Combinatorial Chemistry & High Throughput Screening - Online First
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Qilianshupi Decoction Alleviate Epithelial-mesenchymal Transition to Treat Chronic Atrophic Gastritis
Authors: Mengyi Shen, Chunxiao Wang, Jiapei Zhou, Jing Wang and Hongjie XiangAvailable online: 04 August 2025More LessIntroductionChronic atrophic gastritis (CAG) is an important stage in the occurrence and development of gastric cancer, and the morbidity of CAG is increasing year by year. Qilianshupi Decoction (QLSP) is a Chinese herbal compound which has been proved to reverse CAG, but its mechanism remains unknown. We wanted to identify the main components of QLSP by mass spectrometry and liquid phase analysis, and investigate their potential pathways for CAG treatment in combination with network pharmacology.
MethodsThe main active components of QLSP were identified by liquid chromatography and mass spectrometry. Combined with network pharmacology, the targets where the drugs may act were identified and verified by animal experiments. Rats were randomly divided into control group, model group, QLSP low-dose group, QLSP medium-dose group, QLSP high-dose group and Weifuchun group. Rat CAG model was prepared by “N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) + ethanol intragastric + ranitidine feed”. After the test, gastric tissues were taken for pathological staining and immunohistochemistry.
ResultsWe identified 51 prototype components of QLSP and found that QLSP treatment of CAG was closely related to p53. In animal experiments, CAG results in the decrease of E-cadherin and the increase of N-cadherin, Vimentin, p53, SMAD2 and TGF-β (p<0.05). Both QLSP and Weifuchun can increase E-cadherin and decrease N-cadherin, Vimentin, p53, SMAD2 and TGF-β (p<0.05).
DiscussionQLSP, a traditional Chinese medicine formula with multi-component and multi-target characteristics, has been shown in our study to effectively regulate key EMT (epithelial-mesenchymal transition) markers and their upstream/downstream regulators. In animal experiments, QLSP successfully reversed the EMT process in CAG model rats. This finding provides new therapeutic targets for CAG treatment, though several challenges remain in clinical translation: First, rat CAG models differ from human CAG in pathological features and disease progression, and species-specific physiological and metabolic variations may limit the extrapolation of these findings. Second, network pharmacology analysis identified IL-6, alongside TP53, as another critical target of QLSP in CAG intervention. Therefore, future studies should further clarify the molecular mechanisms by which QLSP modulates EMT via IL-6-related pathways and validate its efficacy through well-designed clinical trials, ultimately providing a comprehensive understanding of QLSP's therapeutic potential in CAG.
ConclusionQLSP inhibits epithelial-mesenchymal transition (EMT) in gastric mucosal epithelial cells and prevents CAG, possibly by regulating p53/TGF-β signaling pathway.
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Gan-Jiang-Ling-Zhu Decoction Prevents Paigen’s Diet-induced Lean Metabolic Dysfunction-associated Steatotic Liver disease by Regulating Bile Acid Metabolism
Authors: Zansong Ma, Milian Chen, Ying Cao, Deji Song and Li ZhangAvailable online: 15 July 2025More LessIntroductionMetabolic dysfunction-associated steatotic liver disease (MASLD) is a global health concern, even among lean individuals. The Gan-Jiang-Ling-Zhu decoction (GZD), a traditional Chinese medicine formula, shows therapeutic potential against MASLD. This study investigated the efficacy of GZD in lean MASLD and explored its mechanisms of action.
MethodsA lean MASLD mouse model was established using C57BL/6 mice fed with a cholesterol-rich Paigen’s diet (PD). Following successful modeling, mice were administered GZD (1.8, 3.6, or 7.2 g/kg) or vehicle control. Body weight, food intake, and liver weight were monitored. Hepatic steatosis and lipid accumulation were assessed via H&E and Oil Red O staining, while serum enzymes were quantified biochemically. Gut microbiota composition was analyzed by 16S rRNA gene sequencing, and bile acid (BA) profiles in feces and serum were measured using UPLC-TQMS.
ResultsTwelve weeks of PD feeding induced a lean MASLD phenotype characterized by reduced body weight alongside hepatic steatosis and dyslipidemia. The GZD treatment dose-dependently ameliorated liver steatosis and lipid accumulation, with the highest dose (7.2 g/kg) showing superior efficacy. GZD restored gut microbiota balance by reducing pathogenic bacteria and enriching taxa involved in BA metabolism, leading to increased fecal excretion of secondary BAs. Conversely, serum levels of secondary BAs were significantly reduced after GZD treatment.
DiscussionOur study highlights the promising role of GZD in lean MASLD, the involvement of gut microbiota and related BA metabolism that aligns with emerging evidence that gut dysbiosis and disrupted BA homeostasis are central to MASLD pathogenesis, even in lean individuals. However, the mechanistic links between specific microbial changes, BA pool composition, and hepatic outcomes remain to be elucidated.
ConclusionGZD ameliorates hepatic steatosis in lean MASLD mice, an effect associated with modulation of gut microbiota composition and increased fecal excretion of secondary BAs. These findings suggest the potential of GZD as a therapeutic option for lean MASLD through gut-liver axis regulation.
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The Potential Mechanisms of Banxia Xiexin Decoction in Treating Chronic Colitis: Insights from UPLC-Q-TOF-MS/MS and Network Pharmacology Studies
Authors: Xinyao Pan, Ruyun Zhang, Mengyuan Wang, Chunjuan Yang, Jinhui Wang, and and Chunli GanAvailable online: 14 July 2025More LessIntroductionBanxia Xiexin Decoction (BXD), traditionally used for gastrointestinal disorders like Chronic Colitis (CC), exerts anti-inflammatory, antibacterial, and intestinal flora-regulating effects. However, CC’s pathogenesis remains unclear, necessitating further research into BXD’s machanism.
MethodsActive BXD components were identified via UPLC-Q-TOF-MS/MS. Databases (TCMSP, HERB, GeneCards,DisGeNET,STRING) were used to identify compound/disease targets. Cytoscape 3.9.1 constructed protein-protein interaction networks, and DAVID database was used for GO and KEGG enrichment analysis of core genes. Finally, PyRx, AutoDockTools and PyMol were used for molecular docking, virtual computation, and visualization analyses of core components and key targets.
ResultsUPLC-Q-TOF-MS/MS detected 482 BXD components, with 165 active ingredients, including quercetin, kaempferol, baicalein, etc. There were 283 targets related to BXD's treatment of CC, of which the core targets included AKT1, IL-6, TP53, ALB, etc. GO enrichment analysis yielded relevant entries including molecular function 60 entries, 257 entries of biological processes, and 31 entries of cellular composition, and KEGG enrichment analysis identified 150 entries involving IL-17, TNF, PI3K-Akt, and other pathways. The molecular docking results demonstrated that the core components exhibited better binding activities with the key targets.
DiscussionQuercetin, kaempferol, baicalein, and naringenin, the main active ingredients in BXD, may play roles in anti-inflammatory, antimicrobial, and regulating intestinal microbiota to achieve the therapeutic purpose of CC treatment by mediating the targets of AKTl, IL-6, TP53, and ALB, and regulating the signaling pathways of IL-17, TNF, and PI3K-Akt.
ConclusionBXD’s active components alleviate CC through multi-target and multi-pathway regulation, providing a mechanistic foundation for clinical application.
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Identification of DNA Replication Stress-Related Genes as Prognostic Biomarkers for Bladder Cancer
Authors: Fei Zhang, Shuai Li, Zhijie Zhang, Jiulong Li, Huiqin Liu, Xudong Ma and Zhigang YangAvailable online: 14 July 2025More LessIntroductionBladder cancer (BLCA) is a highly aggressive malignancy with poor prognosis. DNA replication stress-related genes (DRSGs) hold prognostic significance in multiple cancers, and their expression patterns in BLCA may reveal novel biomarkers and therapeutic targets.
MethodsThis study was designed using a public database and the Cancer Genome Atlas (TCGA). Genes associated with DNA replication stress in BLCA were discovered by analyzing data from the TCGA and GEO databases using bioinformatics tools. The prognostic gene expression profiles in BLCA cell lines were analyzed using Western blotting (WB). The motility capacity of BLCA cells was evaluated using the wound healing and Transwell migration assays, while cell growth was ascertained with the CCK-8 assay.
ResultsFive DRSGs with prognostic significance were identified, and a risk score model was constructed using univariate Cox regression and the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm. Kaplan-Meier (KM) analysis showed worse Overall Survival (OS) in the high-risk group (P < 0.05). Gene Set Enrichment Analysis (GSEA) indicated involvement in tumor-related pathways. The nomogram effectively predicted OS in both training and validation cohorts. WB and functional assays confirmed gene expression and effects on BLCA cell proliferation and migration.
DiscussionThis study first validates DRSGs’ prognostic value in bladder cancer, highlighting potential biomarkers and targets. Limitations include reliance on public data and in vitro tests. Future research should use multicenter cohorts and animal models to confirm clinical relevance.
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Juanbi Lijieqing Decoction Inhibits TLR4/NF-κB Signaling Pathway by Promoting PPARγ Expression to Relieve Acute Gouty Arthritis
Authors: Chengyin Lu, Fangxiao Zhu, Zhiqiang Luo, Hui Xiong and Yuxing GuoAvailable online: 03 July 2025More LessIntroductionThis study aimed to investigate the mechanism of Juanbi Lijieqing Decoction (JLD) in alleviating acute gouty arthritis (AGA) by modulating PPARγ expression to suppress the TLR4/NF-κB pathway.
MethodsA total of 84 male SD rats were divided into 7 groups of 12 rats. One group was randomly selected as the normal control group (Group A), while the remaining 72 rats were used to establish an acute gouty arthritis model through intraperitoneal injection of potassium oxonate combined with MSU ankle joint injection. These rats were randomly assigned to the model group (Group B), the high-dose Juanbi Lijieqing Decoction group (Group C), the medium-dose group (Group D), the low-dose group (Group E), the etoricoxib group (Group F), and the pioglitazone group (Group G), with 12 rats per group. The acute gouty arthritis model was established by intraperitoneal injection of potassium oxonate, followed by monosodium urate (MSU) injection into the ankle joint, and then by pharmacological intervention in each group. The ankle swelling index, pain threshold changes, and serum uric acid levels were observed in each group of rats. The pathological state of synovial tissue in each group was evaluated by hematoxylin-eosin (HE) staining. The levels of TNF-α, IL-6, and IL-1β were detected by enzyme-linked immunosorbent assay (ELISA). The protein expressions of TLR4, NF-κB, and PPARγ were detected in vivo and in vitro using Western blot.
ResultsJLD effectively reduced local swelling, relieved pain, and lowered serum uric acid levels in rats with AGA. Both in vivo and in vitro experiments demonstrated that the Chinese medicine groups showed a significant reduction in TNF-α, IL-1β, and IL-6 levels. Moreover, in in vivo experiments, the expression of PPARγ protein was significantly upregulated in the JLD and pioglitazone groups, whereas the expressions of TLR4 and NF-κB p65 proteins were significantly downregulated, a pattern not observed in the etoricoxib group. In vitro experiments demonstrated significant increases in PPARγ protein expression in the pioglitazone and medicated serum groups, accompanied by significant decreases in TLR4 protein expression. Meanwhile, the NF-κB inhibitor group only exhibited a downregulation of TLR4 protein expression.
DiscussionOur findings demonstrated that JLD alleviated acute gouty arthritis by upregulating PPARγ expression, which subsequently inhibited the TLR4/NF-κB signaling pathway. This mechanism effectively reduced inflammatory cytokine production (TNF-α, IL-1β, and IL-6), explaining the observed anti-swelling and analgesic effects.
ConclusionJLD mitigates AGA symptoms by promoting PPARγ, which in turn inhibits TLR4/NF-κB signaling, thereby reducing inflammation, uric acid, and joint swelling. This highlights the therapeutic potential of JLD for gout management, though long-term effects and molecular targets warrant further study.
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Formononetin Alleviates MNNG-Triggered Chronic Atrophic Gastritis: Its Potential Mechanisms
Available online: 03 July 2025More LessIntroductionChronic atrophic gastritis (CAG) is the initial phase in the carcinogenesis of gastric cancer (GC). Therefore, effective treatment for CAG is important in reducing the risk of GC progression. As an isoflavone compound, formononetin (FMN) has been identified as a potential therapeutic agent for acute gastric ulcers and GC. However, no study has reported the protective effect of FMN against CAG and its underlying mechanism. This study aimed to explore the therapeutic effects of FMN on CAG and its underlying mechanisms in vitro.
MethodsNetwork pharmacology was applied to predict the core targets of FMN therapy in CAG. The CAG cell model was developed using N-methyl-N-nitro-N-nitrosoguanidine (MNNG)-triggered human gastric epithelial cells (GES-1). The CCK-8 assay was applied to estimate cellular viability. The expression of inflammatory cytokines in cell supernatant was detected by ELISA. The protein levels and localization of nuclear receptor coactivator 1 (NCOA1), c-Jun, and c-Fos were evaluated using western blotting and immunofluorescence staining. Cell apoptosis was measured using flow cytometry.
ResultsNetwork pharmacology analysis identified c-Jun as the core target of FMN in the treatment of CAG, with biological processes primarily involving the regulation of apoptosis and inflammation. In vitro, MNNG exposure reduced GES-1 cell viability as well as increased inflammation and cellular apoptosis, and these effects were reversed by FMN treatment. In detail, FMN decreased the protein levels of NCOA1, c-Jun, and c-Fos in MNNG-triggered GES-1 cells. The activator protein-1 (AP-1) inhibitor T-5224 enhanced the effects of FMN treatment on cell viability, inflammatory response, and apoptosis in MNNG-triggered GES-1 cells.
DiscussionThis study employed network pharmacology analysis to identify FMN's therapeutic targets for CAG and validated the underlying mechanisms in vitro. While these results are promising, in vivo validation is required to confirm the efficacy of FMN. A comparative pharmacological evaluation against existing therapeutic agents and bioactive compounds would further elucidate FMN's therapeutic potential for CAG treatment.
ConclusionFMN ameliorated the cell damage that MNNG triggered in GES-1 cells. The mechanism involved the anti-inflammatory and anti-apoptotic effects of FMN via modulation of the NCOA1/AP-1 signaling axis. The present preliminary study found FMN to exhibit a potential therapeutic effect against CAG.
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Mechanisms and Therapeutic Implications of ncRNAs in Regulating the PD-1/PD-L1 Axis Across Cancers
Authors: Huilin Jian, Xitai Li, Xiaoyong Lei, Shengsong Tang and Xiaoyan YangAvailable online: 30 June 2025More LessCancer remains one of the most challenging health issues worldwide. Thus, there is an urgent need to discover effective treatments for cancer. Immune checkpoint blockade targeting the PD-1/PD-L1 axis has revolutionized cancer therapy, yet resistance and limited clinical efficacy remain significant challenges. Emerging evidence highlights ncRNAs as upstream regulators of PD-1/PD-L1, offering novel therapeutic opportunities. This review systematically examines the role of miRNAs, lncRNAs, and circRNAs in modulating PD-1/PD-L1 signaling across diverse cancers, emphasizing their mechanisms and clinical implications. We further discuss the potential of ncRNAs as biomarkers and therapeutic targets to overcome immune evasion and enhance immunotherapy efficacy.
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Profiles of Circulating Exosomal microRNAs in Female College Students with Qi Stagnation and Balanced Constitutions by High-Throughput
Authors: Yunan Zhang, Yali Zhou, Pengfei Zhao, Yuxiu Sun, Yini Li, Lichun Tian, Jianhua Zhen and Guangrui HuangAvailable online: 25 June 2025More LessIntroductionIndividual constitutions are classified into nine types in traditional Chinese medicine (TCM), and qi stagnation constitution (QSC) manifests as disrupted Qi circulation and increased susceptibility to emotional disorders and cancers. However, as a pre-disease state mainly affecting women, the biological basis of QSC and its susceptible mechanism to related diseases are still unclear. Exosomal microRNAs (miRNAs) are the stable regulators of gene expression and intercellular communication, and analysis of miRNAs enables us to understand the QSC better. This study profiles plasma exosomal miRNAs in QSC and balanced constitution (BC) females via high-throughput sequencing, aiming to identify the potential biomarkers of QSC and reveal its biological basis and the mechanism of its susceptible disease.
MethodsIn this cross-sectional observation, female college students were recruited according to the criterion of QSC and BC in Classification and Determination of Constitution in TCM. Exosomal miRNAs were isolated from peripheral blood plasma and then profiled using high-throughput sequencing. Differentially expressed miRNAs (DEMs) were identified with fold change > 2 and P < 0.05, and screened as biomarkers to construct the receiver operating characteristic (ROC) curve. The diagnostic values of these biomarkers in different types of cancers were also validated based on the published data. Functional analysis were explored based on the predicted target genes.
ResultsSubjects with QSC showed significantly higher concentrations of albumin (ALB) and alkaline phosphatase (ALP) compared to those with BC, while there was no significant difference in baseline information and other clinical indicators between groups. A total of 54 DEMs were identified, including 30 up-regulated and 24 down-regulated miRNAs in the QSC group. The area under the ROC curve (AUC) for 7 specific up-regulated DEMs was 1.0, as well as the AUCs for therein 6 DEMs in various cancers were all above 0.9. The enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways included “signal transduction,” “infectious disease,” and “cancers”, and the most associating systems included immune, endocrine, and nervous systems, while the GO (Gene Ontology) function was mainly enriched in “protein binding,” “nucleus” and “transcription, DNA-templated”.
DiscussionThese 7 potential biomarkers of QSC have been confirmed to regulate oncogenic processes through epithelial-mesenchymal transition modulation and metabolic reprogramming, as well as therein 1 can also improve depression by lowering the expression of 5-hydroxytryptamine 1A receptor. The results of this study deepen the understanding of the constitutions in TCM. However, the small single-sex sample limits the application of the conclusion, and a large-scale clinical cohort including both sexes is still needed in future.
ConclusionThe expression of exosomal miRNAs in QSC showed unique features that have the potential to serve as biomarkers, and the related functional changes might be the biological basis for the susceptible diseases of QSC.
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Identification of Shared Gene Signatures Associated with Alzheimer’s Disease and COVID-19 through Bioinformatics Analysis
Authors: Juntu Li, Yanyou Zhou, Linfeng Tao, Chenxi He, Chao Li, Lifang Wu, Ping Yao, Xuefeng Qian and Jun LiuAvailable online: 23 June 2025More LessIntroductionSome studies have shown a link between Alzheimer's disease (AD) and COVID-19. This includes a Mendelian randomization study, which suggests that Alzheimer's disease and COVID-19 may be causally linked in terms of pathogenic mechanisms. However, there are fewer studies related to the two in terms of common pathogenic genes and immune infiltration. We conducted this study to identify key genes in COVID-19 linked to Alzheimer's disease, assess their relevance to immune cell profiles, and explore potential novel biomarkers.
MethodsThe RNA datasets GSE157103 and GSE125583 for COVID-19 and Alzheimer's disease, respectively, were acquired via the GEO database and subsequently processed. Through the utilization of differential expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA), genes associated with Alzheimer's disease and COVID-19 were identified. The immune cell signatures were estimated using the xCell algorithm, and correlation analysis identified links between key genes and significantly different immune cell signatures. Finally, we conducted transcription factor (TF) analysis, mRNA analysis, and sensitivity drug analysis.
ResultsDifferential analysis identified 3560 (2099 up-regulated and 1461 down-regulated) and 1456 (640 up-regulated and 816 down-regulated) differential genes for COVID-19 and AD compared to normal controls, respectively. WGCNA analysis revealed 254 key module genes for COVID-19 and 791 for AD. We combined the differential genes and WGCNA key module genes for each disease to obtain two gene sets. The intersection of these two gene sets was examined to obtain intersecting genes. Subsequently, PPI network analysis was conducted, leading to the identification of 12 hub genes. Then, 12 immune-related hub genes were further identified. Immune infiltration patterns and the correlation between 12 hub genes and 64 immune cell types were analyzed. The analysis revealed a significant positive correlation between the two diseases under study. The relationship network between Transcription Factors and mRNA, as well as the predictions of drugs, further illustrate the strong association between the two diseases. This provides valuable information for further target exploration and drug screening.
DiscussionThis study identified immune-related hub genes and demonstrated their association with natural killer T cell dysfunction in AD and COVID-19, suggesting the existence of common neuroinflammatory pathways. These findings provide molecular evidence for immunological crosstalk between the two diseases.
ConclusionOur study suggests potential shared genes, signalling pathways, and common drug candidates that may be associated with COVID-19 and AD. This may provide insights for future studies of AD patients infected with SARS-CoV-2 and help improve diagnostic and therapeutic approaches.
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Apigenin Regulating PI3K/AKT Pathway to Improve Depressive Behavior in Epileptic Rats
Authors: Zhanfang Xie, Yang Zhao, Yanhong Wang, Weijuan Song and Ganggang LiAvailable online: 23 June 2025More LessIntroductionDepression is a common comorbidity in epilepsy, significantly impacting patients' quality of life. The hippocampus, linked to depression and neurodegeneration, is vulnerable in epilepsy. Epileptogenesis involves inflammation, oxidative stress, and neuronal damage, with the PI3K/AKT pathway playing a key role. Apigenin (API), a flavonoid in fruits and vegetables, shows neuroprotective, anti-inflammatory, and anti-apoptotic effects. This study investigates API's mechanisms in a LiCl-pilocarpine epileptic rat model, focusing on hippocampal neurogenesis and PI3K/AKT signaling as potential therapeutic targets.
MethodsWe studied the effects of API and valproate (VPA) on depressive behavior and astrocytes in Lithium chloride (LiCl)-pilocarpine-induced epileptic rats. Additionally, we predicted the potential molecular targets of API for treating epilepsy using network pharmacology. Finally, we conducted in vivo experiments to validate the predicted mechanism.
ResultsIn the API and VPA groups, there was a reduction in seizure frequency and seizure severity compared with the control group. The model group showed more depressive behavior than the control (CON) group, and these behaviors improved significantly after VPA and API treatment. HE staining showed that both API and VPA treatment improved LiCl-pilocarpine-induced nuclear contraction and cell swelling. Nissl staining demonstrated that Nissl vesicles in the CA3 region of the hippocampus were decreased in the model group, but the neurons were larger, more abundant, and more neatly arranged after API and VPA treatment. In the model group, the p-PI3K/PI3K and p-AKT/AKT protein ratios and PI3K, AKT mRNA expression were reduced, while brain-derived neurotrophic factor (BDNF) and glial fibrillary acidic protein (GFAP) were markedly increased. API and VPA treatment effectively reversed these changes.
DiscussionAPI reduces seizures and depressive behaviors in LiCl-pilocarpine-induced epileptic rats, comparable to VPA API mitigates hippocampal neuronal damage, preserves Nissl bodies, and suppresses astrocyte activation via the PI3K/AKT pathway, suggesting neuroprotective and anti-inflammatory effects. While API shows promise as an antiepileptic and antidepressant agent, further studies are needed to confirm its direct modulation of PI3K/AKT and efficacy in other epilepsy models.
ConclusionOur study suggests that API improves depression in rats and has anti-epilepsy activity, which may be involved in activating the PI3K/AKT pathway to protect astrocytes.
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Antimicrobial Activities of Five Different Soap Types Combined with an Extract from Eucalyptus camaldulensis
Authors: Muna Jalal Ali, Emel Eker, Suzan Adil Rashid Al‐Naqeeb and Manaf AlMatarAvailable online: 12 June 2025More LessIntroductionSoaps are vital for preserving our health and personal hygiene since they not only eliminate germs but also rid the body of pollutants.
MethodThe current study aims to determine the physicochemical and antibacterial properties of Eucalyptus camaldulensis leaves using the agar disc diffusion technique and assess the effectiveness of different branded liquid soaps (25 mg/ml, 50 mg/ml, 75 mg/ml, and 100 mg/ml) with the Eucalyptus leaf extract against skin-infecting human pathogenic bacteria.
ResultsThe combined antimicrobial susceptibility of E. camaldulensis and five liquid soaps showed an inhibition zone of 17.67±0.58, 13.33±0.58, 12.67±0.58, and 15.67±0.58 against Staphylococcus aureus, Streptococcus pyogenes, Pseudomonas aeruginosa, and Escherichia coli. The antibacterial properties of Av soap by itself did not work against S. pyogenes. Nevertheless, the extract and DI together showed a detrimental effect against S. aureus and P. aeruginosa, with no halo forming.
DiscussionThe absence of inhibition zones for the extract combined with DI against S. aureus and P. aeruginosa may indicate antagonistic interactions or reduced efficacy in that formulation. Overall, the data highlight the potential of E. camaldulensis to improve the antimicrobial properties of commercial soaps, though the effectiveness varies with microbial strain and formulation.
ConclusionAntimicrobial activity was observed to increase with higher concentrations of the soap-extract combinations. Although liquid soap (seve) was effective against bacterial isolates, a combination of eucalyptus and aqua vera was shown to be more effective.
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Development, Characterization, and Evaluation of the Antidepressant Potential of Crocus sativus SLN Nasal Spray in a Drosophila melanogaster Model
Available online: 12 June 2025More LessObjectivesTo develop and characterize a Crocus sativus (saffron)-based solid lipid nanoparticle (SLN) nasal spray for treating depression by enabling direct nose-to-brain delivery and evaluating its antidepressant potential in a Drosophila melanogaster model.
Materials and MethodsPhytochemical screening, antioxidant assays, and HPLC quantification of picrocrocin were performed on Crocus sativus extract. The SLN-based nasal spray was formulated and characterized for particle size, zeta potential, polydispersity index (PDI), drug entrapment efficiency, in vitro drug release, and stability over 4 weeks. The antidepressant efficacy was assessed via a climbing assay in Drosophila melanogaster.
ResultsPhytochemical analysis revealed phenolic content (11–36 μg GAE/mg), flavonoid content (43–56 μg QE/mg), and carotenoid content (1.9–30 μg βC/mg). HPLC analysis quantified picrocrocin at 6.3 mg/g, confirming its presence. The SLNs exhibited a particle size of 110–225 nm, a zeta potential of -1 to -0.8 mV, a PDI of 1, and a drug entrapment efficiency of 99.76%. Drug release reached 37% over 270 minutes, and the nasal spray maintained a pH of 5.8, a viscosity of 23.1 cP, and stability over 4 weeks. In vivo, the climbing assay demonstrated improved locomotor activity, indicating significant antidepressant potential.
DiscussionThe favorable physicochemical characteristics of the nasal spray, along with the observed behavioral improvements in the fly model, suggest that Crocus sativus SLNs effectively cross the nasal-brain barrier and exert antidepressant-like effects. These findings support its potential for non-invasive management of treatment-resistant depression.
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Exosomal lncRNA ENST00000592016 rescues the Weakened Viability of HUVEC Cells Caused by Intermittent Hypoxia
Authors: Zhuhua Wu, Xiaoyu Lai, Yuchuan Zhao, Jianming Hong, Yongzhao Liu, Hongdi Liang, Ran Wei, Xunxun Chen and Weilong LiuAvailable online: 03 June 2025More LessIntroductionObstructive sleep apnea syndrome [OSAS] is a common sleep breathing disorder accompanied by multiple organ intermittent hypoxemia. Our previous study has suggested that the expression of a lncRNA termed ENST00000592016 [lnc2016 for short] derived from plasma exosomes is remarkably elevated in OSA patients compared to the normal population, and lnc2016 can improve the diagnostic efficiency of OSA.
ObjectiveTo unmask the role of the lnc2016 in vascular endothelial cells, targeted hypoxia is the goal of the current research.
MethodsPrimary human ADSCs and HUVEC cells were cultured. CCK-8, cytometric assay, transwell, and tubular formation assay were used to determine cell viability, cell apoptosis, cell cycle, cell migration, as well as tubular formation ability.
ResultsAdipose-derived stem cells [ADSCs]-derived exosomes contained robust lnc2016. After co-culture with human umbilical vein endothelial cells [HUVECs], exosomal lnc2016 could enhance cell proliferation, DNA synthesis, migration, and tubular formation, whereas suppress cell apoptosis of HUVECs against hypoxic conditions.
DiscussionUnder hypoxic conditions, ADSCs secrete various reparative factors and transmit them via exosomes; among them, lnc2016 may participate in the regulation of hypoxia-induced injury through the ceRNA network, which requires further investigation.
ConclusionLn2016 can promote the cell growth, migration, DNA synthesis, and tubular formation as well as suppress the cell apoptosis of vascular endothelial cells against hypoxia in vitro.
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ARL6IP1 Inhibits Breast Cancer Tumor Progression by Targeting OLFM4 to Regulate Glycolysis
Authors: Lijun Zhou, Chen Chen, Lingping Zhu and Fei GuAvailable online: 27 May 2025More LessIntroductionARL6IP1 has been linked to cancer progression, but its precise role in BC, particularly in metabolism and its interaction with an OLFM4, remains unclear.
AimsThis study aimed to investigate the role of ADP-ribosylation factor-like 6 interacting protein 1 (ARL6IP1) in breast cancer (BC) cell behavior and metabolism and explore its interaction with an olfactomedin-4 (OLFM4) as a potential therapeutic target.
ObjectiveThe objective of this study was to determine the effects of ARL6IP1 knockdown on BC cell proliferation, invasion, migration, apoptosis, oxidative stress, and glycolysis. Additionally, this study also explored the interaction between ARL6IP1 and OLFM4 and their combined role in BC progression and metabolism.
MethodsKey gene modules in the GSE73540 dataset were identified through weighted gene co-expression network analysis (WGCNA). Three BC-related datasets (GSE73540, GSE22820, and GSE36295) and The Cancer Genome Atlas (TCGA) were applied for additional examination of differentially expressed genes (DEGs). Intersection analysis selected ARL6IP1 as a hub gene for prognostic analysis. In vitro experiments investigated how ARL6IP1 knockdown influences BC cell proliferation, invasion, migration, apoptosis, epithelial-mesenchymal transition (EMT), oxidative stress, and glycolysis. The connection between ARL6IP1 and an OLFM4 was confirmed using Co-immunoprecipitation (Co-IP), and their roles in BC tumor progression and glycolysis were evaluated.
ResultsARL6IP1 was elevated in BC datasets and linked with poor BC prognosis. Experiments demonstrated that knockdown of ARL6IP1 significantly reduced BC cell growth while promoting apoptosis and oxidative stress. Besides, ARL6IP1 knockdown reduced glycolysis, as manifested by decreased extracellular acidification rate (ECAR), glucose consumption, adenosine triphosphate (ATP) levels, and lactate production while increasing mitochondrial respiration (OCR). Co-IP validated the connection between ARL6IP1 and OLFM4, and OLFM4 overexpression partially counteracted the suppression of glycolysis and cell behavior resulting from ARL6IP1 knockdown.
ConclusionARL6IP1 is a critical regulator of BC progression, influencing glycolysis, mitochondrial function, and key cellular behaviors. Targeting the ARL6IP1-OLFM4 axis offers a promising therapeutic strategy for managing BC.
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Effect of Electroacupuncture on Intestinal Mucosal Barrier in IBS-D Rats: Analysis Based on RNA-seq
Authors: Jingru Ruan, Jingwei Zhu, Kuiwu Li, Ziye Wang, Ting Wang, Xiaoyu Han, Xiaomin Li, Yucheng Fang, Xiaoge Song and Haoran ChuAvailable online: 27 May 2025More LessObjectiveTranscriptome-level insights into electroacupuncture (EA)’s mechanisms for alleviating intestinal mucosal barrier damage in diarrhea-predominant irritable bowel syndrome (IBS-D) are limited. This study aimed to construct ceRNA networks and elucidate EA's role in restoring barrier integrity via lncRNA-miRNA-mRNA regulation in IBS-D rats.
MethodsThe IBS-D model was established by neonatal maternal separation (NMS), 4% acetic acid enema and restrain stress (RS). Rats were randomized into control, model, and EA groups. After 2-week EA treatment, colonic morphology was assessed by HE staining and TEM; intestinal barrier biomarkers were analyzed via ELISA and WB. RNA-seq identified differentially expressed RNAs (DE RNAs) to construct ceRNA networks. GO and KEGG analyzed EA-modulated DE mRNAs. RT-qPCR validated RNA-seq; WB and IF confirmed mast cell (MC) involvement in EA-regulated pathways.
ResultsRNA-seq identified 426 up-regulated and 429 down-regulated DE mRNAs, 342 up-regulated and 362 down-regulated DE lncRNAs, and 10 up-regulated and 48 down-regulated DE miRNAs following EA. Constructed ceRNA networks included 7 DE lncRNAs-miR-139-3p-Bid and -miR-378b-Slc4a5. GO analysis linked EA to defense response, hormone regulation, and cytokine function pathways. KEGG implicated antigen processing/presentation, neuroactive ligand-receptor interaction, PPAR signaling, and glutathione metabolism. RT-qPCR validated RNA-seq results.
ConclusionThis RNA-seq study reveals EA mitigates IBS-D intestinal mucosal barrier damage by regulating genes and ceRNA networks, providing novel transcriptomic insights into its therapeutic mechanisms.
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Influence of Mycoplasma Resistance Genes on Pediatric Mycoplasma Pneumonia Treatment and Determinants for Second-line Antimicrobial Adjustment
Authors: Boyin Deng, Wenhui Dong, Jie Cao and Jiwei ZhouAvailable online: 22 May 2025More LessObjectiveThe objective of this study is to evaluate the role of mycoplasma resistance genes in pediatric mycoplasma pneumonia and to identify the factors that necessitate antibiotic adjustments.
MethodsWe retrospectively analyzed clinical data from children diagnosed with mycoplasma pneumonia at Chongqing Medical University Children's Hospital (January-October 2023). We categorized patients based on antibiotic treatment adjustments: the antibiotic adjustment group and the no adjustment group. We compared demographic characteristics, clinical outcomes, and the gene resistance rate that point mutations A2063G and A2064G in the 23S rRNA between groups. Logistic regression was employed to determine the factors prompting a switch from macrolides to alternative antibiotics.
ResultsThe study included 551 cases, with 341 in the no adjustment group and 210 in the antibiotic adjustment group (54 switched to doxycycline, 156 to levofloxacin). There was no significant difference in the prevalence of resistance genes between the groups (71.8% vs. 71.4%; P=0.916). Significant differences were observed in hospital stay duration, C-reactive protein (CRP), D-dimer, fibrinogen, procalcitonin levels, and lung consolidation (P<0.05). Logistic regression identified elevated CRP and procalcitonin levels as independent predictors of the need for alternative antibiotics.
ConclusionResistance genes do not predict the need for second-line antibiotics in pediatric mycoplasma pneumonia; however, elevated CRP, and procalcitonin levels significantly correlate with this necessity.
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Serum Metabolomic Profiles Predict Sensitivity and Toxicity to Platinum-Fluorouracil Chemotherapy in a Gastric Cancer Xenograft Model
Authors: Dong Yang, Yuanlin Liu, Xiangyu Meng, Chao Wang, Meng Zhang, Tao Zhang and Yefu LiuAvailable online: 15 May 2025More LessBackgroundThe mechanisms of chemotherapy sensitivity and toxicity are complex. Metabolomics can better reflect the status of anticancer drugs, tumors, and hosts simultaneously.
MethodsMice were implanted with human gastric cancer cells through subcutaneous xenografting, and then treated with the PF (platinum-fluorouracil) regimen, with saline serving as the control. Tumor growth was monitored by measuring tumor volume, and body weight was recorded on Days 0, 2, 4, 6, and 8. Kidney damage was assessed using H&E staining. To analyze differential responses, PF-treated mice were grouped separately according to chemotherapy sensitivity (high/medium/low via tumor response) and toxicity (high/medium/low via body weight changes). Serum metabolomics was evaluated using Mass Spectrometry.
ResultsPlatinum-Fluorouracil (PF) chemotherapy significantly reduced tumor weight in mice, although it also induced notable body weight loss and renal toxicity compared to controls. Serum metabolomic analysis revealed significant differences between PF and control groups, involving metabolites like deoxymethylmycin and dehydrocorticosterone, associated with AMPK and cortisol synthesis/secretion pathways. Further comparisons highlighted: (1) High- vs. low-sensitivity subgroups differed significantly in metabolites, such as palmitoyl-CoA and indoleacetic acid (linked to AGE-RAGE, insulin resistance, and AMPK pathways). (2) High- vs. low-toxicity subgroups displayed significant metabolic differences, including methylguanosine and methylcytidine (implicated in ferroptosis, ether lipid, and fatty acid metabolism pathways).
ConclusionThe PF regimen effectively inhibits the growth of subcutaneous tumors in nude mice, while causing varying levels of sensitivity and toxicity in tumor chemotherapy. These observed effects of sensitivity and toxicity are linked to underlying metabolic mechanisms.
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Constipation and Psychiatric Disorders: A Bidirectional Mendelian
Authors: Xu Yang, Jie Kang, Xuan Zhang and Nan SuiAvailable online: 14 May 2025More LessBackgroundObservational studies have shown a link between constipation (CN) and psychiatric disorders, including Schizophrenia (SP), Bipolar disorder (BD), Schizoaffective disorder (SD), and Parkinson’s disease (PD). However, it is still unknown whether CN affects the occurrence and development of psychiatric disorders or whether psychiatric disorders cause the occurrence and development of CN. Therefore, this study used Mendelian randomization (MR) analysis to evaluate the relationship between CN and psychiatric disorders.
MethodWe used genome-wide association studies (GWAS) to assess the relationship between constipation (N = 411, 623) and four psychiatric disorders, including SP (N = 77, 096), BD (N = 51, 710), SD (N = 210, 962), PD (N = 482, 730), using bidirectional MR analysis. Inverse variance weighting (IVW), MR Egger (ME) and Weighted median (WM) were used as causal analysis methods. Cochran's Q test, funnel plot, MR Egger intercept test and Leave‐one‐out analysis were used to detect sensitivity. Confounding factors were analyzed and eliminated by LDtrait to avoid influencing the final MR Analysis result.
ResultsThe results of positive MR analysis indicated that there was no evidence of influence of constipation on SP (OR 1.043, 95%CI 0.946 - 1.149, P value = 0.398), BD (OR 1.114, 95%CI 0.995 - 1.248, P value = 0.062), SD (OR 0.934, 95%CI 0.674 - 1.294, P value = 0.682) and PD (OR 1.118, 95%CI 0.918 - 1.361, P value = 0.269) under gene prediction. Reverse MR analysis suggested that SP (OR 1.030, 95% CI 1.001-1.060, P value = 0.042) had a causal relationship with constipation. BD (OR 0.993, 95% CI 0.962-1.025, P value = 0.664), SD (OR 1.021, 95% CI 0.984-1.059, P value = 0.265) and PD (OR 1.004, 95% CI 0.974-1.035, P value = 0.790) were not associated with CN.
ConclusionThere was a positive association between SP and CN. CN may have no exact causal relationship with BD, SD and PD, and the interaction mechanism between these diseases needs to be further explored.
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Identification of Selected Genes Associated With the Prediction of Prognosis in Bladder Cancer
Authors: Xiao-Dong Li, Jun-Ming Zhu, Qi You, Xiao-Hui Wu, Qi Huang, Hai Cai, Yong Wei, Yun-Zhi Lin, Xiong-Lin Sun, Ning Xu, Xue-Yi Xue and Qing-Shui ZhengAvailable online: 13 May 2025More LessBackgroundBladder cancer (BC) is one of the most common urological malignancies, ranking as the eleventh most common cause of cancer-related deaths worldwide. The lack of specific and sensitive prognostic biomarkers presents a significant challenge in the early diagnosis and treatment of BC.
MethodsThis study utilizes the Gene Expression Omnibus (GEO) dataset GSE13507 and the Cancer Genome Atlas (TCGA) database to screen differentially expressed genes related to BC. By using Weighted Gene Co-expression Network Analysis (WGCNA), two modules associated with BC were investigated in GSE13507 and TCGA. Hub genes were identified through Protein-Protein Interaction (PPI) network analysis, and their functions were validated through multiple approaches, including Gene Expression Profiling Interactive Analysis (GEPIA), Western Blotting (WB) assay, Human Protein Atlas (HPA), Oncomine analysis, and quantitative Real-Time PCR (qRT-PCR) analysis. Additionally, miRNAs associated with hub gene expression were identified using various databases to predict the progression and prognosis of BC.
ResultsWGCNA and a differential gene expression analysis identified 171 common genes as target genes. Ten genes (MYH11, ACTA2, TPM2, ACTG2, CALD1, MYL9, TPM1, MYLK, SORBS1, and LMOD1) were identified using the PPI tool. The CALD1 and MYLK genes showed a significant prognostic value for overall survival and disease-free survival in patients with BC. CALD1 and MYLK expression levels were significantly lower in BC tissues than in normal tissues. Furthermore, miR-155 showed a significant positive correlation with MYLK.
ConclusionThis study established MYLK as a direct target gene of miR-155, functioning as an actionable survival-related gene correlated with BC development.
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KLHL17 as a Prognostic Indicator and Therapeutic Target in Cervical Cancer: A Comprehensive Analysis
Authors: Guizhen Lyu, Jinyuan Li and Dongbing LiAvailable online: 13 May 2025More LessIntroductionThis study aims to clarify the role of kelch like family member 17 (KLHL17) in cervical cancer (CESC) is unclear.
ObjectiveTo clarify this uncertainty, our research employed bioinformatics analysis coupled with experimental corroboration.
MethodsWe utilized the Cancer Genome Atlas (TCGA) database to assess the expression of KLHL17 in various cancers, specifically CESC, and to explore its association with clinical characteristics, diagnostic utility, and prognostic significance in CESC. The current investigation delved into the potential regulatory pathways related to KLHL17, examining its connection with the infiltration of immune cells, the expression of immune checkpoint genes, the status of microsatellite instability (MSI), and the efficacy of diverse therapeutic agents in CESC. The research analyzed KLHL17 expression patterns using single-cell sequencing data from CESC samples and investigated the genetic variations of KLHL17 within this context. KLHL17 expression was validated using GSE145372. The presence and levels of KLHL17 in different cell lines were validated through quantitative real-time PCR (qRT-PCR) assays.
ResultsKLHL17 exhibited irregular expression profiles across various cancer types, including CESC. Furthermore, increased KLHL17 levels in CESC patients were significantly associated with a lower progression-free survival (PFS) rate (hazard ratio: 1.62; 95% confidence interval: 1.01–2.60, p = 0.044). Moreover, KLHL17 expression emerged as a distinct prognostic indicator for CESC patients (p = 0.031). It has been associated with various biological pathways, such as cytokine-cytokine receptor interaction, primary immunodeficiency, cell adhesion molecules (CAMs), chemokine signaling pathway, steroid hormone biosynthesis, and others. The expression levels of KLHL17 were found to correlate with the presence of immune cells, the expression of immune checkpoint genes, and the status of MSI within CESC. Furthermore, KLHL17 expression exhibited a significant and inverse correlation with XMD15-27, rTRAIL, Paclitaxel, tp4ek, and tp4ek-k6. Furthermore, KLHL17 was found to be significantly positively regulated in CESC cell lines.
DiscussionThe findings suggest that KLHL17 is involved in the progression of CESC and may serve as a potential prognostic marker and therapeutic target. KLHL17's association with immune cell infiltration and immune checkpoint genes indicates a role in immuneevasion. Future research should focus on validating these findings through independent datasets and experimental studies to elucidate the molecular mechanisms underlying KLHL17's role in CESC progression and immune regulation.
ConclusionKLHL17 is a promising prognostic marker and potential therapeutic target in CESC.
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Exploring Potential Bifunctional Peptides with Anti-tyrosinase and Antioxidant Activities from Porphyra Protolysate Using in Silico Analysis
Authors: Si-Bo Huang, Pei-Xia Feng, Liu-ying Li, Hong-Hui Guo and En-Qin XiaAvailable online: 29 April 2025More LessBackgroundExtracts from Porphyra have been detected to have antioxidant activity and tyrosinase (TYR) inhibitory activity. However, bioactive peptides (BPs) released from Porphyra proteins (PPs) have not been comprehensively reported.
ObjectiveThe aim of this study is to rapidly identify bifunctional peptides with antioxidant and TYR inhibitory activities from a large number of digested peptides from PPs.
MethodsIn this study, a total of 3,288 proteins from six main species of Porphyra were collected, and the antioxidant potential (AP) was evaluated. Hydrolyzed peptides with 2–8 amino acid lengths were collected and known antioxidants were removed. Next, these peptides were further screened using ADMET analysis. Finally, the DPPH· scavenging potential (IC50) and TYR inhibition potential (TIP) of these peptides were further predicted by QSAR models and molecular docking based pharmacophore models, respectively.
ResultsThe most released antioxidant peptides after digestion of all types of PPs were dipeptides with sequences EL, IR and AY. In addition, 44,689 short non-repeatable peptides were swirled in these hydrolysates, which have not yet been reported to have antioxidant activity. Next, 337 of these digested peptides were predicted to be absorbed without hepato-renal toxicity and had virtual metabolic scores > 0.01%. Finally, 138 peptides were predicted to have AP and TIP.
ConclusionPorphyra is a kind of promising source rich in bifunctional peptides. Present study adopted an innovative method with some free scripts to rapid discovery of bifunctional peptides from a large number of unknown PPs.
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Exploring the Active Ingredients and Core Targets of Erxia Decoction in the Treatment of Sleep Disorder by Integration of Network Pharmacology and Proteomics
Authors: Bo Jiang, Huiran Yang, Fei Zhou, Huijun Qu, Xueqian Hu and Zhanwen LiuAvailable online: 29 April 2025More LessAimsFor clarifying the “multi genes and multi targets” characteristic of the treatment of Erxia Decoction (EXD), the aim of this study was to employ network pharmacology technology to perform cluster analysis on selected EXD targets.
BackgroundEXD, a famous Chinese herbal prescription, consisting of Pinelliae Rhizoma (PR) and Prunellae Spica (PS), was mainly used to treat sleep disorder (SLD).
ObjectiveUsing network pharmacology combined with proteomics to find out the main active components and core targets of EXD in the treatment of SLD.
MethodBy constructing the network of drug–component–target, the key protein targets of EXD for the treatment of SLD were screened. Then the interaction of the main active components of EXD and predicted candidate targets were verified. Then the proteomic analysis was used to screen the core targets in BV2 cells treated with EXD or the chemical ingredients, and the expression level was validated by Western blotting. Finally, molecular docking was used to further evaluate the mechanism of the action of the main ingredients and the core targets.
ResultThe 24 components of EXD mainly participate in the SLD treatment process by acting on 15 important key genes, and the core signal pathways were identified in the process of the action of EXD in treating SLD. Four key ingredients and five core targets were revealed from the results of network pharmacological analysis combination with proteomics, and then the AKT1 protein as a key target was validated by PCR and Western blotting.
ConclusionThis study preliminarily revealed EXD, morin (MOR) and quercetin (QUE) mainly inhibited the AKT1 core targets for the treatment of SLD using the network pharmacological analysis, proteomics, Western blotting and molecular docking.
The results elucidated partly the molecular mechanism and provided clues and a basis for further research.
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A Review of Research on the Utilization of Ligularia Plants Based on their Functional Compositions
Authors: Yaqiong Wang, Weifeng Dai, Cheng Yuan, Mengyang Liu, Jingyuan Wen and Mi ZhangAvailable online: 29 April 2025More LessThe genus Ligularia belongs to the family Asteraceae, with approximately 150 species worldwide. It is primarily distributed from Europe and the Himalayas to Japan, and it is rich in resources, with many species possessing medicinal value. According to the research reports on the functional compositions, the research progress and resource utilization of this genus were summarized from 2016 to the present. This paper aims to provide some references for the basic research results of the genus to industrialization. In general, after 2016, combined with the work of chemical and active investigation, some varieties have been applied and explored in drugs, cosmetics, food, daily necessities, pesticides, and feed, reflecting great development and value.
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Exploring the Efficacy and Mechanism of Astragalus Polysaccharide in Treating Allergic Asthma through Network Pharmacology, Bioinformatics, and Experimental Verification
Authors: Linhan Hu, Haiyun Zhang, Yihang Zhang, Lei Wang, Honglei Zhang, Juntong Liu, Linpeng Cong, Yumei Zhou, Ji Wang and Qi WangAvailable online: 29 April 2025More LessIntroductionAllergic asthma is an inflammatory disease of the airways that causes great distress to the patient's normal life. Astragalus Polysaccharide (APS) is the main active ingredient in the traditional Chinese medicine Astragalus mongholicus Bunge, which has the effect of regulating immune function.
ObjectiveThis study aimed to evaluate the effect of APS on allergic asthma and investigate its potential mechanism of action.
MethodsThis study utilized network pharmacology to predict the relevant targets and signaling pathways of APS treatment for allergic asthma. Subsequently, an animal model was established using Ovalbumin (OVA) induction. The efficacy of APS was verified using histopathologic staining and Airway Hyperresponsiveness (AHR) assay. Signaling pathways were examined using Western Blot (WB). Finally, bioinformatics analysis was utilized to explore the correlation between the progression of allergic asthma and signaling pathways.
ResultsNetwork pharmacology analysis identified 15 intersection targets significantly enriched in the PI3K/AKT signaling pathway. The results of molecular docking showed that small molecule drugs have a strong binding ability to target proteins. The experiments confirmed APS successfully suppressed the pathological symptoms in allergic asthma model mice. Subsequently, WB provided evidence supporting that APS has potential therapeutic effects mediated through the PI3K/AKT signaling pathway. The bioinformatics results confirmed that disease progression in allergic asthma patients does correlate with the PI3K/AKT signaling pathway.
ConclusionOur study suggests that APS may treat allergic asthma by targeting the PI3K/AKT signaling pathway. This provides a basis for preliminary research on the clinical application of APS for treating allergic asthma.
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Mutation Mapping of PD-L1 Expression in Advanced Non-small Cell Lung Cancer: A Real-world Retrospective Cohort Study
Authors: Fang Hao, Qing Ma and Diansheng ZhongAvailable online: 25 April 2025More LessIntroductionThe duration of response to immune checkpoint inhibitors (ICIs) varies because of tumor immune heterogeneity, and employing programmed death receptor ligand 1 (PD-L1) expression to evaluate the efficacy of anti-programmed cell death-1 (PD-1)/PD-L1 antibodies remains controversial.
MethodA total of 138 advanced non-small cell lung cancer (NSCLC) patients were subdivided into 2 groups - 52 patients with a PD-L1 Expression≥50% and 86 patients with a PD-L1 Expression <50% - based on next-generation sequencing (NGS) to analyze multiple-dimensional data types, including tumor mutation burden (TMB), gene alterations, gene enrichment analysis, therapy response, and immune-related adverse events (irAEs).
ResultsHigh levels of PD-L1 expression were significantly associated with advanced age and TMB status. The PD-L1≥50% cohort presented mutations of KRAS, NOTCH1, and FAT, while the PD-L1<50% group exhibited mutations of EGFR, PTEN, or LATS1/2. Except for the ascertained DNA damage response regulation. Even though there was no significant difference between PD-L1≥50% and PD-L1<50% cohorts on therapy response, patients with a PD-L1 Expression≥50% elicited a high irAEs incidence rate and increased plasma interleukin 6 (IL-6) concentration.
ConclusionThis real-world retrospective study suggested that high expression of PD-L1 exhibited inappropriate activation of different pathways and collaborated with anti-cytokines and chemokines therapy may optimize clinical therapy efficacy.
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Qishen Huoxue Granule Ameliorates LPS-induced Cardiomyocyte Injury by Suppressing Excessive Autophagy via MasR/PI3K-AKT-mTOR Pathway
Authors: Yu-Fan Du, Zheng Wang, Huan Tang, Zhao-Qing Lu and Guo-Xing WangAvailable online: 24 April 2025More LessIntroductionQishen Huoxue Granule (QHG), a classical Traditional Chinese Medicine prescription, can reduce septic cardiomyopathy in clinic. However, the mechanism of QHG remains unclear. This study aims to investigate the mechanism and effect of QHG-contained serum (QHG-CS) on sepsis-induced cardiomyopathy (SICM).
MethodsQHG was administered to Wistar rats via gavage to obtain QHG-CS. The chemical constituents of QHG-CS were identified via UPLC-Q-TOF-MS. In vitro, rat cardiomyocytes H9c2 cells isolated from embryonic BD1X rat heart tissue, and septic myocardial injury model was established by inducing H9c2 cells with lipopolysaccharide (LPS). Cell viability was assessed through CCK-8. Protein expression was determined using western blot, and gene expression was measured using real-time quantitative PCR. Cell autophagy was investigated by detecting LC3 expression using flow cytometry and immunofluorescence. In addition, three inhibitors, A779 (MasR), wortmannin (PI3K) and rapamycin (mTOR) were used to localize the potential therapeutic targets.
ResultsQHG-CS significantly improved the survival of septic cardiomyocytes (p<0.0001). The expression of autophagy-related markers Beclin1, ATG5, and LC3II/I was increased in LPS-induced cardiomyocytes, which could be inhibited by QHG-CS. QHG-CS upregulated the mRNA expression of MasR, PI3K, and AKT, as well as the phosphorylation of PI3K, AKT, and mTOR. Moreover, A779 markedly lowered mRNA levels of MasR, PI3K, and mTOR, while wortmannin decreased mRNA levels of PI3K and mTOR, whereas rapamycin only suppressed mTOR phosphorylation.
DiscussionBy inhibiting excessive autophagy through upregulation of the MasR/PI3K-AKT-mTOR pathway, QHG can alleviate sepsis-induced cardiomyocyte damage. This study provides novel perspectives for the management of sepsis-induced cardiac damage.
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Shenhuang Liuwei Powder Alleviates Streptozotocin-Induced Diabetic Ulcers in Rats through the Inhibition of the AGE/RAGE Signaling Pathway and Promotion of Antibacterial Activity and Angiogenesis via Activation of the PI3K/Akt/eNOS/HIF-1α Pathway
Authors: Jun Li, Qian Zhang, Shengnan Li, Shu Wang, Fengye Zhou, Haifeng Zhang, and and Jianping ChenAvailable online: 24 April 2025More LessAims and ObjectiveShenhuang Liuwei powder (SHLWP) is frequently used to treat diabetic ulcers (DUs), but its mechanism of action remains poorly understood. This study aimed to identify the active compounds and mechanisms by which SHLWP alleviates DUs.
MethodsThe chemical components of SHLWP were analyzed using high-resolution mass spectrometry (HRMS). Network pharmacology based on HRMS data identified SHLWP-associated targets and signaling pathways. Its antibacterial activity was assessed using Kirby-Bauer disc diffusion and minimum inhibitory concentration (MIC) tests. Its in vivo pharmacological effects were evaluated in a streptozotocin-induced diabetic ulcer model in Sprague-Dawley (SD) rats.
ResultsSeventy-three components were identified in SHLWP, with key constituents including caffeic acid (13.11 ± 0.14 μg/g), ferulic acid (20.40 ± 0.24 μg/g), quercetin (8.49 ± 0.18 μg/g), luteolin (36.63 ± 0.19 μg/g), apigenin (82.14 ± 1.60 μg/g), and linoleic acid (507.59 ± 1.46 μg/g). SHLWP exhibited strong antibacterial activity against Staphylococcus aureus (MIC = 7.8125 μg/mL), Streptococcus pyogenes (MIC < 3.90625 μg/mL), and Streptococcus epidermidis (MIC < 3.90625 μg/mL). Network pharmacology revealed significant enrichment of the AGE/RAGE, HIF-1, and PI3K-Akt pathways, which was validated in vivo using qPCR, immunohistochemistry, and Western blot.
ConclusionSHLWP alleviated streptozotocin-induced diabetic ulcers by inhibiting the AGE/RAGE pathway and promoting antibacterial activity and angiogenesis via the PI3K/Akt/eNOS/HIF-1α pathway, providing a biological basis for its therapeutic effects.
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Eco-friendly Advancements through Fish Waste: A Review of Therapeutic and Industrial Innovations
Available online: 24 April 2025More LessFish waste, a significant by-product of the fisheries industry, presents both an environmental challenge and a valuable resource. This review delves into the innovative approaches to harness the potential of fish waste for various applications, particularly in the biomedical and industrial sectors. Therapeutically, fish waste yields valuable bioactive compounds such as omega-3 fatty acids, collagen peptides, and gelatine, which are known to benefit cardiovascular, skin, and immune health. Fish-derived collagen, for instance, is employed in wound healing, bone regeneration, and cosmetic applications due to its biocompatibility and lower infection risk compared to land-animal sources. Omega-3 fatty acids from fish waste exhibit anti-inflammatory, anticancer adding value to pharmaceutical industries. Industrially, fish waste can be transformed into eco-friendly materials like bioplastics, biofuels, and biofertilizers, contributing to environmental sustainability. Bioplastics synthesized from fish scales and biotextiles developed from collagen-modified polyester exemplify sustainable alternatives to synthetic materials. Additionally, fish-based biofertilizers enhance soil fertility, promoting greener agriculture. Innovations also include the production of fish-based leather, low-cost fish peptones for microbial culture, and fish oil-based biofuel with diesel-like properties, showcasing versatile applications. This review explores the untapped potential of fish waste, emphasizing its underutilized yet high-value therapeutic and industrial applications. Unlike existing studies, it focuses on lesser-explored areas such as fish-derived biofertilizers for precision agriculture and fish-based bioplastics for sustainable packaging. These applications can significantly reduce pollution, promote non-toxic alternatives, and contribute to sustainable industries. By leveraging fish waste, this review aims to address environmental challenges, support global health initiatives, and highlight innovative solutions for a circular economy.
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Identification of the Role of Necroptosis-Related Genes in the Oxidative Damage of Lens Epithelial Cells and Validation in Ultraviolet B-induced Cataract in Rats
Authors: Yongshun Liang, Qingqiao Gan, Xin Zhong, Tian Lan, Yingqin Yang and Hao LiangAvailable online: 17 April 2025More LessIntroductionThe specific role of necroptosis in the pathogenesis of cataracts remains unclear. This study aimed to identify and validate the genes related to necroptosis in the development of cataracts through bioinformatics analysis.
MethodWe utilized RNA sequencing data (GSE161701) from the Gene Expression Omnibus (GEO) database and employed R software to perform differential expression analysis of necroptosis-related genes (NRGs) in lens epithelial cells (LECs) under oxidative stress. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to evaluate the functions of necroptosis-related differentially expressed genes (NRDEGs) and their associated pathways. Additionally, a diagnostic model was established using LASSO regression to select hub genes, and protein-protein interaction (PPI) networks, mRNA-miRNA, and mRNA-drug regulatory networks were constructed. Immune infiltration analysis was performed using the xCell and CIBERSORT algorithms, and the differential expression of hub genes was validated in a UVB-induced rat cataract model using RT-qPCR and immunohistochemistry.
ResultsThe results indicated that oxidative stress promoted necroptosis in LECs, involving 86 NRDEGs and nine hub genes. GO and KEGG analyses revealed significant enrichment in necroptosis-associated pathways. Furthermore, we identified 58 mRNA-miRNA interactions and 131 potential molecular compounds or drugs. The immune infiltration analysis showed that certain immune cells exhibited significantly elevated expression in the cataract group, with notable correlations between some immune cells and hub genes. RT-qPCR and immunohistochemistry confirmed the expression of 9 hub genes and 3 key necroptosis genes. BAX, CXCL1, EPAS1, JUN, LRP1, RBM14, SERTAD1, and TNFAIP3 were highlighted as potential diagnostic and therapeutic targets.
ConclusionThis study identified key NRDEGs involved in the pathogenesis of cataracts under oxidative stress through bioinformatics analyses, potentially providing new targets and research directions for future cataract prevention and treatment.
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Xuebijing Alleviates Microglial Activation after Traumatic Brain Injury via Regulation of NF-κB Pathway: Network Pharmacology and Experimental Validation
Authors: Hongran Fu, Xiaoyu Wang, Xuelin Mo, Jingwei Li and Dongkai GuoAvailable online: 15 April 2025More LessObjectiveXuebijing (XBJ) injection, a Traditional Chinese medicine (TCM) widely used in China for treating sepsis and multiple organ dysfunction, has shown neuroprotective effects in traumatic brain injury (TBI). However, the mechanisms underlying these effects remain unclear. This study aims to elucidate the neuroprotective and pharmacological molecular mechanisms of XBJ and its active monomer, Hydroxy-safflor yellow A (HSYA), in treating TBI through network pharmacology and experimental validation.
MethodsPotential therapeutic targets for TBI were collected from TCMSP, TTD, OMIM, and GeneCards databases. Active compounds and targets of XBJ injection were obtained from TCMSP. The STRING database and Cytoscape software constructed a protein-protein interaction (PPI) network. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the DAVID database and visualized with Bioinformatics tools. Neuroprotective effects of XBJ were verified in vitro using BV2 and primary microglia cells stimulated by Lipopolysaccharide (LPS). Additionally, a TBI mice model was used to identify microglial activation in vivo.
ResultsA total of 161 common targets related to TBI were identified. Network pharmacological analysis suggested that XBJ targets proteins involved in inflammation. In vitro results showed that XBJ and HSYA inhibited LPS-induced microglial activation via the NF-κB pathway. Furthermore, XBJ was found to inhibit microglial activation in TBI mice.
ConclusionThese findings indicate that XBJ and HSYA may treat TBI by repressing microglial activation through the NF-κB pathway. Our study provides valuable evidence supporting XBJ as an effective therapy for TBI.
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Chemistry and Pharmacology of Chenopodium album L. (BATHUA)
Authors: Nagendra Sharma, Pankaj Kumar Chaurasia, Shashi Lata Bharati and Ahmed M. SaqrAvailable online: 08 April 2025More LessIntroductionChenopodium album Linn. is a nutritionally and pharmacologically significant herb that generally grows in the winter season along with other crops. It is rich in fibers, protein, minerals (Mg, Ca, Fe, K, P, and others), vitamins (ascorbic acids, thiamine, riboflavin, and others), and several other biologically active chemical components like flavonoids, saponins, steroids and many more. In this article, the authors briefly describe and assess the chemistry and pharmacology of this nutritionally significant plant.
MethodsThis study is based on several literature searches conducted via Google Scholar, Research Gate, PubMed, and many other online sources.
Result and ConclusionDue to its richness with bioactive phytochemicals, it has become a valuable functional food. C. album has several medicinal properties like antioxidant, antimicrobial, anti-arthritic, anti-diabetic, anti-infection, anti-ulcer, and many others. Even after its rich nutritional values, chemical compositions, and a broad spectrum of pharmacological properties, this is a highly ignored herb worldwide. Therefore, extensive research and awareness regarding the functional role of this herb is needed.
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The Regulatory Effects of Electroacupuncture on the Intestinal Flora of Mice with Ulcerative Colitis
Authors: Xinyu Gao, Enfan Xiao, Shaohui Geng, Haixu Jiang, Hesong Wang, Yuxin Zhao, Jiaxin Xie, Guangrui Huang and Wenrui JiaAvailable online: 07 April 2025More LessIntroductionThis study aimed to investigate the modulation of intestinal flora by electroacupuncture in a murine ulcerative colitis (UC) model, with a focus on analyzing microbial taxa and identifying key regulatory targets and pathways.
MethodsA UC model was established in mice using 5% dextran sodium sulfate (DSS). Electroacupuncture was applied at bilateral “Shangjuxu” (electrostimulation) and “Tianshu” (manual acupuncture) points from days 5–9, while the mesalazine group received 0.5 g/kg/day via gavage. Disease activity index (DAI), colon length, and histopathology (hematoxylin-eosin staining) were evaluated. Intestinal flora composition was analyzed via 16S rDNA sequencing.
ResultsElectroacupuncture significantly reduced DAI scores on days 7 and 9 (P < 0.05; P < 0.01) compared to the model group, improved colon morphology, and reduced inflammation. Linear discriminant analysis and Wilcoxon tests revealed an increased abundance of Roseburia and elevated alpha diversity in the electroacupuncture group. Functional prediction demonstrated suppressed RNA transport and glycerophospholipid metabolism in the model group (P < 0.05), which were significantly enhanced post-electroacupuncture (P < 0.01).
DiscussionElectroacupuncture restored beneficial taxa (e.g., Roseburia) and microbial diversity, suggesting gut homeostasis modulation. Enhanced lipid metabolism and RNA transport pathways may underlie its anti-inflammatory and mucosal repair effects.
ConclusionElectroacupuncture alleviates UC by modulating the structure and function of intestinal flora, with Roseburia and associated metabolic pathways identified as key targets. These findings highlight the potential of electroacupuncture as a UC therapy.
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Curcumin Regulating Primordial Follicle Initiation by Restoring the Oxidative-antioxidant Balance
Authors: Wanjing Li, Jinbang Xu, Dan Shi, Jingyi Wang, Tao Liu, Juan Yang and Disi DengAvailable online: 07 April 2025More LessBackgroundDiminished ovarian reserve (DOR) is accompanied by abnormal initiation and development of primordial follicles. Reporting that curcumin can protect the ovarian reserve, we used rats as a model to explore the regulatory mechanism of curcumin on primordial follicle priming.
ObjectiveCurcumin restores the ovarian microenvironment of DOR model rats by AMPK/SIRT 1 signaling pathway, thus regulating the initiation of primordial follicles.
MethodsThe study used the ovaries of 3-day-old female rats, after replicating the DOR model by triptolide (TP), then used curcumin intervention for 3 days. Histomorphological analysis was counted by H & E staining; ELISA test was used to count ovarian hormone [follicle stimulating hormone (FSH) / luteinizing hormone (LH) ratio and estradiol (E2)] concentration in the culture supernatant. Spectrophotometric measurement was used to count of superoxide dismutase (SOD) and the malondialdehyde (MDA). The protein and mRNA expression of the pathway and key indicators for follicle initiation were determined by Western Blot and Q-PCR (AMPK, SIRT 1, PTEN, PGC-1 α, and AMH).
ResultsAfter curcumin treatment, the number of growing follicles increased (P < 0.05). FSH/LH ratio decreased but the content and expression of E2 and AMH increased (P < 0.05). The protein and mRNA expression of characteristic indicators of inhibiting primordial follicle initiation (PTEN) was decreased (P < 0.05). Oxidation-reduction-related SOD activity increased and the content of MDA decreased (P < 0.05), while the protein and mRNA expression of PGC-1α increased (P < 0.05). The protein and mRNA expression of the pathway (AMPK, SIRT 1) were increased (P < 0.05).
ConclusionCurcumin restored the ovarian local oxidant-antioxidant balance and promoted primordial follicle priming through AMPK/SIRT 1 signaling pathway in the DOR model rats.
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Exploring Mechanisms of Ephx2 in Treating Atherosclerosis Using Independent Cascade Model and Adverse Outcome Pathways
Authors: Caiyuzhen Zhang, Yuanwen Dai, Yong Chen, Bo Cao, Jinbing An and Wei PangAvailable online: 27 March 2025More LessBackgroundAtherosclerosis (AS) is a leading cause of cardiovascular diseases, characterized by lipid accumulation in arterial walls. The gene Ephx2, which encodes soluble epoxide hydrolase (sEH), is implicated in AS development, but its precise mechanisms and therapeutic potential are not fully understood.
ObjectivesThis study aimed to analyze gene expression data from low-density lipoprotein receptor knockout (LDLR−/−) and LDLR−/−sEH−/− mice to identify significant genes associated with AS.
MethodsA directed compound-protein interaction network was constructed based on these genes and related pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In the end, through resistance distance (RD) between any two nodes in this network, the Independent Cascade (IC) model was applied to explore Ephx2 mechanisms in AS, such as important Adverse Outcome Pathways (AOPs).
ResultsSeveral AOPs were identified as critical in AS treatment via Ephx2. The key AOPs included inflammatory response and cytokine release, cholesterol deposition and oxidation, disruption of plaque stability, smooth muscle cell proliferation and migration, and platelet activation and coagulation. Within the top AOPs of inflammatory response and cytokine release, potential target genes were identified, such as Mapk3, Pik3cd, Gnai2, Mapk10, Arnt, and RhoA. Critical paths from Ephx2 to these target genes were established, suggesting mechanisms by which Ephx2 may influence AS pathogenesis.
ConclusionBy defining the AS network and corresponding RD, this study elucidates potential mechanisms by which Ephx2 affects AS through specific KEGG pathways, AOPs, and target genes. These findings enhanced the understanding of AS pathogenesis and highlighte potential targets like Mapk3 for developing therapeutic strategies in AS prevention and treatment.
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Astragalosides Promote MH7A Cell Apoptosis by Suppressing WTAP-mediated m6A Methylation of TRAIL-DR4
Authors: Xiaoya Cui, Linhui Zhang, Huimei Chen and Hui JiangAvailable online: 25 March 2025More LessBackgroundAstragaloside (AST), a natural saponin extracted from Astragalus membranaceus (Fisch.) Bunge., has been consistently utilized in the treatment of rheumatoid arthritis (RA). N6-methyladenosine (m6A), the most prevalent modification of mRNA, is associated with the progression of various diseases, including RA. Nonetheless, the effects of AST on m6A modification in RA remain to be elucidated.
MethodsThe MH7A cell model was established through induction with TNF-α. The effects of AST on the expression levels of WTAP, BAX, BCL2, and TRAIL-DR4 were evaluated utilizing immunofluorescence, RT-qPCR, and Western blot analysis. Furthermore, CCK-8 and flow cytometry were used to assess MH7A cell viability, cell cycle, apoptosis, and proliferation. Then, the m6A modification of TRAIL-DR4 was elucidated via MeRIP-qPCR.
ResultsThe optimal dose administration time was 50 μg/mL at 48 h. AST not only reduced the expression levels of WTAP, BCL2, BAX, TRAIL-DR4, and the m6A modification level of TRAIL-DR4 but also significantly enhanced apoptosis in MH7A cell, while inhibiting cell viability and proliferation. Furthermore, AST was capable of reversing the effect on MH7A cell proliferation and apoptosis induced by WTAP overexpression.
ConclusionThis study elucidates the protective role of AST on MH7A cells by attenuating m6A/WTAP-mediated apoptosis, offering novel insights into the mechanisms of AST.
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Jiawei Danggui Buxue Decoction Reduces Apoptosis and EMT of Renal Interstitial Fibrosis by Regulating JAK2/STAT3 Signaling Pathway
Authors: Xin Jiang, Yinghang Wang, Saiyue Qiu, Lu Tang, Meixiu Luo and Zhi PanAvailable online: 11 March 2025More LessBackgroundRenal interstitial fibrosis (RIF) is the primary pathological progression in chronic kidney disease (CKD). Given the constraints related to cost and adverse effects of current treatments, it is crucial to explore novel and efficacious therapeutic strategies. The purpose of this study was to elucidate the potential of Jiawei Danggui Buxue Decoction (JDBD) to reduce apoptosis and epithelial-mesenchymal transition (EMT) in RIF by regulating the Janus kinase 2 (JAK2)/Signal Transducer and Activator of Transcription 3 (STAT3) pathway.
MethodsAn angiotensin II (Ang II)-induced HK-2 cells model and a unilateral ureteral obstruction (UUO) animal model were employed to replicate the RIF model. A total of 48 male Wistar rats (weighing 200-220g) were acclimated for 1 week and then randomly divided into 6 groups (sham operation, UUO, Losartan potassium tablets, and three JDBD dosage groups: high, medium, and low, n=8). After the acclimatization period, UUO models were established in 40 rats through surgery, excluding the sham operation group. Each group received the corresponding drug via gavage for 2 weeks. After 2 weeks, rats were anesthetized, and tissues were collected for subsequent analysis. Renal function tests and histological stains were used to evaluate renal damage and histopathological alterations in rats. Cell viability was examined using the CCK-8 assay. Apoptosis was identified through the utilization of flow cytometry and assessment of mitochondrial membrane potential, along with other techniques. We identified and examined the expression of EMT and extracellular matrix (ECM)-related factors, as well as the JAK2/STAT3 pathway.
ResultsIn vivo experiments indicated that JDBD effectively reduced renal dysfunction in UUO rats, ameliorated pathological changes in renal tissues, and significantly modulated the JAK2/STAT3 signaling pathway to inhibit EMT and apoptosis, thereby reducing ECM deposition. Furthermore, JDBD markedly increased the survival rate of Ang II-treated HK-2 cells and reduced apoptosis. The in vitro experimental results further confirmed that JDBD ameliorates RIF by regulating the JAK2/STAT3 pathway.
ConclusionJDBD exhibits anti-apoptotic and EMT-inhibiting functions in RIF, potentially mediated by targeting and inhibiting JAK2/STAT3 signaling transduction.
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GLI3 is Inhibited by miR-143-3p and Attenuates Septic-induced Lung Injury and Inflammation by Targeting SFRP1
Authors: Minqing Ma, Haixia Han, Xiaoyan Luo, Jiakai Lin and Bin SunAvailable online: 10 March 2025More LessObjectivesTranscription factors (TF) are the central regulatory hubs of signaling pathways in eukaryotic cells. Here, we explored the abnormal expression of TF in septic-induced lung injury by sequencing.
MethodsThe levels of target proteins were detected using Western Blot and Elisa. Cell function was evaluated using CCK8 and transwell assays. A double luciferase reporter assay was performed to detect interactions between target molecules.
ResultsWe found that TF glioma-associated oncogene (GLI) family zinc finger 3 (GLI3) was abnormally low expressed in a lipopolysaccharide (LPS) induced acute lung injury (ALI) cell model. In an in vitro model, GLI3 overexpression promoted the proliferation and migration and inhibited apoptosis of lung epithelial cells in LPS-induced inflammatory environment. Importantly, GLI3 overexpression inhibited the secretion of inflammatory factors IL-1β, IL-6, and TNF-α. Additionally, miR-143-3p inhibited the expression of GLI3. MiR-143-3p inhibitor alleviated the cell damage caused by LPS, while knocking down GLI3 counteracted this effect, indicating that miR-143-3p downregulated GLI3 and inhibited its anti-inflammatory effect. Secreted frizzled related protein-1 (SFRP1) was upregulated in LPS-treated cells and SFRP1 promoter interacted with GLI3, suggesting that SFRP1 was a target of TF GLI3. Co-transfection with GLI3 knockdown and SFRP1 overexpression plasmids attenuated the secretion of inflammatory factors IL-1β, IL-6, and TNF-α caused by GLI3 knockdown in LPS-treated cells, indicating that SFRP1 plays an anti-inflammatory role as a GLI3 target in the ALI cell model.
ConclusionsmiR-143-3p caused degradation of GLI3 mRNA and thus inhibited the transcription of SFRP1, leading to decreased proliferation and increased levels of inflammatory factors, providing new potential targets for the clinical diagnosis and treatment of ALI.
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The Anti-PEDV Effects and Mechanisms of Forsythia Essential Oil Based on Network Pharmacology and Experimental Validation
Authors: Ruiping Liang, Jianbo Guo, Kai Li, Xuan Wang, Xiaoxiao Ge, Jinhui Wang, Jing Sun, Chongbo Zhao, Huanxian Shi, Rongxia Qiao, Hongqing Zheng and Xiaofei ZhangAvailable online: 10 March 2025More LessObjectivePorcine epidemic diarrhea virus (PEDV), a member of the Coronaviridae, is responsible for acute diarrhea, vomiting, and dehydration, which can lead to high mortality in neonatal piglets. Previous research has indicated the antiviral potential of forsythia essential oil (FEO); however, its active components and mechanisms of action remain inadequately defined. This study aims to investigate the antiviral effects of FEO and elucidate its potential mechanisms for treating PEDV.
MethodsThe primary components of FEO were identified using gas chromatography-mass spectrometry (GC/MS) in conjunction with the National Institute of Standards and Technology Standard Spectrum (NIST) Database. Network pharmacology and weighting coefficients were employed to determine the key signaling pathways associated with PEDV-related diseases. Molecular docking simulations were conducted to explore the interactions between the active ingredients and their corresponding targets. The safety profile of FEO was assessed through cell viability assays utilizing the CCK8 method. Subsequently, immunofluorescence assays (IFA) and reverse transcription-quantitative polymerase chain reaction (RT-Q-PCR) were performed to provide evidence of the anti-PEDV effects. Additionally, the viral replication cycle was analyzed to identify the stages at which FEO exerts its antiviral effects. Finally, key targets were validated through RT-Q-PCR to further investigate the anti-PEDV mechanisms of FEO.
ResultsThe IL-17 signaling pathway was identified as a critical pathway for the treatment of PEDV with FEO based on network pharmacology and weighting coefficient analyses. Furthermore, results from RT-Q-PCR and IFA demonstrated that FEO influenced the replication of PEDV during the attachment and internalization phases. Specifically, during the viral attachment phase, FEO significantly upregulated the expression of HSP90AA1 while downregulating MAPK14 expression, leading to a reduction in associated inflammatory factors. At the high dose of FEO, the expression of HSP90AA1 was higher than that of the model group by about 5-fold, and the expression of MAPK14 was lower than that of the model group by about 2-fold. Cell viability assay showed no significant cytotoxicity of FEO at 0.63 µL/mL, thus confirming its safety.
ConclusionThe findings of this study suggest that FEO possesses potential antiviral properties against PEDV. Its novel mechanisms of action warrant further investigation, which may contribute to the development of effective therapeutic strategies for managing PEDV infections.
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Computational Study for Preparation of Benzoimidazo[1,2-a]pyrimidines from Reaction of Benzaldehyde, Indanedione and 1H-benzo[d]imidazol-2-amine
Authors: Yas Zibaei, Leila Zare Fekri and Mohammad NikpassandAvailable online: 03 March 2025More LessBackgroundBenzoimidazo[1,2-a]pyrimidines are important compounds that have many useful effects in the body. They can help fight cancer, fungal infections, inflammation, and viruses. They can also help with various other health conditions. They can act as antineoplastic, antitubercular, parasitical activity, benzodiazepine receptor agonists, calcium channel blockers, potent P38 MAP kinase inhibitors, TIE-2 and/or VEGFR2 inhibitory activities, protein kinase inhibitors, and T cell activation. There are different methods to make the benzoimidazo[1,2-a]pyrimidines. Some of them dealth with the one-pot threecomponent condensation reactions of β-dicarbonyl compounds, aldehyde and 1H-benzo[d]imidazol-2-amine in the presence of catalyst. Although the synthesis of this group of compounds has been done before, and the products have been identified from the spectroscopic point of view, the kinetics and reaction mechanism have not been investigated. The strength of these calculations is that evaluation of the activation energy of various steps suggests possible mechanisms, probable mechanisms, and valuable synthetic intermediates.
MethodsIn this report, seven possible mechanisms for synthesizing the benzoimidazo[1,2-a]pyrimidines have been investigated using density functional theory (DFT) at the B3LYP/6-311G** level of theory. Each synthetic route involves condensation of the benzaldehyde, indanedione and 1H-benzo[d]imidazol-2-amine molecules to yield the proposed product. The calculations showed that the suggested method has six steps; its initiation step includes the Knoevenagel reaction between indanedione and aldehyde, and the rate determining state is dehydration in the fifth step.
ResultSix potential pathways for the reaction will occur. Then, we focused on the best pathway and studied it in detail. The ways that three chemicals-indanedione (R1), benzaldehyde (R2), and 1H-benzo[d]imidazol-2-amine (R3) react with each other were studied using ab-initio program by ChemBio3D, Gauss View, and Gaussian 09. The Density Functional Theory (DFT) using the B3LYP basis set was used to improve the arrangement of molecules involved in the three-part creation of a specific compound called 12-phenyl-5H-benzo[4,5]imidazo[1,2-a]indeno[1,2-d]pyrimidin-13(12H)-one (P).
ConclusionDuring the study of the six mechanisms, the proposed pathway 2 is the best mechanism for this reaction because its rate-determining step has the lowest activation energy value. This route consists of 6 steps, the fifth step of which is related to the conversion of IM4 to IM5 (relative ∆E: 109.80 Kj/mol), during which a dehydration reaction is performed, and this step occurs by passing through transition state TS5 (Total Energy (Hart./particles: -1194.747403).
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Dry Powder Inhaler of Sustained-Release Microspheres Containing Glycyrrhizin: Factorial Design and Optimization
Authors: Arpita Chakraborty, Riya Mahar and Nidhi NainwalAvailable online: 28 February 2025More LessBackgroundGlycyrrhizin is a saponin glycoside of the liquorice plant. It is commonly used to treat respiratory problems. Inhalable glycyrrhizin formulation in asthma can be a good alternative for widely used inhaled corticosteroids that exhibit side effects upon long-term use.
AimAsthma is a major and prevalent respiratory disease. However, the rate of drug development in this arena is quite slow, as indicated by merely four new drugs approved by the USFDA in the last 6 years for respiratory diseases.
ObjectiveWe herein propose to design and develop Glycyrrhizin-inhalable microspheres for the treatment of asthma.
MethodA 32 full factorial design was applied to show the effect of the two independent variables (polycaprolactone, and polyvinyl alcohol concentration) on each of the selected dependent variables (drug loading and entrapment efficiency).
ResultsThe optimized microspheres were spherical and 1-5 µm in size. The formulation showed a fine particle fraction of 78%, indicating that the powders were suitable for inhalation. The Drug loading and encapsulation efficiency of the optimized formulation were found to be 9.8% and 40.98%, respectively. The aerosolization study on the Anderson cascade impactor showed that deposition of particles of formulation blended with lactose was better than nonblended formulation and drug in the lungs.
ConclusionIn comparison to the pure drug, optimized formulation prolonged drug residency in the lung for more than 12 hrs after inhalation. Inhalable microparticles of glycyrrhizin provide sustained and prolonged drug release in the lungs along with protection of drugs against pulmonary degradation.
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Revealing the Mechanism of Buzhong Yiqi Tang in Ameliorating Autoimmune Thyroiditis via the Toll-like Receptor Pathway
Authors: Zhuo Zhao, Jiayun Li, Donglin Liu, Hao Gao, Zhe Jin, Zhimin Wang, Yiran Chen, Si Chen, Ziyu Liu and Xiao YangAvailable online: 28 February 2025More LessIntroductionEsophageal Squamous Cell Carcinoma (ESCC) remains a significant global health challenge, underscoring the urgent need for the development of innovative therapeutic approaches. Ranunculus ternatus Thunb., a traditional herb, exhibits potential anticancer properties, but its mechanisms against ESCC remain poorly understood. This study integrates network pharmacology and experimental validation to explore the therapeutic effects of the ethyl acetate extract of Ranunculus ternatus Thunb. (RTE).
MethodsPotential targets of RTE and ESCC were screened using public databases. A Protein-Protein Interaction (PPI) network was constructed to identify key targets, followed by GO and KEGG pathway enrichment analyses. The predicted mechanisms were validated using in vitro assays, including cell proliferation analysis and western blot assay in ESCC cell lines.
ResultsNetwork pharmacology analysis identified 274 potential targets, with 14 key genes implicated in the therapeutic effects of RTE. GO analysis revealed significant involvement in the inflammatory response and apoptotic signaling pathways. KEGG pathway analysis highlighted the MAPK, Relaxin, and PI3K/Akt signaling pathways as critical mechanisms. In vitro experiments demonstrated that RTE significantly inhibited the proliferation of EC-109 and TE-13 cells by modulating the MAPK/ERK and PI3K/Akt pathways.
DiscussionThe study reveals that active compounds of RTE target MAPK/ERK and PI3K/Akt pathways, aligning with prior evidence. However, future studies should explore animal models to confirm efficacy.
ConclusionThis study provides a comprehensive understanding of the molecular mechanisms underlying the anticancer effects of RTE against ESCC. These findings underscore the potential of RTE as a promising natural compound for ESCC treatment.
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Agaricus blazei Murill Extract (FA-2-b-β) Induces Ferroptosis in Diffuse Large B-Cell Lymphoma via the Nrf2/HO-1 Pathway
Authors: Rong Li, Dan Huang, Along Wu and Yanqin SunAvailable online: 28 February 2025More LessIntroductionFerroptosis is a recently identified iron-dependent programmed cell death closely linked to the progression of diffuse large B-cell lymphoma (DLBCL). While studies have shown that FA-2-b-β extracted from Agaricus blazei Murill affects various malignancies, its specific role in modulating ferroptosis in DLBCL and the underlying mechanisms are not yet clear. Objectives: This study aims to elucidate the anticancer properties and mechanisms of FA-2-b-β in inducing ferroptosis in DLBCL cells.
MethodsThe cell counting kit 8 assay was carried out to evaluate the inhibition of cellular proliferation. Ferroptosis was evaluated using the ferrous colorimetric method, together with kits for measuring malondialdehyde (MDA), reduced glutathione (GSH), reactive oxygen species (ROS), western blotting, JC-1 assays, and transmission electron microscopy. Reverse transcription-quantitative polymerase chain reaction and western blot were conducted to determine whether FA-2-b-β affected nuclear factor erythroid 2- related factor 2 (Nrf2) and heme oxygenase 1 (HO-1).
ResultsFA-2-b-β induced ferroptosis in DLBCL cells by elevating the ROS and MDA levels, facilitating the accretion of Fe2+, diminishing GSH, upregulating the expression of PTGS2, and downregulating the expression of FTH1, SLC7A11, and GPX4. Furthermore, FA-2-b-β caused structural damage to mitochondria and diminished the mitochondrial membrane potential. The ferroptosis triggered by FA-2-b-β also led to the downregulation of Nrf2 and HO-1, thereby regulating the Nrf2/HO-1 pathway.
ConclusionFA-2-b-β suppressed DLBCL cell growth by inducing ferroptosis through the Nrf2/HO-1 pathway, making it an attractive potential therapeutic option.
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20D-Dynamic Representation of Protein Sequences Combined with K-means Clustering
Authors: Dorota Bielińska-Wąż, Piotr Wąż and Agata BłaczkowskaAvailable online: 26 February 2025More LessObjectiveThe objective of this research is to demonstrate that alignment-free bioinformatics approaches are effective tools for analyzing the similarity and dissimilarity of protein sequences. All numerical parameters representing sequences are expressed analytically, ensuring precision, clarity, and efficient processing, even for large datasets and long sequences. Additionally, a novel approach for identifying previously unknown virus strains is introduced.
MethodsA novel approach is proposed, integrating the unique features of our newly developed method, the 20D-Dynamic Representation of Protein Sequences, with the K-means clustering algorithm. The sequences are represented as clouds of material points in a 20-dimensional space (20D-dynamic graphs), with their spatial distribution being unique to each protein sequence. The numerical parameters, referred to as descriptors in molecular similarity theory, represent quantities characteristic of dynamic systems and serve as input data for the K-means clustering algorithm.
ResultsExamples of the application of the approach are presented, including projections of the 20D-dynamic graphs onto 3D spaces, which serve as a visual tool for comparing sequences. Additionally, cluster plots for the analyzed sequences are provided using the proposed method.
DiscussionCombining the 20D-Dynamic Representation of Protein Sequences with an unsupervised machine learning algorithm (K-means clustering) enhances its scalability. This approach is applicable to large datasets without restrictions on sequence length.
ConclusionIt has been demonstrated that the 20D-Dynamic Representation of Protein Sequences, combined with the K-means clustering algorithm, successfully classifies subtypes of influenza A virus strains.
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Modeling the Physico-Chemical Characteristics of Benzenes through the Application of Zagreb Rho Indices
By İdris ÇiftçiAvailable online: 26 February 2025More LessIntroductionQuantitative Structure–Property Relationship (QSPR) models play a crucial role in predicting the chemical and physical characteristics of molecules.
MethodsThis study introduces Zagreb rho indices derived from graph theory to assess the physico-chemical properties of benzenes. The rho degree of vertices in connected graphs was formulated and used to compute these indices.
ResultsStrong correlations (R> 0.94) were observed between Zagreb rho indices and various molecular properties such as boiling point, molecular weight, and electron energy.
DiscussionThe findings demonstrate that Zagreb rho indices can serve as reliable predictors within QSPR frameworks, offering structural sensitivity and outperforming traditional topological indices in several aspects.
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Advances in Targeting Neutrophil Extracellular Traps as a Promising Approach for Breast Cancer Treatment
Authors: Jiale Mi, Jiani Guo, Kang Kang, Shiqi Wang and Mingde HuangAvailable online: 26 February 2025More LessNeutrophils release neutrophil extracellular traps (NETs), a reticular structure mainly composed of antimicrobial peptides, DNA, and histones. Neutrophil elastase (NE), matrix metalloproteinase-9, and histone G are the key components of NETs critically involved in breast cancer invasion and migration, which suggests an important role of NETs in tumorigenesis and metastasis. Studies have reported that NETs significantly promote breast cancer invasion, intravascular infiltration, and distant metastasis by inducing epithelial-mesenchymal transition (EMT), remodeling the extracellular matrix, and modulating the immune microenvironment. Meanwhile, NETs also function crucially in capturing circulating tumor cells, forming a pre-metastatic microenvironment, and awakening dormant cancer cells. Notably, NETs are also closely associated with chemotherapy and immunotherapy resistance in breast cancer. Therapeutic strategies targeting NETs, including DNase I, PAD4 inhibitors, elastase inhibitors, and histone C inhibitors, have been widely studied. These targeted therapies can effectively suppress the generation of NETs, improve drug efficacy, and delay tumor metastasis. This review aimed to systematically elucidate the mechanism of action of NETs in the progression and drug resistance of breast cancer and explore potential targeted therapeutic strategies against NETs. These strategies could effectively inhibit the generation of NETs, delay the progression of breast cancer, and improve therapeutic efficacy. An in-depth study of the mechanism of action of NETs and the clinical significance of their targeted interventions is expected to provide a new direction for breast cancer treatment.
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Identification of Mitochondrial-related Characteristic Biomarkers in Osteosarcoma using Bioinformatics and Machine Learning
Authors: Jingyi Hou, Yu Zhang, Ning Yang, Bin Chen, Chengbing Chang, Haipeng Gu, Yanqi Liu and Naiqiang ZhuAvailable online: 25 February 2025More LessBackground/AimsOsteosarcoma (OS), a malignant tumor originating in bone or cartilage, primarily affects children and adolescents. Notably, substantial alterations in mitochondrial energy metabolism have been observed in OS; however, the specific contribution of mitochondrial-related genes (MRGs) to OS pathogenesis and prognosis remains unclear. Herein, we identified novel diagnostic biomarkers associated with mitochondrial-related processes in OS via comprehensive bioinformatics analysis.
MethodsOS mRNA expression profiles were retrieved from GSE16088 and GSE19276 databases. Mitochondrial-related differentially expressed genes (MitoDEGs) were identified by integrating differentially expressed analysis with mitochondrial-localized genes. A protein-protein interaction network was constructed, and machine learning algorithms (LASSO regression analysis and SVM-RFE) identified characteristic MitoDEGs. Subsequently, immune cell infiltration, microenvironment analysis, and single-cell RNA sequencing (scRNA-seq) analyzed differences in characteristic MitoDEGs, and RT-PCR was used for in vitro verification of characteristic MitoDEGs.
ResultsMitoDEGs in OS were significantly enriched in the pathways associated with mitochondrial function and immune regulation. Two MitoDEGs, UCP2 and PRDX4, were identified via LASSO and SVM-RFE. Correlation analysis demonstrated a close association between UCP2 and PRDX4 expression levels and immune cell infiltration, particularly in CD8+ T and native CD4+ T cells, as observed in both immune cell and scRNA-seq analyses. Furthermore, RT-PCR confirmed the expression levels of UCP and PRDX4 at the cellular level, which was consistent with the bioinformatics results.
ConclusionThis study identified UCP2 and PRDX4 as characteristic MitoDEGs and potential diagnostic biomarkers for OS using machine learning algorithms. These findings provide novel insights into the clinical applications of these biomarkers for OS diagnosis.
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Rapid Screening and Effective Rabbit-Derived Fab Antibodies Production Based on Yeast Surface Display
Authors: Weili Shen, Tingting Gong and Changli ShaoAvailable online: 24 February 2025More LessIntroduction/ObjectiveAntibodies have broad applications in various fields, such as biology and medicine. The screening and preparation of highly specific and sensitive antibodies are essential research areas. Several techniques for the preparation of mouse-derived antibodies have been developed, but limited studies on rabbit-derived antibodies with a broader antibody profile and easier humanization are reported. An improved yeast surface display technique was used for rapid screening of rabbit-derived Fab antibodies.
MethodsAfter RNA extraction from peripheral rabbit blood, a cDNA library was obtained by reverse transcription. After recombinant vector construction, the expressed sequence in the form of Fab antibody structure was fused to the N-terminal end of Aga2p in the vector; a bidirectional promoter was inserted and successfully expressed in brewer's yeast EBY100. In addition, sequences, such as leucine zipper and inulinase signal peptide (INU), were inserted into the recombinant vector to improve the expression and stability of Fab antibody further.
ResultsA biotin-labeled salbutamol marker was synthesized, and two rabbit-derived salbutamol-Fab antibodies were screened in three weeks using fluorescence-activated cell sorting (FACS).
ConclusionAfter antigen-binding kinetic studies, the screened antibodies demonstrated good affinity and specificity.
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Evaluation of Carbamazepine and Gabapentin’s Safety and Efficacy in Trigeminal Neuralgia Treatment: A Systematic Review and Meta-Analysis
Authors: Yang Yan, Haitao Shang and Tao HanAvailable online: 24 February 2025More LessAimThis study aimed to assess the safety and effectiveness of carbamazepine in treating trigeminal neuralgia in contrast to gabapentin. Hence, a systematic review and meta-analysis of randomised controlled trials had been carried out.
MethodsThe relevant studies were searched in PubMed and filtered according to the inclusion and exclusion criteria. Independently, two reviewers chose the studies, evaluated the quality of the investigations, and retrieved the data. RevMan was used for analysis when the data were collected and entered into the data extraction sheet. In addition to heterogeneity, the overall estimate measures were computed as mean differences with a 95% confidence interval for continuous data and relative risk for dichotomous data. To investigate the impact of outliers on the result, a sensitivity analysis was performed. A funnel plot was used to qualitatively evaluate the publishing bias. A total of 1,650 participants from 19 randomised controlled trials were evaluated.
ResultsThe meta-analysis revealed that the group receiving gabapentin therapy had a similar overall effective rate to the group receiving carbamazepine therapy (OR = 1.94, 95% CI 1.46, 2.57, P = 0.32). Additionally, our meta-analysis revealed that the group receiving gabapentin therapy witnessed a significantly lower risk of adverse reactions than the group receiving carbamazepine therapy (OR= 0.29, 95% CI 0.22, 0.387, P<0.00001).
ConclusionIn summary, the current trials comparing carbamazepine and gabapentin have had inadequate methodological quality. It is not possible to conclude that gabapentin is more effective than carbamazepine in terms of adverse effects based on the evidence that is currently available.
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UPLC-Q-TOF-MS, Network Pharmacology and Molecular Docking to Reveal the Antidepressant Mechanism of the Different Components of Medicinal and Edible Lilies (Lilium sp. pl)
Authors: Zhaoyang Tan, Linghe Huang, Yanqiu Tian, Sai Jiang, Zhi Wang, Hongping Long, Qiaozhen Tong, Shunxiang Li and Lin JiangAvailable online: 24 February 2025More LessBackground and ObjectivesTo explore the mechanism of action of the differential components of medicinal and edible lilies in treating depression by network pharmacology using UPLC-Q-TOF-MS technology.
MethodsThe chemical composition of medicinal and edible lilies was analyzed, screening for unique medicinal compounds. Searched for depression-related targets. Constructed PPI networks. Performed GO and KEGG analyses. Built a network of differential components, and conducted molecular docking. In addition, the contents of regaloside before and after lily processing were compared.
ResultsMedicinal lilies and edible lilies have 17 main differences, including regaloside B and regaloside E. There are 179 targets for actives, 2690 for antidepressants, and 98 intersected. Core targets (7) led to 238 GO processes and 107 KEGG pathways. The molecular docking results showed that 17 components, including regaloside B, regaloside E, (25R)-3β,17α-Dihydroxy-5α- spirostan-6-one 3-O-α-L- rhamnopyranosyl-(1→2)-β- D-glucopyranoside (Named: Lilium lancifolium saponin), etc. could act on 7 potential targets such as EGFR, HSP90AA1, STAT3, TNF, etc. to exert antidepressant effects.
ConclusionThis study employed a network pharmacology combined with a molecular docking approach to compare the active constituents of medicinal and edible lilies in antidepressants, and their pharmacological mechanisms, both theoretically and technically. The phytoconstituents were found to act mainly by inhibiting the inflammatory response in depression. Especially Lilium lancifolium saponin may have a close relationship with antidepressants. These results provide some justification for lilies in the treatment of depression.
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Quercetin Inhibits Ectopic Lesion Formation in Mice by Modulating the MAT2A/PRMT5 Pathway through PPARγ Activation
Authors: Shun Zhang, Yuan-Yuan Zhang, Qiu-Xia Zeng, Li Wang, Kong-Xian Li and Qi ChenAvailable online: 24 February 2025More LessIntroductionThis study aimed to examine the impact of quercetin on a mouse model of endometriosis and elucidate its underlying mechanisms.
MethodsAn endometriosis model was established using C57BL/6 mice, which were divided into three groups: 1) sham group, 2) model group, and 3) model group treated with daily gavage administration of 100 mg/kg/d quercetin. Histopathological examination was performed using hematoxylin and eosin (HE) staining. The microstructure of the lesions was examined using electron microscopy. The expressions levels of related proteins, such as the peroxisome proliferator-activated receptor-γ (PPARγ), methionine adenosyl-transferase 2A (MAT2A), Ki67 and VEGF was measured using Western blotting or Immunohistochemistry.
ResultsCompared to the model group, the medication group showed sparse endometrial stromal cells, irregular morphology, and numerous vacuoles, indicating apoptosis. Compared to the sham group, SAM expression was unchanged (P > 0.05), while PPARγ decreased. MAT2A, PRMT5, cyclin D1, and C-MYC increased, and vimentin, Ki67, VEGF, and caspase-1 were strongly positive (P < 0.05). Quercetin intervention reduced ectopic lesion weights, increased PPARγ, and decreased MAT2A, PRMT5, SAM, cyclin D1, and C-MYC. Vimentin, Ki67, VEGF, and caspase-1 were weakly positive (P < 0.05).
DiscussionThese results indicate that quercetin effectively reduced endometriosis lesions by modulating key protein expressions and promoting apoptosis.
ConclusionQuercetin modulated the transcription of the MAT2A/PRMT5 gene by activating PPARγ activity, thereby influencing the ectopic implantation and growth of endometrial cells.
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Exploring the Blueprint of Life: The Innovation in Antibody and Protein Design
Authors: Zhiwei Yang and Gerald H. LushingtonAvailable online: 20 February 2025More LessThe innovation in antibody and protein design highlights the transformation from empirical approaches to sophisticated strategies integrating computational methods and artificial intelligence (AI). Key principles, such as combinatorial, structure-based, consensus, and computational designs, have been pivotal in predicting structures from sequences (in silico design). Advances in tools, like AlphaFold and Rosetta suite, enable accurate structure prediction, facilitating the development of functional proteins and antibodies. However, challenges remain, including improving prediction accuracy, modeling flexible regions, understanding structural dynamics, and designing catalytic and binding sites. Despite these, the field promises groundbreaking advancements in biomedical sciences, enriching our understanding and serving human health and scientific discovery.
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Investigation of LncRNA Expression Profiles and Analysis of Immune-Related lncRNA-miRNA-mRNA Networks in Neovascular Age-Related Macular Degeneration
Authors: Liying Qin, Xiang Gao, Xiuhai Lu, Wencai Liu, Jingyi Tian, and and Gongqiang YuanAvailable online: 12 February 2025More LessIntroductionAge-related Macular Degeneration (AMD) is a predominant cause of blindness in the elderly. The present study is the first to investigate the alteration of lncRNAs and mRNAs in neovascular AMD.
MethodsNine patients with neovascular AMD were included in the study. The control group comprised seven patients with epiretinal membranes. RNA sequencing was performed to obtain the differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs). Then, the DElncRNA-DEmRNA co-expression network, ceRNA network, and immune-related ceRNA subnetwork were constructed. Functional annotation of DEmRNAs between the two groups and DEmRNAs in networks was conducted. The immune cell distribution in neovascular AMD was also evaluated. Real-time qPCR (RT-qPCR) was used to validate the expression levels of key markers.
ResultsA total of 342 DEmRNAs and 157 DElncRNAs were obtained in neovascular AMD. Functional annotation indicated that these DEmRNAs significantly enriched immune system-related processes, such as positive regulation of B cell activation, immunoglobulin receptor binding, complement activation, and classical pathway. The DElncRNA-DEmRNA co-expression network, including 185 DElncRNA-DEmRNA co-expression pairs, and the ceRNA (DElncRNA-miRNA-DEmRNA) network, containing 45 lncRNA-miRNA pairs and 73 miRNA-mRNA pairs, were constructed. The immune-related ceRNA subnetwork, including 2 lncRNAs, 5 miRNAs, and 3 mRNAs, was constructed. In addition, the distribution of immune cells was slightly different between the neovascular AMD group and the control group. RT-qPCR validation indicated the consistency between the RT-qPCR results and RNA sequencing results.
ConclusionIn conclusion, STC1, S100A1, MEG3, MEG3-hsa-miR-608-S100A1, and MEG3-hsa-miR-130b-3p/hsa-miR-149-3p-STC1 may be related to the occurrence and development of neovascular AMD.
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Therapeutic Potential of Desert Truffles in the Management of Eye Infections: Demystifying the Fact
Available online: 10 February 2025More LessTruffle, an ascomycetous, hypogeous macrofungi, has long been recognized and valued for its therapeutic and dietary properties. Of late, a range of medicinal compounds, such as ergosterol, tuberoside anandamide, polysaccharides, and phenolics exhibiting anti-inflammatory, immunomodulatory, anticancer, antibacterial, and aphrodisiac properties have been identified in truffles. This review provides an update on contemporary truffle research with a focus on antimicrobial potentials and aims to draw the attention of researchers to exploit the therapeutic potential of truffles in the management of eye infections. The scholarly literature pertaining to the utilization of desert truffles in the management of ocular infections was systematically summarized and reviewed from multiple databases, including Scopus, Web of Science Core Collection, PubMed, and others. The essence of truffle is used as a remedy for trachoma and as an anti-inflammatory agent for ocular problems. The most probable inhibitory constituents are the fungal lectins, polysaccharides, and laccases. Truffle lectins possess the ability to identify and remove bacterial exopolysaccharides. In addition, the fungal polysaccharides affect the bacterial defensive systems. Conversely, laccases facilitate the process of oxidizing phenols, resulting in the release of superoxide anion radicals and the production of hydrogen peroxide. The application of desert truffles in addressing ocular issues has been clinically observed to be satisfactory. The existing literature clearly indicates a pressing need for further investigation into the translation of the antimicrobial properties of crude truffle extract into truffle-based pharmaceutical formulations for clinical application.
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Identification of NR4A2 as a Potential Predictive Biomarker for Atherosclerosis
Authors: Lebin Yuan, Ruru Bai, Xinhao Han and Jiajia XiangAvailable online: 10 February 2025More LessIntroduction/ObjectiveAtherosclerosis, a leading cause of death globally, is characterized by the buildup of immune cells and lipids in medium to large-sized arteries. However, its precise mechanism remains unclear. The purpose of this study is to explore innovative and reliable biomarkers as a viable approach for the identification and management of atherosclerosis.
MethodsThe atherosclerosis-related datasets GSE100927 and GSE66360 were retrieved from the Gene Expression Omnibus (GEO) database. The Limma package in the R programming language was utilized, applying the criteria of |logFC| > 1 and P < 0.05. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the 127 identified DEGs using R. Machine learning techniques were then applied to these data to explore and pinpoint potential biomarkers. The diagnostic potential of these markers was assessed via Receiver Operating Characteristic (ROC) curve analysis. Finally, western blot, real-time quantitative PCR (qRT-PCR), and immunohistochemistry (IHC) were employed to confirm the key biomarkers.
ResultsOur research indicated that a total of 127 DEGs linked to atherosclerosis were successfully identified. Through the application of machine learning methods, eight critical genes were highlighted. Among these, Nuclear Receptor Subfamily 4 Group A Member-2 (NR4A2) emerged as the most promising marker for further investigation. CIBERSORT analysis revealed that NR4A2 expression levels were significantly correlated with multiple immune cell types, including B cells, plasma cells, and macrophages. Additional validation experiments confirmed that NR4A2 expression was indeed elevated in atherosclerotic plaques, supporting its potential as a biomarker for atherosclerosis.
ConclusionOur study identified NR4A2 as a potential immune-related biomarker for the diagnosis and treatment of atherosclerosis.
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Causal Mediation Analysis of the Effect of Dietary Habits on Sleep Apnea Risk
Authors: Yingying-Li1, Liang Wu and Wendo- ChenAvailable online: 06 February 2025More LessObjectiveDiet is a modifiable factor that influences several chronic diseases, making lifelong dietary interventions critically important for reducing disease risk. Hence, this study aims to assess the potential causal relationship between diet and sleep apnea (SA).
MethodsWe analyzed genome-wide association study (GWAS) data from approximately 450,000 individuals, focusing on 8 dietary intakes and GWAS statistics for 249 metabolites from the UK Biobank. Sleep apnea-related phenotypic data from 16,761 participants were sourced from the FinnGen Biobank. Furthermore, we conducted a series of two-sample Mendelian Randomization (two-sample MR) to explore the causality between diet and SA. Sensitivity analyses were conducted to assess the robustness of the two-sample MR results, and reverse MR analysis was performed to examine potential reverse causality. Multivariate MR (MVMR) analysis and mediation effect estimation were employed to evaluate the mediating roles of metabolites.
ResultsTwo-sample MR analyses revealed significant causal associations between bread intake (OR=0.56, 95% CI 0.35–0.89, P =0.014), cheese intake (OR=0.67, 95% CI 0.50–0.89, P =0.006), and dried fruit intake (OR=0.61, 95% CI 0.39–0.95, P =0.029) with SA. Reverse MR analysis indicated a causal effect of SA on dried fruit intake (P < 0.05). Univariate MR analyses further identified significant causal effects of bread and cheese intakes on 2 and 32 metabolites, respectively (P < 0.05). Subsequent MVMR analysis demonstrated direct causal effects of bread and cheese intake on SA, independent of metabolite mediation (P < 0.05). Furthermore, the mediating effect of cheese intake on SA through glucose was estimated at 0.023 (90% CI 0.01–0.046), whereas other modeled mediation effects were not statistically significant.
ConclusionThe MR analysis in this study offers genetic evidence indicating that heightened genetic susceptibility to cheese and bread intake potentially reduces SA risk. These findings underscore and validate the significance of diet in preventing SA.
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Adaptability of Thermotoga Maritima's Glycolysis Pathway in Both Oxic and Anoxic Environments
Authors: Raja Lakhal, Manaf AlMatar and Tahani AlkalafAvailable online: 06 February 2025More LessBackgroundThe phylum Thermotogae is composed of five families: Fervidobacteriaceae, Thermatogaceae, Kosmotogaceae, Petrotogaceae, and Mesoaciditogaceae; one class: Thermotogae; and four orders: Kosmotogales, Petrotogales, and Mesoaciditogales. There are thirteen genera in all. The physical and metabolic characteristics of the Thermotogae species reflect the extreme heat from which they were separated. Thermotogae members have a broad spectrum of metabolic capacities, resulting in a pool of valuable chemicals with potential uses in many different sectors.
MethodA 1.5-liter operating capacity bioreactor with a 2.3-liter double-jacket glass volume was utilised to culture Thermotoga maritima in both oxic and anoxic conditions. In addition to temperature, pH, and redox potential, sensors that were installed within the fermentor monitored additional parameters. RNA extraction and cDNA synthesis A total of RNAs was extracted utilising Roche's High Pure RNA reagent. Analysis of glycolysis pathways in T. maritima was performed by NMR spectroscopy
ResultBased on NMR analysis, our findings demonstrate that T. maritima uses the EM route to metabolize 90% of glucose in anoxia and the ED pathway for 10%. On the other hand, T. maritima continues to employ the EM and ED glycolysis routes concurrently when exposed to extended oxidative stress; however, the ED pathway's contribution drops from 10% to around 5%.
ConclusionCompared to the EM route, the ED pathway has more strongly repressed transcripts that encode its unique enzymes.
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Bingqing Gao Facilitates the Healing Process of Full-Thickness Skin Defects in Rat Wounds by Activating the PI3K/AKT Pathway
Authors: Hong’e Ma, Rui Hu, Jiajun Guo, Xinfu Wang, Xin Liu, Ning Zhang, Ruilong Ren, Danyang Wang and Wenxian ZhangAvailable online: 04 February 2025More LessBackgroundTrauma, resulting from mechanical factors, entails damage to human tissues or organs. Whether occurring during times of war or peace, trauma is prevalent, particularly skin defects arising from surgery or external injuries. The development and design of effective wound dressings have become paramount. Bingqing Gao(BQG), rooted in Chinese folk medicine, is employed explicitly in trauma treatment based on traditional Chinese medicine (TCM) theory. This study aims to elucidate how BQG facilitates full-thickness skin wound healing in Sprague Dawley (SD) rats.
MethodsData collection commenced using two approaches: retrieval from TCM system pharmacology databases (TCMSP) and literature mining to compile the practical chemical components and targets of BQG. A drug-target network was constructed. Subsequently, disease targets related to wound healing were collected to select core targets and pathways, building a drug-disease target protein-protein interaction (PPI) network using the ClusterONE algorithm to identify core genes. Gene Ontology (GO) and KEGG enrichment analyses were conducted based on the Metascape database. Finally, molecular docking validation was performed on the screened core targets and core components. In terms of in vivo experimentation, an SD rat full-thickness skin defect model was established, and varying doses of BQG were applied. Healing area, HE staining, Masson staining, ELISA, PCR, and other methods were employed to validate cytokines, differential proteins, and pathways. The study collectively discusses the mechanism and targets by which BQG promotes full-thickness skin wound healing in SD rats.
ResultsThrough network pharmacology screening, we identified various active components, including resveratrol, Lithospermic acid B, sanguiinH-2, asernestioside A_qt, kaempferol, daidzein, quercetin, apigenin, and Medicarpin. The core targets encompass Interleukin-6 (IL-6), Protein Kinase B (AKT1), Vascular Endothelial Growth Factor A (VEGFA), Interleukin-1 beta (IL-1β), Tumor Protein 53 (TP53), Epidermal Growth Factor Receptor (EGFR), Tumor Necrosis Factor (TNF), Albumin (ALB), among others. Potential signaling pathways include Phosphoinositide 3-kinase (PI3K)/AKT, Tumor Necrosis Factor (TNF), Hypoxia-Inducible Factor-1 (HIF-1), and more. Molecular docking studies suggest a robust binding interaction between the active components of BQG and disease targets, indicating a potential regulation of cytokines through the PI3K/AKTsignaling pathway, thereby promoting wound healing. The results of the in vivo experiment revealed that, in comparison to the model group, both the rhb-FGF group and BQG-H group exhibit a noteworthy increase in the expression levels of PI3K and AKT genes. Concurrently, there is a significant decrease in the levels of pro-inflammatory cytokines IL-1β, IL-6, and TNF-α. Additionally, there is a substantial increase in the levels of Transforming Growth Factor-beta (TGF-β) and Vascular Endothelial Growth Factor (VEGF).
ConclusionNetwork pharmacology results indicate that BQG promotes wound healing through multiple components, targets, and pathways. In vivo experimental results suggest that BQG may activate the PI3K/AKTsignaling pathway, inhibit the production and release of related pro-inflammatory cytokines IL-1β, IL-6, and TNF-α, promote VEGF generation at the injury site, and enhance TGF-β signaling transduction, effectively regulates the inflammatory response at the site of injury, promotes vascular regeneration in the injury area, and induces the proliferation and migration of cells in the injury area, ultimately contributing to wound healing. This study establishes the foundation for a more profound understanding of the molecular mechanisms underlying BQG's promotion of wound healing and offers insights for future drug research on BQG.
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Therapeutic Mechanism of Zhishi Decoction Regulating P38/MAPK Signaling Pathway on Functional Constipation (FC)
Available online: 04 February 2025More LessBackgroundZhishi decoction (ZSD) is one of the most common herb decoctions in traditional Chinese medicine (TCM), and it is used for the treatment of FC. However, its main therapeutic mechanism is not yet clear. This study aims to explore the possible pharmacodynamic material basis and potential molecular mechanism from network pharmacology and molecular docking and verify them through animal experiments.
MethodsFirstly, the effective ingredients, potential targets, and key targets of ZSD in the treatment of FC were screened through network pharmacology. Go and KEGG analyses were performed for potential targets. Secondly, molecular docking was used to link the main active components of ZSD with target genes to predict their possible molecular mechanisms. Finally, 30 male BALB/c mice (20±2g) were randomly divided into five groups (n=6), including the blank group, ZSD groups with two dosages (7.15, 14.3g/kg), FC model group, and positive group (lactulose group). All the mice were given difenoxate tablets for 14 days to establish FC model except the blank group. Moreover, the mice in the blank group were given the same volume of normal saline. After admination for 14 days, the whole colon tissues were obtained for the analysis of small intestinal propulsion rate, and the expression of P38MAPK in colon tissues of mice was observed via immunohistochemistry and WesterBlot.
ResultsIn this study, 43 active ingredients in ZSD were identified. Four hundred and thirty potential therapeutic targets were selected, among which AKT1, MAPK12, and MAPK14 were key targets. 164 GO biological processes and 123 KEGG signaling pathways were identified after analysis, such as MAPK signaling pathway, TNF signaling pathway etc. The molecular docking results showed that Prangenin, 4-Hydroxyhomopterocarpin, isoponcimarin, and AKT1, MAPK12, MAPK14 had good binding degree. Additionally, ZSD could relieve the symptoms of FC in mice significantly. Compared with the model group, p38/MAPK positive expression cells and protein expression levels in the colon tissues of ZSD groups significantly increased in a dose-dependent manner (p<0.01).
ConclusionThis study confirmed that ZSD could act on AKT1, MAPK12, and MAPK14 targets to activate the p38/MAPK signaling pathway to relieve FC induced by defenoxate tablets. The further development of ZSD provided a theoretical basis.
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CD4+ Effector Memory T Cells Related Marker Gene Signatures in Osteoporosis and Aging: Insight From Single-Cell Analysis and Mendelian Randomization
Authors: Xiangwen Shi, Linmeng Tang, Mingjun Li, Yipeng Wu and Yongqing XuAvailable online: 04 February 2025More LessObjectiveWith the accelerated aging of the population, aging has emerged as a major risk factor for osteoporosis (OP). This study aims to investigate the relationship and shared molecular mechanisms between OP and aging through various genetic approaches.
MethodsSingle-cell data from the peripheral blood of osteoporosis patients, aging individuals, and healthy controls were integrated to analyze characteristic changes in cell subpopulations. Differentially expressed genes (DEGs) were then identified within core subpopulations, and Mendelian randomization (MR) analysis was employed to explore potential causal links between key genes and OP. Additionally, an OP model was established in rats, and mRNA levels of key genes were measured using RT-qPCR.
ResultsThrough the integration, filtering, and analysis of scRNA-seq data, an increased proportion of CD4+ effector memory T (CD4+ TEM) cells were identified in OP and aging samples, marking them as a core subpopulation. Differential expression analysis identified 49 DEGs, and further analysis through Mendelian Randomization (MR) identified three key genes (KLRB1, NR4A2, and S100A4) significantly associated with OP. Notably, the upregulation of KLRB1 and S100A4 may enhance the interactions within T cells and with other cell subgroups. At the same time, the downregulation of NR4A2 could impede communication between T cells and other cell subpopulations. The RT-qPCR results indicated that NR4A2 was significantly downregulated in the OP group.
ConclusionThis study conducted a comprehensive analysis of the potential link between OP and aging, identifying CD4+ TEM cells as the core cell subgroup in OP and aging samples. It further revealed the causal relationship between KLRB1, NR4A2, and S100A4 and the occurrence of OP. The upregulation of KLRB1 and S100A4 may contribute to OP pathogenesis by promoting interactions between CD4+ TEM cells and other cell subgroups, providing new insights for molecular targeting and immunotherapy of OP.
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A Comparative Chemoinformatics Analysis of Compounds Extracted from Nyctanthes Arbor-tristis
Authors: Nandini Sandeep Kotharkar, Sanket Bapat, Pranav Pathak and Renu VyasAvailable online: 02 February 2025More LessIntroductionNatural products are a rich source of diverse chemical compounds with interesting therapeutic properties. There is a need for in-depth investigation of this reservoir with in-silico tools to assert the molecular diversity with respect to clinical significance. Although studies have been reported on plants such as Nyctanthes arbor-tristis(NAT) and its medicinal importance. A comprehensive study on comparative analysis of all phyto-constituents has not been carried out.
Aimn the present work, we have carried out a comparative study of compounds obtained from the ethanolic extracts of various parts such as calyx, corolla, leaf, and bark of the NAT plant.
MethodsThe extracted compounds were characterized by LCMS and GCMS studies. This was further corroborated by the network analysis, docking, and dynamic simulation studies with validated anti-arthritic targets.
ResultsThe most significant observation from LCMS and GCMS was that the compounds from calyx and corolla were closer in chemical space to the anti-arthritic compounds. To further expand and explore chemical space, the common scaffolds were seeded to enumerate a virtual library. The virtual molecules were prioritized based on the drug-like, leadlike scores and docked against anti-arthritic targets to reveal identical interactions in the pocket region.
ConclusionThe comprehensive study will be of immense value to medicinal chemists for the rational synthesis of molecules as well as bioinformatics professionals for getting useful insight into identifying rich diverse molecules from plant sources.
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Forsythiaside A Ameliorates Inflammation by Regulating the Autophagy in Methotrexate-induced Intestinal Mucositis
Authors: Wuying Lang, Jiayi Zhang, Xuejun Xiao, Min Cheng, Xin Zheng, Haizhou Gong, Ihsan Ali, Yongping Zhao, Feng Jia, Zhe Wang, Jing Wang, Wei Li and Haihua ZhangAvailable online: 29 January 2025More LessBackgroundMethotrexate (MTX) effectively eliminates cancerous cells but can also cause inflammation intestinal, known as mucositis. Forsythiaside A (FTA) from Forsythia suspensa has shown promise in relieving mucositis by targeting the NLRP3 pathways. Since NLRP3 inflammasome activation is negatively regulated by autophagy, this study explores how FTA-mediated autophagy affects NLRP3 inflammasome in treating MTX-induced intestinal inflammation.
MethodsIntestinal mucositis was induced in rats with MTX. FTA's impact was assessed using HE staining and ELISA. The mechanism was studied using immunofluorescence, western blot, and ELISA.
ResultsFTA treatment resulted in reduced levels of D-lactic acid and diamine oxidase (DAO) in MTX-treated rats. Western blot and immunofluorescence analyses revealed up-regulation of Beclin-1 and LC3II/I, accumulation of LC3, and down-regulation of p62 expression levels in MTX-treated rats following 40 or 80 mg/kg FTA intervention. However, when the autophagy inhibitor 3-MA was used, the intestinal pathology was exacerbated, the inflammatory scores increased, and serum levels of TNF-α, IL-1β, and IL-18 were elevated. Western blotting indicated decreased LC3II/I expression, while NLRP3, cleaved caspase 1, and cleaved IL-1β expressions were upregulated.
ConclusionThese findings suggested that FTA alleviated MTX-treated intestinal mucositis by activating autophagy, which in turn inhibits the NLRP3 inflammasome.
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PGD2/PTGDR2 Signaling Affects the Stemness of Gastric Cancer Stem Cells by Regulating Autophagy
Authors: Feifan Wang, Hengjin Tian, Peiyao Gao, Zhanshan Cha and Qiang ZhangAvailable online: 27 January 2025More LessBackgroundProstaglandin D2 (PGD2) can inhibit the development of gastric cancer (GC); however, its role in the autophagic death of GC stem cells (GCSCs) remains elusive. Therefore, this study aims to evaluate the mechanisms by which PGD2 regulates the stemness in GCSCs.
MethodsIn this study, HGC27-derived GCSCs were employed to knock down PGD2 receptor 2 (PTGDR2). Subsequently, cell stemness and autophagic activity in these GCSCs were assessed via sphere-forming capacity, transmission electron microscopy, and western blot analyses.
ResultsThe results revealed that PGD2 suppressed the stemness of GCSCs and induced GCSCs autophagy, whereas the downregulation of PTGDR2 had the opposite effect. Furthermore, PGD2 was also found to inhibit the expression of stemness-associated proteins CD44 and OCT4, which were blocked by 3-MA and enhanced by RAPA. Moreover, the shPTGDR2 + PGD2 group indicated higher stemness than the PGD2 group, with 3-MA enhancing this effect and RAPA reducing this change.
ConclusionIn summary, this study indicated that PGD2/PTGDR2 signaling affects stemness and autophagy in GCSCs. The results suggest that PGD2/PTGDR2 signaling may affect the stemness of GCSCs by regulating autophagy.
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Predicting Polymerase Chain Reaction Success: Integrating the K-Word Order Model, Physicochemical Properties Modeling of Double Bases, and Support Vector Machine
Available online: 23 January 2025More LessIntroductionPolymerase Chain Reaction (PCR) has been a pivotal scientific technique since the twentieth century, and it is widely applied across various domains. Despite its ubiquity, challenges persist in efficiently amplifying specific DNA templates.
MethodWhile PCR experimental procedures have garnered significant attention, the analysis of the DNA template, which is the experiment's focal point, has been notably overlooked. This study addresses the uncertainty surrounding the amplification of DNA fragments using conventional Taq DNA polymerase-based PCR protocols. The imperative need to characterize DNA templates and devise a reliable method for predicting PCR success is underscored.
ResultIn this study, we formulate a 72-dimensional feature vector representing a DNA template through the utilization of k-word order and modeling of physicochemical properties of double bases. Subsequently, a Support Vector Machine (SVM) model is employed to assess PCR results.
ConclusionA jackknife cross-validation test is used to evaluate the anticipated success rates, resulting in an overall accuracy of 95.77%. Sensitivity, specificity, and Matthew's Correlation Coefficient (MCC) stand at 95.75%, 95.79%, and 0.915, respectively.
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Investigation of the Mechanism of Pachyman against Gout Arthritis with Network Pharmacology Analysis and Verification In Vivo
Authors: Qing-xin Kong, Wei-ping Xu, Cheng Fan, Bi-Lin Liu, Li-Ping Reng and Qiao RuanAvailable online: 22 January 2025More LessPurposePachyman, derived from Poria cocos, has been used to treat gouty arthritis (GA) for thousands of years, although its precise role and mechanisms remain unclear. Herein, we investigate the therapeutic effects of pachyman on GA and explore their underlying mechanisms.
MethodsNetwork pharmacology and experimental methods were employed to investigate the therapeutic mechanisms of pachyman against GA. The protein-protein interaction network of shared targets between pachyman and gout was constructed. Furthermore, we elucidated the functions and mechanisms of pachyman against GA. Subsequently, we validated the predicted mechanisms from an experiment on rats.
ResultsThe treatment of GA with pachyman primarily related to tumor necrosis factor (TNF), matrix metalloproteinases (MMP), and relaxation factor signaling pathways. In the experimental validation, pachyman were found to regulate the expression of IL-1β, TNF-α, TGF-β, superoxide dismutase, and glutathione peroxidase of hyperuricemic rats.
ConclusionThese collective findings suggest that pachyman holds promise as an alternative treatment for GA.
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Mechanisms of the Compound of Magnoliae Flos and Xanthii Fructus Essential Oils for the Treatment of Allergic Rhinitis based on the Integration of Network Pharmacology, Molecular Docking, and Animal Experiment
Authors: Tao Lu, Yuqin Yang, Zhenlin Yang, Ziyi Liu, Miao Li, Ziman Lu, Ting Gong and Jincheng ZhangAvailable online: 22 January 2025More LessAim and ObjectiveMagnoliae Flos (Chinese name: Xin-Yi) and Xanthii Fructus (Chinese name: Cang-Er-Zi) are Chinese herbal medicines and have been used to treat allergic rhinitis (AR). However, the therapeutic effect, active ingredients, and probable processes of a compound of Magnoliae Flos and Xanthii Fructus in the form of essential oils (CMFXFEO) in treating AR have not been reported. This study aims to determine the efficacy of the CMFXFEO on ovalbumin (OVA)-induced AR in a rat model and to use network pharmacology and molecular docking to reveal the hub genes, biological functions, and signaling pathways of CMFXFEO against AR.
MethodsAnimal experiments were applied to validate the role of CMFXFEO in the treatment of AR. 20 rats were randomly divided into four groups: control group (CON, n=5), positive control group (AR, n=5), CMFXFEO-treated group (AR+CMFXFEO, n=5), and budesonide-treated group (AR+Budesonide, n=5). Rats were stimulated with OVA to induce AR. Symptom scores assessment and histo-pathomorphological evaluation was performed. The serum level of OVA-specific immunoglobulin (Ig) E was measured. Gas Chromatograph-Mass Spectrometer analysis (GC-MS) was used to identify the monomer chemical composition of CMFXFEO. The target genes of CMFXFEO were obtained by using PubChem and SwissTargetPrediction databases. The target genes of AR were screened using GeneCards, DisGeNET, and OMIM databases. The target genes were intersected using the venny2.1 website to obtain the potential therapeutic targets of CMFXFEO for treating AR and to construct the PPI network. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to reveal associated signaling pathways. The Sybyl tool was used to dock the CMFXFEO with key therapeutic targets molecularly.
ResultsIntranasal CMFXFEO administration significantly suppressed the allergic symptoms, reduced the inflammatory cell infiltration, and the serum level of OVA-specific immunoglobulin (Ig) E. The main components of CMFXFEO obtained through the GC-MS analysis, listed as γ-terpinene (9.4908%), limonene (7.2693%), menthol (7.1821%), β-pinene (7.1190%), β-caryophyllene (7.0396%), eucalyptol (6.1367%), linalool(5.9686%), eugenol (5.0776%). A total of 398 CMFXFEO targets and 488 AR-related targets were screened, of which 42 were common targets. The GO and KEGG pathway analyses unveiled that CMFXFEO were strongly associated with several signaling pathways, including the AGE-RAGE signaling pathway, TNF signaling pathway, and Chemokine signaling pathway. PPI network construction screened six hub genes as therapeutic targets, including STAT3, IL1B, TLR4, PTGS2, ICAM1, and VCAM1. The molecular docking verification indicated that CMFXFEO have good binding activity with therapeutic targets, and β-Pinene’s docking ability with TLR4 is particularly prominent.
ConclusionThe anti-inflammatory and anti-allergic effects of CMFXFEO are to inhibit the infiltration of inflammatory cells in the OVA-induced AR rat model. The results of the network pharmacology and molecular docking deduced that the CMFXFEO may have the potential to treat AR by multiple pathways through relieving inflammatory, anti-oxidative stress response, and modulating the immune system.
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FOLR1 Regulates the Malignant Progression of Glioblastoma through the SRC/ERK1/2 Axis
Authors: Xueshan Jia, Weihang Liang, Junya Yang, Xuejiao Chen, Bin Yi, Zhikun Cao and Qingfeng TianAvailable online: 20 January 2025More LessBackgroundGBM is an aggressive brain tumor with limited treatment options. Prior research has indicated FOLR1 as a pivotal gene involved in cancer pathogenesis.
AimThis study aimed to explore the involvement of folate receptor alpha (FOLR1) in glioblastoma (GBM) and evaluate its potential as a therapeutic target.
ObjectiveThis study investigated the expression pattern of FOLR1 in GBM, its impact on patient prognosis, and its role in GBM cell growth and the SRC/ERK1/2 signaling axis.
MethodsInitially, we conducted an expression analysis of FOLR1 based on public databases and examined its expression pattern in GBM and its impact on patient prognosis. Subsequently, cell experiments were carried out to evaluate the regulation of GBM cells by differential FOLR1 expression. We then downloaded 100 FOLR1 co-expressed genes from the Linkedomics data repository and performed an enrichment analysis. Finally, the role of FOLR1 and SRC/ERK1/2 axis in GBM was analyzed again by cell experiments.
ResultsFOLR1 was found to be substantially expressed in GBM patients and was linked to a poor prognosis. Cell experiments showed that overexpression of FOLR1 promoted GBM cell growth, while low expression of FOLR1 inhibited cell growth. Additionally, genes related to FOLR1 were enriched in the lysosome, toxoplasmosis, and other pathways. This study further indicated that FOLR1 facilitates the activation of the SRC/ERK1/2 signaling pathway in GBM cells, and the attenuation of these pathways can effectively impede the malignancy-promoting effects triggered by FOLR1 in GBM cells.
ConclusionsWe revealed that FOLR1 orchestrates the malignant advancement of GBM by stimulating the SRC/ERK1/2 signaling axis, underscoring its pivotal role in the pathogenesis of GBM.
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Herbal Mucoadhesive Gels for Canker Sores: Analysis of Physicochemical Properties, Efficacy, and Safety
Available online: 20 January 2025More LessAimThe goal of this research was to formulate mucoadhesive gels using hydroglyceric extracts of Cistus creticus L. and Inula viscosa (L.) Aiton, either separately or in combination, utilizes carboxymethyl cellulose and detects their physicochemical characteristics and safety for oromucosal cells and antimicrobial (antibacterial, antifungal, and antiviral) efficacy to assess their performance.
MethodsUsing LC-HRMS, the extracts of C. creticus and I. viscosa were examined. Evaluations were conducted on the formulations' viscosity, cytotoxicity-cell proliferation controls, texture, antibacterial activity, pH, and organoleptic properties. The minimal inhibitory concentrations and microbroth dilution tests were used to assess the effectiveness of the formulations.
ResultsThe pH, organoleptic, and physical characteristics of each formulation have been determined to be appropriate. The research results demonstrated that I. viscosa contributed antiviral efficacy to the formulations linked to dose-dependent activities against all examined mouth pathogens, whereas C. creticus provided antibacterial and antifungal efficacy. The formulation containing C. creticus extract alone was the most cytotoxic, whereas the formulation including I. viscosa extract alone was the least cytotoxic against gingival fibroblast cells, according to the findings of tests on cell proliferation and cytotoxicity.
ConclusionThe formulation contained a 32% 1:1 mixture of I. viscosa and C. creticus hydroglyceric extracts was detected as safe with acceptable cytotoxicity along with antibacterial and antiviral effectiveness, were encouraging for future investigations.
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Transcriptome-Based Analysis of the Oxidative Response of Thermotoga maritima to the O2 Stress
Authors: Raja Lakhal, Manaf AlMatar, Tahani Alkalaf and Osman AlbarriAvailable online: 16 January 2025More LessBackgroundThermotoga maritima is an anaerobic hyperthermophilic eubacterium isolated from geothermally heated maritime surfaces. It can grow at temperatures up to 80 degrees Celsius.
MethodsA 2.3-L bioreactor was specifically designed to cultivate hyperthermophilic bacteria under carefully regulated pH, redox potential, temperature, and dissolved O2.
ResultsUsing this bioreactor, which was adjusted at 80°C and pH 7.0, it was found that Thermotoga maritima demonstrated continued growth even after being exposed to oxygen for an extended period. Transcription studies revealed that following prolonged oxygen exposure, the genes encoding ROS-scavenging systems, alkyl hydroperoxide reductase (ahp), thioredoxin-dependent thiol peroxidase (bcp 2), and, to a lesser extent, neelaredoxin (nlr), were upregulated/overexpressed. When oxygen was available, the metabolism of glucose was diverted to make lactate rather than acetate.
ConclusionBased on the O/R ratio of 1.0 in anaerobiosis and 1.67 in the presence of O2, we may conclude that Thermotoga maritima is capable of semi-oxidative metabolism.
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Artificial Intelligence in Computer-Aided Drug Design (CADD) Tools for the Finding of Potent Biologically Active Small Molecules: Traditional to Modern Approach
Available online: 15 January 2025More LessComputer-Aided Drug Design (CADD) entails designing molecules that could potentially interact with a specific biomolecular target and promising their potential binding. The stereo-arrangement and stereo-selectivity of small molecules (SMs)--based chemotherapeutic agents significantly influence their therapeutic potential and enhance their therapeutic advantages. CADD has been a well-established field for decades, but recent years have observed a significant shift toward acceptance of computational approaches in both academia and the pharmaceutical industry. Recently, artificial intelligence (AI), bioinformatics, and data science have played a significant role in drug discovery to accelerate the development of effective treatments, reduce expenses, and eliminate the need for animal testing. This shift can be attributed to the availability of extensive data on molecular properties, binding to therapeutic targets, and their 3D structures. Increasing interest from legislators, pharmaceutical companies, and academic and industrial scientists is evidence that AI is reshaping the drug discovery industry. To achieve success in drug discovery, it is necessary to optimize pharmacodynamic, pharmacokinetic, and clinical outcome-related properties. Moreover, the advent of on-demand virtual libraries containing billions of drug-like SMs, coupled with abundant computing capacities, has further facilitated this transition. To fully capitalize on these resources, rapid computational methods are needed for effective ligand screening. This includes structure-based virtual screening (SBVS) of vast chemical spaces, aided by fast iterative screening approaches. At the same time, advances in deep learning (DL) predictions of ligand properties and target activities have become very helpful, as they no longer need information about the structure of the receptor. This study examines recent progress in the drug discovery and development (DDD) approach, their potential to reshape the entire DDD process, and the challenges they face. This review examines the role of artificial intelligence as a fundamental component in drug discovery, particularly focusing on small molecules. It also discusses how AI-driven approaches can expedite the identification of diverse, potent, target-specific, and drug-like ligands for protein targets. This advancement has the potential to make drug discovery more efficient and cost-effective, ultimately facilitating the development of safer and more effective therapeutics.
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Mechanism Analysis of the Effect of Cordycepin on Colorectal Cancer via Network Pharmacology and Experiment
Authors: Ya Chen, Peng Wang, Mingzhu Zhang, Hao Yang and Beibei LiangAvailable online: 14 January 2025More LessObjectiveColorectal Cancer (CRC) has attracted much attention due to its high mortality and morbidity. Cordycepin, also known as 3'-deoxyadenosine (3'-dA), exhibits many biological functions, including antibacterial, anti-inflammatory, antiviral, anti-tumor, and immunomodulatory effects. It has been proven to show anticancer activity in both laboratory research studies and living organisms. However, the molecular mechanism of the effect of cordycepin on CRC remains unclear.
MethodsThe genes associated with cordycepin and colorectal cancer have been identified by comparing the toxicogenomics database (CTD) and GeneCards database. The common genes between cordycepin and CRC have been identified using the Venny tool. The Protein-protein Interaction (PPI) network has been drawn using the STRING database. GO and KEGG enrichment analyses of the intersecting genes have been followed by experimental validation, both in vitro and in vivo.
Results24 drug targets have been screened using the CTD database and 1490 disease targets have been obtained from the GeneCards database and GO and KEGG analyses. The effect of cordycepin on the proliferation of SW480 cells has been assessed using CCK-8. The related results have indicated cordycepin to inhibit the proliferation of SW480 cells, promote apoptosis, and activate the p53 signal pathway. The findings obtained from in vivo experiments have been found to be consistent with those obtained from in vitro studies.
ConclusionOur findings have elucidated an effective way to search for cordycepin’s potential mechanism of effect on CRC therapy by employing the network pharmacology and experiment. We have predicted that cordycepin can inhibit tumor growth by regulating the apoptosis pathway. This study has offered valuable insights into the potential mechanism of the effect of cordycepin on CRC and provided a theoretical basis for further validation of its clinical application.
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Mechanism Study on the Regulation of Th1/Th2 in the Treatment of Idiopathic Membranous Nephropathy by Shengyang Yiwei Decoction
Authors: Yuan Wu, Xue-Qin Zhang, Heng-Tong An, Shuai-Jie Wang, Ya-Yun Zhao and Zhi-Qiang ChenAvailable online: 13 January 2025More LessBackgroundShengyang Yiwei Decoction showed efficacy in idiopathic membranous nephropathy treatment, and this study aimed to assess the underlying molecular mechanisms.
MethodsRats with passive Heymann nephritis were divided into the model group, the Shengyang Yiwei Decoction group, the JAK2 inhibitor group, and the STAT3 inhibitor group. Healthy rats served as the normal control. 24-hour urinary protein excretion, IgG deposition, renal histopathology, the expression levels of synaptopodin, nephrin, podocalyxin, interferon-γ, interleukin-4, T-box expressed in T cells, GATA binding protein-3, and relevant pathway proteins were measured.
ResultsWithin the model group, a notable elevation in the 24-h urinary protein level was observed, accompanied by evident IgG deposition, increased glomerular volume, eosinophilic deposits, diminished expression of podocyte marker proteins, and a discernible imbalance in Th1/Th2 cellular immunity. Conversely, in Shengyang Yiwei Decoction and both inhibitor groups, enhancements were observed across the aforementioned indexes.
ConclusionShengyang Yiwei Decoction may reduce glomerular podocyte injury through the suppression of the JAK2/STAT3 signaling pathway and modulation of the Th1/Th2 immune balance.
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The Anaphylactic and Anti-allergenic Properties of Shuanghuanglian: A Review
Authors: Xin Jiang, Ji Li, Xiaohui Yao and Hao DingAvailable online: 13 January 2025More LessShuanghuanglian (SHL) and its primary constituents have demonstrated protective effects against allergenic diseases. This review examines the anaphylactic and anti-allergenic activities of SHL and its constituents. We also discuss potential avenues for future research, particularly regarding the expansion of the clinical applications of SHL formulations (oral or nebulized) for the treatment of allergenic disorders.
For this review, we searched the PubMed, Web of Science, and China National Knowledge Infrastructure databases for relevant publications. Additionally, details of the essential active components and target genes of SHL were obtained from the Traditional Chinese Medicine Systems Pharmacology database (TCMSP), and information on allergy-related genes was collected from the GeneCards and Online Mendelian Inheritance in Man(OMIM) databases. Lists of both the SHL target and disease-related genes were imported into the ‘Draw Venn Diagram’ tool on the website (http://bioinformatics.psb.ugen /web tools/Venn/). A protein–protein interaction network for SHL and disease targets was constructed with reference to the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and the potential pathways were identified based on Kyoto Encyclopaedia of Genes and Genome enrichment analyses.
The allergenic reactions induced by SHL injection (intravenous) and its main constituents (intraperitoneal or intravenous injection) have been verified in animal experiments. Furthermore, the protective effects of SHL injection (intraperitoneal) and its individual Chinese herb components (intragastric administration), namely, Flos Lonicerae, Radix Scutellariae, and Fructus Forsythiae, as well as their main constituents (intraperitoneal or intragastric administration), have been verified in asthma, rhinitis, atopic dermatitis, and both IgE- and non-IgE-mediated systemic allergic responses. The network pharmacology analysis revealed that the therapeutic effects of SHL might be primarily mediated through the regulation of the IL-17 and TNF-α signalling pathways and Th17 cell differentiation.
Accumulated research data provide a theoretical basis for the clinical application of SHL (via extravascular routes) in the treatment of allergenic diseases.
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Betanin Mitigates Inflammation and Ankle Joint Damage by Subduing the MAPK/NF-κB Pathway in Arthritis Triggered by Type II Collagen in Rats
Authors: Yongxiang He, Shaik Althaf Hussain and Wenjie DaiAvailable online: 13 January 2025More LessBackground: Rheumatoid Arthritis (RA), a chronic inflammatory autoimmune illness, is characterized by synovitis, progressive joint damage, and bone erosion. Even though the potent drugs available contain biologics, several patients fail to react to them or cause hostile effects.
ObjectivesBetanin (BTN), the betacyanin present in the red beetroot, has antioxidant, anti-inflammatory, and apoptotic properties. In this study, we assessed the anti-inflammatory and apoptotic effect of BTN on collagen-induced arthritis (CIA).
Materials and MethodsThe rats were arbitrarily separated into four sets: Normal, CIA, CIA+BTN (25 mg/kg bw), and CIA+BTN (50 mg/kg bw). The hematological, biochemical markers, cytokines, inflammatory enzymes, histopathology of the ankle joint, and protein expression of inflammatory and apoptotic proteins were studied.
ResultsInflammatory enzymes, histopathological variations, cytokines generation, and joint inflammation were strongly alleviated, and apoptosis was augmented by BTN in a concentration-dependent manner. Bcl-2 and MAPK/NF-κB proteins were reduced, while the caspase-3, caspase-9, and Bax were intensified. The anti-rheumatic action of BTN was correlated to the attenuation of the MAPK/NF-κB pathway, which suppresses cytokine production, inflammation, and reduced cartilage impairments.
ConclusionThese outcomes recommend that BTN can be employed as a strong healing alternative for RA management.
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Bushen Daozhuo Granules Alleviate Chronic Non-Bacterial Prostatitis in Rats through p38 MAPK and Akt Signaling Pathways Based on Tandem Mass Tag-Based Quantitative Proteomics and Network Pharmacology Analyses
Authors: Dalin Sun, Yuanyuan Liu, Dong Xing, Dandan Wang, Bin Cai, Zhian Tang, Qinglin Hu, Wenjun Ma and Baofang JinAvailable online: 13 January 2025More LessIntroductionThe traditional Chinese medicine formula, Bushen Daozhuo Granules (BSDZG), is used to treat chronic non-bacterial prostatitis (CNP) clinically. However, its mechanism of action is unclear. The aim of our study was to determine the effect of BSDZG on CNP and its underlying mechanisms.
MethodsMale Wistar rats were randomly assigned to control, CNP, and BSDZG groups. CNP was induced using purified prostaglandin solution and Freund's complete adjuvant, after which the BSDZG group received 1.54 g/kg/d of BSDZG for 30 days. Prostate tissues were used to determine apoptosis and inflammatory cytokines. The herb-composition-target network and functional signaling pathways were built using a network pharmacology approach, which was also confirmed in vivo.
ResultsTreatment with BSDZG significantly alleviated the histopathological lesions, inflammation, and apoptosis in the prostate of CNP rats. The herb-composition-target network comprising 42 active compounds and 32 targets of 11 herbs was illustrated, and KEGG pathways analysis identified the Akt and MAPK pathways as related to the effects of BSDZG. Phosphorylation of p38 MAPK, NF-кB, and Bax expression was significantly enhanced and phosphorylated Akt and Bcl-2 levels were decreased in CNP rats, which could be reversed by BSDZG.
ConclusionThis study presented for the first time that BSDZG effectively alleviated CNP symptoms in rats and elucidated the underlying mechanisms mediated by the Akt and MAPK pathways, providing the theoretical basis for the clinical use and promotion of BSDZG.
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TSPOAP1-AS1: A Novel Biomarker for the Prognosis and Therapeutic Target in Cervical Cancer
Authors: Jinyuan Li, Zhen Ye, Yuhong Gan, Dongbing Li and Yibiao ChenAvailable online: 13 January 2025More LessBackgroundTSPOAP1 antisense RNA 1 (TSPOAP1-AS1) is a long non-coding RNA (lncRNA) that has received widespread attention in oncology research in recent years. Its role and mechanism in some cancers have gradually been revealed. However, it is not clear what role TSPOAP1-AS1 plays in cervical cancer (CESC).
ObjectiveIn this study, bioinformatic analysis and experimental validation were carried out to investigate the relationship between TSPOAP1-AS1 and CESC.
MethodsThe relationships between clinical characteristics in patients with CESC, TSPOAP1-AS1 expression, prognostic factors, regulation network, and immune infiltration of TSPOAP1-AS1 were evaluated using statistics and The Cancer Genome Atlas database. Real-Time Quantitative Reverse Transcription PCR was used to test TSPOAP1-AS1, miR-17-5p, and AGFG2 expression in CESC cell lines.
ResultsCESC patients exhibited markedly reduced expression of TSPOAP1-AS1. There was a significant correlation between low expression of TSPOAP1-AS1 in CESC patients and the clinical stage (p < 0.05), weight (p < 0.05), and BMI (p < 0.05). Lower expression of TSPOAP1-AS1 in patients with CESC was associated with poorer overall survival (OS) (p = 0.014) and disease-specific survival (DSS) (p = 0.030). There was also an independent correlation between high expression of TSPOAP1-AS1 (p = 0.036) and DSS in patients with CESC. TSPOAP1-AS1 was involved in the ribosome, oxidative phosphorylation, antigen processing and presentation, cell adhesion molecules (CAMs), the chemokine signaling pathway, neuroactive ligand-receptor interaction, and primary immunodeficiencies. The infiltration of immune cells and the expression of TSPOAP1-AS1 were found to be correlated. A ceRNA network of TSPOAP1-AS1/miR-17-5p/AGFG2 was constructed in CESC. In CESC, a ceRNA network involving TSPOAP1-AS1/miR-17-5p/AGFG2 was successfully established. When comparing CESC cell lines with HcerEpic, the expression of TSPOAP1-AS1 and AGFG2 decreased significantly, and the expression of miR-17-5p increased significantly.
ConclusionIn CESC patients, low expression of TSPOAP1-AS1 was associated with poor survival and immune infiltration. It may be effective to use TSPOAP1-AS1 as a biomarker of prognosis and therapeutic target in CESC.
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Mechanism of Qilong Capsule against Myocardial Ischemia-Reperfusion Injury Based on Network Pharmacology and Experimental Validation
Authors: Lingxu Li, Jingxue Ye, Jiahui Zhou, Zhihui Wang, Ruoyun Li, Min Wang and Guibo SunAvailable online: 10 January 2025More LessIntroductionQilong capsule (QC) has been used clinically to treat ischemic stroke in China. This study evaluated the therapeutic effects of QC on myocardial ischemia-reperfusion injury (MIRI) and its potential mechanisms.
MethodThe components and candidate targets of QC against MIRI were predicted by network pharmacology via relevant databases such as TCMSP, BATMAN-TCM, GeneCards. The potential mechanisms were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and verified by enzyme-linked immunosorbent assay (ELISA) and Western blot.
ResultsNetwork pharmacology analysis indicated that the cardioprotective effect of QC against MIRI was associated with inflammatory pathways. We further confirmed that QC effectively decreased the levels of inflammatory factors, including hs-CRP and MCP-1, and suppressed the expression of TNF-α and the phosphorylation of STAT3.
ConclusionThis study provides evidence for further clinical applications of QC for MIRI therapy.
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Potential Antibacterial of Leaf Sirih Merah Against Enterococcus Faecalis ATCC 29212 Bacteria
Authors: Trisna Yuliana, Devi Meliani and Dikdik KurniaAvailable online: 10 January 2025More LessBackgroundDental root canal failure is a disease caused by gram-positive bacteria, Enterococcus faecalis. The disease is caused by the bacterial cell wall consisting of a peptidoglycan layer that protects the bacteria from internal osmotic pressure. Peptidoglycan biosynthesis includes many enzymes, such as MurA, Penicillin-binding protein (PBP), and SrtA. Herbal plants are a source of bioactive compounds, including antibacterial agents. There is information that red betel leaves, also known as Piper crocatum, contain active substances such as flavonoids, terpenoids, and steroids. However, there is no additional information on the antibacterial properties of P. crocatum and the molecular mechanisms that affect the cell wall of E. faecalis ATCC 29212 bacteria.
ObjectiveThis study aims to determine the antibacterial activity of the extract in vitro, screen and study the antibacterial compounds of red betel leaves against oral pathogenic bacteria, namely E.faecalis ATCC 29212 through molecular docking.
MethodsThe n-hexan:ea (9:1) fraction of P. crocatum extract was tested for inhibition zones against E. faecalis ATCC 29212 bacteria, fractions that had positive results were then identified using the LC-MS method. The LC-MS resulting compounds were tested using In Silico.
ResultsAntibacterial in the n-hexane: ethyl acetate (9:1) fraction of Red Betel Leaf has the best concentration of 10% with a moderate inhibition zone category. LC-MS test results identified compounds including Longicamphenylone, m/z 207, Nootkatone m/z 219, and Tridecanal m/z 221. Molecular interactions between these compounds with target proteins, namely MurA, PBP, and SrtA, show lower binding affinity values than natural ligands and positive controls for each protein.
ConclusionNootkatone compounds demonstrated potential as MurA and PBP inhibitors, while Longicamphenylone compounds showed potential as SrtA inhibitors. Both compounds have the potential to inhibit peptidoglycan biosynthesis and bacterial cell wall formation through docking simulations.
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Causal Association between Arm Fat, Left Leg Fat, and Trunk Fat Masses and Risk of Polycystic Ovarian Syndrome: A Mendelian Randomization Study
Authors: Yuhan Zhang, Wei Zhou, Qiong Su and Qi ChenAvailable online: 09 January 2025More LessBackgroundObservational studies have reported that arm fat, left leg fat, and trunk fat masses have different effects on polycystic ovarian syndrome (PCOS). However, the causal relationship between them remains unknown.
Materials and MethodsA two-sample Mendelian randomization (MR) study was conducted by utilizing pooled data from the largest Genome-Wide Association Study (GWAS). Random effect inverse variance weighted (IVW) method, weighted median (WM), and MR-Egger regression analysis were the main statistical methods utilized. Finally, a sensitivity assessment was conducted. Cochran’s Q test was used to analyze heterogeneity, whereas MR-Egger regression (intercept term) was used to analyze horizontal pleiotropy. The leave-one-out analysis was performed to assess if MR estimates were impacted by a single nucleotide polymorphism (SNP) exhibiting significant horizontal pleiotropy.
ResultsThis study discovered a significant positive correlation between left leg fat mass, arm fat mass, and trunk fat mass and genetic factors of PCOS (odds ratio (OR): 4.452, confidence interval (CI): 2.740−7.232, p < 0.001, OR: 3.321, CI: 2.248−4.907, p < 0.001, and OR: 2.518, CI: 1.722−3.682, p < 0.001, respectively).
ConclusionThis study indicates that arm fat, left leg fat, and trunk fat masses may be genetically correlated with PCOS.
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miR-507 Acts as a Tumor Suppressor in Renal Cell Carcinoma Cells by Targeting STEAP3
Authors: Gong Xiaobo, Huang Jian, Guo Linjie, Tang Zhe, Zhong Guangjun and Feng YeAvailable online: 09 January 2025More LessIntroductionIn recent years, there has been a rise in the incidence of renal cell carcinoma (RCC), with metastatic RCC being a prevalent and significant contributor to mortality. While a regulatory role for microRNAs (miRNAs) in the development and progression of RCC has been recognized, their precise functions, molecular mechanisms, and potential clinical implications remain inadequately elucidated. Hence, this study aimed to explore the role of miR-507 in RCC and identify STEAP3 as a downstream target of miR-507.
MethodsBioinformatics analysis was used to analyze the expression of miR-507 and STEAP3 in RCC specimens. CCK-8, Transwell, and flow cytometry assays were used to assess the function of miR-507 in RCC cells. The connection between miR-507 and STEAP3 was confirmed through a luciferase reporter assay. The expression level of STEAP3, p53, and xCT was analyzed by western blotting.
ResultsBioinformatics analysis showed that miR-507 was expressed at low levels in RCC tissues and was linked to poor overall survival. STEAP3 was found to be significantly upregulated in RCC. Further, STEAP3 was shown to be targeted by miR-507. High levels of miR-507 reduced the expression of STEAP3, leading to stagnant cell viability, apoptosis, and migrative capacity. Whereas miR-507 knockdown reverted such a tendency. The study also discovered that miR-507 exerted its inhibitory effect through the op53/xCT pathway.
ConclusionWithin RCC, miR-507 modulates the expression of SETAP3/p53/xCT axis, exhibiting a tumor suppressive effect. These discoveries offer present prospective biomarkers for both surveillance and treatment of RCC.
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Paederia Foetida Linn (Rubiaceae): Chemical Diversity, Phytopharmacological Potential, Quantitative Analysis and Clinical Approaches
Available online: 07 January 2025More LessThe discovery of novel counteractive pharmaceuticals, which have recently generated much interest, has played a significant role in the development of drugs derived from herbal medicines or botanical sources. Paederia foetida (P. foetida) is one such example of a role in both traditional and traditional medicine. Owing to its popularity in folk medicine, it has been the subject of intense pharmacological and chemical studies for the last 30 years. They are locally known as “Gandhavadulia” or “GandhaPrasarini” (English name “skunkvine”) and belong to the family Rubiaceae. This plant has a broad range of applications in the treatment of several illnesses, including anti-inflammatory, antinociceptive, antitussive, thrombolytic, antidiabetic, antihyperlipidaemic, antioxidant, nephroprotective, anti-inflammatory, hepatoprotective, anthelmintic, and antidiarrheal effects. Additionally, it contains a variety of phytochemicals, such as asperuloside, paederosidic acid, sitosterols, campesterol, lignans, alkaloids, volatile oils, iridoids, methylindooxy substances, stigmasterol, tannins, triterpenoids, ellagic acid, ursolic acid, epifriedelinol, and phenolic compounds. Recently, mounting data on numerous active ingredients have indicated that they may be beneficial for spermatogenesis, wound healing, inflammatory illnesses, and cancer. This review describes the phytochemistry and mechanisms of action of these pharmacological effects and provides insights into potential pharmacological targets. These results highlight the need for additional studies on this medicinal plant and the investigation of new counteractive medications to determine their mode of action before use in healthcare.
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Integrated Network Pharmacology and Transcriptomics Analysis to Elucidate the Mechanism of Huoxue Tongluo Qiwei Decoction in the Treatment of Erectile Dysfunction in Spontaneously Hypertensive Rats through Angii-Activated Pkcε Pathway
Authors: Junlong Feng, Sheng Deng, Bin Wang, Cong Zhao, Kali Zou, Haisong Li and Jisheng WangAvailable online: 07 January 2025More LessBackground and AimAs a classical formula to invigorate blood circulation, Huoxue Tongluo Qiwei Decoction (HTQD) can effectively treat hypertensive erectile dysfunction (ED), but its exact mechanism of action is not yet clear. The goal of this research was to explore the potential mechanism of HTQD in improving hypertensive erectile dysfunction in rats through transcriptomics, network pharmacology, and associated animal experimentations.
MethodsThe HTQD chemical constituents were screened using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Furthermore, transcriptomics analysis was performed via mRNA sequencing to identify significantly differentially expressed proteins. Moreover, the key target proteins of HTQD in the treatment of hypertensive ED were screened by network pharmacology and transcriptomics. In addition, the endothelial cells of the corpus cavernosum were assessed using hematoxylin-eosin staining. The transcript and protein expressions were evaluated via western blotting and Real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR).
ResultsThe network pharmacology and transcriptome mRNA sequencing revealed that KCNE1 may be the target protein of HTQD in improving hypertensive ED. After HTQD treatment, the systolic and diastolic blood pressure (BP) of hypertensive rats decreased, the number of erections increased, and the pathological structure of the penis was improved. Moreover, HTQD downregulated the protein and mRNA expression of AngII, AT1R, DAG, and PKCε, whereas it up-regulated the transcript and protein expression of KCNE1.
ConclusionHTQD may activate the PKCε pathway through AngII, inhibit the expression of KCNE1 protein, relax vascular smooth muscles, and improve erectile function.
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Exploration of the Mechanism of Tanre Qing Injection in Treating Acute Respiratory Distress Syndrome through Network Pharmacology, Molecular Docking, and Animal Experiments
Authors: Liang Wang, Ganqun Lu, Tianyu Cheng, Shuangquan Wen, Wenxiang Ma and Yixuan LiAvailable online: 07 January 2025More LessObjectiveThis study aimed to explore the active components and potential mechanism of Tanre Qing Injection (TRQI) in the treatment of Acute Respiratory Distress Syndrome (ARDS) using network pharmacology, molecular docking, and animal experiments.
MethodsThe targets of active ingredients were identified using the TCMSP and Swiss Target Prediction databases. The targets associated with ARDS were obtained from the GeneCards database, Mala card database, and Open Targets Platform. A Protein-protein Interaction network (PPI) was constructed, and the core targets were subjected to Gene Ontology (GO) function annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Finally, molecular docking technology and a mouse model of lipopolysaccharide-induced acute lung injury validated the experimental results.
ResultsThe results of network pharmacology showed the active components of TRQI in the treatment of ARDS to be baicalin, chenodeoxycholic acid, oroxylin-A, and ursodeoxycholic acid, and the core targets to be TP53, ESR1, AKT1, JUN, and SRC. KEGG analysis showed 181 signaling pathways, primarily including the IL-17 signaling pathway, endocrine resistance, lipid metabolism, and atherosclerosis. Molecular docking results demonstrated that baicalin, chenodeoxycholic acid, oroxylin-A, and ursodeoxycholic acid in TRQI exhibited the strongest affinity for TP53, ESR1, and SRC. Furthermore, the results of animal experiments have indicated TRQI to have a significant inhibitory effect on inflammatory factors TNF-α, IL-1β, and IL-6, and effectively alleviate the pathological damage of ARDS to lung tissue.
ConclusionTRQI may exert its therapeutic effects on ARDS through multiple targets and pathways, providing a research basis for its clinical application and further development.
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Investigation of the Potential Pharmacological Substance Basis and Mechanism of Action of Xuantu Granules in Treating Diabetic Kidney Disease Based on UHPLC-Q-Exactive-HRMS and Bioinformatics
Authors: Jingna Fan, Chang Kong, Bin Yu, Rong Wang and Zhenqiang QiAvailable online: 06 January 2025More LessObjectiveThe objective of this study is to analyze and identify the main chemical components and blood-absorbed components of Xuantu Granules and predict their pharmacological substance basis and mechanism in the treatment of DKD.
MethodsA DKD rat model was established by feeding SD rats a high-fat and high-sugar diet and administering intraperitoneal injections of streptozotocin (STZ). The therapeutic effect of Xuantu granules was evaluated. Drug-containing serum was prepared after gavage, and the major chemical components of Xuantu Granules and the drug-containing serum were detected using UHPLC-Q-Exactive-HRMS. Blood-absorbed components were identified based on retention time, mass-to-charge ratio, and MS/MS spectrum. Blood-absorbed components’ target proteins were searched using the CTD, SwissTarget, BindingDB, and TargetNet databases. DKD disease target genes were screened from the GEO database using WGCNA. A “bioactive blood-absorbed component-target-disease” PPI network was constructed using Cytoscape software, and the key clustering subnetworks were identified by MCODE plugin. GO functional analysis and KEGG pathway enrichment analysis were performed on subnetworks.
ResultsXuantu Granules lowered fasting blood glucose, improved renal function, reduced proteinuria, and improved renal tissue pathological changes in DKD rats. 36 chemical components were identified, among which 12 compounds, including β -Carboline-1-propionic acid, Morin, Afzelin, Schizandrin, Gomisin A were identified as blood-absorbed components. Bioinformatics analysis indicated that AKT1, TNF, TP53, IL6, SRC, IL1B, EGFR, JUN, BCL2, and CASP3 might be the main therapeutic targets. The involved pathways included the IL-17 signaling pathway, PI3K-Akt signaling pathway, AGE-RAGE signaling pathway in diabetic complications and so on.
ConclusionXuantu Granules may exert therapeutic effects on DKD through multiple targets and pathways.
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Unveiling the Interplay between Dopamine-like Molecules and Β-Amyloid Peptide: A Combined Molecular Dynamic and DFT Approach
Available online: 02 January 2025More LessAimsThis study aims explore the impact of catechol, dopamine, and L-DOPA on the stability and toxicity of β-amyloid peptides, which play a key role in the neurodegenerative process of Alzheimer's disease, to assess their potential as therapeutic agents.
BackgroundAlzheimer's disease is marked by the aggregation of β-amyloid peptides, which contribute to neurodegeneration. Exploring how various compounds interact with β-amyloid peptides can offer valuable insights into potential therapeutic strategies.
ObjectiveThe objective of this research is to explore the interaction mechanisms of catechol, dopamine, and L-DOPA with β-amyloid peptides and assess their impact on peptide stability and aggregation.
MethodThis study employs molecular dynamics simulations combined with density functional theory to investigate the interactions between β-amyloid and the three compounds. It evaluates changes in peptide stability and salt bridge lengths and performs electronic structure analyses using the Electron Localization Function (ELF) and Harmonic Oscillator Model of Aromaticity (HOMA).
ResultsThe findings reveal that β-amyloid stability decreases significantly when interacting with dopamine and L-DOPA compared to catechol. All three compounds inhibit β-amyloid, with dopamine and L-DOPA showing stronger effects. Catechol primarily interacts through hydrophobic interactions, while dopamine and L-DOPA also form hydrogen bonds with β-amyloid. Electronic structure analysis shows catechol has higher electron localization and anti-aromatic character, affecting its interactions differently than dopamine and L-DOPA. A decrease in the HOMO-LUMO gap from catechol to L-DOPA to dopamine indicates increasing reactivity towards β-amyloid.
ConclusionDopamine and L-DOPA more effectively disrupt β-amyloid aggregation than catechol, likely due to additional hydrogen bonding and increased electronic reactivity. These insights are crucial for developing therapeutic strategies targeting β-amyloid aggregation in Alzheimer's disease, emphasizing the importance of molecular interactions in modulating peptide stability and toxicity.
The study also provides a comparative analysis of the electronic properties and interaction dynamics of the compounds, which can guide future research in the design of β-amyloid inhibitors. The utilization of advanced simulation techniques underscores the potential for computational methods in understanding complex biological interactions and developing novel therapeutic agents. Furthermore, the insights into the differential effects of hydrophobic interactions versus hydrogen bonding offer valuable information for the synthesis of new compounds aimed at mitigating β-amyloid toxicity.
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Nanomaterials for Temporomandibular Joint Osteoarthritis Therapy: A Mini-Review
Authors: Lulu Chen and Chengcheng LiaoAvailable online: 02 January 2025More LessOsteoarthritis, particularly temporomandibular joint (TMJ) osteoarthritis (OA), poses significant challenges in diagnosis and treatment. Recent studies suggest that nanomaterials hold considerable promise in treating TMJ-OA, showing validated efficacy in animal models. However, further research is required to ensure their long-term safety within the TMJ-OA environment. Nanomaterials can facilitate drug delivery and encapsulate functional cells and extracellular vesicles, offering new avenues for exploration. This paper reviews the current research status of nanomaterials in TMJ-OA treatment, including drug delivery, anti-inflammatory, lubricating and buffering, antioxidant, tissue regeneration, scaffold, and stimuli-responsive nanomaterials. Additionally, the paper explores the development and future prospects of nanomaterials in TMJ-OA treatment, highlighting their unique contributions and aiming to provide new perspectives and solutions for unexplored areas.
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Ferroptosis-related Biotargets and Network Mechanisms of Maslinic Acid Against Myocardial Ischemia-reperfusion Injury: An Integrated Bioinformatic and Experimental Approach
Authors: Qi Li, Guiyuan He, Rujie Zheng, Chunlei Liu, Che Wang, Zhihao Liu, Zhuqing Li and Chengzhi LuAvailable online: 02 January 2025More LessBackgroundMaslinic acid (MA), a pentacyclic triterpenoid compound derived from leaves and fruits of Olea europaea, bears multi-pharmacological properties. Our previous studies found that MA exerted a cardioprotective effect by modulating oxidative stress, inflammation, and apoptosis during myocardial ischemia-reperfusion injury (MIRI). Nevertheless, data regarding the anti-ferroptosis effects of MA on MI/RI remains unidentified.
Aim of the StudyThis study aimed to explore the effects of MA on ferroptosis induced by MI/RI, with a focus on elucidating the underlying mechanisms through an integrated approach of network pharmacology and experimental validation.
Materials and MethodsSeveral public databases and a protein-protein interaction (PPI) network were used to identify the core targets shared by MI/RI, ferroptosis, and MA. The molecular function, cell component, biological process, and potential signaling pathways of core genes were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Subsequently, molecular docking and in vitro experiments were carried out to further validate network pharmacology results.
ResultsA total of 21 unique intersection genes were obtained as potential targets of MA in treating MI/RI-induced ferroptosis. The 10 hub genes with the highest interaction scores were identified from PPI analysis. GO and KEGG enrichment showed the contribution of the core genes to pharmacological actions and mechanisms in MA treatment of MI/RI, especially the ferroptosis-related signaling pathways. Additionally, MA docked well with ranked core targets, including MAPK, MTOR, STAT3, PTGS2, and MDM2. Subsequently, in vitro experiments revealed that MA notably alleviated oxidative damage, reduced ferrous iron overload and ferroptosis, and regulated the expression of ferroptosis-related genes (GPX4, PTGS2, and ACSL4) in erastin-induced H9c2 cells. Meanwhile, MA could significantly reduce phosphorylation of MAPK (ERK1/2) levels in H9c2 cells.
ConclusionBy utilizing network pharmacology and experimental data, our study revealed the correlation between MA and ferroptosis following MI/RI, and concluded that MA might protect against MI/RI by reducing ferroptosis through the ERK1/2 signaling pathway. This finding offered fresh insights into the pharmacological mechanisms of MA against MI/RI.
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KIF4A on TGF-Β1/Smad3 Pathway: A Preliminary Investigation on the Proliferation and Immune Response in In-Vitro Cultured Breast Cancer Cells
Available online: 26 December 2024More LessAimThis study aims to explore the relevant biomarkers in breast cancer (BC).
BackgroundKinesin family member 4A (KIF4A) is a member of the Kinesin 4 subfamily of kinesin-related proteins, which has already been investigated in diverse types of tumors.
ObjectiveOur current study aims to investigate the involvement of KIF4A in BC.
MethodsKIF4A expression level was firstly predicted based on the data from the Cancer Genome Atlas (TCGA) and then assessed in BC cells. Subsequently, after silencing KIF4A, its effects on BC cell proliferation and metastasis, as well as on immune-related cytokines, were assessed by cell counting kit-8 (CCK-8), 5-Ethynyl-2'-deoxyuridine (EdU) staining and quantitative Polymerase Chain Reaction (qPCR). Next, western blotting assays were used to detect the expression and phosphorylation levels of transforming growth factor-beta 1 (TGF-β1) and small mothers against decapentaplegic 3 (Smad3) in BC cells after KIF4A silencing and the role of the pathway was verified by Smad3 inhibitor (SIS3).
ResultsKLF4A was highly expressed in BC, and silencing of KIF4A repressed the proliferation and metastasis potential of in-vitro cultured BC cells, concurrent with the reduction of CDH2, VIM, and SNAIL levels, yet the increase in the expression of CDH1. In the meantime, KIF4A knockdown diminished the levels of IL4, IL10, and TGFB while promoting those of IL1B and IL6 in BC cells. Further, enhanced phosphorylation of Smad3 was observed in BC cells, and the intervention of SIS3 restrained the proliferation and metastasis potential of BC cells and reduced the expression levels of CDH2, VIM, and Snail whilst promoting that of CDH1. Additionally, SIS3 intervention increased IL1B and IL6 levels and decreased IL4, IL10 and TGFB levels in BC cells.
ConclusionThis study preliminarily explored the involvement of KIF4A and TGF-β1/Smad3 together in BC, which may provide another insight into the management of BC in clinical practice.
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Sanggenol L Alleviates Rotenone-induced Parkinson's Disease and Inhibits Mitochondrial Complex I by Apoptosis Via P13K/AKT/mTOR Signalling
Authors: Nan Zhao, Menghai Wu, Periyannan Velu, Annamalai Vijayalakshmi and Jianbin ZhangAvailable online: 13 December 2024More LessBackgroundParkinson’s disease (PD) is the age-associated, second most advanced neurodegenerative illness. Rotenone is an extensively used pesticide to study PD pathology and inhibits mitochondrial complex I. Reports indicate that rotenone exerts neurotoxicity by its capability to produce reactive oxygen species (ROS), which eventually leads to neuronal apoptosis.
ObjectiveSanggenol L (SL) is an eminent flavonoid present in the Morus alba root bark, which exhibits neuroprotective, anticancer, and antioxidant properties. Materials and Methods: Hence, we assessed the neuroprotective activity of SL (5 and 10 µM/ml) on rotenone-stimulated SK-N-SH neuroblastoma cells and elucidated the effect of the P13K/AKT/mTOR signalling.
ResultsThe anti-PD action of SL on proliferation, oxidative stress (OS), intracellular ROS, apoptosis, Bax, cleaved Caspase-12, -9, -3, and Cyt-c, Bcl-2 and P13K/AKT/mTOR signaling was determined by MTT assay, biochemical analysis, DCFDA, AO/EB staining and western blot. It was found that SL (5 and 10 µM/ml) reduced rotenone-triggered OS, ROS levels, and apoptosis in a concentration-related way. SL alleviates Bax, cleaved caspase-12, -9, -3, and Cyt-c, while reducing Bcl-2. Furthermore, SL safer mitochondria by increase MMP and suppresses phosphorylation of P13k/AKT/mTOR pathway, thereby regulating apoptotic signalling.
ConclusionOur findings indicate that SL showed protective effects against rotenone-induced OS, mitochondrial complex-I in neuronal cell damage, which suggests that SL might potentially serve as an anti-PD remedial candidate for PD treatment.
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Bushen Zhuyun Decoction Enhances Endometrial Receptivity via the IL-6/STAT3 Signaling Pathway in Rats
Authors: Yinyin Ding, Yanli Hong, Yeting Zou, Xiaolan Wang, Xinyuan Liu, Xiaoyue Jiang, Minghui Hu, Jinjun Shan, Bei Liu and Huifang ZhouAvailable online: 29 November 2024More LessBackgroundReproductive endocrine disorder can impair endometrial receptivity, preventing embryo implantation and increasing miscarriage risk. Impaired endometrial receptivity contributes significantly to female infertility. Inflammatory signaling pathways including the IL-6/STAT3 pathway help embryos implant. Therefore, it is crucial to explore the relationship between the IL-6/STAT3 signaling pathway and endometrial receptivity.
ObjectiveTo investigate the mechanism by which Bushen Zhuyun decoction (BSZY) enhances endometrial receptivity in rats through the IL-6/STAT3 signaling pathway.
MethodsMifepristone-induced poor endometrial receptivity models of female SD rats were established, followed by histopathological observation. ELISA was used to measure serum sex hormones and VEGF. Western blotting or IHC was used to measure steroid receptors, IGFBP1, and IL-6/STAT3 pathway activation in the uterus during each estrus cycle and early gestation of normal rats. The Treg/Th17 balance was assessed using flow cytometry.
ResultsSignificant differences were found in the protein expressions of steroid receptors, IL-6, STAT3, and p-STAT3 during each estrus cycle and early gestation of normal rats. The protein expressions of STAT3 and PR were strongly correlated with each other. BSZY notably improved uterine morphology increased the expression of implantation markers and raised the serum concentrations of sex hormones and VEGF. BSZY enhanced the expressions of IL-6 and its receptors and restored the expressions of STAT3 and p-STAT3 in the uterus of pregnant rats. In addition, BSZY effectively restored the Treg/Th17 balance in the peripheral blood of pregnant rats.
ConclusionBSZY enhances endometrial receptivity and promotes decidualization in SD rats via the IL-6/STAT3 signaling pathway.
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Mechanisms Underlying the Therapeutic Effects of Yiqi Wenyang Huwei Decoction in Treating Asthma Based on GEO Datasets, Network Pharmacology, Experimental Validation, and Molecular Docking
Authors: Shuangdi Xiang, Yujaio Lu, Linhui Cheng and Hanrong XueAvailable online: 28 November 2024More LessPurposeThe Yiqi Wenyang Huwei Decoction (YWHD) is an herbal formula frequently utilized to treat asthma. Despite its wide usage, the specific mechanism of action remains unknown. Through an in-depth investigation utilizing network pharmacology, molecular docking techniques, and experimental validation, this study aims to uncover the molecular mechanism and material basis of YWHD in the treatment of asthma.
MethodsThe compounds and targets of YWHD were gathered from various databases such as TCMSP, PubMed, and CNKI. Additionally, asthma-related targets were obtained by combining the GEO dataset with GeneCards and OMIM databases. The STRING platform was employed to establish protein-protein interactions. GO and KEGG pathway enrichment analyses were conducted using DAVID. Molecular docking was utilized to assess the binding affinity between potential targets and active compounds. The asthma rat model was established through OVA induction, and a lung function meter was used to detect Mch-induced Max Rrs. HE staining was conducted to observe pathological changes, while ELISA was used to detect levels of inflammatory factors IL4, IL6, IL13, and IgE in BLAF. Furthermore, qPCR was used to detect levels of IL-1β, IL-6, JUN, and PTGS2 mRNA, while Western blot assay was employed to measure phosphorylation levels of NF-κB and IKKα.
ResultsA comprehensive study revealed that YWHD has 188 active compounds and 250 corresponding targets. After conducting a topological analysis of the PPI network, the study identified 14 high-activity targets, including JUN, PTGS2, IL6, IL1B, CXCL8, MMP9, IL10, ALB, TGFB1, CCL2, IFNG, IL4, MAPK3, and STAT3. Further, GO and KEGG pathway enrichment analysis indicated that YWHD targets inflammation-related genes and regulates IL-17 and NF-kappa B signaling pathways. Animal studies have shown that YWHD can effectively minimize airway Max Rrs, reduce the levels of inflammatory factors IL4, IL13, IL6, and IgE in BLAF, and improve airway inflammation in rats with asthma. Molecular experiments have also demonstrated that YWHD achieves this by down-regulating the expression levels of IL-1β, IL-6, JUN, and PTGS2 mRNA, inhibiting the phosphorylation modification levels of NF-κB and IKKα, and reducing the levels of inflammatory cytokines IL4, IL13, IL6, and IgE in BALF of rats. Interestingly, molecular docking has revealed that the active compounds in YWHD have a strong binding ability to the screening targets.
ConclusionThis research endeavor systematically explicated the active constituents, prospective targets, and signaling pathways of YWHD for asthmatic intervention. The study provides an innovative notion and dependable resource for comprehending the molecular mechanism and pharmaceutical screening of YWHD in the context of asthma treatment.
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Dulaglutide Alleviates Alzheimer's Disease by Regulating Microglial Polarization and Neurogenic Activity
Available online: 27 November 2024More LessBackgroundsIncreasing research has proved that microglial activation, polarization, and inflammatory response in the brain affect the pathology of Alzheimer's disease. Hence, employing reagents targeted to microglial functions to optimize the brain microenvironment may become a promising therapeutic method for Alzheimer's disease.
MethodsThe phagocytosis and clearance of Aβ1-42 were detected using western blot and immunofluorescence assay. The cell viability was determined via 3-(4, 5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) or cell counting kit-8 (CCK-8) assay. The load of pro-inflammation, in addition to anti-inflammation factors, was measured through an enzyme-linked immunosorbent (ELISA) assay. Flow cytometry was employed to estimate the apoptotic cells. The protein level related to microglial polarization and neuronal injury was detected via western blot. The length of the neuronal synapse was investigated using an immunofluorescence assay.
ResultsDulaglutide significantly promoted microglia to phagocytose and removed the Aβ plague. Additionally, dulaglutide treatment inhibited the production of pro-inflammatory factors, including tumor necrosis factor (TNF)-α, interleukin -1β, and IL-6, whereas it increased the load of anti-inflammatory molecules, such as IL-10 affected by Aβ1-42 exposure. Further investigation verified that Aβ1-42 down-regulated YM1/2 positive M2 microglial polarization phenotype but up-regulated cyclooxygenase-2 (Cox2) positive M1 microglia. However, treating with dulaglutide effectively counteracted these effects. Moreover, dulaglutide dramatically recovered primary cortical neuron cell viability and inhibited cell apoptosis influenced by Aβ1-42. Furthermore, the dulaglutide also reversed neuronal synapse injury after exposure to Aβ1-42.
ConclusionAltogether, this investigation verified that dulaglutide improved Aβ-induced inflammation and neuronal injury by mediating the activation and polarization of microglia, thereby alleviating Alzheimer's disease efficiently.
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The Prognostic Value and Immunotherapeutic Characteristics of GFPT2 in Pan-cancer
Authors: Yiyi Zhou and Yuchao DongAvailable online: 07 November 2024More LessPurposeThe purpose of this study is to investigate the underlying relationship of diagnosis and therapy between glutamine-fructose-6-phosphate transaminase 2 (GFPT2) and various cancers.
MethodsThe Cancer Genome Atlas (TCGA) database was utilized to get gene expression RNAseq and clinical data for 33 tumors. The immunotherapeutic cohorts, including GSE35640, GSE78220, GSE67501, GSE181815, and IMvigor210, were derived from the Gene Expression Omnibus database (GEO) and a previously released article. Differential expression analysis of GFPT2 was performed using several clinical factors, and prognostic analysis was performed using Cox proportional hazard regression. In addition, the Cell type Identification By Estimating Relative Subsets Of RNA transcripts (CIBERSORT) and the Estimation of STromal and Immune cells in MAlignant Tumor tissues utilizing Expression data (ESTIMATE) algorithms were used to investigate the connection between GFPT2 and the tumor microenvironment. This approach additionally incorporated dynamic immunological indicators, such as tumor mutational burden (TMB) and microsatellite instability (MSI). In addition, a correlation between GFPT2 expression and the effectiveness of anticancer drugs was plotted for discussion.
ResultsGFPT2 expression significantly differed in 11 out of 33 cancers. Although the distinct correlation between GFPT2 expression and clinical parameters had no wide distribution in pan-cancer, it demonstrated the potential prognostic validity of gene expression. GFPT2 demonstrated a strong correlation with immune infiltration, immune modulators, and immune-related biomarkers. Furthermore, a variance analysis demonstrated a significant relationship between GFPT2 and the efficacy of immunotherapy. In addition, GFPT2 was associated with increased sensitivity of drugs such as Olaparib and Lenvatinib and decreased sensitivity of drugs such as Nilotinib.
ConclusionCollectively, GFPT2 is potentially useful as a biomarker for prognostic prediction and immune infiltration in a variety of malignancies, and could lead to exciting new approaches to personalized oncotherapy.
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Preparation of DOX-TPP/HA-ss-OA Nanoparticles, Investigation of Drug Release Behavior In Vitro, and Evaluation of Anti-proliferative Activity In Vitro
Authors: Xuanting Fei and Qiaohong HuAvailable online: 06 November 2024More LessObjectiveThis study aimed to develop and characterize DOX-TPP/HA-ss-OA nanoparticles, utilizing the mitochondria-targeting prodrug doxorubicin-triphenylphosphine (DOX-TPP) and a reduction-sensitive amphiphilic polymer, hyaluronic acid-disulfide-oleic acid (HA-ss-OA). The research focused on evaluating the drug release behavior of these nanoparticles under varying glutathione (GSH) concentrations and their anti-tumor activity in vitro.
MethodsDOX-TPP/HA-ss-OA nanoparticles were prepared using probe ultrasound technology. The study examined the impact of different organic solvents on drug loading capacity and encapsulation efficiency to determine the optimal conditions. A single-factor experimental design was used to optimize the formulation process. Key parameters, including particle size and zeta potential, were measured to assess nanoparticle stability and performance. The dynamic dialysis method was employed to evaluate the reduction-sensitive drug release characteristics in media with different GSH concentrations. The MTT assay was used to analyze the growth-inhibitory effects of the nanoparticles on human breast cancer cells (MCF-7) and drug-resistant cells (MCF-7/ADR).
ResultsThe optimized preparation process for DOX-TPP/HA-ss-OA nanoparticles included a drug dosage of 2.0 mg, an oil-to-water volume ratio of 1:5, ultrasonic power of 500 W, and ultrasonic time of 15 minutes. The nanoparticles had an average particle size of 203.72 ± 2.30 nm and a zeta potential of 25.82 ± 0.58 mV, indicating favorable stability and effective drug delivery properties. The nanoparticles exhibited a slow, sustained release of DOX-TPP in pH 7.4 phosphate buffer solution (PBS) and accelerated release in high GSH concentrations, demonstrating reduction-responsive drug release. In vitro studies showed that DOX-TPP/HA-ss-OA nanoparticles significantly inhibited the proliferation of MCF-7 and MCF-7/ADR cells in a dose-dependent manner, with enhanced efficacy compared to free DOX and other formulations.
ConclusionDOX-TPP/HA-ss-OA nanoparticles demonstrate excellent reduction sensitivity, effective tumor cell growth inhibition in vitro, and the ability to overcome drug resistance. Including particle size and zeta potential measurements supports their suitability as drug carriers, highlighting their potential for targeted cancer therapy and further development.
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Potential Cardiovascular Disease Treatment by Natural Drugs Targeting the HIF-1α Factor and its Pathway
Authors: Weihan Gao, Danyang Wang, Yanmei Shi, Yu Sun, Jinlan Deng, Xiayinan Song, Jie Li and Min ZhangAvailable online: 05 November 2024More LessCardiovascular diseases (CVDs) remain a key contributor to global morbidity and mortality. Being a vital regulator of hypoxia, hypoxia-inducible factor-1α (HIF-1α) is a crucial player in CVD treatment. Recently, increasing attention has been paid to the effect of natural drugs on CVDs. According to some studies, HIF-1α is a potential target for CVD treatment in traditional Chinese medicine. In this study, we describe the mechanism underlying the regulatory role of HIF-1α in CVDs and summarize 30 natural drugs and 3 formulations for CVD treatment through HIF-1α and its signaling pathway. The study provides new ideas for CVD prevention and treatment.
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Research on the Therapeutic Effect of Qizhu Anti Cancer Recipe on Colorectal Cancer Based on RNA Sequencing Analysis
Authors: Pingping Zhai, Xueshen Qian, Guangyao Liu, Jingjing Wang, Lei Xie and Decai TangAvailable online: 04 November 2024More LessBackgroundColorectal cancer is one of the common malignant tumors in clinical practice, and traditional Chinese medicine, as an important adjuvant treatment method, plays important roles in the treatment of malignant tumors.
ObjectiveThis study aims to explore the mechanism of action of the Qizhu anti-cancer recipe on colorectal cancer through transcriptome sequencing.
MethodsThe control group and Qizhu anti-cancer recipe group were established separately, and sequencing of the cells of the two groups was performed using the Illumina sequencing platform. Two sets of Differentially Expressed Genes (DEGs) were screened using the DESeq2 algorithm, and Principal Component Analysis (PCA), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, Disease Ontology (DO), and Protein-Protein Interaction (PPI) were used to comprehensively analyze the molecular functions and signaling pathways enriched by DEGs.
ResultA total of 122 DEGs were identified through differential analysis, including 24 upregulated genes and 98 downregulated genes. GO analysis showed that DEGs were mainly enriched in functions such as alkaline phase activity, ion transport, cell differentiation, etc.; KEGG analysis showed that DEGs were mainly enriched in pathways such as Thiamine metabolism, apoptosis, signaling pathways regulating pluripotency of stem cells, cellular senescence and so on. Reactom analysis showed that DEGs were mainly enriched in response pathways such as EGR1,2,3 bind to the NAB2 promoter, EGR binds ARC gene, EGR-dependent NAB2 gene expression, etc.; DO analysis showed that differentially expressed genes were mainly enriched in diseases such as disease of cellular proliferation, disease of anatomical entity, organ system cancer, etc.; PPI analysis identified key differentially expressed genes, including DDIT3, CHAC1, TRIB3, and ASNS.
ConclusionBased on transcriptome sequencing and bioinformatics analysis, it was found that the Qizhu anti-cancer recipe may involve DEGs and signaling pathways in the treatment of colorectal cancer. Our study may provide potential drug targets for developing new treatment strategies for colorectal cancer.
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Anchored Chitosan-Functionalized Magnetite Nanoparticles for Crystal Violet Decolorization from Aqueous Samples
Authors: Mahsa Bandari, Mohsen Mohammadi Galangash, Shahab Shariati and Atefeh GhavidastAvailable online: 29 October 2024More LessIntroductionIn this research, 3-(triethoxysilyl)propyl isocyanate (TESPIC) functionalized chitosan was successfully synthesized to fabricate silica-coated magnetite nanoparticles (Fe3O4@SiO2-CS MNPs).
MethodThe synthesized MNPs were characterized using XRD, FT-IR, SEM, and TEM instruments and were utilized for the decolorization of Crystal Violet cationic dye (CV). The affecting variables controlling CV removal efficiency were investigated using the Taguchi fractional factorial design method (L16 array).
ResultUnder the optimized removal conditions (adsorbent amount = 0.12 g (4.8 g L-1), pH = 4, ionic strength = 0.05 mol L-1 NaCl, and 30 min stirring), 98.2% of the CV dye was eliminated. The kinetic and equilibrium adsorption isotherms were explained by the pseudo-second-order kinetic (R2 = 0.999) and Freundlich isotherm models, respectively. MATLAB’s fmincon function as an efficient solution was applied in order to compare the Redlich-Peterson three-parametric isotherm model with two-parametric models. Moreover, the Fe3O4@SiO2-CS-TESPIC MNPs showed recyclability and reusability for subsequent runs.
ConclusionThe findings confirmed that these functional MNPs can be considered as proper adsorbents for the removal of CV dye from the aqueous solutions.
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Exploring You-gui Pill for the Treatment of Diabetic Erectile Dysfunction: Data Mining Analysis, Network Pharmacology and Experiments In Vitro
Authors: Jiaqi Chen, Yanan Gao, Yanqiu Zhang, Yue Sun, Yue Jiang, Yong Yang and Mingxing WangAvailable online: 22 October 2024More LessIntroductionThe You-gui pill (YGP) is a classical compound used for treating anti-diabetic erectile dysfunction (DMED). However, the specific active ingredients responsible for its effects on DMED and their mechanisms remain unclear.
MethodsIn this paper, we used data mining techniques to analyze high-frequency herbs and herb combinations used in Chinese medicine for the treatment of DMED based on existing literature. Using network pharmacology to study the active components and mechanism of action of YGP against DMED, molecular docking was used to analyze the interactions of the active components with major structural proteins, nonstructural proteins, and mutants. Also, the therapeutic effect of YGP on hyperglycemic modelling and its underlying mechanisms were experimentally validated in CCEC cells by analyzing the expression of its relevant target mRNAs.
ResultsNetwork pharmacological analysis identified the three core components of YGP as quercetin, kaempferol, and β-sitosterol, and constructed a PPI network map of common targets of YGP and DMED, which included HIF-1α, ALB, Bcl-2, INS, IL-1β, IL-6, TNF-α, CASP3, and TP53. Combined with molecular docking results, these targets had a strong binding affinity between them and the active ingredient compounds, with the highest affinity for HIF-1α and TNF-α. During the in vitro cellular assay validation, the HIF-1α, ALB, Bcl-2, TNF-α, and IL-6 mRNA in CCECs cells showed positive regulation after YGP intervention.
ConclusionThe combination of “data mining - network pharmacology - molecular docking - experimental validation” provides a powerful methodological basis for the study of the main active components and mechanism of action of YGP against DMED, as well as the development and application of the drug.
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To Reveal the Potential Mechanism of Quercetin against NSCLC Based on Network Pharmacology and Experimental Validation
Available online: 21 October 2024More LessPurposeThis study aimed to initially clarify the potential mechanism of quercetin in the treatment of non-small cell lung cancer (NSCLC) based on network pharmacology, molecular docking and in vitro experiments.
MethodTCMSP, SwissTargetPrediction, TCMIP, STITCH, and ETCM databases were applied to obtain the targets of quercetin. NSCLC-related targets were retrieved from GeneCards, OMIM, PharmGKB, TTD, and NCBI databases. Their intersection targets were imported into the STRING database to construct a protein-protein interaction (PPI) network and core targets were identified through the Cytoscape 3.10.0 soft and the CytoHubba tool. Furthermore, Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on the intersection targets. A compound-targets-pathways network was subsequently constructed to screen for key targets and pathways. Molecular docking was performed with Discovery Studio software to verify the interactions between quercetin and core targets. In vitro validations were conducted employing CCK-8 assays, flow cytometry, and Western blotting (WB).
Results193 potential targets of quercetin for treating NSCLC were obtained. The top ten core targets identified within the PPI network included TP53, HSP90AA1, AKT1, JUN, SRC, EGFR, ACTB, TNF, MAPK1, and VEGFA. GO analysis yielded 2319 items, and KEGG analysis resulted in 211 enriched pathways. Molecular docking results demonstrated a high affinity of quercetin towards the core targets. Based on the compound-targets-pathways network and molecular docking, the PI3K/AKT/P53 pathway and its key-related proteins (PIK3R1, AKT1, and TP53) were selected for further validation. Quercetin(20 and 40 μg/mL) significantly decreased the viability of A549 NSCLC cells but not BEAS-2B normal cells via CCK-8 assays. Flow cytometry and WB analyses further corroborated that quercetin could promote apoptosis of A549 cells by downregulating and upregulating the expression of Bcl-2 and Bax (P<0.05), respectively. Notably, quercetin did not significantly alter the total protein levels of PI3K, AKT, and P53 but downregulated the phosphorylation levels of PI3K and AKT (P<0.05) and upregulated the phosphorylation level of P53 (P<0.05).
ConclusionQuercetin exhibits therapeutic potential in NSCLC by regulating the PI3K/AKT/P53 pathway to promote cell apoptosis.
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Wuzi-Yanzong-Wan Prevents the Defect of Cell-Cell Junctions between Sertoli-Germ Cells by Up-Regulating the Expression of TAp73
Authors: Li Li, Min Pan, Ziao Liu, Hongsu Zhao, Fengqing Xu, Xiaohui Tong, Yajuan Wang, Bin Chen, Lihua Yu and Tongsheng WangAvailable online: 15 October 2024More LessBackgroundThe TAp73 gene is an anti-cancer gene that also affects the junction between Sertoli and germ cells. Inhibition of this gene causes infertility in male mice. Our previous research proved that Wuzi-Yanzong-Wan (WZYZW) can protect spermatogenesis and maturation by preventing TAp73 inhibition.
ObjectiveThis study aimed to investigate the effect of drug-containing serum of WZYZW on the defect of cell-cell junctions in the Sertoli-germ cells co-culture system in vitro.
MethodsLC-HRMS was used to analyze the content of active ingredients in WZYZW-medicated serum. Then, primary extraction and co-culture of germ cells and Sertoli cells were carried out. Co-cultured cells were added with PFT-α to induce the TAp73 inhibition model, with WZYZW-medicated serum at 2.5%, 5%, and 10% treated in parallel. Sloughing of germ cells from Sertoli cells was calculated. Transmission electron microscopy (TEM), Immunofluorescence, qRT-PCR, and western blot methods were employed.
ResultsThe drug-containing serum of WZYZW contained schisandrin, hyperoside, geniposidic acid, ellagic acid, and quercetin. Using TEM assay, we observed restoration of the desmosome-like (Des), tight junctions (TJ), and basal ectoplasmic specialization (ES) structure following WZYZW treatment. WZYZW caused inhibition of peptidase and protease inhibitors (tissue inhibitor of metalloproteinase-1 (TIMP1), Serpina3n) by immunofluorescence analysis. Western blot and qRT-PCR analysis revealed that WZYZW was able to ameliorate the expressions of peptidase and protease inhibitors and cell adhesion factors, such as TAp73, TIMP1, Serpina3n, Desmocollin-3, N-cadherin, and Nectin-2.
ConclusionWZYZW-medicated serum could prevent the defect of cell-cell junctions between Sertoli-germ cells co-culture system in vitro by up-regulating the expression of TAp73.
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Label-Free Detection of Biomolecular Interactions Using BioLayer Interferometry for Kinetic Characterization
Authors: Joy Concepcion, Krista Witte, Charles Wartchow, Sae Choo, Danfeng Yao, Henrik Persson, Jing Wei, Pu Li, Bettina Heidecker, Weilei Ma, Ram Varma, Lian-She Zhao, Donald Perillat, Greg Carricato, Michael Recknor, Kevin Du, Huddee Ho, Tim Ellis, Juan Gamez, Michael Howes, Janette Phi-Wilson, Scott Lockard, Robert Zuk and Hong Tan
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