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Stachyose is a typical prebiotic that can be utilized by the probiotic strain Bacillus licheniformis. Pioneering X-ray crystallography has determined the structure of stachyose in complex with the solute-binding protein MsmE in B. licheniformis (BlMsmE). The present work describes a combined strategy for the identification of putative BlMsmE-specific ligands, which can be used for the development of prebiotics. After a ligand-based virtual similarity screening of a large ZINC database containing ∼22 M compounds, we identified 3575 ligands. A total of 600 structures for which the Tanimoto coefficient's value was larger than a cutoff of 0.23 were selected for molecular docking. Based on the docking scores, we identified 100 top-scoring ligands, followed by molecular dynamics (MD) simulations. During simulations, 35 candidates were abandoned because of serious steric clashes in the complexes. Finally, the top 10 ligands with free energies below an energy threshold of -50.84 kcal/mol were selected. The top two ligands were stachyose and raffinose, which have proved their health benefits as prebiotics and their safety. The remaining eight ligands were further analyzed by the in silico ADME tool; only galactinol did not violate any of the criteria required for a lead compound. These three ligands were further analyzed for understanding their binding to BlMsmE. Isothermal titration calorimetry analysis suggested that stachyose, raffinose, and galactinol bound strongly to BlMsmE with Kd values of 299, 170, and 134 nM, respectively. Microsecond MD simulations suggested significant conformational changes of BlMsmE upon ligand binding. Our results provide new insight into the thermodynamics of sugars and MsmE, which would promote the development of novel prebiotics.

Stachyose is a functional oligosaccharide, acting as a potential prebiotic for colonic fermentation. To understand the mechanism of how stachyose promotes the growth of probiotic bacterium, we analyzed the differences of the proteome of Lactobacillus acidophilus grown on stachyose or glucose. By a combination of two-dimensional electrophoresis and mass spectrometry analysis, we observed 16 proteins differentially abundant under these two conditions and identified 9 protein spots. Six of these proteins were highly abundant when stachyose was used as the sole carbon source. They included the phosphotransferase system, the energy coupling factor (ECF) transporter and the mannose-6-phosphate isomerase, involved in the uptake and catabolism of stachyose in Lactobacillus acidophilus CICC22162. Supportively, these observations were validated by quantitative RT-PCR analysis and enzymatic activity determination. Positive correlation was found between the content of the proteins and their mRNA levels. Additionally, we explored the recognition mechanism for stachyose binding to the newly identified ECF transporter by MD simulations and free energy analysis. Taken together, these results provide new insights into the mechanism of stachyose in promoting the growth of probiotic bacterium.

Ginsenoside Re is an active component in ginseng that has attracted much attention because of its evident therapeutic effects on the cardiovascular system. However, little basic information is available on the mechanisms and pharmacological effects of ginsenoside Re. The potential mechanisms and protective effects of Re on H2O2-induced oxidative injury in human umbilical vein endothelial cells (HUVECs) were investigated in this study. An oxidative injury model was established using H2O2. The anti-oxidative effects of Re were determined using a series of experiments, such as MTT and anti-oxidative indicator assays. The potential protective mechanisms of Re were explored at the proteomic level, and differentially expressed proteins were validated by quantitative real-time polymerase chain reaction and western blotting. Results indicated that Re could be a potential anti-oxidant to protect HUVECs against oxidative stress damage. Proteomic analysis showed that the expression of 23 protein spots was upregulated in Re and H2O2 groups to resist oxidative stress, 15 of which were identified by their mass spectrum. These upregulated proteins were involved in stress response, anti-oxidative systems, protein synthesis, regulation of transcription and post-translational modifications, and repair of mitochondrial functions. This study may provide new insights into the mechanisms of ginsenoside Re in protecting the cardiovascular system.

Endothelial cell injury caused by reactive oxygen species (ROS) plays a critical role in the pathogenesis of atherosclerosis. Therefore, phytochemicals or antioxidants that inhibit the production of ROS have clinical value for the treatment of atherosclerosis. Rhein is one of the most important active components of rhubarb (Rheum officinale), a famous traditional Chinese remedy that possesses potent antioxidant properties through undefined mechanism(s). The aim of the present study was to determine whether rhein inhibits hydrogen peroxide (H2O2)-induced injury in human umbilical vein endothelial cells (HUVECs). The oxidative injury model was established with H2O2. HUVECs were treated with different concentrations of rhein in the presence/absence of H2O2. The protective effects of rhein against the injury caused by H2O2 were evaluated. HUVECs incubated with 200 µmol/l H2O2 had significantly decreased cell viability, which was accompanied by cell apoptosis and upregulated Bid and caspase-3, -8 and -9 mRNA expression. Meanwhile, H2O2 treatment induced a marked increase in malondialdehyde (MDA) and lactate dehydrogenase (LDH) content and decreased the nitric oxide (NO) content and nitrogen oxide synthase (NOS), superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX) activity. However, pre-treatment with different rhein concentrations (2, 4, 8 and 16 µmol/l) significantly increased the viability of H2O2-injured HUVECs, decreased the MDA and LDH content, increased the NO content and NOS, SOD and GSH-PX activity in a dose-dependent manner and resulted in significant recovery from H2O2-induced cell apoptosis. In addition, the results of the qRT-PCR indicated that pre‑treatment with rhein downregulates the expression of Bid and caspase-3, -8 and -9 mRNA, which plays a key role in H2O2-induced cell apoptosis. The present study shows that rhein protects endothelial cells against oxidative injury induced by H2O2, suggesting that rhein is a potential compound for the prevention and treatment of atherosclerosis.

Trans fatty acids (TFA) are reported to contribute to inflammation and coronary heart disease. The study aim was to investigate the proapoptotic effects of two double bond TFA (TDTFA) on human umbilical vein endothelial cells (HUVEC). The HUVEC were grown in media supplied with linoelaidic acid (9t,12t-C18:2) at 50, 100, 200, 400 μmol/l for 24 or 48 h to examine the effects of TDTFA on the viability and apoptosis of these cells. Flow cytometry analysis and confocal scanning were used to measure apoptosis, cell binding of Annexin V and propidium iodide uptake. Colorimetric assay and RT-PCR were used to analyze enzyme activities and mRNA expression of caspase-3, -8 and -9 in HUVEC. Results showed that 9t,12t-C18:2 inhibited the viability of HUVEC in a dose-dependent and time-dependent manner. The percentages of 9t,12t-C18:2 induced apoptotic and necrotic cells significantly increased compared with that of the control. The activities and mRNA expression of caspase-8, -9 and -3 were significantly increased in 9t,12t-C18:2 treated cells compared to that of the control. Addition of specific inhibitors of caspase-8 (z-IETD-fmk) and caspase-9 (z-LEHD-fmk) to HUVEC was found to completely inhibit 9t,12t-C18:2-induced activation of caspase-3, and z-IETD-fmk inhibited the activation of caspase-9. Meanwhile, it was found that mRNA expression of Bid, Smac/DIABLO and the release of mitochondrial cytochrome c were significantly elevated by 9t,12t-C18:2 treatment. These results suggest that 9t,12t-C18:2 may induce apoptosis of HUVEC through activating caspase-8, -9 and -3. Both the death receptor pathway and the mitochondrial pathway may be involved in the apoptosis induced by 9t,12t-C18:2.