Quantitative structure-activity relationships for the toxicity of chlorophenols to mammalian submitochondrial particles

New Mechanistic Insights on Carbon Nanotubes' Nanotoxicity Using Isolated Submitochondrial Particles, Molecular Docking, and Nano-QSTR Approaches

Single-walled carbon nanotubes can induce mitochondrial F0F1-ATPase nanotoxicity through inhibition. To completely characterize the mechanistic effect triggering the toxicity, we have developed a new approach based on the combination of experimental and computational study, since the use of only one or few techniques may not fully describe the phenomena. To this end, the in vitro inhibition responses in submitochondrial particles (SMP) was combined with docking, elastic network models, fractal surface analysis, and Nano-QSTR models. In vitro studies suggest that inhibition responses in SMP of F0F1-ATPase enzyme were strongly dependent on the concentration assay (from 3 to 5 µg/mL) for both pristine and COOH single-walled carbon nanotubes types (SWCNT). Besides, both SWCNTs show an interaction inhibition pattern mimicking the oligomycin A (the specific mitochondria F0F1-ATPase inhibitor blocking the c-ring F0 subunit). Performed docking studies denote the best crystallography binding pose obtained for the docking complexes based on the free energy of binding (FEB) fit well with the in vitro evidence from the thermodynamics point of view, following an affinity order such as: FEB (oligomycin A/F0-ATPase complex) = -9.8 kcal/mol > FEB (SWCNT-COOH/F0-ATPase complex) = -6.8 kcal/mol ~ FEB (SWCNT-pristine complex) = -5.9 kcal/mol, with predominance of van der Waals hydrophobic nano-interactions with key F0-ATPase binding site residues (Phe 55 and Phe 64). Elastic network models and fractal surface analysis were performed to study conformational perturbations induced by SWCNT. Our results suggest that interaction may be triggering abnormal allosteric responses and signals propagation in the inter-residue network, which could affect the substrate recognition ligand geometrical specificity of the F0F1-ATPase enzyme in order (SWCNT-pristine > SWCNT-COOH). In addition, Nano-QSTR models have been developed to predict toxicity induced by both SWCNTs, using results of in vitro and docking studies. Results show that this method may be used for the fast prediction of the nanotoxicity induced by SWCNT, avoiding time- and money-consuming techniques. Overall, the obtained results may open new avenues toward to the better understanding and prediction of new nanotoxicity mechanisms, rational drug design-based nanotechnology, and potential biomedical application in precision nanomedicine.

Predicting Uncoupling Toxicity of Organic Acids Based on Their Molecular Structure Using a Biophysical Model

We present a purely mechanistic model to predict protonophoric uncoupling activity EC_w of organic acids. All required input information can be derived from their chemical structure. This makes it a convenient predictive model to gain valuable information on the toxicity of organic chemicals already at an early stage of development of new commercial chemicals (e.g., in agriculture or pharmaceutical industries). A critical component of the model is the consideration of the possible formation of heterodimers from the neutral and anionic monomer, and its permeation through the membrane. The model was tested against literature data measured in chromatophores, submitochondrial particles, isolated mitochondria, and intact green algae cells with good success. It was also possible to reproduce pH-dependencies in isolated mitochondria and intact cells. Besides the prediction of the EC_w, the mechanistic nature of the model allows researchers to draw direct conclusions on the impact of single input factors such as pH- and voltage-gradients across the membrane, the anionic and neutral membrane permeability, and the heterodimerization constant. These insights are of importance in drug design or chemical regulation.

Targeted live-cell nuclear delivery of the DNA 'light-switching' Ru(II) complex via ion-pairing with chlorophenolate counter-anions: the critical role of binding stability and lipophilicity of the ion-pairing complexes

We have found recently that nuclear uptake of the cell-impermeable DNA light-switching Ru(II)-polypyridyl cationic complexes such as [Ru(bpy)2(dppz)]Cl2 was remarkably enhanced by pentachlorophenol (PCP), by forming ion-pairing complexes via a passive diffusion mechanism. However, it is not clear whether the enhanced nuclear uptake of [Ru(bpy)2(dppz)]2+ is only limited to PCP, or it is a general phenomenon for other highly chlorinated phenols (HCPs); and if so, what are the major physicochemical factors in determining nuclear uptake? Here, we found that the nuclear uptake of [Ru(bpy)2(dppz)]2+ can also be facilitated by other two groups of HCPs including three tetrachlorophenol (TeCP) and six trichlorophenol (TCP) isomers. Interestingly and unexpectedly, 2,3,4,5-TeCP was found to be the most effective one for nuclear delivery of [Ru(bpy)2(dppz)]2+, which is even better than the most-highly chlorinated PCP, and much better than its two other TeCP isomers. Further studies showed that the nuclear uptake of [Ru(bpy)2(dppz)]2+ was positively correlated with the binding stability, but to our surprise, inversely correlated with the lipophilicity of the ion-pairing complexes formed between [Ru(bpy)2(dppz)]Cl2 and HCPs. These findings should provide new perspectives for future investigations on using ion-pairing as an effective method for delivering other bio-active metal complexes into their intended cellular targets.

Comparative toxic potency ranking of chlorophenols

Chlorophenols are prevalent in all media of the environment. The most common environmental source of pentachlorophenol (PCP) and other chlorinated phenols are via the lumber industry as a wood preservative and as a pesticide in plant production. The US Environmental Protection Agency’s (EPA) contaminant candidate list (CCL) includes a majority of these compounds as unregulated contaminants. Except for pentachlorophenol, there is a lack of human or animal data base which can be used for human health risk assessment. The specific aim of this study is to develop a rationale to use in vivo nonmammalian, in vitro mammalian and nonmammalian, micro-organism toxicity data base, structural activity, mechanistic and toxicokinetic data bases for developing a relative toxic potency ranking scheme of chlorophenols. Although the toxic potency of chlorophenols was found to increase with the number of chlorines, the potency decreases if the chlorines are attached in the ortho position of the molecules. Based on the LOAELs and mammalian in vitro data, the relative potency of chlorophenols determined to be best estimated by the ratios of log Kow to the 0.55 power. The relationship of the toxic potency derived from such an approach is largely presumptive.

Assessment of phenolic herbicide toxicity and mode of action by different assays

A phytotoxicity assay based on seed germination/root elongation has been optimized and used to evaluate the toxic effects of some phenolic herbicides. The method has been improved by investigating the influence of experimental conditions. Lepidium sativum was chosen as the most suitable species, showing high germinability, good repeatability of root length measurements, and low sensitivity to seed pretreatment. DMSO was the most appropriate solvent carrier for less water-soluble compounds. Three dinitrophenols and three hydroxybenzonitriles were tested: dinoterb, DNOC, 2,4-dinitrophenol, chloroxynil, bromoxynil, and ioxynil. Toxicity was also determined using the Vibrio fischeri Microtox® test, and a highly significant correlation was found between EC50 values obtained by the two assays. Dinoterb was the most toxic compound. The toxicity of hydroxybenzonitriles followed the order: ioxynil >bromoxynil >chloroxynil; L. sativum exhibited a slightly higher sensitivity than V. fischeri to these compounds. A QSAR analysis highlighted the importance of hydrophobic, electronic, and hydrogen-bonding interactions, in accordance with a mechanism of toxic action based on protonophoric uncoupling of oxidative phosphorylation. The results suggest that the seed germination/root elongation assay with L. sativum is a valid tool for the assessment of xenobiotic toxicity and can be recommended as part of a test battery.

Toxicology Strategies for Drug Discovery: Present and Future

Attrition due to nonclinical safety represents a major issue for the productivity of pharmaceutical research and development (R&D) organizations, especially during the compound optimization stages of drug discovery and the early stages of clinical development. Focusing on decreasing nonclinical safety-related attrition is not a new concept, and various approaches have been experimented with over the last two decades. Front-loading testing funnels in Discovery with in vitro toxicity assays designed to rapidly identify unfavorable molecules was the approach adopted by most pharmaceutical R&D organizations a few years ago. However, this approach has also a non-negligible opportunity cost. Hence, significant refinements to the "fail early, fail often" paradigm have been proposed recently to reflect the complexity of accurately categorizing compounds with early data points without taking into account other important contextual aspects, in particular efficacious systemic and tissue exposures. This review provides an overview of toxicology approaches and models that can be used in pharmaceutical Discovery at the series/lead identification and lead optimization stages to guide and inform chemistry efforts, as well as a personal view on how to best use them to meet nonclinical safety-related attrition objectives consistent with a sustainable pharmaceutical R&D model. The scope of this review is limited to small molecules, as large molecules are associated with challenges that are quite different. Finally, a perspective on how several emerging technologies may impact toxicity evaluation is also provided.

How to mechanistically explain the CONDOR study data

Results of the CONDOR study suggest that in osteoarthritis and rheumatoid arthritis patients at elevated risk of gastrointestinal (GI) events, treatment with celecoxib, a cyclooxygenase (COX)-2 selective non-steroidal anti-inflammatory drug (NSAID), demonstrated significantly lower toxicity in the upper and lower (GI) tract when compared to the non-selective NSAID diclofenac plus a proton-pump-inhibitor (PPI), omeprazole. According to current knowledge, traditional NSAIDs (tNSAIDs) as non-selective COX-inhibitors exert their damaging effects on the upper GI tract, largely by reduction of the COX-1 related synthesis of gastro-protective prostaglandins. Thus, the question arises, how NSAIDs do exert their damaging effects especially in the lower GI tract and how to explain the reduced risk of a COX-2 selective inhibitor, celecoxib. Here we hypothesize, that the toxicity of celecoxib on enteral mucosa cells is lower than observed with other NSAIDs, and can be explained COX-independently by typical physicochemical properties of the NSAID substances (e.g., acidic, lipophilic, amphiphilic, surfactant properties). As a consequence these features account for differences in (1) uncoupling effects on mitochondria, (2) effects on cell membrane integrity, and/or (3) formation of "toxic micelles" with bile salts. The evidence for these differences is mainly based on experimental findings. However, several phenomena show differences in extent (e.g., uncoupling effects). The reduced toxicity appears to be rather a substance-specific characteristic. This is an unconditional reason to carry on investigating these phenomena in experimental and large-scale clinical trials.

The QSPR (quantitative structure-property relationship) study about the anaerobic biodegradation of chlorophenols

In this study, based on quantum chemical and physicochemical descriptors, by the use of partial least squares analysis, a good prediction quantitative structure-property relationship for the disappearance rate constant (logK) of chlorophenols (CPs) in the anaerobic culture was obtained. It was found that the resonance energy of the two-center term (J), which described the character of the weakest carbon-chlorine bond, played an important role in the reductive chlorine processes, the greater the sizes of CPs molecules, the higher the logK values. Increasing energy of the lowest unoccupied molecular orbital (E(lumo)) values of the CPs lead to decreasing logK values, and CPs with large absolute hardness values tended to have big logK values.

Quantitative structure activity relationship (QSAR) for toxicity of chlorophenols on L929 cells in vitro

Quantitative structure activity relationship (QSAR) were developed to predict toxicity of chlorophenols by correlating LC50 values with five molecular descriptors, chosen to represent lipophilic, electronic and steric effects: the n-octanol/water partition coefficient (log K(ow)), the constant of Hammett (sigma sigma), the acid dissociation constant (pKa), the order valence molecular connectivity index (1chi(v)) and the perimeter of the efficacious section (sigma D(g)). The results of the regression analysis showed that log K(ow) and sigma D(g) are the dominant (canonical) predictive factors in determining toxicity of chlorophenols to the cells during 24 h exposures, while log K(ow) was the only dominant predictive factor contributing to toxicity during in 48 h exposures. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to investigate predictive relationships of the cytotoxicity of chlorophenols and develop visual 3D-QSAR models. The CoMFA model, in which the contribution of the electrostatic field to the biological activity was greater than that of the steric field, exhibited both high consistency and predictability (r2 = 0.968, Q2 = 0.891 for 24 h exposure; but the relationship was poorer for the 48 h exposure: r2 = 0.727, Q2 = 0.394). The CoMSIA model used in this study contained three fields: electrostatic, hydrophobic and steric, of which the relative contribution to the biological activity was 0.767:0.225:0.008. In addition, according to the models for 24 h and 48 h. The time-dependent toxicity and potential mechanisms for inhibition of L929 cells was discussed.

Drug-induced mitochondrial toxicity

Mitochondria play a critical role in generating most of the cell's energy as ATP. They are also involved in other metabolic processes such as urea generation, haem synthesis and fatty acid beta-oxidation. Disruption of mitochondrial function by drugs can result in cell death by necrosis or can signal cell death by apoptosis (e.g., following cytochrome c release). Drugs that injure mitochondria usually do so by inhibiting respiratory complexes of the electron chain; inhibiting or uncoupling oxidative phosphorylation; inducing mitochondrial oxidative stress; or inhibiting DNA replication, transcription or translation. It is important to test for mitochondrial toxicity early in drug development as impairment of mitochondrial function can induce various pathological conditions that are life threatening or can increase the progression of existing mitochondrial diseases.

QSAR models based on quantum topological molecular similarity

A new method called quantum topological molecular similarity (QTMS) was fairly recently proposed [J. Chem. Inf. Comp. Sc., 41, 2001, 764] to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs. QTMS method uses quantum chemical topology (QCT) to define electronic descriptors drawn from modern ab initio wave functions of geometry-optimised molecules. It was shown that the current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In this article we study seven datasets of medicinal interest : the dissociation constants (pK(a)) for a set of substituted imidazolines , the pK(a) of imidazoles , the ability of a set of indole derivatives to displace [(3)H] flunitrazepam from binding to bovine cortical membranes , the influenza inhibition constants for a set of benzimidazoles , the interaction constants for a set of amides and the enzyme liver alcohol dehydrogenase , the natriuretic activity of sulphonamide carbonic anhydrase inhibitors and the toxicity of a series of benzyl alcohols. A partial least square analysis in conjunction with a genetic algorithm delivered excellent models. They are also able to highlight the active site, of the ligand or the molecule whose structure determines the activity. The advantages and limitations of QTMS are discussed.

C. fumago chloroperoxidase is also a dehaloperoxidase: oxidative dehalogenation of halophenols

We have examined the H2O2-dependent oxidative dehalogenation of 2,4,6-trihalophenols and p-halophenols catalyzed by Caldariomyces fumago chloroperoxidase (CCPO). CCPO is significantly more robust than other peroxidases and can function under harsher reaction conditions, and so its ability to dehalogenate halophenols could lead to its use as a bioremediation catalyst for aromatic dehalogenation reactions. Optimal catalysis occurred under acidic conditions (100 mM potassium phosphate solution, pH 3.0). UV-visible absorption spectroscopy, high-performance liquid chromatography, and gas chromatography/mass spectrometry clearly identified the oxidized reaction product for CCPO-catalyzed dehalogenation of 2,4,6-trihalophenols as the corresponding 2,6-dihalo-1,4-benzoquinones. This reaction has previously been reported for two His-ligated heme-containing peroxidases (see Osborne, R. L.; Taylor, L. O.; Han, K. P.; Ely, B.; Dawson, J. H. Biochem. Biophys. Res. Commun. 2004, 324, 1194-1198), but this is the first example of a Cys-ligated heme-containing peroxidase functioning as a dehaloperoxidase. The relative catalytic efficiency (turnover number) of CCPO reported herein is comparable to that of horseradish peroxidase (Ferrari, R. P.; Laurenti, E.; Trotta, F. J. Biol. Inorg. Chem. 1965, 4, 232-237). The mechanism of dehalogenation has been probed using p-halophenols as substrates. Here the major product is a dimer with 1,4-benzoquinone as the minor product. An electron-transfer mechanism is proposed that accounts for the products formed from both the 2,4,6-trihalo- and p-halophenols. Finally, we note that this is the first case of a peroxidase known primarily for its halogenation ability being shown to also dehalogenate substrates.

Evidence for heterodimers of 2,4,5-trichlorophenol on planar lipid layers. A FTIR-ATR investigation

Trichlorophenols are weak acids of high hydrophobicity and are able to transport protons across the mitochondrial membrane. Thus the proton motive force is dissipated and the ATP production decreased. In situ Fourier Transform Infrared-Attenuated Total Reflection (FTIR-ATR) experiments with 2,4,5-trichlorophenol (TCP) adsorbed to model membranes resulted in good evidence for the formation of the TCP-heterodimer. Two surfaces were examined: a dipalmitoyl phosphatidic acid (DPPA) monolayer and a planar DPPA/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. TCP was adsorbed from 1 to 3 mM solutions at pH 6.0 to the lipid layers leading to surface layers at the water/lipid interface. Difference spectra showed an effect on DPPA acyl chains even when it was covered with POPC. Time-resolved measurements revealed two distinct adsorption processes, which were assigned to TCP and its deprotonated anion (phenoxide), respectively. For DPPA/POPC bilayers, the adsorption of TCP was faster than that of its phenoxide, whereas adsorption of both species to DPPA monolayers proceeded with similar velocity. In both cases, phenoxide formation at the membrane was found to be delayed with respect to phenol adsorption. Phenoxide and phenol were retained after replacing the TCP solution with buffer. For the retained species, we estimated a phenol/phenoxide molar ratio of 1 at pH 6.0 (pKa=6.94 for TCP), demonstrating strong evidence for heterodimer formation.

Molecular Parameters Responsible for the Melting Point of 1,2,3-Diazaborine Compounds

Quantitative structure-property relationships (QSPR) have been determined to predict the melting point temperatures of 1,2,3-diazaborine compounds (n = 72). Electronic and topological descriptors were computed from molecular structures, and a QSPR model was generated by linear multiple regression using reported melting point temperatures as the dependent variable. The most important molecular descriptors describing this physicochemical property were the sum of the atomic charges for the heteroatoms, the sum of Randić connectivity indexes (0)Chi(0), (0)Chi(1), and (0)Chi(2), the total number of atoms in the molecule, and the volume of the box in which the molecule fits. The multiple determination coefficient (R(2)) and standard error of estimation for the model were 0.856 and 16.787 degrees C, respectively. In addition to regression techniques, a back-propagation neural network was used to include nonlinear relationships between molecular structure and melting point temperatures. It is concluded that melting point temperatures for 1,2,3-diazaborine compounds can be described by electrostatic interactions mediated by atomic charges and steric properties. The results of this study demonstrate that multiple linear regression analysis and back-propagation neural network are techniques that can be used to successfully predict the melting point temperatures of 1,2,3-diazaborine compounds. The most accurate prediction results were obtained using the Levenberg-Marquardt neural network algorithm.

Oxidation of 2,4-dichlorophenol catalyzed by horseradish peroxidase: characterization of the reaction mechanism by UV-visible spectroscopy and mass spectrometry

The hydrogen peroxide-oxidation of 2,4-dichlorophenol catalyzed by horseradish peroxidase has been studied by means of UV-visible spectroscopy and mass spectrometry in order to clarify the reaction mechanism. The dimerization of 2,4-dichlorophenol to 2,4-dichloro-6-(2,4-dichlorophenoxy)-phenol and its subsequent oxidation to 2-chloro-6-(2,4-dichlorophenoxy)-1,4-benzoquinone together with chloride release were observed. The reaction rate was found to be pH-dependent and to be influenced by the pK(a) value of 2,4-dichlorophenol. The dissociation constants of the 2,4-dichlorophenol/horseradish peroxidase (HRP) adduct at pH 5.5 and 8.5 were also determined: their values indicate the unusual stability of the adduct at pH 5.5 with respect to several adducts of HRP with substituted phenols.

Comparisons of human-cell-based and submitochondrial particle bioassay responses to the MEIC compounds in reference to human toxicity data

Toxicity results from submitochondrial particle (SMP) bioassays were compared to results from multiple human-cell-based assays to evaluate the SMP tests' ability to indicate cellular toxicity. Correlation analyses between cell-based and SMP responses were conducted on a series of diverse chemicals of human toxicologic interest chosen in the Multicentre Evaluation of In vitro Cytotoxicity (MEIC) study and suggest a high degree of ordering. The r(2) correlation coefficient obtained when comparing the log-transformed SMP results to the average cellular response for all compounds was 0.75 (n=42). When specific mitochondrial inhibitors (to which SMP arc extremely sensitive) and toxic metals (which SMP modeled poorly) were removed, the correlation improved to 0.91 (n=34). When the SMP assay of each individual cell-based assay was compared to the average toxic response of all the cell-based assays for these 34 compounds, the SMP r(2) was greater than the median r(2) of the cell-based assays, indicating its ability to predict cell-based toxic responses with a high degree of accuracy. Comparisons of the SMP data to the human toxicity data are similar to the cell line assays, where removal of the specific mitochondrial toxicants and metals greatly improves the relationship.

Activation of the hsp70 promoter by environmental inorganic and organic chemicals: relationships with cytotoxicity and lipophilicity

Stress proteins (heat shock proteins, HSPs) have been proposed as general markers of cellular aggression and their use for environmental monitoring is often suggested. The aim of this work was to study the potency of various environmentally relevant organic and inorganic chemicals to induce the expression of the HSP70 marker. For this purpose, we used an established HeLa cell line containing the chloramphenicol acetyl transferase (CAT) gene under the control of the hsp70 promoter. The screening of three metallic and 15 organic chemicals revealed differences in their capacities to induce the hsp70 promoter. The three metals tested (cadmium, zinc and mercury) were able to induce a stress response. Some organochlorine compounds (chlorophenol derivatives, tetrachlorohydroquinone, 3, 4-dichloroaniline, ethyl parathion and 1-chloro-2,4-dinitrobenzene) induced a response, whereas other common halogenated pesticides or aromatic hydrocarbons (e.g. benzo(a)pyrene, 2, 4-dichlorophenoxyacetic acid, endosulfan, diuron, 4-nonylphenol) did not. The potency to induce hsp70 was significantly correlated to the octanol-water partition coefficient (log K(ow)) of the inducing chemicals, except for 1-chloro-2,4-dinitrobenzene and ethyl parathion. Cytotoxicity assays run in parallel to the induction measurements revealed that the three metals were effective at non cytotoxic doses whereas all organic compounds, except tetrachlorohydroquinone and 1-chloro-2,4-dinitrobenzene, induced the promoter at cytotoxic doses. These results suggest that hsp70 is induced by different mechanisms of toxicity. We propose that this model can be used in mechanistic studies for the detection of toxic effects of certain pollutants.