Estimation of reliability of predictions and model applicability domain evaluation in the analysis of acute toxicity (LD₅₀)

References

• Zmuidinavicius , D , Japertas , P , Petrauskas , A and Didziapetris , R . 2003 . Progress in toxinformatics: the challenge of predicting acute toxicity . Curr. Top. Med. Chem. , 3 : 1301 – 1314 .
   PubMed Web of Science ®Google Scholar
• The Registry of Toxic Effects of Chemical Substances, RTECS®, Symyx Technologies Inc., Sunnyvale (CA), USA. Available at http://www.symyx.com/products/databases/bioactivity/rtecs/index.jsp
   Google Scholar
• IUCLID Chemical Data Sheets Information System, The Consumer Products Safety and Quality Unit of the Institute for Health and Consumer Protection, Joint Research Centre, European Comission, Ispra (VA), Italy. Available at http://ecb.jrc.ec.europa.eu/esis/index.php?PGM=dat
   Google Scholar
• Didziapetris , R , Reynolds , DP , Japertas , P , Zmuidinavicius , D and Petrauskas , A . 2006 . In silico technology for identification of potentially toxic compounds in drug discovery . Curr. Comput.-Aided Drug Des. , 2 : 95 – 103 .
   Google Scholar
• Jaworska , JS , Comber , M , Auer , C and Van Leeuwen , CJ . 2003 . Summary of a workshop on regulatory acceptance of (Q)SARs for human health and environmental endpoints . Environ. Health Perspect. , 111 : 1358 – 1360 .
   PubMed Web of Science ®Google Scholar
• Simon-Hettich , B , Rothfuss , A and Steger-Hartmann , T . 2006 . Use of computer-assisted prediction of toxic effects of chemical substances . Toxicology , 224 : 156 – 162 .
   PubMed Web of Science ®Google Scholar
• Schultz , TW and Seward , JR . 2000 . Health-effects related structure-toxicity relationships: a paradigm for the first decade of the new millennium . Sci. Total Environ. , 249 : 73 – 84 .
   PubMed Web of Science ®Google Scholar
• Lessigiarska , I , Worth , AP , Netzeva , TI , Dearden , JC and Cronin , MTD . 2006 . Quantitative structure-activity-activity and quantitative structure-activity investigations of human and rodent toxicity . Chemosphere , 65 : 1878 – 1887 .
   PubMed Web of Science ®Google Scholar
• Seibert , H , Balls , M , Fentem , JH , Bianchi , V , Clothier , RH , Dierickx , PJ , Ekwal , B , Garle , MJ , Gomez-Lechon , MJ , Gribaldo , L , Gulden , M , Liebsch , M , Rasmussen , E , Roguet , R , Shrivastava , R and Walum , E . 1996 . Acute toxicity testing in vitro and the classification and labeling of chemicals. The report and recommendations of ECVAM workshop 16 . Altern. Lab. Anim. , 24 : 499 – 510 .
   Google Scholar
• Garle , MJ , Fentem , JH and Fry , JR . 1994 . In vitro cytotoxicity tests for the prediction of acute toxicity in vivo . Toxicol. In Vitro , 8 : 1303 – 1313 .
   PubMed Web of Science ®Google Scholar
• Shrivastava , R , Delomenie , C , Chevalier , A , John , G , Ekwal , B , Walum , E and Massingham , R . 1992 . Comparison of in vivo acute lethal potency and in vitro cytotoxicity of 48 chemicals . Cell Biol. Toxicol. , 8 : 157 – 170 .
   PubMed Web of Science ®Google Scholar
• Phillips , JC , Gibson , WB , Yam , J , Alden , CL and Hard , G . 1990 . Survey of the QSAR and in vitro approaches for developing non-animal methods to supersede in vivo LD50 test . Food Chem. Toxicol. , 28 : 375 – 394 .
   PubMed Web of Science ®Google Scholar
• Enslein , K and Craig , PN . 1978 . A toxicity estimation model . J. Environ. Pathol. Toxicol. , 2 : 115 – 121 .
   PubMed Web of Science ®Google Scholar
• Enslein , K , Lander , TR , Tomb , ME and Craig , PN . 1983 . A Predictive Model for Estimating Rat Oral LD₅₀ Values , Princetor, NJ. : Princeton Scientific Publishers .
   Google Scholar
• Enslein , K , Tuzzeo , TM , Borgstedt , HH , Blake , BW and Hart , JB . 1987 . Prediction of rat oral LD50 from Daphnia Magna LC50 and chemical structure . QSAR Environ. Toxicol. Proc. Int. Workshop , 2 : 91 – 106 .
   Google Scholar
• Enslein , K , Lander , TR , Tomb , ME and Craig , PN . 1989 . A predictive model for estimating rat oral LD50 values . Toxicol. Ind. Health. , 5 : 261 – 387 .
   Google Scholar
• Jaeckel , H and Klein , W . 1991 . Prediction of mammalian toxicity by quantitative structure-activity relationships: aliphatic amines and anilines . Quant. Struct.-Act. Relat. , 10 : 198 – 204 .
   Google Scholar
• Lipnick , RL . 1991 . Outliers: their origin and use in the classification of molecular mechanisms of toxicity . Sci. Total Environ. , 109–110 : 131 – 153 .
   PubMedGoogle Scholar
• Zakarya , D , Larfaoui , EM , Boulaamail , A and Lakhlifi , T . 1996 . Analysis of structure-toxicity relationships for a series of amide herbicides using statistical methods and neural network . SAR QSAR Environ. Res. , 5 : 269 – 279 .
   PubMedGoogle Scholar
• Wang , G and Bai , N . 1998 . Structure-activity relationships for rat and mouse LD50 of miscellaneous alcohols . Chemosphere , 36 : 1475 – 1483 .
   PubMed Web of Science ®Google Scholar
• Eldred , DV and Jurs , PC . 1999 . Prediction of acute mammalian toxicity of organophosphorus pesticide compounds from molecular structure . SAR QSAR Environ. Res. , 10 : 75 – 99 .
   PubMed Web of Science ®Google Scholar
• Cronin , MT , Dearden , JC , Duffy , JC , Edwards , R , Manga , N , Worth , AP and Worgan , AD . 2002 . The importance of hydrophobicity and electrophilicity descriptors in mechanistically-based QSARs for toxicological endpoints . SAR QSAR Environ. Res. , 13 : 167 – 176 .
   PubMed Web of Science ®Google Scholar
• Hansch , C and Kurup , A . 2003 . QSAR of chemical polarizability and nerve toxicity. 2 . J. Chem. Inf. Comput. Sci. , 43 : 1647 – 1651 .
   PubMedGoogle Scholar
• Devillers , J . 2004 . Prediction of mammalian toxicity of organophosphorus pesticides from QSTR modeling . SAR QSAR Environ. Res. , 15 : 501 – 510 .
   PubMed Web of Science ®Google Scholar
• Jean , PA , Gallavan , RH , Kolesar , GB , Siddiqui , WH , Oxley , JA and Meeks , RG . 2006 . Chlorosilane acute inhalation toxicity and development of an LC50 prediction model . Inhal. Toxicol. , 18 : 515 – 522 .
   PubMed Web of Science ®Google Scholar
• Guo , JX , Wu , JJ , Wright , JB and Lushington , GH . 2006 . Mechanistic insight into acetylcholinesterase inhibition and acute toxicity of organophosphorus compounds: a molecular modeling study . Chem. Res. Toxicol. , 19 : 209 – 216 .
   PubMed Web of Science ®Google Scholar
• Freidig , AP , Dekkers , S , Verwei , M , Zvinavashe , E , Bessems , JG and van de Sandt , JJ . 2007 . Development of a QSAR for worst case estimates of acute toxicity of chemically reactive compounds . Toxicol. Lett. , 170 : 214 – 222 .
   Google Scholar
• Toropov , AA , Rasulev , BF and Leszczynski , J . 2007 . QSAR modeling of acute toxicity for nitrobenzene derivatives towards rats: comparative analysis by MLRA and optimal descriptors . QSAR Comb. Sci. , 26 : 686 – 693 .
   Google Scholar
• Zhu , H , Martin , TM , Ye , L , Sedykh , A , Young , DM and Tropsha , A . 2009 . Quantitative structure-activity relationship modeling of rat acute toxicity by oral exposure . Chem. Res. Toxicol. , 22 : 1913 – 1921 .
   PubMed Web of Science ®Google Scholar
• Lipnick , RL . 1999 . Correlative and mechanistic QSAR models in toxicology . SAR QSAR Environ. Res. , 10 : 239 – 248 .
   PubMed Web of Science ®Google Scholar
• Lipnick , RL . 1990 . “ Narcosis: fundamental and baseline toxicity mechanism for non-electrolyte organic chemicals ” . In Practical Applications of Quantitative Structure-Activity Relationships (QSAR) in Environmental Chemistry and Toxicology , Edited by: Karcher , W and Devillers , J . 129 – 144 . Dordrecht : Kluwer Academic Publishers .
   Google Scholar
• TOPKAT®, Accelrys Software Inc., San Diego CA, US, 2007; software available at http://accelrys.com/
   Google Scholar
• Worth , AP , Bassan , A , Gallegos , A , Netzeva , TI , Patlewicz , G , Pavan , M , Tsakovska , I and Vracko , M . 2005 . The characterisation of (quantitative) structure-activity relationships: preliminary guidance , EUR 21866 EN Ispra (VA), , Italy : Institute for Health and Consumer Protection, Joint Research Centre, European Commission . Available at http://ecb.jrc.it/documents/QSAR/QSAR_characterisation_EUR_21866_EN.pdf
   Google Scholar
• Netzeva , TI , Worth , A , Aldenberg , T , Benigni , R , Cronin , MT , Gramatica , P , Jaworska , JS , Kahn , S , Klopman , G , Marchant , CA , Myatt , G , Nikolova-Jeliazkova , N , Patlewicz , GY , Perkins , R , Roberts , D , Schultz , T , Stanton , DW , van de Sandt , JJ , Tong , W , Veith , G and Yang , C . 2005 . Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships. The report and recommendations of ECVAM Workshop 52 . Altern. Lab. Anim. , 33 : 155 – 173 .
   PubMed Web of Science ®Google Scholar
• Tetko , IV . 2002 . Neural network studies. 4. Introduction to associative neural networks . J. Chem. Inf. Comput. Sci. , 42 : 717 – 728 .
   PubMedGoogle Scholar
• Tetko , IV and Bruneau , P . 2004 . Application of ALOGPS to predict 1-octanol/water distribution coefficients, log P, and log D, of AstraZeneca in-house database . J. Pharm. Sci. , 93 : 3103 – 3110 .
   PubMed Web of Science ®Google Scholar
• Tetko , IV and Tanchuk , VY . 2002 . Application of associative neural networks for prediction of lipophilicity in ALOGPS 2.1 program . J. Chem. Inf. Comput. Sci. , 42 : 1136 – 1145 .
   PubMedGoogle Scholar
• Zhu , H , Tropsha , A , Fourches , D , Varnek , A , Papa , E , Gramatica , P , Oberg , T , Dao , P , Cherkasov , A and Tetko , IV . 2008 . Combinatorial QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis . J. Chem. Inf. Model. , 48 : 766 – 784 .
   PubMed Web of Science ®Google Scholar
• Tetko , IV , Sushko , I , Pandey , AK , Zhu , H , Tropsha , A , Papa , E , Oberg , T , Todeschini , R , Fourches , D and Varnek , A . 2008 . Critical assessment of QSAR models of environmental toxicity against Tetrahymena pyriformis: focusing on applicability domain and overfitting by variable selection . J. Chem. Inf. Model. , 48 : 1733 – 1746 .
   PubMed Web of Science ®Google Scholar
• Japertas , P . 2007 . Application of fragmental descriptors and statistical analysis methods in quantitative structure-activity relationships , Ph.D. diss. Vilnius University .
   Google Scholar
• Japertas , P , Sazonovas , A , Didziapetris , R and Petrauskas , A . 2008 . Similarity based assessment of model applicability domain and quantitative evaluation of the reliability of the prediction , New Orleans, LA : The 235th ACS National Meeting .
   Google Scholar
• Regulation (EC) No 1907/2006 of the European Parliament and of the Council of 18 December 2006 concerning the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH), establishing a European Chemicals Agency, amending Directive 1999/45/EC and repealing Council Regulation (EEC) No 793/93 and Commission Regulation (EC) No 1488/94 as well as Council Directive 76/769/EEC and Commission Directives 91/155/EEC, 93/67/EEC, 93/105/EC and 2000/21/EC, The European Parliament and the Council of the European Union, 2006. Available at http://eur-lex.europa.eu/LexUriServ/site/en/oj/2006/l_396/l_39620061230en00010849.pdf
   Google Scholar
• Japertas , P , Didziapetris , R and Petrauskas , A . 2002 . Fragmental methods in the design of new compounds. Applications of Advanced Algorithm Builder . Quant. Struct.-Act. Relat. , 21 : 23 – 37 .
   Web of Science ®Google Scholar
• Japertas , P , Didziapetris , R and Petrauskas , A . 2003 . Fragmental methods in the analysis of biological activities of diverse compound sets . Mini. Rev. Med. Chem. , 3 : 797 – 808 .
   PubMedGoogle Scholar
• Petrauskas , AA and Kolovanov , EA . 2000 . ACD/LogP method description . Perspect. Drug Discov. Design , 19 : 99 – 116 .
   Google Scholar
• Klopman , G . 1984 . Artificial intelligence approach to structure-activity studies. Computer automated structure evaluation of biological activity of organic molecules. . J. Am. Chem. Soc. , 106 : 7315 – 7321 .
   Web of Science ®Google Scholar
• Saiakhov , RD , Stefan , LR and Klopman , G . 2000 . Multpile computer-automated structure evaluation model of the plasma protein binding affinity of diverse drugs . Perspect. Drug Discov. Design , 19 : 133 – 155 .
   Google Scholar
• Klopman , G . 1998 . The MultiCASE Program II. Baseline Activity Identification Algorithm (BAIA) . J. Chem. Inf. Comput. Sci. , 38 : 78 – 81 .
   PubMedGoogle Scholar
• Rosenkranz , HS , Cunningham , AR , Zhang , YP , Claycamp , HG , Macina , OT , Sussman , NB , Grant , SG and Klopman , G . 1999 . Development, characterization and application of predictive-toxicology models . SAR QSAR Environ. Res. , 10 : 277 – 298 .
   PubMed Web of Science ®Google Scholar
• Platts , JA , Butina , D , Abraham , MH and Hersey , A . 1999 . Estimation of molecular linear free energy relation descriptors using a group contribution approach . J. Chem. Inf. Comput. Sci. , 39 : 835 – 845 .
   Google Scholar
• Fukuto , TR . 1990 . Mechanism of action of organophosphorus and carbamate insecticides . Environ. Health. Perspect. , 87 : 245 – 254 .
   PubMed Web of Science ®Google Scholar
• Clarke , DD . 1991 . Fluoroacetate and fluorocitrate: mechanism of action . Neurochem. Res. , 16 : 1055 – 1058 .
   PubMed Web of Science ®Google Scholar
• Povirk , LF and Shuker , DE . 1994 . DNA damage and mutagenesis induced by nitrogen mustards . Mutat. Res. , 318 : 205 – 226 .
   PubMed Web of Science ®Google Scholar
• Van Duuren , BL . 1988 . Direct-acting alkylating and acylating agents. DNA adduct formation, structure-activity, and carcinogenesis . Ann. N. Y. Acad. Sci. , 534 : 620 – 634 .
   PubMed Web of Science ®Google Scholar
• Kaplita , PV and Smith , RP . 1986 . Pathways for the bioactivation of aliphatic nitriles to free cyanide in mice . Toxicol. Appl. Pharmacol. , 84 : 533 – 540 .
   PubMed Web of Science ®Google Scholar
• Casida , JE and Lawrence , LJ . 1985 . Structure-activity correlations for interactions of bicyclophosphorus esters and some polychlorocycloalkane and pyrethroid insecticides with the brain-specific t-butylbicyclophosphorothionate receptor . Environ. Health. Perspect. , 61 : 123 – 132 .
   PubMed Web of Science ®Google Scholar
• Algorithm Builder 1.8, Pharma Algorithms, Inc., Toronto ON, Canada, 2006; software available at http://www.pharma-algorithms.com
   Google Scholar
• Wold , S , Sjostrom , M and Eriksson , L . 1998 . “ PLS in chemistry ” . In The Encyclopedia of Computational Chemistry , Edited by: Schleyer , PvR , Allinger , NL , Clark , T , Gasteiger , J , Kollman , PA , Schaefer III , HF and Schreiner , PR . Vol. 3 , 2006 – 2021 . Chichester : John Wiley & Sons .
   Google Scholar
• Efron , B . 1979 . Bootstrap methods: another look at the jackknife . Ann. Statist. , 7 : 1 – 26 . Available at http://dx.doi.org/10.1214/aos/1176344552
   Web of Science ®Google Scholar
• NCBI PubChem database, National Center for Biotechnology Information of the National Library of Medicine, Bethesda (MD), United States. Available at http://pubchem.ncbi.nlm.nih.gov/
   Google Scholar
• Derwent World Drug Index sample CD, Derwent Information, London, United Kingdom, 2001; software available at www.derwent.com
   Google Scholar