QSPR/QSAR models for prediction of the physicochemical properties and biological activity of polybrominated diphenyl ethers

Molecular structural modeling and physical characteristics of anti-breast cancer drugs via some novel topological descriptors and regression models

Research is continuously being pursued to treat cancer patients and prevent the disease by developing new medicines. However, experimental drug design and development is a costly, time-consuming, and challenging process. Alternatively, computational and mathematical techniques play an important role in optimally achieving this goal. Among these mathematical techniques, topological indices (TIs) have many applications in the drugs used for the treatment of breast cancer. TIs can be utilized to forecast the effectiveness of drugs by providing molecular structure information and related properties of the drugs. In addition, these can assist in the design and discovery of new drugs by providing insights into the structure-property/structure-activity relationships. In this article, a Quantitative Structure Property Relationship (QSPR) analysis is carried out using some novel degree-based molecular descriptors and regression models to predict various properties (such as boiling point, melting point, enthalpy, flashpoint, molar refraction, molar volume, and polarizability) of 14 drugs used for the breast cancer treatment. The molecular structures of these drugs are topologically modeled through vertex and edge partitioning techniques of graph theory, and then linear regression models are developed to correlate the computed values with the experimental properties of the drugs to investigate the performance of TIs in predicting these properties. The results confirmed the potential of the considered topological indices as a tool for drug discovery and design in the field of breast cancer treatment.

Novel control strategies for the endocrine-disrupting effect of PAEs to pregnant women in traffic system

Traffic-related air pollution has become a global issue, and scientific regulation measures are urgently needed to reduce traffic pollution. Phthalates (PAEs) have been widely detected in the traffic environment; thus, they were chosen as target pollutants because of their endocrine-disrupting effects. The pathways of action and mechanisms of PAEs' endocrine-disrupting effects in pregnant women through inhalation were deduced. A novel whole-process 1C + 3D + 5R regulation system was developed to control the endocrine-disrupting effect of PAEs on pregnant women based on the cleaning production concept. (1) For source reduction, the 2D-QSAR model of endocrine-disrupting effects of PAEs in pregnant women was constructed to screen out the key influencing factors as hydrogen bond interaction and hydrophobic interaction. Based on this, a designed PAE substitute molecule with low volatility and endocrine-disrupting effects and no developmental toxicity was screened. The substitute molecule could reduce the volatilization amount of PAEs at the source by 41.76 %; (2) For process interception, selecting C-band UV light to eliminate PAEs molecules in the traffic environment can slow down 19.99 % of the endocrine-disrupting effect of PAEs molecules. The homology modeling method was used to design four kinds of green belt plant proteins with high PAEs absorption efficiency to absorb PAEs molecules in the traffic environment. Compared with the original green belt plant proteins, the absorption amount of PAEs increased by up to 96.08 %, and (3) For terminal prevention, dietary food schemes were designed to regulate PAEs' endocrine-disrupting effect on pregnant women. The optimal dietary food scheme was the simultaneous intake of glutamate, catechin and folic acid, which could reduce the adverse effect of PAEs on maternal and infants by 32.51 %. This study presents theoretical support for regulating PAE exposure to specific populations in the traffic environment and treating other pollutants in the future.

Prediction study on the distribution of polycyclic aromatic hydrocarbons and their halogenated derivatives in the atmospheric particulate phase

Polycyclic aromatic hydrocarbons (PAHs) and their halogenated derivatives (X-PAHs), which generally produced from photochemical and thermal reactions of parent PAHs, widely exist in the environment. They are semi-volatile organic chemicals (SVOCs) and the partitioning between gas/particulate phases affects their environmental migration, transformation and fate, which further impacts their toxicity and health risk to human. However, there is a large data missing of the experimental distribution ratio in the atmospheric particulate phase (f), especially for X-PAHs. In this study, we first checked the correlation between experimental f values of 53 PAH derivatives and their octanol-air partitioning coefficients (log K_OA), which is frequently used to characterize the distribution of chemicals in organic phase, and yielded R² = 0.803. Then, quantum chemical descriptors derived from molecular structural optimization by M06-2X/6-311 +G (d,p) method were further employed to develop Quantitative Structure-Property Relationship (QSPR) model. The model contains two descriptors, the average molecular polarizability (α) and the equilibrium parameter of molecular electrostatic potential (τ), and yields better performance with R² = 0.846 and RMSE = 0.122. The mechanism analysis and validation results by different strategies prove that the model can reveal the molecular properties that dominate the distribution between gas and particulate phases and it can be used to predict f values of other PAHs/X-PAHs, providing basic data for their environmental ecological risk assessment.

A new perspective on the modeling and topological characterization of H-Naphtalenic nanosheets with applications

In the past few years, two-dimensional (2D) layered nanomaterials have greatly attracted the scientific community. Among 2D nanomaterials, the porphyrin-based Naphtalenic nanosheets have been the subject of intense research due to their utilization in photo-dynamic therapy and nanodevices. New technologies based on nanomaterials or Naphtalenic nanosheet are advantageous in overcoming the problems in conventional drug delivery like poor solubility, toxicity and poor release pattern of drugs. In chemical network theory, various molecular descriptors are used to predict the chemical properties of molecules; these molecular descriptors are found to be very useful for Quantitative Structure-Activity/ Quantitative Structure-Property (QSAR/QSPR) relationship analysis in materials engineering, chemical and pharmaceutical industries. Researchers have computed the molecular descriptors for various nanostructures; however, despite intense research, the topology of nanostructures is not yet well understood. Specially, to our knowledge, the computation of topological indices for the line graph of subdivision graph of H-Naphtalenic nanosheet has not been discussed so far, which may open new perspectives for a more accurate and reliable topological characterization of this nanosheet.In this article, we employed some important degree-based topological indices to study the chemical structure of Naphtalenic nanosheet as a chemical network for QSAR/QSPR analysis. We have computed these degree-based topological indices for the line graph of subdivision graph of H-Naphtalenic nanosheet and derived formulas for them. Based on the derived formulas, numerical results are obtained and the physical and chemical properties of the under study nanosheet are investigated.

Reliable Prediction of the Octanol-Air Partition Ratio

The octanol-air equilibrium partition ratio (K_OA ) is frequently used to describe the volatility of organic chemicals, whereby n-octanol serves as a substitute for a variety of organic phases ranging from organic matter in atmospheric particles and soils, to biological tissues such as plant foliage, fat, blood, and milk, and to polymeric sorbents. Because measured K_OA values exist for just over 500 compounds, most of which are nonpolar halogenated aromatics, there is a need for tools that can reliably predict this parameter for a wide range of organic molecules, ideally at different temperatures. The ability of five techniques, specifically polyparameter linear free energy relationships (ppLFERs) with either experimental or predicted solute descriptors, EPISuite's KOAWIN, COSMOtherm, and OPERA, to predict the K_OA of organic substances, either at 25 °C or at any temperature, was assessed by comparison with all K_OA values measured to date. In addition, three different ppLFER equations for K_OA were evaluated, and a new modified equation is proposed. A technique's performance was quantified with the mean absolute error (MAE), the root mean square error (RMSE), and the estimated uncertainty of future predicted values, that is, the prediction interval. We also considered each model's applicability domain and accessibility. With an RMSE of 0.37 and a MAE of 0.23 for predictions of log K_OA at 25 °C and RMSE of 0.32 and MAE of 0.21 for predictions made at any temperature, the ppLFER equation using experimental solute descriptors predicted the K_OA the best. Even if solute descriptors must be predicted in the absence of experimental values, ppLFERs are the preferred method, also because they are easy to use and freely available. Environ Toxicol Chem 2021;40:3166-3180. © 2021 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Molecular Modifications and Control of Processes to Facilitate the Synergistic Degradation of Polybrominated Diphenyl Ethers in Soil by Plants and Microorganisms Based on Queuing Scoring Method

In this paper, a combination of modification of the source and regulation of the process was used to control the degradation of PBDEs by plants and microorganisms. First, the key proteins that can degrade PBDEs in plants and microorganisms were searched in the PDB (Protein Data Bank), and a molecular docking method was used to characterize the binding ability of PBDEs to two key proteins. Next, the synergistic binding ability of PBDEs to the two key proteins was evaluated based on the queuing integral method. Based on this, three groups of three-dimensional quantitative structure-activity relationship (3D-QSAR) models of plant-microbial synergistic degradation were constructed. A total of 30 PBDE derivatives were designed using BDE-3 as the template molecule. Among them, the effect on the synergistic degradation of six PBDE derivatives, including BDE-3-4, was significantly improved (increased by more than 20%) and the environment-friendly and functional evaluation parameters were improved. Subsequently, studies on the synergistic degradation of PBDEs and their derivatives by plants and microorganisms, based on the molecular docking method, found that the addition of lipophilic groups by modification is beneficial to enhance the efficiency of synergistic degradation of PBDEs by plants and microorganisms. Further, while docking PBDEs, the number of amino acids was increased and the binding bond length was decreased compared to the template molecules, i.e., PBDE derivatives could be naturally degraded more efficiently. Finally, molecular dynamics simulation by the Taguchi orthogonal experiment and a full factorial experimental design were used to simulate the effects of various regulatory schemes on the synergistic degradation of PBDEs by plants and microorganisms. It was found that optimal regulation occurred when the appropriate amount of carbon dioxide was supplied to the plant and microbial systems. This paper aims to provide theoretical support for enhancing the synergistic degradation of PBDEs by plants and microorganisms in e-waste dismantling sites and their surrounding polluted areas, as well as, realize the research and development of green alternatives to PBDE flame retardants.

Theoretical investigation of AhR binding property with relevant structural requirements for AhR-mediated toxicity of polybrominated diphenyl ethers

Polybrominated diphenyl ethers (PBDEs) are more frequently suspected with the induction of toxicity via signal transduction pathway of cytosolic aryl hydrocarbon receptor (AhR), the initial binding to which is assumed to be an essential prerequisite during the ligand-dependent activation. However, the AhR binding property and associated toxicity of PBDEs is yet to be clearly known for lacking insights into the structural requirements at molecular level. To understand the AhR binding property of PBDEs, the ligand binding domain (LBD) of AhR was simulatively developed on homologous protein after basic validation of geometrical rationality and the binding interaction profile was visually described using molecular docking approach. For AhR binding, the offset or edge-on π-π stackings with aromatic motifs including Phe289, Phe345 and His285 were shown to be structurally required whereas the electrostatic attraction validated for AhR binding to dioxins might be less effective for 2,2',3,4,4'-pentabromodiphenyl ether (BDE-85). Besides the demands of less steric hindrance from alanines and weak formulation of hydrogen bonds, the dispersion force through large contact and polarization of S-π electrons seemed to be impactful when BDE-85 were closer to Cys327, Met334 or Met342. With theoretical computation of AhR binding energies, the more significant correlativity with bioassays was derived especially for the lowly/moderately brominated congeners, and could be used to predict the AhR binding affinity on certain degree. The informative results would thus not only help well understand the molecular basis of AhR-mediated toxicity but give an approach for accelerative evaluation of AhR binding and toxicity of PBDEs.

Quantitative Structure-Property Relationship Approach in Formulation Development: an Overview

Chemoinformatics is emerging as a new trend to set drug discovery which correlates the relationship between structure and biological functions. The main aim of chemoinformatics refers to analyzing the similarity among molecules, searching the molecules in the structural database, finding potential drug molecule and their property. One of the key fields in chemoinformatics is quantitative structure-property relationship (QSPR), which is an alternative process to predict the various physicochemical and biopharmaceutical properties. This methodology expresses molecules via various numerical values or properties (descriptors), which encodes the structural characteristics of molecules and further used to calculate physicochemical properties of the molecule. The established QSPR model could be used to predict the properties of compounds that have been measured or even have been unknown, which ultimately accelerates the development process of a new molecule or the product. The formulation characteristics (drug release, transportability, bioavailability) can be predicted with the integration of QSPR approach. Therefore, QSPR modeling is an emerging trend to skip conventional drug as well as formulation development process. The current review highlights the overall process involved in the application of the QSPR approach in formulation development.

Releases of brominated flame retardants (BFRs) from microplastics in aqueous medium: Kinetics and molecular-size dependence of diffusion

Microplastics (<5 mm) are increasingly detected in aquatic environment, and the high levels of brominated flame retardants (BFRs) contained in them can potentially impact water quality. This study characterized the release kinetics of polybrominated diphenyl ethers (PBDEs) and 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE) from millimeter-sized microplastic pellets in water at environmentally relevant temperatures. Leaching rates of BFRs from the microplastic pellets made of acrylonitrile butadiene styrene (ABS) were found to be controlled by their diffusion within the plastic matrix, and their diffusion coefficients (D) in the plastic matrices ranged from 10^-28.30 to 10^-20.84 m² s^-1. The apparent activation energies of the BFRs' diffusion coefficients were estimated to be in the range of 64.1-131.8 kJ mol^-1 based on their temperature dependence and the Arrhenius equation. The diffusion coefficients of the BFRs decrease with their molecular diameters, while the activation energies for diffusion increase with the molecular diameters, which are indicative of significant steric hindrance for BFR diffusion within the plastic matrices. A semi-empirical linear relationship was observed between Log₁₀D and the glass transition temperature (T_g) of plastics, which allows prediction of the diffusion coefficients of BFRs in other types of microplastics commonly found in marine environment. The half-lives of BFR leaching (i.e., 50% depletion) from the microplastic pellets would range from tens of thousands to hundreds of billions of years at ambient temperatures if their physical and chemical structures could remain intact. Although the release fluxes of BFRs from microplastics are extremely low under the model conditions, a range of physical and chemical processes in the natural environment and the digestive systems of organisms that ingested them could potentially accelerate their leaching by causing breakdown and swelling of the plastic matrices.

Estimating subcooled liquid vapor pressures and octanol-air partition coefficients of polybrominated diphenyl ethers and their temperature dependence

Both subcooled liquid vapor pressure (P_L) and octanol-air partition coefficient (K_OA) are widely used as descriptors to predict gas-particle partitioning behavior of semi-volatile organic compounds (SVOCs), such as polybrominated diphenyl ethers (PBDEs). These two descriptors are functions of temperature, which are expressed as the Clausius-Clapeyron equations with the coefficients A_L and B_L for P_L (log P_L=A_L+B_L/T) and A_O and B_O for K_OA (log K_OA=A_O+B_O/T), where T is temperature in K. In this study, a simple equation to relate log K_OA and log P_L (log K_OA=-log P_L+6.46) was derived, which also links the coefficients of A_L &B_L and A_O &B_O. Regression analysis of published data of internal energy ΔU_OA for 22 PBDE congeners with their mole mass was made, leading a regression equation to calculate the internal energy for all 209 PBDE congeners. Three datasets of log K_OA at 25°C for all 209 PBDE congeners were evaluated; the one with the best match with experimentally measurements was selected. Using the datasets and equations described above, we calculated the values of Clausius-Clapeyron coefficients A_O &B_O and A_L &B_L for all 209 PBDE congeners at the following steps. First, B_O was computed using the values of ΔU_OA. Next, we calculated the values of A_O using the values of B_O and the values of log K_OA at 25°C. Finally, the values of the parameter A_L and B_L were determined for all 209 PBDE congeners. Results are in consistent with data available in the literature and the accuracy of the data were also evaluated. With these Clausius-Clapeyron coefficients, the values of P_L and K_OA at any environmentally relevant temperature can be calculated for all 209 PBDE congeners, and thus provides a quick reference for environmental monitoring and modeling of PBDEs.

Polybrominated diphenyl ethers (PBDEs) in background air around the Aegean: implications for phase partitioning and size distribution

The occurrence and atmospheric behavior of tri- to deca-polybrominated diphenyl ethers (PBDEs) were investigated during a 2-week campaign concurrently conducted in July 2012 at four background sites around the Aegean Sea. The study focused on the gas/particle (G/P) partitioning at three sites (Ag. Paraskevi/central Greece/suburban, Finokalia/southern Greece/remote coastal, and Urla/Turkey/rural coastal) and on the size distribution at two sites (Neochorouda/northern Greece/rural inland and Finokalia/southern Greece/remote coastal). The lowest mean total (G + P) concentrations of ∑₇PBDE (BDE-28, BDE-47, BDE-66, BDE-99, BDE-100, BDE-153, BDE-154) and BDE-209 (0.81 and 0.95 pg m^-3, respectively) were found at the remote site Finokalia. Partitioning coefficients, K _P, were calculated, and their linear relationships with ambient temperature and the physicochemical properties of the analyzed PBDE congeners, i.e., the subcooled liquid pressure (P _L°) and the octanol-air partition coefficient (K _OA), were investigated. The equilibrium adsorption (P _L°-based) and absorption (K _OA-based) models, as well as a steady-state absorption model including an equilibrium and a non-equilibrium term, both being functions of log K _OA, were used to predict the fraction Φ of PBDEs associated with the particle phase. The steady-state model proved to be superior to predict G/P partitioning of BDE-209. The distribution of particle-bound PBDEs across size fractions < 0.95, 0.95-1.5, 1.5-3.0, 3.0-7.2, and > 7.2 μm indicated a positive correlation between the mass median aerodynamic diameter and log P _L° for the less brominated congeners, whereas a negative correlation was observed for the high brominated congeners. The potential source regions of PBDEs were acknowledged as a combination of long-range transport with short-distance sources.

In silico investigation of gas/particle partitioning equilibrium of polybrominated diphenyl ethers (PBDEs)

Polybrominated diphenyl ethers (PBDEs), a group of typical brominated flame retardants (BFRs), have drawn an increasing concern due to their widespread manufacture, usage and disposal around the world and the frequent detection in a variety of environmental media. In the present study, we investigated the molecular mechanism of the partitioning equilibrium of PBDEs between gas and atmospheric particles, and developed a new temperature-dependent predictive model for the gas/particle partition coefficient (K_P) of these chemicals. Quantum chemical computations were implemented at B3LYP/6-31G (d,p) level of theory based on the neutral electronic ground state of PBDE congeners by Gaussian 09 software package. The model performance was assessed by different validation strategies and the application domain was defined by Williams Plot. Mechanism analysis indicated that the interactions of dispersion, electrostatic and hydrogen bond play crucial roles in the partitioning of PBDEs between the two phases. The developed model can be used to estimate the K_P values of PBDEs for which experimental measurements are restricted. Therefore, this work provides an alternative method in a regulatory context of PBDEs.

Effect analysis of quantum chemical descriptors and substituent characteristics on Henry's law constants of polybrominated diphenyl ethers at different temperatures

Twelve substituent descriptors, 17 quantum chemical descriptors and 1/T were selected to establish a quantitative structure-property relationship (QSPR) model of Henry's law constants for 7 polybrominated diphenyl ethers (PBDEs) at five different temperatures. Then, the lgH of 202 congeners at different temperatures were predicted. The variation rule and regulating mechanism of lgH was studied from the perspectives of both quantum chemical descriptors and substituent characteristics. The R² for modeling and testing sets of the final QSPR model are 0.977 and 0.979, respectively, thus indicating good fitness and predictive ability for Henry' law constants of PBDEs at different temperatures. The favorable hydrogen binding sites are the 5,5',6,6'-positions for high substituent congeners and the O atom of the ether bond for low substituent congeners, which affects the interaction between PBDEs and water molecules. lgH is negatively and linearly correlated with 1/T, and the variation trends of lgH with temperature are primarily regulated by individual substituent characteristics, wherein: the more substituents involved, the smaller the lgH. The significant sequence for the main effect of substituent positions is para>meta>ortho, where the ortho-positions are mainly involved in second-order interaction effect (64.01%). Having two substituents in the same ring also provides a significant effect, with 81.36% of second-order interaction effects, particularly where there is an adjacent distribution (55.02%).

Determination and prediction of octanol-air partition coefficients for organophosphate flame retardants

Organophosphate flame retardants (OPFRs) have attracted wide concerns due to their toxicities and ubiquitous occurrence in the environment. In this work, Octanol-air partition coefficient (K_OA) for 14 OPFRs including 4 halogenated alkyl-, 5 aryl- and 5 alkyl-OPFRs, were estimated as a function of temperature using a gas chromatographic retention time (GC-RT) method. Their log K_OA-GC values and internal energies of phase transfer (Δ_OAU/kJmol^-1) ranged from 8.03 to 13.0 and from 69.7 to 149, respectively. Substitution pattern and molar volume (V_M) were found to be capable of influencing log K_OA-GC values of OPFRs. The halogenated alkyl-OPFRs had higher log K_OA-GC values than aryl- or alkyl-OPFRs. The bigger the molar volume was, the greater the log K_OA-GC values increased. In addition, a predicted model of log K_OA-GC versus different relative retention times (RRTs) was developed with a high cross-validated value (Q²_(cum)) of 0.951, indicating a good predictive ability and stability. Therefore, the log K_OA-GC values of the remaining OPFRs can be predicted by using their RRTs on different GC columns.

The advancement of multidimensional QSAR for novel drug discovery - where are we headed?

INTRODUCTION

The Multidimensional quantitative structure-activity relationship (multidimensional-QSAR) method is one of the most popular computational methods employed to predict interesting biochemical properties of existing or hypothetical molecules. With continuous progress, the QSAR method has made remarkable success in various fields, such as medicinal chemistry, material science and predictive toxicology. Areas covered: In this review, the authors cover the basic elements of multidimensional -QSAR including model construction, validation and application. It includes and emphasizes the very recent developments of multidimensional -QSAR such as: HQSAR, G-QSAR, MIA-QSAR, multi-target QSAR. The advantages and disadvantages of each method are also discussed and typical examples of their application are detailed. Expert opinion: Although there are defects in multidimensional-QSAR modeling, it is still of enormous help to chemists, biologists and other researchers in various fields. In the authors' opinion, the latest more precise and feasible QSAR models should be further developed by integrating new descriptors, algorithms and other relevant computational techniques. Apart from being applied in traditional fields (e.g. lead optimization and predictive risk assessment), QSAR should be used more widely as a routine method in other emerging research fields including the modeling of nanoparticles(NPs), mixture toxicity and peptides.

A solvent free method of analysis to rapidly determine trace levels of ten medium and low brominated diphenyl ethers in soil pore water

A solvent free method to rapidly determine trace levels of ten brominated diphenyl ethers in soil pore water.

Kinetics of Brominated Flame Retardant (BFR) Releases from Granules of Waste Plastics

Plastic components of e-waste contain high levels of brominated flame retardants (BFRs), whose releases cause environmental and human health concerns. This study characterized the release kinetics of polybrominated diphenyl ethers (PBDEs) from millimeter-sized granules processed from the plastic exteriors of two scrap computer displays at environmentally relevant temperatures. The release rate of a substitute of PBDEs, 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE), from the waste plastics, was reported for the first time. Deca-BDE was the most abundant PBDE congeners in both materials (87-89%), while BTBPE was also present at relatively high contents. The release kinetics of BFRs could be modeled as one-dimensional diffusion, while the temperature dependence of diffusion coefficients was well described by the Arrhenius equation. The diffusion coefficients of BFRs (at 30 °C) in the plastic matrices were estimated to be in the range of 10^-27.16 to 10^-19.96 m²·s^-1, with apparent activation energies between 88.4 and 154.2 kJ·mol^-1. The half-lives of BFR releases (i.e., 50% depletion) from the plastic granules ranged from thousands to tens of billions of years at ambient temperatures. These findings suggest that BFRs are released very slowly from the matrices of waste plastics through molecular diffusion, while their emissions can be significantly enhanced with wear-and-tear and pulverization.

Identification of androgen receptor antagonists: In vitro investigation and classification methodology for flavonoid

A tremendous gap exists between the number of potential endocrine disrupting chemicals (EDCs) possibly in the environment and the limitation of traditional regulatory testing. In this study, the anti-androgenic potencies of 21 flavonoids were analyzed in vitro, and another 32 flavonoids from the literature were selected as additional chemicals. Molecular dynamic simulations were employed to obtain four different separation approaches based on the different behaviors of ligands and receptors during the process of interaction. Specifically, ligand-receptor complex which highlighted the discriminating features of ligand escape or retention via "mousetrap" mechanism, hydrogen bonds formed during simulation times, ligand stability and the stability of the helix-12 of the receptor were investigated. Together, a methodology was generated that 87.5% of flavonoids could be discriminated as active versus inactive antagonists, and over 90% inactive antagonists could be filtered out before QSAR study. This methodology could be used as a "proof of concept" to identify inactive anti-androgenic flavonoids, as well could be beneficial for rapid risk assessment and regulation of multiple new chemicals for androgenicity.

Atmospheric occurrence and gas-particle partitioning of PBDEs at industrial, urban and suburban sites of Thessaloniki, northern Greece: Implications for human health

Air samples were collected during the cold and the warm period of the year 2012 and 2013 at three sites in the major Thessaloniki area, northern Greece (urban-industrial, urban-traffic and urban-background) in order to evaluate the occurrence, profiles, seasonal variation and gas/particle partitioning of polybrominated diphenyl ethers (PBDEs). The mean total concentrations of particle phase ∑12PBDE in the cold season were 28.7, 19.5 and 3.87 pg m(-3) at the industrial, urban-traffic and urban-background site, respectively, dropping slightly in the warm season (23.7, 17.5 and 3.14 pg m(-3)), respectively. The corresponding levels of gas-phase ∑12PBDE were 14.4, 7.15 and 4.73 pg m(-3) in the cold season and 21.2, 11.1 and 6.27 pg m(-3) in the warm season, respectively. In all samples, BDE-47 and BDE-99 were the dominant congeners. Absorption of PBDEs in the organic matter of particles appeared to drive their gas/particle partitioning, particularly in the cold season. The estimated average outdoor workday inhalation exposure to ∑12PBDE in the cold and the warm period followed the order: industrial site (288 and 299 pg day(-1)) > urban-traffic site (178 and 191 pg day(-1)) > urban-background site (58 and 63 pg day(-1)). The exposures to BDE-47, BDE-99, BDE-153 and ∑3PBDE via inhalation, for children outdoor worker and seniors were several orders of magnitude lower than their corresponding oral RfD values.

Modification of PBDEs (BDE-15, BDE-47, BDE-85 and BDE-126) biological toxicity, bio-concentration, persistence and atmospheric long-range transport potential based on the pharmacophore modeling assistant with the full factor experimental design

In this study, the properties of AhR binding affinity, bio-concentration factor, half-life and vapor pressure were selected as the typical indicators of biological toxicity, bio-concentration, persistence and atmospheric long-range transport potential for polybrominated diphenyl ethers (PBDEs), respectively. A three-dimensional pharmacophore modeling assistant with a full factor experimental design for each property was used to reveal the significant pharmacophore features and the substituent effects to obtain reasonable modified schemes for the selected target PBDEs. Finally, the performances of the persistent organic pollutant (POP) properties, the synthesis feasibility and the fire resistance of the modified compounds were evaluated. The most influential pharmacophore feature for all POP properties was the hydrophobic group, especially the vinyl and propyl groups. Modified compounds with two additional hydrophobic groups exhibited a better regulatory performance. The average reduction in the proportions of the four POP properties for the modified compounds (except for 3-phenyl-BDE-15) was 70.60%, 52.44%, 47.04% and 70.88%. In addition, the energy and the C-Br bond dissociation enthalpy of the four typical PBDEs were higher than those of the modified compounds (except for 3-phenyl-BDE-15), indicating the synthesis feasibility and the lower energy barrier of the modified compounds to release Br free radicals to provide fire resistance.

Estimation of melting points of large set of persistent organic pollutants utilizing QSPR approach

The presence of polyhalogenated persistent organic pollutants (POPs), such as Cl/Br-substituted benzenes, biphenyls, diphenyl ethers, and naphthalenes has been identified in all environmental compartments. The exposure to these compounds can pose potential risk not only for ecological systems, but also for human health. Therefore, efficient tools for comprehensive environmental risk assessment for POPs are required. Among the factors vital for environmental transport and fate processes is melting point of a compound. In this study, we estimated the melting points of a large group (1419 compounds) of chloro- and bromo- derivatives of dibenzo-p-dioxins, dibenzofurans, biphenyls, naphthalenes, diphenylethers, and benzenes by utilizing quantitative structure-property relationship (QSPR) techniques. The compounds were classified by applying structure-based clustering methods followed by GA-PLS modeling. In addition, random forest method has been applied to develop more general models. Factors responsible for melting point behavior and predictive ability of each method were discussed.

Prediction of the Fate of Organic Compounds in the Environment From Their Molecular Properties: A Review

A comprehensive review of quantitative structure-activity relationships (QSAR) allowing the prediction of the fate of organic compounds in the environment from their molecular properties was done. The considered processes were water dissolution, dissociation, volatilization, retention on soils and sediments (mainly adsorption and desorption), degradation (biotic and abiotic), and absorption by plants. A total of 790 equations involving 686 structural molecular descriptors are reported to estimate 90 environmental parameters related to these processes. A significant number of equations was found for dissociation process (pKa), water dissolution or hydrophobic behavior (especially through the KOW parameter), adsorption to soils and biodegradation. A lack of QSAR was observed to estimate desorption or potential of transfer to water. Among the 686 molecular descriptors, five were found to be dominant in the 790 collected equations and the most generic ones: four quantum-chemical descriptors, the energy of the highest occupied molecular orbital (EHOMO) and the energy of the lowest unoccupied molecular orbital (ELUMO), polarizability (α) and dipole moment (μ), and one constitutional descriptor, the molecular weight. Keeping in mind that the combination of descriptors belonging to different categories (constitutional, topological, quantum-chemical) led to improve QSAR performances, these descriptors should be considered for the development of new QSAR, for further predictions of environmental parameters. This review also allows finding of the relevant QSAR equations to predict the fate of a wide diversity of compounds in the environment.

QSPR study on the octanol/air partition coefficient of polybrominated diphenyl ethers by using molecular distance-edge vector index

BACKGROUND

The quantitative structure property relationship (QSPR) for octanol/air partition coefficient (K OA) of polybrominated diphenyl ethers (PBDEs) was investigated. Molecular distance-edge vector (MDEV) index was used as the structural descriptor of PBDEs. The quantitative relationship between the MDEV index and the lgK OA of PBDEs was modeled by multivariate linear regression (MLR) and artificial neural network (ANN) respectively. Leave one out cross validation and external validation was carried out to assess the predictive ability of the developed models. The investigated 22 PBDEs were randomly split into two groups: Group I, which comprises 16 PBDEs, and Group II, which comprises 6 PBDEs.

RESULTS

The MLR model and the ANN model for predicting the K OA of PBDEs were established. For the MLR model, the prediction root mean square relative error (RMSRE) of leave one out cross validation and external validation is 2.82 and 2.95, respectively. For the L-ANN model, the prediction RMSRE of leave one out cross validation and external validation is 2.55 and 2.69, respectively.

CONCLUSION

The developed MLR and ANN model are practicable and easy-to-use for predicting the K OA of PBDEs. The MDEV index of PBDEs is shown to be quantitatively related to the K OA of PBDEs. MLR and ANN are both practicable for modeling the quantitative relationship between the MDEV index and the K OA of PBDEs. The prediction accuracy of the ANN model is slightly higher than that of the MLR model. The obtained ANN model shoud be a more promising model for studying the octanol/air partition behavior of PBDEs.

Predicting reductive debromination of polybrominated diphenyl ethers by nanoscale zerovalent iron and its implications for environmental risk assessment

The reductive debromination of polybrominated diphenyl ethers (PBDEs) by nanoscale zerovalent iron (nZVI) has proven to be a successful remediation approach. This study simulates the congener profiles and overall ecotoxicological impact of PBDE debromination by nZVI. The relationship between the calculated redox potential values and PBDE debromination rates was sufficiently strong to generate a satisfactory predictive capacity, which was further used to develop a quantitative structure-activity relationship (QSAR) model for the determination of the PBDE debromination patterns and dominant pathways. The predicted results of deca-BDE debromination showed that it would completely disappear within 30 days, but its lower brominated products, particularly tri- to penta-homologues, could exist in the environment even after 5 years. Formation and accumulation of more toxic, low brominated congeners through deca-BDE debromination suggest that deca-BDE may pose prolonged environmental risks. Changes in the toxic equivalent (TEQ) values during deca-BDE debromination parallel the occurrence and transformation of specific low brominated congeners with dioxin-like potency.

Filling the gap: estimating physicochemical properties of the full array of polybrominated diphenyl ethers (PBDEs)

Physicochemical properties of PBDE congeners are important for modeling their transport, but data are often missing. The quantitative structure-property relationship (QSPR) approach is utilized to fill this gap. Individual research groups often report piecemeal properties through experimental measurements or estimation techniques, but these data seldom satisfy fundamental thermodynamic relationships because of errors. The data then lack internal consistency and cannot be used directly in environmental modeling. This paper critically reviews published experimental data to select the best QSPR models, which are then extended to all 209 PBDE congeners. Properties include aqueous solubility, vapor pressure, Henry's law constant, octanol-water partition coefficient and octanol-air partition coefficient. Their values are next adjusted to satisfy fundamental thermodynamic equations. The resulting values then take advantage of all measurements and provide quick references for modeling and PBDE-contaminated site assessment and remediation. PCBs are also compared with respect to their properties and estimation methods.

Predicting network of drug-enzyme interaction based on machine learning method

It is important to correctly and efficiently map drugs and enzymes to their possible interaction network in modern drug research. In this work, a novel approach was introduced to encode drug and enzyme molecules with physicochemical molecular descriptors and pseudo amino acid composition, respectively. Based on this encoding method, Random Forest was adopted to build the drug-enzyme interaction network. After selecting the optimal features that are able to represent the main factors of drug-enzyme interaction in our prediction, a total of 129 features were attained which can be clustered into nine categories: Elemental Analysis, Geometry, Chemistry, Amino Acid Composition, Secondary Structure, Polarity, Molecular Volume, Codon Diversity and Electrostatic Charge. It is further found that Geometry features were the most important of all the features. As a result, our predicting model achieved an MCC of 0.915 and a sensitivity of 87.9% at the specificity level of 99.8% for 10-fold cross-validation test, and achieved an MCC of 0.895 and a sensitivity of 95.7% at the specificity level of 95.4% for independent set test. This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology & Clinical Implications. Guest Editor: Yudong Cai.

Background levels of polybrominated diphenyl ethers (PBDEs) in soils from Mount Meru area, Arusha district (Tanzania)

This study investigates the contamination by 13 polybrominated diphenyl ether (PBDE) congeners in an altitudinal soil transect on Mt. Meru area, Northern Tanzania. A ∑13PBDEs mean concentration of 386±200 pg/g d.w. (4900±3500 pg ∑13PBDEs/g soil organic matter - SOM) was measured, pointing out that, in a prevalently agricultural area from the southern hemisphere, PBDE contamination can be even higher than in similar semi-remote environment of industrialized country of the northern one. The Mt. Meru PBDE pattern of contamination was characterized by the prevalence of intermediate brominated congeners (tetra- and penta-BDEs). Among the detected compounds, BDE-47 was the main congener, followed by BDE-99, BDE-190 and BDE-100. The distribution of PBDEs confirmed that organic carbon had a substantial impact on their accumulation in Tanzanian soils. The altitudinal profile of PBDEs (log TOC-normalized concentrations) fitted a second order polynomial model with altitude, with an initial concentration decrease, interpreted as a dilution effect from local/regional sources, and a following consistent increase with altitude according to the cold condensation theory. Evidences of distillation effect among PBDE congeners were also observed.

QSPR modeling of n-octanol/air partition coefficients and liquid vapor pressures of polychlorinated dibenzo-p-dioxins

The molecular geometries of 75 polychlorinated dibenzo-p-dioxins (PCDDs) were optimized using B3LYP/6-31G(*) method. The calculated structural parameters were taken as theoretical descriptors to establish two new novel QSPR models for n-octanol/air partition coefficients (log K(OA)) and subcooled liquid vapor pressure (log P(L)) of PCDDs. The R(2) values of the two models are 0.983 and 0.985 respectively. Their standard deviations of prediction in modeling (SD) are 0.174 and 0.230 respectively. The results of leave-one-out (LOO) cross-validation for training set show that the two models exhibited optimum stability and good predictive power.

Size-dependent dry deposition of airborne polybrominated diphenyl ethers in urban Guangzhou, China

Gaseous and size-segregated particulate PBDEs (specifically BDE-47, -99, -183, -207, and -209) in the air were measured in urban Guangzhou at 100 and 150 m above the ground in daytime and at night in August and December 2010, to assess dry deposition of these contaminants accurately with regards to influences of meteorological factors but without confounding surface effects. Particulate PBDEs were more abundant at night than in daytime, and slightly higher in winter than in summer, likely from varying meteorological conditions and atmospheric boundary layers. More than 60% of particulate-phase PBDEs was contained in particles with an aerodynamic diameter (D(p)) below 1.8 μm, indicating long-range transport potential. The average daily particle dry deposition fluxes of PBDEs in August ranged from 2.6 (BDE-47) to 88.6 (BDE-209) ng m(-2) d(-1), while those in winter ranged from 2.0 (BDE-47) to 122 (BDE-209) ng m(-2) d(-1). Deposition fluxes of all PBDE congeners were significantly higher in daytime than at night for both months, due to the effect of diurnal variability of meteorological factors. In addition, mean overall particle deposition velocities of individual BDE congeners ranged from 0.11 to 0.28 cm s(-1). These values were within a factor of 2 of assumed values previously used in southern China and the Laurentian Great Lakes, suggesting that such assumptions were reasonable for sites with similar particulate size distributions and PBDE sources. Dry deposition velocities of PBDEs were lower at night than those in the daytime, probably reflecting higher mechanical and thermal turbulence during daytime. Dry deposition of particulate-bound PBDEs is influenced by short-term temporal variability from meteorological factors, and also by particulate size fractions.

Estimation of the physicochemical properties of PCDD/Fs using three-dimensional holographic vector of atomic interaction field

Polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) are a group of important persistent organic pollutants. In the present study, the three-dimensional holographic vector of atomic interaction field (3D-HoVAIF) method is used to describe the chemical structures of PCDD/Fs. After variable screening using a stepwise multiple regression (SMR) technique, the linear relationships among six physicochemical properties of PCDD/Fs and 3D-HoVAIF descriptors are built using a partial least-squares (PLS) regression model. The results show that the 3D-HoVAIF descriptors can be used to express the quantitative structure-property relationships of PCDD/Fs. The predictive capabilities of the models have also been confirmed by leave-one-out cross-validation. The optimum model has been used to estimate values for PCDD/Fs for which no experimental data on physicochemical properties are available. Supplemental materials are available for this article. Go to the publisher's online edition of Journal of Environmental Science and Health: Part A to view the free supplemental file.

Predictive insight into the relationship between AhR binding property and toxicity of polybrominated diphenyl ethers by PLS-derived QSAR

Polybrominated diphenyl ethers (PBDEs) are experimentally indicated to be capable of binding to the cytosolic aryl hydrocarbon receptor (AhR) and show a weak or moderate toxicity. However, little is yet known about the AhR-mediated toxicology. To fully evaluate the structural effects of PBDE ligand on AhR binding affinity and toxicity, quantitative structure-activity relationships (QSARs) were developed by PLS analysis. In this study, a simple but potent QSAR that was qualified with much better or comparable performance of prediction was optimally established for PBDE toxicity. With QSAR analysis, the AhR binding property was carefully described to reflect the origin of AhR binding affinity. Besides the effects from topological characters, the dispersion and electrostatic interactions were of indispensability for AhR binding affinity whereas the dispersion was further suggested to be dominant. The structural requirement for AhR binding affinity and toxicity was also investigated. As was similarly observed for polychlorinated biphenyls (PCBs), the preferential bromination at para- and meta (particularly 3,3'-)-sites was confirmed as a key determinant to improve the AhR binding affinity and the toxicity of PBDEs.

QSAR classification models for the prediction of endocrine disrupting activity of brominated flame retardants

The identification of potential endocrine disrupting (ED) chemicals is an important task for the scientific community due to their diffusion in the environment; the production and use of such compounds will be strictly regulated through the authorization process of the REACH regulation. To overcome the problem of insufficient experimental data, the quantitative structure-activity relationship (QSAR) approach is applied to predict the ED activity of new chemicals. In the present study QSAR classification models are developed, according to the OECD principles, to predict the ED potency for a class of emerging ubiquitary pollutants, viz. brominated flame retardants (BFRs). Different endpoints related to ED activity (i.e. aryl hydrocarbon receptor agonism and antagonism, estrogen receptor agonism and antagonism, androgen and progesterone receptor antagonism, T4-TTR competition, E2SULT inhibition) are modeled using the k-NN classification method. The best models are selected by maximizing the sensitivity and external predictive ability. We propose simple QSARs (based on few descriptors) characterized by internal stability, good predictive power and with a verified applicability domain. These models are simple tools that are applicable to screen BFRs in relation to their ED activity, and also to design safer alternatives, in agreement with the requirements of REACH regulation at the authorization step.

Improved 3D-QSAR analyzes for the predictive toxicology of polybrominated diphenyl ethers with CoMFA/CoMSIA and DFT

With the popular methods of CoMFA and CoMSIA, three-dimensional quantitative structure-activity relationships (QSARs) were newly developed for the toxicity of polybrominated diphenyl ethers (PBDEs). The choice of optimized geometries by density functional theory (DFT) as molecular template and the RMSD-based molecular alignment strategy might mostly contribute to the QSAR improvement, which was highlighted specifically by the increased q2 of 0.870 for CoMFA, 0.887 for CoMSIA, respectively. QSARs analyzes indicated that the steric effects from ortho- and meta-substitution and the correlated hydrophobicities have the greatest impact on the binding affinities of aryl hydrocarbon receptor (AhR) to PBDEs. Though the effects of electrostatics were comparatively inferior in the AhR binding, the aromatic interaction and possible charge transfer proved to be indispensable for toxicity mediation. Consistent with that proposed previously for other structurally similar compounds, such as dioxins and polychlorinated biphenyls, the predictive toxicology was helpful to understand the congener-specificity of toxicity of PBDEs.

QSAR modeling and prediction of the endocrine-disrupting potencies of brominated flame retardants

In the European Union REACH regulation, the chemicals with particularly harmful behaviors, such as endocrine disruptors (EDs), are subject to authorization, and the identification of safer alternatives to these chemicals is required. In this context, the use of quantitative structure-activity relationships (QSAR) becomes particularly useful to fill the data gap due to the very small number of experimental data available to characterize the environmental and toxicological profiles of new and emerging pollutants with ED behavior such as brominated flame retardants (BFRs). In this study, different QSAR models were developed on different responses of endocrine disruption measured for several BFRs. The multiple linear regression approach was applied to a variety of theoretical molecular descriptors, and the best models, which were identified from all of the possible combinations of the structural variables, were internally validated for their performance using the leave-one-out (Q(LOO)(2) = 73-91%) procedure and scrambling of the responses. External validation was provided, when possible, by splitting the data sets in training and test sets (range of Q(EXT)(2) = 76-90%), which confirmed the predictive ability of the proposed equations. These models, which were developed according to the principles defined by the Organization for Economic Co-operation and Development to improve the regulatory acceptance of QSARs, represent a simple tool for the screening and characterization of BFRs.

Persistence of polybrominated diphenyl ethers in agricultural soils after biosolids applications

This study examines polybrominated diphenyl ethers (PBDE) levels, trends in biosolids from a wastewater treatment plant, and evaluates potential factors governing PBDE concentrations and the fate in agricultural soils fertilized by biosolids. The mean concentration of the most abundant PBDE congeners in biosolids ( summation operatorBDE-47, BDE-99, and BDE-209) generated by one wastewater treatment plant was 1250 +/- 134 microg/kg d.w. with no significant change in concentration over 32 months (n = 15). In surface soil samples from the Mid-Atlantic region, average PBDE concentrations in soil from fields receiving no biosolids (5.01 +/- 3.01 microg/kg d.w.) were 3 times lower than fields receiving one application (15.2 +/- 10.2 microg/kg d.w.) and 10 times lower than fields that had received multiple applications (53.0 +/- 41.7 microg/kg d.w.). The cumulative biosolids application rate and soil organic carbon were correlated with concentrations and persistence of PBDEs in soil. A model to predict PBDE concentrations in soil after single or multiple biosolids applications provides estimates which fall within a factor of 2 of observed values.

Do trans-Pacific air masses deliver PBDEs to coastal British Columbia, Canada?

In order to distinguish between 'local' and 'background' sources of polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in coastal British Columbia (Canada) air, we collected samples from two sites: a remote site on western Vancouver Island, and a near-urban site in the Strait of Georgia. Seasonally-integrated samples of vapor, particulate, and rain were collected continuously during 365 days for analysis of 275 PCB and PBDE congeners. While deposition of the legacy PCBs was similar at both sampling sites, deposition of PBDEs at the remote site amounted to 42% (10.4 mg/ha/year) of that at the near-urban site. Additional research into atmospheric circulation in the NE Pacific Ocean will provide more insight into the transport and fate of priority pollutants in this region, but trans-Pacific delivery of PBDEs to the west coast of North America may underlie in part our observations. For example, approximately 40% of >12,000 ten-day back trajectories calculated for the remote site originated over Asia, compared to only 2% over North America.

Mathematical explanation for the non-linear hydrophobicity-dependent bioconcentration processes of persistent organic pollutants in phytoplankton

Phytoplankton play a vital role in determining the fate and transport of persistent organic pollutants (POPs) in aquatic ecosystems. Lipids in phytoplankton cells can accumulate POPs, and equilibrium partitioning of the chemicals between lipids and water can be deduced from the octanol/water partition coefficient (K(ow)). However, there is much uncertainty in the response of the bioconcentration factor (BCF) to K(ow). While distinct level-off and bell-shaped responses of BCF to K(ow) have been confirmed by laboratory experiments, a mathematical basis for the non-linear processes has been lacking. Using two differential equation models (Water-Phytoplankton and Water-Phytoplankton-Dissolved Organic Carbon) we here examine previously reported non-linearity between BCF and K(ow). Our modelling studies suggest that a level-off response of the true BCF (BCF estimated at equilibrium) to K(ow) could be attributed to the presence of dissolved organic carbon (DOC). The alternative bell-shaped response appears to be a consequence of the apparent BCF (BCF estimated at non-equilibrium) for which the slow uptake rate of chemical compounds of relatively large molecular mass by phytoplankton is responsible.

Fate of polybrominated diphenyl ethers in the environment of the Pearl River Estuary, South China

Ninety-six riverine runoff samples collected at eight major outlets in the Pearl River Delta (PRD), South China, during 2005-2006 were analyzed for 17 brominated diphenyl ether (BDE) congeners (defined as Sigma17PBDE). Fourteen and 15 congeners were detected, respectively, in the dissolved and particulate phases. These data were further used to elucidate the partitioning behavior of BDE congeners in riverine runoff. Several related fate processes, i.e. air-water exchange, dry and wet deposition, degradation, and sedimentation, within the Pearl River Estuary (PRE), were examined to estimate the inputs of Sigma10PBDE (sum of the target BDE congeners, BDE-28, -47, -66, -85, -99, -100, -138, -153, -154, and -183) and BDE-209 from the PRD to the coastal ocean based on mass balance considerations. The results showed that annual outflows of Sigma10PBDE and BDE-209 were estimated at 126 and 940 kg/year, respectively from the PRE to coastal ocean. Besides sedimentation and degradation, the majority of Sigma10PBDE and BDE-209 discharged into the PRE via riverine runoff was transported to the coastal ocean.

Anti-androgen activity of polybrominated diphenyl ethers determined by comparative molecular similarity indices and molecular docking

Some polybrominated diphenyl ethers (PBDEs) may have endocrine-disrupting (ED) potencies. In this study, molecular docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) were performed to explore the possible anti-androgenicity of PBDEs. Based on the alignment generated by docking conformations, a highly predictive comparative molecular similarity indices analysis (CoMSIA) model was developed with q(2) value of 0.642 and r(2) value of 0.973. The contributions of the steric, electrostatic, hydrophobic fields to the CoMSIA model are 13.1%, 61.0% and 25.9%, respectively. Br substitutions which are at meta and para positions of PBDEs will be unfavorable for androgen receptor (AR) antagonism and ortho Br substitutions for PBDEs are favorable for anti-androgen activity. Mapping the 3D-QSAR models to the active site of the AR provides new insight into the AR-PBDEs interaction. CoMSIA field contributions showed good consistency with structural features of the AR binding site and can be used to predict anti-androgen activities of other PBDE congeners.