Skip to main content
Log in

True prediction of lowest observed adverse effect levels

  • Full-length paper
  • Published:
Molecular Diversity Aims and scope Submit manuscript

Summary

A database of structurally heterogeneous chemical structures with their experimental values of Lowest Observed Adverse Effect Levels (LOAELs) was modeled using graph theoretical descriptors. Variable selection for multiple linear regression (MLR) and linear discriminant analysis (LDA) was accomplished by the Internal Test Set (ITS) method in order to achieve true predicted LOAEL values. The results obtained can be considered good if we take in count the structural diversity of the training set.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. McNaught, A.D. and Wilkinson, A., IUPAC Compendium of Chemical Terminology, 2nd Edition Blackwell Science, 1997.

  2. Pogliani, L., From molecular connectivity indices to semiempirical connectivity terms: recent trends in graph theoretical descriptors, Chem Rev., 100 (2000) 3827–3858.

    Article  PubMed  CAS  Google Scholar 

  3. Gozalbes, R., Doucet, J.P. and Derouin, F., Application of topological descriptors in QSAR and drug design: history and new trends, Curr. Drug Targets Infect. Disord., 2 (2002) 93–102.

    Article  PubMed  CAS  Google Scholar 

  4. Torrens, F., A new topological index to elucidate apolar hydrocarbons, J. Comput.-Aid. Mol. Des., 15 (2001) 709–719.

    Article  CAS  Google Scholar 

  5. Besalú, E., Gironés, X., Amat, L. and Carbó-Dorca, R., Molecular quantum similarity and the fundamentals of QSAR, Acc. Chem. Res., 35 (2002) 289–295.

    Article  PubMed  CAS  Google Scholar 

  6. Golbraikh, A., Bonchev, D. and Tropsha, A., Novel ZE-isomerism descriptors derived from molecular topology and their application to QSAR analysis, J. Chem. Inf. Comput. Sci., 42 (2002) 769–787.

    Article  PubMed  CAS  Google Scholar 

  7. Tomovic, Z. and Gutman, I., Modeling boiling points of cycloalkanes by means of iterated line graph sequences, J. Chem. Inf. Comput. Sci., 41 (2001) 1041–1045.

    Article  PubMed  CAS  Google Scholar 

  8. Torrens, F., Table of periodic properties of fullerenes based on structural parameters, J. Chem. Inf. Comput. Sci., 44 (2004) 60–67.

    Article  PubMed  CAS  Google Scholar 

  9. Estrada, E., Patlewicz, G., Chamberlain, M., Basketter, D. and Larbey, S., Computer-aided knowledge generation for understanding skin sensitization mechanisms: The TOPS-MODE approach, Chem. Res. Toxicol., 16 (2003) 1226–1235.

    Article  PubMed  CAS  Google Scholar 

  10. Gálvez, J., Julián-Ortiz, J.V. de and García-Domenech, R., General topological patterns of known drugs, J. Mol. Graph. Model., 20 (2001) 84–94.

    Article  PubMed  Google Scholar 

  11. Murcia-Soler, M., Pérez-Giménez, F., García-March, F.J., Salabert-Salvador, M.T., Díaz-Villanueva, W. and Castro-Bleda, M.J., Drugs and nondrugs: An effective discrimination with topological methods and artificial neural networks, J. Chem. Inf. Comput. Sci., 43 (2003) 1688–1702.

    Article  PubMed  CAS  Google Scholar 

  12. Ivanciuc, O. and Klein, D.J., Computing wiener-type indices for virtual combinatorial libraries generated from heteroatom-containing building blocks, J. Chem. Inf. Comput. Sci., 42 (2002) 8–22.

    Article  PubMed  CAS  Google Scholar 

  13. Basak, S.C., Mills, D.R., Balaban, A.T. and Gute, B.D., Prediction of mutagenicity of aromatic and heteroaromatic amines from structure: A hierarchical QSAR approach, J. Chem. Inf. Comput. Sci., 41 (2001) 671–678.

    Article  PubMed  CAS  Google Scholar 

  14. Julián-Ortiz, J.V. de, García-Domenech, R., Gálvez, J. and Pogliani, L., Predictability and prediction of lowest observed adverse effect levels in a structurally heterogeneous set of chemicals, SAR QSAR Environ. Res., 16 (2005) 263–272

    Article  PubMed  Google Scholar 

  15. Mumtaz, M.M., Knauf, L.A., Reisman, D.J., Peirano, W.B., DeRosa, C.T., Gombar, V.K., Enslein, K., Carter, J.R., Blake, B.W., Huque, K.I. and Ramanujam, V.M.S., Assessment of effect levels of chemicals from quantitative structure-activity relationship (QSAR) models. I. Chronic lowest-observed-adverse-effect level (LOAEL), Toxicol Lett., 79 (1995) 131–143.

    Article  PubMed  CAS  Google Scholar 

  16. Venkatapathy, R., Moudgal, C.J. and Bruce, R.M., Assessment of the oral rat chronic lowest observed adverse effect level model in TOPKAT, a QSAR software package for toxicity prediction, J. Chem. Inf. Comput. Sci., 44 (2004) 1623–1629.

    Article  PubMed  CAS  Google Scholar 

  17. García-Domenech, R., DESCRI version 2003. Department of Physical Chemistry. University of Valencia, Spain. It is a home-made PC program for the calculation of 62 molecular structural invariants which accepts lists of MDL MOL files as inputs, freely available to academia upon request to the author (Ramon.Garcia@uv.es).

  18. Hall, L.H., Molconn-Z (version 3.0) EastemNazaree College, Quincy, Massachusetts, USA.

  19. BMDP New System 2.0., Statistical Solutions Ltd., Saugus, MA, USA, 2001.

  20. Furnival, G.M. and Wilson, R.W., Regresions by leaps and bounds, Technometrics, 16 (1974) 499–511.

    Article  Google Scholar 

  21. Livingstone, D.J. and Salt, D.W., Judging the significance of multiple linear regression models, J. Med. Chem., 48 (2005) 661–663.

    Article  PubMed  CAS  Google Scholar 

  22. Besalú, E., Regre v 1.57. Institute of Computational Chemistry. University of Girona. Spain, 2005.

    Google Scholar 

  23. García-García, A., Gálvez, J., Julián-Ortiz, J.V. de, García-Domenech, R., Muñoz, C., Guna, R. and Borrás, R., Search of chemical scaffolds for novel antituberculosis agents, J. Biomol. Screen., 10 (2005) 206–214.

    Article  PubMed  CAS  Google Scholar 

  24. Besalú, E. and Julián-Ortiz, J.V. de, Equivalence of the Pecka-Ponec correlation probability and the statistical F significance for MLR models, J. Math. Chem., 36 (2004) 361–363.

    Article  Google Scholar 

  25. Gálvez, J., García-Domenech, R., Julián-Ortiz, J.V. de and Soler. R., Topological approach to drug design, J. Chem. Inf. Comp. Sci., 35 (1995) 272–284. Errata: J. Chem. Inf. Comp. Sci. 35 (1995) 938.

  26. Kier, L.B., Murray, W.J., Randiċ, M. and Hall, L.H., Molecular connectivity V: connectivity series concept applied to density, J. Pharm. Sci., 65 (1976) 1226–1230.

    Article  PubMed  CAS  Google Scholar 

  27. Julián-Ortiz, J.V. de, Gálvez, J., Muñoz-Collado, C., García–Domenech, R. and Gimeno–Cardona, C., Virtual combinatorial syntheses and computational screening of new potential anti-herpes compounds, J. Med. Chem., 42 (1999) 3308–3314.

    Article  PubMed  CAS  Google Scholar 

  28. Kier, L.B. and Hall, L.H., General definition of valence delta values for molecular connectivity, J. Pharm. Sci., 72 (1983) 1170–1173.

    Article  PubMed  CAS  Google Scholar 

  29. Gálvez, J., García-Domenech, R., Salabert, M.T. and Soler, R., Charge indexes. New topological descriptors, J. Chem. Inf. Comp. Sci., 34 (1994) 520–525.

    Article  Google Scholar 

  30. Hall, L.H. and Kier, L.B., Electrotopological state indices for atom types: a novel combination of electronic, topological, and valence state information, J. Chem. Inf. Comput. Sci., 35 (1995) 1039–1045.

    Article  CAS  Google Scholar 

  31. Kier, L.B., Indexes of molecular shape from chemical graphs, Medicinal Research Reviews, 7 (1987) 417–440.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to R. García-Domenech.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

García-Domenech, R., de Julián-Ortiz, J.V. & Besalú, E. True prediction of lowest observed adverse effect levels. Mol Divers 10, 159–168 (2006). https://doi.org/10.1007/s11030-005-9007-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11030-005-9007-z

Key Words

Navigation