On the toxicity of para-substituted phenols and their quinone metabolites: Quantum chemical study

Clickable APEX2 Probes for Enhanced RNA Proximity Labeling in Live Cells

Although APEX2-mediated proximity labeling has been extensively implemented for studying RNA subcellular localization in live cells, the biotin-phenoxyl radical used for labeling RNAs has a relatively low efficiency, which can limit its compatibility with other profiling methods. Herein, a set of phenol derivatives were designed as APEX2 probes through balancing reactivity, hydrophilicity, and lipophilicity. Among these derivatives, Ph_N3 exhibited reliable labeling ability and enabled two biotinylation routes for downstream analysis. As a proof of concept, we used APEX2/Ph_N3 labeling with high-throughput sequencing analysis to examine the transcriptomes in the mitochondrial matrix, demonstrating high sensitivity and specificity. To further expand the utility of Ph_N3, we employed mechanistically orthogonal APEX2 and singlet oxygen (1O2)-mediated strategies for dual location labeling in live cells. Specifically, DRAQ5, a DNA-intercalating photosensitizer, was applied for nucleus-restricted 1O2 labeling. We validated the orthogonality of APEX2/Ph_N3 and DRAQ5-1O2 at the imaging level, providing an attractive and feasible approach for future studies of RNA translocation in live cells.

Quality preservation and decay reduction of minimally processed seedless barberry fruit via postharvest ultrasonic treatment

Seedless barberry fruit is one of the important horticultural products of Iran, which has health benefits due to great amounts of phenolic compounds, flavonoids, and antioxidant activity. However, fresh barberry fruit has a short shelf life even at cold storage, mainly due to high water content and thin skin that leads to fungal decay and high postharvest loss. We examined the effectiveness of the postharvest ultrasonic technology on the quality preservation and nutritional value of fresh seedless barberry fruit and their decay reduction during cold storage. Experimental treatments were the time and temperature of ultrasound (US) and included: (1) control, fruit without US, (2) 5 min US at 20°C, (3) 5 min US at 30°C, (4) 5 min US at 40°C, (5) 10 min US at 20°C, (6) 10 min US at 30°C, (7) 10 min US at 40°C, (8) 15 min US at 20°C, (9) 15 min US at 30°C, and (10) 15 min US at 40°C. After applying the treatments, the fruits were sealed in polyethylene bags and stored at 4 ± 1°C for 20 days. The results showed that all US treatments had higher titratable acidity, antioxidant activity, phenol content, and vitamin C content than the control. However, the highest titratable acidity and antioxidant activity values were obtained in US treatments at 40°C and 30°C for 15 min. Also, US treatment significantly reduced the total soluble solids, decay percentage, and microbial load of fresh barberry fruit. As the US treatment temperature increased from 20°C to 40°C, the decay and microbial load of fruit significantly decreased. In conclusion, this study proved the potential application of the US for preserving the quality of fresh seedless barberry fruit, and the most optimal US temperature and its application time was 40°C for 15 min.

Methoxylated flavones with potential therapeutic and photo-protective attributes: Theoretical investigation of substitution effect

The molecular and electronic structure of parent flavone and 49 (poly)methoxylated flavones (P)MFs were studied theoretically. Selected group of flavonoids consists of compounds naturally occurring in citrus plants or synthetic derivatives of flavone. These compounds exhibit several bioactivities in vitro and in vivo and can protect plants from solar ultraviolet (UV) radiation. Substitution induced structural changes in (P)MFs were correlated with published experimental values of P-glycoprotein inhibition effect. We have demonstrated that the C5-C10 bond length of 1-benzopyran-4-one moiety represents a suitable structural descriptor for this bioactivity. Obtained linear equations for the compounds with substituted and non-substituted C3 position enable the prediction of the potential anti-cancer chemo-preventive effect of the rest of studied (P)MFs. Consequently, potentially more effective substances were suggested. Optical properties of (P)MFs and their relationship with the molecular structure was examined in detail for methanol environment, as well. The multiple linear regression model was applied to assess the correlation between experimental absorption and fluorescence wavelengths with the theoretically predicted ones. The UV photo-protective potential of studied derivatives was estimated from the calculated optical properties.

Mitigation of membrane biofouling via immobilizing Ag-MOFs on composite membrane surface for extractive membrane bioreactor

The extractive membrane bioreactor (EMBR) combines an extractive membrane process and bioreactor to treat highly saline recalcitrant organic wastewater, in which the organic contaminations diffuse through a semi-permeable polydimethysiloxane (PDMS) composite membrane from the feed wastewater to the receiving biomedium. During the long-term EMBR operation, membrane biofouling is an inevitable phenomenon, which is one of the main obstacles impeding its wide applications. The excessive biofilm deposited on membrane surface could significantly reduce the organic mass transfer coefficient of composite membranes by more than 40%. Therefore, in this work, the silver (Ag)-metal organic frameworks (MOFs) were synthesized and immobilized on the PDMS surface of nanofibrous composite membranes to mitigate the membrane biofouling. The robustness of Ag-MOFs coating on membrane surface was well demonstrated by ultrasonic treatment. In addition, the silver nanoparticles (AgNPs) were coated on the PDMS surface of composite membranes for comparison. In contrast with the unmodified composite membrane #M0, the AgNPs-coated (#M1) and Ag-MOFs modified (#M2) composite membranes possessed less hydrophobic and negatively charged surfaces due to the coating layers. Although the modified membranes exhibited lower phenol mass transfer coefficients (k0's) in the aqueous-aqueous extractive membrane process due to these additional modification layers, both #M1 and #M2 displayed better long-term performance in the 12-days continuous EMBR operations due to their excellent anti-biofouling properties. Moreover, #M2 exhibited the most stable EMBR performance among the composite membranes developed in this work and other reported membranes with a finally stabilized k0 of 33.0 × 10-7 m/s (89% of initial k0). The least amounts of proteins, polysaccharides and total suspended solids (TSS) on the surface of tested #M2 also demonstrated its outstanding biofouling resistance. This excellent anti-biofouling performance should be attributed to the stable, controlled and long-lasting Ag+release from Ag-MOFs, as well as its less hydrophobic and negative charged surface properties, which made #M2 undergo the k0's increasing and gradual stabilization stages in the long-term EMBR operations.

Lipid Digestibility and Polyphenols Bioaccessibility of Oil-in-Water Emulsions Containing Avocado Peel and Seed Extracts as Affected by the Presence of Low Methoxyl Pectin

In this study, the digestibility of oil-in-water (O/W) emulsions using low methoxyl pectin (LMP) as surfactant and in combination with avocado peel (AP) or seed (AS) extracts was assessed, in terms of its free fatty acid (FFA) release and the phenolic compound (PC) bioaccessibility. With this purpose, AP and AS were characterized by UPLC-ESI-MS/MS before their incorporation into O/W emulsions stabilized using LMP. In that sense, AP extract had a higher content of PCs (6836.32 ± 64.66 mg/100 g of extract) compared to AS extract (1514.62 ± 578.33 mg/100 g of extract). Both extracts enhanced LMP's emulsifying properties, leading to narrower distributions and smaller particle sizes compared to those without extracts. Similarly, when both LMP and the extracts were present in the emulsions the FFA release significantly increased. Regarding bioaccessibility, the PCs from the AS extracts had a higher bioaccessibility than those from the AP extracts, regardless of the presence of LMP. However, the presence of LMP reduced the bioaccessibility of flavonoids from emulsions containing either AP or AS extracts. These results provide new insights regarding the use of PC extracts from avocado peel and seed residues, and the effect of LMP on emulsion digestibility, and its influence on flavonoids bioaccessibility.

Solvation Thermodynamics in Different Solvents: Water-Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory

Reliable information on partition coefficients plays a key role in drug development, as solubility decisively affects bioavailability. In a physicochemical context, the partition coefficient of a solute between two different solvents can be described as a function of solvation free energies. Hence, substantial scientific efforts have been made toward accurate predictions of solvation free energies in various solvents. The grid inhomogeneous solvation theory (GIST) facilitates the calculation of solvation free energies. In this study, we introduce an extended version of the GIST algorithm, which enables the calculation for chloroform in addition to water. Furthermore, GIST allows localization of enthalpic and entropic contributions. We test our approach by calculating partition coefficients between water and chloroform for a set of eight small molecules. We report a Pearson correlation coefficient of 0.96 between experimentally determined and calculated partition coefficients. The capability to reliably predict partition coefficients between water and chloroform and the possibility to localize their contributions allow the optimization of a compound's partition coefficient. Therefore, we presume that this methodology will be of great benefit for the efficient development of pharmaceuticals.

An Electronic-structure Informatics Study on the Toxicity of Alkylphenols to Tetrahymena pyriformis

Alkylphenols (APs) dissolved in water are known to be toxic to animals including humans. In this study, regression models describing the toxicity of the 33 AP molecules were investigated for reproducing and thereby making it possible to predict a quantitative structure-activity relationship (QSAR). For this purpose, we tried to derive regression models for the experimental IGC₅₀ (growth inhibition concentration at 50 %) to Tetrahymena pyriformis by using various descriptor sets consisting of electronic and shape descriptors. By applying the multiple linear regression (MLR) analysis, it was successful to derive a quantitative regression model for the IGC₅₀ values. In this analysis, the size parameters of the molecules were found important, suggesting that bulky molecules should be less toxic. We could also obtain, when the size descriptors were excluded, an MLR model indicating that the electron affinity (EA) should be important, which is consistent with the previous QSAR studies. Through the correlation analysis among the descriptors, it was shown that, in the present set of molecules, EA and a size parameter are highly correlated. Since EA was calculated to be negative, indicating that the related process would be energetically unfavourable, it was concluded that the size of the molecules should be a dominant factor determining IGC₅₀ . This implies that a molecular recognition process would play a critical role in the mode of action for the toxicity.

Comparative time-based intermediates study of ozone oxidation of 4-chloro- and 4-nitrophenols followed by LCMS-TOF

Greater insights on the degradation pathways and intermediates formed during the oxidation of organics can be achieved by more suitable and compatible instrumentation. In our research, we sought to explore the relative advantages of the liquid chromatography coupled to a time of flight mass spectrometer (LCMS-TOF) technique for the comparative time-based degradation intermediates and pathways of 4-chlorophenol (4CP) and 4-nitrophenol (4NP). The ozonation of the analytes solution (100 mL of 2 x 10^-3 M) was done in a sintered glass reactor, with an ozone dose of 0.14 mg min^-1 (O₂/O₃ 10 mL/min). The comparative oxidation results revealed that the 4-chloro- and 4-nitrocatechol pathways via hydroxylation were the major degradation route for 4CP and 4NP. Catechol intermediate was present as a primary breakdown product for the two analytes. Hydroquinone was observed as transient degradation intermediate for 4CP, but was absent for 4NP. Rather, a novel ozonation intermediate 2, 4-dinitrophenol was identified which was further oxidized to 3,6-dinitrocatechol. Several dimer products were identified in the oxidation processes, favored by alkaline conditions with more versatility shown by 4CP. The study provided a great insight into the ozone degradation intermediates and pathways, with some intermediates scarce in literature identified.

From phenols to quinones: Thermodynamics of radical scavenging activity of para-substituted phenols

Radical scavenging activity and subsequent oxidation resulting in quinone products represent one of the important features of phenols occurring in plants and other biological systems. However, corresponding thermochemistry data can be still considered scarce. For phenol and 25 para-substituted phenols, we investigate the thermodynamics of the individual reaction steps, including three subsequent hydrogen atom transfers, as well as hydroxyl HO radical addition, leading to final ortho-quinone formation. The substituent and solvent effect of water on corresponding reactions enthalpies is elucidated. Solvent enhances substituent induced changes in the investigated reaction enthalpies. The reliability of employed computational methods for the thermodynamics of hydrogen atom donating ability of studied phenols and catechols is assessed, too. Obtained linear equations enable estimation of studied reaction enthalpies from Hammett constants of substituents.

Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods

The partitioning of compounds between aqueous and other phases is important for predicting toxicity. Although thousands of octanol-water partition coefficients have been measured, these represent only a small fraction of the anthropogenic compounds present in the environment. The octanol phase is often taken to be a mimic of the inner parts of phospholipid membranes. However, the core of such membranes is typically more hydrophobic than octanol, and other partition coefficients with other compounds may give complementary information. Although a number of (cheap) empirical methods exist to compute octanol-water (log k _OW) and hexadecane-water (log k _HW) partition coefficients, it would be interesting to know whether physics-based models can predict these crucial values more accurately. Here, we have computed log k _OW and log k _HW for 133 compounds from seven different pollutant categories as well as a control group using the solvation model based on electronic density (SMD) protocol based on Hartree-Fock (HF) or density functional theory (DFT) and the COSMO-RS method. For comparison, XlogP3 (log k _OW) values were retrieved from the PubChem database, and KowWin log k _OW values were determined as well. For 24 of these compounds, log k _OW was computed using potential of mean force (PMF) calculations based on classical molecular dynamics simulations. A comparison of the accuracy of the methods shows that COSMO-RS, KowWin, and XlogP3 all have a root-mean-square deviation (rmsd) from the experimental data of ≈0.4 log units, whereas the SMD protocol has an rmsd of 1.0 log units using HF and 0.9 using DFT. PMF calculations yield the poorest accuracy (rmsd = 1.1 log units). Thirty-six out of 133 calculations are for compounds without known log k _OW, and for these, we provide what we consider a robust prediction, in the sense that there are few outliers, by averaging over the methods. The results supplied may be instrumental when developing new methods in computational ecotoxicity. The log k _HW values are found to be strongly correlated to log k _OW for most compounds.