Mitochondrial protein targets of thiol-reactive electrophiles

Mapping the cysteine proteome: analysis of redox-sensing thiols

The cysteine (Cys) proteome includes 214,000 Cys with thiol and other forms. A relatively small subset functions in cell signaling, while a larger number coordinate cell functions in response to redox state. The former are redox-signaling thiols while the latter are defined as redox-sensing thiols. Bulk measurements are not very informative for systems biology because reactivity of thiols in proteins differs by seven orders of magnitude. Proteomic databases contain annotation of Cys, for example, disulfides and zinc fingers, but do not include quantitative information necessary to develop functional models. Complementary databases and Cys proteome maps are needed to describe thiol redox circuits and connect these to functional redox-dependent pathways. This article summarizes progress in quantitative redox proteomics to develop such maps.

Cysteinyl peptide capture for shotgun proteomics: global assessment of chemoselective fractionation

The complexity of cell and tissue proteomes presents one of the most significant technical challenges in proteomic biomarker discovery. Multidimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based shotgun proteomics can be coupled with selective enrichment of cysteinyl peptides (Cys-peptides) to reduce sample complexity and increase proteome coverage. Here we evaluated the impact of Cys-peptide enrichment on global proteomic inventories. We employed a new cleavable thiol-reactive biotinylating probe, N-(2-(2-(2-(2-(3-(1-hydroxy-2-oxo-2-phenylethyl)phenoxy)acetamido)ethoxy)-ethoxy)ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide (IBB), to capture Cys-peptides after digestion. Treatment of tryptic digests with the IBB reagent followed by streptavidin capture and mild alkaline hydrolysis releases a highly purified population of Cys-peptides with a residual S-carboxymethyl tag. Isoelectric focusing (IEF) followed by LC-MS/MS of Cys-peptides significantly expanded proteome coverage in Saccharomyces cerevisiae (yeast) and in human colon carcinoma RKO cells. IBB-based fractionation enhanced detection of Cys-proteins in direct proportion to their cysteine content. The degree of enrichment typically was 2-8-fold but ranged up to almost 20-fold for a few proteins. Published copy number annotation for the yeast proteome enabled benchmarking of MS/MS spectral count data to yeast protein abundance and revealed selective enrichment of cysteine-rich, lower abundance proteins. Spectral count data further established this relationship in RKO cells. Enhanced detection of low abundance proteins was due to the chemoselectivity of Cys-peptide capture, rather than simplification of the peptide mixture through fractionation.

Adverse Outcome Pathways: A Way of Linking Chemical Structure to In Vivo Toxicological Hazards

The concept of adverse outcome pathways is presented here as an organising principle to aid assessment and formation of toxicologically meaningful categories for hazard endpoints, especially chronic health effects where different molecular initiating events and different key biological events lead to the same in vivo outcome. A toxicologically meaningful category can be thought of as a group of chemicals whose human health and/or environmental toxicological properties are likely to be similar or follow a regular pattern for a particular hazard. An adverse outcome pathway is a description of plausible causal linkages, which illustrates how the molecular initiating event, leads to the key biochemical, cellular, physiological, behavioural etc. responses, which characterise the biological cascade across the different levels of biological organisation. The concept of the adverse outcome pathway is discussed in the context of the more stringent mechanism of action approach used in pharmacology. The value of this concept is demonstrated with five examples, each with a different type of molecular initiating event. The pathways concept is also discussed in context of elaborate hazards where the in vivo effects may be cumulative or life stage dependent.

Drug bioactivation and protein adduct formation in the pathogenesis of drug-induced toxicity

Adverse drug reactions (ADRs) remain a major complication of drug therapy and can be classified as 'on-target' or 'off-target' (idiosyncratic) reactions. On-target reactions can be predicted from the known primary or secondary pharmacology of the drug and often represent an exaggeration of the pharmacological effect of the drug. In contrast, off-target adverse reactions cannot be predicted from knowledge of the basic pharmacology of the drug. The exact mechanisms of idiosyncratic drug reactions are still unclear; however it is believed that they can be initiated by chemically reactive drug metabolites. It is well known that xenobiotics can undergo metabolic bioactivation reactions which have the potential to cause cellular stress and damage. Bioactivation of drugs is thought to have the potential of initiating covalent linkages between cellular protein and drugs which can be recognised by the adaptive immune system in the absence of detectable cellular stress. This process cannot yet be predicted in pre-clinical models or discovered in clinical trials. Because of this hazard perception, the formation of chemically reactive metabolites in early drug discovery remains a serious impediment to the development of new medicines and can lead to withdrawal of an otherwise effective therapeutic agent. The fear of such reactions occurring at the post-licensing stage - when such problems first become evident - is a major contribution to drug attrition. The first step towards such methodology has been the development of chemically reactive metabolite screens. The chemical basis of drug bioactivation can usually be rationalised and synthetic strategies put in place to prevent such bioactivation. However, there is no simple correlation between drug bioactivation in vitro and adverse drug reactions in the clinic. Such a chemical approach is clearly limited by the facts that (a) not all drugs that can undergo bioactivation by human drug-metabolising enzymes are associated with hypersensitivity in the clinic and (b) drug bioactivation may not always be a mandatory step in drug hypersensitivity. To predict such reactions in early drug development, it will require an integrated understanding of the chemical, immunological and genetic basis of adverse drug reactions in patients, which in turn will depend on the development of novel in vitro experimental systems.

Redox signaling in inflammation: interactions of endogenous electrophiles and mitochondria in cardiovascular disease

Reactive species derived from oxygen and nitric oxide are produced during inflammation and promote oxidation and nitration of biomolecules, including unsaturated fatty acids. Among the products of these reactions are alpha,beta-unsaturated carbonyl and nitro derivatives of fatty acids, electrophilic species whose reactivity with nucleophilic amino acids provides a means of posttranslational protein modification and signaling. These electrophilic fatty acids activate cytosolic and nuclear stress-response pathways (through Nrf2/Keap1 and PPARgamma, for example). There is also growing evidence that mitochondria generate electrophilic species. This appreciation, when combined with the role of mitochondrial dysfunction in conditions where exogenously delivered electrophiles exhibit therapeutic benefit, suggests that mitochondrial electrophile targets are also important in the resolution and prevention of inflammatory injury. Cardioprotective signaling pathways in particular appear to converge on mitochondria, with nitro-fatty acids recently shown to protect against cardiac ischemia/reperfusion injury in a murine model. Although numerous mitochondrial proteins are subject to modification by electrophiles, defining the targets most relevant to cytoprotection during inflammatory stress remains a clinically relevant goal.

Reactive species and mitochondrial dysfunction: mechanistic significance of 4-hydroxynonenal

Mitochondrial dysfunction is a global term used in the context of "unhealthy" mitochondria. In practical terms, mitochondria are extremely complex and highly adaptive in structure, chemical and enzymatic composition, subcellular distribution and functional interaction with other components of cells. Consequently, altered mitochondrial properties that are used in experimental studies as measures of mitochondrial dysfunction often provide little or no distinction between adaptive and maladaptive changes. This is especially a problem in terms of generation of oxidant species by mitochondria, wherein increased generation of superoxide anion radical (O(2*)(-)) or hydrogen peroxide (H(2)O(2)) is often considered synonymously with mitochondrial dysfunction. However, these oxidative species are signaling molecules in normal physiology so that a change in production or abundance is not a good criterion for mitochondrial dysfunction. In this review, we consider generation of reactive electrophiles and consequent modification of mitochondrial proteins as a means to define mitochondrial dysfunction. Accumulated evidence indicates that 4-hydroxynonenal (HNE) modification of proteins reflects mitochondrial dysfunction and provides an operational criterion for experimental definition of mitochondrial dysfunction. Improved means to detect and quantify mitochondrial HNE-protein adduct formation could allow its use for environmental healthrisk assessment. Furthermore, application of improved mass spectrometry-based proteomic methods will lead to further understanding of the critical targets contributing to disease risk.

Reactivity of Zn-, Cd-, and apo-metallothionein with nitric oxide compounds: in vitro and cellular comparison

The reactivity of Zn(7)- and Cd(7)-metallothionein (MT) with S-nitrosopenicillamine (SNAP), S-nitrosoglutathione (GSNO), and 2-(N,N-diethylamino)-diazenolate-2-oxide (DEA/NO) was investigated to explore the hypothesis that metallothionein is a signficant site of cellular reaction of nitric oxide or NO compounds. Zn(7)-MT reacted with SNAP or GSNO only under aerobic conditions and in the presence of light, which stimulates the decomposition of S-nitrosothiolates to NO. Zn(2+) is released, and protein thiols are modified. DEA/NO, which degrades spontaneously to release NO, also reacted with Zn(7)-MT only when oxygen was present. Anaerobically, DEA/NO reacted with Zn(7)-MT in the presence of 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide, which converts NO to NO(2). Glutathione competed effectively with Zn(7)-MT for reactive nitrogen oxide species in reaction mixtures. Reaction of Cd(7)-MT with SNAP also required oxygen and light to react. In this case, only a fraction of the Cd(2+) bound to Cd(7)-MT was displaced by SNAP. Apo-metallothionein was much more reactive with SNAP and DEA-NO than Zn(7)- or Cd(7)-MT. TE671 and LLC-PK(1) cell lines were incubated with DEA/NO to examine the role that MT might play in the cellular reactions of this NO donor compound. Incubation of cells with 0-80 microM Zn(2+) for 24 h resulted in progressively increasing concentrations of Zn-unsaturated MT. One hour of cellular exposure to a range of DEA/NO concentrations followed by 24 h of incubation caused no evident acute toxicity at less than 0.45 mM. Preinduction of MT did not alter this response. The effects of DEA/NO on proteomic, metallothionein, and low molecular weight (LMW) thiol pools, including glutathione (GSH), were measured. Substantial fractions of the proteomic and LMW thiol pools underwent reaction with little dislocation of Zn(2+). In addition, one-third of the MT thiol pool reacted without labilizing any of the bound Zn(2+). These results demonstrated that it was free thiols associated with MT that reacted with DEA/NO not those bound to Zn(2+). Moreover, under the conditions of the experiments, DEA/NO reacted with the spectrum of cellular thiols in proportion to their fraction in the cytosol and did not preferentially react with MT sulfhydryl groups.

Protein adducts of aldehydic lipid peroxidation products identification and characterization of protein adducts using an aldehyde/keto-reactive probe in combination with mass spectrometry

This chapter describes a mass spectrometry-based strategy that facilitates the unambiguous identification and characterization of proteins modified by lipid peroxidation-derived 2-alkenals. The approach employs a biotinylated hydroxyl amine derivative as an aldehyde/keto-reactive probe in conjunction with selective enrichment and tandem mass spectrometric analysis. Methodological details are given for model studies involving a distinct protein and 4-hydroxy-2-nonenal (HNE). The method was also evaluated for an exposure study of a cell culture system with HNE that yielded the major protein targets of HNE in human monocytic THP-1 cells. The application of the approach to complex biological systems is demonstrated for the identification and characterization of endogenous protein targets of aldehydic lipid peroxidation products present in cardiac mitochondria.

Role of reactive metabolites in drug-induced hepatotoxicity

Drugs are generally converted to biologically inactive forms and eliminated from the body, principally by hepatic metabolism. However, certain drugs undergo biotransformation to metabolites that can interfere with cellular functions through their intrinsic chemical reactivity towards glutathione, leading to thiol depletion, and functionally critical macromolecules, resulting in reversible modification, irreversible adduct formation, and irreversible loss of activity. There is now a great deal of evidence which shows that reactive metabolites are formed from drugs known to cause hepatotoxicity, such as acetaminophen, tamoxifen, isoniazid, and amodiaquine. The main theme of this article is to review the evidence for chemically reactive metabolites being initiating factors for the multiple downstream biological events culminating in toxicity. The major objectives are to understand those idiosyncratic hepatotoxicities thought to be caused by chemically reactive metabolites and to define the role of toxic metabolites.

Transduction of redox signaling by electrophile-protein reactions

Over the last 50 years, the posttranslational modification (PTM) of proteins has emerged as a central mechanism for cells to regulate metabolism, growth, differentiation, cell-cell interactions, and immune responses. By influencing protein structure and function, PTM leads to a multiplication of proteome diversity. Redox-dependent PTMs, mediated by environmental and endogenously generated reactive species, induce cell signaling responses and can have toxic effects in organisms. PTMs induced by the electrophilic by-products of redox reactions most frequently occur at protein thiols; other nucleophilic amino acids serve as less favorable targets. Advances in mass spectrometry and affinity-chemistry strategies have improved the detection of electrophile-induced protein modifications both in vitro and in vivo and have revealed a high degree of amino acid and protein selectivity of electrophilic PTM. The identification of biological targets of electrophiles has motivated further study of the functional impact of various PTM reactions on specific signaling pathways and how this might affect organisms.

Methods for the determination and quantification of the reactive thiol proteome

Protein thiol modifications occur under both physiological and pathological conditions and have been shown to contribute to changes in protein structure, function, and redox signaling. The majority of protein thiol modifications occur on cysteine residues that have a low pK(a); these nucleophilic proteins comprise the "reactive thiol proteome." The most reactive members of this proteome are typically low-abundance proteins. Therefore, sensitive and quantitative methods are needed to detect and measure thiol modifications in biological samples. To accomplish this, we have standardized the usage of biotinylated and fluorophore-labeled alkylating agents, such as biotinylated iodoacetamide (IAM) and N-ethylmaleimide (NEM) and BODIPY-labeled IAM and NEM, for use in one- and two-dimensional proteomic strategies. Purified fractions of cytochrome c and glyceraldehyde-3-phosphate dehydrogenase were conjugated to a known amount of biotin or BODIPY fluorophore to create an external standard that can be run on standard SDS-PAGE gels, which allows for the quantification of protein thiols from biological samples by Western blotting or fluorescence imaging. A detailed protocol is provided for using thiol-reactive probes and making external standards for visualizing and measuring protein thiol modifications in biological samples.

Toward an "omic" physiopathology of reactive chemicals: thirty years of mass spectrometric study of the protein adducts with endogenous and xenobiotic compounds

Cancer and degenerative diseases are major causes of morbidity and death, derived from the permanent modification of key biopolymers such as DNA and regulatory proteins by usually smaller, reactive molecules, present in the environment or generated from endogenous and xenobiotic components by the body's own biochemical mechanisms (molecular adducts). In particular, protein adducts with organic electrophiles have been studied for more than 30 [see, e.g., Calleman et al., 1978] years essentially for three purposes: (a) as passive monitors of the mean level of individual exposure to specific chemicals, either endogenously present in the human body or to which the subject is exposed through food or environmental contamination; (b) as quantitative indicators of the mean extent of the individual metabolic processing which converts a non-reactive chemical substance into its toxic products able to damage DNA (en route to cancer induction through genotoxic mechanisms) or key proteins (as in the case of several drugs, pesticides or otherwise biologically active substances); (c) to relate the extent of protein modification to that of biological function impairment (such as enzyme inhibition) finally causing the specific health damage. This review describes the role that contemporary mass spectrometry-based approaches employed in the qualitative and quantitative study of protein-electrophile adducts play in the discovery of the (bio)chemical mechanisms of toxic substances and highlights the future directions of research in this field. A particular emphasis is given to the measurement of often high levels of the protein adducts of several industrial and environmental pollutants in unexposed human populations, a phenomenon which highlights the possibility that a number of small organic molecules are generated in the human organism through minor metabolic processes, the imbalance of which may be the cause of "spontaneous" cases of cancer and of other degenerative diseases of still uncharacterized etiology. With all this in mind, it is foreseen that a holistic description of cellular functions will take advantage of new analytical methods based on time-integrated metabolomic measurements of a new biological compartment, the "adductome," aimed at better understanding integrated organism response to environmental and endogenous stressors.

Reversibility of covalent electrophile-protein adducts and chemical toxicity

The biotin-tagged electrophiles 1-biotinamido-4-(4'-[maleimidoethylcyclohexane]-carboxamido)butane (BMCC) and N-iodoacetyl-N-biotinylhexylenediamine (IAB) have been used as model electrophile probes in complex proteomes to identify protein targets associated with chemical toxicity. Whereas IAB activates stress signaling and apoptosis in HEK293 cells, BMCC does not. Cysteine Michael adducts formed from BMCC and nonbiotinylated analogues rapidly disappeared in the intact cells, whereas the adducts were stable in BMCC-treated subcellular fractions, even in the presence of the cellular reductants reduced glutathione, NADH, and NADPH. In contrast, cysteine thioether adducts formed from IAB and its nonbiotinylated analogues were stable in intact cells. Loss of the BMCC adduct in cells was reduced at 4 degrees C, which suggests the involvement of a metabolic process in adduct removal. Model studies with a glutathione-BMCC conjugate indicated rapid hydrolysis of the adducted imide ring, but neither the conjugate nor its hydrolysis product dissociated to release the electrophile in neutral aqueous buffer at significant rates. The results suggest that low BMCC toxicity reflects facile repair that results in transient adduction, which fails to trigger damage-signaling pathways.

Analytical strategies for the screening and evaluation of chemically reactive drug metabolites

BACKGROUND

Metabolic activation leading to formation of chemically reactive drug metabolites is a long-standing issue for drug development inasmuch as some, but not all, reactive intermediates play a role as mediators of drug-induced toxicities. The risk assessment profile/decision-making guide requires a comprehensive understanding of bioactivation mechanism(s), quantitative magnitude and cellular consequences of this principal and continued safety attrition.

OBJECTIVE

To evaluate analytical methodologies with improved sensitivity, selectivity and throughput for the analysis of reactive metabolites.

CONCLUSIONS

Identification and quantification of short-lived electrophilic intermediates through appropriate trapping experiments have become relatively straightforward. Minimizing the bioactivation potential of drug candidates during the discovery/lead optimization phase has been adopted as a default strategy. Together with advances of proteomics, metabolomics and toxicogenomics, an integrated multitier approach possibly provides a deeper insight into mechanistic aspects of drug-induced toxicities, and contributes to bridging the relationships between metabolic activation, drug-protein adduct formation and their toxicological consequences.

Trivalent methylated arsenical-induced phosphatidylserine exposure and apoptosis in platelets may lead to increased thrombus formation

Trivalent methylated metabolites of arsenic, monomethylarsonous acid (MMA(III)) and dimethylarsinous acid (DMA(III)), have been found highly reactive and toxic in various cells and in vivo animal models, suggesting their roles in the arsenic-associated toxicity. However, their effects on cardiovascular system including blood cells, one of the most important targets for arsenic toxicity, remain poorly understood. Here we found that MMA(III) and DMA(III) could induce procoagulant activity and apoptosis in platelets, which play key roles in the development of various cardiovascular diseases (CVDs) through excessive thrombus formation. In freshly isolated human platelets, treatment of MMA(III) resulted in phosphatidylserine (PS) exposure, a hallmark of procoagulant activation, accompanied by distinctive apoptotic features including mitochondrial membrane potential disruption, cytochrome c release, and caspase-3 activation. These procoagulant activation and apoptotic features were found to be mediated by the depletion of protein thiol and intracellular ATP, and flippase inhibition by MMA(III), while the intracellular calcium increase or reactive oxygen species generation was not involved. Importantly, increased platelet procoagulant activity by MMA(III) resulted in enhanced blood coagulation and excessive thrombus formation in a rat in vivo venous thrombosis model. DMA(III) also induced PS-exposure with apoptotic features mediated by protein thiol depletion, which resulted in enhanced thrombin generation. In summary, we believe that this study provides an important evidence for the role of trivalent methylated arsenic metabolites in arsenic-associated CVDs, giving a novel insight into the role of platelet apoptosis in toxicant-induced cardiovascular toxicity.

Nitro-fatty acid metabolome: saturation, desaturation, beta-oxidation, and protein adduction

Nitrated derivatives of fatty acids (NO2-FA) are pluripotent cell-signaling mediators that display anti-inflammatory properties. Current understanding of NO2-FA signal transduction lacks insight into how or if NO2-FA are modified or metabolized upon formation or administration in vivo. Here the disposition and metabolism of nitro-9-cis-octadecenoic (18:1-NO2) acid was investigated in plasma and liver after intravenous injection in mice. High performance liquid chromatography-tandem mass spectrometry analysis showed that no 18:1-NO2 or metabolites were detected under basal conditions, whereas administered 18:1-NO2 is rapidly adducted to plasma thiol-containing proteins and glutathione. NO2-FA are also metabolized via beta-oxidation, with high performance liquid chromatography-tandem mass spectrometry analysis of liver lipid extracts of treated mice revealing nitro-7-cis-hexadecenoic acid, nitro-5-cis-tetradecenoic acid, and nitro-3-cis-dodecenoic acid and corresponding coenzyme A derivatives of 18:1-NO2 as metabolites. Additionally, a significant proportion of 18:1-NO2 and its metabolites are converted to nitroalkane derivatives by saturation of the double bond, and to a lesser extent are desaturated to diene derivatives. There was no evidence of the formation of nitrohydroxyl or conjugated ketone derivatives in organs of interest, metabolites expected upon 18:1-NO2 hydration or nitric oxide (*NO) release. Plasma samples from treated mice had significant extents of protein-adducted 18:1-NO2 detected by exchange to added beta-mercaptoethanol. This, coupled with the observation of 18:1-NO2 release from glutathione-18:1-NO2 adducts, supports that reversible and exchangeable NO2-FA-thiol adducts occur under biological conditions. After administration of [3H]18:1-NO2, 64% of net radiolabel was recovered 90 min later in plasma (0.2%), liver (18%), kidney (2%), adipose tissue (2%), muscle (31%), urine (6%), and other tissue compartments, and may include metabolites not yet identified. In aggregate, these findings show that electrophilic FA nitroalkene derivatives (a) acquire an extended half-life by undergoing reversible and exchangeable electrophilic reactions with nucleophilic targets and (b) are metabolized predominantly via saturation of the double bond and beta-oxidation reactions that terminate at the site of acyl-chain nitration.

Application of stable isotope-labeled compounds in metabolism and in metabolism-mediated toxicity studies

Stable isotope-labeled compounds have been synthesized and utilized by scientists from various areas of biomedical research during the last several decades. Compounds labeled with stable isotopes, such as deuterium and carbon-13, have been used effectively by drug metabolism scientists and toxicologists to gain better understanding of drugs' disposition and their potential role in target organ toxicities. The combination of stable isotope-labeling techniques with mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy, which allows rapid acquisition and interpretation of data, has promoted greater use of these stable isotope-labeled compounds in absorption, distribution, metabolism, and excretion (ADME) studies. Examples of the use of stable isotope-labeled compounds in elucidating structures of metabolites and delineating complex metabolic pathways are presented in this review. The application of labeled compounds in mechanistic toxicity studies will be discussed by providing an example of how strategic placement of a deuterium atom in a drug molecule mitigated specific-specific renal toxicity. Other examples from the literature demonstrating the application of stable isotope-labeled compounds in understanding metabolism-mediated toxicities are presented. Furthermore, an example of how a stable isotope-labeled compound was utilized to better understand some of the gene changes in toxicogenomic studies is discussed. The interpretation of large sets of data produced from toxicogenomics studies can be a challenge. One approach that could be used to simplify interpretation of the data, especially from studies designed to link gene changes with the formation of reactive metabolites thought to be responsible for toxicities, is through the use of stable isotope-labeled compounds. This is a relatively unexplored territory and needs to be further investigated. The employment of analytical techniques, especially mass spectrometry and NMR, used in conjunction with stable isotope-labeled compounds to establish and understand mechanistic link between reactive metabolite formation, genomic, and proteomic changes and onset of toxicity is proposed. The use of stable isotope-labeled compounds in early human ADME studies as a way of identifying and possibly quantifying all drug-related components present in systemic circulation is suggested.