Skip to main content

The Application of Structure–Activity Relationships to the Prediction of the Mutagenic Activity of Chemicals

  • Protocol
  • First Online:
Genetic Toxicology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 817))

Abstract

Prediction of mutagenicity by computer is now routinely used in research and by regulatory authorities. Broadly, two different approaches are in wide use. The first is based on statistical analysis of data to find patterns associated with mutagenic activity. The resultant models are generally termed quantitative structure–activity relationships (QSAR). The second is based on capturing human knowledge about the causes of mutagenicity and applying it in ways that mimic human reasoning. These systems are generally called knowledge-based system. Other methods for finding patterns in data, such as the application of neural networks, are in use but less widely so.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Ashby J and Tennant R W (1988) Chemical structure, Salmonella Mutagenicity and Extent of Carcinogenicity as Indicators of Genotoxic Carcinogenesis Among 222 Chemicals Tested in Rodents by the US NCI/NTP. Mutagenesis, 204, 17–115.

    CAS  Google Scholar 

  2. Hansch C and Fujita T (1964) A Method for the Correlation of Biological Activity and Chemical Structure. J. Amer. Chem. Soc. 86, 1616–1626.

    Article  CAS  Google Scholar 

  3. Fujita T, Isawa J, and Hansch C (1964) A New Substituent Constant, π, Derived from Partition Coefficient. J. Amer. Chem. Soc., 86, 5175–5180.

    Article  CAS  Google Scholar 

  4. ClogP is supplied by Biobyte Corporation, 201 West 4th. Street, #204, Claremont, CA 91711–4707, USA.

    Google Scholar 

  5. Hall L H, Mohney B, and Kier L B (1991) The Electrotopological State: Structure Information at the Atomic Level for Molecular Graphs. J. Amer. Chem. Soc., 31, 76–82.

    CAS  Google Scholar 

  6. Taft R W, (1956) Separation of Polar, Steric, and Resonance Effects. In: Newmann MS (ed.). Steric Effects in Organic Chemistry, John Wiley, New York, pp. 559–675.

    Google Scholar 

  7. Kamlet MJ, Abboud JML, Abraham MH, and Taft RW (1983) Linear Solvation Energy Relationships. 23. A Comprehensive Collection of the Solvatochromic Parameters, π*, α, and β, and Some Methods for Simplifying the Generalised Solvatochromic Equation, J. Org. Chem., 48, 2877–2887.

    Article  CAS  Google Scholar 

  8. Eriksson L, Johansson E, Kettaneh-Wold N, and Wold S (2001) Multi- and Megavariate Data Analysis, Umetrics AB, Umeå, Sweden.

    Google Scholar 

  9. Hansch C and Leo A (1995) Exploring QSAR: Fundamentals and Applications in Chemistry and Biology, American Chemical Society, Washington DC, USA.

    Google Scholar 

  10. Livingstone D (1995) Data Analysis for Chemists: Applications to QSAR and Chemical Product Design, Oxford University Press, England.

    Google Scholar 

  11. Enslein K, and Craig P N (1982) Carcinogenesis: a Predictive Structure-Activity Model, J. Toxicol. Environ. Health, 10, 521–530.

    Article  PubMed  CAS  Google Scholar 

  12. Enslein K, Gombar V K, and Blake B W (1994) Use of SAR in Computer-Assisted Prediction of Carcinogenicity and Mutagenicity of Chemicals by the TOPKAT Program, Mutation Res., 305, 47–62.

    Article  PubMed  CAS  Google Scholar 

  13. Accelrys Inc., 10188 Telesis Court, Suite 100, San Diego, CA 92121, USA. http://accelrys.com/.

  14. Klopman G (1984) Artificial Intelligence Approach to Structure-Activity Studies: Computer Automated Structure Evaluation of Biological Activity of Organic Molecules, J. Amer. Chem. Soc., 106, 7315–7321.

    Article  CAS  Google Scholar 

  15. Klopman G, Ivanov J, Saiakhov R and Chakravarti S (2005) MC4PC – An Artificial Intelligence Approach to the Discovery of Structure Toxic Activity Relationships (STAR), in Predictive Toxicology, ed. Christoph Helma, CRC Press, Boca Raton, pp. 423–457.

    Google Scholar 

  16. Klopman G, Chakravarti S K, Zhu H, Ivanov J M, and Saiakhov R D (2004) ESP: a Method to Predict Toxicity and Pharmacological Properties of Chemicals Using Multiple MCASE Databases. J. Chem. Inf. Comput. Sci. 44, 704–715.

    Article  PubMed  CAS  Google Scholar 

  17. Kühne R, Kleint F, Ebert R U, and Schüürmann G (1996) Calculation of Compound Properties Using Experimental Data from Sufficiently Similar Chemicals, in Software Development in Chemistry 10, ed. Johann Gasteiger, Gesellschaft Deutscher Chemiker, Frankfurt, Germany, pp. 125–134.

    Google Scholar 

  18. Kühne R, Ebert R-U, and Schüürmann G. (2007) Estimation of Compartmental Half-Lives of Organic Compounds – Structural Similarity vs. EPI-Suite, QSAR Comb. Sci. 26, 542–549.

    Google Scholar 

  19. LeadScope Predictive Data Miner comes from Leadscope Inc., 1393 Dublin Road, Columbus, Ohio 43215, USA.

    Google Scholar 

  20. Quinlan J R (1986) Induction of Decision Trees, Machine Learning, 1, 81–106.

    Google Scholar 

  21. King R D and Srinivasan A (1996) Prediction of Rodent Carcinogenicity Bioassays from Molecular Structure Using Inductive Logic Programming, Environ. Health, Persp., 104, 1031–1040.

    CAS  Google Scholar 

  22. Vracko M, Bandelj V, Barbieri P, Benfenati E, Chaudhry Q, Cronin M, Devillers J, Gallegos A, Gini G, Gramatica P, Helma C, Neagu D, Netzeva T, Pavan M, Patlevicz G, Randic M, Tsakovska I, and Worth A (2006) Validation of Counter Propagation Neural Network Models for Predictive Toxicology According to the OECD Principles. A Case Study, SAR QSAR Environ. Res., 17, 265–284.

    Article  PubMed  CAS  Google Scholar 

  23. Buontempo F V, Zhong Wang X, Mwense M, Horan N, Young A, and Osborn D (2005) Genetic Programming for the Induction of Decision Trees to Model Ecotoxicity Data, J. Chem. Inf. Model., 45, 904–912.

    Article  PubMed  CAS  Google Scholar 

  24. Helma C, Cramer T, Cramer S, and de Raedt L (2004) Data Mining and Machine Learning Techniques for the Identification of Mutagenicity Inducing Substructures and Structure Activity Relationships of Noncongeneric Compounds, J. Chem. Inf. Comput. Sci., 44, 1402–1411.

    Article  PubMed  CAS  Google Scholar 

  25. Kaufman J J, Koski W S, Harihan P, Crawford J, Garmer D M and Chan-Lizardo L. (1983) Prediction of Toxicology and Pharmacology Based on Model Toxicophores and Pharmacophores using the New TOX-MATCH-PHARM-MATCH Program, Int. J. Quantum Chem., Quantum Biol. Symp., 10, 375–416.

    Google Scholar 

  26. Koski W S and Kaufman J J (1988) TOX-MATCH/PHARM-MATCH Prediction of Toxicological and Pharmacological Features by Using Optimal Substructure Coding and Retrieval Systems, Anal. Chim. Acta, 210, 203–7.

    Article  CAS  Google Scholar 

  27. Patlewicz G, Jeliazkova N, Saliner A G, and Worth A P (2008) Toxmatch – a New Software Tool to Aid in the Development and Evaluation of Chemically Similar Groups, SAR and QSAR in Environ. Res., 19, 397–412.

    CAS  Google Scholar 

  28. http://ecb.jrc.it/qsar/qsar-tools/index.php?c=TOXMATCH

  29. Ideaconsult Limited., 4 Angel Kanchev Street, 1000 Sofia, Bulgaria.

    Google Scholar 

  30. Woo Y T, Lai D Y, Argus M F, and Arcos J C, (1995) Development of Structure Activity Relationship Rules for Predicting Carcinogenic Potential of Chemicals, Toxicol. Lett., 79, 219–28.

    Article  PubMed  CAS  Google Scholar 

  31. Lai D Y, Woo Y T, Argus M F, and Arcos J C, (1996) Cancer Risk Reduction Through Mechanism-Based Molecular Design of Chemicals, in Designing Safer Chemicals, eds. S. De Vito and R. Garrett, ACS Symposium Series Vol. 640, American Chemical Society, Washington DC, pp. 62–73.

    Google Scholar 

  32. Woo Y T and Lai D Y (2005) OncoLogic: a Mechanism-Based Expert System for Predicting the Carcinogenic Potential of Chemicals, in Predictive Toxicology, ed. Christoph Helma, Marcel Dekker, New York, 385–413.

    Google Scholar 

  33. http://www.epa.gov/oppt/newchems/tools/oncologic.htm

  34. Smithing M P and Darvas F (1992) HazardExpert – an Expert System for Predicting Chemical Toxicity, in Food Safety Assessment, eds. J. W. Finley, S. F. Robinson, and D. J. Armstrong, ACS Symposium Series Vol. 484, American Chemical Society, Washington DC, pp. 191–200.

    Google Scholar 

  35. CompuDrug International Inc., 115 Morgan Drive, Sedona, AZ 86351, USA.

    Google Scholar 

  36. http://ecb.jrc.ec.europa.eu/

  37. Judson P N, Marchant C A, and Vessey J D (2003) Using Argumentation for Absolute Reasoning About the Potential Toxicity of Chemicals, J. Chem. Inf. Comput. Sci., 43, 1364–1370.

    Article  PubMed  CAS  Google Scholar 

  38. Langton K and Marchant C A (2005) Improvements to the Derek for Windows Prediction of Chromosome Damage, Toxicology Letters, 158, S36–S37.

    Google Scholar 

  39. Derek for Windows and Meteor are developed by, and available from, Lhasa Limited, 22–23 Blenheim Terrace, Woodhouse Lane, Leeds LS2 9HD, United Kingdom.

    Google Scholar 

  40. Sanderson D M, (1989) Computer Prediction of Possible Toxicity from Chemical Structure. Paper presented at the autumn meeting of the British Toxicological Society.

    Google Scholar 

  41. Judson P N (1989) The Use of Expert Systems for Detecting Potential Toxicity. Paper presented at the autumn meeting of the British Toxicological Society.

    Google Scholar 

  42. Sanderson D M, Earnshaw C G, and Judson P N (1991) Computer Prediction of Possible Toxic Action from Chemical Structure; the DEREK System. Human. Exp. Toxicol., 10, 261–273.

    Article  CAS  Google Scholar 

  43. Ridings J E, Barratt M D, Cary R, Earnshaw C G, Eggington E, Ellis M K, Judson P N, . Langowski J J, Marchant C A, Payne M P, Watson W P and Yih T D (1996) Computer Prediction of Possible Toxic Action from Chemical Structure: an Update on the DEREK System. Toxicology, 106, 267–279.

    Article  PubMed  CAS  Google Scholar 

  44. Krause P J, Ambler S, Elvang-Gøransson M, and Fox J (1995) A Logic of Argumentation for Reasoning Under Uncertainty, Computational Intelligence, 11(1), 113–131.

    Article  Google Scholar 

  45. Judson P N and Vessey J D (2003) A Comprehensive Approach to Argumentation, J. Chem. Inf. Comput. Sci., 43, 1356–1363.

    Article  PubMed  CAS  Google Scholar 

  46. Greene N, Judson P N, Langowski J J, and Marchant C A (1999) Knowledge-Based Expert Systems for Toxicity and Metabolism Prediction: DEREK, StAR and METEOR, SAR and QSAR in Environ. Res., 10, 299–314.

    CAS  Google Scholar 

  47. Testa B, Balmat A L, Long A, and Judson P (2005) Predicting Drug Metabolism – an Evaluation of the Expert System METEOR, Chemistry and Biodiversity, 2, 872–885.

    Article  PubMed  CAS  Google Scholar 

  48. Wipke W T, Ouchi G I, and Chou J T (1983) Computer-Assisted Prediction of Metabolism, in Structure-Activity Correlation as a Predictive Tool in Toxicology: Fundamentals, Methods, and Applications, ed. Leon Golberg, Hemisphere, Washington, DC, pp 151–169.

    Google Scholar 

  49. Darvas F (1987) METABOLEXPERT: an Expert System for Predicting Metabolism of Substances, in QSAR. Environmental Toxicology, proceedings of an international workshop 1986, ed. K .L. E. Kaisler, Reidel, Dordrecht, pp. 71–81.

    Google Scholar 

  50. MetabolExpert is supplied by CompuDrug International Inc., 115 Morgan Drive, Sedona, AZ 86351, USA.

    Google Scholar 

  51. Klopman G (1994) Mario Dimayagu, and Joseph Talafous, META. 1. A Program for the Evaluation of Metabolic Transformations of Chemicals, J. Chem. Inf. Comput. Sci., 34 1320–1325.

    Article  PubMed  CAS  Google Scholar 

  52. Talafous J, Sayre L M, Mieyal J J, and Klopman G (1994) META. 2. A Dictionary Model of Mammalian Xenobiotic Metabolism, J. Chem. Inf. Comput. Sci., 34, 1326–1333.

    Article  PubMed  CAS  Google Scholar 

  53. META is supplied by Multicase Inc, 23811 Chagrin Blvd Ste 305, Beachwood, OH, 44122, USA.

    Google Scholar 

  54. Jaworska J, Dimitrov S, Nikolova N, and Mekenyan O (2002) Probabilistic Assessment of Biodegradability Based on Metabolic Pathways: CATABOL System, SAR and QSAR in Environ. Res., 13, 307–323.

    CAS  Google Scholar 

  55. CATABOL is supplied by the Laboratory of Mathematical Chemistry, University “Prof. Assen Zlatarov”, 1 Yakimov Street, Bourgas, 8010 Bulgaria.

    Google Scholar 

  56. International QSAR Foundation, 1501 W. Knife River Road, Two Harbors, Minnesota 55616. Their website address is http://www.qsari.org/.

  57. Laboratory of Mathematical Chemistry, University “Prof. Assen Zlatarov”, 1 Yakimov Street, Bourgas, 8010 Bulgaria.

    Google Scholar 

  58. Information about the (Q)SAR Toolbox Project can be found at http://www.oecd.org/document/23/0,3343,en_2649_34379_33957015_1_1_1_1,00.html and the toolbox can be downloaded from there. The address of the OECD is 2, rue André Pascal, F-75775 Paris, Cedex 16, France.

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Philip Judson .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Judson, P. (2012). The Application of Structure–Activity Relationships to the Prediction of the Mutagenic Activity of Chemicals. In: Parry, J., Parry, E. (eds) Genetic Toxicology. Methods in Molecular Biology, vol 817. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-421-6_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-421-6_1

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-420-9

  • Online ISBN: 978-1-61779-421-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics