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.     

Interference by detergents, chelating agents, and buffers with the Lowry protein determination

EDTA distorts the Lowry method even at the concentration of 0.5 mm. The effect of EDTA, glycine, glycylglycine, Tricine, and Tris on the Lowry method can be calibrated only at a fixed concentration of the chemicals. The effect of succinic acid, sodium citrate, and Bicine on the Lowry method changes depending on the concentration of the chemicals, but the changes were not as significant as in the case of the chemicals mentioned above. Sodium phosphate at pH 8.9, sodium dodecyl sulfate, sucrose, and urea do not affect the Lowry method when a reference containing only the chemical is used.     

The mouse spot test. Evaluation of its performance in identifying chemical mutagens and carcinogens

The published results on 60 chemicals and X-rays investigated in the mouse spot test were compared with data on the same chemicals tested in the bacterial mutation assay (Ames test) and lifetime rodent bioassays. The performance of the spot test as an in vivo complementary assay to the in vitro bacterial mutagenesis test reveals that of 60 agents, 38 were positive in both systems, 6 were positive only in the spot test, 10 were positive only in the bacterial test and 6 were negative in both assays. The spot test was also considered as a predictor of carcinogenesis; 45 chemicals were carcinogenic of which 35 were detected as positive by the spot test and 3 out of 6 non-carcinogens were correctly identified as negative. If the results are regarded in sequence, i.e. that a positive result in a bacterial mutagenicity test reveals potential that may or may not be realized in vivo, then 48 chemicals were mutagenic in the bacterial mutation assay of which 38 were active in the spot test and 31 were confirmed as carcinogens in bioassays. 12 chemicals were non-mutagenic to bacteria of which 6 gave positive responses in the spot test and 5 were confirmed as carcinogens. These results provide strong evidence that the mouse coat spot test is an effective complementary test to the bacterial mutagenesis assay for the detection of genotoxic chemicals and as a confirmatory test for the identification of carcinogens. The main deficiency at present is the paucity of data from the testing of non-carcinogens. With further development and improvement of the test it is probable that the predictive performance of the assay in identifying carcinogens should improve, since many of the false negative responses may be due to inadequate testing.     

Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine

MOTIVATION: Mutagenicity is among the toxicological end points that pose the highest concern. The accelerated pace of drug discovery has heightened the need for efficient prediction methods. Currently, most available tools fall short of the desired degree of accuracy, and can only provide a binary classification. It is of significance to develop a discriminative and informative model for the mutagenicity prediction. RESULTS: Here we developed a mutagenic probability prediction model addressing the problem, based on datasets covering a large chemical space. A novel molecular electrophilicity vector (MEV) is first devised to represent the structure profile of chemical compounds. An extended support vector machine (SVM) method is then used to derive the posterior probabilistic estimation of mutagenicity from the MEVs of the training set. The results show that our model gives a better performance than TOPKAT (http://www.accelrys.com) and other previously published methods. In addition, a confidence level related to the prediction can be provided, which may help people make more flexible decisions on chemical ordering or synthesis. AVAILABILITY: The binary program (ZGTOX_1.1) based on our model and samples of input datasets on Windows PC are available at http://dddc.ac.cn/adme upon request from the authors.     

Developing environmental performance indicators for food and beverage processors in the USA

Despite consumer and regulatory focus on the quality of final food and beverage (F&B) products, little attention is given to the release and management of toxic chemicals by F&B processors. This study develops five plant-level indicators of environmental performance specific to toxic chemicals. Our findings suggest that (i) only few F&B processors invest in toxic chemical prevention activities; (ii) the major toxic chemical management strategy is treatment rather than recycling or energy recovery; (iii) F&B processors, on average, have improved their toxic chemical management rates between 2001 and 2012; and (iv) there is evidence for homogeneous performance across similar producers in the F&B processing industry but there is no evidence for the role of socio-economic characteristics of surrounding communities on the environmental performance of F&B processors.     

ECVAM,ECETOC and the EU chemicals policy

ECVAM's initiatives in validation have received significant support from the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC), especially through the provision of reference chemical data banks, which contain peer-reviewed, high-quality in vivo data on commercially available chemical substances. Chemicals have been selected from these ECETOC data banks for validation studies on alternative methods for skin corrosion and irritation and for eye irritation and, in addition, an ECETOC task force peer-reviewed the selection and classification, on the basis of in vivo data, of chemicals used in the validation of three alternative methods for developmental toxicity. More recently, ECVAM and ECETOC have been pursuing parallel initiatives on the proposed new EU chemicals policy, with the common goals of ensuring that industry and European Commission resources are used to investigate only those chemicals that pose a significant risk to human health and the environment, and that the Policy requires that any testing which is required follows the Three Rs principles of reduction, refinement and replacement.     

Chemical Defense and the Persistence of Pioneer Plant Seeds in the Soil of a Tropical Cloud Forest

We present evidence that differences in soil seedbank persistence among pioneer plants in the cloud forest of Monteverde, Costa Rica, are influenced by differences in seed chemical defense. We used extracted seed chemicals from Bocconia frutescens (Papaveraceae), Guettarda poasana (Rubiaceae) , Phytolacca rivinoides (Phytolaccaceae) , Urera elata (Urticaceae) , Cecropia polyphlebia (Cecropiaceae), and Witheringia meiantha (Solanaceae) to assess seed chemical defense in two ways: (1) a plant pathogen inhibition assay using Pythium irregulare ; and (2) a brine shrimp toxicity assay using Artemia salina . The combined performance of each species in the two assays positively correlated with seedbank persistence. In the pathogen assay, mycelium growth was reduced when Pythium was cultured on media containing seed extracts from the three species with the greatest seed longevity in the soil ( i.e., Bocconia , Guettarda, and Phytolacca ). Bocconia , the most persistent species, was the only species that contained chemicals toxic to brine shrimp , an indication of defense against arthropods. We focused on Bocconia defense by isolating the chemicals toxic to brine shrimp and identified them as dihydrosanguinarine, dihydrochelirubine, and dihydrochelerthrine. We found these alkaloids in Bocconia seeds at much higher concentrations (∼50 mg/g seed material) than in leaves. These chemicals are likely responsible for the exceptional longevity of Bocconia seeds in the soil. Phytolacca and Guettarda seeds also remain viable in the soil for long periods probably due to antipathogen chemicals detected in our analyses. In contrast, the species that do not persist ( i.e., Urera , Cecropia , and Witheringia ) lacked seed defensive chemicals in our assays.
Abstract in Spanish is available at http://www.blackwell-synergy.com/loi/btp .     

CASE, the computer-automated structure evaluation method, correctly predicts the low mutagenicity for Salmonella of nitrated cyclopenta-fused polycyclic aromatic hydrocarbons

Recently Goldring et al. [Mutation Res., 187 (1987) 67-77] reported the synthesis and purification of a series of nitro-substituted cyclopenta-fused polycyclic aromatic hydrocarbons. On the basis of expected charge distributions, these chemicals were predicted to be potent mutagens and, yet, contrary to expectation, they were found to be only weakly mutagenic for Salmonella. In their discussion, the authors suggest that application of CASE, an artificial intelligence system recently developed in these laboratories, would also not predict the low mutagenicity of this group of chemicals. In the present report, it is shown that CASE, in fact, correctly predicts the low mutagenicity of nitro-substituted cyclopenta-fused polycyclic aromatic hydrocarbons.     

A multiple in silico program approach for the prediction of mutagenicity from chemical structure

We have conducted an evaluation of three of the most widely used commercial toxicity prediction programs, Toxicity Prediction by Komputer Assisted Technology (TOPKAT), Deductive Estimation of Risk from Existing Knowledge (DEREK) for Windows (DfW) and CASETOX. The three programs were evaluated for their ability to predict Ames test mutagenicity using 520 proprietary drug candidate (Test set 1) and 94 commercial (Test set 2) compounds. The study demonstrates that these three commercially available programs are useful, with limitations in their ability to predict mutagenicity over a wide range of chemical space, i.e. global predictivity. Individually, each of the programs performed at an acceptable level for overall accuracy, i.e. the ability to predict the correct outcome. However, analysis of the predictions indicates that the overall accuracy figure is heavily weighted by the ability of the programs to correctly predict non-mutagens, whereas none of the programs individually performed well in the prediction of novel mutagenic structures, i.e. Ames positive compounds. The performance of these programs' in predicting Ames positive mutagens appeared to be independent of the chemical utility of the compound, i.e. industrial, agricultural or pharmaceutical. The combination of program predictions provided some improvement in overall accuracy, sensitivity and specificity.     

Relevance of chemical structure and cytotoxicity to the induction of chromosome aberrations based on the testing results of 98 high production volume industrial chemicals

Over a 6-year period (1991-1996), the chromosomal aberration testing of high production volume (HPV) industrial chemicals had been conducted using Chinese hamster lung (CHL/IU) cells according to OECD HPV testing program and the national program in Japan. A total of 98 chemicals were tested for the induction of chromosome aberration (CA), consisting of structural CA and polyploidy. Of the 98 chemicals, structural CA and/or polyploidy were induced by 39 chemicals (40%). Anilines and phenols tended to induce only structural CA. p-tert-Butylphenol had a peculiar feature in inducing not only structural CA but also polyploidy at considerably high frequency (93.2%) after continuous treatment for 48 h, posing an aneugenic potential. Not all, but six of 11 carboxylic acids or esters also showed the simultaneous induction of structural CA and polyploidy. The majority of organic phosphates, alcohols or ethers, alkyl benzenes and non-cyclic alkanes had no CA induction activity. For chemicals which were negative in the bacterial reverse mutation assay (Ames test), the proportion of the chemicals that induced CA at a severely cytotoxic dose (doses manifesting more than 50% cytotoxicity) was similar to that of the CA-negative chemicals manifesting severe cytotoxicity, suggesting that severely cytotoxic chemicals do not always induce CA.     

Effects of Male Germ-Cell Stage on the Frequency,Nature, and Spectrum of Induced Specific-Locus Mutations in the Mouse

By means of the mouse specific-locus test (SLT) with visible markers, which is capable of detecting intragenic mutations as well as larger lesions, about 20 mutagens have been studied comparatively across arrays of male germ-cell stages. In addition, a very large historical control, accumulated over decades, provides data on spontaneous mutations in males. Each mutagen has a characteristic germ-cell-stage sensitivity pattern. Although most chemicals yield their maximum numbers of mutations following exposure of spermatozoa and late spermatids, mutagens have now been identified that peak in each of the major stages of spermatogenesis and spermiogenesis, including those in which effects on recombination can also be induced. Stem-cell spermatogonia have yielded positive results with only five of 15 mutagenic chemicals. In postspermatogonial stages, all chemicals, as well as radiations, induce primarily large lesions (LL). By contrast, in spermatogonia (either stem-cell or differentiating) all chemicals except one (bleomycin) produce very few such lesions. The spectrum of relative mutation frequencies at the seven loci of the SLT is characteristic for treated germ-cell stage and mutagen. Treatments that induce primarily LL are characterized by a great preponderance of s (Ednrb)-locus mutations (possibly due to a paucity of haplo-insufficient genes in the surrounding region); and those that induce very few, if any, LL by a great preponderance of p-locus mutations. Spontaneous locus-spectra differ from both types of treatment-induced spectra; moreover, there are two distinct types of spontaneous spectra, depending on whether mutations occurred in mitotic cells or during the perigametic interval.     

Production of bulk chemicals via novel metabolic pathways in microorganisms

Metabolic engineering has been playing important roles in developing high performance microorganisms capable of producing various chemicals and materials from renewable biomass in a sustainable manner. Synthetic and systems biology are also contributing significantly to the creation of novel pathways and the whole cell-wide optimization of metabolic performance, respectively. In order to expand the spectrum of chemicals that can be produced biotechnologically, it is necessary to broaden the metabolic capacities of microorganisms. Expanding the metabolic pathways for biosynthesizing the target chemicals requires not only the enumeration of a series of known enzymes, but also the identification of biochemical gaps whose corresponding enzymes might not actually exist in nature; this issue is the focus of this paper. First, pathway prediction tools, effectively combining reactions that lead to the production of a target chemical, are analyzed in terms of logics representing chemical information, and designing and ranking the proposed metabolic pathways. Then, several approaches for potentially filling in the gaps of the novel metabolic pathway are suggested along with relevant examples, including the use of promiscuous enzymes that flexibly utilize different substrates, design of novel enzymes for non-natural reactions, and exploration of hypothetical proteins. Finally, strain optimization by systems metabolic engineering in the context of novel metabolic pathways constructed is briefly described. It is hoped that this review paper will provide logical ways of efficiently utilizing ‘big’ biological data to design and develop novel metabolic pathways for the production of various bulk chemicals that are currently produced from fossil resources.     

Comparative efficacy of clove oil and other chemicals in anaesthetization of Pomacentrus amboinensis, a coral reef fish

The efficacy of quinaldine, benzocaine, MS-222, 2-phenoxyethanol and clove oil was compared for anaesthetizing settlement stage Pomacentrus amboinensis , a frequently studied coral reef fish. Induction to anaesthesia, behaviour during anaesthesia, recovery times and survival rates of fish treated with the different chemicals were compared. Clove oil was only marginally less effective than quinaldine and was more effective than other chemicals tested, except at high concentrations. In addition, fish exposed to clove oil exhibited a much calmer induction to anaesthesia than fish exposed to quinaldine. Therefore, clove oil may be an effective alternative to quinaldine as a fish anaesthetic. Recovery time after anaesthesia with clove oil was two to three times longer than recovery from other chemicals, a desirable charcteristic for use in field studies. Survival rates were excellent for all chemicals.     

Trends in Risk Assessment of Chemicals in the European Union

Current legislation in the European Union (EU) requires a risk assessment for industrial chemicals. The underlying procedures and paradigms of such EU risk assessment for new and existing chemicals are explained. The risk assessment is performed according to a harmonised methodology, laid down in the Technical Guidance Documents (TGD). Important new, technical risk assessment aspects covered in a recent revision round of the TGD are highlighted. The most prominent change in the environmental TGD part is the addition of the marine risk assessment, including a Persistent Bioaccumulation and Toxicity (PBT) assessment. In the human health part a significant change is the new data requirement for reproductive toxicity. The performance of both the risk assessment and the risk reduction phase of EU existing chemicals have been evaluated. An important conclusion was that our a priori knowledge on possible risks of chemicals is poor. The European Commission has recently launched a proposal (REACH) for drastically changing the risk management process of industrial chemicals in the EU. Major changes are a shift in responsibility from authorities to industry (including downstream users) for the safe use of chemicals, an acceleration of data collection for ‘non-assessed’ chemicals, and an authorization step for substances of very high concern.     

Olfactory responses of the antennal trichoid sensilla to chemical repellents in the mosquito, Culex quinquefasciatus

Insect repellents are widely used to protect against insect bites and thus prevent allergic reaction and the spread of disease. To gain insight into the mosquito’s response to chemicals repellents, we investigated the interaction between the olfactory system of the mosquito Culex quinquefasciatus Say and chemical repellents using single sensillum recording. The interactions of 50 repellent chemicals with olfactory receptor neurons were measured in six different types of mosquito sensilla: long sharp trichoid (LST), short sharp trichoid (SST), short blunt trichoid I (SBT-I), short blunt trichoid II (SBT-II), short blunt trichoid-curved (SBT-C), and grooved peg (GP). A single olfactory neuron reacted to the chemical repellents in each of the sensilla except for SBT-I and SBT-II, where two neurons were involved. Other than LST and GP, which showed no or very weak responses to the repellents tested, all the sensilla showed significant excitatory responses to certain types of repellents. Terpene-derived chemicals such as eucalyptol, α-pinene, and camphor, stimulated olfactory receptor neurons in a dose-dependent manner and mosquitoes responded more strongly to terpene-derived chemical repellents than to non-terpene-derived chemicals such as dimethyl phthalate. Mosquitoes also exhibited a similar response to stereoisomers of chemicals such as (−)-β-pinene versus (+)-β-pinene, and (−)-menthone versus (+)-menthone. This study not only demonstrates the effects of chemical repellents on the mosquito olfactory system but also provides important information that will assist those screening new mosquito repellents and designing new mosquito control agents.     

An inter-laboratory collaborative study by the Non-Genotoxic Carcinogen Study Group in Japan, on a cell transformation assay for tumour promoters using Bhas 42 cells

The Bhas promotion assay is a cell culture transformation assay designed as a sensitive and economical method for detecting the tumour-promoting activities of chemicals. In order to validate the transferability and applicability of this assay, an inter-laboratory collaborative study was conducted with the participation of 14 laboratories. After confirmation that these laboratories could obtain positive results with two tumour promoters, 12-O-tetradecanoylphorbol-13-acetate (TPA) and lithocholic acid (LCA), 12 coded chemicals were assayed. Each chemical was tested in four laboratories. For eight chemicals, all four laboratories obtained consistent results, and for two of the other four chemicals, only one of the four laboratories showed inconsistent results. Thus, the rate of consistency was high. During the study, several issues were raised, each of which were analysed step-by-step, leading to revision of the protocol of the original assay. Among these issues were the importance of careful maintenance of mother cultures and the adoption of test concentrations for toxic chemicals. In addition, it is suggested that three different types of chemicals show positive promoting activity in the assay. Those designated as T-type induced extreme growth enhancement, and included TPA, mezerein, PDD and insulin. LCA and okadaic acid belonged to the L-type category, in which transformed foci were induced at concentrations showing growth-inhibition. In contrast, M-type chemicals, progesterone, catechol and sodium saccharin, induced foci at concentrations with little or slight growth inhibition. The fact that different types of chemicals similarly induce transformed foci in the Bhas promotion assay may provide clues for elucidating mechanisms of tumour promotion.     

White biotechnology: differences in US and EU approaches?

Several predominantly political movements advocate white, or industrial, biotechnology as a means to alleviate economic, ecological and societal problems in petroleum-dependent industrialized nations worldwide. US and European approaches differ significantly and we believe that, in the long-term, only economic drivers will be able to bring about the broad use of renewable resources and a bio-based economy. As long as the cost of fossil fuel and feedstock for key chemicals have not passed their respective critical thresholds, industrial biotechnology and its products will need political support and funding, particularly in the energy and bulk-chemicals sectors. Other uses of industrial biotechnology, however, such as biocatalytic conversions of fine and specialty chemicals and the manufacture of high-value products, such as nutriceuticals, cosmeceuticals and performance chemicals offer dynamic growth opportunities both for established chemical industries, as well as emerging entrepreneurial enterprises.     

Aneuploidy in Drosophila, II. Further validation of the FIX and ZESTE genetic test systems employing female Drosophila melanogaster

Two sensitive genetic systems for the detection of germline aneuploidy employing Drosophila melanogaster females were described in the first paper of this series (Zimmering et al., submitted to Mutation Research). Designated FIX and ZESTE, these systems permit the rapid and efficient detection of exceptional offspring derived from aneuploid female germ cells. The current report presents test results from a survey of 8 additional chemicals that have been analyzed in both systems. The tested chemicals include: acetonitrile, cadmium chloride, carbendazim, dimethylsulfoxide (DMSO), methylmercury(II) chloride, methoxyethyl acetate, propionitrile and water. Excluding the negative control, water, only the fungicide carbendazim failed to induce aneuploidy in either test system. Of the remaining 6 chemicals one, methylmercury(II) chloride, was positive in the FIX system but not in ZESTE, while MEA was positive in ZESTE and borderline in FIX. The results provide little evidence of germ-cell stage specificity of response to the tested chemicals. Comparison of the induced rates of aneuploidy i indicates that these can exhibit departures from simple additivity to the spontaneous rates: induced rates in the ZESTE system are generally higher and more variable than those from FIX. Possible reasons for the difference in responsiveness between FIX and ZESTE flies are discussed as is the question of the classification of those chemicals which induce chromosome loss events but not chromosome gains.     

Investigations into the biological relevance of in vitro clastogenic and aneugenic activity

In the current study we present a view of events leading to chemically induced DNA damage in vitro from both a cytogenetic and molecular aspect, focusing on threshold mediated responses and the biological relevance of DNA damaging events that occur at low and high cellular toxicity levels. Current regulatory mechanisms do not take into account chemicals that cause significant DNA damage only at high toxicity. Our results demonstrate a defined threshold for micronucleus induction after insult with the alkylating agent MMS. Other results define a significant change in gene expression following treatment with chemicals that give rise to structural DNA damage only at high toxicity. Pairs of chemicals with a similar mode of action but differing toxicity levels were chosen, the chemicals that demonstrated structural DNA damage only at high levels of toxicity showed an increase in heat shock protein gene expression whereas the chemicals causing DNA damage events at all levels of toxicity did not induce changes in heat shock gene expression at identical toxicity levels. The data presented indicates that there are a number of situations where the linear dose response model is not appropriate for risk estimation. However, deviation from linear risk models should be dependent upon the availability of appropriate experimental data such as that shown here.     

Cytotoxicity of the MEIC reference chemicals in antioxidant-enriched, rat hepatoma-derived Fa32 cells

Since vitamin E increases the antioxidant status of cells, its influence on cytotoxicity was investigated. The neutral red uptake (NRU) inhibition effects of 39 MEIC reference chemicals were measured after treatment of rat hepatoma-derived Fa32 cells in the presence of vitamin E for 30 minutes. The results were quantified in terms of the NI50, the concentration of test compound required to reduce the NRU by 50%. Sodium chloride was the only chemical that was more toxic in the presence of vitamin E. This effect was related to the concentration of vitamin E in the cell culture medium. A vitamin E dose-related response was also observed for the decreased toxicity of paracetamol and caffeine. Glutathione levels were slightly increased in the presence of vitamin E, which could contribute to the protective effect of vitamin E. Of the remaining chemicals, 50% were less toxic in the presence of vitamin E, but the correlation with the acute human toxicity data of the MEIC study was not improved. The results imply that reactive oxygen species interfere with the toxicity of a high proportion of toxic chemicals. The assay described provides a quick and easy method for checking whether reactive oxygen species contribute to the toxicity of a chemical.