QSAR model for the prediction of bio-concentration factor using aqueous solubility and descriptors considering various electronic effects

SAR and QSAR in Environmental Research

Volumn 21, Issue 7, 2010, Pages 711-729

  Piir, G ^a   Sild, S ^a   Roncaglioni, A ^b   Benfenati, E ^b   Maran, U ^a  

^a UNIVERSITY OF TARTU   (Estonia)

^b MARIO NEGRI INSTITUTE FOR PHARMACOLOGICAL RESEARCH   (Italy)

Author keywords

Applicability domain; BCF; Bioconcentration; QSAR; Solubility

Indexed keywords

ALCOHOLS; COMPUTATIONAL CHEMISTRY; HYDROGEN BONDS; HYDROPHOBICITY; LINEAR REGRESSION; MOLECULAR GRAPHICS; SURFACE CHEMISTRY;

APPLICABILITY DOMAIN; AQUEOUS SOLUBILITY; BIO-CONCENTRATION FACTORS; BIOCONCENTRATION; DATA SET; DESCRIPTORS; ELECTRONIC EFFECTS; IN-SILICO MODELS; QSAR; QSAR MODEL;

SOLUBILITY;

EID: 78649771398     PISSN: 1062936X     EISSN: 1029046X     Source Type: Journal    
DOI: 10.1080/1062936X.2010.528596     Document Type: Article

References (73)

1. D. Shea, Transport and fate of toxicants, in A Textbook of Modern Toxicology, 3rd ed., E. Hodgson, ed., Wiley-Interscience, New Jersey, 2004, pp. 479-499.
2. G.A. Leblanc, Basics of environmental toxicology, in A Textbook of Modern Toxicology, 3rd ed., E. Hodgson, ed., Wiley-Interscience, New Jersey, 2004, pp. 463-478.
3. D.T.H.M. Sijm, M.G.J. Rikken, E. Rorije, T.P. Traas, M.S. McLachlan, and W.J.G.M. Peijnenburg, Transport, accumulation and transformation processes, in Risk Assessment of Chemicals: An Introduction, 2nd ed., C.J. van Leeuwen, ed., Springer, Dordrecht, 2007, pp. 73-158.
4. OECD, OECD Guidelines for Testing of Chemicals, Guideline 305, Bioconcentration: Flow-through Fish Test, Organization for Economic Co-operation and Development, Paris, 1996.
5. D. Mackay, Correlation of bioconcentration factors, Environ. Sci. Technol. 16 (1982), pp. 274-278.
6. S. Bintein, J. Devillers, and W. Karcher, Nonlinear dependence of fish bioconcentration on n-Octanol/water partition coefficients, SAR QSAR Environ. Res. 1 (1993), pp. 29-39.
7. S.D. Dimitrov, O.G. Mekenyan, and J.D. Walker, Non-linear modeling of bioconcentration using partition coefficients for narcotic chemicals, SAR QSAR Environ. Res. 13 (2002), pp. 177-184.
8. W.M. Meylan, P.H. Howard, R.S. Boethling, D. Aronson, H. Printup, and S. Gouchie, Improved method for estimating bioconcentration/bioaccumulation factor from octanol/water partion coefficient, Environ. Toxicol. Chem. 18 (1999), pp. 664-672.
9. X. Lu, S. Tao, J. Cao, and R.W. Dawson, Prediction of fish bioconcentration factors of nonpolar organic pollutants based on molecular connectivity indices, Chemosphere 39 (1999), pp. 987-999.
10. X. Lu, S. Tao, H. Hu, and R.W. Dawson, Estimation of bioconcentration factors of nonionic organic compounds in fish by molecular connectivity indices and polarity correction factors, Chemosphere 41 (2000), pp. 1675-1688.
11. P. Gramatica and E. Papa, QSAR modeling of bioconcentration factor by theoretical molecular descriptors, QSAR Comb. Sci. 22 (2003), pp. 374-385.
12. M.H. Fatemi, M. Jalali-Heravi, and E. Konuze, Prediction of bioconcentration factor using genetic algorithm and artificial neural network, Anal. Chim. Acta 486 (2003), pp. 101-108.
13. D. Wei, A. Zhang, C. Wu, S. Han, and L. Wang, Progressive study and robustness test of QSAR model based on quantum chemical parameters for predicting BCF of selected polychlorinated organic compounds (PCOCs), Chemosphere 44 (2001), pp. 1421-1428.
14. M. Bermúdez-Saldaña, L. Escuder-Gilabert, M.J. Medina-Hernández, R.M. Villanueva-Camañas, and S. Sagrado, Modelling bioconcentration of pesticides in fish using biopartitioning micellar chromatography, J. Chromatogr. A 1063 (2005), pp. 153-160.
15. M. Fujikawa, K. Nakao, R. Shimizu, and M. Akamatsu, The usefulness of an artificial membrane accumulation index for estimation of the bioconcentration factor of organophosphorus pesticides, Chemosphere 74 (2009), pp. 751-757.
16. S.D. Dimitrov, N.C. Dimitrova, J.D. Walker, G.D. Veith, and O.G. Mekenyan, Predicting bioconcentration factors of highly hydrophobic chemicals. Effects of molecular size, Pure Appl. Chem. 74 (2002), pp. 1823-1830.
17. J.C. Dearden and N.M. Shinnawei, Improved prediction of fish bioconcentration factor of hydrophobic chemicals, SAR QSAR Environ. Res. 15 (2004), pp. 449-455.
18. S. Dimitrov, N. Dimitrova, T. Parkerton, M. Comber, M. Bonnell, and O. Mekenyan, Base-line model for identifying the bioaccumulation potential of chemicals, SAR QSAR Environ. Res. 16 (2005), pp. 531-554.
19. J.D. Dearden, QSAR modeling of bioaccumulation, in Predicting Chemical Toxicity and Fate, M.T.D. Conin and D.J. Livingstone, eds., CRC Press, Boca Raton, 2004, pp. 333-356.
20. M. Pavan, A.P. Worth, and T.I. Netzeva, Review of QSAR Models for Bioconcentration, European Commission, Joint Research Centre. Ispra, Italy, EUR 22327EN, 2006.
21. M.T. Saçan, S.S. Erdem, G.A. Özpinar, and I.A. Balcioglu, QSPR study on the bioconcentration factors of nonionic organic compounds in fish by characteristic root index and semiempirical molecular descriptors, J. Chem. Inf. Comput. Sci. 44 (2004), pp. 985-992.
22. K. Roy, I. Sanyal, and P.P. Roy, QSPR of the bioconcentration factors of non-ionic organic compounds in fish using extended topochemical atom (ETA) indices, SAR QSAR Environ. Res. 17 (2006), pp. 563-582.
23. H. Liu, X. Yao, R. Zhang, M. Liu, Z. Hu, and B. Fan, The accurate QSPR models to predict the bioconcentration factors of nonionic organic compounds based on the heuristic method and support vector machine, Chemosphere 63 (2006), pp. 722-733.
24. H. Qin, J. Chen, Y. Wang, B. Wang, X. Li, F. Li, and Y. Wang, Development and assessment of quantitative structure-activity relationship models for bioconcentration factors of organic pollutants, Chinese Sci. Bull. 54 (2009), pp. 628-634.
25. P. Gramatica and E. Papa, An update of the bcf qsar model based on theoretical molecular descriptors, QSAR Comb. Sci. 24 (2005), pp. 953-960.
26. Y. Wang, Y. Li, J. Ding, Z. Jiang, and Y. Chang, Estimation of bioconcentration factors using molecular electro-topological state and flexibility, SAR QSAR Environ. Res. 19 (2008), pp. 375-395.
27. S. Cui, J. Yang, S. Liu, and L. Wang, Predicting bioconcentration factor values of organic pollutants based on medv descriptors derived QSARs, Sci. China Ser B-Chem. 50 (2007), pp. 587-592.
28. S. Liu, L. Qin, H. Liu, and D. Yin, Molecular electronegativity distance vector model for the prediction of bioconcentration factors in fish, J. Mol. Model. 14 (2008), pp. 83-92.
29. L. Qin, S. Liu, H. Liu, and H. Ge, A new predictive model for the bioconcentration factors of polychlorinated biphenyls (PCBs) based on the molecular electronegativity distance vector (MEDV), Chemosphere 70 (2008), pp. 1577-1587.
30. L. Qin, S. Liu, and H. Liu, QSPR model for bioconcentration factors of nonpolar organic compounds using molecular electronegativity distance vector descriptors, Mol. Divers. 14 (2010), pp. 67-80.
31. E. Papa, J.C. Dearden, and P. Gramatica, Linear QSAR regression models for the prediction of bioconcentration factors by physicochemical properties and structural theoretical molecular descriptors, Chemosphere 67 (2007), pp. 351-358.
32. C. Zhao, E. Boriani, A. Chana, A. Roncaglioni, and E. Benfenati, A new hybrid system of QSAR models for predicting bioconcentration factors (BCF), Chemosphere 73 (2008), pp. 1701-1707.
33. S.H. Jackson, C.E. Cowan-Ellsberry, and G. Thomas, Use of quantitative structural analysis to predict fish bioconcentration factors for pesticides, J. Agric. Food. Chem 57 (2009), pp. 958-967.
34. T. Ivanciuc, O. Ivanciuc, and D.J. Klein, Modeling the bioconcentration factors and bioaccumulation factors of polychlorinated biphenyls with posetic quantitative super-structure/ activity relationships (QSSAR), Mol. Divers. 10 (2006), pp. 133-145.
35. VCCLAB, Virtual Computational Chemistry Laboratory, 2005; software available at http://www.vcclab.org.
36. J.A. Arnot and F.A.P.C. Gobas, A review of bioconcentration factor (BCF) and bioaccumulation factor (BAF) assessments for organic chemicals in aquatic organisms, Environ. Rev. 14 (2006), pp. 257-297.
37. AMBIT, Establishing a bioconcentration factor (BCF) gold standard database. Available at http://ambit.sourceforge.net/euras.
38. E.V. Gordeeva, A.R. Katritsky, V.V. Shcherbukhin, and N.S. Zefirov, Rapid conversion of molecular graphs to three-dimensional representation using the MOLGEO program, J. Chem. Inf. Comput. Sci. 33 (1993), pp. 102-111.
39. Marvin 5.0.3. ChemAxon, 2008; software available at http://www.chemaxon.com/marvin.
40. S.L. Mayo, B.D. Olafson, and W.A. Goddard, DREIDING: A generic force field for molecular simulations, J. Phys. Chem. 26 (1990), pp. 8897-8909.
41. J.J.P. Stewart, Optimization of parameters for semi-empirical methods I-method, J. Comp. Chem. 10 (1989), pp. 209-220.
42. J.J.P. Stewart, MOPAC: A semiempirical molecular orbital program, J. Comput. Aid. Mol. Des. 4 (1990), pp. 1-45.
43. A.R. Katritzky, M. Karelson, and R. Petrukhin, Codessa Pro; software available at http://www.codessa-pro.com.
44. C. Steinbeck, C. Hoppe, S. Kuhn, M. Floris, R. Guha, and E.L. Willighagen, Recent developments of the chemistry development kit (CDK) - an open-source java library for chemoand bioinformatics, Curr. Pharm. Des. 17 (2006), pp. 2111-2120.
45. Chemistry Development Kit 1.0.1, 2007; software available at http://cdk.sourceforge.net.
46. JOELib2 2007-03-03, 2007: software available at http://www.ra.cs.uni-tuebingen.de/software/joelib.
47. I.V. Tetko, J. Gasteiger, R. Todeschini, A. Mauri, D. Livingstone, P. Ertl, V.A. Palyulin, E.V. Radchenko, N.S. Zefirov, A.S. Makarenko, V.Y. Tanchuk, and V.V. Prokopenko, Virtual computational chemistry laboratory - design and description, J. Comput. Aid. Mol. Des. 19 (2005), pp. 453-463.
48. J. Gasteiger and M. Marsili, Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges, Tetrahedron 36 (1980), pp. 3219-3288.
49. N.R. Draper and H. Smith, Applied Regression Analysis, Wiley, New York, 1981.
50. A.R. Katritzky, L. Mu, V.S. Lobanov, and M. Karelson, Correlation of boiling points with molecular structure. 1. A training set of 298 diverse organics and a test set of 9 simple inorganics, J. Phys. Chem. 100 (1996), pp. 10400-10407.
51. A.R. Katritzky, D.A. Dobchev, S. Slavov, and M. Karelson, Legitimate utilization of large descriptor pools for qspr/qsar models, J. Chem. Inf. Model. 48 (2008), pp. 2207-2213.
52. M. Karelson, U. Maran, Y. Wang, and A.R. Katritzky, QSPR and QSAR models derived using large molecular descriptor spaces. a review of codessa applications, Collect. Czech. Chem. Commun. 64 (1999), pp. 1551-1571.
53. A. Colombo, E. Benfenati, M. Karelson, and U. Maran, The proposal of architecture for chemical splitting to optimize QSAR models for aquatic toxicity, Chemosphere 72 (2008), pp. 772-780.
54. I. Kahn, S. Sild, and U. Maran, Modeling the toxicity of chemicals to Tetrahymena pyriformis using heuristic multilinear regression and heuristic back-propagation neural networks, J. Chem. Inf. Model. 47 (2007), pp. 2271-2279.
55. I. Kahn, U. Maran, T.I. Netzeva, E. Benfenati, T.W. Schultz, and M.T.D. Cronin, Comparative quantitative structure-activity relationships for toxicity to Terahymena pyriformis and Pimephales promelas, ATLA 35 (2007), pp. 15-24.
56. U. Maran, S. Sild, P. Mazzatorta, M. Casalegno, E. Benfenati, and M. Romberg, Grid computing for the estimation of toxicity: acute toxicity on fathead minnow (Pimephales promelas), in Distributed, High-Performance and Grid Computing in Computational Biology, W. Dubitzky, A. Schuster, P.M.A. Sloot, M. Schhroeder, and M. Romberg, eds., Springer-Verlag, Berlin Heidelberg, 2007, pp. 60-74.
57. R.G. Brereton, Chemometrics: Data Analysis for the Laboratory and Chemical Plant, John Wiley & Sons, Chichester, 2003.
58. B. Schuller, B. Demuth, H. Mix, K. Rasch, M. Romberg, S. Sild, U. Maran, P. Bala, E. del Grosso, M. Casalegno, N. Piclin, M. Pintore, W. Sudholt, and K.K. Baldridge, Chemomentum - UNICORE 6 based infrastructure for complex applications in science and technology, in Euro-Par 2007 Workshops: Parallel Processing, L. Bougé, M. Forsell, J.L. Trä ff, A. Streit, W. Ziegler, M. Alexander, and S. Childs, eds., Springer-Verlag, Berlin Heidelberg, 2008, pp. 82-93.
59. M. Romberg, The UNICORE grid infrastructure, Sci. Program. 10 (2002), pp. 149-157.
60. S. Sild, U. Maran, A. Lomaka, and M. Karelson, Open computing grid for molecular science and engineering, J. Chem. Inf. Model. 46 (2006), pp. 953-959.
61. A.T. Garcia-Sosa, S. Sild, and U. Maran, Docking and virtual screening using distributed grid technology, QSAR Comb. Sci. 28 (2009), pp. 815-821.
62. Syracuse Research Corporation, Physical/Chemical Property Database (PHYSPROP), SRC Environmental Science Center, Syracuse, New York, 1994.
63. C.T. Chiou, V.H. Freed, D.W. Schmedding, and R.L. Kohnert, Partition coefficient and bioaccumulation of selected organic chemicals, Environ. Sci. Technol. 11 (1977), pp. 475-478.
64. G. Veith, K. Macek, S. Petrocelli, and J. Carroll, An evaluation of using partition coefficients and water solubility to estimate bioconcentration factors for organic chemicals in fish, in Aquatic Toxicology, ASTM STP 707, J.G. Eaton, P.R. Parrish, and A.C. Hendricks, eds., ASTM, Baltimore, 1980, pp. 116-129.
65. E. Kenaga and C. Goring, Relationship between water solubility, soil sorption, octanol-water partitioning, and concentration of chemicals in biota, in Aquatic Toxicology, ASTM STP 707, J.G. Eaton, P.R. Parrish, and A.C. Hendricks, eds., ASTM, Baltimore, 1980, pp. 78-116.
66. J.A. Timbrell, Principles of Biochemical Toxicology, 4th ed., Informa Healthcare, New York, 2009.
67. P. Isnard and S. Lambert, Estimating bioconcentration factors from octanol-water partition coefficient and aqueous solubility, Chemosphere 17 (1988), pp. 21-34.
68. G. Lewandowski, E. Meissner, and E. Milchert, Special applications of fluorinated organic compounds, J. Hazard. Mater. A136 (2006), pp. 385-391.
69. M.L. Hardy, A comparison of the fish bioconcentration factors for brominated flame retardants with their nonbrominated analogues, Environ. Toxicol. Chem. 23 (2004), pp. 656-661.
70. G.J. van Esch, Environmental Health Criteria 185: Chlorendic Acid and Anhydride, World Health Organization, Geneva, 1996.
71. J.W. Deneer, T.L. Sinnige, W. Seinen, and J.L.M. Hermens, Quantitative structure-activity relationships for the toxicity and bioconcentration factor of nitrobenzene derivatives towards the guppy (Poecilia reticulata), Aquat. Toxicol. 10 (1987), pp. 115-129.
72. J.H. Montgomery, Groundwater Chemicals Desk Reference, 3rd ed., CRC Press LLC, Boca Raton, 2000.
73. J. Regeimbal and J.C.A. Bardwell, Disulfide bond formation in prokaryotes and eukaryotes, in Protein Targeting, Transport & Translocation, R.E. Dalbey and G. von Heijne, eds., Academic Press, London, 2002, pp. 131-150.