Comparison and possible use of in Silico tools for carcinogenicity within REACH legislation

Journal of Environmental Science and Health - Part C Environmental Carcinogenesis and Ecotoxicology Reviews

Volumn 29, Issue 4, 2011, Pages 300-323

  Milan, Chiara ^a   Schifanella, Onofrio ^a   Roncaglioni, Alessandra ^a   Benfenati, Emilio ^a  

^a MARIO NEGRI INSTITUTE FOR PHARMACOLOGICAL RESEARCH   (Italy)

Author keywords

alternative methods; carcinogenicity; QSAR; REACH

Indexed keywords

ALTERNATIVE METHODS; ANIMAL STUDIES; CARCINOGENICITY; CRITICAL POINTS; EXPERIMENTAL VALUES; FALSE NEGATIVES; FALSE POSITIVE; IN-SILICO; IN-SILICO MODELS; PREDICTION ACCURACY; QSAR; REACH; TOXICITY PREDICTIONS;

CHEMICAL COMPOUNDS;

COMPUTATIONAL CHEMISTRY;

ENVIRONMENTAL CHEMICAL;

ALGORITHM; ARTICLE; CARCINOGENICITY; COMPUTER MODEL; COMPUTER PROGRAM; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; INTERMETHOD COMPARISON; LAW; ORGANIZATION; PREDICTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; TOXICITY TESTING;

ANIMAL TESTING ALTERNATIVES; CARCINOGENICITY TESTS; CARCINOGENS; COMPUTER SIMULATION; EUROPEAN UNION; MODELS, BIOLOGICAL; MODELS, CHEMICAL; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

ANIMALIA;

EID: 84857806152     PISSN: 10590501     EISSN: 15324095     Source Type: Journal    
DOI: 10.1080/10590501.2011.629973     Document Type: Article

References (33)

1. 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.
2. Benfenati E. Predicting toxicity through computers: A changing world. Chem Cent J. 2007;1:32.
3. European Chemicals Agency. Guidance on information requirements and chemical safety assessment. Chapter 6: QSARs and grouping of chemicals, May 2008.
4. Benfenati E, Benigni R, DeMarini DM, Helma C, Kirkland D, Martin TM, et al. Predictive models for carcinogenicity and mutagenicity: Frameworks, state-ofthe-art, and perspectives. J Environ Sci Health C Environ Carcinog Ecotoxicol Rev. 2009;27:57-90.
5. Gini G, Lorenzini M, Benfenati E, Grasso P, Bruschi M. Predictive carcinogenicity: A model for aromatic compounds, with nitrogen-containing substituents, based on molecular descriptors using an artificial neural network. J Chem In. Comput Sci. 1999;39:1076-1080. (Pubitemid 129579841)
6. Toropova AP, Toropov AA, Gonella Diaza R, Benfenati E, Gini G. Analysis of the co-evolutions of correlations as a tool for QSAR-modeling of carcinogenicity: An unexpected good prediction based on a model that seems untrustworthy. Central European Journal Chemistry. 2011;9:165-174.
7. Ashby J, Tennant RW. Chemical structure, Salmonella mutagenicity and extent of carcinogenicity as indicators of genotoxic carcinogenesis among 222 chemicals tested in rodents by the U.S. NCI/NTP. Mutat Res. 1988;204:17-115. (Pubitemid 18057809)
8. HazardExpert module of Pallas 3.0. User's Manual, 1989, CompuDrug Ltd, Budapest, Hungary. http://www.compudrug.com.
9. Toxtree 1.60. Toxtree User Manual, 2009, Ideaconsult Ltd., Sofia, Bulgaria. http: //ihcp.jrc.ec.europa.eu/our-labs/computational-toxicology/qsar- tools/toxtree.
10. Benigni R, Bossa C, Jeliazkova N, Netzeva T,Worth A. Benigni/Bossa rulebase for mutagenicity and carcinogenicity-A module of Toxtree. JRC Scientific and Technical Reports. 2008.
11. Derek for Windows 11.0, Lhasa Limited, Leeds, UK. http://www. lhasalimited.org.
12. Benigni R, Bossa C. Mechanisms of chemical carcinogenicity and mutagenicity: A review with implications for predictive toxicology. Chem Rev. 2011;111:2507-2536.
13. CAESAR project homepage. http://www.caesar-project.eu.
14. Helma C. Lazy structure-activity relationships (lazar) for the prediction of rodent carcinogenicity and Salmonella mutagenicity. Mol Divers. 2006;10:147-158. (Pubitemid 44092205)
15. Klopman G. Computer automated structure evaluation of organic molecules, J Am Chem Soc. 1984;106:7315-7324.
16. Rosenkranz HS, Cunningham AR, Zhang YP, Claycamp HG, Macina OT, Sussman NB, et al. Development, characterization and application of predictive toxicology models. SAR QSAR Environ Res. 1999;10:277-298.
17. MCASE, Version 1.90. MultiCASE Inc, Beachwood, OH (USA). http://www. multicase.com.
18. TOPKAT, version 6.1. User guide. Accelrys Inc.: San Diego, CA (USA), 2001. http: //accelrys.com.
19. Ferrari T, Gini G, Golbamaki Bakhtyari N, Benfenati E. Mining toxicity structural alerts from SMILES: A new way to derive structure activity relationships. CIDM-IEEE Symposium Series on Computational Intelligence, Paris, April 11-15, 2011.
20. Gold LS, Slone TH, Williams CR, Burch JM, Stewart TW, Swank AE, Beidler J, Richard AM. (2008) DSSTox Carcinogenic Potency Database Summary Tables -All Species: SDF File and Documentation, Updated version: CPDBAS v3b 1481 10Apr2006. http://www.epa.gov/ncct/dsstox/sdf-cpdbas.html.
21. FDA 2009 SAR Carcinogenicity-SAR Structures, Leadscope Inc., Columbus, OH (USA). http://www.leadscope.com.
22. Dragon software homepage, Talete srl, Italy. http://www.talete.mi.it/ products/dragon-description.htm.
23. Fjodorova N, Vracko M, Novic M, Roncaglioni A, Benfenati E. New public QSAR model for carcinogenicity. Chem Cent J. 2010;4 (Suppl 1):S3.
24. Marchant CA, Briggs KA, Long A. In silico tools for sharing data and knowledge on toxicity and metabolism: Derek for Windows, Meteor, and Vitic. Toxicol Mech Method. 2008;18: 177-187. (Pubitemid 351414973)
25. Benfenati E, Gini G. Computational predictive programs (expert systems) in toxicology. Toxicology. 1997;119:213-225. (Pubitemid 27187493)
26. Lazar prediction system, In silico toxicology gmbh, Basel, Switzerland. http:// www.in-silico.de.
27. Matthews EJ, Contrera JF. A new highly specific method for predicting the carcinogenic potential of pharmaceuticals in rodents using enhanced MCASE QSAR-ES software. Regul. Toxicol Pharm. 1998;28:242-264. (Pubitemid 29096166)
28. The Carcinogenic Potency Database (CPDB), Berkeley, CA (USA). http://potency. berkeley.edu.
29. Piegorsch WW, Zeiger E. Measuring intra-assay agreement for the Ames salmonella assay. In: L Hotorn, ed. Statistical Methods in Toxicology, Lecture Notes in Medical Informatics. Berlin: Springer-Verlag; 1991:35-41.
30. Contrera JF, Matthews EJ, Benz RD. Predicting the carcinogenic potential of pharmaceuticals in rodents using molecular structural similarity and E-state indices. Regul Toxicol Pharm. 2003;38:243-259. (Pubitemid 37414815)
31. Guidance document on the validation of (quantitative) structure-activity relationship [(Q)SAR] models, OECD Environmental Health and safety publication series on testing and assessment no. 69, ENV/JM/MONO(2007)2.
32. AMBIT homepage, Ideaconsult Ltd., Sofia, Bulgaria. http://ambit. sourceforge.net.
33. Lombardo A, Gonella Diaza R, Roncaglioni A, Benfenati E. CAESAR's approach for alternative in silico methods for REACH. ALTEX. 2010;27:109-116.