Use of In Silico Evaluation of Chemical Genotoxicity

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Use of In Silico Evaluation of Chemical Genotoxicity

Makoto Hayashi, National Institute of Health Sciences (Japan)

Published: December 6, 2007

About the Author(s)
1999-present: Head, Division of Genetics and Mutagenesis, National Institute of Health Sciences, Tokyo, Japan. B.Sc., M.Sc. and D.Sc. Kwansei Gakuin University. Numerous professional committees, societies, task forces including: President of Japanese Environmental Mutagen Society (JEMS) (2002-2003), President of Mammalian Mutagen Study Group (MMS) (1999-2001), Councilor of US EMS (2001-2003), Member of Japanese Society of Genetics, Member of Japanese Society of Chromosome Research, Member of Japanese Toxicology Society, Editorial Boards.

Makoto Hayashi, D.Sc.
Head, Division of Genetics and Mutagenesis
National Institute of Health Sciences
1-18-1 Kamiyoga
Tokyo 158-8501

Mutagenicity is one of the important endpoints for risk assessment of environmental chemicals. Many short-term in vitro/in vivo assays to evaluate mutagenicity have been developed and some of them are being used routinely. Although these assays can generally be completed within a short period, their throughput is not enough to assess the large number of chemicals that exist in our environment without additional information on their safety.

The other factor to be considered is the movement of 3Rs in the toxicology field. Although genotoxicity started as an alternative assay to assess chemical carcinogenicity using bacteria, we are still using many experimental materials, bacteria, cultured cells, and also rodents. Concerning the 3Rs, we tried to reduce animals to assess chemical genotoxicity, e.g., omitting positive control group in the micronucleus assay, and integrating the micronucleus assay into the general repeat dose toxicological study. However, to further reduce animal testing, and to be able to assess large numbers of chemicals rapidly, use of in silico systems is the ultimate approach.

We have evaluated three commercially available in silico systems, i.e., DEREK, MultiCASE, and ADMEWorks, to assess mutagenicity of existing chemicals. We applied these systems to the 703 chemicals that had been evaluated by the Salmonella/microsome assay from the CGX database published by Kirkland et al. (2005). We also applied these systems to the 206 existing chemicals in Japan that were recently evaluated using the Salmonella/microsome assay under GLP compliance (ECJ database).

Sensitivity (the proportion of positive in Salmonella/microsome assay correctly identified by the in silico system), specificity (the proportion of negative in Salmonella/microsome assay correctly identified) and concordance (the proportion of correct identifications of positive and negative in Salmonella/microsome assay) were increased when we combined the three in silico systems to make a decision in mutagenicity, and accordingly we concluded that in silico evaluation could be optimized by combining the evaluations from different systems (Hayashi et al., 2005)

We also investigated whether there was any correlation between the Salmonella/microsome assay result and the molecular weight of the chemicals. We found that high molecular weight (>3000) chemicals tended to give negative results (Fig. 1). In fact, only 7 (3.6%) of the Ames positive chemicals analyzed had a molecular weight > 3000 and of these, most (4/7) had epoxy groups. Based on this, we proposed a decision tree (Fig. 2) to assess chemical genotoxicity using a combination of the three in silico systems after pre-selection according to their molecular weight and presence of an epoxy group.

We have already done the same analysis substituting the in vitro chromosomal aberration assay for the Salmonella/microsome assay. We obtained similar outcomes though the concordance was a little lower than that of Salmonella/microsome assay. In addition, recently we started a project to establish a database of results from repeat dose studies to establish a (Q)SAR/Category model for the repeat dose toxicology studies as “Development of Hazard Assessment Methodology by using Structure Activity Relationship Method.” The final goal of our project is to establish the decision support system for experts to evaluate chemical safety efficiently and accurately. These studies have been supported by the Health and Labour Sciences Research Grants and New Energy and Industrial Technology Development Organization.

Clearly in silico methods are the way forward for assessing the genotoxicity and potential carcinogenicity/repeat dose general toxicology of large numbers of chemicals. Importantly, these methods will contribute to the reduction of animal use.

Fig. 1 Cumulative percentage of chemicals based on their molecular weight. 194 Ames positive chemcias were analyzed. 7/194 chemicals were more than 3000 molecular weight and Ames positive and 4/7 contained epoxy groups.




Fig. 2 Decision tree. In in silico evaluation, when two or more give positive then the final call is “Positive” and two or more ngative then call “Negative”.
©2007 Makoto Hayashi

Kirkland, D., Aardema, M., Henderson, L. & Mueller, L. (2005). Evaluation of the ability of a battery of three in vitro genotoxicity tests to discriminate rodent carcinogens and non-carcinogens—I. Sensitivity, specificity and relative predictivity. Mutat. Res. 584, 1–256.

Hayashi, M., Kamata, E., Hirose, A., Takahashi, M., Morita, M. & Ema, M. (2005). In silico assessment of chemical mutagenesis in comparison with results of Salmonella microsome assay on 909 chemicals. Mutat. Res. 588, 129-135.