MTD-PLS: A PLS variant of the minimal topologic difference method. III. Mapping interactions between estradiol derivatives and the alpha estrogenic receptor

Journal of Chemical Information and Modeling

Volumn 45, Issue 5, 2005, Pages 1275-1281

  Kurunczi, Ludovic ^a,b   Seclaman, Edward ^a,b   Oprea, Tudor I ^c   Crisan, Luminita ^b   Simon, Zeno ^b  

^a VICTOR BABES UNIVERSITY OF MEDICINE AND PHARMACY   (Romania)

^b ACADEMY OF ROMANIAN SCIENTISTS   (Romania)

^c UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTALLOGRAPHY; DERIVATIVES; HYDROPHOBICITY; TOPOLOGY;

QUANTITATIVE STRUCTURE ACTIVITY; RECEPTOR SITES;

ALCOHOLS;

DRUG DERIVATIVE; ESTRADIOL; ESTROGEN RECEPTOR ALPHA;

ALGORITHM; ANIMAL; ARTICLE; BINDING SITE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; HYDROPHOBICITY; METABOLISM; PROTEIN BINDING; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RAT; REPRODUCIBILITY; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; ANIMALS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ESTRADIOL; ESTROGEN RECEPTOR ALPHA; HYDROPHOBICITY; MODELS, BIOLOGICAL; MOLECULAR STRUCTURE; PROTEIN BINDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RATS; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 26944451315     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050077c     Document Type: Article

References (25)

1. Simon, Z.; Chiriac, A.; Holban, S.; Ciubotaru, D.; Mihalas, G. I. Minimum Steric Difference. The MTD Method for QSAR Studies; Research Studies Press Ltd.: Letchworth, U. K., 1984.
2. Oprea, T. I.; Kurunczi, L.; Olah, M.; Simon, Z. MTD-PLS: A PLS-based variant of the MTD method. A 3-D QSAR analysis of receptor affinities for a series of halogenated dibenzoxin and biphenyl derivatives. SAR QSAR Environ. Res. 2001, 12, 75-92.
3. Kurunczi, L.; Olah, M.; Oprea, T. I.; Bologa, C.; Simon, Z. MTD-PLS: A PLS-based Variant of the MTD Method. II. Mapping Ligand-Receptor Interactions. Enzymatic Acetic Acid Esters Hydrolysis. J. Chem. Inf. Comput. Sci. 2002, 42, 841-846.
4. OCA Advanced Search website. http://oca.ebi.ac.uk/oca-bin/ocamain. Analysis of PDB entry 1ere.
5. PDB Structure Explorer. http://www.rcsb.org/pdb/cgi/explore.cgi?pid= 52851102327638&pdbId=1ERE. Brzozowski, A. M.; Pike, A. C.; Dauter, Z.; Hubbard, R. E.; Bonn, T.; Engstrom, O.; Ohman, L.; Greene, G. L.; Gustafsson, J. A.; Carlquist, M. Human Estrogen Receptor Ligand-Binding Domain in Complex With 17beta-Estradiol.
6. Wold, S.; Albano, C.; Dunn, W. J.; Edlund, U.; Esbensen, K.; Geladi, P.; Hellberg, S.; Johansson, E.; Lindberg, W.; Sjöström, M. Multivariate Data Analysis in Chemistry. In Chemometrics: Mathematics and Statistics in Chemistry; Kowalski, B. R., Ed.; D. Reidel: Dordrecht, The Netherlands, 1984.
7. Wold, S.; Sjöström, M.; Eriksson, L. PLS in Chemistry. In The Encyclopedia of Computational Chemistry; Schleyer, P. V. R., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer, H. F., III., Schreiner, P. R., Eds.; John Wiley and Sons: Chichester, U. K., 1999; pp 2006-2020.
8. Anstead, G. M.; Carlson, K. E.; Katzenellenbogen, J. A. The estradiol pharmacophore: ligand structure-estrogen binding affinity relationships and a model for the receptor binding site. Steroids 1997, 62, 268-303.
9. HyperChem 5.11 Pro; ChemPlus 1.6; HyperCube Inc.: Gainesville, FL. http://www.hyper.com.
10. Ciubotariu, D.; Deretey, E.; Oprea, T. I.; Sulea, T.; Simon, Z.; Kurunczi, L.; Chiriac, A. Multiconformational Minimal Steric Difference. Structure - Acetylcholinesterase Hydrolysis Rates Relations for Acetic Acid Esters. Quant. Struct.-Act. Relat. 1993, 12, 367-372.
11. Kotani, T.; Higashiura, K. Comparative Molecular Active Site Analysis (COMASA). 1. An Approach to Rapid Evaluation of 3D QSAR. J. Med. Chem. 2004, 47, 2732-2742.
12. Olah, M. Molecular fragment volume calculation for QSAR studies. Rev. Roum. Chim. 2000, 45 (12), 1123-1125.
13. Rekker, R. The Hydrophobic Fragmental Constant; Elsevier: Amsterdam, 1977.
14. Volkenstein, M. V. Stroenie i fizicheskie svoistva molecul; Izd. Akad. Nauk: Moscow, 1955; pp 230, 296.
15. Raevsky, O. A.; Grigor'ev, V. Ju.; Kireev, D. B.; Zefirov, N. S. Complete Thermodynamic Description of H - Bonding in the Framework of Multiplicative Approach. Quant. Struct.-Act. Relat. 1992, 11, 49-63.
16. SIMCA P, version 9.0; Umetrics AB: Umeå, Sweden. http://www.umetrics.com.
17. Eriksson, L.; Johansson, E.; Kettaneh-Wold, N.; Wold, S. Multi- and Megavariate Data Analysis. Principles and Applications. Umetrics AB: Umeå, Sweden, 2001; p 94-97.
18. Basic Local Alignement Search Tool, http://au.expasy.org/tools/blast/.
19. MDL Chime, version 2.6 SP4; MDL Information Systems, Inc.: San Leandro, CA (http://www.mdlchime.com/chime).
20. Martz, E.; Noncovalent Bond Finder (NCBF), 2002 (http://www.umass.edu/ microbio/chime/find-ncb/).
21. Eriksson, L.; Johansson, E.; Kettaneh-Wold, N.; Wold, S. Multi- and Megavariate Data Analysis. Principles and Applications. Umetrics AB: Umeå, Sweden, 2001; pp 101-103, 507-509.
22. Brzozowski, A. M.; Pike, A. C. W.; Dauter, Z.; Hubbard, R. E.; Bonn, T.; Engstrom, O.; Öhman, L.; Greene, G. L.; Gustafsson, J. A.; Carlquist, M. Molecular basis of agonism and antagonism in the oestrogen receptor. Nature 1997, 389, 753-758.
23. Endocrine disrupter knowledge base, http://edkb.fda.gov/.
24. 2! J. Mol. Graph. Mod. 2002, 20, 269-276.
25. Topliss, J. G.; Costello, R. J. Chance correlations in structure-activity studies using multiple regression analysis. J. Med. Chem. 1972, 15, 1066-1069.