Quantitative structure-activity relationship for prediction of the toxicity of phenols on Photobacterium phosphoreum

Ligand-Based Compound Activity Prediction via Few-Shot Learning

Predicting the activities of new compounds against biophysical or phenotypic assays based on the known activities of one or a few existing compounds is a common goal in early stage drug discovery. This problem can be cast as a "few-shot learning" challenge, and prior studies have developed few-shot learning methods to classify compounds as active versus inactive. However, the ability to go beyond classification and rank compounds by expected affinity is more valuable. We describe Few-Shot Compound Activity Prediction (FS-CAP), a novel neural architecture trained on a large bioactivity data set to predict compound activities against an assay outside the training set, based on only the activities of a few known compounds against the same assay. Our model aggregates encodings generated from the known compounds and their activities to capture assay information and uses a separate encoder for the new compound whose activity is to be predicted. The new method provides encouraging results relative to traditional chemical-similarity-based techniques as well as other state-of-the-art few-shot learning methods in tests on a variety of ligand-based drug discovery settings and data sets. The code for FS-CAP is available at https://github.com/Rose-STL-Lab/FS-CAP.

Acute toxicity assessment of indoor dust extracts by luminescent bacteria assays with Photobacterium Phosphoreum T3

In the last decades, there has been an increasing concern about the human exposure to indoor dust. Therefore, it is imperative to assess the toxicity of indoor dust and associated dust extracts. In this study, the acute toxicity assessment of indoor dust was performed using a bioluminescence test, with Photobacterium phosphoreum T₃ (PPT₃) chosen as the test bacterium. The different indoor dust samples were collected from residences, offices, dormitories and laboratories in Shanghai, China. Our data reveal that PPT₃ is more active to water-soluble ions and organic contaminants at low concentrations, while extract solutions elicit increased bacterial toxicity at high concentrations. The results of a bioluminescence assay by PPT₃ indicated that the dust organic extracts exhibited increased toxicity compared with the water exacts. Dust extracts from the laboratory exhibited the greatest bacterial toxicity when compared with office, dormitory and residence samples. Moreover, office dust exhibited higher bacterial toxicity than residence dust. Furthermore, the comprehensive toxicity of dust on PPT₃ was assessed by extracts toxicity -addition (i.e. IR_addition). The calculated values were close to the corresponding experimental data. The bioluminescence test showed the indoor dust samples are weakly toxic to PPT₃, which are equivalent to 0.046-0.123 mg Hg•L^-1. Different dust extracts among the different sampling sites showed varying toxicity to PPT₃. This study provides some important information to understand the potential health risk from different indoor environment using a rapid bioluminescence assay.

Toxicity of binary mixtures of pesticides and pharmaceuticals toward Vibrio fischeri: Assessment by quantitative structure-activity relationships

Pollutants in real aquatic systems commonly occur as chemical mixtures. Yet, the corresponding risk assessment is still mostly based on information on single-pollutant toxicity, accepting the assumption that pollutant mixtures exhibit additive toxicity effect which is often not the case. Therefore, it is still better to use the experimental approach. Unfortunately, experimental determination of toxicity for each mixture is practically unfeasible. In this study, quantitative structure-activity relationship (QSAR) models for the prediction of toxicity of binary mixtures towards bioluminescent bacteria Vibrio fischeri were developed at three toxicity levels (EC₁₀, EC₃₀ and EC₅₀). For model development, experimentally determined toxicity values of 14 pollutants (pharmaceuticals and pesticides) were correlated with their structural features, applying multiple linear regression together with genetic algorithm. Statistical analysis, internal validation and external validation of the models were carried out. The toxicity is accurately predicted by all three models. EC₃₀ and EC₅₀ values are mostly influenced by geometrical distances between nitrogen and sulfur atoms. Furthermore, the simultaneous presence of oxygen and chlorine atoms in mixture can induce the increase in toxicity. At lower effect levels (EC₁₀), nitrogen atom bonded to different groups has the highest impact on mixture toxicity. Thus, the analysis of the descriptors involved in the developed models can give insight into toxic mechanisms of the binary systems.

Correlation between the uncoupling metabolism induced by 2,4,6-trichlorophenol and sludge toxicity in sequence batch reactors

The correlation between sludge reduction induced by 2,4,6-trichlorophenol (2,4,6-TCP) as an uncoupler and sludge toxicity was investigated in sequence batch reactors over a 100-d operation period. The influent concentrations of 2,4,6-TCP tested were 10 mg/L, 30 mg/L, and 50 mg/L. Sludge reduction, chemical oxygen demand (COD) removal rate, and sludge toxicity were measured. The results showed that from 30 to 80 d, when the COD removal rate was at an acceptable level, the sludge reduction levels for the 10 mg/L, 30 mg/L, and 50 mg/L groups were 9.7%, 31.6%, and 41.5%, respectively, and the average sludge toxicity values were 24.2%, 38.0%, and 53.0%, respectively. Sludge reduction was positively correlated with sludge toxicity. The two-dimensional polyacrylamide gel electrophoresis/results showed that extracellular and intracellular proteins secreted by the activated sludge during uncoupling metabolism were positively correlated with sludge toxicity. Taking the COD removal rate, sludge reduction, and sludge toxicity into consideration, the optimal influent concentration of the uncoupler 2,4,6-TCP was 30 mg/L when the initial mixed liquid suspended solids of sludge was 2,500 mg/L.

Effects of 4-chlorophenol wastewater treatment on sludge acute toxicity, microbial diversity and functional genes expression in an activated sludge process

In this study, the effects of 4-chlorophenol (4-CP) wastewater treatment on sludge acute toxicity of luminescent bacteria, microbial diversity and functional genes expression of Pseudomonas were explored. Results showed that in the entire operational process, the sludge acute toxicity acclimated by 4-CP in a sequencing batch bioreactor (SBR) was significantly higher than the control SBR without 4-CP. The dominant phyla in acclimated SBR were Proteobacteria and Firmicutes, which also existed in control SBR. Some identified genera in acclimated SBR were responsible for 4-CP degradation. At the stable operational stages, the functional genes expression of Pseudomonas in acclimated SBR was down-regulated at the end of SBR cycle, and their expression mechanisms needed further research. This study provides a theoretical support to comprehensively understand the sludge performance in industrial wastewater treatment.

Toxicity assessment of the extractables from multi-layer coextrusion poly ethylene bags exposed to pH=5 solution containing 4% benzyl alcohol and 0.1 M sodium acetate

A non-target analysis was developed for the analysis of extractables from multi-layer coextrusion bags exposed to 4% benzyl alcohol solution and 0.1 M sodium acetate at pH = 5 for defined periods (15 day, 45 day and 90 day) according to manufacturer instructions based on the ultra-performance liquid chromatography (UPLC) quadrupole-time of flight mass spectrometry (Q-TOF MS). In order to confirm the extractables, principal component analysis (PCA) was used to indicate the differences among samples of different periods. Then, the extractables were identified based on searching the self-built library or online searching. The total content of extractables of 90 day samples was 589.78 μg/L, and the content was in the range of acceptable levels for pharmaceutical manufacturers. The risk assessment of the extractables were evaluated by Toxtree and T.E.S.T. software to avoid the animals bioexperiment.

Effect of ultrasonic waves on the water turbidity during the oxidation of phenol. Formation of (hydro)peroxo complexes

Analysis of the kinetics of aqueous phenol oxidation by a sono-Fenton process reveals that the via involving ortho-substituted intermediates prevails: catechol (25.0%), hydroquinone (7.7%) and resorcinol (0.6%). During the oxidation, water rapidly acquires color that reaches its maximum intensity at the maximum concentration of p-benzoquinone. Turbidity formation occurs at a slower rate. Oxidant dosage determines the nature of the intermediates, being trihydroxylated benzenes (pyrogallol, hydroxyhydroquinone) and muconic acid the main precursors causing turbidity. It is found that the concentration of iron species and ultrasonic waves affects the intensity of the turbidity. The pathway of (hydro)peroxo-iron(II) complexes formation is proposed. Operating with 20.0-27.8mgFe²⁺/kW rates leads to formation of (hydro)peroxo-iron(II) complexes, which induce high turbidity levels. These species would dissociate into ZZ-muconic acid and ferrous ions. Applying relationships around 13.9mgFe²⁺/kW, the formation of (hydro)peroxo-iron(III) complexes would occur, which could react with carboxylic acids (2,5-dioxo-3-hexenedioic acid). That reaction induces turbidity slower. This is due to the organic substrate reacting with two molecules of the (hydro)peroxo complex. Therefore, it is necessary to accelerate the iron regeneration, intensifying the ultrasonic irradiation. Afterwards, this complex would dissociate into maleic acid and ferric ions.

Evaluation of ecotoxicological effects of benzophenone UV filters: Luminescent bacteria toxicity, genotoxicity and hormonal activity

The widespread use of organic ultraviolet (UV) filters in personal care products raises concerns about their potentially hazardous effects on human and ecosystem health. In this study, the toxicities of four commonly used benzophenones (BPs) UV filters including benzophenone (BP), 2-Hydroxybenzophenone (2HB), 2-Hydroxy-4-methoxybenzophenone (BP3), and 2-Hydroxy-4-methoxybenzophenone-5-sulfonicacid (BP4) in water were assayed in vitro using Vibrio fischeri, SOS/umu assay, and yeast estrogen screen (YES) assay, as well as in vivo using zebrafish larvae. The results showed that the luminescent bacteria toxicity, expressed as logEC₅₀, increased with the lipophilicity (logKow) of BPs UV filters. Especially, since 2HB, BP3 and BP4 had different substituent groups, namely -OH, -OCH₃ and -SO₃H, respectively, these substituent functional groups had a major contribution to the lipophilicity and acute toxicity of these BPs. Similar tendency was observed for the genotoxicity, expressed as the value of induction ratio=1.5. Moreover, all the target BPs UV filters showed estrogenic activity, but no significant influences of lipophilicity on the estrogenicity were observed, with BP3 having the weakest estrogenic efficiency in vitro. Although BP3 displayed no noticeable adverse effects in any in vitro assays, multiple hormonal activities were observed in zebrafish larvae including estrogenicity, anti-estrogenicity and anti-androgenicity by regulating the expression of target genes. The results indicated potential hazardous effects of BPs UV filters and the importance of the combination of toxicological evaluation methods including in vitro and in vivo assays.

The investigation of different pollutants and operation processes on sludge toxicity in sequencing batch bioreactors

The influence of different target pollutants and operation modes in sequencing batch bioreactors (SBRs) on sludge toxicity was compared in this study. Sludge toxicity was characterized by the inhibiting luminosity through using luminescent bacterium Photobacterium phosphoreum (P. phosphoreum) during either gradual acclimation or impaction processes with synthetic wastewater containing high-strength bisphenol A (BPA) or N, N-dimethylformamide (DMF). When the activated sludge was first acclimated with either 120 mg/L DMF or 20 mg/L BPA, and then respectively increased to 200 mg/L DMF and 40 mg/L BPA it was defined as gradual acclimation process, whereas when the activated sludge was, respectively, injected with 200 mg/L DMF and 40 mg/L BPA directly it was defined as impaction process. Results showed that the toxicity of the impacted sludge was greater than that of the gradual acclimated sludge, especially in the initial stage before 10 d. Activated sludge treating BPA synthetic wastewater exhibited higher toxicity due to the more inhibition of BPA to sludge activity compared to that of DMF. The proteomics analysis indicated that the stress responses of activated sludge to DMF and BPA stimulation were both significant. In turn, the secretions from two kinds of sludge under stress conditions contributed to sludge toxicity.

High-accuracy QSAR models of narcosis toxicities of phenols based on various data partition, descriptor selection and modelling methods

The environmental protection agency thinks that quantitative structure–activity relationship (QSAR) analysis can better replace toxicity tests.

Acute toxicity of benzophenone-type UV filters for Photobacterium phosphoreum and Daphnia magna: QSAR analysis, interspecies relationship and integrated assessment

The hazardous potential of benzophenone (BP)-type UV filters is becoming an issue of great concern due to the wide application of these compounds in many personal care products. In the present study, the toxicities of BPs to Photobacterium phosphoreum and Daphnia magna were determined. Next, density functional theory (DFT) and comparative molecular field analysis (CoMFA) descriptors were used to obtain more detailed insight into the structure - activity relationships and to preliminarily discuss the toxicity mechanism. Additionally, the sensitivities of the two organisms to BPs and the interspecies toxicity relationship were compared. Moreover, an approach for providing a global index of the environmental risk of BPs to aquatic organisms is proposed. The results demonstrated that the mechanism underlying the toxicity of BPs to P. phosphoreum is primarily related to their electronic properties, and the mechanism of toxicity to D. magna is hydrophobicity. Additionally, D. magna was more sensitive than P. phosphoreum to most of the BPs, with the exceptions of the polyhydric BPs. Moreover, comparisons with published data revealed a high interspecies correlation coefficient among the experimental toxicity values for D. magna and Dugesia japonica. Furthermore, hydrophobicity was also found to be the most important descriptor of integrated toxicity. This investigation will provide insight into the toxicity mechanisms and useful information for assessing the potential ecological risk of BP-type UV filters.

Effect of Fenton oxidation on biodegradability, biotoxicity and dissolved organic matter distribution of concentrated landfill leachate derived from a membrane process

The treatment of concentrated landfill leachate from membrane process is a troublesome issue due to high concentrations of biorecalcitrant pollutants. In this study, the effect of Fenton process on dissolved organic matter (DOM) distribution (i.e. humic acid (HA), fulvic acid (FA) and hydrophilic fraction (HyI)), chemical forms of toxic organic compounds and metals, and their biotoxicity were investigated. In the concentrated leachate, toluene, ethylbenzene and chlorobenzene predominated in the HyI fraction, while phthalate esters (PAEs) were mainly absorbed on the HA and FA fractions. PAEs were more readily removed from the HA and FA fractions than that from the HyI fraction in the Fenton process. The complexing abilities of DOM varied with types of metal in the concentrated leachate. The biotoxicities of the DOM fractions to luminescent bacteria (Photobacterium phosphoreum T3 mutation) were HA > FA > - HyI. The biotoxicities of the hydrophobic organic contaminants to luminescent bacteria were not obvious in the concentrated leachate due to their low concentrations. Metals might be the main contributor to the biotoxicity to luminous bacteria in the concentrated leachate. These results indicated that Fenton process could influence the pollutants distribution in DOM and their biotoxicities through the breakdown of HA and FA in the concentrated leachate.

Oxidative toxicity of perfluorinated chemicals in green mussel and bioaccumulation factor dependent quantitative structure-activity relationship

Concerns regarding perfluorinated chemicals (PFCs) have risen in recent years because of their ubiquitous presence and high persistency. However, data on the environmental impacts of PFCs on marine organisms are very limited. Oxidative toxicity has been suggested to be one of the major toxic pathways for PFCs to induce adverse effects on organisms. To investigate PFC-induced oxidative stress and oxidative toxicity, a series of antioxidant enzyme activities and oxidative damage biomarkers were examined to assess the adverse effects of the following 4 commonly detected compounds: perfluoro-octanesulfonate, perfluoro-ocanoic acid, perfluorononanoic acid, and perfluorodecanoic acid, on green mussel (Perna viridis). Quantitative structure-activity relationship (QSAR) models were also established. The results showed that all the tested PFCs are able to induce antioxidant response and oxidative damage on green mussels in a dose-dependent manner. At low exposure levels (0 µg/L-100 µg/L), activation of antioxidant enzymes (catalase [CAT] and superoxide dismutase [SOD]) was observed, which is an adaptive response to the excessive reactive oxygen species induced by PFCs, while at high exposure levels (100 µg/L-10 000 µg/L), PFCs were found to inhibit some enzyme activity (glutathione S-transferase and SOD) where the organism's ability to respond in an adaptive manner was compromised. The oxidative stress under high PFC exposure concentration also led to lipid and DNA damage. PFC-induced oxidative toxicity was found to be correlated with the bioaccumulation potential of PFCs. Based on this relationship, QSAR models were established using the bioaccumulation factor (BAF) as the molecular descriptor for the first time. Compared with previous octanol-water partition coefficient-dependent QSAR models, the BAF-dependent QSAR model is more suitable for the impact assessment of PFCs and thus provides a more accurate description of the toxic behavior of these compounds.

The influence of SBR parameters on the sludge toxicity of synthetic wastewater containing bisphenol A

Synthetic wastewater with bisphenol A (BPA) concentrations of 7.5, 20, and 40 mg/L was treated with activated sludge sequential batch reactors (SBRs). The sludge acute toxicity indicated by the inhibitory ratio to luminous bacteria T3 was evaluated. The influent COD was controlled at approximately 300 mg/L, and aerobic conditions were maintained in the SBR. It was found that the process of BPA biodegradation, as opposed to BPA adsorption, contributed to the formation of sludge toxicity; there was a positive relationship between sludge toxicity and influent BPA concentration, and the toxicity centralized in intracellular regions and the intersection of extracellular polymeric substances (EPS) in sludge flocs. Since the BPA biodegradation process dedicated to sludge toxicity, the influence of key operational parameters such as sludge retention time (SRT) and hydraulic retention time (HRT) on sludge toxicity were investigated. It was founded that sludge toxicity decreased significantly when SRT and HRT were shortened from 20 to 10 days and 12 to 8 h, respectively. The results of Pearson correlation analysis indicated that the Shannon index H of the bacterial community correlated significantly to sludge toxicity. The results from both similarity analysis and UPGMA indicated that influent quality characteristic contributes much more to bacterial community than operation parameters, and then leads to difference between blank and control sludge toxicity.

Toxicity formation and distribution in activated sludge during treatment of N,N-dimethylformamide (DMF) wastewater

The organic toxicity of sludge in land applications is a critical issue; however, minimal attention has been given to the mechanism of toxicity formation during high-strength wastewater treatment. To investigate the relevant factors that contribute to sludge toxicity, synthetic wastewater with N,N-dimethylformamide (DMF) was treated in a sequential aerobic activated sludge reactor. The acute toxicity of sludge, which is characterised by the inhibition rate of luminous bacteria T3, is the focus of this study. Using an operational time of 28 days and a hydraulic retention time of 12h, the study demonstrated a positive relationship between the acute toxicity of sludge and the influent DMF concentration; the toxicity centralised in the intracellular and inner sections of extracellular polymeric substances (EPS) in sludge flocs. Due to increased concentrations of DMF, which ranged from 40 to 200mgL(-1), the sludge toxicity increased from 25 to 45%. The organic toxicity in sludge flocs was primarily contributed by the biodegradation of DMF rather than adsorption of DMF. Additional investigation revealed a significant correlation between the properties of the bacterial community and sludge toxicity.

Analysis of Ah receptor binding affinities of polybrominated diphenyl ethers via in silico molecular docking and 3D-QSAR

Polybrominated diphenyl ethers (PBDEs) have become ubiquitous contaminations due to their use as flame retardants. The structural similarity of PBDE to some dioxin-like compounds suggested that they may share similar toxicological effects: they might activate the aryl hydrocarbon receptor (AhR) signal transduction pathway and thus might have adverse effects on wildlife and humans. In this study, in silico computational workflow combining molecular docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) was performed to investigate the binding interactions between PBDEs and AhR and the structural features affecting the AhR binding affinity of PBDE. The molecular docking showed that hydrogen-bond and hydrophobic interactions were the major driving forces for the binding of ligands to AhR, and several key amino acid residues were also identified. The CoMSIA model was developed from the conformations obtained from molecular docking and exhibited satisfactory results as q (2) of 0.605 and r (2) of 0.996. Furthermore, the derived model had good robustness and statistical significance in both internal and external validations. The 3D contour maps generated from CoMSIA provided important structural features influence the binding affinity. The obtained results were beneficial to better understand the toxicological mechanism of PBDEs.

Exploring QSTR analysis of the toxicity of phenols and thiophenols using machine learning methods

There is an increasing need for the rapid safety assessment of chemicals by both industries and regulatory agencies throughout the world. In silico techniques are practical alternatives in the environmental hazard assessment. In this background, quantitative structure-toxicity relationship (QSTR) analysis has been performed on toxicity of phenols and thiophenols to Photobacterium phosphoreum. The techniques of classification and regression trees (CART) and least squares support vector regressions (LS-SVR) were applied successfully as variable selection and mapping tools, respectively. Four descriptors selected by the CART technique have been used as inputs of the LS-SVR for prediction of toxicities. The best model explains 91.8% leave-one-out predicted variance and 93.0% external predicted variance. The predictive performance of the CART-LS-SVR model was significantly better than the previous reported models based on CoMFA/CoMSIA and stepwise MLR techniques, suggesting that the present methodology may be useful to predict of toxicity, safety and risk assessment of chemicals.