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Original Articles

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

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Pages 711-729 | Received 28 May 2010, Accepted 01 Sep 2010, Published online: 29 Nov 2010

References

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

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