The Mechanism of C-H Bond Oxidation by Aqueous Permanganate.

The permanganate ion (MnO) has been widely used as a reagent for water treatment for over a century. It is a strong enough oxidant to activate carbon-hydrogen bonds, one of the most important reactions in biological and chemical systems. Our current textbook understanding of the oxidation mechanism in aqueous solution involves an initial, rate-limiting hydride abstraction by permanganate followed by reaction of the carbocation with bulk water to form an alcohol.

DoseSim: a tool for pharmacokinetic/pharmacodynamic analysis and dose reconstruction.

Unlabelled: Assessing and improving the safety of chemicals and the efficacy of drugs depends on an understanding of the biodistribution, clearance and biological effects of the chemical(s) of interest. A promising methodology for the prediction of these phenomena is physiologically based pharmacokinetic/pharmacodynamic modeling, which centers on the prediction of chemical absorption, distribution, metabolism and excretion (pharmacokinetics) and the biological effects (pharmacodynamics) of the chemical on the organism. Strengths of this methodology include modeling across multiple scales of biological organization and facilitate the extrapolation of results across routes of exposure, dosing levels and species.

Tools and techniques.

This chapter lists some of the software and tools that are used in computational toxicology, as presented in this volume.

What is computational toxicology?

Computational toxicology is a vibrant and rapidly developing discipline that integrates information and data from a variety of sources to develop mathematical and computer-based models to better understand and predict adverse health effects caused by chemicals, such as environmental pollutants and pharmaceuticals. Encompassing medicine, biology, biochemistry, chemistry, mathematics, computer science, engineering, and other fields, computational toxicology investigates the interactions of chemical agents and biological organisms across many scales (e.g.

A physiologically based pharmacokinetic model for capreomycin.

The emergence of multidrug-resistant tuberculosis (MDR-TB) has led to a renewed interest in the use of second-line antibiotic agents. Unfortunately, there are currently dearths of information, data, and computational models that can be used to help design rational regimens for administration of these drugs. To help fill this knowledge gap, an exploratory physiologically based pharmacokinetic (PBPK) model, supported by targeted experimental data, was developed to predict the absorption, distribution, metabolism, and excretion (ADME) of the second-line agent capreomycin, a cyclic peptide antibiotic often grouped with the aminoglycoside antibiotics.

Prediction of contaminant persistence in aqueous phase: a quantum chemical approach.

At contaminated field sites where active remediation measures are not feasible, monitored natural attenuation is sometimes the only alternative for surface water or groundwater decontamination. However, due to slow degradation rates of some contaminants under natural conditions, attenuation processes and their performance assessment can take several years to decades to complete. Here, we apply quantum chemical calculations to predict contaminant persistence in the aqueous phase.

Rapid estimation of activation enthalpies for cytochrome-P450-mediated hydroxylations.

Cytochrome P450 (CYP) enzymes play a critical role in detoxication and bioactivation of xenobiotics; thus, the ability to predict the biotransformation rates and regioselectivity of CYP enzymes toward substrates is an important goal in toxicology and pharmacology. Here, we present the use of the semiempirical quantum chemistry method SAM1 to rapidly estimate relative activation enthalpies (ΔH(‡)) for the hydroxylation of aliphatic carbon centers of various substrates. The ΔH(‡) were determined via a reaction path calculation, in the reverse direction (RRP), using the iron-hydroxo-porphine intermediate and the substrate radical.

Quantum chemical prediction of redox reactivity and degradation pathways for aqueous phase contaminants: an example with HMPA.

Models used to predict the fate of aqueous phase contaminants are often limited by their inability to address the widely varying redox conditions in natural and engineered systems. Here, we present a novel approach based on quantum chemical calculations that identifies the thermodynamic conditions necessary for redox-promoted degradation and predicts potential degradation pathways. Hexamethylphosphoramide (HMPA), a widely used solvent and potential groundwater contaminant, is used as a test case.

Predicting activation enthalpies of cytochrome-P450-mediated hydrogen abstractions. 2. Comparison of semiempirical PM3, SAM1, and AM1 with a density functional theory method.

Predicting the biotransformation of xenobiotics is important in the chemical and pharmaceutical industries, as well as in toxicology. Here, we extend and evaluate the rapid methodology of Korzekwa, Jones, and Gillette (J. Am.

Computational toxicology of chloroform: reverse dosimetry using Bayesian inference, Markov chain Monte Carlo simulation, and human biomonitoring data.

Background: One problem of interpreting population-based biomonitoring data is the reconstruction of corresponding external exposure in cases where no such data are available.

Objectives: We demonstrate the use of a computational framework that integrates physiologically based pharmacokinetic (PBPK) modeling, Bayesian inference, and Markov chain Monte Carlo simulation to obtain a population estimate of environmental chloroform source concentrations consistent with human biomonitoring data. The biomonitoring data consist of chloroform blood concentrations measured as part of the Third National Health and Nutrition Examination Survey (NHANES III), and for which no corresponding exposure data were collected.

Cytochromes P450: a structure-based summary of biotransformations using representative substrates.

Cytochromes P450 (CYPs) are a superfamily of enzymes that metabolize the majority of xenobiotics in humans. This review presents a structure-based outline of CYP-catalyzed biotransformations of selected substrates, representing diverse structural classes of chemicals, ranging from drugs to toxicants. Data are presented in a tabular format for easy reference, with visual representations of all substrates and sites-of-attack.

Biochemical reaction network modeling: predicting metabolism of organic chemical mixtures.

All organisms are exposed to multiple xenobiotics, through food, environmental contamination, and drugs. These xenobiotics often undergo biotransformation, a complex process that plays a critical role in xenobiotic elimination or bioactivation to toxic metabolites. Here we describe the results of a new computer-based simulation tool that predicts metabolites from exposure to multiple chemicals and interconnects their metabolic pathways, using four common drinking water pollutants (trichloroethylene, perchloroethylene, methylchloroform, and chloroform) as a test case.

A novel, sensitive method for determining benzo[a]pyrene-diones using high-performance liquid chromatography with post-column zinc reduction.

A novel and sensitive high-performance liquid chromatography (HPLC) method was developed to analyze dione metabolites of benzo[a]pyrene (BaP). Because BaP-diones do not fluoresce, detection of low concentrations is difficult to achieve when analyzing these chemicals with a simple HPLC system. We developed a method to increase the detection sensitivities for BaP-diones using reduction by zinc after the chromatographic separation.

On-line HPLC-tandem mass spectrometry analysis of contaminants of L-tryptophan associated with the onset of the eosinophilia-myalgia syndrome.

The structural characterization of a number of contaminants of L-tryptophan (Trp) associated with eosinophilia myalgia syndrome has been performed for the first time by the powerful structural elucidation technique of tandem mass spectrometry coupled with on-line HPLC (LC-ESI-MS/MS). The identity of the contaminants: peaks UV-5, 3-(phenylamino)alanine, (PAA); E 1,1'-ethylidenebis(tryptophan); 200, 2-(3-indolylmethyl)-L-tryptophan; (all identified as case related) and peaks 1, 3-carboxy-1,2,3,4-tetrahydro-beta-carboline; 2, 3-carboxy-1-methyl-1,2,3,4-tetrahydro-beta-carboline; 100, 2-(2,3 dihydroxy-1-[3-indolyl]propyl)-L-tryptophan; and 300 and 400, diastereomers of 3-carboxy-1-[3-indolyl-methyl]-1,2,3,4-tetrahydro-beta-carboline, have been confirmed by this technique. By comparison of tandem MS (MS/MS) data from these compounds with the MS/MS data of several other impurities, we have structurally characterized peaks CC, KK and OO, as well as two previously unreported components labeled as peak P18 and peak P31.

Lidocaine in bronchoalveolar lavage fluid (BALF) is an inhibitor of eosinophil-active cytokines.

Eosinophils and eosinophil granule proteins may play an important role in the pathogenesis of asthma. BALF from 40 patients with symptomatic asthma were analysed for cytokine activity by the eosinophil survival assay. BALF from 15 patients showed increased survival activity.

EBT, a tryptophan contaminant associated with eosinophilia myalgia syndrome, is incorporated into proteins during translation as an amino acid analog.

The tryptophan dimer 1,1'-ethylidenebis[L-tryptophan] was identified as a contaminant of tryptophan preparations associated with Eosinophilia-Myalgia Syndrome. In this paper, we describe experiments examining the hypothesis that 1,1'-ethylidenebis[L-tryptophan] acts as an amino acid analog replacing L-tryptophan during the synthesis of proteins. We propose further that proteins containing 1,1'-ethylidenebis[L-tryptophan] are rejected in an autoimmune process identified clinically as Eosinophilia-Myalgia Syndrome.

1,1'-Ethylidenebis[L-tryptophan], an impurity in L-tryptophan associated with eosinophilia-myalgia syndrome, stimulates type I collagen gene expression in human fibroblasts in vitro.

Eosinophilia-myalgia syndrome (EMS), a recently described inflammatory disorder characterized by myalgia, peripheral eosinophilia, and multisystem inflammation is associated with L-tryptophan consumption. Fibrosis of various tissues due to excessive accumulation of type I collagen is a prominent late manifestation of the syndrome. 1,1'-Ethylidenebis[L-tryptophan] (EBT), an impurity distinct from L-tryptophan found in case-associated lots, has been implicated in function in vitro.

Biotransformation of 3-(phenylamino)-1,2-propanediol to 3-(phenylamino)alanine: a chemical link between toxic oil syndrome and eosinophilia-myalgia syndrome.

During late 1989, the eosinophilia-myalgia syndrome (EMS) developed as an epidemic in the United States, with numerous additional cases reported in several other countries worldwide. Eight years earlier, a closely-related disease, the toxic oil syndrome (TOS), occurred in Spain as a massive food-borne epidemic. Although EMS was linked to the ingestion of tainted L-tryptophan, and TOS to aniline-denatured rapeseed oil, the etiologic agent(s) responsible for both diseases remains undetermined.

Eosinophil-active cytokine from mononuclear cells cultured with L-tryptophan products: an unexpected consequence of endotoxin contamination.

Background: The eosinophilia-myalgia syndrome, caused by a contaminant or contaminants in epidemiologically implicated L-tryptophan products, is characterized by eosinophilia and eosinophil degranulation. We hypothesized that immune cells are stimulated by implicated L-tryptophan and produce eosinophil-active cytokines.

Objectives: This study was designed to identify substances in L-tryptophan causing the eosinophilia-myalgia syndrome.

1,1'-Ethylidenebis[tryptophan] induces pathologic alterations in muscle similar to those observed in the eosinophilia-myalgia syndrome.

1,1'-Ethylidenebis[tryptophan] (EBT), a derivative of L-tryptophan (LT), is a trace contaminant in batches of LT implicated by epidemiologic evidence in the pathogenesis of the eosinophilia-myalgia syndrome (EMS). We treated female Lewis rats with EBT or unimplicated LT (4 mg per 100 grams daily) by intraperitoneal injection. No rash or weakness occurred in either group.

Eosinophilia-myalgia syndrome and tryptophan production: a cautionary tale.

An epidemic of a new disease, termed eosinophilia-myalgia syndrome, occurred in the USA in 1989. This syndrome was linked to the consumption of L-tryptophan manufactured by a single company utilizing a fermentation process. All the findings indicate that the illness was probably triggered by an impurity formed when the manufacturing conditions were modified.

Studies with 1,1'-ethylidenebis(tryptophan), a contaminant associated with L-tryptophan implicated in the eosinophilia-myalgia syndrome.

L-Tryptophan binds to a rat liver nuclear envelope protein, and this binding is saturable, stereospecific, and of high affinity. Utilizing an in vitro assay of [3H]tryptophan binding to rat hepatic nuclear envelopes, we have previously determined that the L-tryptophan obtained from Showa Denko and which was implicated in cases of the eosinophilia-myalgia syndrome (EMS) inhibited [3H]tryptophan binding differently than did control L-tryptophan (not implicated in EMS). Therefore, in this study we investigated whether the addition of 1,1'-ethylidenebis(tryptophan) (EBT), a contaminant or impurity in L-tryptophan implicated in EMS, would have an effect.

3-(Phenylamino)alanine, a novel aniline-derived amino acid associated with the eosinophilia-myalgia syndrome: a link to the toxic oil syndrome?

The eosinophilia-myalgia syndrome (EMS) is an inflammatory disease that occurred in epidemic proportions in the United States during 1989. Cases of EMS were also reported in Europe and elsewhere. Clinically, EMS resembles the Spanish toxic oil syndrome.

Granule-associated flavin adenine dinucleotide (FAD) is responsible for eosinophil autofluorescence.

Unstained human eosinophils exhibit marked autofluorescence in comparison to other leukocytes due to a granule-associated fluorescent substance. Fluorescence spectroscopy of granule extracts reveals excitation maxima at approximately 380 and approximately 450 nm with a single emission at approximately 520, characteristic of flavins. The fluorescent material from eosinophil granule extracts was characterized by fluorescence, high-performance liquid chromatographic, and enzymatic analyses.