In Silico Model for Chemical-Induced Chromosomal Damages Elucidates Mode of Action and Irrelevant Positives
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data set of Chemical Substances
2.1.1. Data Acquisition and Classification
- Positives: (a) chemicals with “positive results in in vitro mammalian cell genotoxicity tests” in Kirkland et al. [12] (25 chemicals) and (b) positive chemicals (70 chemicals) and “chemicals with minimal or some concern” (12 chemicals) in Morita et al [11]. Although o-Dichlorobenzene (CAS No. 95-50-1) had been classified into “missed chemicals with negligible concern” in Morita et al. [11], it was recategorized into positives because positive results were recently reported in both in vivo [20] and in vitro [15] micronucleus tests under the current OECD test guidelines [14]. In total, 108 chemicals were classified as positives.
- Misleading positives: (a) chemicals that “should give negative results in in vitro mammalian cell genotoxicity tests, but have been reported to induce gene mutations in mouse lymphoma cells, chromosomal aberrations, or micronuclei, often at high concentrations or at high levels of cytotoxicity” in Kirkland et al. [12] (17 chemicals), (b) “chemicals with negligible concern” (25 chemicals) in Morita et al. [11], and (c) among chemicals with negative Ames tests in Morita et al. [11], chemicals that were suggested to be misleading positives owing to cytotoxicity [16] and showed negative retest results using in vitro micronucleus test in Fujita et al. [15] (8 chemicals). In total, 50 chemicals were classified as misleading positives. Basically, misleading positive chemicals do not induce genotoxicity in in vivo conditions and induce irreverent positives in in vitro conditions.
2.1.2. Reselection of Chemicals via OFG Extraction
2.2. Prediction Model Development
2.3. Performance Evaluation of Models
2.4. Visualization of Structural Alerts (OFGs)
3. Results
3.1. Prediction Performances of Developed Model
3.2. OFGs Related to Test Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Accuracy (%) | Sensitivity (%) | Specificity (%) | |
---|---|---|---|
P | 85.6 | 72.6 | 92.7 |
N | 80.3 | 71.0 | 85.2 |
MP | 87.9 | 71.6 | 94.8 |
OFG | Odds Ratio | Reported Main Toxicological Effect or Mechanisms Likely Related to Positive Results | REF |
---|---|---|---|
Epoxide | 13.94 | DNA binding (a) | [35] |
Fused unsaturated carbocycles | 10.84 | metabolites: DNA binding (c) * | [21] |
Alkoxysilane | 10.21 | DNA binding (a) | [11] |
Sulfonate ester | 9.16 | DNA binding (a) | [35] |
Fused heterocyclic aromatic | 9.14 | DNA intercalation (c) | [35] |
N. Nitroso | 9.09 | DNA binding (a) | [35] |
Amidine | 8.34 | DNA minor groove binders (b) | [36] |
Isocyanate | 8.34 | DNA acylation (a) | [35] |
Dianilines | 8.28 | DNA binding (c) | [21] |
OFG | Odds Ratio | Reported Main Toxicological Effects or Mechanisms Likely Related to Misleading Positive Results | REF |
---|---|---|---|
Oxazole/Izoxazole | 12.32 | Anti-tuberculosis activity (a) | [37] |
Benzthiazolinone/Benzoisothiazolinone | 11.83 | Reaction with amino groups of lysine residues (b) | [38] |
Phosphonium, salt | 7.68 | Cytotoxicity (b) | [39] |
Acetoxy | 4.09 | Low pH (a) | [11] |
Methacrylate | 4.05 | DNA reactivity in vitro-specific and/or cytotoxicity (b) | [11] |
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Fujita, Y.; Morita, O.; Honda, H. In Silico Model for Chemical-Induced Chromosomal Damages Elucidates Mode of Action and Irrelevant Positives. Genes 2020, 11, 1181. https://doi.org/10.3390/genes11101181
Fujita Y, Morita O, Honda H. In Silico Model for Chemical-Induced Chromosomal Damages Elucidates Mode of Action and Irrelevant Positives. Genes. 2020; 11(10):1181. https://doi.org/10.3390/genes11101181
Chicago/Turabian StyleFujita, Yurika, Osamu Morita, and Hiroshi Honda. 2020. "In Silico Model for Chemical-Induced Chromosomal Damages Elucidates Mode of Action and Irrelevant Positives" Genes 11, no. 10: 1181. https://doi.org/10.3390/genes11101181
APA StyleFujita, Y., Morita, O., & Honda, H. (2020). In Silico Model for Chemical-Induced Chromosomal Damages Elucidates Mode of Action and Irrelevant Positives. Genes, 11(10), 1181. https://doi.org/10.3390/genes11101181