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

Journal of Receptor and Signal Transduction Research

Volumn 17, Issue 42007, 1997, Pages 459-473

  Klebe, Gerhard ^a   Böhm, Hans Joachim ^a,b  

^a BASF SE   (Germany)

^b F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CONFERENCE PAPER; ENTHALPY; ENTROPY; HYDROGEN BOND; LIGAND BINDING; PROTEIN BINDING; RECEPTOR AFFINITY; RECEPTOR BINDING;

ANIMALS; ENTROPY; HYDROGEN BONDING; KINETICS; LIGANDS; PROTEINS;

EID: 1842411345     PISSN: 10799893     EISSN: None     Source Type: Journal    
DOI: 10.3109/10799899709036621     Document Type: Article

References (62)

1. Andrews P. R., Craik D. J., Martin J. L. Functional group contributions to drug-receptor interactions. J. Med. Chem. 1984; 27: 1648 – 1657
2. 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
3. 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
4. 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
5. 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
6. Sussman J. L., Page M. I. Entropy, binding, energy, and enzymic catalysis. Angew. Chem. Int. Ed. Engl. 1977; 16: 449 – 459
7. Jencks W. P. On the attribution and additivity of binding energies. Proc. Natl. Acad. Sci. USA 1981; 78: 4046 – 4050
8. Searle M. S., Williams D. H. The cost of conformational order: Entropy changes in molecular associations. J. Am. Chem. Soc. 1992; 114: 10690 – 10697
9. 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
10. Jeffrey G. A., Saenger W. Hydrogen Bonding in Biological Structures. Springer-Verlag, Berlin 1991
11. 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
12. 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
13. 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
14. Dunitz J. D. The entropic cost of bound water in crystals and biomolecules. Science 1994; 264: 670
15. 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
16. Tanford C. The Hydrophobic Effect2nd ed. Wiley, New York 1980
17. Ben-Naim A. Application of the Kirkwood-Buff theory to the problem of hydrophobic interactions. Faraday Symp. Chem. Soc. 1982; 17: 121 – 127
18. Burley S. K., Petsko G. A. Aromatic-aromatic interaction: A mechanism of protein structure stabilization. Science 1985; 229: 23 – 28
19. 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
20. Hunter C. A. Meldola Lecture: The role of aromatic interaction in molecular recognition. Chem. Soc. Rev. 1994; 101 – 109
21. 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
22. 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
23. 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
24. Dougherty D. A., Staufer D. A. Acetylcholine binding by a synthetic receptor: Implications for biological recognition. Science 1990; 250: 1558 – 1560
25. 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
26. 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
27. 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
28. 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
29. 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
30. 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
31. 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
32. 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
33. 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
34. 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
35. Pace C. N. Contribution of the hydrophobic effect to globular protein stability. J. Mol. Biol. 1992; 226: 29 – 35
36. Cohen J. L., Connors K. A. Stability and structure of some organic molecular complexes in aqueous solution. J. Pharm. Sci. 1970; 59: 1271
37. 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
38. Richards F. M. Areas, volumes, packing and protein structure. Ann. Rev. Biophys. Bioeng. 1977; 6: 151 – 176
39. Chothia C. Structural invariants in protein folding. Nature 1975; 254: 304 – 308
40. 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
41. 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
42. 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
43. Wiley R. A., Rich D. H. Peptidomimetics derived from natural products. Med. Res. Rev. 1993; 13: 327 – 384
44. 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
45. 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
46. Jencks W. P. Binding energy, specificity, and enzymic catalysis: The circe effect. Adv. Enzymol. 1975; 43: 219 – 410
47. b) Fersht, A. Enzyme Structure and Mechanism, 2nd ed., Freeman, New York
48. 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
49. 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
50. 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
51. 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
52. 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
53. 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
54. Hitzemann R. Thermodynamic aspects of drug-receptor interactions. Trends Pharmacol. Sci. 1988; 9: 408 – 411
55. Hitzemann R., Murphy M., Currell J. Opiate receptor thermodynamics: Agonist and antagonist binding. Eur. J. Pharmacol. 1985; 108: 171 – 177
56. 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
57. 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
58. 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
59. 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
60. Grunewald E., Steel C. Solvent reorganization and thermodynamic enthalpyentropy compensation. J. Am. Chem. Soc. 1992; 117: 5687 – 5692
61. 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
62. 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