Designing ligands to bind tightly to proteins

Physical Biology: From Atoms to Medicine

Volumn , Issue , 2008, Pages 189-215

  Whitesides, George M ^a   Snyder, Phillip W ^a   Moustakas, Demetri T ^a   Mirica, Katherine A ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84967638953     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9781848162013_009     Document Type: Chapter

References (89)

1. Lehn JM. (1990) Perspectives in supramolecular chemistry - from molecular recognition towards molecular information-processing and self-organization. Angew Chem 29: 1304-1319.
2. Cram DJ. (1992) Molecular container compounds. Nature 356: 29-36.
3. Hof F, Craig SL, Nuckolls C, Rebek J. (2002) Molecular encapsulation. Angew Chem Int Ed 41: 1488-1508.
4. Houk KN, Leach AG, Kim SP, Zhang XY. (2003) Binding affinities of host-guest, protein-ligand, and protein-transition-state complexes. Angew Chem Int Ed 42: 4872-4897.
5. Meyer EA, Castellano RK, Diederich F. (2003) Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed 42: 1210-1250.
6. Williams DH, Stephens E, O’Brien DP, Zhou M. (2004) Understanding noncovalent interactions: Ligand binding energy and catalytic efficiency from ligand-induced reductions in motion within receptors and enzymes. Angew Chem Int Ed 43: 6596-6616.
7. Hof F, Diederich F. (2004) Medicinal chemistry in academia: Molecular recognition with biological receptors. Chem Commun 477-480.
8. Reed CA. (2005) Molecular architectures - guest editorial. Acc Chem Res 38: 215-216.
9. Butlin NG, Meares CF. (2006) Antibodies with infinite affinity: Origins and applications. Acc Chem Res 39: 780-787.
10. Hirsch AKH, Fischer FR, Diederich F. (2007) Phosphate recognition in structural biology. Angew Chem Int Ed 46: 338-352.
11. Gitlin I, Carbeck JD, Whitesides GM. (2006) Why are proteins charged? Networks of charge-charge interactions in proteins measured by charge ladders and capillary electrophoresis. Angew Chem Int Ed 45: 3022-3060.
12. Homans SW. (2007) Water, water everywhere - except where it matters? Drug Discov Today 12: 534-539.
13. Homans SW. (2007) Dynamics and thermodynamics of ligand-protein interactions, Bioactive conformation i, Vol. 272, Topics in Current Chemistry, pp. 51-82.
14. Dill KA, Truskett TM, Vlachy V, Hribar-Lee B. (2005) Modeling water, the hydrophobic effect, and ion solvation. Annu Rev Biophys Biomol Struct 34: 173-199.
15. Paulini R, Muller K, Diederich F. (2005) Orthogonal multipolar interactions in structural chemistry and biology. Angew Chem Int Ed Engl 44: 1788-1805.
16. Kauzmann W. (1959) Some factors in the interpretation of protein denaturation. Adv Protein Chem 14: 1-63.
17. Jencks WP, Page MI. (1974) Orbital steering, entropy, and rate accelerations. Biochem Biophys Res Commun 57: 887-892.
18. Page MI, Jencks WP. (1971) Entropic contributions to rate accelerations in enzymic and intramolecular reactions and chelate effect. Proc Natl Acad Sci USA 68: 1678-1683.
19. Tanford C. (1962) Contribution of hydrophobic interactions to stability of globular conformation of proteins. J Am Chem Soc 84: 4240-&.
20. Mirsky AE, Pauling L. (1936) On the structure of native, denatured, and coagulated proteins. Proc Natl Acad Sci USA 22: 439-447.
21. Makhatadze GI, Privalov PL. (1993) Contribution of hydration to protein-folding thermodynamics. 1. The enthalpy of hydration. J Mol Biol 232: 639-659.
22. Privalov PL, Makhatadze GI. (1993) Contribution of hydration to protein-folding thermodynamics. 2. The entropy and gibbs energy of hydration. J Mol Biol 232: 660-679.
23. Rebek J. (2005) Simultaneous encapsulation: Molecules held at close range. Angew Chem Int Ed 44: 2068-2078.
24. Whitesides GM, Simanek EE, Mathias JP, Seto CT, Chin DN, Mammen M, Gordon DM. (1995) Noncovalent synthesis - using physicalorganic chemistry to make aggregates. Acc Chem Res 28: 37-44.
25. Pal SK, Zewail AH. (2004) Dynamics of water in biological recognition. Chem Rev 104: 2099-2123.
26. Jayaram B, Jain T. (2004) The role of water in protein-DNA recognition. Annu Rev Biophys Biomol Struct 33: 343-361.
27. Ball P. (2008) Water as an active constituent in cell biology. Chem Rev 108: 74-108.
28. Head-Gordon T. (1995) Is water structure around hydrophobic groups clathrate-like? Proc Natl Acad Sci USA 92: 8308-8312.
29. Head-Gordon T, Hura G. (2002) Water structure from scattering experiments and simulation. Chem Rev 102: 2651-2669.
30. Beattie JK, Djerdjev AM. (2004) The pristine oil/water interface: Surfactant-free hydroxide-charged emulsions. Angew Chem Int Ed 43: 3568-3571.
31. Beattie JK, Djerdjev AM, Franks GV, Warr GG. (2005) Dipolar anions are not preferentially attracted to the oil/water interface. J Phys Chem B 109: 15675-15676.
32. Chandler D. (2005) Interfaces and the driving force of hydrophobic assembly. Nature 437: 640-647.
33. Arnett EM, McKelvey DR. (1969) Solvent isotope effect on thermodynamics of nonreacting solutes. In: Coetzee JF & Ritchie CD (eds), Solute-Solvent Interactions, pp. 343-398. Marcel Dekker, New York.
34. Caravella JA, Carbeck JD, Duffy DC, Whitesides GM, Tidor B. (1999) Long-range electrostatic contributions to protein-ligand binding estimated using protein charge ladders, affinity capillary electrophoresis, and continuum electrostatic theory. J Am Chem Soc 121: 4340-4347.
35. Kangas E, Tidor B. (1999) Charge optimization leads to favorable electrostatic binding free energy. Phys Rev E 59: 5958-5961.
36. Kangas E, Tidor B. (2000) Electrostatic specificity in molecular ligand design. J Chem Phys 112: 9120-9131.
37. Sheinerman FB, Norel R, Honig B. (2000) Electrostatic aspects of protein-protein interactions. Curr Opin Struct Biol 10: 153-159.
38. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE, 3rd. (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc Chem Res 33: 889-897.
39. Massova I, Kollman P. (2000) Combined molecular mechanical and continuum solvent approach (mm-pbsa/gbsa) to predict ligand binding. Persp Drug Discov 18: 113-135.
40. Swanson JM, Henchman RH, McCammon JA. (2004) Revisiting free energy calculations: A theoretical connection to mm/pbsa and direct calculation of the association free energy. Biophys J 86: 67-74.
41. Schafer H, Mark AE, Gunsteren WFv. (2000) Absolute entropies from molecular dynamics simulation trajectories. J Chem Phys 113: 7809- 7817.
42. Karplus M, Kushick JN. (1981) Method for estimating the configurational entropy of macromolecules. Macromolecules 14: 325-332.
43. Gilson MK, Given JA, Bush BL, McCammon JA. (1997) The statisticalthermodynamic basis for computation of binding affinities: A critical review. Biophys J 72: 1047-1069.
44. Gilson MK, Zhou HX. (2007) Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct 36: 21-42.
45. Ruvinsky AM, Kozintsev AV. (2005) New and fast statisticalthermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy. J Comput Chem 26: 1089-1095.
46. Wang J, Deng Y, Roux B. (2006) Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J 91: 2798-2814.
47. Woo HJ, Roux B. (2005) Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci USA 102: 6825-6830.
48. Homans SW. (2005) Probing the binding entropy of ligand-protein interactions by nmr. ChemBioChem 6: 1585-1591.
49. Lundquist JJ, Toone EJ. (2002) The cluster glycoside effect. Chem Rev 102: 555-578.
50. Mammen M, Choi SK, Whitesides GM. (1998) Polyvalent interactions in biological systems: Implications for design and use of multivalent ligands and inhibitors. Angew Chem Int Ed 37: 2755-2794.
51. Wold S, Exner O. (1973) Statistics of enthalpy-entropy relationship 4. Temperature-dependent activation parameters. Chemica Scripta 3: 5-11.
52. Krug RR, Hunter WG, Grieger RA. (1976) Statistical interpretation of enthalpy-entropy compensation. Nature 261: 566-567.
53. Liu YF, Sturtevant JM. (1997) Significant discrepancies between van’t Hoff and calorimetric enthalpies. 3. Biophys Chem 64: 121-126.
54. Cornish-Bowden A. (2002) Enthalpy-entropy compensation: A phantom phenomenon. J Biosci 27: 121-126.
55. Beasley JR, Doyle DF, Chen LX, Cohen DS, Fine BR, Pielak GJ. (2002) Searching for quantitative entropy-enthalpy compensation among protein variants. Proteins: Struct Funct Genet 49: 398-402.
56. Mukherjee M, Dutta K, White MA, Cowburn D, Fox RO. (2006) Nmr solution structure and backbone dynamics of domain iii of the e protein of tick-borne langat flavivirus suggests a potential site for molecular recognition. Protein Sci 15: 1342-1355.
57. Frederick KK, Marlow MS, Valentine KG, Wand AJ. (2007) Conformational entropy in molecular recognition by proteins. Nature 448: 325-U3.
58. Igumenova TI, Frederick KK, Wand AJ. (2006) Characterization of the fast dynamics of protein amino acid side chains using nmr relaxation in solution. Chem Rev 106: 1672-1699.
59. Horovitz A, Fersht AR. (1990) Strategy for analyzing the cooperativity of intramolecular interactions in peptides and proteins. J Mol Biol 214: 613-617.
60. Hunt JA, Ahmed M, Fierke CA. (1999) Metal binding specificity in carbonic anhydrase is influenced by conserved hydrophobic core residues. Biochemistry 38: 9054-9062.
61. McCall KA, Fierke CA. (2004) Probing determinants of the metal ion selectivity in carbonic anhydrase using mutagenesis. Biochemistry 43: 3979-3986.
62. Nair SK, Calderone TL, Christianson DW, Fierke CA. (1991) Altering the mouth of a hydrophobic pocket - structure and kinetics of human carbonic anhydrase-ii mutants at residue val-121. J Biol Chem 266: 17320-17325.
63. Agarwal PK, Billeter SR, Rajagopalan PTR, Benkovic SJ, Hammes- Schiffer S. (2002) Network of coupled promoting motions in enzyme catalysis. Proc Natl Acad Sci USA 99: 2794-2799.
64. Parr RG, Yang W. (1995) Density-functional theory of the electronic structure of molecules. Annu Rev Phys Chem 46: 701-728.
65. Bingham RJ, Findlay JBC, Hsieh SY, Kalverda AP, Kjeliberg A, Perazzolo C, Phillips SEV, Seshadri K, Trinh CH, Turnbull WB, Bodenhausen G, Homans SW. (2004) Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein. J Am Chem Soc 126: 1675-1681.
66. Freire E. (1994) Statistical thermodynamic analysis of differential scanning calorimetry data - structural deconvolution of heat-capacity function of proteins, Numerical computer methods, pt b, Vol. 240, Methods in Enzymology, pp. 502-530.
67. Chervenak MC, Toone EJ. (1994) A direct measure of the contribution of solvent reorganization to the enthalpy of ligand-binding. J Am Chem Soc 116: 10533-10539.
68. Christensen T, Gooden DM, Kung JE, Toone EJ. (2003) Additivity and the physical basis of multivalency effects: A thermodynamic investigation of the calcium edta interaction. J Am Chem Soc 125: 7357-7366.
69. Malham R, Johnstone S, Bingham RJ, Barratt E, Phillips SEV, Laughton CA, Homans SW. (2005) Strong solute-solute dispersive interactions in a protein-ligand complex. J Am Chem Soc 127: 17061-17067.
70. Leavitt S, Freire E. (2001) Direct measurement of protein binding energetics by isothermal titration calorimetry. Curr Opin Struct Biol 11: 560-566.
71. Ladbury JE, Chowdhry BZ. (1996) Sensing the heat: The application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions. Chem Biol 3: 791-801.
72. Connelly PR, Thomson JA, Fitzgibbon MJ, Bruzzese FJ. (1993) Probing hydration contributions to the thermodynamics of ligand-binding by proteins - enthalpy and heat-capacity changes of tacrolimus and rapamycin binding to fk506 binding-protein in d2o and h2o. Biochemistry 32: 5583-5590.
73. Oas TG, Toone EJ. (1997) Thermodynamic solvent isotope effects and molecular hydrophobicity. Adv Biophys Chem 6: 1-52.
74. Wiseman T, Williston S, Brandts JF, Lin LN. (1989) Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal Biochem 179: 131-137.
75. Krishnamurthy VM, Kaufman GK, Urbach AR, Gitlin I, Gudiksen KL, Weibel DB, Whitesides GM. (In press) Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chem Rev.
76. Boriack PA, Christianson DW, Kingery-Wood J, Whitesides GM. (1995) Secondary interactions significantly removed from the sulfonamide binding pocket of carbonic anhydrase ii influence inhibitor binding constants. J Med Chem 38: 2286-2291.
77. Gao JM, Qiao S, Whitesides GM. (1995) Increasing binding constants of ligands to carbonic-anhydrase by using greasy tails. J Med Chem 38: 2292-2301.
78. Jain A, Huang SG, Whitesides GM. (1994) Lack of effect of the length of oligoglycine-derived and oligo(ethylene-glycol)-derived para-substituents on the affinity of benzenesulfonamides for carbonicanhydrase- ii in solution. J Am Chem Soc 116: 5057-5062.
79. Jain A, Whitesides GM, Alexander RS, Christianson DW. (1994) Identification of 2 hydrophobic patches in the active-site cavity of human carbonic-anhydrase-ii by solution-phase and solid-state studies and their use in the development of tight-binding inhibitor. J Med Chem 37: 2100-2105.
80. Carbeck JD, Colton IJ, Gao J, Whitesides GM. (1998) Protein charge ladders, capillary electrophoresis, and the role of electrostatics in biomolecular recognition. Acc Chem Res 31: 343-350.
81. Grzybowski BA, Ishchenko AV, Kim C-Y, Topalov G, Chapman R, Christianson DW, Whitesides GM, Shakhnovich EI. (2002) Combinatorial computational method gives new picomolar ligands for a known enzyme. Proc Natl Acad Sci USA 99: 1270-1273.
82. Krishnamurthy VM, Bohall BR, Kim C-Y, Moustakas DT, Christianson DW, Whitesides GM. (2007) Thermodynamic parameters for the association of fluorinated benzenesulfonamides with bovine carbonic anhydrase ii. Chem-Asia J 2: 94-105.
83. Krishnamurthy VM, Bohall BR, Kim CY, Moustakas DT, Christianson DW, Whitesides GM. (2007) Thermodynamic parameters for the association of fluorinated benzenesulfonamides with bovine carbonic anhydrase ii. Chem-Asia J 2: 94-105.
84. Krishnamurthy VM, Semetey V, Bracher PJ, Shen N, Whitesides GM. (2007) Dependence of effective molarity on linker length for an intramolecular protein-ligand system. J Am Chem Soc 129: 1312- 1320.
85. Krishnamurthy VM, Bohall BR, Semetey V, Whitesides GM. (2006) The paradoxical thermodynamic basis for the interaction of ethylene glycol, glycine, and sarcosine chains with bovine carbonic anhydrase ii: An unexpected manifestation of enthalpy/entropy compensation. J Am Chem Soc 128: 5802-5812.
86. Dunitz JD. (1995) Win some, lose some - enthalpy-entropy compensation in weak intermolecular interactions. Chem Biol 2: 709-712.
87. Ishikawa H, Finkelstein IJ, Kim S, Kwak K, Chung JK, Wakasugi K, Massari AM, Fayer MD. (2007) Neuroglobin dynamics observed with ultrafast 2d-ir vibrational echo spectroscopy. Proc Natl Acad Sci USA 104: 16116-16121.
88. Ishikawa H, Kim S, Kwak K, Wakasugi K, Fayer MD. (2007) Disulfide bond influence on protein structural dynamics probed with 2d-ir vibrational echo spectroscopy. Proc Natl Acad Sci USA 104: 19309- 19314.
89. Park S, Kwak K, Fayer MD. (2007) Ultrafast 2d-ir vibrational echo spectroscopy: A probe of molecular dynamics. Laser Phys Lett 4: 704- 718.