Energetic and Entropic Factors Determining Binding Affinity in Protein-Ligand Complexes

References

• Andrews P. R., Craik D. J., Martin J. L. Functional group contributions to drug-receptor interactions. J. Med. Chem. 1984; 27: 1648–1657
   PubMed Web of Science ®Google Scholar
• Böhm H. J., Klebe G. What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs. Angew. Chem. 1996, in press
   Google Scholar
• Morgan B. P., Scholtz J. M., Ballinger M. D., Zipkin I. D., Bartlett P. A. Differential binding energy: A detailed evaluation of the influence of hydrogen-bonding and hydrophobic groups on the inhibition of thermolysin by phosphorus-containing inhibitors. J. Am. Chem. Soc. 1991; 113: 297–307
   Web of Science ®Google Scholar
• Tronrud D. E., Holden H. M., Matthews B. W. Structures of two thermolysin-inhibitor complexes that differ by a single hydrogen boncl. Science 1987; 235: 571–574
   PubMed Web of Science ®Google Scholar
• Livnah O., Bayer E. A., Wilchek M. Three-dimensional structures of avidin and the avidin-biotin complex. Proc. Natl. Acad. Sci. USA 1993; 90: 5076–5080
   PubMed Web of Science ®Google Scholar
• Sussman J. L., Page M. I. Entropy, binding, energy, and enzymic catalysis. Angew. Chem. Int. Ed. Engl. 1977; 16: 449–459
   Web of Science ®Google Scholar
• Jencks W. P. On the attribution and additivity of binding energies. Proc. Natl. Acad. Sci. USA 1981; 78: 4046–4050
   PubMed Web of Science ®Google Scholar
• Searle M. S., Williams D. H. The cost of conformational order: Entropy changes in molecular associations. J. Am. Chem. Soc. 1992; 114: 10690–10697
   Web of Science ®Google Scholar
• Searle M. S., Williams D. H., Gerhard U. Partitioring of free energy contributions in the estimation of binding constants: Residual motions and consequences for amide-amide hydrogen bond strengths. J. Am. Chem. Soc. 1992; 114: 10697–10704
   Web of Science ®Google Scholar
• Jeffrey G. A., Saenger W. Hydrogen Bonding in Biological Structures. Springer-Verlag, Berlin 1991
   Google Scholar
• Chalasinski G., Szczesniak M. M. Origins of structure and energetics of van der Waals clusters from ab initio calculations. Chem. Rev. 1994; 94: 1723–1765
   Web of Science ®Google Scholar
• Kim K. S., Mhin B. J., Choi U. S., Lee K. J. Ab initio studies on the water dimer using large basis sets: The structure and thermodynamic energies. Chem. Phys. 1992; 97: 6649–6662
   Web of Science ®Google Scholar
• Chervenak M. C., Toone E. J. A direct measure of the contribution of solvent reorganization to the enthalpy of ligand binding. J. Am. Chem. Soc. 1994; 116: 10533–10539
   Web of Science ®Google Scholar
• Dunitz J. D. The entropic cost of bound water in crystals and biomolecules. Science 1994; 264: 670
   PubMed Web of Science ®Google Scholar
• Cowan S. W., Newcomer M. E., Jones T. A. Crystallographic refinement of human serum retinol binding protein at 2Å resolution. Proteins, Struct, Funct. Genetics 1990; 8: 44–61
   PubMed Web of Science ®Google Scholar
• Tanford C. The Hydrophobic Effect2nd ed. Wiley, New York 1980
   Google Scholar
• Ben-Naim A. Application of the Kirkwood-Buff theory to the problem of hydrophobic interactions. Faraday Symp. Chem. Soc. 1982; 17: 121–127
   Google Scholar
• Burley S. K., Petsko G. A. Aromatic-aromatic interaction: A mechanism of protein structure stabilization. Science 1985; 229: 23–28, b) Hunter, C. A.; Singh, J.; and Thornton, J. M. π-π interactions: The geometry and energetics of phenylalanine-phenylalanine interactions in proteins. J. Mol. Biol. 218, 837–846, 1991
   PubMed Web of Science ®Google Scholar
• Hunter C. A. Meldola Lecture: The role of aromatic interaction in molecular recognition. Chem. Soc. Rev. 1994; 101–109
   Web of Science ®Google Scholar
• Smithrud D. B., Wyman T. B., Diederich F. Enthalpically driven cyclophane-arene inclusion complexation: Solvent-dependent calorimetric studies. J. Am. Chem. Soc. 1991; 113: 5420–5426
   Web of Science ®Google Scholar
• Klebe G., Diederich F. A. Comparison of the crystal packing in benzene with the geometry seen in crystalline cyclophane-benzene complexes: Guidelines for rational receptor design. Phil. Trans. R. Soc. Lond. A. 1993; 345: 37–48
   Web of Science ®Google Scholar
• Sussman J. L., Harel M., Frolow F., Oefher C., Goldman A., Toker L., Silman I. Atomic structure of acetylcholinesterase from Torpedo californica: A prototypic acetylcholine-binding protein. Science 1991; 253: 872–879
   PubMed Web of Science ®Google Scholar
• Dougherty D. A., Staufer D. A. Acetylcholine binding by a synthetic receptor: Implications for biological recognition. Science 1990; 250: 1558–1560
   PubMed Web of Science ®Google Scholar
• Fersht A. R., Shi J. P., Knill-Jones J., Lowe D. M., Wilkinson A. J., Blow D. M., Brick P., Carter P., Waye M. M. Y., Winter G. Hydrogen bonding and biological specificity analysed by protein engineering. Nature 1985; 34: 235–238, b) Thorson, J. S.; Chapman, E.; and Schultz, P. G. Analysis of hydrogen bonding strengths in proteins using unnatural amino acids. J. Am. Chem. Soc. 117, 9361–9362, 1995
   Google Scholar
• Connelly P. R., Aldape R. A., Bruzzese F. J., Chambers S. P., Fitzgibbon M. J., Fleming M. A., Itoh S., Livingston D. J., Navia M. A., Thomson J. A., Wilson K. P. Enthalpy of hydrogen bond formation in a protein-ligand binding reaction. Proc. Natl. Acad. Sci. USA 1994; 91: 1964–1968
   PubMed Web of Science ®Google Scholar
• Shirley B. A., Stanssens P., Hahn U., Pace C. N. Contribution of hydrogen bonding to the conformational stability of ribonuclease Tl. Biochemistry 1992; 31: 725–732
   PubMed Web of Science ®Google Scholar
• Chen Y. W., Fersht A. R., Henrick K. Contribution of buried hydrogen bonds to protein stability. The crystal structures of two barnase mutants. J. Mol. Biol. 1993; 234: 1158–1170
   PubMed Web of Science ®Google Scholar
• Jandu S. K., Ray S., Brooks L., Leatherbarrow R. J. Role of arginine 67 in the stabilization of chymotrypsin inhibitor 2: Examination of amide proton exchange rates and denaturation thermodynamics of an engineered protein. Biochem. 1990; 29: 6264–6269
   PubMed Web of Science ®Google Scholar
• Bohacek R. S., McMartin C. Definition and display of steric, hydrophobic, and hydrogen-bonding properties of ligand binding sites in proteins using Lee and Richards accessible surface: Validation of a high-resolution graphical tool for drug design. J. Med. Chem. 1992; 35: 1671–1684
   PubMed Web of Science ®Google Scholar
• Schneider H. J., Schiestel T., Zimmermann P. The incremental approach to noncovalent interactions: Coulomb and van der Waals effects in organic ion pairs. J. Am. Chem. Soc. 1992; 114: 7698–7703
   Web of Science ®Google Scholar
• Vajda S., Weng Z., Rosenfeld R., DeLisi C. Effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry 1994; 33: 13977–13988
   PubMed Web of Science ®Google Scholar
• Krystek S., Stouch T., Novotny J. Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures. J. Mol. Biol. 1993; 234: 661–679
   PubMed Web of Science ®Google Scholar
• Pace C. N. Contribution of the hydrophobic effect to globular protein stability. J. Mol. Biol. 1992; 226: 29–35
   PubMed Web of Science ®Google Scholar
• Cohen J. L., Connors K. A. Stability and structure of some organic molecular complexes in aqueous solution. J. Pharm. Sci. 1970; 59: 1271
   PubMed Web of Science ®Google Scholar
• Gao J., Qiao S., Whitesides G. M. Increasing binding constants of ligands to carbonic anhydrase by using, greasy tails”. J. Med. Chem. 1995; 38: 2292–2301
   PubMed Web of Science ®Google Scholar
• Richards F. M. Areas, volumes, packing and protein structure. Ann. Rev. Biophys. Bioeng. 1977; 6: 151–176
   PubMedGoogle Scholar
• Chothia C. Structural invariants in protein folding. Nature 1975; 254: 304–308
   PubMed Web of Science ®Google Scholar
• Matsumura M., Becktel W. J., Matthews W. Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of Ile 3. Nature 1988; 334: 406–41
   PubMed Web of Science ®Google Scholar
• Sharp K. A., Nicholls A., Friedman R., Honig B. Extracting hydrophobic free energies from experimental data. Relationship to protein folding and theoretical models. Biochemistry 1991; 30: 9686–9697
   PubMed Web of Science ®Google Scholar
• Kaplan A. P., Bartlett P. A. Synthesis and evaluation of an inhibitor of carboxypeptidase A with a K1 value in the femtomolar range. Biochemistry 1991; 30: 8165–8170
   PubMed Web of Science ®Google Scholar
• Wiley R. A., Rich D. H. Peptidomimetics derived from natural products. Med. Res. Rev. 1993; 13: 327–384
   PubMed Web of Science ®Google Scholar
• Lim M. S. L., Johnston E. R., Kettner C. A. The solution conformation of (D)Phe-Pro-containing peptides: Implications on the activity of Ac-(D)Phe-Pro-boroArg-OH,1 a potent thrombin inhibitor. J. Med. Chem. 1993; 36: 1831–1838
   PubMed Web of Science ®Google Scholar
• Sakamoto H., Shimohigashi Y., Ogawa T., Kawano K., Ohno M. Dipeptide side chain-side chain hydrophobic interactions as conformational core for chymotrypsin inhibition. Bull. Chem. Soc. Jpn. 1991; 64: 2519–2523
   Web of Science ®Google Scholar
• Jencks W. P. Binding energy, specificity, and enzymic catalysis: The circe effect. Adv. Enzymol. 1975; 43: 219–410, b) Fersht, A. Enzyme Structure and Mechanism, 2nd ed., Freeman, New York
   PubMedGoogle Scholar
• Mack H., Pfeiffer T., Hornberger W., Böhm H. J., Höffken H. W. Design, synthesis and biological activity of novel rigid amidino-phenylalanine derivatives as inhibitors of thrombin. J. Enzyme Inhibition 1995; 9: 73–86
   Google Scholar
• Raag R., Poulos T. L. Crystal structures of cytochrome P-450cam complexed with camphane, thiocamphor, and adamantane: Factors controlling P-450 substrate hydroxylation. Biochemistry 1991; 30: 2674–2684
   PubMed Web of Science ®Google Scholar
• Paulsen M. D., Ornstein R. L. Predicting the preduct specificity and coupling of cytochrome P-45cam. J. Comp. Aided Molec. Des. 1992; 6: 449–460
   PubMed Web of Science ®Google Scholar
• Weber P. C., Pantoliano M. W., Simons D. M., Salemme F. R. Structure-based design of synthetic azobenzene ligands for streptavidin. J. Am. Chem. Soc. 1994; 116: 2717–2724
   Web of Science ®Google Scholar
• Inoue Y., Hakushi T., Liu Y., Tong L. H., Shen B. L., Jin D. S. Thermodynamics of molecular recognition by cyclodextrins. J. Caorimetric titration of inclusion complexation of naphthalenesulfonates with α-, β-, and γ-cyclodextrins: Enthalpyentropy compensation. J. Am. Chem. Soc. 1993; 115: 475–481
   Web of Science ®Google Scholar
• Wieseman T., Williston S., Brandts J. F., Lin L. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Analyt. Biochem. 1989; 179: 131–137
   PubMed Web of Science ®Google Scholar
• Hitzemann R. Thermodynamic aspects of drug-receptor interactions. Trends Pharmacol. Sci. 1988; 9: 408–411
   PubMed Web of Science ®Google Scholar
• Hitzemann R., Murphy M., Currell J. Opiate receptor thermodynamics: Agonist and antagonist binding. Eur. J. Pharmacol. 1985; 108: 171–177
   PubMed Web of Science ®Google Scholar
• Weiland G. A., Minnemann G. P., Molinoff P. B. Thermodynamics of agonist and antagonist interactions with mammalian β-adrenergic receptors. Mol. Pharmacol. 1985; 18: 341–347
   Google Scholar
• Epps D. E., Cheney J., Schostarez H., Sawyer T. K., Prairie M., Krueger W. C., Mandel F. J. Thermodynamics of the interaction of inhibitors with the binding site of recombinant human renin. Med. Chem. 1990; 33: 2080–2086, b) Braden, B. C.; Dall'Asqua, W.; Eisenstein, E.; Fields, B. A.; Goldbaum, F. A.; Malchiodi, E. L.; Mariuzza, R. A.; Schwartz, F. P.; Ysern, X.; and Poljak, R. J.; Protein motion and lock and key complementarity in antigen-antibody reactions. Pharm. Acta Helv. 69, 225–230, 1995
   Web of Science ®Google Scholar
• Weber P. C., Wendoloski J. J., Panoliano M. W., Salemme F. R. Crystallographic and thermodynamic comparison of natural and synthetic ligands bound to streptavidin. J. Am. Chem. Soc. 1992; 114: 3197–3200
   Web of Science ®Google Scholar
• Grunewald E., Steel C. Solvent reorganization and thermodynamic enthalpyentropy compensation. J. Am. Chem. Soc. 1992; 117: 5687–5692
   Google Scholar
• Williams D. H., Searle M. S., Mackay J. P., Gerhard U., Maplestone R. A. Toward an estimation of binding constants in aqueous solution: Studies of associations of vancomycin group antibiotics. Proc. Natl. Acad. Sci. USA 1993; 90: 1172–1178
   PubMed Web of Science ®Google Scholar
• Murphy K. P., Xie D., Thompson K. S., Amzel L. M., Freire E. Entropy in biological binding processes: Estimation of translational entropy loss. Protein-Struct. Funct. Genet. 1994; 18: 63–67
   PubMed Web of Science ®Google Scholar