Structure-activity and mechanistic relationships: the effect of chemical overlap on structural overlap in data bases of varying size and composition

Database composition can affect the structure-activity relationship prediction

The percent active (A) and inactive (I) chemicals in a database can directly affect the sensitivity (% active chemicals predicted correctly) and specificity (% inactive chemicals predicted correctly) of structure-activity relationship (SAR) analyses. Subdividing the National Center for Toxicological Research (NCTR) liver cancer database (NCTRlcdb) into various A/I ratios, which varied from 0.2 to 5.5, resulted in sensitivity/specificity ratios that varied from 0.1 to 6.5. As percent active chemicals increased (increasing A/I ratio), the sensitivity rose, the specificity decreased, and the concordance (% total chemicals predicted correctly) remained fairly constant. The numbers of chemicals in the various data sets ranged from 187 to 999 and appeared to have no affect on any of the 3 predictors of sensitivity, specificity, or concordance.

Computer systems for the prediction of toxicity: an update

In order to survive in the current economic climate, the pharmaceutical, agrochemical and personal product companies are required to produce large numbers of new, effective products whilst significantly reducing development time and costs. With the advent of combinatorial chemistry and high-throughput screening (HTS), the numbers of new candidate structures coming out of the discovery cycle has increased significantly. This has created a demand for faster screening of the toxicological properties of these candidates. Not surprisingly, computer methods for toxicity prediction offer an attractive solution to this problem because of their ability to screen large numbers of structures even before synthesis has occurred. In this paper the major, commercially available computer software systems for toxicity prediction are discussed together with their main strengths and limitations.

Direct oxidation of guanine and 7,8-dihydro-8-oxoguanine in DNA by a high-valent chromium complex: a possible mechanism for chromate genotoxicity

Intracellular reductive activation of the human carcinogen chromate, Cr(VI), is a necessary step in the formation of DNA lesions that lead to cancer. Reductive activation forms the transient metastable high-valent oxidation state of Cr(V) as a precursor to the final intracellularly stable oxidation state, Cr(III). In this study, we have used a model high-valent Cr(V) complex, N,N'-ethylenebis(salicylideneanimato)oxochromium(V), Cr(V)-Salen, to probe the mechanism of interaction between this oxidation state of chromium and DNA. This interaction was found to be specific toward the oxidation of the nucleic acid base guanine in unmodified single- and double-stranded oligonucleotides as measured by an increased level of DNA strand cleavage at these sites following piperidine treatment. Replacement of a single guanine residue in DNA with a more readily oxidized 7,8-dihydro-8-oxoguanine (8-oxo-G) base allowed for site-specific oxidation at this modified site within the DNA strand by the Cr(V)-Salen complex. HPLC and ESI-mass spectrometry were used to identify the modified guanine base lesions formed in the reaction of this high-valent chromium complex with the 8-oxo-G-containing DNA substrate. Two of these modified base lesions, identified as guanidinohydantoin and spiroiminodihydantoin, were found in the reaction of the Cr(V)-Salen complex with 8-oxo-G-modified DNA, while only one, spiroiminodihydantoin, was formed from oxidation of the 8-oxo-G nucleoside. A primer extension assay using the exo(-) Klenow fragment demonstrated polymerase arrest at the site of these base modifications as well as a high degree of misincorporation of adenine opposite the site of modification. These results suggest that mutations arising from G --> T transversions would predominate with these lesions. The mechanism of damage and base oxidation products for the interaction between high-valent chromium and DNA described herein may be relevant to the in vivo formation of DNA damage leading to cancer in chromate-exposed human populations. These results also suggest how high-valent chromium can act as a cocarcinogen with 8-oxo-G-forming xenobiotics.

SAR modeling of unbalanced data sets

The increased acceptance of SAR approaches to hazard identification has led us to investigate methods to improve the predictive performance of SAR models. In the present study we demonstrate that although on theoretical grounds the ratio of active to inactive chemicals in the learning set should be unity, SAR models can "tolerate" an unbalanced range in ratios from 3:1 (i.e., 75% actives) to 1:2 (i.e., 33% actives) and still perform adequately. On the other hand SAR models derived from learning sets with ratios in excess of 4:1 (80% actives), even when corrected for the initial ratio do not perform satisfactorily.

Knowledge discovery and data mining in toxicology

Knowledge discovery and data mining tools are gaining increasing importance for the analysis of toxicological databases. This paper gives a survey of algorithms, capable to derive interpretable models from toxicological data, and presents the most important application areas. The majority of techniques in this area were derived from symbolic machine learning, one commercial product was developed especially for toxicological applications. The main application area is presently the detection of structure-activity relationships, very few authors have used these techniques to solve problems in epidemiological and clinical toxicology. Although the discussed algorithms are very flexible and powerful, further research is required to adopt the algorithms to the specific learning problems in this area, to develop improved representations of chemical and biological data and to enhance the interpretability of the derived models for toxicological experts.

Structural Basis of the Toxicity of Chemicals in Cultured Human HeLa Cells

The newly developed "chemical diversity approach" was used to determine whether or not it is likely that a panel of in vitro cell toxicity assays capable of predicting in vivo eye irritation could be assembled. The analyses, based upon available and validated structure-activity relationship models of toxicity in cultured human HeLa cells and murine Balb/c 3T3 cells, indicate that a battery of cytotoxicity tests could provide a viable alternative to the animal-based procedure.

Modeling the mouse lymphoma forward mutational assay: the Gene-Tox program database

An SAR model of the induction of mutations at the tk(+/-) locus of L5178Y mouse lymphoma cells (MLA, for mouse lymphoma assay) was derived based upon a re-evaluation of experimental results reported by a Gene-Tox (GT) working group [A.D. Mitchell, A.E. Auletta, D. Clive, P.E. Kirby, M.M. Moore, B.C. Myhr, The L5178Y/tk(+/-) mouse lymphoma specific gene and chromosomal mutation assay. A phase III report of the U.S. Environmental Protection Agency Gene-Tox Program, Mutation Res. 394 (1997) 177-303.]. The predictive performance of the GT MLA SAR model was similar to that of a Salmonella mutagenicity model containing the same number of chemicals. However, the structural determinants (biophores) derived from the GT MLA SAR model include both electrophilic as well as non-electrophilic moieties, suggesting that the induction of mutations in the MLA may occur by both direct interaction with DNA and by non-DNA-related mechanisms. This was confirmed by the observation that the set of biophores associated with MLA overlapped significantly with those associated with phenomena related to loss of heterozygosity, chromosomal rearrangements and aneuploidy. The MLA SAR model derived from the GT data evaluation was significantly more predictive than an SAR model previously derived from MLA data reported by the US National Toxicology Program [B. Henry, S.G. Grant, G. Klopman, H.S. Rosenkranz, Induction of forward mutations at the thymidine kinase locus of mouse lymphoma cells: evidence for electrophilic and non-electrophilic mechanisms, Mutation Res. 397 (1998) 331-335.]. Moreover, the latter model appeared to be more complex than the former, suggesting that the GT induction data was both simpler mechanistically and more homogeneous than that of the NTP.

SOS chromotest and mutagenicity in Salmonella: evidence for mechanistic differences

An examination of the relationship of the experimental results obtained with chemicals tested in the SOS chromotest and for mutagenicity in Salmonella indicates that the two assays respond to different genotoxic stimuli. Furthermore, the relationship between results obtained in these assays and in rodents carcinogenicity bioassays suggests that the short-term assays respond to a different spectrum of carcinogens. The same conclusions were reached based upon an analysis of the structural features associated with these three phenomena. With respect to using these short-term assays to predict carcinogens, the present results suggest that they are not equivalent, but complement one another.

Structural determinants of developmental toxicity in hamsters

A CASE/MULTICASE structure activity relationship (SAR) model of developmental toxicity of chemicals in hamsters (HaDT) was developed. The model exhibited a predictive performance of 74%. The model's overall predictivity and informational content were similar to those of an SAR model of mutagenicity in Salmonella. However, unlike the Salmonella mutagenicity model, the HaDT model did not identify overtly chemically reactive moieties as associated with activity. Moreover, examination of the number and nature of significant structural determinants suggested that developmental toxicity in hamsters was not the result of a unique mechanism or attack on a specific molecular target. The analysis also indicated that the availability of experimental data on additional chemicals would improve the performance of the SAR model.

Human developmental toxicity and mutagenesis

A previously described SAR model of human developmental toxicity was analyzed further. The model shows a number of mechanistic similarities with SAR models of other toxicological phenomena (systemic toxicity, chromosomal and genomic effects). This implies that there are many targets associated with developmental effects. Surprisingly the analyses revealed no significant mechanistic overlap between developmental toxicity in humans and mutagenicity in Salmonella, a surrogate for the occurrence of point mutations. Our study indicates that this lack of similarity is likely the result of the pre-screening strategies which largely eliminate Salmonella mutagens from among the therapeutics introduced into human medicine.

Chromium(III) decreases the fidelity of human DNA polymerase beta

Certain particulate compounds of hexavalent chromium are well-known occupational and environmental human carcinogens. Hexavalent chromium primarily enters the cells and undergoes metabolic reduction; however, the ultimate trivalent oxidation state of chromium, Cr(III), predominates within the cell. DNA-bound Cr(III) has been previously shown to decrease the fidelity of replication in the M13 phage mutation assay. This study was done to understand how Cr(III), in the presence of physiological concentrations of magnesium, affects the kinetic parameters of steady-state DNA synthesis in vitro across site-specific O6-methylguanine (m6dG) residues by DNA polymerase beta (pol beta). Cr(III) binds to the short oligomer templates in a dose-dependent manner and stimulates the activity of pol beta. Cr(III) stimulates the mutagenic incorporation of dTTP opposite m6dG more than the nonmutagenic incorporation of dCTP, and thereby Cr(III) further decreases the fidelity of DNA synthesis across m6dG by pol beta. In contrast, Cr(III) does not affect the fidelity of DNA synthesis across the normal template base, dG. Both the enhanced activity and the mutagenic lesion bypass in the presence of Cr(III) may be associated with Cr(III)-dependent stimulation of pol beta binding to DNA as reported here. This study shows some of the mechanisms by which mutagenic chromium affects DNA synthesis.

Structure-based methods for predicting mutagenicity and carcinogenicity: are we there yet?

There is a great deal of current interest in the use of commercial, automated programs for the prediction of mutagenicity and carcinogenicity based on chemical structure. However, the goal of accurate and reliable toxicity prediction for any chemical, based solely on structural information remains elusive. The toxicity prediction challenge is global in its objective, but limited in its solution, to within local domains of chemicals acting according to similar mechanisms of action in the biological system; to predict, we must be able to generalize based on chemical structure, but the biology fundamentally limits our ability to do so. Available commercial systems for mutagenicity and/or carcinogenicity prediction differ in their specifics, yet most fall in two major categories: (1) automated approaches that rely on the use of statistics for extracting correlations between structure and activity; and (2) knowledge-based expert systems that rely on a set of programmed rules distilled from available knowledge and human expert judgement. These two categories of approaches differ in the ways that they represent, process, and generalize chemical-biological activity information. An application of four commercial systems (TOPKAT, CASE/MULTI-CASE, DEREK, and OncoLogic) to mutagenicity and carcinogenicity prediction for a particular class of chemicals-the haloacetic acids (HAs)-is presented to highlight these differences. Some discussion is devoted to the issue of gauging the relative performance of commercial prediction systems, as well as to the role of prospective prediction exercises in this effort. And finally, an alternative approach that stops short of delivering a prediction to a user, involving structure-searching and data base exploration, is briefly considered.

Induction of forward mutations at the thymidine kinase locus of mouse lymphoma cells: evidence for electrophilic and non-electrophilic mechanisms

A database of 209 chemicals tested for induction of forward mutations at the heterozygous thymidine kinase (TK +/-) locus in L5178Y mouse lymphoma cells was analyzed for structure-activity relationships using the MultiCASE expert system. Consistent with evidence of several contributing biological mechanisms, these studies suggest that such mutations may occur by more than one mechanism. As might be expected, there was evidence for a component involving direct electrophilic attack on the cellular DNA, in a manner previously established as causative in the induction of mutations in Salmonella. In addition, however, there was also strong evidence for another mechanism or mechanisms involving chromosome missegregation, cellular toxicity or an alternate site of action, such as the microtubules.

Intercellular communication, tumor promotion and non-genotoxic carcinogenesis: relationships based upon structural considerations

An SAR model for inhibition of metabolic cooperation (iMC) was developed. The structural and physicochemical features associated with the ability to cause iMC are primarily lipophilic moieties consistent with the possibility that they represent receptor-binding ligands. There are also significant parallels between the structural descriptors associated with iMC and those associated with tumor promotion and with carcinogenesis in rodents. Overall, the present study provides structural evidence that iMC is a feature associated with the carcinogenic process.