Combined 3D-QSAR, molecular docking and molecular dynamics study on thyroid hormone activity of hydroxylated polybrominated diphenyl ethers to thyroid receptors β

Structure-based modeling to assess binding and endocrine disrupting potential of polycyclic aromatic hydrocarbons in Daniorerio

Environmental contaminants, such as polycyclic aromatic hydrocarbons (PAHs), have raised concerns regarding their potential endocrine-disrupting effects on aquatic organisms, including fish. In this study, molecular docking and molecular dynamics techniques were employed to evaluate the endocrine-disrupting potential of PAHs in zebrafish, as a model organism. A virtual screening with 72 PAHs revealed a correlation between the number of PAH aromatic rings and their binding affinity to proteins involved in endocrine regulation. Furthermore, PAHs with the highest binding affinities for each protein were identified: cyclopenta[cd]pyrene for AR (-9.7 kcal/mol), benzo(g)chrysene for ERα (-11.5 kcal/mol), dibenzo(a,e)pyrene for SHBG (-8.7 kcal/mol), dibenz(a,h)anthracene for StAR (-11.2 kcal/mol), and 2,3-benzofluorene for TRα (-9.8 kcal/mol). Molecular dynamics simulations confirmed the stability of the protein-ligand complexes formed by the PAHs with the highest binding affinities throughout the simulations. Additionally, the effectiveness of the protocol used in this study was demonstrated by the receiver operating characteristic curve (ROC) analysis, which effectively distinguished decoys from true ligands. Therefore, this research provides valuable insights into the endocrine-disrupting potential of PAHs in fish, highlighting the importance of assessing their impact on aquatic ecosystems.

Integrated Studies on Male Reproductive Toxicity of Bis(2-ethylhexyl)-tetrabromophthalate: in Silico, in Vitro, ex Vivo, and in Vivo

Bis(2-ethylhexyl)tetrabromophthalate (TBPH) has been widely detected in the environment and organisms; thus, its toxic effects on male reproduction were systematically studied. First, we found that TBPH can stably bind to the androgen receptor (AR) based on in silico molecular docking results and observed an antagonistic activity, but not agonistic activity, on the AR signaling pathway using a constructed AR-GRIP1 yeast assay. Subsequently, we validated the adverse effects on male germ cells by observing inhibited androgen production and proliferation in Leydig cells upon in vitro exposure and affected general motility and motive tracks of zebrafish sperm upon ex vivo exposure. Finally, the in vivo reproductive toxicity was demonstrated in male zebrafish by reduced mating behavior in F0 generation when paired with unexposed females and abnormal development of their offspring. In addition, reduced sperm motility and impaired germ cells in male zebrafish were also observed, which may be related to the disturbed homeostasis of sex hormones. Notably, the specifically suppressed AR in the brain provides further evidence for the antagonistic effects as above-mentioned. These results confirmed that TBPH affected male reproduction through a classical nuclear receptor-mediated pathway, which would be helpful for assessing the ecological and health risks of TBPH.

Update of the risk assessment of polybrominated diphenyl ethers (PBDEs) in food

The European Commission asked EFSA to update its 2011 risk assessment on polybrominated diphenyl ethers (PBDEs) in food, focusing on 10 congeners: BDE-28, -47, -49, -99, -100, -138, -153, -154, -183 and ‑209. The CONTAM Panel concluded that the neurodevelopmental effects on behaviour and reproductive/developmental effects are the critical effects in rodent studies. For four congeners (BDE-47, -99, -153, -209) the Panel derived Reference Points, i.e. benchmark doses and corresponding lower 95% confidence limits (BMDLs), for endpoint-specific benchmark responses. Since repeated exposure to PBDEs results in accumulation of these chemicals in the body, the Panel estimated the body burden at the BMDL in rodents, and the chronic intake that would lead to the same body burden in humans. For the remaining six congeners no studies were available to identify Reference Points. The Panel concluded that there is scientific basis for inclusion of all 10 congeners in a common assessment group and performed a combined risk assessment. The Panel concluded that the combined margin of exposure (MOET) approach was the most appropriate risk metric and applied a tiered approach to the risk characterisation. Over 84,000 analytical results for the 10 congeners in food were used to estimate the exposure across dietary surveys and age groups of the European population. The most important contributors to the chronic dietary Lower Bound exposure to PBDEs were meat and meat products and fish and seafood. Taking into account the uncertainties affecting the assessment, the Panel concluded that it is likely that current dietary exposure to PBDEs in the European population raises a health concern.

3D- and 2D-QSAR models’ study and molecular docking of novel nitrogen-mustard compounds for osteosarcoma

Background: The dipeptide-alkylated nitrogen-mustard compound is a new kind of nitrogen-mustard derivative with a strong anti-tumor activity, which can be used as a potential anti-osteosarcoma chemotherapy drug.

Objective: 2D- and 3D-QSAR (structure–activity relationship quantification) models were established to predict the anti-tumor activity of dipeptide-alkylated nitrogen-mustard compounds.

Method: In this study, a linear model was established using a heuristic method (HM) and a non-linear model was established using the gene expression programming (GEP) algorithm, but there were more limitations in the 2D model, so a 3D-QSAR model was introduced and established through the CoMSIA method. Finally, a series of new dipeptide-alkylated nitrogen-mustard compounds were redesigned using the 3D-QSAR model; docking experiments were carried out on several compounds with the highest activity against tumors.

Result: The 2D- and 3D-QSAR models obtained in this experiment were satisfactory. A linear model with six descriptors was obtained in this experiment using the HM through CODESSA software, where the descriptor “Min electroph react index for a C atom” has the greatest effect on the compound activity; a reliable non-linear model was obtained using the GEP algorithm model (the best model was generated in the 89th generation cycle, with a correlation coefficient of 0.95 and 0.87 for the training and test set, respectively, and a mean error of 0.02 and 0.06, respectively). Finally, 200 new compounds were designed by combining the contour plots of the CoMSIA model with each other, together with the descriptors in the 2D-QSAR, among which compound I1.10 had a high anti-tumor and docking ability.

Conclusion: Through the model established in this study, the factors influencing the anti-tumor activity of dipeptide-alkylated nitrogen-thaliana compounds were revealed, providing direction and guidance for the further design of efficient chemotherapy drugs against osteosarcoma.

2D, 3D-QSAR study and docking of vascular endothelial growth factor receptor 3 (VEGFR3) inhibitors for potential treatment of retinoblastoma

Background: Retinoblastoma is currently the most common malignant tumor seen in newborns and children's eyes worldwide, posing a life-threatening hazard. Chemotherapy is an integral part of retinoblastoma treatment. However, the chemotherapeutic agents used in clinics often lead to drug resistance. Thus there is a need to investigate new chemotherapy-targeted agents. VEGFR3 inhibitors are anti-tumour-growth and could be used to develop novel retinoblastoma-targeted agents. Objective: To predict drug activity, discover influencing factors and design new drugs by building 2D, 3D-QSAR models. Method: First, linear and non-linear QSAR models were built using heuristic methods and gene expression programming (GEP). The comparative molecular similarity indices analysis (COMISA) was then used to construct 3D-QSAR models through the SYBYL software. New drugs were designed by changing drug activity factors in both models, and molecular docking experiments were performed. Result: The best linear model created using HM had an R², S², and R²cv of 0.82, 0.02, and 0.77, respectively. For the training and test sets, the best non-linear model created using GEP had correlation coefficients of 0.83 and 0.72 with mean errors of 0.02 and 0.04. The 3D model designed using SYBYL passed external validation due to its high Q² (0.503), R² (0.805), and F-value (76.52), as well as its low standard error of SEE value (0.172). This demonstrates the model's reliability and excellent predictive ability. Based on the molecular descriptors of the 2D model and the contour plots of the 3D model, we designed 100 new compounds using the best active compound 14 as a template. We performed activity prediction and molecular docking experiments on them, in which compound 14.d performed best regarding combined drug activity and docking ability. Conclusion: The non-linear model created using GEP was more stable and had a more substantial predictive power than the linear model built using the heuristic technique (HM). The compound 14.d designed in this experiment has the potential for anti-retinoblastoma treatment, which provides new design ideas and directions for retinoblastoma-targeted drugs.

A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma

BACKGROUND

Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32).

AIM

The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL.

METHODOLOGY

Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds.

RESULT

MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies.

CONCLUSION

Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.

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.

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.

Structural studies on the endocrine-disrupting role of polybrominated diphenyl ethers (PBDEs) in thyroid diseases

Polybrominated diphenyl ethers (PBDEs) are synthetic brominated flame retardants with extensive applications in daily-life consumer products. However, PBDEs have become ubiquitous environmental contaminants due to their leach-out capability. The hazardous human health effects and endocrine-disrupting activity of PBDEs have led many governmental organizations to impose ban on their manufacture, causing their gradual phase out from commercial products. However, PBDEs and their metabolites are still being detected from biological and environmental samples owing to their persistence and bioaccumulation. The PDBE metabolites in these samples are present in concentrations often higher and even with higher toxic potential than parent PBDEs. The two commonly detected environmental PBDE congeners, 2,2',4,4'-tetra-bromodiphenyl ether (BDE-47) and 2,2',4,4',5-penta-bromodiphenyl ether (BDE-99), and their HO- and MeO- metabolites were considered in this study for their potential disrupting activity on thyroid hormone transport. Specifically, the study involved structural binding characterization of BDE-47 and BDE-99 including their two HO- and two MeO- metabolites with thyroxine-binding globulin (TBG), which is the main thyroid hormone transport protein in blood. The results showed that the binding pattern and molecular interactions of above two PBDEs and their metabolites exhibited overall similarity to native ligand, thyroxine in dock score, binding energy, and amino acid interactions with TBG. The BDE-99 and its metabolites were predicted to have stronger binding to TBG than BDE-47 with the metabolite 5-MeO-BDE-99 showing equal binding affinity to that of thyroxine. It is concluded that BDE-47 and BDE-99 and their metabolites have the potential to disrupt thyroid hormone transport and interfere in thyroid function.

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

A multi-activity three-dimensional quantitative structure-activity relationship (3D-QSAR) model was established based on the comprehensive evaluation index (CEI) of polychlorinated naphthalenes (PCNs). The CEI values were calculated using the vector analysis method in combination with the following parameters: biological toxicity (predicted by logEC₅₀), bioconcentration (predicted by logK_ow), long-distance migration (predicted by logP_L), and biodegradation (predicted by total-score). Additionally, sixty-four CN-70 derivatives with lower CEI values were designed, among which three derivatives with reduced CEI values were selected for verification based on an evaluation of their persistent organic pollutant properties and practicability. Finally, an environmental behavior simulation was conducted via molecular dynamics simulation aided by the Taguchi experimental design by considering the degradation characteristics of the three aforementioned CN-70 derivatives as an example. Only two of the selected CN-70 derivatives were observed to be more easily degraded when compared with the CN-70 molecule (ascending range: 11.57 %-13.57 %) in a real-world setting, which was consistent with the biodegradability prediction results (ascending range: 14.94 %-22.49 %) obtained through the molecular docking studies. The multi-activity 3D-QSAR model established in this study overcame the limitations of generating molecular designs based on single-effect models from the source because it focused on the multiple effects of the pollutants.

Evaluation and mechanistic study of chlordecone-induced thyroid disruption: Based on in vivo, in vitro and in silico assays

The present study aimed to evaluate the thyroid-disrupting potency of chlordecone, and reveal the underlying mechanism. In the in vivo assays, rare minnow embryos were exposed to 0, 0.01, 0.1, 1 and 10 μg·L^-1 chlordecone until sexually mature. The results showed decreased T4 but increased T3 concentrations in plasma, upregulated mRNA levels of thyrotropin-releasing hormone receptor (trhr) and sodium-iodide symporter (nis) in the brain, and transthyretin (ttr), thyroid hormone receptor α (trα) and deiodinase enzymes (dio1 and dio2) in the liver of adult fish. In the in vitro assays, single chlordecone treatments promoted growth hormone (GH) and prolactin (PRL) secretion in GH3 cells. Transcription of thyroid receptor (trβ) was inhibited, but this is not likely responsible for chlordecone-induced GH secretion and altered transcription. When co-treated with T3, chlordecone acted independently of the effect of T3 on GH secretion; chlordecone-induced GH/PRL secretion and mRNA expression were further promoted when co-treated with E2, but inhibited when co-treated with ICI, indicating an important role for estrogen receptors (ERs) in chlordecone-induced changes in GH3 cells. Furthermore, in silico prediction suggested no stable interactions between chlordecone and thyroid hormone-related proteins, as well as a regulatory role for ERs in thyroid systems. Overall, our results indicated that chlordecone may have adverse effects on thyroid systems upon long-term exposure. However, rather of TRs, ERs may be responsible for thyroid disruption following chlordecone exposure.

Detection Method of Environmentally Friendly Non-POP PBDEs by Derivatization-Enhanced Raman Spectroscopy Using the Pharmacophore Model

Background:

Polybrominated diphenyl ethers (PBDEs) are dangerous for the environment and human health because of their persistent organic pollutant (POP) characteristics, which have attracted extensive research attention. Raman spectroscopy is a simple highly sensitive detection operation. This study was performed to obtain environmentally friendly non-POP PBDE derivatives with simple detection-based molecular design and provide theoretical support for establishing enhanced Raman spectroscopic detection techniques.

Methods:

A three-dimensional quantitative structure-activity relationship (3DQSAR) pharmacophore model of characteristic PBDE Raman spectral was established using 20 and 10 PBDEs as training and test sets, respectively. Full-factor experimental design was used to modify representative commercial PBDEs, and their flame retardancy and POP characteristics were evaluated.

Results:

The pharmacophore model (Hypo1) exhibited good predictive ability with the largest correlation coefficient (R2) of 0.88, the smallest root mean square (RMS) value of 0.231, and total cost of 81.488 with a configuration value of 12.56 (˂17).74 monosubstituted and disubstituted PBDE derivatives were obtained based on the Hypo 1 pharmacophore model and full-factor experimental design auxiliary. Twenty PBDE derivatives were screened, and their flame-retardant capabilities were enhanced and their migration and bio-concentration were reduced (log(KOW) <5), with unchanged toxicity and high biodegradability. The Raman spectral intensities increased up to 380%. In addition, interference analysis of the Raman peaks by group frequency indicated that the 20 PBDE derivatives were easily detected with no interference in gaseous environments.

Conclusion:

Nine pharmacophore models were constructed in this study; Hypo 1 was the most accurate. Twenty PBDE derivatives showed Raman spectral intensities increased up to 380%; these were classified as new non-POP environmentally friendly flame retardants with low toxicity, low migration, good biodegradability, and low bio-concentrations. 2D QSAR analysis showed that the most positive Milliken charge and lowest occupied orbital energy were the main contributors to the PBDE Raman spectral intensities. Raman peak analysis revealed no interference between the derivatives in gaseous environments.

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

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).

Identifying the Antiproliferative Effect of Astragalus Polysaccharides on Breast Cancer: Coupling Network Pharmacology With Targetable Screening From the Cancer Genome Atlas

Background:Astragalus polysaccharides (APS), natural plant compounds, have recently emerged as a promising strategy for cancer treatment, but little is known concerning their effects on breast cancer (BC) tumorigenesis.

Methods: We obtained breast cancer genetic data from The Cancer Genome Atlas (TCGA) database, network pharmacology to further clarify its biological properties. Survival analysis and molecular docking techniques were implemented for the final screening to obtain key target information. Our experiments focused on the detection of intervention effects of APS on BC cells (MCF-7 and MDA-MB-231), and quantitative RT-PCR (qRT-PCR) was used to assess the expression of key targets.

Results: A total of 1,439 differentially expressed genes (DEGs) were identified by TCGA and used to build disease networks. Module analysis, gene ontology and pathway analysis revealed characteristic of the DEGs network. Topological properties were used to identify key targets, survival analysis and molecular docking finally found that the targets of APS regulation of BC cells may be CCNB1, CDC6, and p53. Through cell viability, migration and invasion assays, we found that APS interferes with the development of breast cancer in MCF7 and MDA-MB-231 cells in a dose-dependent manner. Furthermore, qRT-PCR verification suggested that the expression of CCNB1 and CDC6 in breast cancer cells was significantly downregulated in response to APS, while expression of the tumor suppressor gene P53 was significantly increased.

Conclusion: Results of this study suggest therapeutic potential for APS in BC treatment, possibly through interventions with CCNB1, CDC6, and P53. Furthermore, these findings illustrate the feasibility of using network pharmacology to connect large-scale target data as a way to discover the mechanism of natural products interfering with disease.

Designing modified polybrominated diphenyl ether BDE-47, BDE-99, BDE-100, BDE-183, and BDE-209 molecules with decreased estrogenic activities using 3D-QSAR, pharmacophore models coupled with resolution V of the 210-3 fractional factorial design and molecular docking

A 3D-QSAR model was constructed to predict polybrominated diphenyl ether (PBDE) estrogenic activities expressed as median effective concentrations (pEC₅₀), and resolution V of the 2^10-3 fractional factorial design and a pharmacophore model were used to modify the target PBDE molecules BDE-47, BDE-99, BDE-100, BDE-183, and BDE-209 to decrease the estrogenic activities. The persistent-organic-pollutant-related and flame-retardant properties of the modified molecules were evaluated. The mechanisms involved in decreasing PBDE estrogenic activities were explored through molecular docking. The 3D-QSAR model gave a cross-validated correlation coefficient (q²) of 0.682 (i.e., >0.5) and a non-cross-validated correlation coefficient (r²) of 0.980 (i.e., >0.9). Mono- and di-substitutions and hydrophobic substituent groups gave 40 modified molecules with decreased estrogenic activities, including modified BDE-47 and BDE-99 with pEC₅₀ decreased by >10% and modified BDE-100, BDE-183, and BDE-209 with pEC₅₀ decreased by >20%. The modified molecules had similar flame-retardancy to the unmodified molecules, and lower biotoxicities (by a maximum of 17.27%), persistences (by a maximum of 55.68%), bioconcentration (by 4.28%-23.91%), and long-range transport potentials (by 0.72%-18.47%). Docking indicated that hydrophobic interactions were the main factors affecting PBDE estrogenic activities. The results provide a theoretical basis for designing less estrogenic flame retardants than are currently available.

Environmentally friendly polychlorinated naphthalenes (PCNs) derivatives designed using 3D-QSAR and screened using molecular docking, density functional theory and health-based risk assessment

A complete design and screening system for environmental-friendly polychlorinated naphthalene (PCN) derivatives was established through three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, density functional theory (DFT) methods and health-based risk assessment based on dynamic multimedia fugacity model. Two types of 3D-QSAR models were established for PCNs using the experimental biological toxicity (logEC₅₀) of 14 PCNs to carry out a modification to lower the logEC₅₀ of CN-70. Consequently, 67 new monosubstituted and disubstituted derivatives with a lower biological toxicity than CN-70 were designed. Furthermore, 21 new CN-70 derivatives were selected through the evaluation of their persistent organic pollutant properties (biological toxicity, bio-concentration, long-range transport potential, biodegradability) and practicability (stability, insulativity, flame retardancy) using 3D-QSAR, molecular docking and DFT methods. Finally, the non-carcinogenic and carcinogenic risks of 19 new CN-70 derivatives in different exposure pathways were reduced, and 5 derivatives with a significant decrease both in biological toxicity (amplitude reduction: 12.73%-32.51%) and risk (amplitude reduction: 32.18%-59.19%) were selected as environmental-friendly PCN derivatives, which had been screened using the health-based risk assessment system associated with dynamic multimedia fugacity model. This study provides a theoretical basis for the design of environmental-friendly flame retardants and insulating materials.

Combined molecular docking, homology modelling and density functional theory studies to modify dioxygenase to efficiently degrade aromatic hydrocarbons

To promote the biodegradation of aromatic hydrocarbons in petroleum-contaminated soils, naphthalene dioxygenase (NDO), which is the key metabolic enzyme that degrades aromatic hydrocarbons, was modified using molecular docking and homology modelling. The novel NDO enzymes screened can efficiently degrade the target aromatic hydrocarbons naphthalene, anthracene, pyrene and benzo[a]pyrene. The docking showed that the key amino acid residues at the binding site of the NDO enzyme include both hydrophilic residues (Asn201, Asp205, His208, His213, His295 and Asn297) and hydrophobic residues (Phe202, Ala206, Val209, Leu307, Phe352 and Trp358), and the hydrophilic residues were replaced by hydrophobic residues to design 54 kinds of NDO enzyme modification schemes. A total of 14 kinds of novel NDO enzymes designed were found to simultaneously increase the binding affinity to the target aromatic hydrocarbons. The energy barrier and rate constant of the degradation reaction for the NDO enzyme modification were calculated using Gaussian09 software and the KiSThelP program. The novel NDO-7 enzyme exhibited decreases in the energy barrier of 76.28, 26.35, 4.39 and 1.88 kcal mol⁻¹ and increases in the rate constant of 54, 18, 12 and 5 orders of magnitude in the degradation reactions with naphthalene, anthracene, pyrene and benzo[a]pyrene, respectively. These results provide a theoretical basis for the efficient degradation of aromatic hydrocarbons and the modification of their key metabolic enzymes.

To promote the biodegradation of aromatic hydrocarbons in petroleum-contaminated soils, naphthalene dioxygenase (NDO), which is the key metabolic enzyme that degrades aromatic hydrocarbons, was modified using molecular docking and homology modelling.

Virtual Screening, Biological Evaluation, and 3D-QSAR Studies of New HIV-1 Entry Inhibitors That Function via the CD4 Primary Receptor

Human immunodeficiency virus type 1 (HIV-1) is responsible for the majority of HIV infections worldwide, and we still lack a cure for this infection. Blocking the interaction of HIV-1 and its primary receptor CD4 is one strategy for identifying new anti-HIV-1 entry inhibitors. Here we report the discovery of a novel ligand that can inhibit HIV-1 entry and infection via CD4. Biological and computational analyses of this inhibitor and its analogs, using bioactivity evaluation, Rule of Five (RO5), comparative molecular field analysis (CoMFA)/comparative molecular similarity index analysis (CoMSIA) models, and three-dimensional quantitative structure-activity relationship (3D-QSAR), singled out compound 3 as a promising lead molecule for the further development of therapeutics targeting HIV-1 entry. Our study demonstrates an effective approach for employing structure-based, rational drug design techniques to identify novel antiviral compounds with interesting biological activities.

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.

Relationship between the binding free energy and PCBs' migration, persistence, toxicity and bioaccumulation using a combination of the molecular docking method and 3D-QSAR

The molecular docking method was used to calculate the binding free energies between biphenyl dioxygenase and 209 polychlorinated biphenyl (PCB) congeners. The relationships between the calculated binding free energies and migration (octanol-air partition coefficients, KOA), persistence (half-life, t1/2), toxicity (half maximal inhibitory concentration, IC50), and bioaccumulation (bioconcentration factor, BCF) values for the PCBs were used to gain insight into the degradation of PCBs in the presence of biphenyl dioxygenase. The relationships between the calculated binding free energies and the molecular weights, KOA, BCF, and t1/2 values for the PCBs were statistically significant (P < 0.01), whereas the relationship between the calculated binding free energies and the IC50 for the PCBs was not statistically significant (P > 0.05). The electrostatic field, derived from three-dimensional quantitative structure-activity relationship studies, was a primary factor governing the binding free energy, which agreed with literature findings for KOA, t1/2, and BCF. Comparative molecular field analysis and comparative molecular similarity indices analysis contour maps showed that the binding free energies, KOA, t1/2, and BCF values for the PCBs decreased simultaneously when substituents with electropositive groups at the 3-position or electronegative groups at the 3'-position were introduced. This indicated the binding free energy was correlated with the persistent organic pollutant characteristics of PCBs. Furthermore, low binding free energies improved the degradation of the PCBs and simultaneously decreased the KOA, t1/2, and BCF values, thereby reducing the persistent organic pollutant characteristics of PCBs in the environment. These results are expected to be beneficial in providing a theoretical foundation for further elucidation of the degradation and molecular modification of PCBs.

Pentachlorophenol molecule design with lower bioconcentration through 3D-QSAR associated with molecule docking

A three-dimensional quantitative structure activity relationship (3D-QSAR) model is built by using a comparative molecular similarity indices analysis (CoMSIA) technique with an experimentally determined logarithm of bioconcentration factors (logBCFs) for 36 phenols in fish. Meanwhile, with the pentachlorophenol (PCP) molecule as target molecules, contributions of the molecular fields indicate that the electrostatic fields are the main influences on the bioconcentration of the PCP molecule. Based on the analytical results of CoMSIA contour map of PCP and PCP molecular docking with SOD protease (PDB ID: 4A7T), the R₆ substituent positions of PCP were modified to give seven new modified PCP molecules with low bioconcentration in this paper. The energy barrier calculation of the new modified PCP molecular reaction pathways can infer the order of the substitution reaction s as -SCl > -CH₂Cl > -COCl > -CCl₃ > -CH=CH₂ > -NO₂ > -SH. These calculations, combined with anaerobic biodegradation, ecotoxic effect, and mobility of new modified PCP molecules, enable a new environmentally friendly compound when the Cl at the R₆ position of PCP was replaced with -COCl substituent with low bioconcentration (reduced by 32.89%), ecotoxic effect basically unchanged (increased by 1.37%), anaerobic biodegradation increased (increased by 24.81%), and mobility basically unchanged (reduced by 0.94%) to be designed.

Quantum chemical and molecular dynamics modelling of hydroxylated polybrominated diphenyl ethers

A series of 19 hydroxylated polybrominated diphenyl ethers (OH-PBDEs) have been studied using density functional theory (DFT) and molecular dynamics simulations with the purpose of investigating eventual correlations between their physicochemical properties and toxic action. Dissociation constants (pK_a), solvation free energies and octanol-water partition coefficients (log P) have been computed. Additionally, metadynamics simulations of OH-PBDEs passing through a lipid bilayer have been carried out for four OH-PBDE species. No correlations between computed pK_a values and toxicity data have been found. Medium correlations were found between partition coefficients and the ability of OH-PBDEs to alter membrane potential in cell cultures, which is attributed to higher uptake of molecules with larger log P parameters. It was also demonstrated that in lipid bilayers, OH-PBDE molecules differ in their orientational distributions and can adopt different conformations which can affect the uptake of these molecules and influence the pathways of their toxic action.

Pentachlorophenol affected both reproductive and interrenal systems: In silico and in vivo evidence

The present study investigated the effects on reproductive and interrenal system by pentachlorophenol (PCP) using in silico and in vivo assays. Molecular docking results indicated interacting potency of PCP with steroid receptors (ERα, ERβ, AR, GR) but not Cytochrome P450 enzymes (CYPs). In the in vivo assay, sexually matured rare minnow (Gobiocypris rarus) was exposed to environmental relevant concentrations of PCP (0, 0.5, 5, 50 μg L^-1). In male fish, 14-d exposure caused up-regulation of mRNA levels of hepatic erα, erβ, ar, gr, vtg and gonadal erα, vtg, ar, dmrt1, providing evidence for agonistic activities for steroid receptors by PCP. The up-regulated mRNA of gnrh, crf, pomc in the brain also indicated feed-forward responses of the hypothalamic-pituitary-gonadal/interrenal (HPG/I) axis. However, at 28th d the feed-forward response of the HPG axis seemed eased back and the HPI axis showed negative feedback responses. Corresponding changes including increases of plasma steroid hormones, inhibition of spermatogenesis, and decreased RSI were observed in male fish upon 28-d exposure to PCP. In the females, a transition from feed-forward responses to negative feedbacks of the HPG/I axis was also indicated by the transcriptional profiles at 14th and 28th day. Corresponding changes including increased E2, T and decreased C levels, degenerated ovaries, and decreased GSI and RSI were also observed. Overall, we concluded that PCP could interfere with steroid receptors, evoke responses of HPG/I axis, and finally result in adverse effects on reproductive and interrenal system in rare minnow at environmental relevant concentrations.

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.

Prediction of octanol-air partition coefficients for polychlorinated biphenyls (PCBs) using 3D-QSAR models

Based on the experimental data of octanol-air partition coefficients (KOA) for 19 polychlorinated biphenyl (PCB) congeners, two types of QSAR methods, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), are used to establish 3D-QSAR models using the structural parameters as independent variables and using logKOA values as the dependent variable with the Sybyl software to predict the KOA values of the remaining 190 PCB congeners. The whole data set (19 compounds) was divided into a training set (15 compounds) for model generation and a test set (4 compounds) for model validation. As a result, the cross-validation correlation coefficient (q(2)) obtained by the CoMFA and CoMSIA models (shuffled 12 times) was in the range of 0.825-0.969 (>0.5), the correlation coefficient (r(2)) obtained was in the range of 0.957-1.000 (>0.9), and the SEP (standard error of prediction) of test set was within the range of 0.070-0.617, indicating that the models were robust and predictive. Randomly selected from a set of models, CoMFA analysis revealed that the corresponding percentages of the variance explained by steric and electrostatic fields were 23.9% and 76.1%, respectively, while CoMSIA analysis by steric, electrostatic and hydrophobic fields were 0.6%, 92.6%, and 6.8%, respectively. The electrostatic field was determined as a primary factor governing the logKOA. The correlation analysis of the relationship between the number of Cl atoms and the average logKOA values of PCBs indicated that logKOA values gradually increased as the number of Cl atoms increased. Simultaneously, related studies on PCB detection in the Arctic and Antarctic areas revealed that higher logKOA values indicate a stronger PCB migration ability. From CoMFA and CoMSIA contour maps, logKOA decreased when substituents possessed electropositive groups at the 2-, 3-, 3'-, 5- and 6- positions, which could reduce the PCB migration ability. These results are expected to be beneficial in predicting logKOA values of PCB homologues and derivatives and in providing a theoretical foundation for further elucidation of the global migration behaviour of PCBs.

Structure–activity relationship and binding mode studies for a series of diketo-acids as HIV integrase inhibitors by 3D-QSAR, molecular docking and molecular dynamics simulations

We explored the main factors affecting the activity of compounds by different statistical and computational methods.

Identification of triazolo[4,5-b]pyrazine derivatives as hepatocyte growth factor receptor inhibitors through structure-activity relationships and molecular docking simulations

c-MET is a receptor tyrosine kinase and potential oncological target for cancer therapy. The activities of 1,2,3-triazolo[4,5-b]pyrazine series of c-MET inhibitors were analyzed according to the three-dimensional quantitative structure-activity relationship and molecular docking methods. The results indicated that the hydrophobic and electrostatic fields play key roles in activity and QSAR model was reliable enough for activity prediction. Moreover, the docking results do validate the predicted 3D-QSAR scores, vital residues Asp1222, Asp1231, Met1160, Tyr1259 and Tyr1230 found in binding site. Four new c-MET inhibitor analogs designed in this Letter which are being currently synthesized by our laboratories.

Effects of HO-/MeO-PBDEs on androgen receptor: in vitro investigation and helix 12-involved MD simulation

Hydroxylated and methoxylated polybrominated diphenyl ethers (HO-/MeO-PBDEs) have received increasing attention for their potential endocrine disrupting activities and widely environmental distribution. However, little information is available for the anti-androgenic activities, and the molecular mechanism of interactions with androgen receptor (AR) is not fully understood. In the present study, cell line assay and computational simulation were integrated to systematically explore the molecular mechanism of interactions between chemicals and AR. The metabolites with similar molecular structures exhibited different anti-androgenic activity while none of them showed androgenic activity. According to the multisystem molecular dynamics simulation, minute differences in the structure of ligands induced dramatic different conformational transition of AR-ligand binding domain (LBD). The Helix12 (H12) component of active ligands occupied AR-LBD could become stable, but this component continued to fluctuate in inactive ligands occupied AR-LBD. Settling time and reposition of H12 obtained in dynamics process are important factors governing anti-androgenic activities. The related settling times were characteristic of anti-androgenic potencies of the tested chemicals. Overall, in our study, the stable reposition of H12 is characterized as a computational mark for identifying AR antagonists from PBDE metabolites, or even other various environmental pollutants.