Validation of a novel molecular orbital approach (COMPACT) for the prospective safety evaluation of chemicals, by comparison with rodent carcinogenicity and Salmonella mutagenicity data evaluated by the U.S. NCI/NTP

Non-clinical safety assessment of Annona atemoya leaf extract: evaluation of genotoxicity

The leaves, stems, and fruits of Annona atemoya (A. atemoya; AA), a fruit-bearing plant of the family Annonaceae, exhibit anti-angiogenic, anti-oxidative, anti-inflammatory, and neuroprotective activities. However, the safety of AA has not been comprehensively elucidated. In this study, we evaluated the potential genotoxicity of an AA leaf (AAL) ethanol extract using a standard three-test battery constituting in vitro mammalian chromosomal aberration, in vivo micronucleus, and bacterial reverse mutation (also known as the Ames test) tests, as recommended by the Ministry of Food and Drug Safety of Korea. In vitro chromosomal aberration assay revealed that AAL extract did not induce structural or numerical aberrations, with or without metabolic activation (S9). In vivo micronucleus assay revealed that the number of micronucleated polychromatic erythrocytes (PCEs) and the PCE/normochromatic erythrocyte ratio after AAL extract treatment were not substantially different from those in the negative control. Changes in body weight and mortality were not observed. However, AAL extract partially induced mutagenic activity in all three bacterial strains in the bacterial reverse mutation assay, indicating that it could potentially aid in determining the genotoxic safety of AAL. QuantSeq 3' mRNA sequencing analysis to elucidate the genotoxicity mechanisms of AAL extract using TK6 cells revealed that the genotoxic effects of AAL may be associated with cellular morphology-associated (cell development and keratinization), nucleotide metabolism, and electron transport chain functions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43188-024-00241-4.

Safety evaluation of mutagenicity, genotoxicity, and cytotoxicity of Lactobacillus spp. isolates as probiotic candidates

BACKGROUND

Probiotics promote a healthy balance of gut bacteria and have many beneficial effects on human digestive physiology. Although, few side effects of probiotics have been reported. This study aimed to assess the safety of five probiotic candidate Lactobacillus strains isolated from healthy individuals by examining mutagenicity, genotoxicity, and oral toxic effects.

METHODS

Five selected candidate probiotic (SCPs) strains were evaluated for genotoxicity (Ames test with Salmonella typhimurium), in vitro mammalian chromosome aberration test and an in vivo mouse micronucleus assay on peripheral blood of mice. To evaluate the oral dose toxicity, BALB/c mice models were treated repeatedly (2000, 1000, and 500 mg/kg body weight /day) for 28-days.

RESULTS

The Ames test performed for two S. typhimurium strains TA 98 and TA100 (both in the absence and in the presence of S-9 metabolic activation system) did not show an increase in reverse mutation because of exposure to the SCPs in any of the doses (5.0, 2.5, 1.25, 0.625, and 0.3125 mg/plate). There was no genotoxicity in the SCPs treatment in the vitro chromosome aberration assay with Chinese hamster ovary cells (CHO-K1). In addition, none of the tested strains increased the frequency of micronucleated reticulocytes in reticulocytes, the SCPs with the studied doses caused no substantial variation in the experimental groups compared to the negative control group (p > 0.05). SCPs were not acutely toxic when administered to male and female BALB/c mice by single gavage at (2000, 1000, and 500 mg/kg b.w/day) with no mortality or clinical signs, change in body weight or macroscopic abnormalities were observed in this dose range.

CONCLUSION

As a result, SCPs did not induce mutagenic potential in vitro with bacterial reverse mutation, clastogenicity, and in vivo tests in the ranges of concentrations evaluated in our study.

A Comparison between COMPACT and Hazardexpert Evaluations for 80 Chemicals Tested by the NTP/NCI Rodent Bioassay

A total of 80 structurally diverse chemicals for which rodent carcinogenicity data are known, have been evaluated by two predictive computer-based systems, COMPACT and Hazardexpert. The results demonstrate that these two predictive test procedures are, to some extent, complementary, in that COMPACT can identify carcinogens which require metabolic activation, whereas Hazardexpert is able to provide an alert for potentially direct-acting agents. In this study, COMPACT was able to identify correctly most rodent carcinogens, and the Hazardexpert system showed a high concordance with non-carcinogens, in particular. It is suggested that some form of combined approach to the use of predictive methods in chemical safety evaluation may represent a way forward for the future.

Bioaccessibility of BDE 47 in a simulated gastrointestinal system and its metabolic transformation mechanisms in Caco-2 cells

Polybrominated diphenyl ethers (PBDEs) have been regarded as ubiquitous environmental pollutants. However, the absorption and transformation of these compounds after ingestion are not well understood yet. In this study, the bioaccessibility and metabolic pathway of 2,2',4,4'- tetrabromodiphenyl ether (BDE47) was investigated in an in vitro digestion/Caco-2 cell. Gastric and intestinal bioaccessibilities of BDE47 in 5 kinds of spiked soil samples were ranging from 11.39 ± 0.83% to 36.02 ± 4.34%, and 48.24 ± 3.24% to 81.52 ± 6.43%, respectively. Upon exposure to differentiated Caco-2 cells for 6 h, it was found that only a small amount of BDE47 in the gastrointestinal (GI) solution could pass through Caco-2 cells, and might enter the body. Moreover, BDE47 was found to be metabolized or transformed into BDE28, BDE75, BDE37, BDE32, BDE15 and BDE8 in Caco-2 cells. The metabolic pathway could be explained by using the Becke three-parameter hybrid functional (B3Lucifer yellow CHP) in the Density Functional Theory (DFT), denoted as the values of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) at the atoms of BDE47 and its metabolic products. The obtained results suggest that oral intake of PBDEs is associated with low bioaccessibility, but also emphasize the risks associated with oral ingestion, namely toxicity resulting from the debromination of highly brominated diphenyl ethers. Although highly brominated diphenyl ethers are known to be the least toxic PBDEs, the debrominated products in human intestinal epithelia may elicit greater than expected toxicity.

Mutagenic and cytotoxic activities of Limonium globuliferum methanol extracts

Unmonitored use of plant extractions alone or in combination with drugs may cause important health problems and toxic effects. Limonium (Plumbaginaceae) plants are known as antibacterial, anticancer and antivirus agent. But it is possible that this genus may have toxic effects. This study evaluated the mutagenic and cytotoxic effects of Limonium globuliferum (Boiss. et Heldr.) O. Kuntze (Plumbaginaceae) acetone/methanol (2:1), and methanol extracts of root, stem, and leaf. Different parts of this species were used in order to compare the mutagenic and cytotoxic effects of these parts. Ames test was carried out with S. typhimurium TA98, and TA100 strains. Strains were incubated at 37 °C for 72 h. MDBK cell line was used in MTT test. 10,000, 1000, 100, 10, 1 and 0.1 µg/plate concentrations of plant extracts were used in Ames test. 50, 25, 12.5, 6.25 and 3.125 µg/ml concentrations of root, stem and leaf acetone/methanol (2:1) and methanol extracts were used in MTT test. Ames test results indicated that only methanol leaf extract (10,000 µg/plate) had mutagenic activity. L. globuliferum root methanol extracts (3.125 and 6.25 µg/ml) increased the proliferation rates. Root acetone/methanol (2:1) extracts were found highly cytotoxic in all treatments. The results indicated that leaf extracts had lower cytotoxic effects than root and stem extracts. High concentrations of L. globuliferum stem and leaf methanol extracts showed cytotoxic activity in all treatment periods while low concentrations of the stem methanol extracts increased the proliferation rates.

Dopamine D2-Receptor Antagonists Down-Regulate CYP1A1/2 and CYP1B1 in the Rat Liver

Dopaminergic systems regulate the release of several hormones including growth hormone (GH), thyroid hormones, insulin, glucocorticoids and prolactin (PRL) that play significant roles in the regulation of various Cytochrome P450 (CYP) enzymes. The present study investigated the role of dopamine D₂-receptor-linked pathways in the regulation of CYP1A1, CYP1A2 and CYP1B1 that belong to a battery of genes controlled by the Aryl Hydrocarbon Receptor (AhR) and play a crucial role in the metabolism and toxicity of numerous environmental toxicants. Inhibition of dopamine D₂-receptors with sulpiride (SULP) significantly repressed the constitutive and benzo[a]pyrene (B[a]P)-induced CYP1A1, CYP1A2 and CYP1B expression in the rat liver. The expression of AhR, heat shock protein 90 (HSP90) and AhR nuclear translocator (ARNT) was suppressed by SULP in B[a]P-treated livers, whereas the AhRR expression was increased by the drug suggesting that the SULP-mediated repression of the CYP1 inducibility is due to inactivation of the AhR regulatory system. At signal transduction level, the D₂-mediated down-regulation of constitutive CYP1A1/2 and CYP1B1 expression appears to be mediated by activation of the insulin/PI3K/AKT pathway. PRL-linked pathways exerting a negative control on various CYPs, and inactivation of the glucocorticoid-linked pathways that positively control the AhR-regulated CYP1 genes, may also participate in the SULP-mediated repression of both, the constitutive and induced CYP1 expression. The present findings indicate that drugs acting as D₂-dopamine receptor antagonists can modify several hormone systems that regulate the expression of CYP1A1, CYP1A2 and CYP1B1, and may affect the toxicity and carcinogenicity outcome of numerous toxicants and pre-carcinogenic substances. Therefore, these drugs could be considered as a part of the strategy to reduce the risk of exposure to environmental pollutants and pre-carcinogens.

Adaptation of high-throughput screening in drug discovery-toxicological screening tests

High-throughput screening (HTS) is one of the newest techniques used in drug design and may be applied in biological and chemical sciences. This method, due to utilization of robots, detectors and software that regulate the whole process, enables a series of analyses of chemical compounds to be conducted in a short time and the affinity of biological structures which is often related to toxicity to be defined. Since 2008 we have implemented the automation of this technique and as a consequence, the possibility to examine 100,000 compounds per day. The HTS method is more frequently utilized in conjunction with analytical techniques such as NMR or coupled methods e.g., LC-MS/MS. Series of studies enable the establishment of the rate of affinity for targets or the level of toxicity. Moreover, researches are conducted concerning conjugation of nanoparticles with drugs and the determination of the toxicity of such structures. For these purposes there are frequently used cell lines. Due to the miniaturization of all systems, it is possible to examine the compound's toxicity having only 1-3 mg of this compound. Determination of cytotoxicity in this way leads to a significant decrease in the expenditure and to a reduction in the length of the study.

Expert Systems for Toxicity Prediction

Expert systems offer the facility to predict a toxicity endpoint, as well sometimes as additional relevant information, simply by inputting the chemical structure of a compound. There is now a number of expert systems available, mostly on a commercial basis although a few are free to use or download. This chapter discusses nineteen currently available expert systems, and their performances (if known). Published studies of consensus predictions with these expert systems indicate that these give better results than do individual expert systems.

A test set of compounds with Tetrahymena pyriformis toxicities has been run through the two expert systems known to predict these toxicities; the predictions were quite good, with standard errors of prediction of 0.395 and 0.433 log unit. A further test set of compounds with local lymph node assay skin sensitisation data has been run through seven expert systems, and it was found that consensus predictions were better than were those from any individual expert system.

Molecular orbital studies on brominated diphenyl ethers. Part II--reactivity and quantitative structure-activity (property) relationships

Polybrominated diphenyl ethers (PBDEs) are widely used as flame retardants and are increasingly turning up in the environment. Their structural similarities to polychlorinated biphenyls and thyroid hormones suggest they may be a risk to human health. The present study examines the reactivity of brominated diphenyl ethers (BDEs) on the basis of the electronic structures as calculated by semiempirical AM1 self-consistent field molecular orbital (SCF-MO) method. Frontier orbital energies were used to elucidate the reactivity of BDEs in electrophilic, nucleophilic and photolytic reactions. From an examination of the frontier electron densities, the regioselectivity, or orientation, of metabolic reactions of BDEs was predicted. Furthermore, satisfactory quantitative structure-activity (property) relationship (QSAR and QSPR) models were derived to calculate gas chromatographic and ultraviolet spectral properties and luciferase induction activities from the AM1-computed electronic parameters.

Quantitative structure-activity relationships (QSARs) within the cytochrome P450 system: QSARs describing substrate binding, inhibition and induction of P450s

Quantitative structure-activity relationships (QSARs) within substrates, inducers and inhibitors of cytochromes P450 involved in xenobiotic metabolism are reported, together with QSARs associated with induction, inhibition and metabolic rate. The importance of frontier orbitals and shape descriptors, such as planarity (estimated by the area/depth(2) parameter) and rectangularity (estimated by the length/width parameter) is discussed, particularly in the context of the COMPACT system which discriminates between several P450 families associated with the activation and detoxication of xenobiotics. The use of parameters, particularly those derived from homology modelling of mammalian (especially human) P450s that are involved in exogenous metabolism, in generating QSARs for P450 substrates is discussed in the context of explaining differences in the binding affinities of human P450 substrates which are pharmacologically active.

In silico prediction of drug toxicity

It is essential, in order to minimise expensive drug failures due to toxicity being found in late development or even in clinical trials, to determine potential toxicity problems as early as possible. In view of the large libraries of compounds now being handled by combinatorial chemistry and high-throughput screening, identification of putative toxicity is advisable even before synthesis. Thus the use of predictive toxicology is called for. A number of in silico approaches to toxicity prediction are discussed. Quantitative structure-activity relationships (QSARs), relating mostly to specific chemical classes, have long been used for this purpose, and exist for a wide range of toxicity endpoints. However, QSARs also exist for the prediction of toxicity of very diverse libraries, although often such QSARs are of the classification type; that is, they predict simply whether or not a compound is toxic, and do not give an indication of the level of toxicity. Examples are given of all of these. A number of expert systems are available for toxicity prediction, most of them covering a range of toxicity endpoints. Those discussed include TOPKAT, CASE, DEREK, HazardExpert, OncoLogic and COMPACT. Comparative tests of the ability of these systems to predict carcinogenicity show that improvement is still needed. The consensus approach is recommended, whereby the results from several prediction systems are pooled.

A quantitative structure-activity relationship (QSAR) study of mutagenicity in several series of organic chemicals likely to be activated by cytochrome P450 enzymes

The results of quantitative structure-activity relationship (QSAR) studies on six series of compounds exhibiting indirect mutagenic activity are reported. These findings demonstrate the importance of frontier orbital energies and, in some cases, frontier orbital electronic populations to overall mutagenicity in diverse polyaromatic hydrocarbons, benzidines and aminobiphenyls, benzonitrofurans, nitrogenous cooked-food mutagens, benzanthracenes, and chrysenes. The correlations between structural parameters and mutagenic potency vary from R=0.81 to R=0.97, and these findings are discussed in the context of possible molecular mechanisms of mutagenicity. In particular, it is generally regarded that cytochrome P450-mediated activation of polyaromatic hydrocarbons and their amino derivatives plays an important role in mutagenic activity. In this respect, it is apparent that enzymes of the cytochrome P4501 (CYP1) family are closely associated with the metabolic activation of polyaromatic mutagens and carcinogens via the generation of reactive intermediates (usually electrophilic in nature) that attack DNA. The findings presented in this study indicate that QSAR analyses on several series of compounds are consistent with the known evidence of procarcinogen activation mechanisms, particularly for polyaromatic hydrocarbons and their heterocyclic/amino derivatives, pointing to the importance of frontier orbital energy values in particular.

Extended quantitative structure-activity relationships for 80 aromatic and heterocyclic amines: structural, electronic, and hydropathic factors affecting mutagenic potency

The mutagenic/carcinogenic heterocyclic amines formed during the cooking of protein foods have been determined to be probable or possible human carcinogens. As part of a comprehensive study of the food mutagens, our laboratory has produced a series of quantitative structure-activity relationships (QSARs) of aromatic and heterocyclic amines, to attempt to elucidate the mechanisms of mutagenesis/carcinogenesis. Amines are genotoxically active only after activation by a series of reactions converting the parent compound to an electrophilic derivative, which is postulated to be a nitrenium ion that covalently binds to and damages DNA. An important agent in this conversion is cytochrome P450. In this report we develop a QSAR for 80 amines of diverse structure and a range of 10 orders of magnitude in mutagenic potency. New structural factors and quantum chemical ab initio and Hückel calculations are included. The results are interpreted to show that a main determinant of mutagenic potency is the extent of the aromatic pi-electron system. Small contributions are made by both the dipole moment and the calculated stability of the nitrenium ion. Multiple linear regression models account for nearly two-thirds of the variance in potency, leaving room for additional unknown factors. The role of cytochrome P450 1A in amine toxification is supported, and further theoretical and experimental research on its reaction mechanisms and modeling of its active site are proposed.

A combined COMPACT and HazardExpert study of 40 chemicals for which information on mutagenicity and carcinogenicity is known, including the results of human epidemiological studies

The COMPACT approach for defining structural criteria for substrates and inducers of cytochrome P450 (CYP) enzymes which mediate the formation of reactive intermediates is discussed in the context of prediction of potential carcinogenicity. This is broadened to encompass structural studies on mammalian P450s, including those relevant to genetic polymorphism in man. The use of the COMPACT system, in parallel with the structure alert program HazardExpert (now incorporated into the Pallas system), for evaluating human carcinogenicity data is reported, as an example of the possible employment of a battery of short-term test procedures for safety evaluation. In particular, the importance of using the log P value (as a measure of compound lipophilicity) to assess the likelihood of a potentially toxic compound reaching the site of activation, is emphasized by the finding that most procarcinogens requiring metabolic activation by P450s are lipophilic in nature.

Quantitative structure-based modeling applied to characterization and prediction of chemical toxicity

Quantitative modeling methods, relating aspects of chemical structure to biological activity, have long been applied to the prediction and characterization of chemical toxicity. The early linear free-energy approaches of Hansch and Free Wilson provided a fundamental scientific framework for the quantitative correlation of chemical structure with biological activity and spurred many developments in the field of quantitative structure-activity relationships (QSARs). In addition to modeling of chemical toxicity, these methods have been extensively applied to modeling of medicinal properties of chemicals. However, there are important differences in the nature and objectives of these two applications, which have led to the evolution of different modeling approaches (namely, the need for treating sets of noncongeneric toxic compounds). In this paper are discussed those approaches to chemical toxicity that have taken a more "personalized" configuration and have undergone implementation into software programs able to perform the various steps of the assessment of the hazard posed by the chemicals. These models focus both on a variety of toxicological endpoints and on key elements of toxicity mechanisms, such as metabolism.

Further evaluation of COMPACT, the molecular orbital approach for the prospective safety evaluation of chemicals

The molecular dimensions and electronic structures of the first group of 100 US NCI/NTP miscellaneous chemicals, evaluated for potential carcinogenicity by computer-optimized molecular parametric analysis for chemical toxicity (COMPACT) have been re-determined. Using improved criteria for cytochrome P450 (CYP) substrate specificity, re-defined for CYP1 as having a COMPACT radius [square root of (deltaE - 9.5)2 + (a/d(2) - 7.8)2] of < 6.5, and for CYP2E as having a collision diameter of 6.5 angstroms or less and deltaE < 15.5, the likely substrates of CYP1 and CYP2E, which are regarded as potential carcinogens, have been identified. In addition, log P values have been taken into account; those chemicals with log P < 0 are non-lipophilic substrates unlikely to reach the activating cytochrome enzymes, and have been regarded as non-carcinogens. The second group of 100 US NCI/NTP chemicals have also now been categorized by COMPACT into CYP1 and CYP2E substrates, and their potential carcinogenicities evaluated. Of the 203 chemicals in the 2 groups, those positive in the rodent two-species life-span carcinogenicity study (rodent assay) were 53%, those positive in the Ames test (mutagenicity) were 48%, and those positive in the COMPACT programme (carcinogenicity, mutagenicity, cytotoxicity) were 54%. Concordance between the COMPACT prediction of carcinogenicity/cytotoxicity and rodent two species life-span carcinogenicity data for the 203 chemicals is 69%, and correlation of COMPACT with Ames test data is 61%. The sensitivity of COMPACT for predicting rodent carcinogenicity is 72%, whereas the sensitivity of the Ames test for predicting carcinogenicity for the 203 chemicals was only 57%. The degree (severity) of rodent carcinogenicity also showed correlation with the COMPACT predictive evaluations of the chemicals.

Computational predictive programs (expert systems) in toxicology

The increasing number of pollutants in the environment raises the problem of the toxicological risk evaluation of these chemicals. Several so called expert systems (ES) have been claimed to be able to predict toxicity of certain chemical structures. Different approaches are currently used for these ES, based on explicit rules derived from the knowledge of human experts that compiled lists of toxic moieties for instance in the case of programs called HazardExpert and DEREK or relying on statistical approaches, as in the CASE and TOPKAT programs. Here we describe and compare these and other intelligent computer programs because of their utility in obtaining at least a first rough indication of the potential toxic activity of chemicals.

Defective expression of cytochrome P450 proteins in the liver of the genetically obese Zucker rat

The hepatic expression of xenobiotic-metabolising cytochrome P450 isoforms in the genetically obese Zucker rat, a model of obesity, was compared to that of its lean littermate. Cytochrome P450 (CYP) levels were determined using diagnostic substrates and/or immunologically in Western blot analyses. When compared with the lean Zucker rat, the obese animal exhibited hyperglycaemia, hypercholesterolaemia, marked hyperinsulinaemia and hypertriglyceridaemia but was normoketonaemic. CYP3A and CYP1A2 levels were higher in the obese Zucker rat when compared with the lean littermate but, in contrast, a protein recognised by human CYP2D6 and, to a lesser extent, CYP2C11 levels were lower. Pretreatment with acetone, dexamethasone and clofibrate resulted in enhanced p-nitrophenol hydroxylase (CYP2E), erythromycin N-demethylase (CYP3A) and lauric acid hydroxylase (CYP4A) activities respectively in the liver of the lean Zucker rat but, in contrast, the obese Zucker rat was refractive to such treatment; similarly, hepatic apoprotein levels of the CYP2E and CYP4A subfamilies were increased markedly only in the lean Zucker rat. It is concluded that CYP2E, CYP3A and CYP4A subfamilies are poorly expressed in the obese Zucker rat, and this rat strain may serve as a good model for elucidating the molecular mechanisms of induction of these cytochrome P450 proteins.

Quantitative structure-activity relationships and COMPACT analysis of a series of food mutagens

Quantitative structure-activity relationships between chemical structure and Ames mutagenicity for a group of 24 food mutagens, including 17 cooked-food heterocyclic amines, have been determined. For the TA98 strain of Salmonella typhimurium (frameshift mutagens) the best correlation of mutagenicity is with molecular diameter (R = 0.91), while for the TA100 strain (base-pair mutations) the best correlation is with delta E, the energy difference between the lowest unoccupied and highest occupied molecular orbitals. High mutagenicity is related to high values of molecular diameter, hence to planarity and to high values of the COMPACT ratio ([area/depth2]/delta E). High mutagenicity is also related to low values of delta E. Consequently, highly mutagenic and potentially carcinogenic food chemicals can readily be identified as substrates of cytochrome P4501 (CYP1) and may therefore be detected by the COMPACT procedure. Highly mutagenic compounds also exhibit high values of dipole moment.

Extrahepatic expression of P450 proteins in insulin-dependent diabetes mellitus

1. Male Wistar rats were rendered diabetic by the administration of a single intraperitoneal dose of streptozotocin; the levels of the xenobiotic-inducible P450 proteins were determined in the lung and kidney using diagnostic substrates and immunoblotting employing polyclonal antibodies. The glutathione conjugation system in the cytosol of these tissues was also investigated. 2. The onset of insulin-dependent diabetes did not influence the O-dealkylations of methoxyresorufin, ethoxyresorufin and pentoxyresorufin in either kidney or lung. 3. Lauric acid hydroxylase activity, however, was induced in the kidney but no activity was detectable in the lung. Immunoblot analysis of kidney microsomes using antibodies to P4504A1 revealed the presence of two bands, both of which were clearly inducible in diabetes. In pulmonary microsomes a single faint band was detected which also appeared to be higher in the diabetic rats. 4. Aniline p-hydroxylase activity was not detectable in the kidney, but activity was measurable in the lung and was suppressed in diabetes. Immunoblot analysis of pulmonary microsomes using antibodies to P4502E1 immunodetected a single band which was suppressed in diabetes. In the kidney microsomes a single band was also detected which was, however, markedly elevated in diabetes. 5. Glutathione S-transferase activity was modestly higher in the kidney, but not lung, of the diabetic animals. Glutathione reductase and total glutathione levels were not influenced by the presence of diabetes. 6. It is concluded that streptozotocin-induced insulin-dependent diabetes modulates extrahepatic P450 proteins, the effect being both tissue- and isoform-specific.

Molecular modelling of members of the P4502A subfamily: application to studies of enzyme specificity

1. Using the recently published crystal structure of a bacterial P450, namely 102 (also termed P450bm3), as a template molecular models of mammalian 2A1, 2A4, 2A5 and 2A6 were constructed. 2. Substrate interaction studies demonstrated that in keeping with known catalytic activities the putative binding sites of mouse hepatic P4502A4 and 2A5 oriented testosterone for 15 alpha-hydroxylation and coumarin for 7-hydroxylation respectively. 3. Substrate interaction studies with the putative binding site of human liver P4502A6 demonstrated that coumarin was oriented for 7-hydroxylation. However, in keeping with previous site-directed mutagenesis studies with P4502A4 and 2A5, changing a single phenylalanine residue to leucine in 2A6 gave rise to a mutant enzyme, which could bind testosterone as a substrate for 15 alpha-hydroxylation rather than coumarin. 4. Substrate interaction studies with the putative binding site of rat hepatic P4502A1 suggested that this isoenzyme would hydroxylate coumarin at the 3- rather than at the 7-position. 5. The results of these molecular modelling studies demonstrate that apparently minor modifications to P4502A subfamily amino acid sequences can result in major alterations in enzyme specificity. 6. Molecular modelling is thus a useful technique that can aid in elucidating substrate specificities of P450 isoenzymes and species differences in xenobiotic metabolism. The technique can also be utilized to complement site-directed mutagenesis studies in order to identify critical structural features of P450s and other enzymes.

A retrospective evaluation of COMPACT predictions of the outcome of NTP rodent carcinogenicity testing

The carcinogenic potentials of 40 National Toxicology Program chemicals previously predicted by Computer Optimised Molecular Parametric Analysis for Chemical Toxicity (COMPACT), based on the identification of potential substrates of cytochromes P4501A and 2E (CYP1A and CYP2E), have been compared with new rodent carcinogenicity results. The COMPACT predictions have also been compared with published Ames mutagenicity data and with our own Hazardexpert predictions for carcinogenicity. Concordance evaluations between rodent carcinogenicity (1/4 segments positive) and predictions by COMPACT or Hazardexpert were 64% for COMPACT (CYP1A only), 72% for COMPACT (CYP1A plus CYP2E), 70% for Hazardexpert alone, and 86% for COMPACT (CYP1A plus CYP2E) plus Hazardexpert. Sensitivities of the predictions were for COMPACT, 75%; Hazardexpert, 60%; and Ames, 54%. Positive predictivities were for COMPACT, 75%; Hazardexpert, 78%; and Ames 81%. Negative predictivites were for COMPACT, 62%; Hazardexpert, 52%; and Ames, 42%.

Safety evaluations of food chemicals by "COMPACT". 1. A study of some acyclic terpenes

A group of 19 acyclic terpenes have been evaluated for potential toxicity/carcinogenicity by molecular orbital determinations of their spatial and electronic parameters, and hence prediction of their metabolic activation or detoxication by the cytochrome P-450 (CYP) superfamily of mixed-function oxidase enzymes. Previous studies have characterized the spatial dimensions of the CYP1A1, 1A2 and 2E1 enzymes, which are known to activate mutagens and carcinogens and to be involved in other mechanisms of toxicity. None of the terpenes was found to have shape or electronic parameters appropriate for metabolic activation by CYP1A1 or 1A2, and hence they are unlikely to be carcinogenic or mutagenic. Furthermore, none of these chemicals had spatial parameters critical for substrates of CYP2E, and they are therefore unlikely to induce the formation of reactive oxygen species (ROS) or to initiate or promote malignancy or toxicity by mechanisms involving ROS. However, citral, and others of these terpenes, are known to undergo metabolism to carboxylic acids that may induce CYP4, and are therefore possible inducers of hepatic peroxisomal proliferation at high dosage, which may have implications for possible hepatotoxicity.

The cytochromes P450 and mechanisms of chemical carcinogenesis

This article reviews mechanisms of chemical carcinogenesis, from metabolic activation and generation of reactive oxygen species by cytochromes P4511 and P4502E to DNA damage, activation of protein kinase C and ocogenes, hyperplasia, and proteoglycan changes in the cell glycocalyx and lysosomal enzymes which mediate invasion and metastasis.

The use of computers in the safety evaluation of drugs and other chemicals

The toxicity and carcinogenicity of drugs and other chemicals is, in most cases, mediated by highly reactive intermediates which are generated following metabolism catalysed by the enzymic apparatus of the exposed organisms. These reactive intermediates readily interact covalently with vital cellular components to provoke toxicity and carcinogenicity. The ubiquitous cytochrome P450-dependent mixed-function oxidases are the most important enzyme system in the activation of chemicals. This enzyme system comprises a number of families, each of which contains one or more subfamilies. The CYPIA and CYP2E subfamilies are the most closely associated with the production of reactive intermediates and, consequently, the manifestation of toxicity and carcinogenicity. A computer based molecular structure procedure (COMPACT) has been developed which, via a calculation of the molecular and electronic structure of the chemical, determines whether the chemical will interact with either of these two cytochrome P450 subfamilies and hence be metabolised to form reactive intermediates that manifest toxicity. As the basal levels of these two subfamilies are generally low, the ability of a chemical to induce them selectively, on repeated administration, is an important determinant of its toxic and carcinogenic potential. This inductive capability may be determined in short-term studies (ENACT) using only a small number of animals. Thus the combination of COMPACT and ENACT provides a rapid and inexpensive means for the preliminary screening of chemicals for toxicity and carcinogenicity before undertaking the long-term and expensive rodent lifetime bioassays.

Interaction of a series of nitriles with the alcohol-inducible isoform of P450: computer analysis of structure-activity relationships

1. Structural studies are reported on a series of 20 nitriles of varying rates of P4502E-mediated oxidative metabolism. 2. Parameters of molecular and electronic structure have been calculated for the generation of quantitative structure-activity relationships (QSARs) with the rates of oxidative metabolism of the nitriles, and with their acute toxicity. 3. Correlations between molecular polarizability, excitation energy and biological activity are presented as a result of QSAR analysis.