A novel pharmacophore model on PAEs' estrogen and thyroid hormone activities using the TOPSIS and its application in molecule modification

In the proposed model, the estrogen activity values and thyroid hormone activity values of PAEs molecules were normalized using the TOPSIS method by eliminating the dimension coefficients, and the comprehensive activity values of estrogen and thyroid hormone were obtained by analyzing the activity of each hormone and assigning the corresponding weight. The five pharmacophore models of hormone combined activity were constructed using the comprehensive activity values. Hypol 1 was the optimal pharmacophore model, showing good predictive power and significance. Then, the DBP, DNOP, and DMP molecules in environmental priority control pollutants were selected as the target molecules to perform common substitution reactions of hydrogen bond donor. Eleven PAEs derivative molecules with significantly reduced combined activity and single activity were screened. In analysis of the differences before and after modification of the docking parameters and amino acid residues before and after modification of PAEs and their derivatives, the reduced closeness between ligand and receptor leads to the decrease of thyroid hormones and estrogen activities. Moreover, the establishment of the models, not only shows that the PAEs hormone activity has certain linear relationships with the physical parameters of molecules but also shows that thyroid hormone activity and estrogen activity of PAEs is consistent with the hormone combined activity. The results confirmed the feasibility of the modified PAEs modification scheme with reduced combined activities of hormones, providing an important theoretical method for the construction of the pharmacophore model of combined activities of hormones and the study of PAEs derivative molecules.

Combined QSAR/QSPR and molecular docking study on fluoroquinolones to reduce biological enrichment

With the aim of reducing the adverse effects of fluoroquinolones in the environment, a complete design and screening system for the low biological enrichment and high photodegradabilities of 29 fluoroquinolones was established through a three-dimensional quantitative structure-activity relationship (3D-QSAR) model and molecular docking. The interaction mechanisms of the fluoroquinolones with Gram-negative bacteria (DNA gyrase in Escherichia coli) and Gram-positive bacteria (Topoisomerase IV in Staphylococcus aureus) were also evaluated. Consequently, the 3D-QSAR model showed that the 3- and 18-positions of the fluoroquinolones strongly affected their biological enrichment, and that the introduction of electropositive or hydrophobic groups at these positions reduced the logarithm of the octanol-water partition coefficient. Using nadifloxacin as a template, 23 derivatives with lower biological enrichment than nadifloxacin (decreased by 30.12%-94.18%) were designed. Meanwhile, the photodegradabilities of 15 derivatives were increased compared with nadifloxacin. Finally, the further screening by molecular docking of nadifloxacin and the above 15 derivatives with DNA gyrase and Topoisomerase IV showed that 13 of the derivatives had lower biological enrichment (decreased by 0.30%-16.76%) than nadifloxacin in the bacteria.

Modified neonicotinoid insecticide with bi-directional selective toxicity and drug resistance

A three-dimensional quantitative structure-activity relationship (3D-QSAR) model was established based on the molecular structures and the negative logarithm of experimental lethal concentration 50 values (pLC₅₀) of neonicotinoid insecticides. Then, the mechanisms of bi-directional selective toxic effects and drug resistance were determined using homology modeling and molecular docking analyses. The results of the model showed that the 1-, 2-, 4-, and 12- positions of neonicotinoid insecticides strongly affected their toxicity, and that the introduction of bulky or electropositive groups at these positions could increase the pLC₅₀ values. Using Compound 19 as a template, we designed 37 derivatives with greater toxicity (increased by 0.04-11.45%). Among them, 20 derivatives had bioconcentrations lower than that of Compound 19 (reduced by 0.38-147.88%). Further screening of Compound 19 and the 20 derivatives mentioned above by homology modeling and acetylcholine receptors (AChRs) molecular docking analyses showed that 10 derivatives had bi-directional selective toxic effects against pests and bees. Further docking analyses of Compound 19 and these 10 derivatives identified that Derivative-33 showed decreased docking with superoxide dismutase (SOD) and glutathione S transferase (GST) in pests and enhanced docking with these enzymes in bees, indicating bi-directional selective resistance for pests and bees. Accordingly, Derivative-33 was selected as a new insecticide with high toxicity to pests and low toxicity to bees (bi-directional selective toxicity), low resistance in pest populations, and high resistance in bee populations. This study provides valuable reference data and will be useful for the development of strategies to produce new environmentally friendly pesticides.

Modification of Hexachlorobenzene to Molecules with Lower Long-Range Transport Potentials Using 3D-QSAR Models with a Full Factor Experimental Design

In this study, the hexachlorobenzene molecule was modified by three-dimensional quantitative structure-activity relationship (3D-QSAR) models and a full factor experimental design to obtain new hexachlorobenzene molecules with low migration ability. The 3D-QSAR models (comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA)) were constructed by SYBLY-X 2.0 software, using experimental data of octanol-air partition coefficients (K_OA) for 12 chlorobenzenes (CBs) congeners as the dependent variable, and the structural parameters of CBs as independent variables, respectively. A target molecule (hexachlorobenzene; HCB: its long-distance migration capability leads to pollution of the marine environment in Antarctic and Arctic) was modified using the 3D-QSAR contour maps associated with resolution V of the 2^10-3 full-factorial experimental design method, and 11 modified HCB molecules were produced with a single chlorine atom (-Cl₂) and three chlorine atoms (-Cl₁, -Cl₃, and -Cl₅) replaced with electropositive groups (-COOH, -CN, -CF₃, -COF, -NO₂, -F, -CHF₂, -ONO₂, and -SiF₃) to increase the logK_OA. The new molecules had essentially similar biological enrichment functions and toxicities as HCB but were found to be more easily degraded. A 2D-QSAR model and molecular docking technology indicated that both dipole moments and highest occupied orbital energies of the substituents markedly affected migration and degradation of the new molecules. The abilities of the compounds to undergo long distance migration were assessed. The modified HCB molecules (i.e. 2-CN-HCB, 2-CF₃-HCB, 1-F-3-COOH-5-NO₂-HCB, 1-NO₂-3-CN-5-CHF₂-HCB and 1-CN-3-F-5-NO₂-HCB) moved from a long-range transport potential of the modified molecules to a relatively low mobility class, and the transport potentials of the remaining modified HCB molecules (i.e. 2-COOH-HCB, 2-COF-HCB, 1-COF-3-ONO₂-5-NO2-HCB, 1-F-3-CN-5-SiF₃-HCB, 1-F-3-COOH-5-SiF₃-HCB and 1-CN-3-SiF₃-5-ONO₂-HCB) also significantly decreased. These results provide a basic theoretical basis for designing environmentally benign molecules based on HCB.