Active Target Research Articles

Network-Pharmacology-Based Study on Active Phytochemicals and Molecular Mechanism of Cnidii Fructus in Treating Colorectal Cancer.

Cnidii Fructus (CF) is known for its antibacterial, anti-inflammatory, and antitumor properties, as well as its activities against kidney deficiency and impotence. In this study, we aimed to explore the anti-CRC cancer effect and molecular mechanism of CF via network pharmacology and in vitro antitumor experiments. Network pharmacology was used to investigate the anti-CRC mechanism of CF. First, a series of databases was used to screen the active phytochemical targets and anti-CRC core targets. Then, the GO and KEGG pathways were analyzed to predict possible mechanisms. Molecular docking analysis explore core targets-phytochemicals interactions. In vitro antitumor experiments were carried on verifying anti-CRC mechanism of CF. In this study, 20 active ingredient targets and 50 intersecting targets were analyzed by Cytoscape software 3.9.1 to obtain the core genes and phytochemicals. Then, the GO and KEGG pathways of 50 intersecting targets were analyzed to predict possible mechanisms. The results from GO and KEGG indicated that CF has significant antitumor efficacy, which involves many signaling pathways, such as PI3K/AKT and p53. The five core targets and five core phytochemicals were screened for molecular docking to show protein-ligand interactions. According to the results of molecular docking, the compound O-acetylcolumbianetin was selected for the anti- CRC functional verification in vitro. MTT assay showed that O-acetylcolumbianetin significantly inhibited the proliferation of colorectal HCT116 cells in a time- and quantity-dependent manner. O-acetylcolumbianetin can promote the expression of CASP3 protein, induce HCT116 cells apoptosis, thus exert anti-CRC effect. This study preliminarily verified the anti-CRC effect and molecular mechanism of CF and provided a reference for Traditional Chinese Medicine anti-tumor subsequent research.

Damage features and mechanism of prestressed hollow square piles subjected to non-contact underwater explosion

Critical hydraulic structures are increasingly vulnerable to underwater explosion attacks, with the supporting piles being prime targets for terrorist activities. This study investigates the damage effects and mechanisms of prestressed concrete hollow square (PCHS) piles under non-contact underwater explosions. A series of underwater explosion experiments was conducted on four PCHS piles. The dynamic response of PCHS piles throughout the underwater explosion process was simulated using a coupled fluid-solid numerical model. The mechanisms of dynamic damage to the PCHS piles were elucidated through an integrated analysis of both experimental and numerical results. The research indicates that the damage characteristics of PCHS piles include longitudinal and oblique cracks on the lateral surfaces, transverse cracks on the rear side, and localized fragmentation of concrete. Three primary damage modes have been identified: bending failure(L¯c= 0.59 m/kg1/3), combined bending-shear failure(L¯c= 0.36 m/kg1/3), and punching failure(L¯c= 0.24 m/kg1/3). The local and global responses induced by shock waves are the primary causes of structural damage. Furthermore, as the stand-off distance decreases, the impact of explosive bubbles increases the magnitude of the overall response. A comparative analysis also examined the impact of prestress and axial load on the damage behavior of hollow square piles.

Network Pharmacology and Molecular Docking Analysis on Mechanisms of Scutellariae Radix in the Treatment of Cerebral Ischemia-reperfusion Injury.

Multiple brain disorders are treated by Scutellaria Radix (SR), including cerebral ischemia-reperfusion (CI/R). However, more studies are needed to clarify the molecular mechanism of SR for CI/R. The active substances and potential targets of SR and CI/R-related genes were obtained through public databases. Overlapping targets of SR and CI/R were analyzed using proteinprotein interaction (PPI) networks. GO and KEGG enrichment analyses were performed to predict the pathways of SR against CI/R, and the key components and targets were screened for molecular docking. The results of network pharmacology analysis were verified using in vitro experiments. 15 components and 64 overlapping targets related to SR and CI/R were obtained. The top targets were AKT1, IL-6, CAS3, TNF, and TP53. These targets have been studied by GO and KEGG to be connected to a number of signaling pathways, including MAPK, PI3K-Akt pathway, and apoptosis. Molecular docking and cell experiments helped to further substantiate the network pharmacology results. The active compound of SR was able to significantly decrease the apoptosis of HT- 22 cells induced by OGD/R. This finding suggests that SR is a potentially effective treatment for CI/R by modulating the MAPK and PI3K-Akt pathways.

Evaluation of the Mechanism of Yishan Formula in Treating Breast Cancer Based on Network Pharmacology and Experimental Verification.

Yishan formula (YSF) has a significant effect on the treatment of breast cancer, which can improve the quality of life and prolong the survival of patients with breast cancer; however, its mechanism of action is unknown. In this study, network pharmacology and molecular docking methods have been used to explore the potential pharmacological effects of the YSF, and the predicted targets have been validated by in vitro experiments. Active components and targets of the YSF were obtained from the TCMSP and Swiss target prediction website. Four databases, namely GeneCards, OMIM, TTD, and DisGeNET, were used to search for disease targets. The Cytoscape v3.9.0 software was utilized to draw the network of drug-component-target and selected core targets. DAVID database was used to analyze the biological functions and pathways of key targets. Finally, molecular docking and in vitro experiments have been used to verify the hub genes. Through data collection from the database, 157 active components and 618 genes implicated in breast cancer were obtained and treated using the YSF. After screening, the main active components (kaempferol, quercetin, isorhamnetin, dinatin, luteolin, and tamarixetin) and key genes (AKT1, TP53, TNF, IL6, EGFR, SRC, VEGFA, STAT3, MAPK3, and JUN) were obtained. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that the YSF could affect the progression of breast cancer by regulating biological processes, such as signal transduction, cell proliferation and apoptosis, protein phosphorylation, as well as PI3K-Akt, Rap1, MAPK, FOXO, HIF-1, and other related signaling pathways. Molecular docking suggested that IL6 with isorhamnetin, MAPK3 with kaempferol, and EGFR with luteolin have strong binding energy. The experiment further verified that YSF can control the development of breast cancer by inhibiting the expression of the hub genes. This study showed that resistance to breast cancer may be achieved by the synergy of multiple active components, target genes, and signal pathways, which can provide new avenues for breast cancer-targeted therapy.

Combining single-cell RNA sequencing and network pharmacology to explore the target of cangfu daotan decoction in the treatment of obese polycystic ovary syndrome from an immune perspective

BackgroundPolycystic ovary syndrome (PCOS) is a heterogeneous gynecological endocrine disorder linked to immunity. Cangfu Daotan Decoction (CFDT), a classic Chinese medicine prescription, is particularly effective in treating PCOS, specifically in patients with obesity; however, its specific mechanism remains unclear.MethodsPart 1: Peripheral blood mononuclear cells were collected on egg retrieval day from obese and normal-weight patients with PCOS and healthy women undergoing in vitro fertilization (IVF)-embryo transfer. Next, scRNA-seq was performed to screen the key genes of bese patients with PCOS. Part 2: Active ingredients of CFDT and obesity-related PCOS targets were identified based on public databases, and the binding ability between the active ingredients and targets was analyzed. Part 3: This part was a monocentric, randomized controlled trial. The obese women with PCOS were randomized to CFDT (6 packets/day) or placebo, and the healthy women were included in the blank control group (43 cases per group). The clinical manifestations and laboratory outcomes among the three groups were compared.ResultsBased on the scRNA-seq data from Part 1, CYLD, ARPC3, CXCR4, RORA, JUN, FGL2, ZEB2, GNLY, FTL, SMAD3, IL7R, KIR2DL1, CTSD, BTG2, CCL5, HLA, RETN, CTSZ, and NCF2 were potential key genes associated with obese PCOS were identified. The proportions of T, B, and natural killer cells were higher in patients with PCOS compared to healthy women, with even higher proportions observed in obese patients with PCOS. Gene ontology and the Kyoto encyclopedia of genes and genomes analysis depicted that the differentially expressed genes were related to immune regulation pathways. Network pharmacology analysis identified that the key active components in CFDT were quercetin, carvacrol, β-sitosterol, cholesterol, and nobiletin, and TP53, AKT1, STAT3, JUN, SRC, etc. were the core targets. The core targets and their enrichment pathways overlapped with those in Part 1. Clinical trials in Part 3 found that CFDT reduced the dosage of gonadotropins use in patients with PCOS, increased the number of high-quality embryos, and improved the ongoing pregnancy rate.ConclusionCFDT can improve the immune microenvironment of patients to some extent, reduce their economic burden, and enhance IVF outcomes. The improvement in the immune microenvironment in obese patients with PCOS may be linked to targets such as JUN and AKT.

Traditional Chinese Herbal Formula, Fuzi-Lizhong Pill, Produces Antidepressant-like Effects in Chronic Restraint Stress Mice through Systemic Pharmacology.

Fuzi-Lizhong Pill (FLP) is a well-validated traditional Chinese medicine (TCM) formula that has long been used in China for gastrointestinal disease and adjunctive therapy for depression. In our previous study, we reported that the principal herb of FLP, Aconitum carmichaelii Debx. (Fuzi), exhibits antidepressant-like effects. However, there have been no reports on whether FLP produces antidepressant-like effects and its potential molecular mechanisms. We aim to demonstrate the antidepressant-like effects of FLP in chronic restraint stress (CRS) mice and to explore the associated molecular mechanisms. The active components and probable molecular targets of FLP, as well as the targets related to depression, were identified through network pharmacology. A protein-protein interaction (PPI) network was generated using the overlapping targets, followed by the visualization as well as identification of the core targets associated with the antidepressant-like action of FLP. Subsequently, KEGG and GO enrichment analyses were conducted. UHPLC-MS/MS was employed to further detect the active compounds in FLP. Molecular docking was applied to assess the connections between the active components as well as the core targets. The efficacy of FLP in treating depression and its molecular mechanisms were examined using western blotting, ELISA, 16S rRNA sequencing, HE staining, Nissl staining, and Golgi-Cox staining in a CRS-induced mouse model. Network pharmacology and UHPLC-MS/MS analyses indicated that the active compounds of FLP comprised taraxerol, songorine, neokadsuranic acid B, ginkgetin, hispaglabridin B, quercetin, benzoylmesaconine and liquiritin. KEGG pathway analysis implicated that the PI3K/Akt/mTOR as well as MAPK signaling pathways are closely related to the therapeutic effects of FLP on depression. Molecular docking analysis demonstrated that the main components of FLP bind to PI3K, AKT, mTOR, BDNF and MAPK. FLP significantly decreased immobility in mice that were elevated by CRS in the FST and the TST. FLP also significantly increased sucrose preference in mice after CRS in the SPT. FLP upregulated proteins associated with BDNF-TrkB and PI3K/Akt/mTOR signaling and downregulated proteins associated with MAPK signaling. Serum levels of CORT, IL-6, IL-1β, and TNF-α in CRS mice were significantly decreased following treatment with FLP. In addition, FLP ameliorated CRS-induced gut microbiota dysbiosis as demonstrated by 16S rRNA sequencing analysis. FLP ameliorated CRS-induced intestinal inflammation and neuronal damage. Finally, antidepressant-like effects and concomitant increases in dendritic spine density induced by FLP administration were also reduced after rapamycin treatment. These results demonstrate that FLP has antidepressant-like effects in mice exposed to CRS that involve activation of the PI3K/Akt/mTOR signaling pathway, increase in spinogenesis, inhibition of the MAPK signaling pathway, decrease in inflammation, and amelioration of gut microbiota dysbiosis. These findings provide novel evidence for the clinical application of FLP on depression.

A Network Pharmacological Study of Qianjin Sanhuang Decoction in the Treatment of Osteoarthritic Knee Disease

Objective: To predict the action targets of Qianjin Sanhuang decoction in the treatment of knee osteoarthritis through network pharmacology, to explore its potential multi component, multi target, multi, pathway mechanism of action, and to elaborate the relationship between the pharmacological effects of the drug and the disease from the perspective of molecular mechanism. Methods: The Chinese herbal composition of Qianjin Sanhuang decoction was determined by reading ancient texts and reviewing data, and the chemical components of Qianjin Sanhuang decoction were collected through the Traditional Chinese Medicine Systematic Pharmacology Database and Analysis Platform (TCMSP), and the active ingredients of the drug were obtained after oral utilization (OB) and drug-like properties (DL) screening, and the active ingredient target prediction was performed, while the active ingredient targets were retrieved from GeneCards, OMIM, and DisGeNet database to retrieve knee osteoarthritis-related targets. After taking the intersecting targets, a software called cytoscape 3.9.0 was used for mapping, with the goal of constructing a component-target network map, followed by a string database for mapping, with the goal of making a network map of target protein-target protein interactions, and finally, a gene ontology (GO) enrichment analysis and a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, this analysis process was performed in the metascape database. Results: A total of 1272 targets related to osteoarthritis of the knee were collected in this study, 89 active ingredients of Qianjin Sanhuang decoction, involving 267 targets, and 121 therapeutic targets involving osteoarthritis of the knee, and the results of GO enrichment analysis showed that it involved the response to inorganic substances, positive regulation of cell migration, response to oxygen content, response to lipopolysaccharide, response to peptides, regulation of cell adhesion, response to extracellular stimuli, negative regulation of cell differentiation, positive regulation of cell death, glandular development, regulation of apoptotic signaling pathways, development of reproductive structures, response to trauma, response to growth factors, regulation of inflammatory response, cellular response to organic recycling compounds, regulation of proteolysis, etc. After KEGG analysis, the results showed that signaling pathways such as AGE-RAGE pathway and HIF-1 pathway were involved. Conclusion: Qianjin Sanhuang decoction can improve the inflammatory response of knee osteoarthritis through potential multi-pathways, multi-targets and multi-pathways, and can have potential therapeutic effects on osteoarthritis.

An operational risk assessment method for petrochemical plants based on deep learning

The petrochemical industry is an important guarantee for the development of people’s lives, and the operational risk assessment method of personnel in the operation of petrochemical enterprises is the most important. Based on a deep learning algorithm, a new method based on the micro-Doppler effect and fuzzy analytic hierarchy process is proposed to evaluate the operational risk of personnel in petrochemical enterprises. The original monitoring image of petrochemical equipment is invoked, and micro-Doppler analysis is performed based on the original image to identify the activity target of the personnel on the job site and generate the activity map of the petrochemical plant operators. Based on the analysis data of the micro-Doppler effect, the fuzzy function and hierarchical analysis method are combined. The fuzzy theory is introduced into the analytic hierarchy process, and the inherent expert evaluation scores are transformed into fuzzy numbers. It makes the expert evaluation of petrochemical plants more accurate in the subsequent coupling and improves the objectivity of the traditional analytic hierarchy process. The scheme proposed in this paper can monitor real-time operation safety and provide a guarantee for the personal safety of field operators. This method plays an important role in improving the safety of petrochemical plants.

Device-measured vigorous intermittent lifestyle physical activity (VILPA) and major adverse cardiovascular events: evidence of sex differences.

Vigorous intermittent lifestyle physical activity (VILPA) refers to brief bouts of intense physical activity embedded into daily life. To examine sex differences in the dose-response association of VILPA with major adverse cardiovascular events (MACE) and its subtypes. Using multivariable-adjusted cubic splines, we examined the associations of daily VILPA duration with overall MACE and its subtypes (incident myocardial infarction, heart failure and stroke) among non-exercisers (individuals self-reporting no leisure-time exercise and no more than one recreational walk per week) in the UK Biobank. We also undertook analogous analyses for vigorous physical activity among exercisers (individuals self-reporting participation in leisure-time exercise and/or recreational walking more than once a week). Among 13 018 women and 9350 men, there were 331 and 488 all MACE, respectively, over a 7.9-year follow-up. In women, daily VILPA duration exhibited a near-linear dose-response association with all MACE, myocardial infarction and heart failure. In men, dose-reponse curves were less clear with less evidence of statistical signifigance. Compared with women with no VILPA, women's median daily VILPA duration of 3.4 min was associated with hazard ratios (HRs; 95% confidence intervals) of 0.55 (0.41 to 0.75) for all MACE and 0.33 (0.18 to 0.59) for heart failure. Women's minimum doses of 1.2-1.6 min of VILPA per day were associated with HRs of 0.70 (0.58 to 0.86) for all MACE, 0.67 (0.50 to 0.91) for myocardial infarction, and 0.60 (0.45 to 0.81) for heart failure. The equivalent analyses in UK Biobank's accelerometry sub-study exercisers suggested no appreciable sex differences in dose-response. Among non-exercising women, small amounts of VILPA were associated with a substantially lower risk of all MACE, myocardial infarction and heart failure. VILPA may be a promising physical activity target for cardiovascular disease prevention, particularly in women unable or not willing to engage in formal exercise.

Integrating network pharmacology, molecular docking, and experimental validation to reveal the mechanism of Radix Rehmanniae in psoriasis.

Radix Rehmanniae (RR) plays an important role in treating psoriasis. However, the active compounds of RR and potential mechanisms are unclear. The current study was designed to investigate the potential active ingredients, targets, and mechanisms of RR in treating psoriasis through network pharmacology, molecular docking, and vitro experiments. Initially, the TCMSP database and literature retrieval were used to access the active ingredients of RR. The psoriasis target proteins were obtained from Therapeutic Target Database, OMIM, GeneCards, and DrugBank databases. The target proteins were then converted into target genes using Uniprot. Secondly, overlapping genes were obtained through Venn online tool. Then, protein-protein interactions network diagram is finished by STRING database. Next, Cytoscape software was used to acquire the top 10 hub proteins; gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis were then used to predict possible mechanisms. Afterwards, molecular docking validation of the active ingredients with the main targets was performed by AutoDock software. Finally, lipopolysaccharides induced RAW264.7, to assess the effects and molecular mechanisms by MTT, RT-qPCR, and Western blot assays. Overall, there are 20 effective compounds and 33 targets involved in biological processes including apoptosis, intracellular signaling, vasodilation, and mitogen-activated protein kinase (MAPK) signaling cascade. The docking results showed strong binding capacity between the active ingredients and targets. We verified aucubin as the key active ingredient, tumor necrosis factor α, and IL6 as the core targets, and focused on the p38MAPK protein pathway. Cellular experiments showed that aucubin down-regulated the phosphorylated p38MAP protein and reduced the expression of tumor necrosis factor α mRNA, IL6 mRNA, and IL1βmRNA. In summary, RR is featured with multicomponent, multi-target, and multi-pathway in treating psoriasis; the preliminary mechanism may be associated with the down-regulation of p38MAPK phosphorylation and curbing the expression of inflammatory factor by aucubin. This paper provides the scientific basis for Traditional Chinese medicine treating psoriasis.

Virus-mimicking nanodrug active crossing of the blood-brain barrier via transcytosis against central nervous system leukemia

The poor central nervous system leukemia (CNSL) clinical efficacy of conventional doses of chemotherapy is mainly attributed to the limited permeability of chemotherapy agents caused by the blood-brain barrier (BBB). Effectively enhancing the accumulation of drugs across the BBB in the central nervous system is one of the key challenges in improving patient compliance and clinical efficacy of CNSL. Here, we find that the VP1 protein, the functional module of the John Cunningham (JC) virus, can safely penetrate the BBB through a sialic acid receptor-mediated transcytosis mechanism. Based on this, we develop a JC virus-mimicking nanodrug delivery platform based on VP1 protein-conjugated self-assembled nanoparticles (MFHV), which can active target and cross the BBB via a receptor-mediated transcytosis for safe and effective low-dose chemotherapy against CNSL after systemic administration. The results demonstrate that such a platform can penetrate the BBB through the dual mechanism of clathrin-mediated endocytosis and micropinocytosis pathway. When further synergistic with ferroptosis and histamine metabolism, the long-term survivors of low-dose MTX are significantly enhanced by 83.3 % and 56.7 % in two CNSL mice models. Collectively, this study takes a new perspective on natural living materials and molecule targeting of the BBB to present a promising strategy for low-dose chemotherapy against CNSL with safety and efficacy, which might provide a clinically translatable option for the prevention and treatment of CNSL.

Mechanism of Gastrodin against neurotoxicity based on network pharmacology, molecular docking and experimental verification

BackgroundDisorders of glutamate metabolism and excessive release participat in multiple neuronal pathologies including ischemic stroke (IS), Alzheimer's disease (AD), or Parkinson's disease (PD). Recently, herbal medicines have been widely used and have shown satisfactory results in the treatment of neurological disorders. Gastrodin is a traditional Chinese medicine (TCM) used for the treatment of nerve injuries, spinal cord injuries, and some central nervous system diseases as well. This research examines the neuroprotective effects of Gastrodin against glutamate-induced neurotoxicity in neuronal cells. MethodsThe HERB database was used to explore the active ingredients and target genes of Gastrodia Elata. The STRING database and Cytoscape software were used to screen and construct the Protein-Protein Interaction (PPI). Furthermore, we used molecular docking to predict the potential targets of Gastrodin. The effects of Gastrodin were revealed by western blot, calcium imaging, membrane clamp, CCK8 and flow cytometry. Neuronal oxidative stress and damage were assessed by measuring malondialdehyde (MDA) levels and superoxide dismutase (SOD) activity. Neuronal morphology was examined using Golgi-Cox staining. Finally, animal behavior was examined using novel object recognition and fear conditioning tests. ResultsWe have obtained 22 components such as TM10, TM17, TM25 (Gastrodin), and 281 targets such as AKT, EGFR, and CDK1 through network pharmacology. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed these genes were significantly enriched in protein phosphorylation, protein serine/threonine/tyrosine kinase activity, apoptosis and HIF-1 signaling pathways, etc. A higher affinity between Gastrodin and AKT was revealed by PPI analysis and molecular docking. Further, Gastrodin significantly inhibited Ca2+ influxes and excitatory synaptic transmission in cortical neurons. In addition, Gastrodin effectively alleviated neuron apoptosis, oxidative stress and damage. ConclusionGastrodin has neuroprotective effects against glutamate-induced neurotoxicity.

Study on the anti-atherosclerosis mechanisms of Tanyu Tongzhi formula based on network pharmacology, Mendelian randomization, and experimental verification

Context Tanyu Tongzhi Formula (TTF) exhibits potential against atherosclerosis; however, its mechanisms remain unclear. Objective This study explores the pharmacological mechanisms of TTF in treating atherosclerosis. Materials and methods Network pharmacology, molecular docking, mendelian randomization (MR), and liquid chromatography-mass spectrometry (LC-MS) analyses were utilized to reveal potential targets and compounds of TTF against atherosclerosis. After exploring the appropriate concentration of TTF to treat HCAECs using Cell Counting Kit-8 (CCK-8), the HCAECs were divided into three groups: control, oxidized low-density lipoprotein (ox-LDL, 50 μg/mL), and ox-LDL (50 μg/mL) + TTF (1 mg/mL). After 24-h incubation, the efficacy of TTF was verified by CCK-8, Oil red O staining, and ELISA. The expression of key targets was detected by real-time polymerase chain reaction (qPCR) and western blotting. Results A total of 137 active compounds and 127 potential TTF targets against atherosclerosis were identified. MR identified ALB, TNF, PPARα, and PPARγ as key targets. Molecular docking indicated that baicalin, naringenin, and curcumin exhibited suitable binding activities to these targets, further confirming by LC-MS analysis. The IC50 of TTF in HCAECs was 18.25 mg/mL. TTF treatment significantly improved atherosclerosis by enhancing cell viability, reducing lipid accumulation, and inhibiting inflammation factors (IL6, IL1B and TNF-α) in ox-LDL-treated HCAECs. Moreover, qPCR or western blotting indicated that TTF could up-regulate PPARα and PPARγ while down-regulate TNF expression. Discussion and conclusions Our results revealed active compounds, key pathways, and core targets of TTF against atherosclerosis, providing experimental support for its application in treating of atherosclerosis.

Application of Network Pharmacology, Molecular Docking, and In Vitro Experimental Evaluation to Decipher the Anti-Inflammatory Mechanisms of Cirsium japonicum

Cirsium japonicum, a traditional herb, exhibits significant anti-inflammatory activity. However, the main components and potential mechanisms of C. japonicum remain unclear. The aim of this study is to investigate the anti-inflammatory mechanism of Cirsium japonicum through network pharmacology and cellular experiments. The effective components of and potential targets for the anti-inflammatory activity of C. japonicum were identified using a traditional Chinese medicine systematic pharmacology database, the TCMSP analysis platform, and the GeneCards database. The drug–component–target–disease network diagram was constructed using Cytoscape 3.8.0 software, while the protein interaction network diagram was created using the STRING database and Cytoscape 3.8.0 software. Gene ontology (GO) enrichment and KEGG pathway enrichment analysis were carried out using the DAVID database. Molecular docking between key targets and active components was constructed with AutoDock 4.2.6 software to determine the best binding target. The results revealed that 14 active components of C. japonicum targeted 171 anti-inflammatory proteins. GO function enrichment analysis yielded 173 items, while KEGG pathway enrichment analysis identified 48 signaling pathways related to inflammation regulation. Molecular docking showed a strong affinity of sitosterol, stigmasterol, and other components with key targets such as peroxisome proliferator-activated receptor α recombinant protein (PPARA) and cyclooxygenase-2 (PTGS2). Vanillin, one active ingredient of C. japonicum, inhibited the release of lipopolysaccharide (LPS)-induced inflammatory factors in RAW264.7 cells. These findings suggest that C. japonicum may exert its anti-inflammatory effects by modulating the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) signal pathway (PI3K-Akt) and apoptin signal pathway, highlighting the multi-component, multi-target, and multi-channel molecular mechanism underlying its anti-inflammatory properties. Finally, the anti-inflammatory effect of vanillin, an effective component of C. japonicum, was verified by cell experiments. This study provides a new understanding of the pharmacological mechanisms of C. japonicum in the treatment of inflammatory conditions.

Exploring the material basis and molecular targets of Changma Xifeng tablet in treating Tourette syndrome: an integrative approach of network pharmacology and miRNA analysis.

This study was to investigate the mechanism of Changma Xifeng tablet, a traditional Chinese medicine in the treatment of Tourette syndrome. Network pharmacology was utilized to pinpoint blood-entering constituents of Changma Xifeng and explore their potential targets. Additionally, differential microRNA expression analysis was conducted to predict Tourette syndrome-associated targets, complemented by molecular docking and dynamics simulations to support the interactions of the active compounds with these targets. The study identified 98 common targets between Changma Xifeng and Tourette syndrome, which may be involved in the treatment process. A protein-protein interaction network and a drug-active ingredient-disease target network highlighted the formulation's multi-component, multi-target therapeutic approach. Eight pivotal targets-AR, GRM5, MET, RORA, HTR2A, CNR1, PDE4B, and TOP1-were identified at the intersection of microRNA and drug targets. Molecular docking revealed 12 complexes with favorable binding energies below - 7kcal/mol, specifically: AR with Alfacalcidol, TOP1 with Albiflorin, GRM5 with Arachidic Acid, GRM5 with Palmitic Acid, AR with Arachidic Acid, AR with 2-Hydroxyoctadecanoic Acid, RORA with Pinellic Acid, RORA with Palmitic Acid, AR with Acoronene, AR with Epiacoronene, AR with 4,4'-Methylenediphenol, and HTR2A with Calycosin. Our molecular docking and molecular dynamics simulations suggest potential stable interactions between the formulation's active components and target proteins. These computational methods provide a preliminary theoretical framework that will guide our future experimental work. The study provides a scientific rationale for the use of traditional Chinese medicine in Tourette syndrome management and offers new insights for drug development.

Anti-inflammatory Activities and Mechanisms of New Compounds Isolated from the Fruits of Foeniculum vulgare Mill.

Forty-nine compounds, including six previously unknown together with forty-three known ones, were isolated from the fruits of Foeniculum vulgare Mill. Their structures were elucidated using high-resolution electrospray ionization mass spectrometry (HR-ESI-MS), infrared spectroscopy (IR), ultraviolet-visible spectroscopy (UV), nuclear magnetic resonance (NMR), and electronic circular dichroism (ECD) methods. All isolates were evaluated their anti-inflammatory activity. The results indicated that compounds 1, 6, 35 and 45 inhibit lipopolysaccharide(LPS)-induced nitric oxide production in RAW 264.7 macrophages with IC50 values of 17.13 ± 0.74, 14.40 ± 0.54, 112.13 ± 2.08 and 77.02 ± 3.62 μg/mL, respectively. Moreover, the potential targets of the four active ingredients were explored through network pharmacology, revealing that SRC, TP53, AKT1, and PIK3CA may serve as key anti-inflammatory targets. To confirm the potential binding mode, molecular docking was employed, which demonstrated that all active targets except SRC exhibited favorable binding energy with compound 35. Additionally, the anti-inflammatory activities of compounds 1-6 were first observed in this experiment.

Prediction of potential conflicts between active targets in airport flight zones based on LSTM

Aiming at the problem of constant conflicts in airport flight zones, a method based on LSTM to predict potential conflicts of active targets in airport flight zones is proposed. Firstly, based on the complex network theory, two types of active targets, aircraft and vehicles, are taken as the research objects, and the flight zone active target network is established. The network dynamic evolution model is set up, and the operation data is input to calculate multiple network characteristic indicators. The principal component analysis of the indicator time series is performed to fit the potential conflict index; then, the Keras framework is used to build a long short-term memory neural network (LSTM) model, and the indicator time series is input into LSTM for training and prediction, and compared with other prediction methods; finally, the actual operation data of Xi'an Xianyang Airport is used for experiments, and the predicted values are compared with the true values. The mean square errors of the prediction results of each indicator are respectively 1.61%、13.13%、0.72%、0.004%、0.014%; The research shows that by establishing the flight zone active target network model, the network characteristic indicators can be used to characterize potential conflicts from different angles; LSTM can effectively predict the potential conflicts of the flight zone active target network, remind relevant personnel to pay attention to preventing conflicts and reducing the probability of conflicts.

Integrating network pharmacology and experimental verification to explore the pharmacological mechanisms of Guanxin Shutong capsule in treating heart failure.

The Guanxin Shutong capsule (GXST), a traditional Chinese medicine, is commonly used for treating cardiovascular disease, it has shown efficacy in improving symptoms and enhancing the quality of life for patients with heart failure (HF). However, the specific mechanism of action of GXST in HF remains unclear. In this study, we employed a comprehensive approach combining network pharmacology, molecular dynamics (MD) simulations, and in vitro validations to investigate the potential targets and molecular mechanisms of GXST against HF. We collected active ingredients and target genes of GXST, as well as related genes of HF, from multiple public databases. Using bioinformatics analysis, we constructed networks of ingredients-disease-targets and performed functional annotations of the core targets. MD simulations were conducted to verify the binding between the core protein-ligand complexes. In vitro evaluations, including cell proliferation, apoptosis, and protein expression in human umbilical vein endothelial cells (HUVECs) and H9C2 cells were treated with GXST, were performed for pharmacodynamics evaluation. Network analysis revealed 320 intersection genes and 74 active ingredients in the Herbs-ingredients-target genes-disease network. We identified key active ingredients and target genes that overlapped. The KEGG pathways of the intersection genes were primarily enriched in the PI3K-Akt signaling pathway and apoptosis. The protein-protein interaction network highlighted proteins such as AKT1, VEGFR2, and eNOS. MD simulations confirmed stable docking and lower binding energy between 4 identified ingredients (kaempferol, quercetin, (2R)-5,7-dihydroxy-2-(4-hydroxyphenyl) chroman-4-one, and ellagic acid) and their respective core proteins (VEGFR2, eNOS, and AKT). In vitro experiments demonstrated the protective effects of GXST against H2O2-induced apoptosis in both HUVECs and H9C2 cells. Notably, consistent with the in silico predictions, GXST effectively activates the VEGFR2/AKT/eNOS signaling pathways in HUVECs. This study provides insights into the underlying mechanism of GXST's therapeutic effects in heart failure. The involvement of the VEGFR2/AKT/eNOS signaling pathways suggests their importance in further elucidating and applying GXST in the clinical treatment of heart failure.

Modulation of heteromeric glycine receptor function through high concentration clustering.

Ion channels are targeted by many drugs for treating neurological, musculoskeletal, renal and other diseases. These drugs bind to and alter the function of individual channels to achieve desired therapeutic effects. However, many ion channels function in high concentration clusters in their native environment. It is unclear if and how clustering modulates ion channel function. Human heteromeric glycine receptors (GlyRs) are the major inhibitory neurotransmitter receptors in the spinal cord and are active targets for developing chronic pain medications. We show that the α2β heteromeric GlyR assembles with the master postsynaptic scaffolding gephyrin (GPHN) into micron-sized clustered at the plasma membrane after heterologous expression. The inhibitory trans- synaptic adhesion protein neuroligin-2 (NL2) further increases both the cluster sizes and GlyR concentration. The apparent glycine affinity increases monotonically as a function of GlyR concentration but not with cluster size. We also show that ligand re-binding to adjacent GlyRs alters kinetics but not chemical equilibrium. A positively charged N- terminus sequence of the GlyR β subunit was further identified essential for glycine affinity modulation through clustering. Taken together, we propose a mechanism where clustering enhances local electrostatic potential, which in turn concentrates ions and ligands, modulating the function of GlyR. This mechanism is likely universal across ion channel clusters found ubiquitously in biology and provides new perspectives in possible pharmaceutical development.

Exploring the mechanism of Danggui Sini Decoction in the treatment of myocardial infarction: A systematic review, network pharmacology, and molecular docking.

Myocardial infarction (MI) is one of the leading causes of death worldwide because of its high morbidity and mortality. Traditional Chinese Medicine compounds play a crucial role in preventing cardiovascular diseases. Danggui Sini Decoction (DSD) is widely used clinically for cardiovascular diseases. However, the mechanism, main components, and main targets of DSD in treating MI are still unclear. In this study, we utilized network pharmacology and molecular docking for exploration. MI-related genes were examined using the Genecards database, and the active ingredients of DSD were screened based on System Pharmacology Database and Analysis Platform of Traditional Chinese Medicine by oral bioavailability ≥ 30% and drug-likeness ≥ 0.18. The protein-protein interaction network diagram was generated using the STRING database. The DAVID web platform was used to carry out gene ontology and Kyoto encyclopedia of gene and genome signaling pathway analysis. DSD's screening study revealed 120 primary active ingredients and 561 putative active target genes. The main therapeutic targets were TP53, EGFR, AKT1, IL6, TNF, STAT3, IL1B, CTNNB1, SRC, MYC, JUN, and INS. Gene ontology and Kyoto encyclopedia of gene and genome analyses revealed that DSD treatment of MI mainly involves the positive regulation of the ERK1 and ERK2 cascades, positive regulation of cell proliferation, inflammatory responses, aging, and the MAPK cascade, along with other biological processes. The molecular docking results indicate that DSD drugs may interact with AKT1, EGFR, TP53, and TNF through formononetin, isorhamnetin, β-Sitosterol, and kaempferol, potentially contributing to the treatment of MI. By utilizing a multi-component, multi-pathway, and multi-target mode of action, DSD may have the potential to prevent MI.