Ligand solvation in molecular docking

Proteins: Structure, Function and Genetics

Volumn 34, Issue 1, 1999, Pages 4-16

  Shoichet, Brian K ^a   Leach, Andrew R ^b,c   Kuntz, Irwin D ^b  

^a NORTHWESTERN UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c GLAXOSMITHKLINE   (United Kingdom)

Author keywords

Computer aided drug design; Database search; Molecular docking; Solvation; Structure based drug design

Indexed keywords

DOCKING PROTEIN; LIGAND; PROTEIN; RECEPTOR;

ARTICLE; COMPUTER AIDED DESIGN; DRUG DESIGN; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; SOLVATION;

ANILINE COMPOUNDS; BINDING SITES; COMPUTER SIMULATION; DATABASES, FACTUAL; INDOLES; KINETICS; LIGANDS; LYSOSOMES; MODELS, MOLECULAR; PROTEIN BINDING; PTERIDINES; TETRAHYDROFOLATE DEHYDROGENASE; THYMIDINE MONOPHOSPHATE;

EID: 0032939345     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990101)34:1<4::AID-PROT2>3.0.CO;2-6     Document Type: Article

References (61)

1. Boobbyer DN, Goodford PJ, McWhinnie PM, Wade RC. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J Med Chem 1989;32:1083-1094.
2. Moon JB, Howe WJ. Computer design of bioactive molecules: A method for receptor-based de novo ligand design. Proteins 1991;11: 314-328.
3. Miranker A, Karplus M. Functionality maps of binding sites: A multicopy simultaneous search method. Proteins 1991;11:29-34.
4. Bartlett PA, Shea GT, Telfer ST, Waterman S. CAVEAT: A program to facilitate the structure-derived design of biologically active molecules. In: Roberts SM, editor. Molecular Recognition. London: Royal Society of Chemistry; 1989. p 182-196.
5. DesJarlais RL, Seibel GL, Kuntz ID et al. Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. Proc Natl Acad Sci USA 1990;87:6644-6648.
6. Lawrence MC, Davis PC. CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure. Proteins 1992;12:31-41.
7. Shoichet BK, Perry KM, Santi DV, Stroud RM, Kuntz ID. Structure-based discovery of inhibitors of thymidylate synthase. Science 1993;259:1445-1450.
8. Bodian DL, Yamasaki RB, Buswell RL, Stearns JF, White JM, Kuntz ID. Inhibition of the fusion-inducing conformational change of the influenza hemagglutinin by bensoquinones and hydroquinones. Biochemistry 1993;32:2967-2978.
9. Lybrand TP, Ghose I, McCammon JA. Hydration of chloride and bromide anions - determination of relative free-energy by computer-simulation. J Am Chem Soc 1985;107:7793-7794.
10. Bash PA, Singh UC, Langridge R, Kollman PA. Free energy calculations by computer simulation. Science 1987;236:564-568.
11. Warshel A, Sussman F, Hwang J-K. Evaluation of Catalytic Free Energies in Genetically Modified Proteins. J Mol Biol 1988;201: 139-159.
12. Straatsma TP, McCammon JA. Theoretical calculations of relative affinities of binding. Methods Enzymol 1991;202:497-511.
13. Shi YY, Mark AE, Wang CX, Huang F, Berendsen HJ, Gunsteren WFv. Can the stability of protein mutants be predicted by free energy calculations? Protein Eng 1993;6:289-295.
14. Pearlman DA Connelly PR. Determination of the differential effects of hydrogen bonding and water release on the binding of FK506 to native and Tyr82-Phe82 FKBP-12 proteins using free energy simulations. J Mol Biol 1995;248:696-717.
15. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 1983;4: 187-217.
16. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S, Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984;106: 765-784.
17. Gunsteren WFv, Berendsen HJC. GROMOS Library Manual. Groningen: Biomos; 1987.
18. Hansch C, Leo AJ. Substituent Constants for Correlation Analysis in Chemistry and Biology. New York: John Wiley & Sons; 1979. 339 p.
19. Nozaki Y, Tanford C. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. J Biol Chem 1971;246:2211-2217.
20. Wolfenden R. Affinities of amino acid side chains for solvent water. Biochemistry 1981;20:849-855.
21. Fauchere JL, Charton M, Kier LB, Verloop A, Pliska V. Amino acid side chain parameters for correlation studies in biology and pharmacology. Int J Pept Protein Res 1988;32:269-278.
22. Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986;319:199.
23. Ooi T, Oobatake M, Nemethy G, Scheraga H. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci USA 1987;84:3086-3090.
24. Tokarski JS, Hopfinger AJ. Prediction of ligand-receptor binding thermodynamics by free energy force field (FEFF) 3D-QSAR analysis: application to a set of peptidomimetic renin inhibitors. J Chem Inf Comput Sci 1997;37:792-811.
25. Still WC, Tempczyk A, Hawley RC, Hendrickson T. A Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990;112:6127.
26. Gilson MK, Honig B. The inclusion of electrostatic hydration energies in molecular mechanics calculations. J Comput Aided Mol Des 1991;5:5-20.
27. Rashin AA. Hydration phenomena, classical electrostatics and the boundary element method. J Phys Chem 1990;94:1725-1733.
28. Andrews PR, Craik DJ, Martin JL. Functional group contributions to drug-receptor interactions. J Med Chem 1984;27:1648-1657.
29. Williams DH, Cox JPL, Doig AJ, Gardner M, Gerhard U, Kaye PT, Lal AR, Nicolls IA, Salte CJ, Mitchell RC. Towards the semiquantitative estimation of binding constants. Guides for peptide-peptide binding in aqueous solution. J Am Chem Soc 1991;113: 7020-7030.
30. Head RD, Smyte ML, Oprea TI, Waller CL, Green SM, Marshall GR. VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands. J Am Chem Soc 1996;118: 3959-3969.
31. Bohm H-J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des 1994;8:243-256.
32. DeWitte RS, Shakhnovich EI. SMoG: de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence. J Am Chem Soc 1996;118: 11733-11744.
33. Wilson C, Mace JE, Agard DA. A computational method for designing enzymes with altered substrate specificity. J Mol Biol 1991;220:495-506.
34. Wilson C, Gregoret LM, Agard DA. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J Mol Biol 1993;229:996-1006.
35. Shoichet B, Bodian DL, Kuntz ID. Molecular docking using sphere descriptors. J Comp Chem 1992;13:380-397.
36. Meng EC, Shoichet B, Kuntz ID. Automated docking with grid-based energy evaluation. J Comp Chem 1992;13:505-524.
37. Ho CMW, Marshall GR. FOUNDATION-A program to retrieve all possible structures containing a user defined minimum number of matching query elements from 3-dimensional databases. J Comput Aided Mol Des 1993;7:3-22.
38. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982;161:269-288.
39. Connolly ML. Solvent-accessible surfaces of proteins and nucleic acids. Science 1983;221:709-713.
40. Ewing TJA, Kuntz ID. Critical evaluation of search algorithms for automated molecular docking and database screening. J Comp Chem 1997;18:1175-1189.
41. Gilson MK, Honig BH. Calculation of electrostatic potentials in an enzyme active site. Nature 1987;330:84-86.
42. Gasteiger J, Marsili M. Electrostatic charges. Tetrahedron 1980; 36:3219.
43. Rashin AA, Namboodiri K. A simple method for the calculation of hydration enthalpies of polar molecules with arbitrary shapes. J Phys Chem 1987;91:6003-6012.
44. Rashin AA, Honig B. Reevaluation of the Born Model of Ion Hydration. J Phys Chem 1985;89:5588.
45. Jean-Charles A, Nichols A, Sharp K et al. Electrostatic contributions to solvation energies: Comparison of free energy perturbation and continuum calculations. J Am Chem Soc 1991;113:1454-1455.
46. Cramer CJ, Truhlar DG. AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution. J Comput Aided Mol Des 1992;6:629-666.
47. Shoichet BK, Kuntz ID. Matching chemistry and shape in molecular docking. Protein Eng 1993;6:723-732.
48. Guner OF, Hughes DW, Dumont LM. An integrated approach to three dimensional information management with MACCS-3D. J Chem Inf Comput Sci 1991;31:408-414.
49. Finer-Moore J, Fauman EB, Foster PG, Perry KM, Santi DV, Stroud RM. Refined structures of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei. J Mol Biol 1993;232:1101-1116.
50. Meng EC, Gschwend DC, Blaney JM, Kuntz ID. Orientational sampling and rigid-body minimization in molecular docking. Proteins 1993;17:266-278.
51. Bernstein FC, Koetzle TF, Williams GJB et al. The protein data bank: A computer-based archival file for macromolecular structure. J Mol Biol 1977;112:535-542.
52. Bolin JT, Filman DJ, Matthews DA, Hamlin RC, Kraut J. Crystal structures of E. coli and L. casei DHFR refined to 1.7 angstrom resolution. 1. General features and binding of methotrexate. J Biol Chem 1982;257:13650-62.
53. Santi DV, Danenberg PV. In: Blakely RL, Benkovic SJ, editors. Folates and Pterins. Vol. 1. New York: John Wiley & Sons, Inc.; 1984. p 345-398.
54. Santi DV, Ouyang TM, Tan AK, Gregory DH, Scanlan T, Carreras CW. Interaction of thymidylate synthase with pyridoxal-5'-phosphate as studied by UV/visible difference spectroscopy and molecular modeling. Biochemistry 1993;32:11819-11824.
55. Blaney JM, Hansch C, Silipo C, Vittoria A. Structure-activity relationships of dihydrofolate reductase inhibitors. Chem Rev 1984;84:333-407.
56. Eriksson AE, Baase WA, Wosniak JA, Matthews BW. A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene. Nature 1992;355:371-373.
57. Morton A, Matthews BW. Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: Linkage of dynamics and structural plasticity. Biochemistry 1995;34:8576-8588.
58. Lorber DM, Shoichet BK. Flexible ligand docking using conformational ensembles. Protein Sci 1998;7:151-158.
59. Bardi JS, Luque I, Freire E. Structure-based thermodynamic analysis of HIV-1 protease inhibitors. Biochemistry 1997;36:6588-6596.
60. Luque I, Gomez J, Semo N, Freire E. Structure-based thermodynamic design of peptide ligands: Application to peptide inhibitors of the aspartic protease endothiapepsin. Proteins 1998;30:74-85.
61. Ferrin TE, Huang CC, Jarvis LE, Langridge R. The MIDAS Display Program. J Mol Graphics 1988;6:13-27.