Structure–activity relationships for thiol reactivity and rat or human hepatocyte toxicity induced by substitutedp‐benzoquinone compounds

Hydrothermal Synthesis of Siderite and Application as Catalyst in the Electro-Fenton Oxidation of p-Benzoquinone

A weak aspect of the electro-Fenton (EF) oxidation of contaminants is the dependence of the Fenton reaction on acidic pH values. Therefore, the rationale of this work was to develop a novel catalyst capable of promoting the EF oxidation process at near-neutral and basic pH values. In this framework, rhombohedral FeCO3 was synthesized hydrothermally and used as a catalyst in the EF oxidation of p-benzoquinone (BQ). The catalyst was characterized using various surface and spectroscopic methods. Moreover, the effects of applied current (100-500 mA), time (1-9 h), catalyst dosage (0.25-1.00 g L-1), and initial concentration of BQ (0.50-1.00 mM) on the total organic carbon removal efficiency were determined. The results indicated that a 400 mA current was sufficient for a 95% total organic carbon removal and that the increase in catalyst dosage had a positive effect on the mineralization of BQ. It was determined that at pH 3, FeCO3 behaved like a homogeneous catalyst by releasing Fe3+ ions; whereas, at the pH range of 5-7, it shifted to a homogeneous/heterogeneous catalyst. At pH 9, it worked solely as a heterogeneous catalyst due to the decrease of Fe ions passing into the solution. Finally, the spent catalyst did not undergo structural deformations after the EF treatment at higher pH values and could be regenerated and used several times.

Sensitive Detection of Industrial Pollutants Using Modified Electrochemical Platforms

Water pollution is nowadays a global problem and the effective detection of pollutants is of fundamental importance. Herein, a facile, efficient, robust, and rapid (response time < 2 min) method for the determination of important quinone-based industrial pollutants such as hydroquinone and benzoquinone is reported. The recognition method is based on the use of screen-printed electrodes as sensing platforms, enhanced with carbon-based nanomaterials. The enhancement is achieved by modifying the working electrode of such platforms through highly sensitive membranes made of Single- or Multi-Walled Carbon Nanotubes (SWNTs and MWNTs) or by graphene nanoplatelets. The modified sensing platforms are first carefully morphologically and electrochemically characterized, whereupon they are tested in the detection of different pollutants (i.e., hydroquinone and benzoquinone) in water solution, by using both cyclic and square-wave voltammetry. In particular, the sensors based on film-deposited nanomaterials show good sensitivity with a limit of detection in the nanomolar range (0.04 and 0.07 μM for SWNT- and MWNT-modified SPEs, respectively) and a linear working range of 10 to 1000 ppb under optimal conditions. The results highlight the improved performance of these novel sensing platforms and the large-scale applicability of this method for other analytes (i.e., toxins, pollutants).

Drug Discovery Insights from Medicinal Beetles in Traditional Chinese Medicine

Traditional Chinese medicine (TCM) was the primary source of medical treatment for the people inhabiting East Asia for thousands of years. These ancient practices have incorporated a wide variety of materia medica including plants, animals and minerals. As modern sciences, including natural products chemistry, emerged, there became increasing efforts to explore the chemistry of this materia medica to find molecules responsible for their traditional use. Insects, including beetles have played an important role in TCM. In our survey of texts and review articles on TCM materia medica, we found 48 species of beetles from 34 genera in 14 different families that are used in TCM. This review covers the chemistry known from the beetles used in TCM, or in cases where a species used in these practices has not been chemically studied, we discuss the chemistry of closely related beetles. We also found several documented uses of beetles in Traditional Korean Medicine (TKM), and included them where appropriate. There are 129 chemical constituents of beetles discussed.

Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites

Adverse drug metabolism often severely impacts patient morbidity and mortality. Unfortunately, drug metabolism experimental assays are costly, inefficient, and slow. Instead, computational modeling could rapidly flag potentially toxic molecules across thousands of candidates in the early stages of drug development. Most metabolism models focus on predicting sites of metabolism (SOMs): the specific substrate atoms targeted by metabolic enzymes. However, SOMs are merely a proxy for metabolic structures: knowledge of an SOM does not explicitly provide the actual metabolite structure. Without an explicit metabolite structure, computational systems cannot evaluate the new molecule's properties. For example, the metabolite's reactivity cannot be automatically predicted, a crucial limitation because reactive drug metabolites are a key driver of adverse drug reactions (ADRs). Additionally, further metabolic events cannot be forecast, even though the metabolic path of the majority of substrates includes two or more sequential steps. To overcome the myopia of the SOM paradigm, this study constructs a well-defined system-termed the metabolic forest-for generating exact metabolite structures. We validate the metabolic forest with the substrate and product structures from a large, chemically diverse, literature-derived dataset of 20 736 records. The metabolic forest finds a pathway linking each substrate and product for 79.42% of these records. By performing a breadth-first search of depth two or three, we improve performance to 88.43 and 88.77%, respectively. The metabolic forest includes a specialized algorithm for producing accurate quinone structures, the most common type of reactive metabolite. To our knowledge, this quinone structure algorithm is the first of its kind, as the diverse mechanisms of quinone formation are difficult to systematically reproduce. We validate the metabolic forest on a previously published dataset of 576 quinone reactions, predicting their structures with a depth three performance of 91.84%. The metabolic forest accurately enumerates metabolite structures, enabling promising new directions such as joint metabolism and reactivity modeling.

BIreactive: A Machine-Learning Model to Estimate Covalent Warhead Reactivity

In the past decade, the pharmaceutical industry has paid closer attention to covalent drugs. Differently from standard noncovalent drugs, these compounds can exhibit peculiar properties, such as higher potency or longer duration of target inhibition with a potentially lower dosage. These properties are mainly driven by the reactive functional group present in the compound, the so-called warhead that forms a covalent bond with a specific nucleophilic amino-acid on the target. In this work, we report the possibility to combine ab initio activation energies with machine-learning to estimate covalent compound intrinsic reactivity. The idea behind this approach is to have a precise estimation of the transition state barriers, and thus of the compound reactivity, but with the speed of a machine-learning algorithm. We call this method "BIreactive". Here, we demonstrate this approach on acrylamides and 2-chloroacetamides, two warhead classes that possess different reaction mechanisms. In combination with our recently implemented truncation algorithm, we also demonstrate the possibility to use BIreactive not only for fragments but also for lead-like molecules. The generic nature of this approach allows also the extension to several other warheads. The combination of these factors makes BIreactive a valuable tool for the covalent drug discovery process in a pharmaceutical context.

VASPIN, ADIPONECTIN AND LEPTIN LEVELS IN TYPE 1 DIABETIC RATS INDUCED BY STREPTOZOTOCIN

Background

Adiponectin, vaspin and leptin are only a few of these numerous adipocytokines. Little is known about the behavior of adipocytokines and how adipose tissue metabolism is affected in this Type 1 DM model. In this study we investigated the serum levels of adiponectin, leptin, vaspin in streptozotocin(STZ) induced diabetic rats.

Material and methods

Twelve Spraque Dawley albino rats were included in the study. The animals were divided into two groups. The first group was diabetic (D) (n: 6) and 60mg / kg STZ was administered intraperitoneally (i.p.) to these rats. The second group was the non-diabetic control (ND) group (n: 6). All the animals were euthanized by cervical dislocation. Quantification of vaspin, Adiponectin, leptin in serum was performed using the ELISA kit.

Results

Adiponectin, vaspin levels of diabetic group were found to be statistically lower than of control group (p<0.05). Leptin levels were significantly higher in the diabetic group (P<0.05).

Conclusion

There is a need for new researches that can explain the relationship between Vaspin, Leptin and Adiponectin and Type 1 diabetes. New studies in this area will open new horizons for the identification of new biomarkers in the diagnosis and treatment of Type 1 diabetes.

Modification of Cys residues in human thioredoxin-1 by p-benzoquinone causes inhibition of its catalytic activity and activation of the ASK1/p38-MAPK signalling pathway

Quinones can modify biological molecules through both redox-cycling reactions that yield radicals (semiquinone, superoxide and hydroxyl) and via covalent adduction to nucleophiles (e.g. thiols and amines). Kinetic data indicate that Cys residues in GSH and proteins are major targets. In the studies reported here, the interactions of a prototypic quinone compound, p-benzoquinone (BQ), with the key redox protein, thioredoxin-1 (Trx1) were examined. BQ binds covalently with isolated Trx1 forming quinoprotein adducts, resulting in a concentration-dependent loss of enzyme activity and crosslink formation. Mass spectrometry peptide mass mapping data indicate that BQ forms adducts with all of the Trx1 Cys residues. Glutathione (GSH) reacts competitively with BQ, and thereby modulates the loss of activity and crosslink formation. Exposure of macrophage-like (J774A.1) cells to BQ results in a dose-dependent loss of Trx and thioredoxin reductase (TrxR) activities, quinoprotein formation, and a decrease in GSH levels without a concomitant increase in oxidized glutathione. GSH depletion aggravates the loss of Trx and TrxR activity. These data are consistent with adduction of GSH to BQ being a primary protective pathway. Reaction of BQ with Trx in cells resulted in the activation of apoptosis signal-regulating kinase 1 (ASK1), and p38 mitogen-activated protein kinase (MAPK) leading to apoptotic cell death. These data suggest that BQ reacts covalently with Cys residues in Trx, including at the active site, leading to enzyme inactivation and protein cross-linking. Modification of the Cys residues in Trx also results in activation of the ASK1/p38-MAPK signalling pathway and promotion of apoptotic cell death.

•

Quinone (e.g. p-benzoquinone, BQ) toxicity is linked to Michael adduction reactions.

•

Adduction of BQ to Cys residues in proteins are rapid (≤10⁵ M⁻¹ s⁻¹) and selective.

•

BQ reaction with Cys inactivates thioredoxin (Trx) and yields quinone- and disulfide-linked dimers.

•

GSH reacts competitively with BQ and modulates damage, without GSSG formation.

•

BQ activates ASK1 and p38 pathways and induced apoptosis in cells via Trx damage.

A Fast Ab Initio Predictor Tool for Covalent Reactivity Estimation of Acrylamides

Thanks to their unique mode of action, covalent drugs represent an exceptional opportunity for drug design. After binding to a biologically relevant target system, covalent compounds form a reversible or irreversible covalent bond with a nucleophilic amino acid. Due to the inherently large binding energy of a covalent bond, covalent binders exhibit higher potencies and thus allow potentially lower drug dosages. However, a proper balancing of compound reactivity is key for the design of covalent binders, to achieve high levels of target inhibition while minimizing promiscuous covalent binding to nontarget proteins. In this work, we demonstrated the possibility to apply the electrophilicity index concept to estimate covalent compound reactivity. We tested this approach on acrylamides, one of the most prominent classes of covalent warheads. Our study clearly demonstrated that, for compounds with molecular weight (MW) below 250 Da, the electrophilicity index can be directly used to estimate compound reactivity. On the other hand, for leadlike molecules (MW > 250 Da) we implemented a new truncation algorithm that has to be applied before reactivity calculations. This algorithm can ensure the localization of HOMO/LUMO orbitals on the compound warhead and thus a correct estimation of its reactivity. Our results also indicate that caution should be used when employing the electrophilicity index to estimate the reactivity of nonterminal acrylamides. The nonparametric nature of this method and its reasonable computational cost make it a suitable tool to support covalent drug design.

Studying the chemical reactivity properties of the target tumor-environment tripeptides NGR (asparagine-glycine-arginine) and RGD (arginine-glycine-aspartic acid) in their interactions with tamoxifen through conceptual density functional theory

Here, we report theoretical research into the interaction of the drug tamoxifen drug with tripeptides found in the tumor environment-specifically, asparagine-glycine-arginine (NGR) and arginine-glycine-aspartic acid (RGD). Reactivity parameters of these tripeptides were calculated and their intrinsic reactivities and cross-reactivities were analyzed. The interactions of the tripeptides with the nanodiamond-tamoxifen (ND-TAM) complex where the nanodiamond acts as a nanocarrier were also examined theoretically. In addition, their intestinal absorption was predicted based on the polar surface area. The results showed that tamoxifen interacts with RGD, and this interaction remained after the addition of the nanodiamond. An analysis of the chemical hardnesses of the tripeptides was carried out to explore their possible use as synthetic vectors when joined to the nanodiamond. Results indicated that NGR is the most stable of the tripeptides and could be used for active targeting. All calculations were implemented using the conceptual framework of density functional theory.

Monohalogenated acetamide-induced cellular stress and genotoxicity are related to electrophilic softness and thiol/thiolate reactivity

Haloacetamides (HAMs) are cytotoxic, genotoxic, and mutagenic byproducts of drinking water disinfection. They are soft electrophilic compounds that form covalent bonds with the free thiol/thiolate in cysteine residues through an S_N2 reaction mechanism. Toxicity of the monohalogenated HAMs (iodoacetamide, IAM; bromoacetamide, BAM; or chloroacetamide, CAM) varied depending on the halogen substituent. The aim of this research was to investigate how the halogen atom affects the reactivity and toxicological properties of HAMs, measured as induction of oxidative/electrophilic stress response and genotoxicity. Additionally, we wanted to determine how well in silico estimates of electrophilic softness matched thiol/thiolate reactivity and in vitro toxicological endpoints. Each of the HAMs significantly induced nuclear Rad51 accumulation and ARE signaling activity compared to a negative control. The rank order of effect was IAM>BAM>CAM for Rad51, and BAM≈IAM>CAM for ARE. In general, electrophilic softness and in chemico thiol/thiolate reactivity provided a qualitative indicator of toxicity, as the softer electrophiles IAM and BAM were more thiol/thiolate reactive and were more toxic than CAM.

The electrophilic character of quinones is essential for the suppression of Bach1

The activation of nuclear factor erythroid 2-related factor 2 (Nrf2) is the most important cellular defense mechanisms against oxidative attack. BTB and CNC homology-1 (Bach1), like Kelch-like ECH-associated protein 1 (Keap1), is one of a negative regulator of Nrf2 that control antioxidant response elements (ARE)-dependent gene expressions. In the current study, we found that quinones show greater capacity than hydroquinones in nuclear Bach1 export, as well as ubiquitin-dependent Bach1 degradation in our experimental time frame. Consistently, quinones are easier than hydroquinones in Nrf2 activation and ARE-driven antioxidant protein expressions. Considering the redox cycling potential of quinone-hydroquinone couple, we investigated the effect of transit metal oxidation on the regulation of Nrf2 activity. As shown, Fe³⁺ enhanced hydroquinone-induced Nrf2 activation and ARE-driven gene expressions, suggesting quinones rather than hydroquinone activate Nrf2 through Bach1 arylation. Taking together, our investigation illustrated that the electrophilic character of quinones ensure their conjugation with Bach1, which is important for the downregulation of Bach1 and the upregulation of Nrf2 signaling.

Experimental type 2 diabetes induction reduces serum vaspin, but not serum omentin, in Wistar rats

Vaspin and omentin are adipose tissue adipokines that have often been related to obesity and its comorbidities. The aim of this study was to investigate the behaviour of serum omentin and vaspin in models of type 2 diabetes. To do this, Wistar rats (~200 g) were randomly divided into two groups: a non-diabetic group (n = 6) and a diabetic group fed on a high-fat diet (n = 6) and a low dose of streptozotocin (Sigma^® ). All procedures were approved by the Brazilian Ethics Committee. Body weight (BW) and food intake were recorded daily. Tail blood glucose levels were assessed at the end of the diabetes induction period. The insulin tolerance test (ITT) was performed after the diabetes induction period (7 weeks). The serum and tissues (liver, pancreas, and retroperitoneal (RET), epididymal (EPI) and visceral (VIS) white adipose tissues) were immediately removed and weighed. Analyses of levels of insulin, omentin, vaspin, adiponectin and inflammatory cytokines IL-6, IL-8 (CXCL8), TNF-α and C-reactive protein (CRP) in serum were performed using the enzyme-linked immunosorbent assay (ELISA). Our results showed that IL-8 and CRP serum levels in the diabetic group were significantly higher than in the non-diabetic group. Vaspin and adiponectin values were lower for the diabetic group than for the non-diabetic group. Omentin, IL-6 and TNF-α values did not differ between the groups. Our results showed that both the metabolism of the adipose tissue and the secretion of adipokines may be affected in diabetic rats. Omentin showed no difference between the groups, although the vaspin values decreased in the diabetic group.

Discovery of the first dual GSK3β inhibitor/Nrf2 inducer. A new multitarget therapeutic strategy for Alzheimer's disease

The formation of neurofibrillary tangles (NFTs), oxidative stress and neuroinflammation have emerged as key targets for the treatment of Alzheimer’s disease (AD), the most prevalent neurodegenerative disorder. These pathological hallmarks are closely related to the over-activity of the enzyme GSK3β and the downregulation of the defense pathway Nrf2-EpRE observed in AD patients. Herein, we report the synthesis and pharmacological evaluation of a new family of multitarget 2,4-dihydropyrano[2,3-c]pyrazoles as dual GSK3β inhibitors and Nrf2 inducers. These compounds are able to inhibit GSK3β and induce the Nrf2 phase II antioxidant and anti-inflammatory pathway at micromolar concentrations, showing interesting structure-activity relationships. The association of both activities has resulted in a remarkable anti-inflammatory ability with an interesting neuroprotective profile on in vitro models of neuronal death induced by oxidative stress and energy depletion and AD. Furthermore, none of the compounds exhibited in vitro neurotoxicity or hepatotoxicity and hence they had improved safety profiles compared to the known electrophilic Nrf2 inducers. In conclusion, the combination of both activities in this family of multitarget compounds confers them a notable interest for the development of lead compounds for the treatment of AD.

Precise simultaneous quantification of methadone and cocaine in rat serum and brain tissue samples following their successive i.p. administration

A sensitive high-performance liquid chromatography (HPLC) assay with dual UV detection has been developed and validated for the simultaneous quantification of methadone and cocaine in rat serum and brain tissue samples. Liquid-liquid extraction using hexanes was applied for samples extraction with Levo-Tetrahydropalmatine (L-THP) as the internal standard. Chromatographic separation of the analytes was achieved on a reversed-phase Waters Symmetry^® C₁₈ column (150mm×4.6mm, 5μm). A gradient elution was employed with a mobile phase consisting of 5mM potassium phosphate containing 0.1% triethylamine (pH=6.5) (A) and acetonitrile (B) with a flow rate of 1mL/min. UV detection was employed at 215nm and 235nm for the determination of methadone and cocaine, respectively. The calibration curves were linear over the range of 0.05-10μg/mL for both methadone and cocaine. The assay was validated according to FDA guidelines for bioanalytical method validation and results were satisfactory and met FDA criteria. Inter-day accuracy values of serum and brain samples ranged from 96.97 to 105.59% while intra-day accuracy values ranged from 91.49 to 111.92%. Stability assays showed that both methadone and cocaine were stable during sample storage, preparation, and analytical procedures. The method was successfully used to analyze biological samples obtained from a drug- drug interaction pharmacokinetics (PK) study conducted in rats to investigate the effect of methadone on cocaine PK. Our method not only can be used for bioanalysis of samples obtained from rats but also can potentially be applied to human biological serum samples to monitor compliance to methadone maintenance therapy (MMT) and to detect possible cocaine-methadone co-abuse.

Deep Learning to Predict the Formation of Quinone Species in Drug Metabolism

Many adverse drug reactions are thought to be caused by electrophilically reactive drug metabolites that conjugate to nucleophilic sites within DNA and proteins, causing cancer or toxic immune responses. Quinone species, including quinone-imines, quinone-methides, and imine-methides, are electrophilic Michael acceptors that are often highly reactive and comprise over 40% of all known reactive metabolites. Quinone metabolites are created by cytochromes P450 and peroxidases. For example, cytochromes P450 oxidize acetaminophen to N-acetyl-p-benzoquinone imine, which is electrophilically reactive and covalently binds to nucleophilic sites within proteins. This reactive quinone metabolite elicits a toxic immune response when acetaminophen exceeds a safe dose. Using a deep learning approach, this study reports the first published method for predicting quinone formation: the formation of a quinone species by metabolic oxidation. We model both one- and two-step quinone formation, enabling accurate quinone formation predictions in nonobvious cases. We predict atom pairs that form quinones with an AUC accuracy of 97.6%, and we identify molecules that form quinones with 88.2% AUC. By modeling the formation of quinones, one of the most common types of reactive metabolites, our method provides a rapid screening tool for a key drug toxicity risk. The XenoSite quinone formation model is available at http://swami.wustl.edu/xenosite/p/quinone .

Inhibition effect of aromatic aldehydes on butanol fermentation by Clostridium acetobutylicum

The ortho-substituted 2-hydroxybenzaldehyde caused 20-fold stronger inhibition than meta- and para-substituted analogues of 3- and 4-hydroxybenzaldehydes.

Combined Toxic Effects of Polar and Nonpolar Chemicals on Human Hepatocytes (HepG2) Cells by Quantitative Property-Activity Relationship Modeling

We determined the toxicity of mixtures of ethyl acetate (EA), isopropyl alcohol (IPA), methyl ethyl ketone (MEK), toluene (TOL) and xylene (XYL) with half-maximal effective concentration (EC₅₀) values obtained using human hepatocytes cells. According to these data, quantitative property-activity relationships (QPAR) models were successfully proposed to predict the toxicity of mixtures by multiple linear regressions (MLR). The leave-one-out cross validation method was used to find the best subsets of descriptors in the learning methods. Significant differences in physico-chemical properties such as boiling point (BP), specific gravity (SG), Reid vapor pressure (rVP) and flash point (FP) were observed between the single substances and the mixtures. The EC₅₀ of the mixture of EA and IPA was significantly lower than that of contained TOL and XYL. The mixture toxicity was related to the mixing ratio of MEK, TOL and XYL (MLR equation EC₅₀ = 3.3081 − 2.5018 × TOL − 3.2595 × XYL − 12.6596 × MEK × XYL), as well as to BP, SG, VP and FP (MLR equation EC₅₀ = 1.3424 + 6.2250 × FP − 7.1198 × SG × FP − 0.03013 × rVP × FP). These results suggest that QPAR-based models could accurately predict the toxicity of polar and nonpolar mixtures used in rotogravure printing industries.

Modeling Reactivity to Biological Macromolecules with a Deep Multitask Network

Most small-molecule drug candidates fail before entering the market, frequently because of unexpected toxicity. Often, toxicity is detected only late in drug development, because many types of toxicities, especially idiosyncratic adverse drug reactions (IADRs), are particularly hard to predict and detect. Moreover, drug-induced liver injury (DILI) is the most frequent reason drugs are withdrawn from the market and causes 50% of acute liver failure cases in the United States. A common mechanism often underlies many types of drug toxicities, including both DILI and IADRs. Drugs are bioactivated by drug-metabolizing enzymes into reactive metabolites, which then conjugate to sites in proteins or DNA to form adducts. DNA adducts are often mutagenic and may alter the reading and copying of genes and their regulatory elements, causing gene dysregulation and even triggering cancer. Similarly, protein adducts can disrupt their normal biological functions and induce harmful immune responses. Unfortunately, reactive metabolites are not reliably detected by experiments, and it is also expensive to test drug candidates for potential to form DNA or protein adducts during the early stages of drug development. In contrast, computational methods have the potential to quickly screen for covalent binding potential, thereby flagging problematic molecules and reducing the total number of necessary experiments. Here, we train a deep convolution neural network-the XenoSite reactivity model-using literature data to accurately predict both sites and probability of reactivity for molecules with glutathione, cyanide, protein, and DNA. On the site level, cross-validated predictions had area under the curve (AUC) performances of 89.8% for DNA and 94.4% for protein. Furthermore, the model separated molecules electrophilically reactive with DNA and protein from nonreactive molecules with cross-validated AUC performances of 78.7% and 79.8%, respectively. On both the site- and molecule-level, the model's performances significantly outperformed reactivity indices derived from quantum simulations that are reported in the literature. Moreover, we developed and applied a selectivity score to assess preferential reactions with the macromolecules as opposed to the common screening traps. For the entire data set of 2803 molecules, this approach yielded totals of 257 (9.2%) and 227 (8.1%) molecules predicted to be reactive only with DNA and protein, respectively, and hence those that would be missed by standard reactivity screening experiments. Site of reactivity data is an underutilized resource that can be used to not only predict if molecules are reactive, but also show where they might be modified to reduce toxicity while retaining efficacy. The XenoSite reactivity model is available at http://swami.wustl.edu/xenosite/p/reactivity.

Inhibition of Zinc-Dependent Histone Deacetylases with a Chemically Triggered Electrophile

Unbiased binding assays involving small-molecule microarrays were used to identify compounds that display unique patterns of selectivity among members of the zinc-dependent histone deacetylase family of enzymes. A novel, hydroxyquinoline-containing compound, BRD4354, was shown to preferentially inhibit activity of HDAC5 and HDAC9 in vitro. Inhibition of deacetylase activity appears to be time-dependent and reversible. Mechanistic studies suggest that the compound undergoes zinc-catalyzed decomposition to an ortho-quinone methide, which covalently modifies nucleophilic cysteines within the proteins. The covalent nature of the compound-enzyme interaction has been demonstrated in experiments with biotinylated probe compound and with electrospray ionization-mass spectrometry.

Emerging Disinfection Byproducts, Halobenzoquinones: Effects of Isomeric Structure and Halogen Substitution on Cytotoxicity, Formation of Reactive Oxygen Species, and Genotoxicity

Halobenzoquinones (HBQs) are a structurally diverse class of water disinfection byproducts. Here, we report a systematic study on the effects of isomeric structure and the type and number of halogen substitutions of HBQs on their cytotoxicity, formation of reactive oxygen species (ROS), and genotoxicity. Dynamic responses and IC50 histograms were obtained using real-time cell analysis, clearly ranking the cytotoxicity of the HBQs in Chinese hamster ovary (CHO-K1) cells. Strong isomeric structure effects were shown with 2,5-HBQ isomers inducing greater cytotoxicity than their corresponding 2,6-HBQ isomers (P < 0.05). HBQ-halogen substitution groups also influence cytotoxicity, as cytotoxicity increases across the dihalogenated HBQs: iodo- > bromo- > chloro-HBQs (P < 0.05). Determination of HBQ-induced ROS further supports isomeric structure and halogen substitution effects. HBQ-induced genotoxicity was shown as increased levels of 8-hydroxy-2'-deoxyguanosine and p53 protein. Pearson correlation analysis of the HBQ toxicity measurements with their physicochemical parameters demonstrates that dipole moment and the lowest unoccupied molecular orbital energy are two major structural influences on toxicity (r = -0.721 or -0.766, P < 0.05). Dipole moment also correlates with isomer toxicity. This study suggests that formation and occurrence of highly toxic iodo-HBQs and 2,5-HBQs warrant further investigation to fully assess the impact of HBQs in drinking water.

New melatonin–cinnamate hybrids as multi-target drugs for neurodegenerative diseases: Nrf2-induction, antioxidant effect and neuroprotection

Background: Neurodegenerative diseases share many pathological pathways, such as abnormal protein aggregation, mitochondrial dysfunction, extensive oxidative stress and neuroinflammation. Cells have an intrinsic mechanism of protection, the Nrf2 transcriptional factor, known as the master regulator of redox homeostasis. Results: Based on the common features of these diseases we have designed a multi-target hybrid structure derived from melatonin and ethyl cinnamate. The obtained derivatives were Nrf2 inducers and potent-free radical scavengers. These new compounds showed a very interesting neuroprotective profile in several in vitro models of oxidative stress, Alzheimer's disease and brain ischemia. Conclusion: We have designed a new hybrid structure with complementary activities. We have identified compound 5h as an interesting Nrf2 inducer, very potent antioxidant and neuroprotectant.

Detoxification of biomass hydrolysates with nucleophilic amino acids enhances alcoholic fermentation

Carbonyl compounds generated in biomass pretreatment hinder the biochemical conversion of biomass hydrolysates to biofuels. A novel approach of detoxifying hydrolysates with amino acids for ethanol production was developed. Among the 20 amino acids assessed for their detoxification efficiency and nucleophilicity, cysteine was the most effective one. It increased both ethanol productivity and final yield of biomass hydrolysates from 0.18 (untreated) to 1.77 g/L/h and from 0.02 to 0.42 g/g, respectively. Detoxification efficiency was followed by histidine and it increased the final yield to 0.42 g/g, then by lysine, tryptophan and asparagine. It was observed all five effective amino acids contained reactive side-chain functional groups, which played important roles in the amino acid detoxification reaction. The study further showed cysteine and glycine detoxifications were temperature and pH dependent. The mechanistic study using mass spectrometry revealed thiazolidine carboxylic acid, a Schiff base, was formed by condensation of aldehyde and cysteine.

Site of reactivity models predict molecular reactivity of diverse chemicals with glutathione

Drug toxicity is often caused by electrophilic reactive metabolites that covalently bind to proteins. Consequently, the quantitative strength of a molecule's reactivity with glutathione (GSH) is a frequently used indicator of its toxicity. Through cysteine, GSH (and proteins) scavenges reactive molecules to form conjugates in the body. GSH conjugates to specific atoms in reactive molecules: their sites of reactivity. The value of knowing a molecule's sites of reactivity is unexplored in the literature. This study tests the value of site of reactivity data that identifies the atoms within 1213 reactive molecules that conjugate to GSH and builds models to predict molecular reactivity with glutathione. An algorithm originally written to model sites of cytochrome P450 metabolism (called XenoSite) finds clear patterns in molecular structure that identify sites of reactivity within reactive molecules with 90.8% accuracy and separate reactive and unreactive molecules with 80.6% accuracy. Furthermore, the model output strongly correlates with quantitative GSH reactivity data in chemically diverse, external data sets. Site of reactivity data is nearly unstudied in the literature prior to our efforts, yet it contains a strong signal for reactivity that can be utilized to more accurately predict molecule reactivity and, eventually, toxicity.

Effect of carbonyl inhibitors and their H₂O₂ detoxification on lactic acid fermentation

Biomass degradation compounds significantly inhibit biochemical conversion of biomass prehydrolysates to biofuels and chemicals, such as lactic acid. To characterize the structure-activity relationship of carbonyl inhibition on lactic acid fermentation, we examined effects of eight carbonyl compounds (furfural, 5-hydroxymethyl furfural, vanillin, syringaldehyde, 4-hydroxybenzaldehyde, phthalaldehyde, benzoic acid, and pyrogallol aldehyde) and creosol on lactic acid production by Lactobacillus delbrueckii. Pyrogallol aldehyde reduced the cell growth rate by 35 % at 1.0 mM and inhibited lactic acid production completely at 2.0 mM. By correlating the molecular descriptors to the inhibition constants in lactic acid fermentation, we found a good relationship between the hydrophobicity (Log P) of aldehydes and their inhibition constants in fermentation. The inhibitory effect of carbonyl inhibitors appeared to correlate with their thiol reactivity as well. In addition, we found that H2O2 detoxified pyrogallol aldehyde and phthalaldehyde inhibitory activity. H2O2 detoxification was applied to real biomass prehydrolysates in lactic acid fermentation.

Sorption mechanism and predictive models for removal of cationic organic contaminants by cation exchange resins

Understanding the sorption mechanism of organic contaminants on cation exchange resins (CXRs) will enable application of these resins for the removal of cationic organic compounds from contaminated water. In this study, sorption of a diverse set of 12 organic cations and 8 neutral aromatic solutes on two polystyrene CXRs, MN500 and Amberlite 200, was examined. MN500 showed higher sorbed concentrations due to its microporous structure. The sorbed concentrations followed the same trend of aromatic cations > aliphatic cations > neutral solutes for both resins. Generally, solute-solvent interactions, nonpolar moiety of the solutes, and resin matrix can affect selectivity of the cations. Sorbed concentrations of the neutral compounds were significantly less than those of the cations, indicating a combined effect of electrostatic and nonelectrostatic interactions. By conducting multiple linear regression between Gibbs free energy of sorption and Abraham descriptors for all 20 compounds, polarity/polarizability (S), H-bond acidity (A), induced dipole (E), and electrostatic (J(+)) interactions were found to be involved in the sorption of the cations by the resins. After converting the aqueous sorption isotherms to sorption from the ideal gas-phase by water-wet resins, a more significant effect of J(+) was observed. Predictive models were then developed based on the linear regressions and validated by accurately estimating the sorption of different test set compounds with a root-mean-square error range of 0.91-1.1 and 0.76-0.85 for MN500 and Amberlite 200, respectively. The models also accurately predicted sorption behavior of aniline and imidazole between pH 3 and 10.

Inhibitory activity of carbonyl compounds on alcoholic fermentation by Saccharomyces cerevisiae

Aldehydes and acids play important roles in the fermentation inhibition of biomass hydrolysates. A series of carbonyl compounds (vanillin, syringaldehyde, 4-hydroxybenzaldehyde, pyrogallol aldehyde, and o-phthalaldehyde) were used to examine the quantitative structure-inhibitory activity relationship of carbonyl compounds on alcoholic fermentation, based on the glucose consumption rate and the final ethanol yield. It was observed that pyrogallol aldehyde and o-phthalaldehyde (5.0 mM) reduced the initial glucose consumption rate by 60 and 89%, respectively, and also decreased the final ethanol yield by 60 and 99%, respectively. Correlating the molecular descriptors to inhibition efficiency in yeast fermentation revealed a strong relationship between the energy of the lowest unoccupied molecular orbital (ELUMO) of aldehydes and their inhibitory efficiency in fermentation. On the other hand, vanillin, syringaldehyde, and 4-hydroxybenzaldehyde (5.0 mM) increased the final ethanol yields by 11, 4, and 1%, respectively. Addition of vanillin appeared to favor ethanol formation over glycerol formation and decreased the glycerol yield in yeast fermentation. Furthermore, alcohol dehydrogenase (ADH) activity dropped significantly from 3.85 to 2.72, 1.83, 0.46, and 0.11 U/mg at 6 h of fermentation at vanillin concentrations of 0, 2.5, 5.0, 10.0, and 25.0 mM correspondingly. In addition, fermentation inhibition by acetic acid and benzoic acid was pH-dependent. Addition of acetate, benzoate, and potassium chloride increased the glucose consumption rate, likely because the salts enhanced membrane permeability, thus increasing glucose consumption.

Synthesis and properties of fluorous benzoquinones and their application in deprotection of silyl ethers

1,4-Benzoquinone derivatives bearing perfluoroalkyl groups were prepared and used as a recyclable catalyst in the selective desilylation of silyl ethers.

Substituent effects on the reactivity of benzoquinone derivatives with thiols

Benzoquinone (BQ) is an extremely potent electrophilic contact allergen that haptenates endogenous proteins through Michael addition (MA). It is also hypothesized that BQ may haptenate proteins via free radical formation. The objective of this study was to assess the inductive effects (activating and deactivating) of substituents on BQ reactivity and the mechanistic pathway of covalent binding to a nucleophilic thiol. The BQ binding of Cys34 on human serum albumin was studied, and for reactivity studies, nitrobenzenethiol (NBT) was used as a surrogate for protein binding of the BQ and benzoquinone derivatives (BQD). Stopped flow techniques were used to determine pseudofirst order rate constants (k) of methyl-, t-butyl-, and chlorine-substituted BQD reactions with NBT, whereas electron pair resonance (EPR) studies were performed to investigate the presence of the free radical mediated binding mechanism of BQD. Characterization of adducts was performed using mass spectrometry and nuclear magnetic resonance spectroscopy (NMR). The rate constant values demonstrated the chlorine-substituted (activated) BQD to be more reactive toward NBT than the methyl and t-butyl-substituted (deactivated) BQD, and this correlated with the respective EPR intensities. The EPR signal, however, was quenched in the presence of NBT suggesting MA as the dominant reaction pathway. MS and NMR results confirmed adduct formation to be a result of MA onto the BQ ring with vinylic substitution also occurring for chlorine-substituted derivatives. The binding positions on BQ and NBT/BQ(D) stoichiometric ratios were affected by whether the inductive effects of the substituents on the ring were positive or negative. The reactivity of BQ and BQD is discussed in terms of the potential relationship to potential allergenic potency.

Drug discovery for a new generation of covalent drugs

INTRODUCTION

The design of target-specific covalent inhibitors is conceptually attractive because of increased biochemical efficiency through covalency and increased duration of action that outlasts the pharmacokinetics of the agent. Although many covalent inhibitors have been approved or are in advanced clinical trials to treat indications such as cancer and hepatitis C, there is a general tendency to avoid them as drug candidates because of concerns regarding immune-mediated toxicity that can arise from indiscriminate reactivity with off-target proteins.

AREAS COVERED

The review examines potential reason(s) for the excellent safety record of marketed covalent agents and advanced clinical candidates for emerging therapeutic targets. A significant emphasis is placed on proteomic techniques and chemical/biochemical reactivity assays that aim to provide a systematic rank ordering of pharmacologic selectivity relative to off-target protein reactivity of covalent inhibitors.

EXPERT OPINION

While tactics to examine selective covalent modification of the pharmacologic target are broadly applicable in drug discovery, it is unclear whether the output from such studies can prospectively predict idiosyncratic immune-mediated drug toxicity. Opinions regarding an acceptable threshold of protein reactivity/body burden for a toxic electrophile and a non-toxic electrophilic covalent drug have not been defined. Increasing confidence in proteomic and chemical/biochemical reactivity screens will require a retrospective side-by-side profiling of marketed covalent drugs and electrophiles known to cause deleterious toxic effects via non-selective covalent binding.

Electrospray ionization tandem mass spectrometry analysis of the reactivity of structurally related bromo-methyl-benzoquinones toward oligonucleotides

We report the use of electrospray ionization tandem mass spectrometry (ESI-MS/MS) as a tool for rapid screening of structurally related chemicals toward oligonucleotides using the binding of five bromobenzoquinones with single-stranded (ss) and double-stranded (ds) oligonucleotides (ODNs) as a model. We found that these compounds interact differentially with oligonucleotides depending on the extent of their bromination and methylation. Three dibromobenzoquinones, 2,6-dibromo-1,4-benzoquinone (2,6-DBBQ), 2,5-dibromo-1,4-benzoquinone (2,5-DBBQ), and 2,5-dimethyl-3,6-dibromo-1,4-benzoquinone (DMDBBQ), bound to ssODN to form 1:1 adducts, and the binding constant of DMDBBQ bound to ssODN was 100-fold lower than those of 2,6-DBBQ and 2,5-DBBQ to ssODN, indicating that methyl groups hindered interactions of the bromoquinones with ODNs. Collision-induced dissociation (CID) of the 1:1 and 1:2 adducts of ODN with 2,6-DBBQ and 2,5-DBBQ demonstrated neutral loss of DBBQ and charge separations. Incubation of two tetrabromobenzoquinones (TBBQ), 2,3,5,6-tetrabromo-1,4-benzoquinone and 3,4,5,6-tetrabromo-1,2-benzoquinone, with the same ODNs did not form any adducts of TBBQ with ssODN or dsODN; however, bromide-ODNs were detected. Fragmentation of the bromide-ODN adducts showed loss of the HBr molecule, supporting the presence of bromide on ODNs. High-resolution MS and MS/MS analysis of the mixtures of dinucleotides (AA, GG, CC, and TT) and TBBQ confirmed the presence of bromide on the dinucleotides, supporting the transfer of bromide to ODNs through interaction with TBBQ. This study presents evidence of differential interactions of structurally related bromo and methyl-benzoquinones with oligonucleotides and demonstrates a potential application of ESI-MS/MS analysis of chemical interactions with ODN for rapid screening of the reactivity of other structurally related environmental contaminants toward DNA.

Thymoquinone supplementation induces quinone reductase and glutathione transferase in mice liver: possible role in protection against chemical carcinogenesis and toxicity

Thymoquinone (TQ), the main constituents of the volatile oil from Nigella sativa seeds is reported to protect laboratory animals against chemical carcinogenesis and toxicity through mechanism(s) that is not fully understood. Among possible mechanism(s), protection could be mediated via induction of detoxifying enzymes, including quinone reductase and glutathione transferase. This study was undertaken to investigate whether oral administration of TQ increases the activities of quinone reductase and glutathione transferase in mice liver. Overdose of TQ, when administered intraperitoneally, caused a marked depletion of hepatic glutathione in both a time- and dose- dependent manner, a characteristic of a group of compounds known as Michael reaction acceptors which are known to act as inducers of enzymes that protect against chemical carcinogenesis and toxicity. TQ was given (1, 2 and 4 mg/kg/day p.o.) for five days to test the chemical inducibility of quinone reductase and glutathione transferase in mice liver. TQ administration produced significant increase in the activities of quinone reductase (147, 196 and 197% of control, respectively) and glutathione transferase (125, 152 and 154% of control, respectively). In conclusion, oral administration of TQ is effective in increasing the activities of quinone reductase and glutathione transferase and makes TQ a promising prophylactic agent against chemical carcinogenesis and toxicity.

The In Chemico–In Silico Interface: Challenges for Integrating Experimental and Computational Chemistry to Identify Toxicity

A number of toxic effects are brought about by the covalent interaction between the toxicant and biological macromolecules. In chemico assays are available that attempt to identify reactive compounds. These approaches have been developed independently for pharmaceuticals and for other non-pharmaceutical compounds. The assays vary widely in terms of the macromolecule (typically a peptide) and the analytical technique utilised. For both sets of methods, there are great opportunities to capture in chemico information by using in silico methods to provide computational tools for screening purposes. In order to use these in chemico and in silico methods, integrated testing strategies are required for individual toxicity endpoints. The potential for the use of these approaches is described, and a number of recommendations to improve this extremely useful technique, in terms of implementing the Three Rs in toxicity testing, are presented.

Application of structure-activity relationships to investigate the molecular mechanisms of hepatocyte toxicity and electrophilic reactivity of alpha,beta-unsaturated aldehydes

Covalent binding of reactive electrophiles to cellular targets is a molecular interaction that has the potential to initiate severe adverse biological effects. Therefore, a measure for electrophilic reactivity with biological nucleophiles could serve as an important correlate to toxic effects such as hepatocyte death. To determine if electrophile reactivity correlates with rat hepatocyte cytotoxicity, the inherently electrophilic alpha,beta-unsaturated aldehydes were chosen for investigation. Reactivity was measured with simple assays that used glutathione, a soft nucleophile, and butylamine, a harder nucleophile, as models for protein thiol and amine nucleophilic sites, respectively. Despite their higher reactivity with thiols, a linear relationship was only observed between hepatocyte cytotoxicity and amine reactivity. Structure-activity relationships were also investigated for hepatocyte toxicity, and results showed toxicity was well modelled by log P and electronic parameters E(LUMO) and partial charge of the carbonyl carbon (C'(carb)). Hydrophobicity and electronic descriptors were only significant in separate distinct models, suggesting that there were simultaneously occurring mechanisms that affected toxicity. Log P was linked to the ease of oxidation by a microsomal aldehyde dehydrogenase enzyme, while the electronic descriptors and amine reactivity were linked to direct alkylation. Even with the presence of electrophile characteristics, alpha,beta-unsaturated aldehyde hepatocyte toxicity could not be predicted exclusively by electrophilic reactivity as oxidative metabolism was also a factor for toxicity.