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Volumn 60, Issue 13, 2017, Pages 5791-5799

Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; METALLOPROTEINASE INHIBITOR; THERMOLYSIN; THERMOLYSIN INHIBITOR; UNCLASSIFIED DRUG; ENZYME INHIBITOR;

EID: 85023759573     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/acs.jmedchem.7b00490     Document Type: Article
Times cited : (35)

References (36)
  • 1
    • 84857421328 scopus 로고    scopus 로고
    • Hydration Shells of Molecules in Molecular Association: A Mechanism for Biomolecular Recognition
    • Lim, V. I.; Curran, J. F.; Garber, M. B. Hydration Shells of Molecules in Molecular Association: A Mechanism for Biomolecular Recognition J. Theor. Biol. 2012, 301, 42-48 10.1016/j.jtbi.2012.02.008
    • (2012) J. Theor. Biol. , vol.301 , pp. 42-48
    • Lim, V.I.1    Curran, J.F.2    Garber, M.B.3
  • 2
    • 84916623121 scopus 로고    scopus 로고
    • Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase
    • Mondal, J.; Friesner, R. A.; Berne, B. J. Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase J. Chem. Theory Comput. 2014, 10, 5696-5705 10.1021/ct500584n
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 5696-5705
    • Mondal, J.1    Friesner, R.A.2    Berne, B.J.3
  • 3
    • 0008863560 scopus 로고
    • Some Factors in the Interpretation of Protein Denaturation
    • Kauzmann, W. Some Factors in the Interpretation of Protein Denaturation Adv. Protein Chem. 1959, 14, 1-63 10.1016/S0065-3233(08)60608-7
    • (1959) Adv. Protein Chem. , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 4
    • 67449084506 scopus 로고    scopus 로고
    • Dewetting and Hydrophobic Interaction in Physical and Biological Systems
    • Berne, B. J.; Weeks, J. D.; Zhou, R. Dewetting and Hydrophobic Interaction in Physical and Biological Systems Annu. Rev. Phys. Chem. 2009, 60, 85-103 10.1146/annurev.physchem.58.032806.104445
    • (2009) Annu. Rev. Phys. Chem. , vol.60 , pp. 85-103
    • Berne, B.J.1    Weeks, J.D.2    Zhou, R.3
  • 5
    • 34447108978 scopus 로고    scopus 로고
    • Water, Water Everywhere - Except Where It Matters?
    • Homans, S. W. Water, Water Everywhere-except Where It Matters? Drug Discovery Today 2007, 12, 534-539 10.1016/j.drudis.2007.05.004
    • (2007) Drug Discovery Today , vol.12 , pp. 534-539
    • Homans, S.W.1
  • 8
    • 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 10.1021/ct1003077
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 2866-2871
    • Setny, P.1    Baron, R.2    McCammon, J.A.3
  • 9
    • 84985995059 scopus 로고    scopus 로고
    • Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces
    • Haider, K.; Wickstrom, L.; Ramsey, S.; Gilson, M. K.; Kurtzman, T. Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces J. Phys. Chem. B 2016, 120, 8743-8756 10.1021/acs.jpcb.6b01094
    • (2016) J. Phys. Chem. B , vol.120 , pp. 8743-8756
    • Haider, K.1    Wickstrom, L.2    Ramsey, S.3    Gilson, M.K.4    Kurtzman, T.5
  • 10
    • 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 10.1002/anie.201208561
    • (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
  • 11
    • 84898006931 scopus 로고    scopus 로고
    • Methyl, Ethyl, Propyl, Butyl: Futile but Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors
    • Krimmer, S. G.; Betz, M.; Heine, A.; Klebe, G. Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors ChemMedChem 2014, 9, 833-846 10.1002/cmdc.201400013
    • (2014) ChemMedChem , vol.9 , pp. 833-846
    • Krimmer, S.G.1    Betz, M.2    Heine, A.3    Klebe, G.4
  • 12
    • 85003422164 scopus 로고    scopus 로고
    • Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands
    • Krimmer, S. G.; Cramer, J.; Betz, M.; Fridh, V.; Karlsson, R.; Heine, A.; Klebe, G. Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands J. Med. Chem. 2016, 59, 10530-10548 10.1021/acs.jmedchem.6b00998
    • (2016) J. Med. Chem. , vol.59 , pp. 10530-10548
    • Krimmer, S.G.1    Cramer, J.2    Betz, M.3    Fridh, V.4    Karlsson, R.5    Heine, A.6    Klebe, G.7
  • 13
    • 84867342383 scopus 로고    scopus 로고
    • Water Mediated Ligand Functional Group Cooperativity: The Contribution of a Methyl Group to Binding Affinity Is Enhanced by a COO- Group Through Changes in the Structure and Thermodynamics of the Hydration Waters of Ligand-Thermolysin Complexes
    • Nasief, N. N.; Tan, H.; Kong, J.; Hangauer, D. Water Mediated Ligand Functional Group Cooperativity: The Contribution of a Methyl Group to Binding Affinity Is Enhanced by a COO- Group Through Changes in the Structure and Thermodynamics of the Hydration Waters of Ligand-Thermolysin Complexes J. Med. Chem. 2012, 55, 8283-8302 10.1021/jm300472k
    • (2012) J. Med. Chem. , vol.55 , pp. 8283-8302
    • Nasief, N.N.1    Tan, H.2    Kong, J.3    Hangauer, D.4
  • 14
    • 84897471228 scopus 로고    scopus 로고
    • Influence of Neighboring Groups on the Thermodynamics of Hydrophobic Binding: An Added Complex Facet to the Hydrophobic Effect
    • Nasief, N. N.; Hangauer, D. Influence of Neighboring Groups on the Thermodynamics of Hydrophobic Binding: An Added Complex Facet to the Hydrophobic Effect J. Med. Chem. 2014, 57, 2315-2333 10.1021/jm401609a
    • (2014) J. Med. Chem. , vol.57 , pp. 2315-2333
    • Nasief, N.N.1    Hangauer, D.2
  • 15
    • 84900498772 scopus 로고    scopus 로고
    • Is It the Shape of the Cavity, or the Shape of the Water in the Cavity?
    • Snyder, P. W.; Lockett, M. R.; Moustakas, D. T.; Whitesides, G. M. Is It the Shape of the Cavity, or the Shape of the Water in the Cavity? Eur. Phys. J.: Spec. Top. 2014, 223, 853-891 10.1140/epjst/e2013-01818-y
    • (2014) Eur. Phys. J.: Spec. Top. , vol.223 , pp. 853-891
    • Snyder, P.W.1    Lockett, M.R.2    Moustakas, D.T.3    Whitesides, G.M.4
  • 16
    • 84940501243 scopus 로고    scopus 로고
    • Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip?
    • Geschwindner, S.; Ulander, J.; Johansson, P. Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip? J. Med. Chem. 2015, 58, 6321-6335 10.1021/jm501511f
    • (2015) J. Med. Chem. , vol.58 , pp. 6321-6335
    • Geschwindner, S.1    Ulander, J.2    Johansson, P.3
  • 17
    • 56549131177 scopus 로고    scopus 로고
    • The Thermodynamics of Protein-Ligand Interaction and Solvation: Insights for Ligand Design
    • Olsson, T. S. G.; Williams, M. A.; Pitt, W. R.; Ladbury, J. E. The Thermodynamics of Protein-Ligand Interaction and Solvation: Insights for Ligand Design J. Mol. Biol. 2008, 384, 1002-1017 10.1016/j.jmb.2008.09.073
    • (2008) J. Mol. Biol. , vol.384 , pp. 1002-1017
    • Olsson, T.S.G.1    Williams, M.A.2    Pitt, W.R.3    Ladbury, J.E.4
  • 18
    • 84944352692 scopus 로고    scopus 로고
    • Thermodynamics of Protein-Ligand Interactions as a Reference for Computational Analysis: How to Assess Accuracy, Reliability and Relevance of Experimental Data
    • Krimmer, S. G.; Klebe, G. Thermodynamics of Protein-Ligand Interactions as a Reference for Computational Analysis: How to Assess Accuracy, Reliability and Relevance of Experimental Data J. Comput.-Aided Mol. Des. 2015, 29, 867-883 10.1007/s10822-015-9867-y
    • (2015) J. Comput.-Aided Mol. Des. , vol.29 , pp. 867-883
    • Krimmer, S.G.1    Klebe, G.2
  • 19
    • 84904735461 scopus 로고    scopus 로고
    • Statistical Comparison of the Slopes of Two Regression Lines: A Tutorial
    • Andrade, J. M.; Estévez-Pérez, M. G. Statistical Comparison of the Slopes of Two Regression Lines: A Tutorial Anal. Chim. Acta 2014, 838, 1-12 10.1016/j.aca.2014.04.057
    • (2014) Anal. Chim. Acta , vol.838 , pp. 1-12
    • Andrade, J.M.1    Estévez-Pérez, M.G.2
  • 20
    • 85019607617 scopus 로고    scopus 로고
    • Elucidating the Origin of Long Residence Time Binding for Inhibitors of the Metalloprotease Thermolysin
    • Cramer, J.; Krimmer, S. G.; Fridh, V.; Wulsdorf, T.; Karlsson, R.; Heine, A.; Klebe, G. Elucidating the Origin of Long Residence Time Binding for Inhibitors of the Metalloprotease Thermolysin ACS Chem. Biol. 2017, 12, 225-233 10.1021/acschembio.6b00979
    • (2017) ACS Chem. Biol. , vol.12 , pp. 225-233
    • Cramer, J.1    Krimmer, S.G.2    Fridh, V.3    Wulsdorf, T.4    Karlsson, R.5    Heine, A.6    Klebe, G.7
  • 21
    • 84864400966 scopus 로고    scopus 로고
    • Water Makes the Difference: Rearrangement of Water Solvation Layer Triggers Non-Additivity of Functional Group Contributions in Protein-Ligand Binding
    • Biela, A.; Betz, M.; Heine, A.; Klebe, G. Water Makes the Difference: Rearrangement of Water Solvation Layer Triggers Non-Additivity of Functional Group Contributions in Protein-Ligand Binding ChemMedChem 2012, 7, 1423-1434 10.1002/cmdc.201200206
    • (2012) ChemMedChem , vol.7 , pp. 1423-1434
    • Biela, A.1    Betz, M.2    Heine, A.3    Klebe, G.4
  • 22
    • 36849117971 scopus 로고
    • Free Volume and Entropy in Condensed Systems III. Entropy in Binary Liquid Mixtures; Partial Molal Entropy in Dilute Solutions; Structure and Thermodynamics in Aqueous Electrolytes
    • Frank, H. S.; Evans, M. W. Free Volume and Entropy in Condensed Systems III. Entropy in Binary Liquid Mixtures; Partial Molal Entropy in Dilute Solutions; Structure and Thermodynamics in Aqueous Electrolytes J. Chem. Phys. 1945, 13, 507-532 10.1063/1.1723985
    • (1945) J. Chem. Phys. , vol.13 , pp. 507-532
    • Frank, H.S.1    Evans, M.W.2
  • 23
    • 85009971479 scopus 로고    scopus 로고
    • An Allyl Protection and Improved Purification Strategy Enables the Synthesis of Functionalized Phosphonamidate Peptides
    • Cramer, J.; Klebe, G. An Allyl Protection and Improved Purification Strategy Enables the Synthesis of Functionalized Phosphonamidate Peptides Synthesis 2017, 49, 1857-1866 10.1055/s-0036-1588393
    • (2017) Synthesis , vol.49 , pp. 1857-1866
    • Cramer, J.1    Klebe, G.2
  • 24
    • 84861840835 scopus 로고    scopus 로고
    • High-Precision Isothermal Titration Calorimetry with Automated Peak Shape Analysis
    • Keller, S.; Vargas, C.; Zhao, H.; Piszczek, G.; Brautigam, C. A.; Schuck, P. High-Precision Isothermal Titration Calorimetry with Automated Peak Shape Analysis Anal. Chem. 2012, 84, 5066-5073 10.1021/ac3007522
    • (2012) Anal. Chem. , vol.84 , pp. 5066-5073
    • Keller, S.1    Vargas, C.2    Zhao, H.3    Piszczek, G.4    Brautigam, C.A.5    Schuck, P.6
  • 25
    • 84925455000 scopus 로고    scopus 로고
    • SEDPHAT - A Platform for Global ITC Analysis and Global Multi-Method Analysis of Molecular Interactions
    • Zhao, H.; Piszczek, G.; Schuck, P. SEDPHAT-A Platform for Global ITC Analysis and Global Multi-Method Analysis of Molecular Interactions Methods 2015, 76, 137-148 10.1016/j.ymeth.2014.11.012
    • (2015) Methods , vol.76 , pp. 137-148
    • Zhao, H.1    Piszczek, G.2    Schuck, P.3
  • 26
    • 76449106188 scopus 로고    scopus 로고
    • Integration, Scaling, Space-Group Assignment and Post-Refinement
    • Kabsch, W. Integration, Scaling, Space-Group Assignment and Post-Refinement Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66, 133-144 10.1107/S0907444909047374
    • (2010) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.66 , pp. 133-144
    • Kabsch, W.1
  • 30
    • 84855757480 scopus 로고    scopus 로고
    • Chemical Computing Group Inc. Montreal, QC, Canada
    • Molecular Operating Environment (MOE); Chemical Computing Group Inc.: Montreal, QC, Canada.
    • Molecular Operating Environment (MOE)
  • 31
    • 70349597601 scopus 로고    scopus 로고
    • Electronic Ligand Builder and Optimization Workbench (eLBOW): A Tool for Ligand Coordinate and Restraint Generation
    • Moriarty, N. W.; Grosse-Kunstleve, R. W.; Adams, P. D. Electronic Ligand Builder and Optimization Workbench (eLBOW): A Tool for Ligand Coordinate and Restraint Generation Acta Crystallogr., Sect. D: Biol. Crystallogr. 2009, 65, 1074-1080 10.1107/S0907444909029436
    • (2009) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.65 , pp. 1074-1080
    • Moriarty, N.W.1    Grosse-Kunstleve, R.W.2    Adams, P.D.3
  • 32
    • 0028103275 scopus 로고
    • The CCP4 Suite: Programs for Protein Crystallography
    • CCP4
    • CCP4 The CCP4 Suite: Programs for Protein Crystallography Acta Crystallogr., Sect. D: Biol. Crystallogr. 1994, 50, 760-763 10.1107/S0907444994003112
    • (1994) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.50 , pp. 760-763
  • 33
    • 0000243829 scopus 로고
    • PROCHECK: A Program to Check the Stereochemical Quality of Protein Structures
    • Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK: A Program to Check the Stereochemical Quality of Protein Structures J. Appl. Crystallogr. 1993, 26, 283-291 10.1107/S0021889892009944
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 34
    • 0000252066 scopus 로고
    • The G Turn. Evidence for a New Folded Conformation in Proteins
    • Matthews, B. W. The G Turn. Evidence for a New Folded Conformation in Proteins Macromolecules 1972, 5, 818-819 10.1021/ma60030a031
    • (1972) Macromolecules , vol.5 , pp. 818-819
    • Matthews, B.W.1
  • 35
    • 85023768803 scopus 로고    scopus 로고
    • Unpublished Program; Uppsala University: Uppsala, Sweden
    • Kleywegt, G. J. MOLEMAN-Unpublished Program; Uppsala University: Uppsala, Sweden.
    • MOLEMAN
    • Kleywegt, G.J.1


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