Differential substrate behaviour of phenol and aniline derivatives during conversion by horseradish peroxidase

For the first time saturating overall k(cat) values for horseradish peroxidase (HRP) catalysed conversion of phenols and anilines are described. These k(cat) values correlate quantitatively with calculated ionisation potentials of the substrates. The correlations for the phenols are shifted to higher k(cat) values at similar ionisation potentials as compared to those for anilines. (1)H-NMR T(1) relaxation studies, using 3-methylphenol and 3-methylaniline as the model substrates, revealed smaller average distances of the phenol than of the aniline protons to the paramagnetic Fe(3+) centre in HRP. This observation, together with a possibly higher extent of deprotonation of the phenols than of the anilines upon binding to the active site of HRP, may contribute to the relatively higher HRP catalysed conversion rates of phenols than of anilines.     

Kinetic and molecular orbital studies on the rate of oxidation of monosubstituted phenols and anilines by horseradish peroxidase compound II

The second-order rate constant (k4) for the oxidation of a series of aromatic donor molecules (monosubstituted phenols and anilines) by horseradish peroxidase (HRP) compound II was examined with a stopped-flow apparatus. The electronic states of these substrates were calculated by an ab initio molecular orbital method. It was found that in both phenols and anilines log k4 values correlate well with the highest occupied molecular orbital (HOMO) energy level and the lowest unoccupied molecular orbital (LUMO) energy level, but not with the net charge or frontier electron density on atoms of these molecules. The HOMO and LUMO energy levels of phenols and anilines further showed linear relationships with Hammett's sigma values with negative slopes. Similar results were obtained in the oxidation of substrates by HRP compound I, except that the rate of reaction was much higher than in the case of HRP compound II. In addition, the rates of oxidation of phenols by compound I or II were found to be about 1000 times higher than those of anilines with similar HOMO energy levels. On the basis of these results, the mechanism of electron transfer from the substrate to the heme iron of HRP compound II is discussed.     

Chromatographic evaluation of the toxicity in fish of pesticides

Ecotoxicity assessment is essential before placing new chemical substances on the market. An investigation of the use of the chromatographic retention (log k) in biopartitioning micellar chromatography (BMC) as an in vitro approach to evaluate the toxicity in fish of pesticides (acute toxicity levels as pLC(50)) is proposed. A heterogeneous data set of 85 pesticides from six chemical families with available experimental fish toxicity data (ECOTOX database from U.S. Environmental Protection Agency (EPA)) was used. For pesticides exhibiting non-polar narcosis mechanism in fish (non-specific toxicity), more reliable models and precise pLC(50) estimations are obtained from log k (quantitative retention-activity relationships, QRAR) than from log P (quantitative structure-activity relationships, QSAR) or ECOSAR (ECOSAR program from U.S. EPA).     

Antifungal and cytotoxic activities of some N-substituted aniline derivatives bearing a hetaryl fragment

Diverse N-substituted anilines bearing hetaryl fragments were easily prepared from corresponding aldimines derived from commercially available aromatic aldehydes and anilines. 2-Furyl substituted anilines showed very good antifungal activities against dermatophytes, particularly against Trichophyton rubrum (MIC=3.12-6.25microg/mL). In addition, all active compounds, 45-47, 73, and 74, were tested for cytotoxic activities against breast (MCF-7), lung (H-460), and central nervous system (SF-268) human cancer cell lines with the NCI-anticancer-drug screen. The activity of amines described in this paper, along with the low toxicity of most of them, shows promise for the future development of non-toxic new antimycotic agents.     

Determination of phenolic compounds by a polyphenol oxidase amperometric biosensor and artificial neural network analysis

The determination of phenolic compounds is significant given its toxicity, even at very low concentration levels. Amperometric determination of phenols is a simple technique available. Direct oxidation of phenols can be used, but another possibility is the use of polyphenol oxidase (tyrosinase) enzyme biosensors that oxidises the phenolic compounds into their corresponding quinones. Reduction of the resulting quinones accomplishes the amplification of the amperometric signal, as long as the result of the reduction process is the corresponding cathecol, this being able to be oxidised again by the polyphenol oxidase immobilized on the surface of the biosensor. In this communication, simultaneous determination of different phenols was carried out combining biosensor measurements with chemometric tools, in what is known as electronic tongue. The departure information used was the overlapped reduction voltammogram generated with the amperometric biosensor based on polyphenol oxidase. Artificial Neural Networks (ANN) were used for extraction and quantification of each compound. Phenol, cathecol and m-cresol formed the three-analyte study case resolved in this work. Good prediction ability was attained, and so, the separate quantification of these three phenols was accomplished.     

Accurate gas phase acidities of carboxylic acids estimated by scaling the vibrational contribution of ab initio gibbs free energies

The gas phase Gibbs free energies deltaG(T) of dissociation reaction of 14 carboxylic acids were calculated on the SCF, as well as G3 and CBS-Q levels. Corresponding accuracies were critically compared with experimental data. Since all of the results suffer from systematic errors, the procedure of scaling of thermal contribution to Gibbs free energy was applied for minimizing differences between theoretical and experimental values of deltaG(T). Two parameters were adjusted, namely the scaling of thermal contribution to Gibbs free energy of neutral and anionic forms. The presented results suggest the great effectiveness of such a procedure since for all applied basis sets within the SCF framework the achieved accuracy was below the experimental error. Besides, the proposed low-cost approximation method leads to precision comparable to or even exceeding the quality offered by more sophisticated composite quantum chemistry methods. The extension of the set of training molecules up to 82 has an insignificant impact on the overall quality of deltaG(T) estimation, which suggests that a wisely chosen set of reference data may be used for the characteristics of the whole class of compounds. There is a straightforward way for the analysis of acidities/basicities of other classes of chemicals such as DNA bases, alcohols, phenols, amines, amino acids, etc.     

Interaction with functional membrane proteins--a common mechanism of toxicity for lipophilic environmental chemicals?

1. The effects of several phenols, anilines and aliphatic alcohols on yeast plasma membrane H(+)-ATPase and purine transport system as well as on Na+, K(+)-ATPase and adenosine uptake by Chinese hamster ovary cells (CHO) were investigated. 2. In all cases an inhibition was observed, which could be correlated with the octanol/water partition coefficients of the substances tested, thus making quantitative structure-activity predictions possible. 3. The observed effects correlated well with the influence of the chemicals on cell growth. 4. The results suggest a common mechanism of toxicity by the action of hydrophobic xenobiotics on biomembranes.     

Rhamnolipid biosurfactants decrease the toxicity of chlorinated phenols to Pseudomonas putida DOT-T1E

Aims:  To investigate the effect of a mixture of rhamnolipid R1 and R2 biosurfactants produced by a Pseudomonas aeruginosa strain on the toxicity of phenol and chlorophenols to Pseudomonas putida DOT-T1E.
Methods and Results:  Toxicity was quantified by the effective concentration 50% (EC50), that is the concentration that causes a 50% inhibition of bacterial growth. The presence of 300 mg l⁻¹ rhamnolipids, that is at about twice their critical micelle concentration (CMC), increased the EC50 of phenol, 4-chlorophenol, 2,4-dichlorophenol and 2,4,5-trichlorophenol by about 12, 19, 32 and 40%, respectively, and consequently reduced the bioavailability and the freely dissolved concentration of the toxic phenolic compounds. The reduction was related to the phenols' octanol–water partition coefficients ( K _ow).
Conclusions:  The reduction in toxicity of the phenols can be explained by a combination of toxin accumulation in biosurfactant micelles and hydrophobic interactions of the phenols with rhamnolipid-based dissolved organic carbon.
Significance and Impact of the Study:  Results provide evidence that next to the effect of the micelle formation also hydrophobic interactions with rhamnolipid-based dissolved organic carbon affects the bioavailability of the phenols. Quantifying the effect of biosurfactants on the toxicity of hydrophobic compounds such as phenols thus appears to be a useful approach to assess their bioavailable equilibrium concentration.     

N-甲基取代苯基氨基甲酸酯的系列合成及其对家蝇的生物活性

利用酰氯水相简易工艺合成了52个N-甲基取代苯基氨基甲酸酯类化合物, 并测定了它们对家蝇Musca domestica的室内毒力。结果表明：烷基单取代化合物中,间位取代物的活性大于邻、对位;单卤素取代物中,邻位取代活性大于间位和对位,邻溴代物大于邻氯代物;对位硫甲基和邻位硫乙基取代物的活性均较高。对于烷基间位苯环取代化合物,在一定限度内随烷基分子量增大,化合物对家蝇的毒力增高,其次序为异丙基>乙基>甲基>未取代基。     

Differential substrate behaviour of phenol and aniline derivatives during oxidation by horseradish peroxidase: kinetic evidence for a two-step mechanism

The catalytic constant (k(cat)) and the second-order association constant of compound II with reducing substrate (k(5)) of horseradish peroxidase C (HRPC) acting on phenols and anilines have been determined from studies of the steady-state reaction velocities (V(0) vs. [S(0)]). Since k(cat)=k(2)k(6)/k(2)+k(6), and k(2) (the first-order rate constant for heterolytic cleavage of the oxygen-oxygen bond of hydrogen peroxide during compound I formation) is known, it has been possible to calculate the first-order rate constant for the transformation of each phenol or aniline by HRPC compound II (k(6)). The values of k(6) are quantitatively correlated to the sigma values (Hammett equation) and can be rationalized by an aromatic substrate oxidation mechanism in which the substrate donates an electron to the oxyferryl group in HRPC compound II, accompanied by two proton additions to the ferryl oxygen atom, one from the substrate and the other the protein or solvent. k(6) is also quantitatively correlated to the experimentally determined (13)C-NMR chemical shifts (delta(1)) and the calculated ionization potentials, E (HOMO), of the substrates. Similar dependencies were observed for k(cat) and k(5). From the kinetic analysis, the absolute values of the Michaelis constants for hydrogen peroxide and the reducing substrates (K(M)(H(2)O(2)) and K(M)(S)), respectively, were obtained.     

Interpretation of the reactivity of peroxidase compound II with phenols and anilines using the Marcus equation

The catalytic cycle of heme peroxidases involves three processes: the formation of compound I, its conversion to compound II and regeneration of the native enzyme. Each of the processes consists of a reversible binding stage followed by an irreversible transformation stage. Our group has proposed a continuous, sensitive and reliable chronometric method for measuring the steady-state rate of peroxidase activity. Furthermore, we have derived an analytical expression for the steady-state rate and simplified it, taking into consideration the experimental values of the rate constants of some stages previously determined by other authors in stopped-flow assays. We determined the value of the constant for the transformation of a series of phenols and anilines by compound II, and found that it involves a deprotonation step and an electron transfer step. Study of the solvent deuterium isotope effect on the oxidation of phenol revealed the non-rate-limiting character of the deprotonation step in a proton inventory study. Usage of the Marcus equation showed that the electronic transfer step is rate-limiting in both cases, while phenols and anilines were oxidised at different rates for the same potentials. This can be attributed to the shorter electron-tunnelling distance for electron transfer to the iron ion in the phenols than in the anilines.     

Categorization of metabolome in bacterial systems

Analyses of biological databases such as those of genome, proteome, metabolome etc., have given insights in organization of biological systems. However, current efforts do not utilize the complete potential of available metabolome data. In this study, metabolome of bacterial systems with reliable annotations are analyzed and a simple method is developed to categorize pathways hierarchically, using rational approach. Ninety-four bacterial systems having for each ≥ 250 annotated metabolic pathways were used to identify a set of common pathways. 42 pathways were present in all bacteria which are termed as Core/Stage I pathways. This set of pathways was used along with interacting compounds to categorize pathways in the metabolome hierarchically. In each metabolome non-interacting pathways were identified including at each stage. The case study of Escherichia coli O157, having 433 annotated pathways, shows that 378 pathways interact directly or indirectly with 41 core pathways while 14 pathways are noninteracting. These 378 pathways are distributed in Stage II (289), Stage III (75), Stage IV (13) and Stage V (1) category. The approach discussed here allows understanding of the complexity of metabolic networks. It has pointed out that core pathways could be most ancient pathways and compounds that interact with maximum pathways may be compounds with high biosynthetic potential, which can be easily identified. Further, it was shown that interactions of pathways at various stages could be one to one, one to many, many to one or many to many mappings through interacting compounds. The granularity of the method discussed being high; the impact of perturbation in a pathway on the metabolome and particularly sub networks can be studied precisely. The categorizations of metabolic pathways help in identifying choke point enzymes that are useful to identify probable drug targets. The Metabolic categorizations for 94 bacteria are available at http://115.111.37.202/mpe/.     

Numerical modeling and uncertainties in rate coefficients for methane utilization and TCE cometabolism by a methane-oxidizing mixed culture

The rates of methane utilization and trichloroethylene (TCE) cometabolism by a methanotrophic mixed culture were characterized in batch and pseudo-steady-state studies. Procedures for determination of the rate coefficients and their uncertainties by fitting a numerical model to experimental data are described. The model consisted of a system of differential equations for the rates of Monod kinetics, cell growth on methane and inactivation due to TCE transformation product toxicity, gas/liquid mass transfer of methane and TCE, and the rate of passive losses of TCE. The maximum specific rate of methane utilization (k(CH(4) )) was determined by fitting the numerical model to batch experimental data, with the initial concentration of active methane-oxidizing cells (X(0) (a)) also used as a model fitting parameter. The best estimate of k(CH(4) ) was 2.2 g CH(4)/g cells-d with excess copper available, with a single-parameter 95% confidence interval of 2.0-2.4 mg/mg-d. The joint 95% confidence region for k(CH(4) ) and X(0) (a) is presented graphically. The half-velocity coefficient (K(S,CH(4) )) was 0.07 mg CH(4)/L with excess copper available and 0.47 mg CH(4)/L under copper limitation, with 95% confidence intervals of 0.02-0.11 and 0.35-0.59 mg/L, respectively. Unique values of the TCE rate coefficients k(TCE) and K(S,TCE) could not be determined because they were found to be highly correlated in the model fitting analysis. However, the ratio k(TCE)/K(S,TCE) and the TCE transformation capacity (T(C)) were well defined, with values of 0.35 L/mg-day and 0.21 g TCE/g active cells, respectively, for cells transforming TCE in the absence of methane or supplemental formate. The single-parameter 95% confidence intervals for k(TCE)/K(S,TCE) and T(C) were 0.27-0.43 L/mg-d and 0.18-0.24 g TCE/g active cells, respectively. The joint 95% confidence regions for k(TCE)/K(S,TCE) and T(C) are presented graphically. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 320-331, 1997.     

Toxicity Screening of a Combinatorial Library: Correlation of Cytotoxicity and Gene Induction to Compound Structure

Combinatorial chemistry has increased the number of compounds available for efficacy and safety assessment by several orders of magnitude and has made high throughput assays essential. To test whether higher throughput toxicity assays could be of utility in screening compounds in early development, a selected set of combinatorial chemistry compounds was screened for induction of 70-Kd heat shock protein (HSP70) and 45-Kd growth arrest and DNA damage protein (GADD45) mRNA levels as well as cytotoxicity, in HepG2 cells, using a 96-well microtiter plate format. Both assays, the branched DNA (Quantigene) assay for mRNA levels and MTT for cytotoxicity, were robust enough to be incorporated into a screening format using a single replicate and a single concentration of compound. Significantly, a structure/toxicity correlation was established with this set of compounds with cytotoxicity and gene induction patterns linked to compound structure. Therefore, this type of early screening may be useful in identifying toxic substituents, enabling the design of libraries with less potential for toxicity. While structure/toxicity correlations were observed, no relationship was observed between GADD45 gene induction and mutagenesis as measured by the Ames bacterial reverse mutation assay.     

An improved generalized AMBER force field (GAFF) for urea

We describe an improved force field parameter set for the generalized AMBER force field (GAFF) for urea. Quantum chemical computations were used to obtain geometrical and energetic parameters of urea dimers and larger oligomers using AM1 semiempirical MO theory, density functional theory at the B3LYP/6-31G(d,p) level, MP2 and CCSD ab initio calculations with the 6-311++G(d,p), aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets, and with the CBS-QB3 and CBS-APNO complete basis set methods. Seven different urea dimer structures were optimized at the MP2/aug-cc-pVDZ level to obtain accurate interaction energies. Atomic partial charges were calculated at the MP2/aug-cc-pVDZ level with the restrained electrostatic potential (RESP) fitting approach. The interaction energies computed with these new RESP charges in the force field are consistent with those obtained from CCSD and MP2 calculations. The linear dimer structure calculated using the force field with modified geometrical parameters and the new RESP charge set agrees well with available experimental data.     

Development and validation of a robust QSAR model for prediction of carcinogenicity of drugs

Carcinogenicity is one of the toxicological endpoints causing the highest concern. Also, the standard bioassays in rodents used to assess the carcinogenic potential of chemicals and drugs are extremely long, costly and require the sacrifice of large numbers of animals. For these reasons, we have attempted development of a global quantitative structure-activity relationship (QSAR) model using a data set of 1464 compounds (the Galvez data set available from http://www.uv.es/-galvez/tablevi.pdf), including many marketed drugs for their carcinogenesis potential. Though experimental toxicity testing using animal models is unavoidable for new drug candidates at an advanced stage of drug development, yet the developed global QSAR model can in silico predict the carcinogenicity of new drug compounds to provide a tool for initial screening of new drug candidate molecules with reduced number of animal testing, money and time. Considering large number of data points with diverse structural features used for model development (n(training) = 732) and model validation (n(test) = 732), the model developed in this study has an encouraging statistical quality (leave-one-out Q2 = 0.731, R2pred = 0.716). Our developed model suggests that higher lipophilicity values and conjugated ring systems, thioketo and nitro groups contribute positively towards drug carcinogenicity. On the contrary, tertiary and secondary nitrogens, phenolic, enolic and carboxylic OH fragments and presence of three-membered rings reduce the carcinogenicity. Branching, size and shape are found to be crucial factors for drug-induced carcinogenicity. One may consider all these points to reduce carcinogenic potential of the molecules.     

Benznidazole/Itraconazole Combination Treatment Enhances Anti-Trypanosoma cruzi Activity in Experimental Chagas Disease

The nitroheterocyclic drugs nifurtimox and benznidazole are first-line drugs available to treat Chagas disease; however, they have limitations, including long treatment courses and toxicity. Strategies to overcome these limitations include the identification of new drugs with specific target profiles, re-dosing regimens for the current drugs, drug repositioning and combination therapy. In this work, we evaluated combination therapy as an approach for optimization of the current therapeutic regimen for Chagas disease. The curative action of benznidazole/itraconazole combinations was explored in an established infection of the mice model with the T. cruzi Y strain. The activities of the benznidazole/itraconazole combinations were compared with the results from those receiving the same dosage of each individual drug. The administration of benznidazole/itraconazole in combination eliminated parasites from the blood more efficiently than each drug alone. Here, there was a significant reduction of the number of treatment days (number of doses) necessary to induce parasitemia suppression with the benznidazole/itraconazole combination, as compared to each compound administered alone. These results clearly indicate the enhanced effects of these drugs in combination, particularly at the dose of 75 mg/kg, as the effects observed with the drug combinations were four times more effective than those of each drug used alone. Moreover, benznidazole/itraconazole treatment was shown to prevent or decrease the typical lesions associated with chronic experimental Chagas disease, as illustrated by similar levels of inflammatory cells and fibrosis in the cardiac muscle tissue of healthy and treated mice. These results emphasize the importance of exploring the potential of combination treatments with currently available compounds to specifically treat Chagas disease.     

Application of long-range order to predict unfolding rates of two-state proteins

Predicting the experimental unfolding rates of two-state proteins and models describing the unfolding rates of these proteins is quite limited because of the complexity present in the unfolding mechanism and the lack of experimental unfolding data compared with folding data. In this work, 25 two-state proteins characterized by Maxwell et al. (Protein Sci 2005;14:602–616) using a consensus set of experimental conditions were taken, and the parameter long-range order (LRO) derived from their three-dimensional structures were related with their experimental unfolding rates ln(k(u)). From the total data set of 30 proteins used by Maxwell et al. (Protein Sci 2005;14:602–616), five slow-unfolding proteins with very low unfolding rates were considered to be outliers and were not included in our data set. Except all beta structural class, LRO of both the all-alpha and mixed-class proteins showed a strong inverse correlation of r = -0.99 and -0.88, respectively, with experimental ln(k(u)). LRO shows a correlation of -0.62 with experimental ln(k(u)) for all-beta proteins. For predicting the unfolding rates, a simple statistical method has been used and linear regression equations were developed for individual structural classes of proteins using LRO, and the results obtained showed a better agreement with experimental results.