MCnebula: Critical Chemical Classes for the Classification and Boost Identification by Visualization for Untargeted LC-MS/MS Data Analysis.

Untargeted mass spectrometry is a robust tool for biology, but it usually requires a large amount of time on data analysis, especially for system biology. A framework called Multiple-Chemical nebula (MCnebula) was developed herein to facilitate the LC-MS data analysis process by focusing on critical chemical classes and visualization in multiple dimensions. This framework consists of three vital steps as follows: (1) abundance-based classes (ABC) selection algorithm, (2) critical chemical classes to classify "features" (corresponding to compounds), and (3) visualization as multiple Child-Nebulae (network graph) with annotation, chemical classification, and structure. Notably, MCnebula can be used to explore the classification and structural characteristic of unknown compounds beyond the limit of the spectral library. Moreover, it is intuitive and convenient for pathway analysis and biomarker discovery because of its function of ABC selection and visualization. MCnebula was implemented in the R language. A series of tools in R packages were provided to facilitate downstream analysis in an MCnebula-featured way, including feature selection, homology tracing of top features, pathway enrichment analysis, heat map clustering analysis, spectral visualization analysis, chemical information query, and output analysis reports. The broad utility of MCnebula was illustrated by a human-derived serum data set for metabolomics analysis. The results indicated that "Acyl carnitines" were screened out by tracing structural classes of biomarkers, which was consistent with the reference. A plant-derived data set was investigated to achieve a rapid annotation and discovery of compounds in E. ulmoides.

A deep clustering-based mass spectral data visualization strategy for anti-renal fibrotic lead compound identification from natural products.

Natural products have been a key source of drug lead discovery. However, their identification has long been a challenge even with the state-of-the-art analysis technologies like high-resolution mass spectrometry (MS) due to their complexity. Emerging in silico chemical structure prediction tools have provided time-saving and highly efficient approaches for identification of these complex samples. Nevertheless, the interpretation of these MS annotations into key supporting evidence towards specific questions is still a bottleneck in medicinal and biological fields. Here we present a deep clustering-based MS data visualization strategy (MCnebula), integrated with the influential open-source automatic MS annotation platform SIRIUS and in vivo and in vitro methods, to screen and validate potential lead compounds from natural products. MCnebula could provide multi-layer clustering profiles with chemical ontologies and comparative analysis of differential treatments. Plantaginis Semen (PS) is commonly used for treating kidney disease and usually stir-fried with salt water to enhance its anti-renal fibrosis effect, but the reason behind this remains unclear. Taking PS as an example, we comprehensively identified and compared the raw and processed PS extracts with SIRIUS-MCnebula, and screened potential anti-renal fibrotic lead compounds using weighted fold change analysis. Eighty-nine components were identified in PS with isoacteoside, calceolarioside B, 2'-acetylacteoside, and plantainoside D being screened and validated to treat renal fibrosis. The novel developed mass spectral data visualization strategy combined with biological function investigation and validation workflow could not only accelerate the discovery of lead compounds from medicinal natural products, but also shed new light on the traditional processing theory.

Integrated gut microbiota and serum metabolomics reveal the protective effect of oleanolic acid on liver and kidney-injured rats induced by Euphorbia pekinensis.

Euphorbia pekinensis (EP) is a commonly used Chinese medicine treating edema with potential hepatorenal toxicity. However, its toxic mechanism and prevention are remained to be explored. Oleanolic acid (OA) is a triterpene acid with potential hepatorenal protective activities. We investigated the protective effect and potential mechanism of OA on EP-induced hepatorenal toxicity. In this study, rats were given total diterpenes from EP (TDEP, 16 mg/kg) combined with OA (10, 20, 40 mg/kg) by gavage for 4 weeks. The results showed that TDEP administration could lead to a 3-4-fold increasement in hepatorenal biochemical parameters with histopathological injuries, while OA treatment could ameliorate them in a dose-dependent manner. At microbial and metabolic levels, intestinal flora and host metabolism were perturbed after TDEP administration. The disturbance of bile acid metabolism was the most significant metabolic pathway, with secondary bile acids increasing while conjugated bile acids decreased. OA treatment can improve the disorder of intestinal flora and metabolic bile acid spectrum. Further correlation analysis screened out that Escherichia-Shigella, Phascolarctobacterium, Acetatifactor, and Akkermansia were closely related to the bile acid metabolic disorder. In conclusion, oleanolic acid could prevent hepatorenal toxicity induced by EP by regulating bile acids metabolic disorder via intestinal flora improvement.

[Effect of mild hypothermia on macrophage polarization in lipopolysaccharide-induced acute lung injury mice].

OBJECTIVE: To investigate the effect of mild hypothermia on macrophage polarization in lipopolysaccharide (LPS)-induced acute lung injury (ALI) mice and to clarify its role in lung injury. METHODS: According to a random number table method, 18 male C57BL/6 mice were divided into sham operation group (Sham group), ALI normothermic model group (NT group) and ALI mild hypothermia treatment group (HT group), with 6 mice in each group. The ALI model in mice was established by the method of tracheal instillation of LPS, and temperature control was administered at 1 hour after surgery. The anus temperature in NT group was kept at 36-38?centigrade, while the anus temperature in HT group was kept at 32-34?centigrade. The target anus temperature in both groups were maintained for 6 hours and then slowly rewarmed to 36-38 centigrade. The Sham group was infused with an equal amount of physiological saline through the trachea without temperature control. After 24 hours of modeling, serum was collected and mice were sacrificed to obtain lung tissue. Pathological changes in lung tissue were observed under light microscopy and semi-quantitative lung injury score was performed. Enzyme linked immunosorbent assay (ELISA) was used to detect the serum levels of interleukins (IL-1ß, IL-10). Real-time quantitative polymerase chain reaction (RT-qPCR) was used to test the indicators of macrophage polarization, such as the mRNA expressions of CD86, IL-6, CD206 and arginase 1 (Arg1) in the lung tissue. The protein expression of M1 macrophage marker inducible nitric oxide synthase (iNOS) and M2 macrophage marker Arg1 were detected by Western blotting. RESULTS: Compared with the Sham group, the NT group appeared significant pulmonary hemorrhage and edema, thickened lung septum, inflammatory cell infiltration, and lung injury score was significantly increased; serum IL-1ß level was significantly elevated; IL-10 level was increased without statistical significance; the expressions of CD86 mRNA, IL-6 mRNA and iNOS protein were significantly elevated, and CD206 mRNA was significantly decreased; the mRNA and protein expressions of Arg1 decreased, but there were no significant differences. Compared with the NT group, the pathological injury of lung tissue in HT group was significantly reduced, and the lung injury score was significantly decreased (4.78±0.96 vs. 8.56±1.98, P < 0.01); serum IL-1ß level was decreased (ng/L: 13.52±1.95 vs. 27.18±3.87, P < 0.01), and IL-10 level was significantly increased (ng/L: 42.59±15.79 vs. 14.62±4.47, P < 0.01); IL-6 mRNA expression was decreased in lung tissue (2-ΔΔCt: 3.37±0.92 vs. 10.04±0.91, P < 0.05), the expression of M1 macrophage markers CD86 mRNA and iNOS protein were significantly decreased [CD86 mRNA (2-ΔΔCt): 0.52±0.16 vs. 1.95±0.33, iNOS protein (iNOS/ß-actin): 0.57±0.19 vs. 1.11±0.27, both P < 0.05], the expression of M2 macrophage markers CD206 mRNA, Arg1 mRNA and Arg1 protein were significantly increased [CD206 mRNA (2-ΔΔCt): 3.99±0.17 vs. 0.34±0.17, Arg1 mRNA (2-ΔΔCt): 2.33±0.73 vs. 0.94±0.23, Arg1 protein (Arg1/ß-actin): 0.96±0.09 vs. 0.31±0.11, all P < 0.05]. CONCLUSIONS: Mild hypothermia can alleviate the inflammatory response and protect lung tissue in ALI mice, which may be related to the inhibition of M1 macrophage polarization and promotion of M2 macrophage polarization.

Expanding annotation of chemical compounds in hawthorn fruits and their variations in thermal processing using integrated mass spectral similarity networking.

Chemical structural characterization of chemical compounds from hawthorn fruits and its thermal processed products was carried out in present study. By linking Global Natural Products Social (GNPS) Molecular Networking and MolNetEnhancer workflow, seventy-four chemical compounds in hawthorn fruits and its thermal processed products were tentatively identified. Three quercetagetin derivatives (quercetagetin-3-O-glucoside, quercetagetin-di-glucoside and its isomer), five quercetin or kaempferol derivatives (quercetin-acetylapiosyl-hexoside, quercetin-3-O-(6″-malonyl-hexoside), quercetin-3-O-(6″-malonyl-hexoside)-(1 â†’ 2)-O-hexoside, quercetin-3-O-(6″-malonyl-hexoside)-(1 â†’ 2)-O-deoxyhexoside, kaempferol-3-O-(6″-malonyl-hexoside)), six procyanidins including four (E)C-ethyl-procyanidins and two A-type procyanidins digallate, as well as 13 triterpenoids including ursolic aldehyde, triterpenoid glycosides, and triterpene acids were reported for the first time in hawthorn fruits. In addition, triterpenoids exhibited considerable thermal stability, while all of flavonoid glycosides, proanthocyanidins and 10 in 13 organic acids showed dramatic decrease after thermal processing.

Traditional application and modern pharmacological research of Eucommia ulmoides Oliv.

As a Traditional Chinese Medicine, Eucommia ulmoides Oliv. has been used for the treatment of various diseases since ancient times, involving lumbar pain, knee pain, osteoporosis, hepatoprotection, paralysis, intestinal haemorrhoids, vaginal bleeding, abortion, spermatorrhoea, foot fungus, anti-aging etc. With the developing discovery of E. ulmoides extracts and its active components in various pharmacological activities, E. ulmoides has gained more and more attention. Up to now, E. ulmoides has been revealed to show remarkable therapeutic effects on hypertension, hyperglycemia, diabetes, obesity, osteoporosis, Parkinson's disease, Alzheimer's disease, sexual dysfunction. E. ulmoides has also been reported to possess antioxidant, anti-inflammatory, neuroprotective, anti-fatigue, anti-aging, anti-cancer and immunoregulation activities etc. Along these lines, this review summarizes the traditional application and modern pharmacological research of E. ulmoides, providing novel insights of E. ulmoides in the treatment of various diseases.

Evaluating the Therapeutic Mechanisms of Selected Active Compounds in Cornus Officinalis and Paeonia Lactiflora in Rheumatoid Arthritis via Network Pharmacology Analysis.

Cornus officinalis Sieb et. Zucc and Paeonia lactiflora Pall. have exhibited favorable therapeutic effects against rheumatoid arthritis (RA), but the specific mechanisms of their active compounds remain unclear. The aim of this study was to comprehensively analyze the therapeutic mechanisms of selected active compounds in Cornus officinalis (loganin, ursolic acid, and morroniside) and Paeonia lactiflora (paeoniflorin and albiflorin) via network pharmacology. The pharmacological properties of the five active compounds were evaluated and their potential target genes were identified by database screening. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional analysis were performed to determine the enriched molecular pathways associated with the active compounds. Using network pharmacology tools, eight genes (IL1ß, VEGFA, STAT3, TP53, IL6, TNF, FOS, and LGALS3) were identified as common targets between RA and the five active compounds. Molecular docking simulation revealed the compound-target relationship between the five active compounds and three selected targets from the eight common ones (LGALS3, STAT3, and VEGFA). The compound-target relationships were subsequently validated via preliminary in vivo experiments in a rat model of collagen-induced arthritis. Rats subjected to collagen-induced arthritis showed increased protein expression of LGALS3, STAT3, and VEGFA in synovial tissues. However, treatment using Cornus officinalis or/and Paeonia lactiflora, as well as their most drug-like active compounds (ursolic acid or/and paeoniflorin, respectively, identified based on pharmacological properties), attenuated the expression of these three targets, as previously predicted. Collectively, network pharmacology allowed the pharmacological and molecular roles of Cornus officinalis and Paeonia lactiflora to be systematically revealed, further establishing them as important candidate drugs in the treatment and management of RA.

Combined Cornus Officinalis and Paeonia Lactiflora Pall Therapy Alleviates Rheumatoid Arthritis by Regulating Synovial Apoptosis via AMPK-Mediated Mitochondrial Fission.

Rheumatoid arthritis (RA) is a chronic autoimmune disease that leads to cartilage destruction and bone erosion. In-depth exploration of the pathogenesis of RA and the development of effective therapeutic drugs are of important clinical and social value. Herein, we explored the medicinal value of Cornus officinalis Sieb. and Paeonia lactiflora Pall. in RA treatment using a rat model of collagen-induced arthritis (CIA). We compared the therapeutic effect of Cornus officinalis and Paeonia lactiflora with that of their main active compounds, ursolic acid and paeoniflorin, respectively. We demonstrated that the combination of Cornus officinalis and Paeonia lactiflora effectively inhibited the release of factors associated with oxidative stress and inflammation during RA, therein ameliorating the symptoms and suppressing the progression of RA. We further showed that the underlying mechanisms may be related to the regulation of apoptosis in synovial tissues, and we investigated the potential involvement of AMPK-mediated mitochondrial dynamics in the therapeutic action of the two drugs and their active components.