Computational Insights into Cyclodextrin Inclusion Complexes with the Organophosphorus Flame Retardant DOPO.

Cyclodextrins (CDs) were used as green char promoters in the formulation of organophosphorus flame retardants (OPFRs) for polymeric materials, and they could reduce the amount of usage of OPFRs and their release into the environment by forming [host:guest] inclusion complexes with them. Here, we report a systematic study on the inclusion complexes of natural CDs (α-, ß-, and γ-CD) with a representative OPFR of DOPO using computational methods of molecular docking, molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations. The binding modes and energetics of [host:guest] inclusion complexes were analyzed in details. α-CD was not able to form a complete inclusion complex with DOPO, and the center of mass distance [host:guest] distance amounted to 4-5 Å. ß-CD and γ-CD allowed for a deep insertion of DOPO into their hydrophobic cavities, and DOPO was able to frequently change its orientation within the γ-CD cavity. The energy decomposition analysis based on the dispersion-corrected density functional theory (sobEDAw) indicated that electrostatic, orbital, and dispersion contributions favored [host:guest] complexation, while the exchange-repulsion term showed the opposite. This work provides an in-depth understanding of using CD inclusion complexes in OPFRs formulations.

Repurposing Drugs for Inhibition against ALDH2 via a 2D/3D Ligand-Based Similarity Search and Molecular Simulation.

Aldehyde dehydrogenase-2 (ALDH2) is a crucial enzyme participating in intracellular aldehyde metabolism and is acknowledged as a potential therapeutic target for the treatment of alcohol use disorder and other addictive behaviors. Using previously reported ALDH2 inhibitors of Daidzin, CVT-10216, and CHEMBL114083 as reference molecules, here we perform a ligand-based virtual screening of world-approved drugs via 2D/3D similarity search methods, followed by the assessments of molecular docking, toxicity prediction, molecular simulation, and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis. The 2D molecular fingerprinting of ECFP4 and FCFP4 and 3D molecule-shape-based USRCAT methods show good performances in selecting compounds with a strong binding behavior with ALDH2. Three compounds of Zeaxanthin (q = 0), Troglitazone (q = 0), and Sequinavir (q = +1 e) are singled out as potential inhibitors; Zeaxanthin can only be hit via USRCAT. These drugs displayed a stronger binding strength compared to the reported potent inhibitor CVT-10216. Sarizotan (q = +1 e) and Netarsudil (q = 0/+1 e) displayed a strong binding strength with ALDH2 as well, whereas they displayed a shallow penetration into the substrate-binding tunnel of ALDH2 and could not fully occupy it. This likely left a space for substrate binding, and thus they were not ideal inhibitors. The MM-PBSA results indicate that the selected negatively charged compounds from the similarity search and Vina scoring are thermodynamically unfavorable, mainly due to electrostatic repulsion with the receptor (q = -6 e for ALDH2). The electrostatic attraction with positively charged compounds, however, yielded very strong binding results with ALDH2. These findings reveal a deficiency in the modeling of electrostatic interactions (in particular, between charged moieties) in the virtual screening via the 2D/3D similarity search and molecular docking with the Vina scoring system.

Repurposing of World-Approved Drugs for Potential Inhibition against Human Carbonic Anhydrase I: A Computational Study.

Human carbonic anhydrases (hCAs) have enzymatic activities for reversible hydration of CO2 and are acknowledged as promising targets for the treatment of various diseases. Using molecular docking and molecular dynamics simulation approaches, we hit three compounds of methyl 4-chloranyl-2-(phenylsulfonyl)-5-sulfamoyl-benzoate (84Z for short), cyclothiazide, and 2,3,5,6-tetrafluoro-4-piperidin-1-ylbenzenesulfonamide (3UG for short) from the existing hCA I inhibitors and word-approved drugs. As a Zn2+-dependent metallo-enzyme, the influence of Zn2+ ion models on the stability of metal-binding sites during MD simulations was addressed as well. MM-PBSA analysis predicted a strong binding affinity of -18, -16, and -14 kcal/mol, respectively, for these compounds, and identified key protein residues for binding. The sulfonamide moiety bound to the Zn2+ ion appeared as an essential component of hCA I inhibitors. Vina software predicted a relatively large (unreasonable) Zn2+-sulfonamide distance, although the relative binding strength was reproduced with good accuracy. The selected compounds displayed potent inhibition against other hCA isoforms of II, XIII, and XIV. This work is valuable for molecular modeling of hCAs and further design of potent inhibitors.

In-silico annotation of the chemical composition of Tibetan tea and its mechanism on antioxidant and lipid-lowering in mice.

BACKGROUND/OBJECTIVES: Tibetan tea is a kind of dark tea, due to the inherent complexity of natural products, the chemical composition and beneficial effects of Tibetan tea are not fully understood. The objective of this study was to unravel the composition of Tibetan tea using knowledge-guided multilayer network (KGMN) techniques and explore its potential antioxidant and hypolipidemic mechanisms in mice. MATERIALS/METHODS: The C57BL/6J mice were continuously gavaged with Tibetan tea extract (T group), green tea extract (G group) and ddH2O (H group) for 15 days. The activity of total antioxidant capacity (T-AOC) and superoxide dismutase (SOD) in mice was detected. Transcriptome sequencing technology was used to investigate the molecular mechanisms underlying the antioxidant and lipid-lowering effects of Tibetan tea in mice. Furthermore, the expression levels of liver antioxidant and lipid metabolism related genes in various groups were detected by the real-time quantitative polymerase chain reaction (qPCR) method. RESULTS: The results showed that a total of 42 flavonoids are provisionally annotated in Tibetan tea using KGMN strategies. Tibetan tea significantly reduced body weight gain and increased T-AOC and SOD activities in mice compared with the H group. Based on the results of transcriptome and qPCR, it was confirmed that Tibetan tea could play a key role in antioxidant and lipid lowering by regulating oxidative stress and lipid metabolism related pathways such as insulin resistance, P53 signaling pathway, insulin signaling pathway, fatty acid elongation and fatty acid metabolism. CONCLUSIONS: This study was the first to use computational tools to deeply explore the composition of Tibetan tea and revealed its potential antioxidant and hypolipidemic mechanisms, and it provides new insights into the composition and bioactivity of Tibetan tea.

Effects of Pu-erh and Dian Hong tea polyphenols on the gut-liver axis in mice.

Tea polyphenols (TP) are the most biologically active components in tea, with antioxidant, antiobesity, and antitumor properties, as well as the ability to modulate the composition and function of intestinal microbiota. This experimental study evaluated the chemical constituents of polyphenols in Pu-erh (PTP) and Dian Hong tea (DHTP). It also investigated the co-regulatory effects of PTP and DHTP on intestinal flora and liver tissues in mice using 16 S rRNA gene and transcriptome sequencing. The results revealed that DHT had higher concentrations of EGC (epigallocatechin), C (catechin), EC (epicatechin), and EGCG (epigallocatechin gallate). In contrast, PT had higher concentrations of GA (gallic acid), ECG (epicatechin-3-gallate), TF (theaflavin), and TB (theabrownin). PTP and DHTP consumption significantly reduced the rates of weight gain in mice. Microbial community diversity was significantly higher in PTP and DHTP-treated mice than in the control group. Notably, beneficial microbes such as Lactobacillus increased significantly in PTP-treated mice, whereas Lachnospiraceae increased significantly in DHTP-treated mice. Both PTP and DHTP improved the activity of the antioxidant enzymes (SOD) and total antioxidant capacity (T-AOC) in the liver. The transcriptome analysis revealed that the beneficial effects of PTP and DHTP were due to changes in various metabolic pathways, the majority of which were related to antioxidant and lipid metabolism. This study discovered that PTP and DHTP had beneficial effects in mice via the gut-liver axis.

Photocatalytic Regioselective [2 + 2 + 1] Radical Annulation of Alkenes with tert-Butyl Nitrite and gem-Dihalides.

A visible-light photocatalytic regioselective [2 + 2 + 1] radical annulation reaction of alkenes, tert-butyl nitrite, and gem-dihalides has been developed. The protocol provides an efficient and practical approach to obtain isoxazolines in good yields under mild conditions. Significantly, gem-dihalides serve as C1 synthons, while cheap tert-butyl nitrite acts as an ideal "N-O" synthon.

Visible-Light-Induced 1,6-Enynes Triggered C-Br Bond Homolysis of Bromomalonates: Solvent-Controlled Divergent Synthesis of Carbonylated and Hydroxylated Benzofurans.

Visible-light-induced 1,6-enyne-triggered C-Br bond homolysis of bromomalonates has been developed. This transition-metal-free, photocatalyst-free, and oxidant- and additive-free protocol affords an efficient approach for divergent synthesis of carbonylated and hydroxylated benzofurans from 1,6-enynes and bromomalonates under mild conditions. Significantly, mechanistic studies reveal that the homolysis of C-Br bonds appears to experience an energy-transfer pathway, and the atom-transfer radical addition products are the key intermediates to generate carbonylated and hydroxylated benzofurans.

XGBoost-based intelligence yield prediction and reaction factors analysis of amination reaction.

Buchwald-Hartwig amination reaction catalyzed by palladium plays an important role in drug synthesis. In the last few years, machine learning-assisted strategies emerged and quickly gained attention. In this article, an importance and relevance-based integrated feature screening method is proposed to effectively filter high-dimensional feature descriptor data. Then, a regularized machine learning boosting tree model, eXtreme Gradient Boosting, is introduced to intelligently predict reaction performance in multidimensional chemistry space. Furthermore, convergence, interpretability, generalization, and the internal association between reaction conditions and yields are excavated, which provides intelligent assistance for the optimal design of coupling reaction system and evaluating the reaction conditions. Compared with recently published results, the proposed method requires fewer feature descriptors, takes less time, and achieves more accurate prediction accuracy.

Gold-Catalyzed One-Pot Synthesis of Polyfluoroalkylated Oxazoles from N-Propargylamides Under Visible-Light Irradiation.

A gold-catalyzed synthesis of polyfluoroalkylated oxazoles from N-propargylamides under visible-light irradiation has been developed. These reactions display excellent compatibility of radicals and gold catalysts under visible-light irradiation. Mechanistic experiments indicate that polyfluoroalkyl iodides play a dual role in enhanced compatibility of radicals and gold catalysts through assisted protodeauration of vinyl gold and reactivated the gold catalyst. In addition, PPh3 AuNTf2 not only activates N-propargylamide to generate vinyl gold intermediate, but also greatly promotes homolysis of polyfluoroalkyl iodides under blue light irradiation.

Polymer functionalization and solubilization of carbon nanosheets.

Few-layer graphene materials or "carbon nanosheets" were covalently functionalized with poly(vinyl alcohol) via ester linkages, and the resulting functionalized sample became soluble, allowing solution-phase processing for various purposes such as the fabrication of polymer-carbon nanosheets composites containing no dispersion agents or any other foreign substances.

Single-walled carbon nanotube as a unique scaffold for the multivalent display of sugars.

Single-walled carbon nanotube (SWNT) is a pseudo-one-dimensional nanostructure capable of carrying/displaying a large number of bioactive molecules and species in aqueous solution. In this work, a series of dendritic beta-D-galactopyranosides and alpha-D-mannopyranosides with a terminal amino group were synthesized and used for the functionalization of SWNTs, which targeted the defect-derived carboxylic acid moieties on the nanotube surface. The higher-order sugar dendrons were more effective in the solubilization of SWNTs, with the corresponding functionalized nanotube samples of improved aqueous solubility characteristics. Through the functionalization, the nanotube apparently serves as a unique scaffold for displaying multiple copies of the sugar molecules in pairs or quartets. Results on the synthesis and characterization of these sugar-functionalized SWNTs and their biological evaluations in binding assays with pathogenic Escherichia coli and with Bacillus subtilis (a nonvirulent simulant for Bacillus anthracis or anthrax) spores are presented and discussed.

Metallic single-walled carbon nanotubes for conductive nanocomposites.

This article reports an unambiguous demonstration that bulk-separated metallic single-walled carbon nanotubes offer superior performance (consistently and substantially better than the as-produced nanotube sample) in conductive composites with poly(3-hexylthiophene) and also in transparent conductive coatings based on PEDOT:PSS. The results serve as a validation on the widely held view that the carbon nanotubes are competitive in various technologies currently dominated by conductive inorganic materials (such as indium tin oxide).