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

The q-RASPR approach for predicting the property and fate of persistent organic pollutants

This study presents a quantitative read-across structure-property relationship (q-RASPR) approach that integrates the chemical similarity information used in read-across with traditional quantitative structure-property relationship (QSPR) models. This novel framework is applied to predict the physicochemical properties and environmental behaviors of persistent organic pollutants, specifically polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs). By utilizing a curated dataset and incorporating similarity-based descriptors, the q-RASPR approach improves the accuracy of predictions, particularly for compounds with limited experimental data. The models' performances were assessed using internal cross-validation and external testing, demonstrating significant enhancements in predictive reliability compared to conventional QSPR models. The findings highlight the potential of q-RASPR for use in regulatory risk assessments and optimizing remediation strategies by providing more precise insights into the environmental fate of these contaminants.

Analysis of factors affecting microbial degradation of cyanobacterial toxins based on theoretical calculations

Cyanobacterial toxins are the most common algal toxins, which are highly toxic and can persist in the aquatic environment without easy degradation, posing risks to the ecosystem and human health that cannot be ignored. Although microbiological methods for the removal of cyanobacterial toxins from aqueous environments are highly efficient, their degradation efficiency is susceptible to many abiotic environmental factors. In this paper, Microcystin-LR (MC-LR) and its microbial degrading enzymes were selected to study the effects of common environmental factors (temperature (T), NO3-, NH4+, Cu2+, Zn2+) and their levels during microbial degradation of cyanobacterial toxins in aqueous environments by using molecular docking, molecular dynamics simulation, analytical factor design, and the combined toxicokinetics of TOPKAT (toxicity prediction). It was found that the addition of T, NO3- and Cu2+ to the aqueous environment promoted the microbial degradation of MC-LR, while the addition of NH4+ and Zn2+ inhibited the degradation; The level effect study showed that the microbial degradation of MC-LR was promoted by increasing levels of added T and NO3- in the aqueous environment, whereas it was inhibited and then promoted by increasing levels of NH4+, Cu2+ and Zn2+. In addition, the predicted toxicity of common Microcystins (MCs) showed that MC-LR, Microcystin-RR (MC-RR) and Microcystin-YR (MC-YR) were not carcinogenic, developmentally toxic, mutagenic or ocular irritants in humans. MC-LR and MC-RR are mild skin irritants and MC-YR is not a skin irritant. MC-YR has a higher chronic and acute toxicity in humans than MC-LR and MC-RR. Acute/chronic toxicity intensity for aquatic animals: MC-YR > MC-LR > MC-RR and for aquatic plants: MC-LR > MC-YR > MC-RR. This suggests that MC-YR also has a high environmental health risk. This paper provides theoretical support for optimizing the environmental conditions for microbial degradation of cyanobacterial toxins by studying the effects of common environmental factors and their level effects in the aquatic environment.

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.

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.

Mitigating the Adverse Effects of Polychlorinated Biphenyl Derivatives on Estrogenic Activity via Molecular Modification Techniques

The aim of this paper is to explore the mechanism of the change in oestrogenic activity of PCBs molecules before and after modification by designing new PCBs derivatives in combination with molecular docking techniques through the constructed model of oestrogenic activity of PCBs molecules. We found that the weakened hydrophobic interaction between the hydrophobic amino acid residues and hydrophobic substituents at the binding site of PCB derivatives and human oestrogen receptor alpha (hERα) was the main reason for the weakened binding force and reduced anti-oestrogenic activity. It was consistent with the information that the hydrophobic field displayed by the 3D contour maps in the constructed oestrogen activity CoMSIA model was one of the main influencing force fields. The hydrophobic interaction between PCB derivatives and oestrogen-active receptors was negatively correlated with the average distance between hydrophobic substituents and hydrophobic amino acid residues at the hERα-binding site, and positively correlated with the number of hydrophobic amino acid residues. In other words, the smaller the average distance between the hydrophobic amino acid residues at the binding sites between the two and the more the number of them, and the stronger the oestrogen activity expression degree of PCBS derivative molecules. Therefore, hydrophobic interactions between PCB derivatives and the oestrogen receptor can be reduced by altering the microenvironmental conditions in humans. This reduces the ability of PCB derivatives to bind to the oestrogen receptor and can effectively modulate the risk of residual PCB derivatives to produce oestrogenic activity in humans.