Conformal prediction to define applicability domain - A case study on predicting ER and AR binding.

A fundamental element when deriving a robust and predictive in silico model is not only the statistical quality of the model in question but, equally important, the estimate of its predictive boundaries. This work presents a new method, conformal prediction, for applicability domain estimation in the field of endocrine disruptors. The method is applied to binders and non-binders related to the oestrogen and androgen receptors. Ensembles of decision trees are used as statistical method and three different sets (dragon, rdkit and signature fingerprints) are investigated as chemical descriptors. The conformal prediction method results in valid models where there is an excellent balance in quality between the internally validated training set and the corresponding external test set, both in terms of validity and with respect to sensitivity and specificity. With this method the level of confidence can be readily altered by the user and the consequences thereof immediately inspected. Furthermore, the predictive boundaries for the derived models are rigorously defined by using the conformal prediction framework, thus no ambiguity exists as to the level of similarity needed for new compounds to be in or out of the predictive boundaries of the derived models where reliable predictions can be expected.

Non-dioxin-like PCBs inhibit [(3)H]WIN-35,428 binding to the dopamine transporter: a structure-activity relationship study.

Non-dioxin-like polychlorinated biphenyls (NDL-PCBs) are neurotoxic compounds with known effects at the dopaminergic system in the brain. In a previous study we demonstrated that NDL-PCBs inhibit uptake of dopamine into rat brain synaptosomes, an effect most likely mediated by inhibition of the dopamine transporter (DAT). Here, using the cocaine analogue [(3)H]WIN-35,428 binding assay and synaptosomes, we directly investigate whether NDL-PCBs act via DAT and explore the structure-activity relationship of this effect. In total, thirty PCBs were investigated, including a previously selected training set of twenty PCBs covering the structural variation within tri- to hepta-chlorinated NDL-PCBs, and an additional set of ten NDL-PCB congeners selected to validate the structure-activity pattern of neurotoxic PCBs. Since previous work has demonstrated that NDL-PCBs can also inhibit the vesicular monoamine transporter 2 (VMAT2), we additionally examined whether some PCB congeners favour an effect on VMAT2 and others on DAT. Our results show that NDL-PCBs are potent inhibitors of [(3)H]WIN-35,428 binding to DAT. In fact, we identify a PCB congener (PCB 110) with similar potency for [(3)H]WIN-35,428 binding inhibition as cocaine. All active congeners were ortho-chlorinated PCBs, and in particular, tetra- and penta-chlorinated with 2-3 chlorine atoms in the ortho position were potent inhibitors of [(3)H]WIN-35,428 binding. Notably, the most active PCBs are highly prevalent in commercial mixtures of PCBs (Aroclor 1242, 1254 and 1260), which indicates that DAT inhibition could be one of the factors contributing to behavioural effects after Aroclor exposure. Derived data correlated well with the recently derived neurotoxic equivalency factors (NEQs), indicating the generality and applicability of the NEQ scheme in risk assessments of PCBs.

On the use of electronic descriptors for QSAR modelling of PCDDs, PCDFs and dioxin-like PCBs.

The electronic properties of 29 polychlorinated dibenzo-p-dioxins and dibenzofurans and dioxin-like polychlorinated biphenyls that have been included in the toxic equivalency factor system have been investigated and used to derive quantum mechanical (QM) chemical descriptors for QSAR modelling. Their utility in this context was investigated alongside descriptors based on ultraviolet absorption data and traditional 2D descriptors including log K(ow), polarizability, molecular surface properties, van der Waals volume and selected connectivity indices. The QM descriptors were calculated using the semi-empirical AM1 method and the density functional theory method B3-LYP/6-31G**. Atom-specific and molecular quantum chemical descriptors were calculated to compare the electronic properties of dioxin-like compounds regardless of their chemical class, with particular emphasis on the lateral positions. Multivariate analysis revealed differences between the chemical classes in terms of their electronic properties and also highlighted differences between congeners. The results obtained demonstrated the importance of considering molecular orbital energies, but also indicated that the ratios of the coefficients of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) at the lateral carbons were important. In addition, the digitalized UV spectra contained chemical information that provided crucial insights into dioxin-like activity.

Gender-specific proteomic responses in zebrafish liver following exposure to a selected mixture of brominated flame retardants.

Proteomic effect screening in zebrafish liver was performed to generate hypotheses following exposure (21 days) to a structurally diverse mixture of brominated flame retardants (BFRs). Fish were exposed to two doses (10 and 100 nmol/g feed). Two-dimensional gel-electrophoresis, image analysis and MALDI-TOF mass-spectrometry revealed 13 and 19 significant responses in males and females, respectively. Effects on proteins related to cellular maintenance and stress were observed in both genders. Regulated proteins were gender-specific, but functionally indicated common protective responses (peroxiredoxin 6 and Zgc:92891 in males and transketolase in females) suggesting oxidative stress. Betaine homocysteine methyltransferase (BHMT) was induced in both genders. In addition a female-specific downregulation of ironhomeostatic proteins (iron-regulatory protein 1 and transferrin) were observed. Our proteomic approach revealed novel responses that suggest important gender-specific sensitivity to BFRs that should be considered when interpreting adverse effects of BFRs.

An overview of OSPAR priority compounds and selection of a representative training set.

The aim of our study was to chemically characterize a set of priority substances in order to systematically select a representative set of heterogeneous substances for experimental studies of their persistence, bioaccumulation and toxicity (PBT). By including structurally diverse compounds in a PBT-screening protocol, structure-based knowledge would be achieved as a basis for more detailed studies of specific compounds from certain regions of the chemical domain. Initially compounds on the Draft Preliminary List of Substances of Possible Concern presented by the Oslo & Paris Commission (OSPAR) were subjected to broad chemical characterization using Principal Component Analysis (PCA). Molecular weight and seven physico-chemical descriptors collected from the literature, five calculated properties and 25 constitutional descriptors were used in this characterization. The OSPAR list represents a broad spectrum of substances, and thus provides a good basis for selecting heterogeneous substances. D-optimal design was applied to the first four principal components derived in the PCA. In total, 19 structurally diverse substances were chosen as representatives of the chemical domain including 353 substances.

Effect of polychlorinated biphenyls on the uptake of dopamine into rat brain synaptic vesicles: a structure-activity study.

PCBs are neurotoxic compounds that have a known effect on the dopaminergic system in the brain. In a previous work it was established that PCBs are potent inhibitors of the uptake of dopamine into rat brain synaptic vesicles. In this work we further investigated the vesicular dopamine uptake in response to different PCBs to explore the structure-activity relationship involved in this effect. Twenty PCB congeners were selected, based on multivariate chemical characterization, to cover the chemical variation within tetra- to hepta-chlorinated PCBs. PCBs of large structural variation were tested and the general finding was that only the ortho-substituted PCBs inhibited the dopamine uptake. The most active congeners were the penta- and hexa-chlorinated PCBs. Furthermore, the uptake was correlated with parameters describing the absolute hardness, the octanol-water partition coefficient, and the Henry's law constant. These parameters are correlated to the number of chlorine atoms in ortho positions and to the size of the molecule. Notably the most active PCBs are highly prevalent in the environment and are disposed to bioaccumulate in wildlife. Thus, these neurotoxic effects should be included in the risk assessment of PCBs.

Bioaccumulation of selected PCBs in zebrafish, three-spined stickleback, and arctic char after three different routes of exposure.

The uptake and elimination of 20 structurally diverse tetra- to heptachlorinated biphenyls were studied in zebrafish (Danio rerio), three-spined stickleback (Gasterosteus aculeatus), and Arctic char (Salvelinus alpinus). The polychlorinated biphenyls (PCBs) were administered to the fish through food, intraperitoneal injection of peanut oil, or intraperitoneal implantation of silicone capsules. The retention of the PCBs in fish exposed through their diet was related with the substitution patterns of the compounds. Ortho-substituted congeners with no unsubstituted meta-para positions had high biomagnification potential. PCBs with low biomagnification all had adjacent vicinal hydrogens, indicating that congeners with this feature may have been metabolically eliminated. The retention characteristics of the PCBs in the diet-exposed and the injected zebrafish were similar. The pattern of congeners in Arctic char indicates that they have a lower capacity to metabolize PCBs compared to three-spined sticklebacks and zebrafish. The levels in the fish exposed to the PCBs through a silastic implant were negatively correlated with the hydrophobicity of the congeners. Most probably congener-specific release rates of the PCBs from the implants mask their retention characteristics. It is suggested that food, mimicking the natural intake route, should be used in PCB exposure studies to validate extrapolations to natural situations.

Structure dependent induction of CYP1A by polychlorinated biphenyls in hepatocytes of male castrated pigs.

Hepatocytes cultures prepared from castrated pig hepatocytes (Great Yorkshire x Dutch Landrace), as a model for human liver, were used to study the effect of twenty polychlorinated biphenyls (PCBs) on CYP1A activity, measured as the dealkylation of either ethoxyresorufin or methoxyresorufin. The selection of the PCBs was based on their differences in physico-chemical properties. The non-ortho and mono-ortho substituted PCBs were the most potent CYP1A inducers in pig hepatocytes. In addition, several multiple-ortho substituted congeners, with five or more chlorine atoms, were inducers of CYP1A activity as well. Their relative effect potencies (REP) were proximately 10,000 times lower than the most potent congener, 3,3',4,4',5 PeCB (PCB#126). Using partial least-squares (PLS) modeling, predictions of CYP1A activity could be made for all tetra to hepta substituted congeners. Several multiple-ortho substituted PCBs, which are highly abundant in the biotic and abiotic environment, have been found to induce CYP1A activity in pig hepatocytes. Because induction of CYP1A activity is used as biomarker for Ah-receptor mediated responses, it is suggested to include these congeners in future risk assessment.

Activation of respiratory burst in human granulocytes by polychlorinated biphenyls: A structure-activity study.

The respiratory burst in human granulocytes activated by 33 different congeners of polychlorinated biphenyls (PCBs) was measured as luminol-amplified chemoluminescence. The selection of 20 (training set) compounds was based on multivariate chemical characterization, laying the groundwork for covering the whole chemical series of tetra- through hepta-chlorinated PCBs. In addition 6 congeners were used as a validation set, and 7 were mono- to tri-chlorinated congeners representing low-chlorinated compounds not covered by the training set. Only ortho-substituted biphenyls activate respiratory burst. There is a correlation between activated respiratory burst and the total surface area of congeners up to 230 x 10(-20) m(2). Congeners of larger size show a reduced activity. There is also a correlation between respiratory burst activity and the number of ortho-substituents. Furthermore, there is also a correlation with parameters that describe absolute hardness of the molecule and respiratory burst activity. Congeners with a 2,4, 6-substitution on one biphenyl ring are optimal activators. In conclusion, all three factors, size, rotation, and electronic properties, which are not independent of each other, are important for the activity of the PCBs.

Impact of polychlorinated naphthalenes (PCNs) in juvenile Baltic salmon, Salmo salar: evaluation of estrogenic effects, development, and CYP1A induction.

Juvenile Baltic salmon, Salmo salar, were fed commercial salmon food contaminated with different concentrations of polychlorinated naphthalenes (PCNs; 0.1, 1, 2, or 10 microg PCN/g food). Among other effects, possible estrogenic impact caused by PCNs were evaluated. Fish were therefore fed a diet contaminated with 17beta-estradiol (E2; 0.94 or 9.4 microg E2/g food), as a positive control. After 8, 13, 17, and 41 weeks, sampling took place. Growth, liver somatic index (LSI), EROD activity, and vitellogenin content in blood plasma were measured along with morphological studies of gonads and chemical analyses to determine the effects caused by PCNs. Exposure to PCNs did not seem to have any effects on body weight gain, since the group fed the high dose followed the growth in the control group during the entirely experimental period. After 41 weeks of exposure the groups fed 2 and 10 microg PCN/g food had significantly lower LSIs compared with the control, indicating liver toxic effects of PCNs. Furthermore, a dose-dependent induction of EROD activity was found. At week 41, the control group had an activity of 4.9 +/- 4.8 pmol/mg prot/min, whereas it was between 69 +/- 21 and 720 +/- 370 pmol/mg prot/min in the exposed groups, respectively. Examination of gonadal morphology showed that PCNs also had negative effects on ovaries in Baltic salmon, including delayed development. The distribution between females and males, gonadal morphology, and vitellogenin content in blood plasma did, however, indicate that PCNs are not capable of causing effects similar to E2 or xenoestrogens. Exposure to both of the concentrations of E2 resulted in decreased body weight gain, increased LSI, and feminization of the gonads. E2 did, however, not induce any EROD activity.

The impact of musk ketone on reproduction in zebrafish (Danio rerio).

Nitro musks are a group of nitrated benzenes mainly used by the fragrance industry as a substitute for natural musk. Two of the most common nitro musks, musk xylene and musk ketone, have been detected in water, fish, human adipose tissue, as well as in human breast milk. In this study, female zebrafish were dietary-exposed to musk ketone, prior to spawning with unexposed males. The fish were exposed for 8 weeks at two different dose levels. Accumulation of the compound in the fish as well as reproductive success were studied. Exposed females had reduced body weight and length, as well as reduced liver- and gonad somatic index. The results from the reproduction study showed a dose-dependent reduction in fecundity. Early life-stage mortality was increased and the median survival time was reduced. In addition, an embryo/larvae toxicity test was performed, using newly fertilized zebrafish eggs from unexposed parental fish. Eggs were exposed to a series of different concentrations of musk ketone via the surrounding water. A NOEC value of 10 micrograms/l and a LOEC value of 33 micrograms/l was determined. Conclusively, the present study clearly shows that musk ketone negatively affects reproduction and early life-stage survival in zebrafish.

Assessment of PCBs and hydroxylated PCBs as potential xenoestrogens: In vitro studies based on MCF-7 cell proliferation and induction of vitellogenin in primary culture of rainbow trout hepatocytes.

In the present study, four structurally diverse polychlorinated biphenyls (PCBs) were chosen from a set of 20 PCBs selected to represent the 154 tetra- through hepta-chlorinated biphenyls. The purpose was to determine estrogenic activities of the chosen PCBs and five of their hydroxylated derivatives (OH-PCBs). A human breast cancer cell line (MCF-7) and primary cultures of rainbow trout (Oncorhyncus mykiss) hepatocytes were used to determine estrogenic effects. The PCBs 2,2',4,6,6'-pentachlorobiphenyl (104) and 2,2',3, 4', 5,6,6'-heptachlorobiphenyl (188), and the hydroxylated PCBs 2,2', 4',6'-tetrachloro-4-biphenylol (4'-50), 2',4', 6'-trichloro-4-biphenylol (4'-30), 2',3,5, 5'-tetrachloro-4-biphenylol (4'-72), 2',3,3',5', 6'-pentachloro-4-biphenylol (4'-112), and 2',3,4',5, 6'-pentachloro-4-biphenylol (4'-121) significantly increased MCF-7 cell proliferation. The coaddition of hydroxytamoxifen, an estrogen antagonist, inhibited increased cell proliferation. The activity of the hydroxylated PCBs 4'-50 and 4'-30 was significantly higher at all nominal concentrations tested as compared to the corresponding PCB, viz., PCB 104. The hydroxylated PCBs 4'-50, 4'-30, 4'-72 and 4'-112 induced vitellogenin synthesis in rainbow trout hepatocytes. Significant differences were found in the MCF-7 system between the parent PCB and its hydroxylated derivative, viz., for 4'-50/4'-30 and 104, and in the rainbow trout hepatocyte assay between 4'-112 and 112, respectively. No activity was observed for PCB 58 in any of the two assays in the present study. Even though cells from two different species (human and fish) are used in the present study, the results obtained by the two methods agree fairly well. In both studies the hydroxylated PCBs were more active than the PCBs, and 4'-30 was the most active compound second only to 17beta-estradiol. http://link.springer-ny. com/link/service/journals/00244/bibs/37n2p145.html

Structure-dependent induction of CYP1A by polychlorinated biphenyls in hepatocytes of cynomolgus monkeys (Macaca fascicularis).

Until now structure-activity relationships (SARs) for in vitro or in vivo CYP1A induction by polychlorinated biphenyls (PCBs) have only been determined in rodents and birds. This study describes the first development of such a SAR in a primate species by using hepatocyte cultures of cynomolgus monkey (Macaca fascicularis). Hepatocyte cultures of primate species might be a more suitable model for humans than those of rodents. For 20 PCBs, the in vitro induction of CYP1A activity was determined by measuring dealkylation of either methoxyresorufin or ethoxyresorufin. Selection of PCBs was based on multivariate physical-chemical characterization of all tetra- through heptachlorinated congeners. The non-ortho-substituted congeners were found to be the most potent inducers, followed by the mono-ortho-substituted PCBs. Multiple-ortho-substituted congeners, with more than five chlorine atoms, were inducers of CYP1A activity in monkey hepatocytes as well, with EC50 values approximately 10,000 times higher than 3,3',4,4',5 PeCB (PCB 126), the most potent congener. Using partial least-squares (PLS) modeling, predictions of CYP1A activity were established for all other tetra- to hepta-substituted congeners. Several congeners, which are abundant in the (a)biotic environment, were predicted to have CYP1A activity in cynomolgus monkey hepatocytes. Because induction of CYP1A activity is generally used as an early and sensitive biomarker for the Ah-receptor-mediated potential of a chemical, further studies are recommended to determine the possible risks of these multiple-ortho PCBs to humans.

The impact on reproduction of an orally administered mixture of selected PCBs in zebrafish (Danio rerio).

Zebrafish (Danio rerio) were orally exposed to a mixture of 20 PCBs in three different dose levels (0.008, 0.08, and 0.4 microg of each congener per gram of freeze-dried chironomids). Generally, the PCBs accumulated in a dose-related manner. After 13 weeks of exposure body, liver, and ovary weights, as well as the liver and ovary somatic index, were significantly lower in exposed groups. In addition, the PCB mixture was an effective inducer of hepatic EROD activity. The reproduction study performed with exposed females and unexposed males after 9 weeks revealed that median survival time for larvae was only 7.7 days in the high-dose group as compared with 14 days in controls. Furthermore, egg production was reduced in all three groups exposed. No differences in hatching frequency or median hatching time were recorded. Histologically, females in both the intermediate and high-dose groups contained a reduced number of mature oocytes. The present study demonstrates that the potency of the mixture of selected PCBs induces hepatic EROD activity and has a clearly negative effect on zebrafish reproduction.

The internal barriers of rotation for the 209 polychlorinated biphenyls.

The internal barrier of rotation (Erot) was calculated for all 209 polychlorinated biphenyls (PCBs) by using a semi-empirical method, viz. the Austin Model 1 (AMI) Hamiltonian. The difference in total energy between a forced planar state and an optimised twisted structure was defined as Erot. The Erot values were in the range of 8.33 to 483 kJ/mol, and were significantly influenced by the number of chlorine atoms in ortho position. An additional structural characteristic of the PCBs influencing Erot of ortho substituted congeners was substitution by chlorine atoms in vicinal meta positions, which is assumed to prevent outward bending of ortho substituents. This so-called buttressing effect contributed with 4 to 31 kJ/mol per added chlorine atom. In conclusion, the internal barrier of rotation, calculated for all 209 PCBs, provides an important structure dependent physico-chemical parameter for multivariate modelling of future quantitative structure-activity and structure-property relationships (QSARs/QSPRs).