Computational Analysis of CRTh2 receptor antagonist: A Ligand-based CoMFA and CoMSIA approach

Exposure to high-performance benzotriazole ultraviolet stabilizers: Advance in toxicological effects, environmental behaviors and remediation mechanism using in-silica methods

Benzotriazole ultraviolet stabilizers (BUVSs), as light stabilizers, have attracted widespread attention because of their easy migration in the environment and their acute toxicity and biological toxicity effects, such as immunotoxicity and hepatotoxicity. Accordingly, the treatment and remediation mechanisms of high-performance, environmentally friendly, and low human health risk BUVS substitutes were analyzed. Firstly, the weights and the comprehensive effect (CE) values of migration and toxicity of BUVSs were determined by Topsis assisted by the coefficient of variation (CV) method. From this, a three-dimensional quantitative structure activity relationship (3D-QSAR) model based on the CE values of the 13 BUVSs was constructed. Secondly, EPI software was used to predict the functionality and environmental friendliness of BUVS substitutes, and a partial least squares regression machine learning (ML-PLSR) model was used to analyze the mechanism. Then, ADMET (absorption, distribution, metabolism, excretion, toxicity), TOPKAT, and exposure dose models were used to evaluate the ecological and human health risks of BUVSs and their substitutes. Finally, the key charge information affecting the UV-326 substitutes was deduced by time dependent density functional theory (TDDFT). Using UV-326 as an example, 15 UV-326 substitutes with reduced CE values were designed (reductions of 2.61%-23.18%). Compared with ML-PLSR models of acute toxicity, immunotoxicity, and hepatotoxicity, it was found that the decrease of DM and Q_yy values and the increase of Q_zz value could further decrease the toxicity of the UV-326 substitutes. Ecological and human health risk assessment showed that the exposure risks of the six UV-326 substitutes were within acceptable limits. TDDFT showed that the change of electron distribution and electron excitation type were the key factors affecting the performance of the UV-326 substitutes, and a charge transfer excitation type was more conducive to obtaining high-performance, environmentally friendly UV-326 substitutes. This study aims to alleviate the toxic damage to the ecological environment and human health caused by BUVS exposure.

Isolation, bioassay and 3D-QSAR analysis of 8-isopentenyl flavonoids from Epimedium sagittatum maxim. as PDE5A inhibitors

BACKGROUND

As known, inhibition of phosphodiesterase 5 (PDE5) has the therapeutic effect on male erectile dysfunction (ED), and the processed folium of Epimedium sagittatum Maxim. (PFES) characterized by 8-isopentenyl flavonoids is a famous herb for treating ED. However, the main flavonoids inhibitory activities, structure-activity relationship (SAR) and signaling pathway have been not systematically studied so that its pharmacodynamic mechanism is unclear.

METHODS

We aimed to initially reveal the PFES efficacy mechanism for treating ED. For the first time, 6 main 8-isopentenyl flavonoids (1-6) from PFES were isolated and identified. Then based on HPLC detection, we proposed a novel method to screen inhibitors among them. We further analyze the three-dimensional quantitative structure-activity relationship (3D-QSAR) for those inhibitors.

RESULTS

The results were verified by cellular effects of the screened flavonoids. Among 6 compounds, Icariin: (1), 2-O''rhamnosylicaridide II (2) and Baohuoside I (3) were identified with significant activities (IC₅₀ = 8.275, 3.233, 5.473 μM). Then 3D-QSAR studies showed that the replacement of C8 with bulky steric groups as isopentenyl, C3 with positive charge groups and C4' with a hydrogen bond acceptor substituent could increase inhibitory effects. In contrast, the substitution of C7 with bulky steric groups or hydrophilic groups tended to decrease the efficacies. And compounds 1, 2, 3 could increase cGMP level and decrease cytoplasmic Ca²⁺ of rat corpus cavernosum smooth muscle cells (CCSMCs)by activating PKG.

CONCLUSION

8-isopentenyl flavonoids could be the main pharmacodynamic substances of PFES in the treatment for ED, and some had significant PDE5A1 inhibitory activities so as to activate cGMP/PKG/Ca²⁺ signaling pathway in CCSMCs, that was related to the substituents at the key sites such as C8, C3, C4' and C7 in the characteristic compounds.

A 3D-QSAR model for the comprehensive bioenrichment and biodegradation effect of benzotriazole ultraviolet stabilisers and application of the model in molecular modification

Ultraviolet (UV) absorber, a type of light stabiliser, has received considerable attention because of its high bioenrichment ability and low biodegradability. In this study, benzotriazole ultraviolet stabilisers (BUVSs) were used as the research object, and the bioenrichment and biodegradation data of 13 types of BUVS molecules were subjected to dimensionless processing through quartile data transformation. Additionally, a three-dimensional quantitative structure-activity relationship (3D-QSAR) model was constructed for the investigation of the comprehensive effect of molecular bioenrichment and biodegradation of BUVSs, and improved derivative molecules were designed. Furthermore, the validity of the model was predicted using EPI simulation software, and finally, the biodegradability of BUVSs and their bioenrichment and biological effect before and after modification in the food chain and in the aerobic and anaerobic bacteria in sewage were analysed through the molecular docking technology. A total of 10 derivatives with reduced enrichment ability and enhanced degradability were designed using the CoMFA model analysis (reduction: combined effect value, 0.32-20.55%; log BCF, 2.37-17.59%; and log HL, 0.47-16.94%). Molecular docking showed that the bioenrichment ability of two derivative molecules in the four organisms was decreased by 1.87-27.67%, and the biodegradation ability of four derivative molecules in the three sewage bacteria was enhanced by 1.60-33.38% compared with those before modification. The molecular modification method of UV absorbent developed in this study provides a new perspective for further studies on environment-friendly UV absorbent and helps reduce the risks of these emerging pollutants on the environment and human body.

Effects of Phthalate Esters (PAEs) on Cell Viability and Nrf2 of HepG2 and 3D-QSAR Studies

Phthalate esters (PAEs) are a widespread environmental pollutant, and their ecological and environmental health risks have gradually attracted attention. To reveal the toxicity characteristics of these compounds, ten PAEs were selected as research objects to establish a cell model. CCK-8 was used to determine cell viability, Western blots were used to determine the content of Nrf₂ in HepG2, and the LD₅₀ collected for the 13 PAEs administered to rats. On this basis, 3D-QSAR models of IC₅₀, LD₅₀ and Nrf2 were established. The experimental results showed that as the time of PAEs exposure increased (24, 48 and 72 h), cell viability gradually decreased. The test concentration (62.5 /125/250 μM) of PAEs exposed for 48 h could significantly increase the content of Nrf2, and the 1000 μM PAEs could inhibit the content of Nrf2. The model is relatively stable and predicts well that the introduction of large and hydrophobic groups may significantly affect the toxic effects of PAEs on cells. The present study provided a potential tool for predicting the LD50 and Nrf2 of new PAEs, and provide a reference for the design of new less toxic PAEs in the future.

A Modified 3D-QSAR Model Based on Ideal Point Method and Its Application in the Molecular Modification of Plasticizers with Flame Retardancy and Eco-Friendliness

The addition of plasticizers makes plastics flammable, and thus, poses a potential risk to the environment. In previous researches, plasticizers with flame retardancy had been synthesized, but their eco-friendliness had not been tested or described. Thus, in this paper, eco-friendliness plasticizers with flame retardancy were designed based on phthalic acid esters (PAEs), which are known as common plasticizers and major plastic additives. For a comprehensive analysis, such as flammability, biotoxicity, and enrichment effects, 17 PAEs’ comprehensive evaluation values were calculated based on the ideal point method. Further, a multi-effect three-dimensional quantitative structure-activity relationship (3D-QSAR) model of PAEs’ flammability, biotoxicity and enrichment effects was constructed. Thus, 18 dimethyl phthalate (DMP) derivatives and 20 diallyl phthalate (DAP) derivatives were designed based on three-dimensional contour maps. Through evaluation of eco-friendliness and flammability, six eco-friendly PAE derivatives with flame retardancy were screened out. Based on contour maps analysis, it was confirmed that the introduction of large groups and hydrophobic groups was beneficial to the simultaneous improvement of PAEs’ comprehensive effects, and multiple effects. In addition, the group properties were correlated significantly with improved degrees of the comprehensive effects of corresponding PAE derivatives, confirming the feasibility of the comprehensive evaluation method and modified scheme.

A 3D-QSAR Study on the Antitrypanosomal and Cytotoxic Activities of Steroid Alkaloids by Comparative Molecular Field Analysis

As part of our research for new leads against human African trypanosomiasis (HAT), we report on a 3D-QSAR study for antitrypanosomal activity and cytotoxicity of aminosteroid-type alkaloids recently isolated from the African medicinal plant Holarrhena africana A. DC. (Apocynaceae), some of which are strong trypanocides against Trypanosoma brucei rhodesiense (Tbr), with low toxicity against mammalian cells. Fully optimized 3D molecular models of seventeen congeneric Holarrhena alkaloids were subjected to a comparative molecular field analysis (CoMFA). CoMFA models were obtained for both, the anti-Tbr and cytotoxic activity data. Model performance was assessed in terms of statistical characteristics (R², Q², and P² for partial least squares (PLS) regression, internal cross-validation (leave-one-out), and external predictions (test set), respectively, as well as the corresponding standard deviation error in prediction (SDEP) and F-values). With R² = 0.99, Q² = 0.83 and P² = 0.79 for anti-Tbr activity and R² = 0.94, Q² = 0.64, P² = 0.59 for cytotoxicity against L6 rat skeletal myoblasts, both models were of good internal and external predictive power. The regression coefficients of the models representing the most prominent steric and electrostatic effects on anti-Tbr and for L6 cytotoxic activity were translated into contour maps and analyzed visually, allowing suggestions for possible modification of the aminosteroids to further increase the antitrypanosomal potency and selectivity. Very interestingly, the 3D-QSAR model established with the Holarrhena alkaloids also applied to the antitrypanosomal activity of two aminocycloartane-type compounds recently isolated by our group from Buxus sempervirens L. (Buxaceae), which indicates that these structurally similar natural products share a common structure⁻activity relationship (SAR) and, possibly, mechanism of action with the Holarrhena steroids. This 3D-QSAR study has thus resulted in plausible structural explanations of the antitrypanosomal activity and selectivity of aminosteroid- and aminocycloartane-type alkaloids as an interesting new class of trypanocides and may represent a starting point for lead optimization.

Ribosome profiling reveals translational regulation of mammalian cells in response to hypoxic stress

Background

Retinal pigment epithelium (RPE) cells transfer oxygen and nutrients from choroid to the neural retina. Reduced oxygen to RPE perturbs development and functions of blood vessels in retina. Previous efforts of genome-wide studies have been largely focused on transcriptional changes of cells in response to hypoxia. Recently developed ribosome profiling provides an opportunity to study genome-wide translational changes. To gain systemic insights into the transcriptional and translational regulation of cellular in response to hypoxic stress, we used simultaneous RNA sequencing and ribosome profiling on an RPE cells line, ARPE-19, under hypoxia condition.

Results

Both HIF-1α and EPAS1 (HIF-2α) proteins were stabilized in ARPE-19 under hypoxic stress treatment at 1 h, 2 h and 4 h. Analysis of simultaneous RNA sequencing and ribosome profiling data showed genome-wide gene expression changes at both transcriptional and translational levels. Comparative analysis of ribosome profiling and RNA-seq data revealed that hypoxia induced changes of more genes at the translational than the transcriptional levels. Ribosomes densities at 5′ untranslated region (UTR) significantly increased under hypoxic stress. Interestingly, the increase in ribosome densities at 5′ UTR is positively correlated with the presence of upstream open reading frames (uORFs) in the 5′ UTR of mRNAs.

Conclusion

Our results characterized translational profiles of mRNAs for a RPE cell line in response to hypoxia. In particular, uORFs play important roles in the regulation of translation efficiency by affecting ribosomes loading onto mRNAs. This study provides the first attempt to understand translational response of mammalian cells under hypoxic condition.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3996-8) contains supplementary material, which is available to authorized users.

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.

The effect of N-methylation of amino acids (Ac-X-OMe) on solubility and conformation: a DFT study

N-Methylation of amino acid derivatives (Ac-X-OMe, X = Gly, Val, Leu, Ile, Phe, Met, Cys, Ser, Asp and His) leads to an increase in aqueous solubility, lipophilicity and lowering of the cis/trans amide conformational energy barrier (E_A).