Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis

Journal of Medicinal Chemistry

Volumn 43, Issue 9, 2000, Pages 1780-1792

  Tomic, Sanja ^a,b   Nilsson, Lennart ^c   Wade, Rebecca C ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b RUDER BO KOVI INSTITUTE   (Croatia)

^c KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS RECEPTOR; DNA; ESTROGEN RECEPTOR; GLUCOCORTICOID RECEPTOR; RETINOIC ACID RECEPTOR; STEROID RECEPTOR; THYROID HORMONE RECEPTOR; VITAMIN D RECEPTOR;

ARTICLE; BINDING AFFINITY; GENE EXPRESSION REGULATION; GENE MUTATION; HORMONE RECEPTOR INTERACTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RECEPTOR BINDING;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; DNA; ENTROPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; RECEPTORS, CYTOPLASMIC AND NUCLEAR; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSCRIPTION FACTORS;

EID: 0034069171     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm9911175     Document Type: Article

References (52)

1. Beato, M. Gene regulation by steroid hormones. Cell 1989, 56, 335-344.
2. Evans, R. M. The steroid and thyroid hormone receptor superfamily. Science 1988, 240, 889-895.
3. Laudet, V.; Hanni, C.; Coll, J.; Catzefils, F.; Stehelin, D. Evolution of the nuclear receptor gene superfamily. EMBO J. 1992, 11, 1003-1013.
4. Mandel-Gutfreund, Y.; Schueler, O.; Margalit, H. Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. J. Mol. Biol. 1995, 253, 370-382.
5. Mandel-Gutfreund, Y.; Margalit, H. Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Nucl. Acid Res. 1998, 26, 2306-2312.
6. Eriksson, M. A. L.; Nilsson, L. Structure, Thermodynamics and Cooperativity of the GR DBD in Complex with Different REs. MD Simulation and Free Energy Pertubation Studies. J. Mol. Biol. 1995, 253, 453-472.
7. Komeiji, Y.; Fujita, I.; Honda, N.; Tsutsui, M.; Tamara, T.; Yamato, I. Glycine 85 of the trp-repressor of E.coli is important in forming the hydrophobic tryptophan binding pocket: experimental and computational approaches. Protein Eng. 1994, 7, 1239-1247.
8. Zacharias, M.; Luty, B. A.; Davis, M. E.; McCammon, J. A. Poisson-Boltzmann analysis of the lambda repressor-operator interaction. Biophys. J. 1992, 63, 1280-1285.
9. Zacharias, M.; Luty, B. A.; Davis, M. E.; McCammon, J. A. Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor-operator complex. J. Mol. Biol. 1994, 238, 455-465.
10. Misra, V. K.; Hecht, J. L.; Yang, A. S.; Honig, B. Electrostatic contributions to the binding free energy of the lambdacI repressor to DNA. Biophys. J. 1998, 75, 2262-2273.
11. Brown, L. M.; Bruccoleri, R. E.; Novotny, J. Empirical free energy calculations of phage 434 repressor- and cro-DNA complexes support the 'indirect readout' hypothesis of specificity. Pac. Symp. Biocomput. 1998, 339-348.
12. Fogolari, F.; Elcock, A. H.; Esposito, G.; Viglino, P.; Briggs, J. M.; McCammon, J. A. Electrostatic effects in homeodomain-DNA interactions. J. Mol. Biol. 1997, 267, 368-381.
13. Cramer, R. D., III; Patterson, D. E.; Bunce, J. D. Comparative molecular field analysis (CoMFA): 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc., 1988, 110,
14. Holloway, M. K.; Wai, J. M.; Halgren, T. A.; Fitzgerald, P. M.; Vacca, J. P.; Dorsey, B. D.; Levin, R. B.; Thompson, W. J.; Chen, L. J.; deSolms, S. J. A priori prediction of activity for HTV-1 protease inhibitors employing energy minimization in the active site. J. Med. Chem. 1995, 38, 305-17.
15. Grootenhuis, P. D. J.; van Galen, P. J. M. Correlation of binding affinities with nonbonded interaction energies of thrombin-inhibitor complexes. Acta Crystallogr. 1995, D51, 560-566.
16. Ortiz, A. R.; Pisabarro, M. T.; Gago, F.; Wade, R. C. Prediction of drug binding affinities by comparative binding energy analysis. J. Med. Chem. 1995, 38, 2681-2691.
17. Wade, R. C.; Ortiz, A. R.; Gago, F. Comparative Binding Energy Analysis. Perspect. Drug Des. Discov. 1998, 9, 19-34.
18. Wold, S.; Johansson, E.; Cocchi, M. PLS-Partial Least-Squares Projections to Latent Structures; ESCOM: Leiden, 1993.
19. Zilliacus, J.; Wright, A. P.; Norinder, U.; Gustafsson, J. A.; Carlstedt-Duke, J. Determinants for DNA-binding site recognition by the glucocorticoid receptor. J. Biol. Chem. 1992, 267, 24941-24947.
20. Zilliacus, J.; Wright, A. P.; Norinder, U.; Gustafsson, J. A.; Carlstedt-Duke, J. DNA-binding specificity of mutant glucocorticoid receptor DNA-binding domains. Ann. N. Y. Acad. Sci. 1993, 684, 253-255.
21. Zilliacus, J.; Wright, A. P.; Carlstedt-Duke, J.; Gustafsson, J. A. Structural determinants of DNA-binding specificity by steroid receptors. Mol. Endocrinol. 1995, 9, 389-400.
22. Zilliacus, J.; Wright, A. P.; Carlstedt-Duke, J.; Nilsson, L.; Gustafsson, J. A. Modulation of DNA-binding specificity within the nuclear receptor family by substitutions at a single amino acid position. Proteins: Struct. Funct. Genet. 1995, 21, 57-67.
23. Hard, T.; Gustafsson, J. A. Structure and function of the DNA-binding domain og the glucocorticoid receptor and other members of the nuclear receptor supergene family. Acc. Chem. Res. 1993, 26, 644-650.
24. Klock, G. S.; U.; Schuetz, G Oestrogen and glucocorticoid response elements are closely related dut distinct. Nature (London) 1987, 329, 734-736.
25. Hard, T.; Kellenbach, E.; Boelens, R.; Kaptein, R.; Dahlman, K.; Carlstedt-Duke, J.; Freedman, L. P.; Maler, B. A.; Hyde, E. I.; Gustafsson, J. A.; et al. 1H NMR studies of the glucocorticoid receptor DNA-binding domain: sequential assignments and identification of secondary structure elements. Biochemistry 1990, 29, 9015-9023.
26. Tsai, S. Y.; Carlstedt-Duke, J.; Weigel, N. L.; Dahlman, K.; Gustafsson, J. A.; Tsai, M. J.; O'Malley, B. W. Molecular interactions of steroid hormone receptor with its enhancer element: evidence for receptor dimer formation. Cell 1988, 55, 361-369.
27. Luisi, B. F.; Xu, W. X.; Otwinowski, Z.; Freedman, L. P.; Yamamoto, K. R.; Sigler, P. B. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature 1991, 352, 497-505.
28. Free, S. M.; Wilson, J. A. A mathematical contribution to structure-activity studies. J. Med. Chem. 1964, 7, 395-399.
29. Kubinyi, H. The Free-Wilson method and its relationship to the extrathermodynamic approach; Pergamon Press: Oxford, 1990; Vol. 4, pp 589-643.
30. Wold, S.; C.; A.; Dunn, W. J., III; Edlund, U.; Esbensen, K.; Geladi, P.; Hellberg, S.; Johansson, E.; Lindberg, W.; Sjoestroem, M. In Chemometrics-Mathematics and Statistics in Chemistry; Kowalski, B. R., Ed.; Reidel: Dordrecht, 1984; pp 17-95.
31. Baroni, M.; Costantino, G.; Cruciani, G.; Riganelli, D.; Valigi, R.; Clementi, S. Generating Optimal Linear PLS Estimations (GOLPE): An Advanced Chemometric Tool For Handling 3D-QSAR Problems. Quant. Struct.-Act. Relat. 1993, 12, 9-20.
32. GOLPE; Multivariate Infometric Analysis S.r.l.: Perugia, Italy, 1997.
33. Eriksson, M. A. L.; Nilsson, L. Structural and dynamic effects of point mutations in the recognition helix of the glucocorticoid receptor DNA-binding domain. Protein Eng. 1998, 11, 589-600.
34. Eriksson, M. A. L.; Nilsson, L. Structural and dynamic differences of the estrogen receptor DNA-binding domain, binding as a dimer and as a monomer to DNA: molecular dynamics simulations studies. Eur. Biophys. J. 1999, 28, 102-111.
35. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: A program for macromolecular enegy, minimization and dynamics calculations. J. Comput. Chem. 1983, 4, 187-217.
36. Cornell, W. D.; Cieplak, P.; Payly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
37. Besler, B. H.; Merz, K. M. J.; Kollman, P. A. Atomic charges derived from semiempirical methods. J. Comput. Chem. 1990, 11, 431-439.
38. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. AM1: A new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 1985, 107, 3902-3909.
39. Creighton, T. E. Proteins: Structures and Molecular Properties; W. H. Freeman and Co.: New York, 1993.
40. Fauchere, J. L.; Pliska, V. Eur. J. Med. Chem.-Chim. Ther. 1983, 18, 369-375.
41. Wimley, W. C.; Creamer, T. P.; White, S. H. Solvation Energies of Amino Acid Side Chains and Backbone in a Family of Host-Guest Pentapeptides. Biochemistry 1996, 35, 5109-5124.
42. Kollman, P. Free Energy Calculations: Application to Chemical and Biochemical Phenomena. Chem. Rev. 1993, 93, 2395-2417.
43. Shih, P.; Pedersen, L. G.; Gibbs, P. R.; Wolfenden, R. Hydrophobicities of the Nucleic Acid Bases: Distribution Coefficients from Water to Cyclohexane. J. Mol. Biol. 1998, 280, 421-430.
44. Lee, B.; Richards, F. M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 1971, 55, 379-400.
45. Hubbard, S. J.; Thornton, J. M. NACCESS; Department of Biochemistry and Molecular Biology, University College London: London, 1993.
46. INSIGHTII; Molecular Simulations Inc., San Diego, 1997.
47. Plaxco, K. W.; Goddard, W. A. I. Contributions of the thymine methyl group to the specific recognition of poly and mononucleotides: An analysis of the relative free energies of solvation of thymin and uracil. Biochemistry 1994, 33, 3050-3054.
48. Perez, C.; Pastor, M.; Ortiz, A. R.; Gago, F. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design. J. Med. Chem. 1998, 41, 836-852.
49. Ortiz, A. R.; Pastor, M.; Palomer, A.; Cruciani, G.; Gago, F.; Wade, R. C. Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors. J. Med. Chem. 1997, 40, 1136-1148.
50. Eriksson, M.; Haerd, T.; Nilsson, L. Molecular Dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution. Biophys. J. 1995, 68, 402-426.
51. Williams, D. H.; Maguire, A. J.; Tsuzuki, W.; Westwell, M. S. An analysis of the origins of a cooperative binding energy of dimerization. Science 1998, 280, 711-714.
52. Kosztin, D.; Bishop, T. C.; Schulten, K. Binding of the Estrogen Receptor to DNA. The Role of Waters. Biophys. J. 1997, 73, 557-570.