
    • García-Sosa, A. T.; Firth-Clark, S.; Mancera, R. L. Including tightly-bound water molecules in de novo drug design. Exemplification through the in silico generation of poly(ADP-Ribose) polymerase ligands J. Chem. Inf. Model. 2005, 45, 624-633
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 624-633
    • García-Sosa, A.T.1    Firth-Clark, S.2    Mancera, R.L.3
  • 32
    • 84867384558 scopus 로고    scopus 로고
    • Hydrophobic association and volume-confined water molecules
    • In, 1st ed. Gohlke, H. Wiley-VCH Verlag: Weinheim, Germany, Series: Methods and Principles in Medicinal Chemistry
    • Baron, R.; Setny, P.; McCammon, J. A. Hydrophobic association and volume-confined water molecules. In Protein-Ligand Interactions, 1st ed.; Gohlke, H., Ed.; Wiley-VCH Verlag: Weinheim, Germany, 2012; Series: Methods and Principles in Medicinal Chemistry.
    • (2012) Protein-Ligand Interactions
    • Baron, R.1    Setny, P.2    McCammon, J.A.3
  • 33
    • 0028228418 scopus 로고
    • The entropic cost of bound water in crystals and biomolecules
    • Dunitz, J. D. The entropic cost of bound water in crystals and biomolecules Science 1994, 264, 670
    • (1994) Science , vol.264 , pp. 670
    • Dunitz, J.D.1
  • 34
    • 0030442990 scopus 로고    scopus 로고
    • Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
    • Hooft, R. W. W.; Sander, C.; Vriend, G. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures Proteins: Struct., Funct., Genet. 1996, 26, 363-376
    • (1996) Proteins: Struct., Funct., Genet. , vol.26 , pp. 363-376
    • Hooft, R.W.W.1    Sander, C.2    Vriend, G.3
  • 35
    • 0030059689 scopus 로고    scopus 로고
    • Forces contributing to the conformational stability of proteins
    • Pace, N. N.; Shirley, B. A.; McNutt, M.; Gajiwala, K. Forces contributing to the conformational stability of proteins FASEB J. 1996, 10, 75-83
    • (1996) FASEB J. , vol.10 , pp. 75-83
    • Pace, N.N.1    Shirley, B.A.2    McNutt, M.3    Gajiwala, K.4
  • 36
    • 77956305291 scopus 로고    scopus 로고
    • Free energy, entropy, and enthalpy of a water molecule in various protein environments
    • Yu, H.; Rick, S. W. Free energy, entropy, and enthalpy of a water molecule in various protein environments J. Phys. Chem. B 2010, 114, 11552-11560
    • (2010) J. Phys. Chem. B , vol.114 , pp. 11552-11560
    • Yu, H.1    Rick, S.W.2
  • 37
    • 0031556719 scopus 로고    scopus 로고
    • Orientational disorder and entropy of water in protein cavities
    • Denisov, V. P.; Venu, K.; Peters, J.; Horlein, H. D.; Halle, B. Orientational disorder and entropy of water in protein cavities J. Phys. Chem. B 1997, 101, 9380-9389
    • (1997) J. Phys. Chem. B , vol.101 , pp. 9380-9389
    • Denisov, V.P.1    Venu, K.2    Peters, J.3    Horlein, H.D.4    Halle, B.5
  • 38
    • 0031592453 scopus 로고    scopus 로고
    • Predicting conserved water-mediated and polar ligand interactions and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm
    • Raymer, M. L.; Sanschagrin, P. C.; Punch, W. F.; Venkataraman, S.; Goodman, E. D.; Kuhn, L. A. Predicting conserved water-mediated and polar ligand interactions and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm J. Mol. Biol. 1997, 265, 445-464
    • (1997) J. Mol. Biol. , vol.265 , pp. 445-464
    • Raymer, M.L.1    Sanschagrin, P.C.2    Punch, W.F.3    Venkataraman, S.4    Goodman, E.D.5    Kuhn, L.A.6
  • 39
    • 33847655150 scopus 로고    scopus 로고
    • Classification of water molecules in protein binding suites
    • Barillari, C.; Taylor, J.; Viner, R.; Essex, J. W. Classification of water molecules in protein binding suites J. Am. Chem. Soc. 2007, 129, 2577-2587
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 2577-2587
    • Barillari, C.1    Taylor, J.2    Viner, R.3    Essex, J.W.4
  • 40
    • 0001700714 scopus 로고    scopus 로고
    • Inhomogeneous fluid approach to solvation thermodynamics. 1. Theory
    • Lazaridis, T. Inhomogeneous fluid approach to solvation thermodynamics. 1. Theory J. Phys. Chem. B 1998, 102, 3531-3541
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3531-3541
    • Lazaridis, T.1
  • 41
    • 33846524439 scopus 로고    scopus 로고
    • Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding
    • Young, T.; Abel, R.; Kim, B.; Berne, B. J.; Friesner, R. A. Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 808-813
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 808-813
    • Young, T.1    Abel, R.2    Kim, B.3    Berne, B.J.4    Friesner, R.A.5
  • 42
    • 40949163431 scopus 로고    scopus 로고
    • Role of the active-site solvent in the thermodynamics of factor Xa ligand binding
    • Abel, R.; Young, T.; Farid, R.; Berne, B. J.; Friessner, R. A. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding J. Am. Chem. Soc. 2008, 130, 2817-2831
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 2817-2831
    • Abel, R.1    Young, T.2    Farid, R.3    Berne, B.J.4    Friessner, R.A.5
  • 43
    • 77951997162 scopus 로고    scopus 로고
    • Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations
    • Guimaraes, C. R.; Mathiowetz, A. M. Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations J. Chem. Inf. Model 2010, 50, 547-559
    • (2010) J. Chem. Inf. Model , vol.50 , pp. 547-559
    • Guimaraes, C.R.1    Mathiowetz, A.M.2
  • 45
    • 77950022453 scopus 로고    scopus 로고
    • Non-additivity of functional group contributions in protein-ligand binding: A comprehensive study by crystallography and isothermal titration calorimetry
    • Baum, B.; Muley, L.; Smolinski, M.; Heine, A.; Hangauer, D.; Klebe, G. Non-additivity of functional group contributions in protein-ligand binding: A comprehensive study by crystallography and isothermal titration calorimetry J. Mol. Biol. 2010, 397, 1042-1054
    • (2010) J. Mol. Biol. , vol.397 , pp. 1042-1054
    • Baum, B.1    Muley, L.2    Smolinski, M.3    Heine, A.4    Hangauer, D.5    Klebe, G.6
  • 46
    • 78650214391 scopus 로고    scopus 로고
    • Free energy calculations of mutations involving a tightly bound water molecule and ligand substitutions in a ligand-protein complex
    • García-Sosa, A. T.; Mancera, R. L. Free energy calculations of mutations involving a tightly bound water molecule and ligand substitutions in a ligand-protein complex Mol. Inf. 2010, 29, 589-600
    • (2010) Mol. Inf. , vol.29 , pp. 589-600
    • García-Sosa, A.T.1    Mancera, R.L.2
  • 48
    • 4344593122 scopus 로고    scopus 로고
    • The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models
    • Lloyd, D. G.; García-Sosa, A. T.; Alberts, I. L.; Todorov, N. P.; Mancera, R. L. The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models J. Comput.-Aided Mol. Des. 2004, 18, 89-100
    • (2004) J. Comput.-Aided Mol. Des. , vol.18 , pp. 89-100
    • Lloyd, D.G.1    García-Sosa, A.T.2    Alberts, I.L.3    Todorov, N.P.4    Mancera, R.L.5
  • 49
    • 80054892853 scopus 로고    scopus 로고
    • Combined approach using ligand efficiency, cross-docking, and antitarget hits for wild-type and drug-resistant Y181C HIV-1 reverse transcriptase
    • García-Sosa, A. T.; Sild, S.; Takkis, K.; Maran, U. Combined approach using ligand efficiency, cross-docking, and antitarget hits for wild-type and drug-resistant Y181C HIV-1 reverse transcriptase J. Chem. Inf. Model. 2011, 51, 2595-2611
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2595-2611
    • García-Sosa, A.T.1    Sild, S.2    Takkis, K.3    Maran, U.4
  • 50
    • 0032961895 scopus 로고    scopus 로고
    • The particle concept: Placing discrete water molecules during protein-ligand docking predictions
    • Rarey, M.; Kramer, B.; Lengauer, T. The particle concept: placing discrete water molecules during protein-ligand docking predictions Proteins: Struct., Funct., Bioinf. 1999, 34, 17-28
    • (1999) Proteins: Struct., Funct., Bioinf. , vol.34 , pp. 17-28
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 52
    • 70349683018 scopus 로고    scopus 로고
    • Prediction of the water content in protein binding sites
    • Michel, J.; Tirado-Rives, J.; Jorgensen, W. L. Prediction of the water content in protein binding sites J. Phys. Chem. B 2010, 113, 13337-13346
    • (2010) J. Phys. Chem. B , vol.113 , pp. 13337-13346
    • Michel, J.1    Tirado-Rives, J.2    Jorgensen, W.L.3
  • 53
    • 84857748866 scopus 로고    scopus 로고
    • Rapid and accurate prediction and scoring of water molecules in protein binding sites
    • Ross, G. A.; Morris, G. M.; Biggin, P. C. Rapid and accurate prediction and scoring of water molecules in protein binding sites PLoS One 2012, 7, e32036
    • (2012) PLoS One , vol.7 , pp. 32036
    • Ross, G.A.1    Morris, G.M.2    Biggin, P.C.3
  • 54
    • 80052654567 scopus 로고    scopus 로고
    • Systematic placement of structural water molecules for improved scoring of protein-ligand interactions
    • Huggins, D. J.; Tidor, B. Systematic placement of structural water molecules for improved scoring of protein-ligand interactions Protein Eng., Des. Sel. 2011, 24, 777-789
    • (2011) Protein Eng., Des. Sel. , vol.24 , pp. 777-789
    • Huggins, D.J.1    Tidor, B.2
  • 55
    • 34547774584 scopus 로고    scopus 로고
    • Prediction of solvation sites at the interface of src SH2 domain complexes using molecular dynamics simulations
    • Geroult, S.; Hooda, M.; Virdee, S.; Waksman, G. Prediction of solvation sites at the interface of src SH2 domain complexes using molecular dynamics simulations Chem. Biol. Drug Des. 2007, 70, 87-99
    • (2007) Chem. Biol. Drug Des. , vol.70 , pp. 87-99
    • Geroult, S.1    Hooda, M.2    Virdee, S.3    Waksman, G.4
  • 56
    • 2942659093 scopus 로고    scopus 로고
    • Standard free energy of releasing a localized water molecule from the binding pockets of protein: Double-decoupling method
    • Hamelberg, D.; McCammon, J. A. Standard free energy of releasing a localized water molecule from the binding pockets of protein: double-decoupling method J. Am. Chem. Soc. 2004, 24, 7683-7689
    • (2004) J. Am. Chem. Soc. , vol.24 , pp. 7683-7689
    • Hamelberg, D.1    McCammon, J.A.2
  • 57
    • 0032054675 scopus 로고    scopus 로고
    • Computational alchemy to calculate absolute protein-ligand binding free energy
    • Helms, V.; Wade, R. C. Computational alchemy to calculate absolute protein-ligand binding free energy J. Am. Chem. Soc. 1998, 120, 2710-2713
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 2710-2713
    • Helms, V.1    Wade, R.C.2
  • 59
    • 50249094315 scopus 로고    scopus 로고
    • Exploiting ordered waters in molecular docking
    • Huang, N.; Shoichet, B. K. Exploiting ordered waters in molecular docking J. Med. Chem. 2008, 51, 4862-4865
    • (2008) J. Med. Chem. , vol.51 , pp. 4862-4865
    • Huang, N.1    Shoichet, B.K.2
  • 61
    • 70449558129 scopus 로고    scopus 로고
    • Molecular recognition at the active site of the catechol-o- methyltransferase: Energetically favorable replacement of a water molecule imported by a bisubstrate inhibitor
    • Ellermann, M.; Jakob-Roetne, R.; Lerner, C.; Borroni, E.; Schlatter, D.; Roth, D.; Ehler, A.; Rudolph, M. G.; Diederich, F. Molecular recognition at the active site of the catechol-o-methyltransferase: energetically favorable replacement of a water molecule imported by a bisubstrate inhibitor Angew. Chem., Int. Ed. 2009, 48, 9092-9096
    • (2009) Angew. Chem., Int. Ed. , vol.48 , pp. 9092-9096
    • Ellermann, M.1    Jakob-Roetne, R.2    Lerner, C.3    Borroni, E.4    Schlatter, D.5    Roth, D.6    Ehler, A.7    Rudolph, M.G.8    Diederich, F.9
  • 62
    • 84856397848 scopus 로고    scopus 로고
    • A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking
    • Forli, S.; Olson, A. J. A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking J. Med. Chem. 2012, 55, 623-638
    • (2012) J. Med. Chem. , vol.55 , pp. 623-638
    • Forli, S.1    Olson, A.J.2
  • 63
    • 80052010268 scopus 로고    scopus 로고
    • AcquaAlta: A directional approach to the solvation of ligand-protein complexes
    • Rossato, G.; Ernst, B.; Vedani, A.; Smiesko, M. AcquaAlta: a directional approach to the solvation of ligand-protein complexes J. Chem. Inf. Model. 2011, 51, 1867-1881
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 1867-1881
    • Rossato, G.1    Ernst, B.2    Vedani, A.3    Smiesko, M.4
  • 64
    • 79958143460 scopus 로고    scopus 로고
    • Modulators of protein-protein interactions - Novel approaches in targeting protein kinases and other pharmaceutically relevant biomolecules
    • Rechfeld, F.; Gruber, P.; Hofmann, J.; Kirchmair, J. Modulators of protein-protein interactions-novel approaches in targeting protein kinases and other pharmaceutically relevant biomolecules Curr. Top. Med. Chem. 2011, 11, 1305-1319
    • (2011) Curr. Top. Med. Chem. , vol.11 , pp. 1305-1319
    • Rechfeld, F.1    Gruber, P.2    Hofmann, J.3    Kirchmair, J.4
  • 65
    • 84861118556 scopus 로고    scopus 로고
    • Outstanding challenges in protein-ligand docking and structure-based virtual screening
    • Waszkowycz, B.; Clark, D. E.; Gancia, E. Outstanding challenges in protein-ligand docking and structure-based virtual screening Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 229-259
    • (2011) Wiley Interdiscip. Rev.: Comput. Mol. Sci. , vol.1 , pp. 229-259
    • Waszkowycz, B.1    Clark, D.E.2    Gancia, E.3
  • 67
    • 48749127628 scopus 로고    scopus 로고
    • What has virtual screening ever done for drug discovery?
    • Clark, D. E. What has virtual screening ever done for drug discovery? Expert Opin. Drug Discovery 2008, 3, 841-851
    • (2008) Expert Opin. Drug Discovery , vol.3 , pp. 841-851
    • Clark, D.E.1
  • 68
    • 52949093889 scopus 로고    scopus 로고
    • Structural and kinetic analysis of pyrrolidine-based inhibitors of the drug-resistant Ile84Val mutant of HIV-1 protease
    • Bottcher, J.; Blum, A.; Heine, A.; Diederich, W. E.; Klebe, G. Structural and kinetic analysis of pyrrolidine-based inhibitors of the drug-resistant Ile84Val mutant of HIV-1 protease J. Mol. Biol. 2008, 383, 347-357
    • (2008) J. Mol. Biol. , vol.383 , pp. 347-357
    • Bottcher, J.1    Blum, A.2    Heine, A.3    Diederich, W.E.4    Klebe, G.5
  • 69
    • 49449105293 scopus 로고    scopus 로고
    • AIScore - Chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes
    • Raub, S.; Steffen, A.; Kamper, A.; Marian, C. M. AIScore-chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes J. Chem. Inf. Model. 2008, 48, 1492-1510
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1492-1510
    • Raub, S.1    Steffen, A.2    Kamper, A.3    Marian, C.M.4
  • 72
    • 84879579915 scopus 로고    scopus 로고
    • Structure-based drug design: Docking and scoring
    • Kroemer, R. T. Structure-based drug design: docking and scoring Curr. Protein. Pept. Sci. 2007, 50, 5712-5719
    • (2007) Curr. Protein. Pept. Sci. , vol.50 , pp. 5712-5719
    • Kroemer, R.T.1
  • 73
    • 33646165863 scopus 로고    scopus 로고
    • Determination of the interfacial water content in protein-protein complexes from free energy simulations
    • Monecke, P.; Borosch, T.; Brickmann, R.; Kast, S. M. Determination of the interfacial water content in protein-protein complexes from free energy simulations Biophys. J. 2006, 3, 841-850
    • (2006) Biophys. J. , vol.3 , pp. 841-850
    • Monecke, P.1    Borosch, T.2    Brickmann, R.3    Kast, S.M.4
  • 74
  • 75
    • 10644222723 scopus 로고    scopus 로고
    • The role of virtual screening in computer-aided structure-based drug design
    • Branson, K. M.; Smith, B. J. The role of virtual screening in computer-aided structure-based drug design Aust. J. Chem. 2004, 57, 1029-1037
    • (2004) Aust. J. Chem. , vol.57 , pp. 1029-1037
    • Branson, K.M.1    Smith, B.J.2
  • 76
    • 83455200053 scopus 로고    scopus 로고
    • A role for hydration in interleukin-2 inducible T cell kinase (lth) selectivity
    • Knegtel, R. M. A.; Robinson, D. D. A role for hydration in interleukin-2 inducible T cell kinase (lth) selectivity Mol. Inf. 2011, 30, 950-959
    • (2011) Mol. Inf. , vol.30 , pp. 950-959
    • Knegtel, R.M.A.1    Robinson, D.D.2
  • 77
    • 77949345618 scopus 로고    scopus 로고
    • Computational approaches for fragment-based and de novo design
    • Loving, K.; Alberts, I.; Sherman, W. Computational approaches for fragment-based and de novo design Curr. Top. Med. Chem. 2010, 10, 14-32
    • (2010) Curr. Top. Med. Chem. , vol.10 , pp. 14-32
    • Loving, K.1    Alberts, I.2    Sherman, W.3
  • 78
    • 79955419410 scopus 로고    scopus 로고
    • Synopsis of some recent tactical application of bioisosteres in drug design
    • Meanwell, N. A. Synopsis of some recent tactical application of bioisosteres in drug design J. Med. Chem. 2011, 54, 2529-2591
    • (2011) J. Med. Chem. , vol.54 , pp. 2529-2591
    • Meanwell, N.A.1
  • 79
    • 77954787493 scopus 로고    scopus 로고
    • De novo design: Balancing novelty and continued chemical space
    • Kutchukian, P. S.; Shakhnovich, E. I. De novo design: balancing novelty and continued chemical space Expert Opin. Drug Discovery 2010, 5, 789-812
    • (2010) Expert Opin. Drug Discovery , vol.5 , pp. 789-812
    • Kutchukian, P.S.1    Shakhnovich, E.I.2
  • 80
    • 38949121610 scopus 로고    scopus 로고
    • Cluster analysis of hydration waters around the active sites of bacterial alanine racemase using a 2-ns MD simulation
    • Huang, H. C.; Jupiter, D.; Qiu, M.; Briggs, J. M.; VanBuren, V. Cluster analysis of hydration waters around the active sites of bacterial alanine racemase using a 2-ns MD simulation Biopolymers 2008, 89, 210-219
    • (2008) Biopolymers , vol.89 , pp. 210-219
    • Huang, H.C.1    Jupiter, D.2    Qiu, M.3    Briggs, J.M.4    Vanburen, V.5
  • 81
    • 84873635524 scopus 로고    scopus 로고
    • Water PMF for predicting the properties of water molecules in protein binding site
    • Zheng, M.; Li, Y.; Xiong, B.; Jiang, H.; Shen, J. Water PMF for predicting the properties of water molecules in protein binding site J. Comput. Chem. 2013, 34, 583-592
    • (2013) J. Comput. Chem. , vol.34 , pp. 583-592
    • Zheng, M.1    Li, Y.2    Xiong, B.3    Jiang, H.4    Shen, J.5
  • 82
    • 77949443500 scopus 로고    scopus 로고
    • Polarizable water molecules in ligand-macromolecule recognition. Impact on the relative affinities of competing pyrrolopyrimidine inhibitors for FAK kinase
    • de Courcy, B.; Piquemal, J.-P.; Garbay, C.; Gresh, N. Polarizable water molecules in ligand-macromolecule recognition. Impact on the relative affinities of competing pyrrolopyrimidine inhibitors for FAK kinase J. Am. Chem. Soc. 2010, 132, 3312-3320
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 3312-3320
    • De Courcy, B.1    Piquemal, J.-P.2    Garbay, C.3    Gresh, N.4
  • 83
    • 79959561253 scopus 로고    scopus 로고
    • Polarizable water networks in ligand-metalloprotein recognition. Impact on the relative complexation energies of Zn-dependent phosphomannose isomerase with D-mannose 6-phosphate surrogates
    • Gresh, N.; de Courcy, B.; Piquemal, J.-P.; Foret, J.; Courtiol-Legourd, S.; Salmon, L. Polarizable water networks in ligand-metalloprotein recognition. Impact on the relative complexation energies of Zn-dependent phosphomannose isomerase with D-mannose 6-phosphate surrogates J. Phys. Chem. B 2011, 115, 8304-8316
    • (2011) J. Phys. Chem. B , vol.115 , pp. 8304-8316
    • Gresh, N.1    De Courcy, B.2    Piquemal, J.-P.3    Foret, J.4    Courtiol-Legourd, S.5    Salmon, L.6
  • 84
    • 36649014257 scopus 로고    scopus 로고
    • Synthesis of urea picket porphyrins and their use in the education of the role buried solvent plays in the selectivity and stoichiometry of anion binding receptors
    • Calderon-Kawasaki, K.; Kularatne, S.; Li, Y. H.; Noll, B. C.; Scheidt, W. R.; Burns, D. H. Synthesis of urea picket porphyrins and their use in the education of the role buried solvent plays in the selectivity and stoichiometry of anion binding receptors J. Org. Chem. 2007, 72, 9081-9087
    • (2007) J. Org. Chem. , vol.72 , pp. 9081-9087
    • Calderon-Kawasaki, K.1    Kularatne, S.2    Li, Y.H.3    Noll, B.C.4    Scheidt, W.R.5    Burns, D.H.6
  • 85
    • 0029134561 scopus 로고
    • The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: Synthesis, biological activity, and crystallographic analysis with cyclophilin A
    • Mikol, V.; Papageorgiou, C.; Borer, X. The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: synthesis, biological activity, and crystallographic analysis with cyclophilin A J. Med. Chem. 1995, 38, 3361-3367
    • (1995) J. Med. Chem. , vol.38 , pp. 3361-3367
    • Mikol, V.1    Papageorgiou, C.2    Borer, X.3
  • 86
    • 34247559015 scopus 로고    scopus 로고
    • Structure-based design and synthesis of Nw-nitro-L-arginine-containing peptidomimetics as selective inhibitors of neuronal nitric oxide synthase. Displacement of the heme structural water
    • Seo, J.; Igarashi, J.; Li, H.; Martásek, P.; Roman, L. J.; Poulos, T. L.; Silverman, R. B. Structure-based design and synthesis of Nw-nitro-L-arginine-containing peptidomimetics as selective inhibitors of neuronal nitric oxide synthase. Displacement of the heme structural water J. Med. Chem. 2007, 50, 2089-2099
    • (2007) J. Med. Chem. , vol.50 , pp. 2089-2099
    • Seo, J.1    Igarashi, J.2    Li, H.3    Martásek, P.4    Roman, L.J.5    Poulos, T.L.6    Silverman, R.B.7
  • 90
    • 84860359784 scopus 로고    scopus 로고
    • Finding the sweet spot: The role of nature and nurture in medicinal chemistry
    • Hann, M. M.; Keserü, G. M. Finding the sweet spot: the role of nature and nurture in medicinal chemistry Nat. Rev. Drug Discovery 2012, 11, 355-365
    • (2012) Nat. Rev. Drug Discovery , vol.11 , pp. 355-365
    • Hann, M.M.1    Keserü, G.M.2
  • 91
    • 77952849162 scopus 로고    scopus 로고
    • ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
    • Konc, J.; Janežič, D. ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment Bioinformatics 2010, 26, 1160-1168
    • (2010) Bioinformatics , vol.26 , pp. 1160-1168
    • Konc, J.1    Janežič, D.2
  • 93
    • 1942453243 scopus 로고    scopus 로고
    • Ligand efficiency: A useful metric for lead selection
    • Hopkins, A. L.; Groom, C. R. Ligand efficiency: a useful metric for lead selection Drug Discovery Today 2004, 9, 430-431
    • (2004) Drug Discovery Today , vol.9 , pp. 430-431
    • Hopkins, A.L.1    Groom, C.R.2
  • 95
    • 56449084239 scopus 로고    scopus 로고
    • Design of multi-binding-site inhibitors, ligand efficiency, and consensus screening of avian influenza H5N1 wild-type neuraminidase and of the oseltamivir-resistant H274Y variant
    • García-Sosa, A. T.; Sild, S.; Maran, U. Design of multi-binding-site inhibitors, ligand efficiency, and consensus screening of avian influenza H5N1 wild-type neuraminidase and of the oseltamivir-resistant H274Y variant J. Chem. Inf. Model. 2008, 48, 2074-2080
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 2074-2080
    • García-Sosa, A.T.1    Sild, S.2    Maran, U.3
  • 96
    • 70350370859 scopus 로고    scopus 로고
    • Docking and virtual screening using distributed grid technology
    • García-Sosa, A. T.; Sild, S.; Maran, U. Docking and virtual screening using distributed grid technology QSAR Comb. Sci. 2009, 28, 815-821
    • (2009) QSAR Comb. Sci. , vol.28 , pp. 815-821
    • García-Sosa, A.T.1    Sild, S.2    Maran, U.3
  • 97
    • 72449144245 scopus 로고    scopus 로고
    • Drug efficiency indices for improvement of molecular docking scoring functions
    • García-Sosa, A. T.; Hetényi, C.; Maran, U. Drug efficiency indices for improvement of molecular docking scoring functions J. Comput. Chem. 2010, 31, 174-184
    • (2010) J. Comput. Chem. , vol.31 , pp. 174-184
    • García-Sosa, A.T.1    Hetényi, C.2    Maran, U.3
  • 98
    • 84865457697 scopus 로고    scopus 로고
    • DrugLogit: Logistic discrimination between drugs and nondrugs including disease-specificity by assigning probabilities based on molecular properties
    • García-Sosa, A. T.; Oja, M.; Hetényi, C.; Maran, U. DrugLogit: Logistic discrimination between drugs and nondrugs including disease-specificity by assigning probabilities based on molecular properties J. Chem. Inf. Model. 2012, 52, 2165-2180
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2165-2180
    • García-Sosa, A.T.1    Oja, M.2    Hetényi, C.3    Maran, U.4
  • 99
    • 20444422149 scopus 로고    scopus 로고
    • The PDBBind database: Methodologies and updates
    • Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. The PDBBind database: methodologies and updates J. Med. Chem. 2005, 48, 4111-4119
    • (2005) J. Med. Chem. , vol.48 , pp. 4111-4119
    • Wang, R.1    Fang, X.2    Lu, Y.3    Yang, C.-Y.4    Wang, S.5
  • 100
    • 84860506903 scopus 로고    scopus 로고
    • Molecular property filters describing pharmacokinetics and drug binding
    • García-Sosa, A. T.; Maran, U.; Hetényi, C. Molecular property filters describing pharmacokinetics and drug binding Curr. Med. Chem. 2012, 19, 1646-1662
    • (2012) Curr. Med. Chem. , vol.19 , pp. 1646-1662
    • García-Sosa, A.T.1    Maran, U.2    Hetényi, C.3
  • 101
    • 84860505355 scopus 로고    scopus 로고
    • Disease-specific differentiation between drugs and non-drugs using principal component analysis of their molecular descriptor space
    • García-Sosa, A. T.; Oja, M.; Hetényi, C.; Maran, U. Disease-specific differentiation between drugs and non-drugs using principal component analysis of their molecular descriptor space Mol. Inf. 2012, 31, 369-383
    • (2012) Mol. Inf. , vol.31 , pp. 369-383
    • García-Sosa, A.T.1    Oja, M.2    Hetényi, C.3    Maran, U.4
  • 102
    • 84891510691 scopus 로고    scopus 로고
    • Drugs, non-drugs, and disease category specificity: Organ effects by ligand pharmacology
    • [online] DOI: http://dx.doi.org/ 10.1080/1062936X.2013.773373
    • García-Sosa, A. T.; Maran, U. Drugs, non-drugs, and disease category specificity: organ effects by ligand pharmacology. SAR QSAR Environ. Res. 2013, [online] DOI: http://dx.doi.org/ 10.1080/1062936X.2013.773373.
    • (2013) SAR QSAR Environ. Res.
    • García-Sosa, A.T.1    Maran, U.2
  • 103
    • 52249114682 scopus 로고    scopus 로고
    • Limitations and lessons in the use of X-ray structural information in drug design
    • Davis, A. M.; St-Gallay, S. A.; Kleywegt, G. J. Limitations and lessons in the use of X-ray structural information in drug design Drug Discovery Today 2008, 13, 831-841
    • (2008) Drug Discovery Today , vol.13 , pp. 831-841
    • Davis, A.M.1    St-Gallay, S.A.2    Kleywegt, G.J.3
  • 104
    • 79961135005 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing: Vienna, Austria. (accessed January 1)
    • R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria. http://www.R-project.org (accessed January 1, 2011).
    • (2011) R: A Language and Environment for Statistical Computing
  • 107
    • 0033820007 scopus 로고    scopus 로고
    • Calculating partition coefficient by atom-additive method
    • Wang, R.; Gao, Y.; Lai, L. Calculating partition coefficient by atom-additive method Perspect. Drug Discovery Des. 2000, 19, 47-66
    • (2000) Perspect. Drug Discovery Des. , vol.19 , pp. 47-66
    • Wang, R.1    Gao, Y.2    Lai, L.3
  • 108
    • 79751507801 scopus 로고    scopus 로고
    • version 5.6.0.1; ChemAxon: Budapest, Hungary
    • Marvin Beans, version 5.6.0.1; ChemAxon: Budapest, Hungary, 2011.
    • (2011) Marvin Beans
  • 109
    • 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 Discovery 2007, 6, 881-890
    • (2007) Nat. Rev. Drug Discovery , vol.6 , pp. 881-890
    • Leeson, P.D.1    Springthorpe, B.2
  • 110
    • 65349195698 scopus 로고    scopus 로고
    • Molecular docking and ligand specificity in fragment-based inhibitor discovery
    • Chen, Y.; Shoichet, B. K. Molecular docking and ligand specificity in fragment-based inhibitor discovery Nat. Chem. Biol. 2009, 5, 358-364
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 358-364
    • Chen, Y.1    Shoichet, B.K.2
  • 111
    • 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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