scholarly journals Potential Environmental Risk Characteristics of PCB Transformation Products in the Environmental Medium

Toxics ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 213
Author(s):  
Minghao Li ◽  
Wei He ◽  
Hao Yang ◽  
Shimei Sun ◽  
Yu Li
Keyword(s):  
Environmental Risk ◽  
Polychlorinated Biphenyl ◽  
Degradation Products ◽  
Organic Pollutant ◽  
Environmentally Friendly ◽  
3D Qsar ◽  
Transformation Products ◽  
Qsar Model ◽  
Environmental Risks ◽  
Environmental Media

The complementary construction of polychlorinated biphenyl (PCB) phytotoxicity and the biotoxicity 3D-QSAR model, combined with the constructed PCB environmental risk characterization model, was carried out to evaluate the persistent organic pollutant (POP) properties (toxicity (phytotoxicity and biotoxicity), bioconcentration, migration, and persistence) of PCBs and their corresponding transformation products (phytodegradation, microbial degradation, biometabolism, and photodegradation). The transformation path with a significant increase in environmental risks was analyzed. Some environmentally friendly PCB derivatives, exhibiting a good modification effect, and their parent molecules were selected as precursor molecules. Their transformation processes were simulated and evaluated for assessing the environmental risks. Some transformation products displayed increased environmental risks. The environmental risks of plant degradation products of the PCBs in the environmental media showed the maximum risk, indicating that the potential risks of the transformation products of the PCBs and their environmentally friendly derivatives could not be neglected. It is essential to further improve the ability of plants to degrade their transformation products. The improvement of some degradation products for environmentally friendly PCB derivatives indicates that the theoretical modification of a single environmental feature cannot completely control the potential environmental risks of molecules. In addition, this method can be used to analyze and evaluate environmentally friendly PCB derivatives to avoid and reduce the potential environmental and human health risks caused by environmentally friendly PCB derivatives.

scholarly journals Environmentally Friendly Quinolones Design for a Two-Way Choice between Biotoxicity and Genotoxicity through Double-Activity 3D-QSAR Model Coupled with the Variation Weighting Method

2020 ◽  
Vol 17 (24) ◽  
pp. 9398
Author(s):  
Peixuan Sun ◽  
Yuanyuan Zhao ◽  
Luze Yang ◽  
Zhixing Ren ◽  
Wenjin Zhao
Keyword(s):  
Molecular Dynamics ◽  
Structural Parameters ◽  
Environmentally Friendly ◽  
3D Qsar ◽  
Qsar Model ◽  
Binding Energies ◽  
Combined Toxicity ◽  
Weighting Method ◽  
Environmental Friendliness ◽  
Before And After

Quinolone (QN) antibiotics are widely used, which lead to their accumulation in soil and toxic effects on ryegrass in pasture. In this study, we employed ryegrass as the research object and selected the total scores of 29 QN molecules docked with two resistant enzyme structures, superoxide dismutase (SOD, PDB ID: 1B06) and proline (Pro, PPEP-2, PDB ID: 6FPC), as dependent variables. The structural parameters of QNs were used as independent variables to construct a QN double-activity 3D-QSAR model for determining the biotoxicity on ryegrass by employing the variation weighting method. This model was constructed to determine modification sites and groups for designing QNs molecules. According to the 3D contour map of the model, by considering enrofloxacin (ENR) and sparfloxacin (SPA) as examples, 23 QN derivatives with low biotoxicity were designed, respectively. The functional properties and environmental friendliness of the QN derivatives were predicted through a two-way selection between biotoxicity and genotoxicity before and after modification; four environmentally friendly derivatives with low biotoxicity and high genotoxicity were screened out. Mixed toxicity index and molecular dynamics methods were used to verify the combined toxicity mechanism of QNs on ryegrass before and after modification. By simulating the combined pollution of ENR and its derivatives in different soils (farmland, garden, and woodland), the types of combined toxicity were determined as partial additive and synergistic. Binding energies were calculated using molecular dynamics. The designed QN derivatives with low biotoxicity, high genotoxicity, and environmental friendliness can highly reduce the combined toxicity on ryegrass and can be used as theoretic reserves to replace QN antibiotics.

scholarly journals Biological enrichment prediction of polychlorinated biphenyls and novel molecular design based on 3D-QSAR/HQSAR associated with molecule docking

2019 ◽  
Vol 39 (5) ◽  
Author(s):  
Jiawen Yang ◽  
Wenwen Gu ◽  
Yu Li
Keyword(s):  
Partition Coefficients ◽  
Polychlorinated Biphenyl ◽  
Molecular Design ◽  
3D Qsar ◽  
Qsar Model ◽  
Quantitative Structure Activity Relationship ◽  
Field Analysis ◽  
Similarity Indices ◽  
Qsar Models ◽  
Molecule Docking

Abstract Based on the experimental data of octanol-water partition coefficients (Kow, represents bioaccumulation) for 13 polychlorinated biphenyl (PCB) congeners, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to establish 3D-QSAR models, combined with the hologram quantitative structure–activity relationship (HQSAR), the substitution sites (mono-substituted and bis-substituted) and substituent groups (electron-withdrawing hydrophobic groups) that significantly affect the octanol-water partition coefficients values of PCBs were identified, a total of 63 monosubstituted and bis-substituted were identified. Compared with using 3D-QSAR model alone, the coupling of 3D-QSAR and HQSAR models greatly increased the number of newly designed bis-substituted molecules, and the logKow reduction in newly designed bis-substituted molecules was larger than that of monosubstituted molecules. This was established to predict the Kow values of 196 additional PCBs and carry out a modification of target molecular PCB-207 to lower its Kow (biological enrichment) significantly, simultaneously maintaining the flame retardancy and insulativity after calculation by using Gaussian09. Simultaneously, molecular docking could further screen out three more environmental friendly low biological enrichment newly designed PCB-207 molecules (5-methyl-PCB-207, 5-amino-PCB-207, and 4-amino-5-ethyl-PCB-207).

scholarly journals Integration of Fuzzy Matter-Element Method and 3D-QSAR Model for Generation of Environmentally Friendly Quinolone Derivatives

2020 ◽  
Vol 17 (9) ◽  
pp. 3239
Author(s):  
Xixi Li ◽  
Baiyu Zhang ◽  
Wendy Huang ◽  
Cuirin Cantwell ◽  
Bing Chen
Keyword(s):  
Density Functional ◽  
Molecular Design ◽  
Environmentally Friendly ◽  
3D Qsar ◽  
Qsar Model ◽  
Spectral Intensity ◽  
Field Analysis ◽  
Genetic Toxicity ◽  
Quinolone Derivatives ◽  
Element Method

The environmental pollution of quinolone antibiotics (QAs) has caused rising public concern due to their widespread usage. In this study, Gaussian 09 software was used to obtain the infrared spectral intensity (IRI) and ultraviolet spectral intensity (UVI) of 24 QAs based on the Density Functional Theory (DFT). Rather than using two single-factor inputs, a fuzzy matter-element method was selected to calculate the combined effects of infrared and ultraviolet spectra (CI). The Comparative Molecular Field Analysis (CoMFA) was then used to construct a three-dimensional quantitative structure–activity relationship (3D-QSAR) with QAs’ molecular structure as the independent variable and CI as the dependent variable. Using marbofloxacin and levofloxacin as target molecules, the molecular design of 87 QA derivatives was carried out. The developed models were further used to determine the stability, functionality (genetic toxicity), and the environmental effects (bioaccumulation, biodegradability) of these designed QA derivatives. Results indicated that all QA derivatives are stable in the environment with their IRI, UVI, and CI enhanced. Meanwhile, the genetic toxicity of the 87 QA derivatives increased by varying degrees (0.24%–29.01%), among which the bioaccumulation and biodegradability of 43 QA derivatives were within the acceptable range. Through integration of fuzzy matter-element method and 3D-QSAR, this study advanced the QAs research with the enhanced CI and helped to generate the proposed environmentally friendly quinolone derivatives so as to aid the management of this class of antibiotics.

scholarly journals Theoretical Design and Process Control of Neonicotinoids Insecticides Suitable for Synergistic Degradation of Rhizobia and Carbon-fixing Bacteria in Soil

2021 ◽  
Author(s):  
Zhengyang Deng ◽  
Zhixing Ren ◽  
Shuhai Sun ◽  
Yujun Wang
Keyword(s):  
Evaluation Method ◽  
Comprehensive Evaluation ◽  
Orthogonal Experiment ◽  
Environmentally Friendly ◽  
3D Qsar ◽  
Qsar Model ◽  
Binding Ability ◽  
Comprehensive Evaluation Method ◽  
Contour Maps ◽  
Synergistic Degradation

Abstract This study studied and developed the modification schemes of environmentally friendly substitutes of NNIs along with the regulatory measures that effectively enhanced the synergistic degradation of NNIs by soil rhizobia and carbon-fixing bacteria. Firstly, the binding ability of NNIs to the two key proteins was characterized by molecular docking; Secondly, the mean square deviation decision method, which is a comprehensive evaluation method was used to investigate the binding ability of NNI molecules with the two Rubisco rate-limiting enzymes. The 3D-QSAR model was established for the synergistic degradation and single effect of rhizobia and carbon fixing bacteria, subsequently. Finally, after combining the 3D-QSAR model with a contour maps analysis of the synergistic degradation effect of soil rhizobia and carbon-fixing bacteria, 102 NNI derivatives were designed. 4 NNI derivatives passed the functional and environmentally friendly evaluation. Taguchi orthogonal experiment and factorial experiment assisted molecular dynamics method were used to simulate the effects of 32 regulation schemes on the synergistic degradation of NNIS and its derivatives by rhizobia and carbon fixing bacteria. The synergistic degradation capacity of soil rhizobia and carbon-fixing bacteria was increased to 33.32% after right nitrogen supplementation. This indicated that supplementing the correct amount of nitrogen was beneficial to the microbial degradation of NNIs and their derivatives.

Generation of Pharmacophore and Atom Based 3D-QSAR Model of Novel Isoquinolin-1-one and Quinazolin-4-one-type Inhibitors of TNFα

2012 ◽  
Vol 8 (3) ◽  
pp. 436-451 ◽  
Author(s):  
Pradeep Hanumanthappa ◽  
Mahesh K. Teli ◽  
Rajanikant G. Krishnamurthy
Keyword(s):  
3D Qsar ◽  
Qsar Model

scholarly journals Degradation Products of Polychlorinated Biphenyls and Their In Vitro Transformation by Ligninolytic Fungi

Toxics ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 81
Author(s):  
Kamila Šrédlová ◽  
Kateřina Šírová ◽  
Tatiana Stella ◽  
Tomáš Cajthaml
Keyword(s):  
Polychlorinated Biphenyls ◽  
Extracellular Enzymes ◽  
Degradation Products ◽  
Transformation Products ◽  
Irpex Lacteus ◽  
Chlorobenzoic Acid ◽  
Ligninolytic Fungi ◽  
Wide Range ◽  
Pcb Metabolites

Metabolites of polychlorinated biphenyls (PCBs)—hydroxylated PCBs (OH‑PCBs), chlorobenzyl alcohols (CB‑OHs), and chlorobenzaldehydes (CB‑CHOs)—were incubated in vitro with the extracellular liquid of Pleurotus ostreatus, which contains mainly laccase and low manganese-dependent peroxidase (MnP) activity. The enzymes were able to decrease the amount of most of the tested OH‑PCBs by > 80% within 1 h; the removal of more recalcitrant OH‑PCBs was greatly enhanced by the addition of the laccase mediator syringaldehyde. Conversely, glutathione substantially hindered the reaction, suggesting that it acted as a laccase inhibitor. Hydroxylated dibenzofuran and chlorobenzoic acid were identified as transformation products of OH‑PCBs. The extracellular enzymes also oxidized the CB‑OHs to the corresponding CB‑CHOs on the order of hours to days; however, the mediated and nonmediated setups exhibited only slight differences, and the participating enzymes could not be determined. When CB‑CHOs were used as the substrates, only partial transformation was observed. In an additional experiment, the extracellular liquid of Irpex lacteus, which contains predominantly MnP, was able to efficiently transform CB‑CHOs with the aid of glutathione; mono‑ and di-chloroacetophenones were detected as transformation products. These results demonstrate that extracellular enzymes of ligninolytic fungi can act on a wide range of PCB metabolites, emphasizing their potential for bioremediation.

Computational Atom-based Three-Dimensional Quantitative Structure-Activity Relationship (3D QSAR) Model for Predicting Anti-Dengue Agents

2021 ◽  
Vol 16 (10) ◽  
pp. 50-58
Author(s):  
Ali Qusay Khalid ◽  
Vasudeva Rao Avupati ◽  
Husniza Hussain ◽  
Tabarek Najeeb Zaidan
Keyword(s):  
Dengue Fever ◽  
Three Dimensional ◽  
3D Qsar ◽  
Qsar Model ◽  
Quantitative Structure Activity Relationship ◽  
Activity Relationship ◽  
Quantitative Structure ◽  
Contour Maps ◽  
Structure Activity ◽  
Bioactive Ligands

Dengue fever is a viral infection spread by the female mosquito Aedes aegypti. It is a virus spread by mosquitoes found all over the tropics with risk levels varying depending on rainfall, relative humidity, temperature and urbanization. There are no specific medications that can be used to treat the condition. The development of possible bioactive ligands to combat Dengue fever before it becomes a pandemic is a global priority. Few studies on building three-dimensional quantitative structure-activity relationship (3D QSAR) models for anti-dengue agents have been reported. Thus, we aimed at building a statistically validated atom-based 3D-QSAR model using bioactive ligands reported to possess significant anti-dengue properties. In this study, the Schrodinger PhaseTM atom-based 3D QSAR model was developed and was validated using known anti-dengue properties as ligand data. This model was also tested to see if there was a link between structural characteristics and anti-dengue activity of a series of 3-acyl-indole derivatives. The established 3D QSAR model has strong predictive capacity and is statistically significant [Model: R2 Training Set = 0.93, Q2 (R2 Test Set) = 0.72]. In addition, the pharmacophore characteristics essential for the reported anti-dengue properties were explored using combined effects contour maps (coloured contour maps: blue: positive potential and red: negative potential) of the model. In the pathway of anti-dengue drug development, the model could be included as a virtual screening method to predict novel hits.

scholarly journals STRUCTURAL EXPLORATION AND PHARMACOPHORIC INVESTIGATION OF PYRAZOLE BASED ANALOGS AS NOVEL HISTONE DEACETYLASE 1 INHIBITOR USING COMBINATORIAL STUDIES

2018 ◽  
Vol 10 (3) ◽  
pp. 90
Author(s):  
Avineesh Singh ◽  
Harish Rajak
Keyword(s):  
Molecular Docking ◽  
Histone Deacetylase ◽  
Histone Deacetylase Inhibitors ◽  
Research Work ◽  
3D Qsar ◽  
Qsar Model ◽  
Docking Studies ◽  
Inhibition Activity ◽  
Design Strategies ◽  
Histone Deacetylase 1

Objective: Histone deacetylase inhibitors (HDACi) have four essential pharmacophores as cap group, connecting unit, a linker moiety and zinc binding group for their anticancer and histone deacetylase (HDAC) inhibition activity. On the basis of this fact, the objective of this research was to evaluate the exact role of pyrazole nucleus as connecting unit and its role in the development of newer HDACi.Methods: Ligand and structure-based computer-aided drug design strategies such as pharmacophore and atom based 3D QSAR modelling, molecular docking and energetic based pharmacophore mapping have been frequently applied to design newer analogs in a precise manner. Herein, we have applied these combinatorial approaches to develop the structure-activity correlation among novel pyrazole-based derivatives.Results: the Pharmacophore-based 3D-QSAR model was developed employing Phase module and e-pharmacophore on compound 1. This 3D-QSAR model provides fruitful information regarding favourable and unfavourable substitution on pyrazole-based analogs for HDAC1 inhibition activity. Molecular docking studies indicated that all the pyrazole derivatives bind with HDAC1 proteins and showed critical hydrophobic interaction with 5ICN and 4BKX HDAC1 proteins.Conclusion: The outcome of the present research work clearly indicated that pyrazole nucleus added an essential hydrophobic feature in cap group and could be employed to design the ligand molecules more accurately.

scholarly journals Non-Negligible Effects of UV Irradiation on Transformation and Environmental Risks of Microplastics in the Water Environment

2021 ◽  
Vol 12 (1) ◽  
pp. 1-12
Author(s):  
Fangyuan Cheng ◽  
Tingting Zhang ◽  
Yue Liu ◽  
Yanan Zhang ◽  
Jiao Qu
Keyword(s):  
Environmental Factors ◽  
Uv Irradiation ◽  
Water Environment ◽  
Oxidative Degradation ◽  
Environmental Risks ◽  
Important Process ◽  
Environmental Behaviors ◽  
Environmental Media ◽  
Different Types ◽  
Harmful Effects

Microplastics (MPs) are ubiquitous in environmental media, and their harmful effects on MPs on the ecosystem have attracted more and more attention. Once released into the environment, MPs can trigger oxidative degradation through ultraviolet (UV) to cause photoaging. Photoaging significantly affects the properties of MPs, which leads to changing their environmental behaviors and increasing environmental risks. In this review, the generation of MPs under UV irradiation and the influence of environmental factors on the photoaging of MPs were discussed. Photoaging of MPs is an important process affecting the migration, transformation and interaction of pollutants in water and soil. In order to fully predict the fate and environmental interaction of MPs, more researches are needed in the future to explore the photoaging behavior of different types of MPs under natural environmental conditions.

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