DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data.

The identification of molecular structure is essential for understanding chemical diversity and for developing drug leads from small molecules. Nevertheless, the structure elucidation of small molecules by Nuclear Magnetic Resonance (NMR) experiments is often a long and non-trivial process that relies on years of training. To achieve this process efficiently, several spectral databases have been established to retrieve reference NMR spectra. However, the number of reference NMR spectra available is limited and has mostly facilitated annotation of commercially available derivatives. Here, we introduce DeepSAT, a neural network-based structure annotation and scaffold prediction system that directly extracts the chemical features associated with molecular structures from their NMR spectra. Using only the 1H-13C HSQC spectrum, DeepSAT identifies related known compounds and thus efficiently assists in the identification of molecular structures. DeepSAT is expected to accelerate chemical and biomedical research by accelerating the identification of molecular structures.

Cell extraction method coupled with LC-QTOF MS/MS analysis for predicting neuroprotective compounds from Polygonum tinctorium.

The cell extraction method coupled with LC-QTOF-MS/MS is a biological screening technique in which cells are incubated with extracts of natural products, which results in potential bioactive compounds selectively combining with various extracellular and intracellular targets. Although the neuroprotective effects of the plant Polygonum tinctorium are unknown, the ethyl acetate (EtOAc) fraction exhibits significant neuroprotective effects against ʟ-glutamate-induced cytotoxicity in HT22 cells. In this study, we attempted to identify the neuroprotective compounds in the EtOAc fraction of P. tinctorium using the cell extraction method coupled with LC-QTOF MS/MS. Potential neuroprotective components derived from P. tinctorium were combined selectively with HT22 cells, and cell-derived metabolites were identified. A new flavonoid compound, 3,5,3',4'-tetrahydroxy-6,7-methylendioxyflavone-3-O-ß-ᴅ-glucopyranoside (1), and 14 known compounds (2-15), with compounds 2, 3, 8, 13, and 15 detected by the cell extraction method, were isolated from the EtOAc fraction of P. tinctorium. Compounds 2, 8, 12, and 14 showed strong neuroprotective effects, with compounds 2 and 14 identified in this plant for the first time in this study. Our results indicate that the cell extraction method coupled with LC-QTOF MS/MS is a useful tool for screening and identifying neuroprotective compounds in natural products.

Influence of Panax ginseng formulation on skin microbiota: A randomized, split face comparative clinical study.

Background: Skin microbiota is important for maintenance of skin homeostasis; however, its disturbance may cause an increase in pathogenic microorganisms. Therefore, we aimed to develop a red ginseng formulation that can selectively promote beneficial bacteria. Methods: The effects of red ginseng formulation on microorganism growth were analyzed by comparing the growth rates of Staphylococcus aureus, S. epidermidis, and Cutibacterium acnes. Various preservatives mixed with red ginseng formulation were evaluated to determine the ideal composition for selective growth promotion of S. epidermidis. Red ginseng formulation with selected preservative was loaded into a biocompatible polymer mixture and applied to the faces of 20 female subjects in the clinical trial to observe changes in the skin microbiome. Results: Red ginseng formulation promoted the growth of S. aureus and S. epidermidis compared to fructooligosaccharide. When 1,2-hexanediol was applied with red ginseng formulation, only S. epidermidis showed selective growth. The analysis of the release rates of ginsenoside-Rg1 and -Re revealed that the exact content of Pluronic F-127 was around 11%. The application of hydrogel resulted in a decrease in C. acnes in all subjects. In subjects with low levels of S. epidermidis, the distribution of S. epidermidis was significantly increased with the application of hydrogel formulation and total microbial species of subjects decreased by 50% during the clinical trial. Conclusion: We confirmed that red ginseng formulation with 1,2-hexanediol can help maintain skin homeostasis through improvement of skin microbiome.

Lignans from Machilus thunbergii as Thymic Stromal Lymphopoietin Inhibitors.

Thymic stromal lymphopoietin (TSLP) plays an important role in the pathophysiology of various allergic diseases that are mediated by T helper cell type-2 (Th2) responses, including asthma and atopic dermatitis. The primary focus of this study was the identification of potent inhibitors of the TSLP signaling pathway for potential therapeutic use. The 80% methanol extract of Machilus thunbergii bark significantly inhibited the signal transducer and activator of transcription 5 (STAT5) phosphorylation in human mast cell (HMC)-1 cells. Through activity-guided isolation, three lignans (1-3) were obtained and identified as (+)-galbelgin (1), meso-dihydroguaiaretic acid (2), and machilin A (3). Among them, two lignans (1 and 2) significantly inhibited STAT5 phosphorylation and TSLP/TSLPR interaction, as determined by ELISA. Our results indicated that lignans isolated from M. thunbergii are a promising resource for the treatment of allergic diseases.

Blockade of transforming growth factor ß2 by anti-sense oligonucleotide improves immunotherapeutic potential of IL-2 against melanoma in a humanized mouse model.

BACKGROUND AIMS: IL-2 is a potent cytokine that activates natural killer cells and CD8+ cytotoxic T lymphocytes (CTLs) and has been approved for the treatment of metastatic renal cell carcinoma and metastatic melanoma. However, the medical use of IL-2 is restricted because of its narrow therapeutic window and potential side effects, including the expansion of regulatory T cells (Tregs). METHODS: In this study, the authors investigated the complementary effects of transforming growth factor-ß2 (TGF-ß2) anti-sense oligodeoxynucleotide (TASO) on the immunotherapeutic potential of IL-2 in a melanoma-bearing humanized mouse model. RESULTS: The authors observed that the combination of TASO and IL-2 facilitated infiltration of CTLs into the tumor, thereby potentiating the tumor killing function of CTLs associated with increased granzyme B expression. In addition, TASO attenuated the increase in Tregs by IL-2 in the peripheral blood and spleen and also inhibited infiltration of Tregs into the tumor, which was partly due to decreased CCL22. Alteration of T-cell constituents at the periphery by TGF-ß2 inhibition combined with IL-2 might be associated with the synergistic augmentation of serum pro-inflammatory cytokines (such as interferon Î³ and tumor necrosis factor α) and decreased ratio of Tregs to CTLs in tumor tissues, which consequently results in significant inhibition of tumor growth CONCLUSIONS: These results indicate that the application of TASO improves IL-2-mediated anti-tumor immunity, thus implying that blockade of TGF-ß2 in combination with IL-2 may be a promising immunotherapeutic strategy for melanoma.

In vitro growth culture in a medium with reduced sodium chloride improves maturation and developmental competence of pig oocytes derived from small antral follicles.

The objective of this study was to evaluate the effects of reducing the sodium chloride content in in vitro growth (IVG) medium to 61.6 mM on in vitro maturation (IVM) and embryonic development of pig oocytes derived from small antral follicles (SAF) less than 3 mm in diameter. SAF oocytes were cultured for 2 days to induce IVG in alpha-minimal essential medium with 108 mM NaCl (αMEM-108) or porcine zygote medium (PZM) containing 61.6 mM (PZM-61.6) or 108 mM (PZM-108) NaCl. These media were further supplemented with 1 mM dibutyryl cyclic adenosine monophosphate (dbcAMP) and 10% (v/v) fetal bovine serum. After IVG culture, oocytes were matured for 44 h in our standard IVM medium. The IVG culture in PZM-61.6 significantly increased nuclear maturation (88.0 ±â€¯2.2%) of SAF oocytes compared to that in PZM-108 (77.3 ±â€¯3.9%) or αMEM-108 (75.9 ±â€¯3.8%). After parthenogenesis (PA), the proportions of blastocysts, based on the number of metaphase II (MII) oocytes, induced for PA were not different among IVG oocytes cultured in PZM-61.6 (50.2 ±â€¯3.0%), PZM-108 (46.8 ±â€¯2.9%), or αMEM-108 (45.6 ±â€¯2.9%). The IVM oocytes derived from IVG in PZM-61.6 showed increased perivitelline space (PVS) (12.1 ±â€¯0.6 µm) and intra-oocyte glutathione (GSH) content (1.19 ±â€¯0.04 pixels/oocyte) compared to PVS (8.0 ±â€¯0.5 and 7.4 ±â€¯0.4 µm) and GSH (1.03 ±â€¯0.04 and 1.00 ±â€¯0.04 pixels/oocyte) of oocytes derived from PZM-108 and αMEM-108, respectively. The IVG culture in PZM-61.6 stimulated meiotic resumption after IVG and faster nuclear progression after IVM than that in αMEM-108. After somatic cell nuclear transfer (SCNT), the blastocyst formation of SAF oocytes grown in PZM-61.6 (17.8 ±â€¯3.3%) was higher than that of oocytes grown in PZM-108 (7.5 ±â€¯2.7%) but not different from that of oocytes in αMEM-108 (11.4 ±â€¯3.4%). Regardless of the different osmotic pressures, nuclear maturation was significantly increased by IVG culture in PZM with reduced NaCl (86.8 ±â€¯2.3 and 84.9 ±â€¯4.2% in PZM-61.6 and PZM-61.6 with sorbitol, respectively) than in PZM-108 (70.5 ±â€¯3.4%). Blastocyst formation was not affected by the differences in NaCl content and osmotic pressure of the IVG medium, whereas the mean number of cells in blastocysts was significantly higher following IVG culture in PZM-61.6 than in the other groups. In conclusion, the results demonstrate that, following SCNT in pigs, IVG culture of SAF oocytes in a medium with a reduced NaCl concentration stimulates oocyte maturation and improves subsequent embryonic development.

Characterization and Optimization of the Tyrosinase Inhibitory Activity of Vitis amurensis Root Using LC-Q-TOF-MS Coupled with a Bioassay and Response Surface Methodology.

Vitis amurensis roots have been reported to have the potential for skin whitening through the evaluation of melanogenesis and tyrosinase inhibitory activities. In this study, V. amurensis roots were utilized to quickly select whitening ingredients using LC-Q-TOF-MS coupled with tyrosinase inhibitory assay, and to optimize the extraction process for use as a skin whitening functional material by response surface methodology. Results showed that V. amurensis roots exhibited tyrosinase inhibitory effects by two stilbene oligomers, ε-viniferin (1) and vitisin B (2), as predicted by LC-Q-TOF-MS coupled with bioassay. The optimal extraction conditions (methanol concentration 66%, solvent volume 140 mL, and extraction time 100 min) for skin whitening ingredients were established with the yields 6.20%, and tyrosinase inhibitory activity was 87.27%. The relationship between each factor and its corresponding response was confirmed by Pearson's correlation analysis. The solvent volume showed clear linear relationship with yields, and methanol concentration had a strong linear relationship with tyrosinase inhibitory activity for compounds 1 and 2, as well as their combination. Overall, LC-Q-TOF-MS coupled with bioassay was proved to have the potential to effectively find new active constituents, as well as known active constituents; vitisin B can be proposed as a new natural potential whitening agent.

Structure elucidation of a new triterpene from Inonotus obliquus.

Ethyl acetate (EtOAc) fraction of the Inonotus obliquus (Hymenochaetaceae) significantly inhibited nitric oxide production in lipopolysaccharide (LPS)-induced murine BV2 microglial cells. A new triterpene, characterized as inonotusol H (1), was isolated from the EtOAc fraction using the bioactivity-guided fractionation together with four known triterpenes, inotodiol (2), trametenolic acid (3), inonotsutriols A (4), and inonotusol A (5). Among them, Compounds 2-4 significantly reduced LPS-induced nitric oxide production to 4.5 ± 0.8%, 47.4 ± 4.4%, and 2.8 ± 1.7%, respectively, at a concentration of 30 µM.

Characterization of Anti-Inflammatory and Antioxidant Constituents from Scutellaria baicalensis Using LC-MS Coupled with a Bioassay Method.

An effective and previously demonstrated screening method for active constituents in natural products using LC-MS coupled with a bioassay was reported in our earlier studies. With this, the current investigation attempted to identify bioactive constituents of Scutellaria baicalensis through LC-MS coupled with a bioassay. Peaks at broadly 17-20 and 24-25 min on the MS chromatogram displayed an inhibitory effect on NO production in lipopolysaccharide-induced BV2 microglia cells. Similarly, peaks at roughly 17-19 and 22 min showed antioxidant activity with an 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS)/2,2-diphenyl-1- picrylhydrazyl (DPPH) assay. For confirmation of LC-MS coupled with a bioassay, nine compounds (1-9) were isolated from an MeOH extract of S. baicalensis. As we predicted, compounds 1, 8, and 9 significantly reduced lipopolysaccharide (LPS)-induced NO production in BV2 cells. Likewise, compounds 5, 6, and 8 exhibited free radical-scavenging activities with the ABTS/DPPH assay. In addition, the structural similarity of the main components was confirmed by analyzing the total extract and EtOAc fractions through molecular networking. Overall, the results suggest that the method comprised of LC-MS coupled with a bioassay can effectively predict active compounds without an isolation process, and the results of molecular networking predicted that other components around the active compound node may also be active.

Author Correction: Structure-Activity Relationships of Baicalein and its Analogs as Novel TSLP Inhibitors.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Antithyroid cancer effects of human neural stem cells expressing therapeutic genes on anaplastic thyroid cancer cells.

Stem cells that express therapeutic proteins have been identified to have an anticancer effects on various types of cancer. In the present study study, human neural stem cells (hNSCs) that were genetically engineered to express cytosine deaminase (CD) and human interferon-ß (IFN-ß) were used for anaplastic thyroid cancer (ATC) treatment owing to their tumor-tropic properties and therapeutic effects. CD is an enzyme that converts 5-fluorocytosine (5-FC), a prodrug, to 5-fluorouracil (5-FU) which is a medication to suppress tumor growth through DNA synthesis inhibition. Also, IFN-ß suppresses tumor growth by the induction of apoptotic process. In water soluble tetrazolium salt (WST) assay, SNU-80 cells which are human female ATC cells were cocultured with three cell types including engineered hNSCs such as HB1.F3, HB1.F3.CD, and HB1.F3.CD.IFN-ß cells on transwells and treated with 5-FC for 72 hours. Finally, the SNU-80 cell viability was reduced by the coculture with HB1.F3.CD and HB1.F3.CD.IFN-ß cells. In dichlorofluorescein diacetate (DCF-DA) and TdT-mediated dUTP nick-end labeling (TUNEL) assays, the production of reactive oxygen species (ROS) and the number of apoptotic cells were increased by HB1.F3.CD and HB1.F3.CD.IFN-ß cells in the presence of 5-FC. In Western blot assay, ROS, and apoptosis-related genes were increased in SNU-80 cells when they were cocultured with HB1.F3.CD and HB1.F3.CD.IFN-ß cells. In transwell migration assay, hNSCs selectively migrated to SNU-80 cells because hNSCs interacted with chemoattractant factors like SDF-1α, uPAR, and CCR2 secreted by SNU-80 cells. Taken together, engineered hNSCs were revealed to selectively migrate to ATC cells and to inhibit growth as well as to induce apoptosis of ATC cells via ROS production through the actions of transgenes such as CD and IFN-ß. Therefore, these engineered hNSCs can be promising candidates for the treatment of metastatic ATC.

Structure-Activity Relationships of Baicalein and its Analogs as Novel TSLP Inhibitors.

Thymic stromal lymphopoietin (TSLP) plays an important role in the differentiation and proliferation of Th2 cells, resulting in eosinophilic inflammation and numerous allergic diseases. Baicalein (1), a major component of Scutellaria baicalensis, was found to be the first small molecule to block TSLP signaling pathways. It inhibited effectively eosinophil infiltration in house dust mite-induced and ovalbumin-challenged mouse models. Structure-activity relationship studies identified compound 11a, a biphenyl flavanone analog, as a novel human TSLP inhibitor for the discovery and development of new anti-allergic drugs.

Antitumor Effect of Various Phytochemicals on Diverse Types of Thyroid Cancers.

Thyroid cancers developed from the tissues of the thyroid gland are classified into papillary (PTC), follicular (FTC), medullary (MTC), and anaplastic thyroid cancer (ATC). Although thyroid cancers have been generally known as mild forms of cancer, undifferentiated MTC and ATC have a more unfavorable prognosis than differentiated PTC and FTC because they are more aggressive and early metastatic. A variety of therapies such as surgery, radiotherapy, and chemotherapy have been currently used to treat thyroid cancer, but they still have limitations including drug resistance or unfavorable side effects. Phytochemicals are plant-derived chemicals having various physiological activities that are expected to be effective in cancer treatment. In this review, anticancer efficacy of phytochemicals, such as resveratrol, genistein, curcumin, and other substances in each type of thyroid cancer was introduced with their chemopreventive mechanisms. English articles related with thyroid cancer and anti-thyroid cancer of phytochemicals were searched from PubMed and Google Scholar. This article mainly focused on in vitro or animal studies on phytochemicals with anti-thyroid cancer activity. These various phytochemicals have been shown to induce apoptosis in all types of thyroid cancer cells, inhibit cell proliferation and invasion, and to be helpful in enhancing the effect of radioiodine therapy that is a typical therapy to thyroid cancer. These results suggest that thyroid cancer can be more effectively treated by the combinations of phytochemicals and the existing therapies or substances.

Anti-acne properties of hydrophobic fraction of red ginseng (Panax ginseng C.A. Meyer) and its active components.

Acne is a chronic inflammatory disease of the skin that occurs when bacteria abnormally grow in hair follicles. The most common treatment is antibiotics, but they are limited due to antibiotic resistance. The purpose of this study was to identify the active ingredients of the antimicrobial effects of red ginseng (Panax ginseng C.A. Meyer), compare it to existing antibacterial substances, and determine its potential efficacy as a natural drug product. The hydrophobic fraction in red ginseng ethanol extract (RGEF) showed the same or better antimicrobial activity against Propionibacterium acnes than benzoyl peroxide or azelaic acid. In addition, the antimicrobial component derived from red ginseng selectively showed a high antimicrobial effect on P. acnes. Nuclear magnetic resonance spectroscopic analysis showed that the active antimicrobial substance in this fraction was panaxynol and panaxydol. Twenty subjects who had acne symptoms were treated with cream containing 3 mg/g of RGEF for 4 weeks. It was found that oxidized sebum contents and redness of the skin were reduced, and symptoms of the early to middle stage of acne were effectively improved. This study showed that red ginseng extract containing panaxynol and panaxydol can effectively control the symptoms of acne.

Comparison of antibacterial activity and phenolic constituents of bark, lignum, leaves and fruit of Rhus verniciflua.

Rhus verniciflua is commonly known as a lacquer tree in Korea. The bark of R. verniciflua has been used as an immunostimulator in traditional medicine, but also causes allergic dermatitis due to urushiol derivatives. For the development of active natural resources with less toxicity, the antibacterial activity of various parts of R. verniciflua such as bark, lignum, leaves and fruit, together with chemical composition, were investigated. Among the various parts of R. verniciflua, lignum showed the most potent antibacterial activity against fish pathogenic bacteria such as Edwardsiella tarda, Vibrio anguillarum and Streptococcus iniae. Measurement of total phenolic content and flavonoid content clearly showed a high content of phenolic and flavonoids in lignum among the various parts of R. verniciflua. Further analysis showed a close correlation between antibacterial activity and phenolic content. In addition, methyl gallate and fustin, the major constituents of bark and lignum, showed antibacterial activity, which suggested phenolic constituents as active constituents. The content of urushiols, however, was highest in bark, but there was a trace amount in lignum. LC-MS-MS and PCA analysis showed good discrimination with the difference of phenolic composition in various parts of R. verniciflua. Taken together, phenolic compounds are responsible for the antibacterial activity of R. verniciflua. The lignum of R. verniciflua contains high content of phenolic compounds with less urushiols, which suggests efficient antibacterial activity with less toxicity. Therefore, the lignum of R. verniciflua is suggested as a good source for antibacterial material to use against fish bacterial diseases.

Characterization of inhibitory constituents of NO production from Catalpa ovata using LC-MS coupled with a cell-based assay.

An effective screening method for inhibitors of NO production in natural products using LC-QTOF MS/MS coupled with a cell-based assay was proposed. The ethyl acetate fraction of Catalpa ovata exhibited a strong inhibitory effect on NO production in lipopolysaccharide-induced BV2 microglia cells. We attempted to identify the active constituents of C. ovata by using LC-QTOF MS/MS coupled with a cell-based assay. Peaks at approximately 14-15 min on the MS chromatogram were estimated to be the bioactive constituents. A new iridoid compound, 6-O-trans-feruloyl-3ß-hydroxy-7-deoxyrehamaglutin A (4), and nine known compounds (1-3, 5-10) were isolated from the ethyl acetate fraction of C. ovata by repeated column chromatography. Compounds 3, 4, 5, 7, and 8 significantly attenuated lipopolysaccharide-stimulated NO production in BV2 cells. Our results indicate that LC-QTOF MS/MS coupled with a cell-based NO production inhibitory assay successfully predicted active compounds without a time-consuming isolation process.

Identification of Polygonum orientale constituents using high-performance liquid chromatography high-resolution tandem mass spectrometry.

Our primary focus in this research was to identify and characterize its bioactive compounds for potential therapeutic use. Twenty-seven metabolites of Polygonum orientale were identified using LC-QTOF tandem mass spectrometry. Interestingly, P. orientale extracts included several highly oxygenated flavonoids were isolated from P. orientale by column chromatography. 13C NMR data of highly oxygenated flavonoids (1-7) are reported here for the first time. In addition, nitric oxide, 1,1-diphenyl-2-picrylhydrazyl, and water-soluble tetrazolium salt assays were carried out on the isolated compounds to investigate their anti-inflammatory, anti-oxidant, and neuroprotective activities, respectively. Compounds 1, 2, 3, 5, 7, and 8 significantly attenuated lipopolysaccharide-stimulated NO production in BV2 cells without affecting cell viability. Compounds 9-12 exhibited significant antioxidant activity, while compounds 8, 9, and 12 exhibited protective effects against glutamate-induced neurotoxicity in HT22 cells. Our results indicate that P. orientale is a promising source of natural agents for the potential treatment of inflammation and neurodegenerative diseases.

Screening and identification of neuroprotective compounds from Scrophularia buergeriana using cell extraction coupled with LC-MS.

In the cell extraction_LC-MS method, when cells are incubated with natural product extracts, bioactive compounds selectively bind to extracellular or intracellular targets. The extracts and major compounds (phenylpropanoids and iridoid glycosides) of Scrophularia buergeriana Miquel have been reported to show neuroprotective effects both in vitro and in vivo. In this study, the cell extraction_LC-MS strategy was applied to screen and identify potential neuroprotective compounds from S. buergeriana by using immortalized mouse hippocampal HT22 cells. The results showed that two known compounds from S. buergeriana selectively bound HT22 cells. Additionally, metabolomics analyses were performed using the Mass Profiler Professional and Limma differential expression package of R to identify significant differences between HT22 cells treated with S. buergeriana and untreated cells. The cell extraction approach more accurately reflects in vivo conditions compared with other methods and can be readily used for screening bioactive components from natural products.

Anti-inflammatory effects of Viola yedoensis and the application of cell extraction methods for investigating bioactive constituents in macrophages.

BACKGROUND: Viola yedoensis (VY, Violaceae) is a popular medicinal herb used in traditional eastern medicine for treating lots of diseases, including inflammation and its related symptoms. However, the anti-inflammatory properties of VY have not been demonstrated. In the present study, we investigated the anti-inflammatory effects of VY ethanol extract (VYE) on macrophages and attempted to identify the bioactive components of VYE. METHODS: We assessed the effects of VYE on secretion of nitric oxide (NO) and inflammatory cytokines such as tumor necrosis factor (TNF)-α, interleukin (IL)-6, and IL-1ß. In addition, we explored the expression of inducible nitric oxide synthase (iNOS), cyclooxygenase (COX)-2, and changes in heme oxygenase (HO)-1, nuclear factor (NF)-kB, and mitogen-activated protein kinase (MAPK) signaling pathways in RAW 264.7 macrophages stimulated by lipopolysaccharide (LPS). In addition, a rapid and useful approach to identify potential bioactive components in VYE with anti-inflammatory effects was developed using murine macrophage cell extraction coupled with high-performance liquid chromatography tandem mass spectrometry (LC-MS). RESULTS: We found that VYE exerted anti-inflammatory activity by inhibiting the production of key inflammation mediators and related products, as well as suppression of HO-1, NF-kB, and MAPK signaling pathway activation in RAW 264.7 cells. In addition, we identified two compounds in VYE via the cell extraction method. CONCLUSIONS: Our results revealed that VYE exerts anti-inflammatory activities and its detailed inhibitory mechanism in macrophages. Furthermore, we identified bioactive components of VYE.