Integrated strategy of LC-MS and network pharmacology for predicting active constituents and pharmacological mechanisms of Ranunculus japonicus Thunb. for treating rheumatoid arthritis

Neem Leaf Extract Exhibits Anti-Aging and Antioxidant Effects from Yeast to Human Cells

Neem leaves have long been used in traditional medicine for promoting longevity. However, the precise mechanisms underlying their anti-aging effects remain elusive. In this study, we investigated the impact of neem leaf extract (NLE) extracted from a 50% ethanol solution on the chronological lifespan of Saccharomyces cerevisiae, revealing an extension in lifespan, heightened oxidative stress resistance, and a reduction in reactive oxygen species. To discern the active compounds in NLE, LC/MS and the GNPS platform were employed. The majority of identified active compounds were found to be flavonoids. Subsequently, compound-target pharmacological networks were constructed using the STP and STITCH platforms for both S. cerevisiae and Homo sapiens. GOMF and KEGG enrichment analyses of the predicted targets revealed that "oxidoreductase activity" was among the top enriched terms in both yeast and human cells. These suggested a potential regulation of oxidative stress response (OSR) by NLE. RNA-seq analysis of NLE-treated yeast corroborated the anti-oxidative effect, with "oxidoreductase activity" and "oxidation-reduction process" ranking high in enriched GO terms. Notably, CTT1, encoding catalase, emerged as the most significantly up-regulated gene within the "oxidoreductase activity" cluster. In a ctt1 null mutant, the enhanced oxidative stress resistance and extended lifespan induced by NLE were nullified. For human cells, NLE pretreatment demonstrated a decrease in reactive oxygen species levels and senescence-associated β-galactosidase activity in HeLa cells, indicative of anti-aging and anti-oxidative effects. This study unveils the anti-aging and anti-oxidative properties of NLE while delving into their mechanisms, providing novel insights for pharmacological interventions in aging using phytochemicals.

Integrated network pharmacology and metabolomics reveal the mechanisms of Jasminum elongatum in anti-ulcerative colitis

Jasminum elongatum (JE), an ethnic Chinese medicine, is widely used in the Lingnan region of China, because of its analgesic and antidiarrheal action, as well as its anti-inflammatory effects in gastrointestinal diseases. However, whether JE could against ulcerative colitis (UC) remains unclear. This research aims to reveal JE in treating UC and clarify the underlying mechanism. We used the 2.5% dextran sulfate sodium (DSS)-induced UC mice (C57BL/6J) to evaluate the therapeutic effects of JE. Metabolomics of serum and network pharmacology were combined to draw target-metabolite pathways. Apart from that, the targets of associated pathways were confirmed, and the mechanism of action was made clear, using immunohistochemistry. The pharmacodynamic results, including disease activity index (DAI), histological evaluation, and inflammatory cytokines in colon tissues, demonstrated that JE significantly relieved the physiological and pathological symptoms of UC. Network pharmacology analysis indicated 25 core targets, such as TNF, IL-6, PTGS2 and RELA, and four key pathways, including the NF-κB signaling pathway and arachidonic acid metabolism pathway, which were the key connections between JE and UC. Metabolomics analysis identified 45 endogenous differential metabolites and 9 metabolic pathways by enrichment, with the arachidonic acid metabolism pathway being the main metabolism pathway, consistent with the prediction of network pharmacology. IκB, p65 and COX-2 were identified as key targets and this study demonstrated for the first time that JE reverses 2.5% DSS-induced UC in mice via the IκB/p65/COX-2/arachidonic acid pathway. This study reveals the complex mechanisms underlying the therapeutic effects of JE on UC and provides a new approach to identifying the underlying mechanisms of the pharmacological action of Chinese natural medicines such as JE.

Appraisals on the chemical characterization and biological potentials of Ranunculus constantinopolitanus extracts using chromatographic, computational, and molecular network approaches

In this context, phytochemicals were extracted from Ranunculus constantinopolitanus using ethyl acetate (EA), ethanol, ethanol/water (70%), and water solvent. The analysis encompassed quantification of total phenolic and flavonoid content using spectrophotometric assays, chemical profiling via high performance liquid chromatography-mass spectrometry/mass spectrometry (HPLC-MS/MS) for the extracts, and assessment of antioxidant activity via 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS), Cupric reducing antioxidant capacity (CUPRAC), ferric reducing antioxidant power (FRAP), metal chelating (MCA), and phosphomolybdenum (PBD) assays. Moreover, antimicrobial activity was assessed against four different bacterial strains, as well as various yeasts. Enzyme inhibitory activities were evaluated against five types of enzymes. Additionally, the extracts were examined for their anticancer and protective effects on several cancer cell lines and the human normal cell line. All of the extracts exhibited significant levels of ferulic acid, kaempferol, and caffeic acid. All tested extracts demonstrated antimicrobial activity, with Escherichia coli and Pseudomonas aeruginosa being most sensitive to EA and ethanol extracts. Molecular docking studies revealed that kaempferol-3-O-glucoside strong interactions with AChE, BChE and tyrosinase. In addition, network pharmacology showed an association between gastric cancer and kaempferol-3-O-glucoside. Based on the results, R. constantinopolitanus can be a potential reservoir of bioactive compounds for future bioproduct innovation and pharmaceutical industries.

Chemical profiling and mechanistic studies of Zhi-Shang-Feng granules against influenza virus by high-performance liquid chromatography coupled with Q exactive focus hybrid quadrupole orbitrap high-resolution mass spectrometry in combination with network pharmacology analysis

Zhi-Shang-Feng Granules are used in the clinical treatment of influenza to relieve headaches, chills and fever, bronchitis, nasal congestion, neuralgia and other symptoms. To decipher the components responsible for therapeutic effects of Zhi-Shang-Feng g ranules against influenza virus, an analytical method based on high-performance liquid chromatography coupled with Q exactive focus hybrid quadrupole orbitrap high resolution mass spectrometry was developed and the chemical profile of Zhi-Shang-Feng granules was characterized. Then, the identified components were used to conduct network pharmacological analysis and determine the potential mechanism of Zhi-Shang-Feng Granules. As a result, 177 compounds were putatively identified through comprehensive analysis by liquid chromatography coupled with high-resolution mass spectrometry, of which 23 compounds were unambiguously confirmed with reference standards. Components in Zhi-Shang-Feng Granules were found to specifically act on different enzymes, G-protein-coupled receptors, ion channels and transporters in the immune, endocrine, nervous, and circulatory systems. The potential mechanism was related to several biological processes, including cell growth and death, pattern recognition receptor signalling, signalling by interleukins, and lipid metabolism. The combination of chemical profile characterization and network construction provided useful insight into the overall chemical composition of Zhi-Shang-Feng granules and revealed their potential anti-infection, anti-inflammatory and immunoregulatory mechanisms against influenza virus infected disease.

Full-length transcriptome analysis provides insights into flavonoid biosynthesis in Ranunculus japonicus

Ranunculus japonicus Thunb. is a traditional Chinese herb. Plants in the genus Ranunculus are generally rich in flavonoids, which have antibacterial, anti-infective, and other pharmacological effects. However, owing to the lack of reference genomes, little is known about the flavonoid biosynthetic pathway in R. japonicus. In this study, PacBio isoform sequencing (PacBio iso-seq) and DNA nanoball sequencing (DNB-seq) were combined to build a full-length transcriptome database for three different tissues of R. japonicus. A total of 395,402 full-length transcripts were obtained, of which 308,474 were successfully annotated. A Kyoto Encyclopedia of Genes and Genomes analysis identified 29 differentially expressed genes encoding nine key enzymes for flavonoid biosynthesis. Correlation analysis indicated that flavanone 3-hydroxylase and flavonol synthase genes might have key roles in the accumulation of flavonoid substances in the different tissues of R. japonicus. The structures of chalcone synthase and chalcone isomerase enzymes were spatially modeled. Reverse-transcription quantitative PCR was used to verify gene expression levels of key enzymes associated with flavonoid biosynthesis. In addition, 22 MYB transcription factors involved in flavonoid biosynthesis and phenylpropanoid biosynthesis were discovered. The reliable transcriptomic data from this study provide genetic information about R. japonicus as well as insights into the molecular mechanism of flavonoid biosynthesis. The results also provide a basis for developing the medicinal value R. japonicus.

Green tea EGCG inhibits naïve CD4+ T cell division and progression in mice: An integration of network pharmacology, molecular docking and experimental validation

Dietary green tea epigallocatechin-3-gallate (EGCG) could attenuate experimental autoimmune encephalomyelitis via the modification of the balance of CD4⁺ T helper (Th) cells. Moreover, EGCG administration in vitro has a direct impact on the regulatory cytokines and differentiation of CD4⁺ T cells. Here, we aim to determine whether EGCG directly affects the cell division and progression in naive CD4⁺ T cells. We first investigate the effect of EGCG on naïve CD4⁺ T cell division and progression in vitro. An integrated analysis of network pharmacology and molecular docking was utilized to further identify the targets of EGCG for T cell-mediated autoimmune diseases and multiple sclerosis (MS). EGCG treatment prevented naïve CD4⁺ T cells from progressing through the cell cycle when stimulated with anti-CD3/CD28 antibodies. This was achieved by increasing the proportion of cells arrested in the G0/G1 phase by 8.6% and reducing DNA synthesis activity by 51% in the S phase. Furthermore, EGCG treatment inhibited the expression of cyclins (cyclin D1, cyclin D3, cyclin A, and cyclin B1) and CDKs (CDK2 and CDK6) during naïve CD4⁺ T cell activation in response to anti-CD3/CD28 stimulation. However, EGCG inhibited the decrease of P27^Kip1 (CDKN1B) during naïve CD4⁺ T cell activation, whereas it inhibited the increase of P21^Cip1 (CDKN1A) expression 48 h after mitogenic stimulation. The molecular docking analysis confirmed that these proteins (CD4, CCND1, and CDKN1A) are the primary targets for EGCG, T cell-mediated autoimmune diseases, and MS. Finally, target enrichment analysis indicated that EGCG may affect the cell cycle, T cell receptor signaling pathway, Th cell differentiation, and NF-κB signaling pathway. These findings reveal a crucial role of EGCG in the division and progression of CD4⁺ T cells, and underscore other potential targets of EGCG in T cell-mediated autoimmune diseases such as MS.

Berberine inhibits RA-FLS cell proliferation and adhesion by regulating RAS/MAPK/FOXO/HIF-1 signal pathway in the treatment of rheumatoid arthritis

AIMS

Rheumatoid arthritis (RA) is a common chronic immune disease. Berberine, as its main active ingredient, was also contained in a variety of medicinal plants such as Berberaceae, Buttercup, and Rutaceae, which are widely used in digestive system diseases in traditional Chinese medicine with anti-inflammatory and antibacterial effects. The aims of this article were to explore the therapeutic effect and mechanism of berberine on rheumatoid arthritis.

METHODS

Cell Counting Kit-8 was used to evaluate the effect of berberine on the proliferation of RA fibroblast-like synoviocyte (RA-FLS) cells. The effect of berberine on matrix metalloproteinase (MMP)-1, MMP-3, receptor activator of nuclear factor kappa-Β ligand (RANKL), tumour necrosis factor alpha (TNF-α), and other factors was determined by enzyme-linked immunoassay (ELISA) kit. Transcriptome technology was used to screen related pathways and the potential targets after berberine treatment, which were verified by reverse transcription-polymerase chain reaction (RT-qPCR) and Western blot (WB) technology.

RESULTS

Berberine inhibited proliferation and adhesion of RA-FLS cells, and significantly reduced the expression of MMP-1, MMP-3, RANKL, and TNF-α. Transcriptional results suggested that berberine intervention mainly regulated forkhead box O (FOXO) signal pathway, prolactin signal pathway, neurotrophic factor signal pathway, and hypoxia-inducible factor 1 (HIF-1) signal pathway.

CONCLUSION

The effect of berberine on RA was related to the regulation of RAS/mitogen-activated protein kinase/FOXO/HIF-1 signal pathway in RA-FLS cells.Cite this article: Bone Joint Res 2023;12(2):91-102.

Transcriptomic profiling revealed the role of apigenin-4'-O-α-L-rhamnoside in inhibiting the activation of rheumatoid arthritis fibroblast-like synoviocytes via MAPK signaling pathway

BACKGROUND

Activated fibroblast-like synoviocyte (FLS) played a significant role in the pathogenesis and progression of rheumatoid arthritis (RA). Apigenin-4'-O-α-L-rhamnoside showed remarkable effects against RA, however, no relevant studies on pharmacology of apigenin-4'-O-α-L-rhamnoside yet, the effects and underlying molecular mechanism of apigenin-4'-O-α-L-rhamnoside on RA are still unclear.

PURPOSE

This study aimed to investigate the therapeutic effects and mechanisms of apigenin-4'-O-α-L-rhamnoside on RA-FLS cells by transcriptomic analysis.

METHODS

In vitro, RA-FLS cell viability and migration were measured by CCK-8 and scratch assays, respectively. The effects of apigenin-4'-O-α-L-rhamnoside on inflammatory levels of MMP-1, MMP-3, RANKL and TNF-α in RA-FLS cells were detected using ELISA kits. High-throughput transcriptome analysis was performed to screen the key genes and related pathways of apigenin-4'-O-α-L-rhamnoside inhibit RA-FLSs, and the result of which were validated by RT-qPCR and western blot. Furthermore, in vivo, we also evaluated the effects of apigenin-4'-O-α-L-rhamnoside in rat with CIA.

RESULTS

Apigenin-4'-O-α-L-rhamnoside significantly suppressed RA-FLS migration, exerted remarkable inhibiting effects on the expression levels on MMP-1, MMP3, RANKL and TNF-α in RA-FLS cells. It seemed that MAPK signaling pathway might be closely related to the pathogenesis of RA by down-regulated relevant core targets (MAPK1, HRAS, ATF-2, p38 and JNK). Moreover, apigenin-4'-O-α-L-rhamnoside attenuated the severity of arthritis in CIA rat.

CONCLUSION

Apigenin-4'-O-α-L-rhamnoside inhibited pro-inflammatory cytokine, chemokine and MMPs factors production of RA-FLS by targeting the MAPK signaling pathway, which provided a scientific basis for potential application in the treatment of RA.

Investigation of Molecular Mechanism of Banxia Xiexin Decoction in Colon Cancer via Network Pharmacology and In Vivo Studies

Objective

Banxia Xiexin decoction (BXD) is widely used in the treatment of gastrointestinal and other digestive diseases. This study is based on network pharmacology to explore the molecular mechanism of BXD in the treatment of colon cancer.

Methods

The bioactive components and potential targets of BXD were obtained from public database. The protein-protein interaction (PPI) network of the potential targets of BXD for colon cancer was constructed based on the STRING database, cytoscape software, gene ontology (GO), and kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis of the PPI network. Finally, we established a xenograft nude mouse model to verify the effect of BXD in colon cancer treatment.

Results

We have acquired a total of 55 bioactive components and 136 cross-targets of BXD. The results of enrichment analysis suggested that the oxidate stress and diet were the key factors of colon cancer occurrence, and AGE-RAGE signaling pathway plays an essential role in the treatment of colon cancer with BXD. Animal experiments revealed that BXD could suppress tumor growth and induce tumor cell apoptosis in the xenograft nude mouse model with HCT116 cells.

Conclusion

This study uncovered that BXD inhibits the malignant progression of colon cancer that may be related to multiple compounds (berberine, quercetin, baicalein, etc.), multiple targets (Bcl2, Bax, IL6, TNFα, CASP3, etc.), and multiple pathways (human cytomegalovirus infection, AGE-RAGE signaling pathway in diabetic complications, etc.).

Integrate UPLC-QE-MS/MS and Network Pharmacology to Investigate the Active Components and Action Mechanisms of Tea Cake Extract for Treating Cough

OBJECTIVE

Investigate the active components and mechanisms of tea cake extract (TCE) for treating cough.

METHODS

The components of TCE were tentatively identified by ultrahigh performance liquid chromatography coupled with Q-Exactive MS/MS (UPLC-QE-MS/MS), whose targets were obtained from databases of Swiss Target Prediction and traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP). Cough-related targets were retrieved from databases of Gene cards and Online Mendelian Inheritance in Man (OMIM). After intersection targets were obtained, enrichment analysis of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was performed, and protein-protein interactions (PPI) network and active compound-intersection target-KEGG pathway network was constructed. Core active compounds and their targets were validated with molecular docking.

RESULTS

Total of 78 compounds were identified from TCE, including 24 flavonoids, 17 phenolic acids, 10 alkaloids, 7 organic acids, 5 triterpenes, 5 amino acids, 5 coumarins, 3 carbohydrates, 1 anthraquinone and 1 other. 347 intersection targets were obtained. The top 5 GO terms with most significant P-values were response to oxygen-containing compound, response to organic substance, response to chemical, cellular response to chemical stimulus, and regulation of biological quality. The top 5 KEGG pathways with most significant P-values were: PI3K-Akt signaling pathway, lipid and atherosclerosis, human cytomegalovirus infection, fluid shear stress and atherosclerosis, and proteoglycans in cancer. The top 5 core active compounds were: quercetin, genistein, luteolin, kaempferol and emodin. The top 5 core targets were: protein kinase B (Akt1), prostaglandin-endoperoxide synthase 2 (PTGS2), mitogen-activated protein kinase 1/3 (MAPK1/3), and phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1). The top 5 core active compounds could stably bind to their targets with LibDockScore higher than 100.

CONCLUSION

TCE plays the antitussive role by multiple components and targets. Core targets (AKT1, MAPK1, MAPK3 and PIK3R1) and core components (quercetin, genistein, luteolin and kaempferol) involved in the PI3K-Akt signaling pathway are worth more attention in subsequent validation experiments.

Therapeutic Potential of Ranunculus Species (Ranunculaceae): A Literature Review on Traditional Medicinal Herbs

The genus Ranunculus includes approximately 600 species and is distributed worldwide. To date, several researchers have investigated the chemical and biological activities of Ranunculus species, and my research team has found them to have antimalarial effects. This review is based on the available information on the traditional uses and pharmacological studies of Ranunculus species. The present paper covers online literature, particularly from 2010 to 2021, and books on the ethnopharmacology and botany of Ranunculus species. Previous studies on the biological activity of crude or purified compounds from Ranunculus species, including R. sceleratus Linn., R. japonicus Thunb., R. muricatus Linn., R. ternatus Thunb., R. arvensis Linn., R. diffusus DC., R. sardous Crantz, R. ficaria Linn., R. hyperboreus Rotlb., and R. pedatus Waldst. & Kit., have provided new insights into their activities, such as antibacterial and antiprotozoal effects as well as antioxidant, immunomodulatory, and anticarcinogenic properties. In addition, the anti-inflammatory and analgesic effects of plants used in traditional medicine applications have been confirmed. Therefore, there is a need for more diverse studies on the chemical and pharmacological activities of highly purified molecules from Ranunculus species extracts to understand the mechanisms underlying their activities and identify novel drug candidates.

Inhibitory Activities of Ranunculus japonicus Thunb. Ethanol Extract against Hepatitis B Virus

The chronic hepatitis B virus (HBV) infection is a worldwide public health problem, which cannot be cured by current therapeutics due to the persistence of viral CCC DNA in the infected hepatocytes. Screening from medicinal herbs for anti-HBV activities showed that the ethanol extract from Ranunculus japonicus Thunb. could decrease the production of HBV e antigen (HBeAg). Further study showed that the extract had no effect on core protein expression but significantly reduced the efficiency of viral capsid assembly. The levels of viral pgRNA and total core DNA were not affected significantly. However, the ratio of RC DNA/SS DNA decreased, indicating that the conversion of RC DNA from SS DNA was delayed by the extract. More interestingly, though similar levels of RC DNA were accumulated, the CCC DNA level and its formation efficiency were reduced significantly, which was also consistent with the decreased level of HBeAg, indicating that Ranunculus japonicus Thunb. extract could inhibit the CCC DNA formation. Together, this study found that Ranunculus japonicus Thunb. extract could inhibit HBV replication at multiple steps, especially showed significant inhibitory effects on capsid assembly and CCC DNA formation. This article is protected by copyright. All rights reserved.

The complete chloroplast genome sequence of Japanese buttercup Ranunculus japonicus Thunb

Ranunculus japonicus is an important medicinal herb widely used in East Asia. In this study, we report the first complete chloroplast genome sequence of Ranunculus japonicus using next-generation sequencing technology. The chloroplast genome size of R. japonicus was 156,981 bp. A total of 129 genes were included, consisting 84 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Thirteen protein-coding genes had intron (ycf3 gene, rps12 gene, rps12 gene, clpP gene contained two introns). A further phylogenomic analysis of Ranunculaceae, including 10 taxa, was conducted for assessing the placement of R. japonicus. It will provide valuable genetic information for this medicinally important species.