Environment-friendly PCN derivatives design and environmental behavior simulation based on a multi-activity 3D-QSAR model and molecular dynamics

Reduced estrogenic risks of a sunscreen additive: Theoretical design and evaluation of functionally improved salicylates

Salicylic esters (SEs), the widely used ultraviolet (UV) absorbers in sunscreen products, have been found to have health risks such as skin sensitization and estrogenic effects. This study aims to design SE substitutes that maintain high UV absorbance while reducing estrogenicity. Using molecular docking and Gaussian09 software for initial assessments and further application of a combination of two-dimensional and three-dimensional quantitative structure-activity relationships (2D-QSAR and 3D-QSAR, respectively) models, we designed 73 substitutes. The best-performing molecules, ethylhexyl salicylate (EHS)-5 and EHS-15, significantly reduced estrogenicity (44.54 % and 17.60 %, respectively) and enhanced UV absorbance (249.56 % and 46.94 %, respectively). Through screening for human health risks, we found that EHS-5 and EHS-15 were free from skin sensitivity and eye irritation and exhibited reduced skin permeability compared with EHS. Furthermore, the photolysis and synthetic pathways of EHS-5 and EHS-15 were deduced, demonstrating their good photodegradability and potential synthesizability. In addition, we analyzed the mechanisms underlying the changes in estrogenic effects and UV absorption properties. We identified covalent hydrogen bond basicity and acidity Propgen value for atomic molecular properties and the highest occupied molecular orbital eigenvalue as the main factors affecting the estrogenic effect and UV absorbance of SEs, respectively. This study focuses on the design and screening of SEs, exhibiting enhanced functionality, reduced health risks, and synthetic feasibility.

Toxicity assessment of dioxins and their transformation by-products from inferred degradation pathways

Due to the significant POPs characteristics, dioxins caused concern in public health and environmental protection. Evaluating the toxicity risk of dioxin degradation pathways is critical. OCDD, 1,2,3,4,6,7,8-HpCDD, and 1,2,3,4,6,7,8-HpCDF, which are highly abundant in the environment and have strong biodegradation capabilities, were selected as precursor molecules in this study. Firstly, their transformation pathways were deduced during the metabolism of biometabolism, microbial aerobic, microbial anaerobic, and photodegradation pathways, and density function theory (DFT) was used to calculate the Gibbs free energy to infer the possibility of the occurrence of the transformation pathway. Secondly, the carcinogenic potential of the precursors and their degradation products was evaluated using the TOPKAT modeling method. With the help of the positive indicator (0-1) normalization method and heat map analysis, a significant increase in the toxic effect of some of the transformation products was found, and it was inferred that it was related to the structure of the transformation products. Meanwhile, the strength of the endocrine disrupting effect of dioxin transformation products was quantitatively assessed using molecular docking and subjective assignment methods, and it was found that dioxin transformation products with a higher content of chlorine atoms and molecules similar to those of thyroid hormones exhibited a higher risk of endocrine disruption. Finally, the environmental health risks caused by each degradation pathway were comprehensively assessed with the help of the negative indicator (1-2) standardization method, which provides a theoretical basis for avoiding the toxicity risks caused by dioxin degradation transformation. In addition, the 3D-QSAR model was used to verify the necessity and rationality of this study. This paper provides theoretical support and reference significance for the toxicity assessment of dioxin degradation by-products from inferred degradation pathways.

Risk mitigation strategy and mechanism analysis of neonicotinoid pesticides on earthworms

Neonicotinoid insecticides (NNIs) are a new class of widely used insecticides with certain risks to non-target organisms, like earthworms. The gray correlation method was used to calculate the comprehensive risk effect value of acute toxicity (LC50) and bioaccumulation (logKow) of NNIs on earthworms. A comprehensive effects three-dimensional quantitative structure-activity relationship (3D-QSAR) model was constructed, using NNIs molecular structures and the comprehensive effect value as the independent and dependent variables, respectively. One of the representatives guadipyr (GUA) was selected as the template molecule for the molecular design and modification. A total of 63 NNIs alternatives were designed with a reduced comprehensive value higher than 10%, and as high as 42%. After screening, 15 NNIs alternatives were screened with decreased acute toxicity to earthworms, bioaccumulation effects and improved functional property. The calculated primary acute risk quotient of earthworms shows that the designed NNIs alternatives have lower earthworm risks (reduction of 70.48-99.99%). Results also found that the electronic, geometric and topological parameters of NNIs are the key descriptors that affect NNIs alternatives' toxicity. The number of hydrophobic interaction amino acid residues in NNIs molecules also contributes to the acute toxicity and the bioaccumulation of NNIs alternatives on earthworms. This study aims to design and screen functionally improved and environmentally friendly NNIs alternatives that have low risk to earthworms and provide theoretical methods and new ideas for the risk control and development of pesticides represented by NNIs.

Inhibition of algal blooms by residual antibiotics in aquatic environments: Design, screening, and validation of antibiotic alternatives

Water blooms frequently appear in the aquatic environment with global warming. However, traditional methods for treating water bloom usually require the addition of algaecides, which may lead to secondary environmental pollution problems in the water environment. To solve this problem, researchers have initiated efforts to harness pre-existing chemical substances within aquatic environments to regulate algal blooms, thereby pioneering novel avenues for water body management. Therefore, an integrated approach involving molecular docking, molecular dynamics simulations, three-dimensional quantitative structure-activity relationship (3D-QSAR), and toxicokinetics methods were utilized for the molecular modification of fluoroquinolone antibiotics, to design and screen fluoroquinolone substitutes with improved toxicity of cyanobacteria and green algae, functionality, and environmental friendliness. A total of 143 fluoroquinolone alternatives were designed in this study, and lomefloxacin-6 (LOM6) was found as the optimum alternative to lomefloxacin (LOM), with increased toxicity to cyanobacteria and green algae by 31 % and 72 %. Molecular docking of LOM before and after modification with seven other cyanobacterial and green algal photosynthetic proteins revealed that LOM6 exhibited varying degrees of increased toxicity towards 6 of these photosynthetic proteins, of which 2J96 protein increased the most (136.25 %). It shows that the residual LOM6 in the water environment has a certain inhibitory effect on the algae bloom. In addition, results showed that LOM6 had synergistic toxic effects on cyanobacteria and green algae with other pollutants residual in the aqueous environment, such as trichloroethyl phosphate, triethyl phosphate, perfluorononanoic acid, perfluorooctanoic acid. This indicates that LOM6 has better algal removal effectiveness in aqueous environments where organophosphate flame retardants and perfluorinated compounds exist together. In this paper, a novel method was developed to remove cyanobacteria and green algae in water environment and reduce the secondary pollution through theoretical simulation, which provides theoretical support for the control of water blooms.

Multi-process regulation of novel brominated flame retardants: Environmentally friendly substitute design, screening and environmental risk regulation

Novel brominated flame retardants (NBFRs), one of the most widely used synthetic flame-retardant materials, have been considered as a new group of pollutants that potentially affect human health. To overcome the adverse effects of NBFRs, a systematic approach for molecular design, screening, and performance evaluation was developed to generate environmentally friendly NBFR derivatives with unaltered functionality. In the present study, the features of NBFRs (long-distance migration, biotoxicity, bioenrichment, and environmental persistence) were determined and characterized by the multifactor comprehensive characterization method with equal weight addition, and the similarity index analysis (CoMSIA) model was constructed. Based on the three-dimensional equipotential diagram of the target molecule 2-ethylhexyl tetrabromobenzoic acid (TBB), 23 TBB derivatives were designed. Of these, 22 derivatives with decreased environmental impact and unaltered functional properties (i.e., flame retardancy and stability) were selected using 3D-QSAR models and density functional theory methods. The health risks of these derivatives to humans were assessed by toxicokinetic analysis; the results narrowed down the number of candidates to three (Derivative-7, Derivative-10, and Derivative-15). The environmental impact of these candidates was further evaluated and regulated in the real-world environment by using molecular dynamics simulation assisted by the Taguchi experimental design method. The relationship between the binding effects and the nonbonding interaction resultant force (TBB derivatives-receptor proteins) was also studied, and it was found that the larger the modulus of the binding force, the stronger the binding ability of the two. This finding indicated that the environmental impact of the designed NBFR derivatives was decreased. The present study aimed to provide a new idea and method for designing NBFR substitutes and to provide theoretical support for restraining the potential environmental risks of NBFRs.

Molecular design of environment-friendly amide herbicide substitutes with high efficacy, low phytotoxicity and medication safety

The primary goal of this investigation was to formulate an ecologically sustainable alternative to amide herbicides (AHs) characterized by robust herbicidal effectiveness, minimal corn phytotoxicity, and commendable pharmaceutical safety. We employed comparative molecular similarity index analysis (CoMSIA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) model, which systematically outlined parameters such as herbicidal effectiveness, corn phytotoxicity, and AHs biodegradability. Subsequently, after thorough evaluation, we carefully selected a group of fourteen stable AH-substitute compounds known for their safety and environmental compatibility, considering aspects like pharmacokinetics, toxicokinetics, functional properties, and environmental friendliness. This resulted in a significant increase in herbicidal effectiveness, ranging from 21.64% to 34.07%, alongside a decrease in corn phytotoxicity within the range of 12.19-20.87%. Furthermore, we achieved an improvement in biodegradability, measured within the spectrum of 4.92-9.40%. Importantly, these changes also correlated with the reduction of hepatotoxicity, mutagenicity, and cutaneous health risks. Finally, we delved into the mechanisms underlying the improved herbicidal effectiveness, reduced corn phytotoxicity, and enhanced biodegradability of AHs substitutes through molecular docking and analysis of amino acid interactions. The investigation concluded that non-covalent forces governing the interaction between AHs substitutes and receptor proteins are crucial in determining herbicidal effectiveness, corn phytotoxicity, and biodegradability. Specifically, Van der Waals and electrostatic forces emerged as key factors governing the binding affinities of AH molecules with receptor proteins, both before and after modification. In summary, this study introduces innovative approaches in the field of agricultural chemical weeding technology and provides a theoretical framework for the environmentally responsible management of AHs herbicides.

Mechanism analysis and improved molecular modification: Design of high efficiency and environmentally friendly triazole fungicide substitutes

The adverse effects of triazole fungicides (TFs) on the soil and the environmental damage caused by their residues have attracted the attention of the international community. To effectively prevent and control the above problems, this paper designed 72 substitutes of TFs with significantly better molecular functionality (>40%) using Paclobutrazol (PBZ) as the template molecule. Then, the comprehensive scores for environmental effects calculated after normalization by "extreme value method-entropy weight method-weighted average method" was the dependent variable, the structural parameters of TFs molecules was the independent variable (PBZ-214 was the template molecule) to construct the 3D-QSAR model of integrated environmental effects of TFs with high degradability, low bioenrichment, low endocrine disruption effects, and low hepatotoxicity and designed 46 substitutes of TFs with significantly better comprehensive environmental effects (>20%). After confirming the above effects of TFs and assessing human health risk and the universality of biodegradation and endocrine disruption, we screened PBZ-319-175 as the eco-friendly substitute of TF, which had high efficiency (improved functionality) and better environmental effects than those of the target molecule by 51.63% and 36.09%, respectively. Finally, the results of the molecular docking analysis showed that non-bonding interactions (hydrogen bonding, electrostatic, or polar force) predominantly affected the association between PBZ-319-175 and its biodegradable protein, and the hydrophobic effect of the amino acids distributed around PBZ-319-175 played a significant role. Additionally, we determined the microbial degradation path of PBZ-319-175 and found that the steric hindrance of the substituent group after molecular modification promoted its biodegradability. In this study, we enhanced molecular functionality twice and also reduce the major damage of TFs to the environment by performing iterative modifications. This paper provided theoretical support for the development and application of high-performance, eco-friendly substitutes of TFs.

New insights into enhanced electrochemical advanced oxidation mechanism of B-doped graphene aerogel: Experiments, molecular dynamics simulations and DFT

B-doped graphene, as an efficient and environmental-friendly metal-free catalyst, has aroused much attention in the electrochemical advanced oxidation process (EAOP), but the bottleneck in this field is to determine the relationship between the surface structure regulation and activity of catalysts. Herein, the B-doped graphene aerogel (BGA) fabricated gas diffusion electrode was prepared and used as a cathode for EAOP to remove tetracycline (TC). Higher free radical yield (169.59 μM), faster reaction speed (0.35 min^-1) and higher TC removal rate (99.93%) were found in the BGA system. Molecular dynamics simulation unveiled the interaction energy of BGA was greater than the raw graphene aerogel (GA). The adsorption-activation process of H₂O₂ and the degradation process of TC occurred in the first adsorption layer of catalysts. And both processes turned more orderly after B doping, which accelerated the reaction efficiency. Results of density functional theory displayed the contribution of three B-doped structures to improve the binding strength between H₂O₂ and BGA was: - BCO₂ (-0.23 eV) > - BC₂O (-0.16 eV) > - BC₃ (-0.09 eV). -BCO₂ was inferred to be the main functional region of H₂O₂ in-situ activation to hydroxyl radical (•OH), while -BC₂O and -BC₃ were responsible for improving H₂O₂ production.

Efficient and synergistic degradation of fluoroquinolones by bacteria and microalgae: Design of environmentally friendly substitutes, risk regulation and mechanism analysis

Fluoroquinolones (FQs) are widely used as antimicrobial agents, and their nonbiodegradable in sewage has become an increasingly concerning. High-biochemical substitutes of FQs were designed with bacteria and microalgae as driving forces of biodegradation, and this is the first study on efficient synergistic degradation of FQs by multiple microorganisms. Among 143 designed FQ substitutes, only one was screened with high biodegradability (increased by 120.51 %), improved functional properties (genotoxicity: 13.66 %), less environmental impacts (bio-accumulation: -44.81 %), less human health and ecological risk (hepatotoxicity: -106.21 %). The complex functional protein with the synergistic degradation effect of bacteria and microalgae was constructed, which proved their synergistic degradation and realized the effect of "1 + 1 > 2″. The best risk regulation scheme determined using molecular dynamics simulation proved the degradation ability of complex functional protein and found the CIP-129 was easy to be degraded in real environment compared with CIP, and the degradation rate increased by 70.42 %. The synthesis path of CIP-129 and CIP were inferred and calculated, and the results showed the Gibbs free energies of three CIP-129 synthetic paths (40.64 a.u.; 40.61 a.u.; 40.65 a.u.) were close to the energy required for the CIP (39.43 a.u.), indicating there was no significant difference in the energy consumption of CIP-129 in laboratory synthesis.

Potential Toxicity Risk Assessment and Priority Control Strategy for PAHs Metabolism and Transformation Behaviors in the Environment

In this study, 16 PAHs were selected as the priority control pollutants to summarize their environmental metabolism and transformation processes, including photolysis, plant degradation, bacterial degradation, fungal degradation, microalgae degradation, and human metabolic transformation. Meanwhile, a total of 473 PAHs by-products generated during their transformation and degradation in different environmental media were considered. Then, a comprehensive system was established for evaluating the PAHs by-products' neurotoxicity, immunotoxicity, phytotoxicity, developmental toxicity, genotoxicity, carcinogenicity, and endocrine-disrupting effect through molecular docking, molecular dynamics simulation, 3D-QSAR model, TOPKAT method, and VEGA platform. Finally, the potential environmental risk (phytotoxicity) and human health risks (neurotoxicity, immunotoxicity, genotoxicity, carcinogenicity, developmental toxicity, and endocrine-disrupting toxicity) during PAHs metabolism and transformation were comprehensively evaluated. Among the 473 PAH's metabolized and transformed products, all PAHs by-products excluding ACY, CHR, and DahA had higher neurotoxicity, 152 PAHs by-products had higher immunotoxicity, and 222 PAHs by-products had higher phytotoxicity than their precursors during biological metabolism and environmental transformation. Based on the TOPKAT model, 152 PAH by-products possessed potential developmental toxicity, and 138 PAH by-products had higher genotoxicity than their precursors. VEGA predicted that 247 kinds of PAH derivatives had carcinogenic activity, and only the natural transformation products of ACY did not have carcinogenicity. In addition to ACY, 15 PAHs produced 123 endocrine-disrupting substances during metabolism and transformation. Finally, the potential environmental and human health risks of PAHs metabolism and transformation products were evaluated using metabolic and transformation pathway probability and degree of toxic risk as indicators. Accordingly, the priority control strategy for PAHs was constructed based on the risk entropy method by screening the priority control pathways. This paper assesses the potential human health and environmental risks of PAHs in different environmental media with the help of models and toxicological modules for the toxicity prediction of PAHs by-products, and thus designs a risk priority control evaluation system for PAHs.

Insights into toxicity of polychlorinated naphthalenes to multiple human endocrine receptors: Mechanism and health risk analysis

This study explored the combined disruption mechanism of polychlorinated naphthalenes (PCNs) on the three key receptors (estrogen receptor, thyroid receptor, and adrenoceptor) of the human endocrine system. The intensity of PCN endocrine disruption on these receptors was first determined using a molecular docking method. A comprehensive index of PCN endocrine disruption to human was quantified by analytic hierarchy process and fuzzy analysis. The mode of action between PCNs and the receptors was further identified to screen the molecular characteristics influencing PCN endocrine disruption through molecular docking and fractional factorial design. Quantitative structure-activity relationship (QSAR) models were established to investigate the toxic mechanism due to PCN endocrine disruption. The results showed that the lowest occupied orbital energy (E_LUMO) was the most important factor contributing to the toxicity of PCNs on the endocrine receptors, followed by the orbital energy difference (ΔE) and positive Millikan charge (q⁺). Furthermore, the strategies were formulated through adjusting the nutritious diet to reduce health risk for the workers in PCN contaminated sites and the effectiveness and feasibility were assessed by molecular dynamic simulation. The simulation results indicated that the human health risk caused by PCN endocrine disruption could be effectively decreased by nutritional supplementation. The binding ability between PCNs and endocrine receptors significantly declined (up to -16.45%) with the supplementation of vitamins (A, B₂, B₁₂, C, and E) and carotene. This study provided the new insights to reveal the toxic mechanism of PCNs on human endocrine systems and the recommendations on nutritional supplements for health risk reduction. The methodology and findings could serve as valuable references for screening of potential endocrine disruptors and developing appropriate strategies for PCN or other persistent organic pollution control and health risk management.

Identifying molecular structural features by pattern recognition methods

Identification of molecular structural features is a central part of computational chemistry. It would be beneficial if pattern recognition techniques could be incorporated to facilitate the identification. Currently, the quantification of the structural dissimilarity is mainly carried out by root-mean-square-deviation (RMSD) calculations such as in molecular dynamics simulations. However, the RMSD calculation underperforms for large molecules, showing the so-called "curse of dimensionality" problem. Also, it requires consistent ordering of atoms in two comparing structures, which needs nontrivial effort to fulfill. In this work, we propose to take advantage of the point cloud recognition using convex hulls as the basis to recognize molecular structural features. Two advantages of the method can be highlighted. First, the dimension of the input data structure is largely reduced from the number of atoms of molecules to the number of atoms of convex hulls. Therefore, the dimensionality curse problem is avoided, and the atom ordering process is saved. Second, the construction of convex hulls can be used to define new molecular descriptors, such as the contact area of molecular interactions. These new molecular descriptors have different properties from existing ones, therefore they are expected to exhibit different behaviors for certain machine learning studies. Several illustrative applications have been carried out, which provide promising results for structure-activity studies.

Molecular design of high-efficacy and high drug safety Fluoroquinolones suitable for a variety of aerobic biodegradation bacteria

The present study attempted to improve the biodegradation removal rate of Fluoroquinolones (FQs) in sewage treatment plants. The similarity index analysis (CoMSIA) model for combined biodegradability was constructed, and 33 kinds of molecular derivatives of FQs suitable for a variety of aerobic biodegradation microorganisms were designed. Further, derivative-20 and derivative-28, with high drug efficiency, drug safety, and environmental friendliness were selected through pharmacokinetics (ADMET), toxicokinetics (TOPKAT), FQs functional characteristics, and environmental friendliness evaluations. Compared with the target molecules, the combined biodegradability of the above two FQ-derivative molecules were increased by 193.57 % and 205.07 %, respectively, while their environment-friendly characteristics were improved to a certain degree. Through molecular docking and molecular dynamic simulation analysis, it showed that van der Waals force (decreased by 2.73 %-61.74 %) was the main factor influencing the binding ability of the modified FQ molecules to the receptor proteins. In addition, the relationship among the non-bonding interaction resultant force, the binding effect of the FQ-derivative molecules, and the receptor protein-related amino acid residues were studied for the first time. It was observed that the higher the value of the non-bonding interaction resultant force, the better was the binding effect, which demonstrating the significantly improved biodegradability of the designed FQ-derivative molecules.

Control strategies for the vertical gene transfer of quinolone ARGs in Escherichia coli through molecular modification and molecular dynamics

This study investigates the regulation of the vertical gene transfer of quinolones' antibiotic resistance genes (ARGs) through a combination of source modification and process control. In source prevention, 29 Escherichia coli (E. coli) DNA gyrase subunit A mutant proteins were constructed, the B-G mutant protein displayed the greatest reduction in binding effect (-25.98%). Based on this, a 3D-QSAR model was constructed, and LEV-2 and LEV-9 QNs derivatives were designed based on Levofloxacin (LEV), and their binding effect with B-G mutant protein was found be increased by 13.24% and 19.40%. The drug resistance mechanism of E. coli was explored based on molecular docking technology and protein hydrophobic interaction theory. Most of the amino acid resistance mutations changed from hydrophilic to lipophilic, which inhibited the binding of QNs to mutant protein A subunit, and further reduced the bactericidal effect of QNs. In process control, Huoxiang-Zhengqi, stroke-physiological saline solution (SPSS), and Lycium barbarum (L. barbarum) was found to be 164.82% higher than that of the blank control group. The purpose of this study is to provide a theoretical support for the joint regulation of QNs' ARGs in organisms and the research and development on green alternatives to QNs compounds.

Functional modification of HHCB: Strategy for obtaining environmentally friendly derivatives

Galaxolide (HHCB), one of the most widely used synthetic musks in personal care products (PCPs), has been recognized as an emerging contaminant with potential human health concerns. To overcome such adverse effects, a systematic molecular design, screening and performance evaluation approach was developed to generate functionally improved and environmentally friendly HHCB derivatives. Among the 90 designed HHCB derivatives, 15 were screened with improved functional properties (i.e., odor stability and intensity) and less environmental impacts (i.e., lower bio-toxicity, bio-accumulation ability, and mobility) using 3D-QSAR models and density functional theory methods. Their human health risks were then assessed by toxicokinetic analysis, which narrowed the candidates to four. Derivative 7, the designed molecule with the least dermal adsorption potential, was evaluated for its interaction with other PCPs additives (i.e., anti-photosensitivity materials and moisturizer) and such impacts on human health risks using molecular docking and molecular dynamic simulation. The environmental fate of Derivative 7 after transformation (i.e., photodegradation, biotransformation, and chlorination) was also discussed. Biotransformation and chlorination were recognized as optimum options for Derivative 7 mitigation. This study provided the theoretical basis for the design of functionally improved and environmentally friendly HHCB alternatives and advanced the understanding of their environmental behaviors and health risks.

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.

Identification and regulation of ecotoxicity of polychlorinated naphthalenes to aquatic food Chain (green algae-Daphnia magna-fish)

Polychlorinated naphthalenes (PCNs) are widely distributed in the aquatic environment and can be transmitted through the food chain, which can amplify their toxic effects on human. To inhibit their transmission in the trophic level, this study aimed to predict the joint toxicity mechanism of polychlorinated naphthalenes (PCNs) to the key organisms and control scheme of its toxicity in the aquatic food chain (green algae-Daphnia magna-fish). The toxic effect grade and mode of action (MoA) of PCNs on the food chain were first predicted to guide the establishment of toxic mechanism model. QSAR models were constructed to quantify the mechanism of aquatic toxicity due to PCNs. The results showed the PCN compounds studied were highly toxic at all the trophic levels of the aquatic food chain. The binding ability of PCNs to the aquatic organisms was the main factor causing the toxicity of PCNs in the food chain, followed by electronic parameters E_HOMO and E_LUMO. Moreover, the binding ability between PCNs and food chain receptors was related to the molecular hydrophobicity, the hydrophobicity can be changed by adjusting the ability of PCNs to be adsorbed by sediment and their chlorine substituents, while the effect of PCNs electronic parameters (E_HOMO and E_LUMO) can be adjusted by their solvation effect. In addition, the macro-control scheme of PCN-based aquatic toxicity mechanism was established, and the molecular dynamics (MD) simulation confirmed its effectiveness and accessibility. The MD simulation showed the inhibition effect of nutrition-grade toxicity in the food chain was significant when the external stimulation conditions of solvation, anaerobic dechlorination and molecular adsorption were improved, with the decrease range of 66.26-263.16%, 198.93-323.98% and 189.24-549.48%, respectively. This work reveals new insights into the mechanism of PCNs joint toxicity to aquatic ecosystem food chain and develop appropriate strategies for its ecological risk management.

Combined remediation of polychlorinated naphthalene-contaminated soil under multiple scenarios: An integrated method of genetic engineering and environmental remediation technology

This study explored the types of polychlorinated naphthalene (PCN)-contaminated soil and determined the practicable scheme of combined remediation using an integrated method of genetic engineering and environmental remediation technology. A multi-scenario comprehensive evaluation system of a plant-microbial combined bioremediation of PCN-contaminated soil was established using the intelligent integration of analytic hierarchy process and formula evaluation methods based on the current situation of PCN contamination in China, which showed the bioremediation of PCN-contaminated soil by the plant-microbial system could be divided into four scenarios. QSAR models were constructed to quantify the remediation mechanism that electronic parameter ∆E was the key factor changing the efficiency of combined bioremediation. Moreover, the macro-control scheme of PCN-contaminated soil was established, which indicated that four new multifunctional proteins promoted the absorption, degradation, and mineralization of PCNs in specific soil pollution types significantly, were obtained through cross gene recombination. The molecular dynamics (MD) simulation results showed the efficiency of the plant-microbial combined bioremediation were increased by 15.45% (Scenario 1, 2, 3) and 20.02% (Scenario 4) under the optimal regulation scheme. The findings will be helpful to realize the regional control of PCN-contaminated soil.

Structure-based molecular modeling in SAR analysis and lead optimization

In silico methods like molecular docking and pharmacophore modeling are established strategies in lead identification. Their successful application for finding new active molecules for a target is reported by a plethora of studies. However, once a potential lead is identified, lead optimization, with the focus on improving potency, selectivity, or pharmacokinetic parameters of a parent compound, is a much more complex task. Even though in silico molecular modeling methods could contribute a lot of time and cost-saving by rationally filtering synthetic optimization options, they are employed less widely in this stage of research. In this review, we highlight studies that have successfully used computer-aided SAR analysis in lead optimization and want to showcase sound methodology and easily accessible in silico tools for this purpose.

Establishment of a CoMFA Model Based on the Combined Activity of Bioconcentration, Long-Range Transport, and Highest Infrared Signal Intensity and Molecular Design of Environmentally Friendly PBB Derivatives

In the current study, a comparative molecular field analysis (CoMFA) model with the combined activity of polybrominated biphenyls (PBBs) bioconcentration, long-range transport, and the highest infrared signal intensity (weight ratio of 5:4:1) was constructed based on the threshold method and was further evaluated and analyzed. PBB-153 derivatives with improved combined activity values of bioconcentration, long-range transport, and the highest infrared signals intensity were designed based on contour maps of the CoMFA model. The environmental stability and functionality of the derivatives were also evaluated. The constructed model showed good prediction ability, fitting ability, stability, and external prediction ability. The contribution rates of electrostatic and steric fields to the combined activity of PBBs were 53.4% and 46.6%, respectively. Four PBB-153 derivatives with significantly improved bioconcentration, long-range transport and the highest infrared signal intensity (the combined activity value of these three parameters decreased) were screened with good environmental stability and functionality. Results validated the accuracy and reliability, and ability of the generated model to realize the simultaneous modification of the three activities of the target molecule. The binding ability of the designed derivatives to food chain biodegradation enzymes increased, thereby verifying the improvement in the bioconcentration. The half-lives of the derivatives in air and their ability to be absorbed by the plants significantly improved compared to the target molecule, further showing that the long-range transport of derivatives was reduced. In addition, the introduction of the –NO group caused the N =O stretching vibration of the derivatives to increase the infrared signal intensity. The present model provides a theoretical design method for the molecular modification of environmentally friendly PBBs.

Enhanced Biodegradation/Photodegradation of Organophosphorus Fire Retardant Using an Integrated Method of Modified Pharmacophore Model with Molecular Dynamics and Polarizable Continuum Model

A comprehensive 3D-quantitative structure-activity relationship (QSAR) pharmacophore model was constructed using the values of comprehensive biodegradation/photodegradation effects of 17 organophosphorus flame retardants (OPFRs) evaluated by a normalization method to modify OPFRs with high biodegradation/photodegradation, taking tris(chloro-isopropyl) phosphate (TCPP), tris(2-chloroethyl) phosphate (TCEP) and tris(1-chloro-2-propyl) phosphate (TCIPP)-which occur frequently in the environment, and are the most difficult to degrade as target molecules. OPFR-derivative molecules TCPP-OH shows the highest improvement in biodegradation and photodegradation (55.48% and 46.37%, respectively). On simulating the biodegradation path and photodegradation path, it is found that the energy barrier of TCPP-OH for phosphate bond cleavage is reduced by 15.73% and 52.52% compared to TCPP after modification, respectively. Finally, in order to further significantly improve its biodegradability and photodegradation, the efficiency enhancement in the biodegradation and photodegradation of TCPP-OH are analyzed under the simulated environment by molecular dynamics and polarizable continuum model, respectively. The results of molecular dynamics show that the biodegradation efficiency of the TCPP-OH increased by 75.52% compared to TCPP. The UV spectral transition energy (4.07 eV) of TCPP-OH under the influence of hydrogen peroxide solvation effect is 44.23% lower than the actual transition energy (7.29 eV) of TCPP.

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

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.