Network-based Approaches in Pharmacology

In Silico-Based Identification of Natural Inhibitors from Traditionally Used Medicinal Plants that can Inhibit Dengue Infection

Dengue fever (DF) is an endemic disease that has become a public health concern around the globe. The NS3 protease-helicase enzyme is an important target for the development of antiviral drugs against DENV (dengue virus) due to its impact on viral replication. Inhibition of the activity of the NS3 protease-helicase enzyme complex significantly inhibits the infection associated with DENV. Unfortunately, there are no scientifically approved antiviral drugs for its prevention. However, this study has been developed to find natural bioactive molecules that can block the activity of the NS3 protease-helicase enzyme complex associated with DENV infection through molecular docking, MM-GBSA (molecular mechanics-generalized born surface area), and molecular dynamics (MD) simulations. Three hundred forty-two (342) compounds selected from twenty traditional medicinal plants were retrieved and screened against the NS3 protease-helicase protein by molecular docking and MM-GBSA studies, where the top six phytochemicals have been identified based on binding affinities. The six compounds were then subjected to pharmacokinetics and toxicity analysis, and we conducted molecular dynamics simulations on three protein-ligand complexes to validate their stability. Through computational analysis, this study revealed the potential of the two selected natural bioactive inhibitors (CID-440015 and CID-7424) as novel anti-dengue agents.

Network-based pharmacological and experimentally validated study on the therapeutic effects and mechanisms of Polygonatum Rhizoma Ginseng Formula in immunocompromised mice

ETHNOPHARMACOLOGICAL RELEVANCE

Polygonatum Rhizoma Ginseng Formula (HJRS) is a traditional Chinese medicine preparation commonly used to enhance immunity. Traditionally, it is believed to "moisten dryness and nourish yin, tonify the spleen, and benefit qi." However, a systematic evaluation of its efficacy and mechanism of action is still lacking.

AIM OF THE STUDY

To explore the pharmacodynamic effects and underlying mechanisms of HJRS in cyclophosphamide (CTX)-induced immunocompromised model mice.

METHOD

To explore the immunomodulatory effects of HJRS, we used cyberpharmacology combined with in vivo experiments. An immunocompromised mouse model was established using CTX, and different doses of HJRS were administered by gavage during the modeling period. The efficacy of HJRS was evaluated by assessing immune-related parameters, including body weight, heat pain threshold, and behavioral activity. Biochemical markers (acid phosphatase, total nitric oxide synthase, and lactate dehydrogenase), immune function indicators (C3, C4, secretory immunoglobulin A [sIgA]), and immune organ indices (spleen and thymus coefficients) were measured. Additionally, intestinal mucosal immunity (Peyer's patches, sIgA, and IgM), cellular immunity (delayed-type hypersensitivity [DTH]), and humoral immunity (serum hemolysin, hemolysin, and IgM) were analyzed in the model mice. To further investigate the underlying mechanisms, we used 16S RNA sequencing, western blotting, gas chromatography-mass spectrometry, and other techniques to examine the intestinal microbiota, the short-chain fatty acids-G protein-coupled receptor 41 (SCFAs-GPR41) pathway, and the downstream mitogen-activated protein kinase (MAPK) signaling pathway.

RESULT

Network pharmacology analysis identified 34 active compounds and predicted 154 potential targets in HJRS that may regulate immune function by interacting with multiple targets (tumor-necrosis factor [TNF], PIK3CG, JUN, AKT1, and MAPK) and immune-related signaling pathways (MAPK and TNF-signaling pathway). Experimental validation demonstrated that HJRS alleviated symptoms of weakness and reduced behavioral activity in the model mice. It significantly enhanced the DTH response, elevated serum hemolysin levels, and restored the balance of white blood cells, lymphocytes, red blood cells, and hemoglobin percentages. HJRS also rebalanced the serum CD3+CD4+/CD3+CD8+ ratio and increased C3 and C4 levels. Furthermore, it improved immune organ function by raising the thymus and spleen coefficients and increasing serum IgA, IgA, and IgM levels. Histopathological examination revealed that HJRS ameliorated CTX-induced pathological damage in the thymus, spleen, and intestines. HJRS regulated gut microbiota composition by enhancing the richness of Bacteroidetes and increasing the Firmicutes/Bacteroidetes ratio, while reducing the abundance of Firmicutes. It decreased the relative abundance of harmful genera, such as Bacteroides and Enterorhabdus, and promoted the growth of beneficial genera, including Muribaculaceae, Clostridia, and Alloprevotella. Additionally, HJRS increased the fecal acetic acid, propionic acid, hexanoic acid, and total SCFA levels in the model mice. It activated the SCFAs-GPR41 pathway and downstream MAPK signaling, thereby enhancing intestinal mucosal immune function.

CONCLUSION

HJRS effectively improved immune function in CTX-induced immunocompromised mice. Its mechanism of action may be associated with the regulation of intestinal microbiota dysbiosis, activation of the intestinal "SCFA-GPR41" pathway, and modulation of the downstream MAPK signaling pathway.

The Paeonol of Total Glucosides of White Peony Regulates the Differentiation of CD4+Treg Cells through the EP300/Foxp3 Axis to Relieve Pulmonary Fibrosis in Mice

Pulmonary fibrosis is a chronic progressive lung disease that can lead to lung structural damage and respiratory failure. This study aimed to investigate whether paeonol could improve pulmonary fibrosis in mice by regulating through the EP300/Foxp3 axis. We established a mouse model of pulmonary fibrosis. Total glucosides of white peony (TGP) were used to treat the animal model, and lung injury was observed using HE and Masson staining. Inflammatory factor levels in bronchoalveolar lavage fluid were detected using ELISA. Network pharmacology analysis was conducted to explore the components, shared targets, and signaling pathways of pulmonary fibrosis and TGP. Molecular docking was performed to observe the binding of paeonol, a component of TGP, to the target EP300. CD4+T cells were collected and co-cultured with MPPF cells, followed by intervention with TGP and paeonol. The ratio of CD4+T/Treg cells was measured in vitro, and immunofluorescence was used to detect the intensity of α-SMA. Network pharmacology revealed that one of the key components of TGP is paeonol, and the signaling pathway associated with pulmonary fibrosis is the Foxp3 signaling pathway. TGP effectively inhibited the secretion of lung inflammatory factors TGF-β1, IFN-γ, IL-2, and IL-17 in mic. Paeonol, an effective component of TGP, could bind to EP300 at the molecular level. Both TGP and paeonol inhibited the expression of EP300 in CD4+T and MPPF cells, enhanced the proportion of Treg cells in CD4+T, and reduced the expression of Collagen I and α-SMA in MPPF cells. TGP can effectively inhibit lung inflammation and fibrosis progression in mice. Paeonol regulating CD4+Treg cell differentiation through the EP300/Foxp3 axis. This study may provide new insights into how TGP improves pulmonary fibrosis in mice.

A Direct Relationship Between 'Blood Stasis' and Fibrinaloid Microclots in Chronic, Inflammatory, and Vascular Diseases, and Some Traditional Natural Products Approaches to Treatment

'Blood stasis' (syndrome) (BSS) is a fundamental concept in Traditional Chinese Medicine (TCM), where it is known as Xue Yu (). Similar concepts exist in Traditional Korean Medicine ('Eohyul') and in Japanese Kampo medicine (Oketsu). Blood stasis is considered to underpin a large variety of inflammatory diseases, though an exact equivalent in Western systems medicine is yet to be described. Some time ago we discovered that blood can clot into an anomalous amyloid form, creating what we have referred to as fibrinaloid microclots. These microclots occur in a great many chronic, inflammatory diseases are comparatively resistant to fibrinolysis, and thus have the ability to block microcapillaries and hence lower oxygen transfer to tissues, with multiple pathological consequences. We here develop the idea that it is precisely the fibrinaloid microclots that relate to, and are largely mechanistically responsible for, the traditional concept of blood stasis (a term also used by Virchow). First, the diseases known to be associated with microclots are all associated with blood stasis. Secondly, by blocking red blood cell transport, fibrinaloid microclots provide a simple mechanistic explanation for the physical slowing down ('stasis') of blood flow. Thirdly, Chinese herbal medicine formulae proposed to treat these diseases, especially Xue Fu Zhu Yu and its derivatives, are known mechanistically to be anticoagulatory and anti-inflammatory, consistent with the idea that they are actually helping to lower the levels of fibrinaloid microclots, plausibly in part by blocking catalysis of the polymerization of fibrinogen into an amyloid form. We rehearse some of the known actions of the constituent herbs of Xue Fu Zhu Yu and specific bioactive molecules that they contain. Consequently, such herbal formulations (and some of their components), which are comparatively little known to Western science and medicine, would seem to offer the opportunity to provide novel, safe, and useful treatments for chronic inflammatory diseases that display fibrinaloid microclots, including Myalgic Encephalopathy/Chronic Fatigue Syndrome, long COVID, and even ischemic stroke.

A Meta-Analysis: Anti-Inflammatory Medicinal Plants for Age-Related Menopause-Like Symptoms and Psychological Problems in Breast Cancer and Healthy Perimenopausal Women

BACKGROUND

Medicinal plant supplements (MPS) have benefits in improving menopause-like symptoms (MLS).

OBJECTIVES

To investigate the effectiveness of MPS in reducing MLS in healthy women and those with breast cancer (BC).

SEARCH STRATEGY

PubMed, Web of Science, Embase, Cochrane Library, China National Knowledge Infrastructure, Wanfang database and Chinese Scientific Journals Database were searched from the date of library construction until 30 January 2024.

SELECTION CRITERIA

Randomised controlled trials were selected that involved healthy perimenopausal women, BC patients treated with herbal medicines, and the effects of plant-based compounds on MLS.

DATA COLLECTION AND ANALYSIS

The review included 12 studies with 917 patients with BC and 15 studies with 2104 healthy perimenopausal women. The data were analysed using the Meta-mar tool.

MAIN RESULTS

MPS improved Kupperman's Index (KMI) and menopause rating scale (MRS) scores compared with the comparator. Patients with BC experienced a greater reduction in KMI and MRS because of treatment than healthy perimenopausal women. Patients with BC had a more significant reduction in KMI than women who received hormone therapy. In both healthy perimenopausal women and women with BC, MPS treatment resulted in significantly higher response rates and fewer psychological problems. Women with BC experienced a decrease in anxiety and insomnia by MPS. Network analysis showed that the response rate was the factor most associated with MPS use.

CONCLUSIONS

Anti-inflammatory MPS may assist women with BC or healthy perimenopausal women experience less MLS.

Identification of potential mechanisms of Schisandrin B in the treatment of idiopathic pulmonary fibrosis by integrating network pharmacology and experimental validation

Idiopathic pulmonary fibrosis (IPF) is a worsening fibrotic condition characterized by a short survival rate and limited treatment options. This study evaluates the potential anti-fibrotic properties of Schisandrin B (Sch B) through network pharmacology and experimental validation. A mouse model of bleomycin-induced pulmonary fibrosis was established, and the modeled mice were treated with Sch B at three doses (20 mg/kg/day, 40 mg/kg/day, and 80 mg/kg/day). A fibrotic model was developed in NIH/3T3 cells by treating them with TGF-β (10 ng/mL) and administering Sch B at various concentrations (10, 20, and 40 µM). The results revealed that Sch B treatment delayed the development of bleomycin-induced pulmonary fibrosis and substantially decreased the transcription levels of collagen I and α-SMA in TGF-β-induced fibroblasts. Core targets were screened with protein-protein interaction network analysis, molecular complex detection (MCODE), and CytoHubba plugin. The application of Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and molecular docking highlighted the significance of the HIF-1α signaling pathway in the potential mechanism of Sch B in IPF therapy. Western blot, PCR, and immunofluorescence were performed to validate the effects of Sch B on HIF-1α. In vivo and in vitro, Sch B administration reduced HIF-1α expression. These outcomes provide valuable insights into the potential mechanism by which Sch B delays IPF development, with HIF-1α potentially serving as a key target. However, further investigation is warranted to assess the safety and efficacy of Sch B in clinical settings.

Strategies for Reducing the Homogenization Phenomenon in the Screening of Key Components in Network Pharmacology Based on the Detectability of Components

BACKGROUND

The ingredients of traditional Chinese medicine (TCM) are complex and diverse and are often identified using the TCM systems pharmacology (TCMSP) database. However, the ingredients in this database exhibit significant homogeneity, which limits the comprehensive understanding of TCM's ingredient diversity and biological activity. Consequently, liquid chromatography-mass spectrometry (LC-MS) has become a key tool for the precise identification of TCM components.

METHODS

In this study, the LC-MS was used to identify the components of a TCM herb. The identified components were then compared with the component data in the TCMSP database. A network pharmacological prediction of the components was subsequently performed.

RESULTS

An analysis of the four herb formula prescriptions (Ganmai Dazao decoction, Bazhen granule, Shaoyao Gancao decoction, and Zixue san) was conducted, revealing significant discrepancies between the LC-MS identification results and the components in the TCMSP database. The database components were found to be highly homogeneous.

CONCLUSION

This study underscores the pivotal function of LC-MS in the analysis of components of TCM, particularly in addressing issues of database homogeneity. The employment of LC-MS technology enhances the precision of ingredient identification and streamlines the identification of potential pharmacodynamic ingredients, thereby propelling TCM toward a more contemporary standing.

Qingqi Guxue Decoction induces S cell cycle arrest to inhibit replication of severe fever with thrombocytopenia syndrome virus

Severe fever with thrombocytopenia syndrome (SFTS) is a novel emerging acute infectious disease caused by severe fever with thrombocytopenia syndrome virus (SFTSV), characterized by high fever and thrombocytopenia. It has been proved that traditional Chinese medicine (TCM) has displayed definite therapeutic effects on viral hemorrhagic fever, indicating its potential to treat SFTS. In this study, SFTS-relative key targets were predicted via gene ontology (GO) analysis and kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis. Molecular docking was then used to select stable binders. Molecules matched TCMs were identified, and a new prescription, Qingqi Guxue decoction (QQGX), was formulated to clear heat and nourish blood, with a resulting drug composition network. We explored the optimal drug proportion for QQGX. Through an in-depth study of molecular mechanisms, we found that QQGX induces S phase arrest by promoting the degradation of cyclin A2 (CCNA2) and cyclin-dependent kinase 2 (CDK2), thereby inhibiting SFTSV replication. Finally, we verified the effectiveness and safety of QQGX based on the mouse liver bile duct organoid model infected with SFTSV. In summary, our study prepared a TCM decoction using the method of network pharmacology. This decoction has a significant inhibitory effect on the replication of SFTSV and provides a new treatment strategy for hemorrhagic fever with TCM.

Integrating metabolomics, network pharmacology and pharmacological verification analysis provides new insights into the anti-inflammatory and anti-tussive properties of Fritillaria cirrhosa bulbs

ETHNOPHARMACOLOGICAL RELEVANCE

Fritillaria cirrhosa bulbs, referred to as Chuanbeimu in traditional Chinese medicine (TCM), are extensively used for recognized anti-inflammatory and anti-tussive effects. Both Songbei (SB) and Qingbei (QB), which are from this plant, have been used separately in medicine. However, the differences and similarities in their bioactive components and anti-inflammatory effects remain unclear.

OBJECTIVE

We aimed to analyse the metabolic profiles of F. cirrhosa bulbs across different growth years and explore the anti-inflammatory and anti-tussive properties of two distinct medicinal materials.

METHODS

With nontargeted metabolic technology, the main components of bulbs were detected. Principal component analysis (PCA) and pathway enrichment analysis were carried out to determine the differentially expressed metabolites between growth years. Network pharmacology was subsequently used to analyse the relationships among the components, diseases, key targets, and metabolic pathways by constructing a network model. The effects of drug-containing serum on cellular inflammatory factors were analysed through in vitro assays.

RESULTS

A total of 1349 compounds were identified from the different bulb samples. PCA revealed metabolic differences between SB bulbs (1- and 2-year-old) and QB bulbs (3-, 4-, and 5-year-old). Notably, 4-methoxycinnamaldehyde, tenuifoliside A, LysoPC 20:4, and morpholine-4-carboximidamide hydrobromide were identified as potential components for distinguishing SB and QB. Network pharmacology revealed more common targets related to anti-inflammatory (PPARG, PPARA, PTGS1, and XDH) and anti-tussive (PPARG, PTGS1, PPARA, OPRM1, DRD2, SLC6A4, and HTR2A) effects in SB than in QB. KEGG analysis revealed that inflammation and cough, including tryptophan metabolism and arachidonic acid metabolism, were enriched in the SB group. Cellular assays revealed anti-inflammatory effects, with SB having greater effects on IL-6 and QB on TNF-α and IL-1β having overall anti-inflammatory effects.

CONCLUSION

By integrating metabolomic and network analyses, the traditional classification of F. cirrhosa into SB and QB based on bulb characteristics and the observed differences are justified to a certain extent. This study provides new insights, guiding the clinical use of these treatments for inflammation and cough.

Network pharmacological evaluation of Cressa cretica L.- an integrated approach of modern and ancient pharmacology

Cressa cretica L. is immensely valuable in pharmacology. Computational approach through network pharmacology has been attempted to understand lead molecules of Cressa and their interactions with multiple targets. The phytochemical components of methanolic extracts of Cressa leaves were identified using GC-MS analysis, revealing 16 compounds. Using the identified lead molecules, target proteins were predicted using SWISS-target prediction and were analyzed using Cytoscape. This led to the identification of 56 candidate protein targets, which were used to construct a network using CytoHubba, Centiscape, MCODE, and KEGG pathways. The STRING network was created using Cytoscape for analyzing protein-protein interactions, and the top 5 genes were chosen from a total of 12 algorithms in CytoHubba. The antioxidant effects of C. cretica were investigated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, which showed an increase in the trend activity of the plant extract with an inhibition percentage of 51.53 ± 0.003%. This was further validated by ferric reducing antioxidant power (FRAP) assay that resulted in an antioxidant activity of 6.64 µg/mL at a high concentration of 500 µg/mL. Molecular docking and simulation were performed to study the interaction of human cyclooxygenase-2 (PDB ID: 5KIR) with Cressa metabolites. 5KIR exhibited a higher interaction with methyl stearate, forming two H-bond interactions with Arg 120 and Tyr 355. Molecular dynamics simulation analysis confirmed the stability of the protein-ligand complex. The network pharmacology analysis of putative proteins obtained from C. cretica revealed that the peroxisome proliferator-activated receptor gamma (PPARG) gene is found in numerous cancer pathways and can be inhibited.

Decoding Drug Discovery: Exploring A-to-Z In Silico Methods for Beginners

The drug development process is a critical challenge in the pharmaceutical industry due to its time-consuming nature and the need to discover new drug potentials to address various ailments. The initial step in drug development, drug target identification, often consumes considerable time. While valid, traditional methods such as in vivo and in vitro approaches are limited in their ability to analyze vast amounts of data efficiently, leading to wasteful outcomes. To expedite and streamline drug development, an increasing reliance on computer-aided drug design (CADD) approaches has merged. These sophisticated in silico methods offer a promising avenue for efficiently identifying viable drug candidates, thus providing pharmaceutical firms with significant opportunities to uncover new prospective drug targets. The main goal of this work is to review in silico methods used in the drug development process with a focus on identifying therapeutic targets linked to specific diseases at the genetic or protein level. This article thoroughly discusses A-to-Z in silico techniques, which are essential for identifying the targets of bioactive compounds and their potential therapeutic effects. This review intends to improve drug discovery processes by illuminating the state of these cutting-edge approaches, thereby maximizing the effectiveness and duration of clinical trials for novel drug target investigation.

Network pharmacology combined with molecular docking and experimental validation of the mechanism of action of columbianetin acetate in the treatment of ovarian cancer

Background

Ovarian cancer is the most prevalent malignant tumor of the female reproductive system and has the highest mortality rate among gynecological cancers. Columbianetin acetate (CE) is one of the active ingredients of Angelica sinensis, which has good antifungal and anti-inflammatory activities. However, its potential mechanism of action in ovarian cancer remains unclear. This study used network pharmacology and molecular docking technology to investigate the molecular mechanism and material basis of CE in the treatment of ovarian cancer, and further verified by in vitro experiments.

Methods

Relevant targets for CE were obtained from TCMSP and SwissTargetPrediction databases. OMIM, GeneCards and DisGeNET databases were applied to screen ovarian cancer-related targets. The STRING database to obtain protein-protein interaction (PPI) network. Then key targets were obtained using Cytoscape software, followed by expression, survival and ROC diagnostic analyses of core genes using R software. GO and KEGG enrichment analyses were performed using the DAVID database. Binding ability of CE to core targets was assessed by molecular docking. KEGG sites were used to predict core gene-related pathways. Subsequently, in vitro cellular experiments were performed to further investigate the molecular mechanism of CE treatment for ovarian cancer.

Results

A total of 55 CE-ovarian cancer interaction targets were identified using network pharmacology techniques. Among these, eight key targets -ESR1, GSK3B, JAK2, MAPK1, MDM2, PARP1, PIK3CA, and SRC-were screened using Cytoscape software. Core genes ESR1, GSK3B and JAK2 were obtained based on expression, prognostic and diagnostic values using R software. GO and KEGG enrichment analyses indicated that CE treatment of ovarian cancer might be related to PI3K/Akt signaling pathway, MAPK signaling pathway, ErbB signaling pathway and Ras signaling pathway. The molecular docking results showed that CE had good binding ability with core targets ESR1, GSK3B and JAK2. The results of in vitro cellular experiments indicated that CE may inhibit the proliferation and metastasis of ovarian cancer and promote apoptosis by inhibiting the PI3K/AKT/GSK3B pathway.

Conclusions

Based on the network pharmacology approach, we predicted the potential mechanism of CE for the treatment of ovarian cancer, which provided a new idea for further research on its pharmacological mechanism.

General expert consensus on the application of network pharmacology in the research and development of new traditional Chinese medicine drugs

The research and development of new traditional Chinese medicine (TCM) drugs have progressively established a novel system founded on the integration of TCM theory, human experience, and clinical trials (termed the "Three Combinations"). However, considering TCM's distinctive features of "syndrome differentiation and treatment" and "multicomponent formulations and complex mechanisms", current TCM drug development faces challenges such as insufficient understanding of the material basis and the overall mechanism of action and an incomplete evidence chain system. Moreover, significant obstacles persist in gathering human experience data, evaluating clinical efficacy, and controlling the quality of active ingredients, which impede the innovation process in TCM drug development. Network pharmacology, centered on the "network targets" theory, transcends the limitations of the conventional "single target" reductionist research model. It emphasizes the comprehensive effects of disease or syndrome biological networks as targets to elucidate the overall regulatory mechanism of TCM prescriptions. This approach aligns with the holistic perspective of TCM, offering a novel method consistent with TCM's holistic view for investigating the complex mechanisms of TCM and developing new TCM drugs. It is internationally recognized as a "next-generation drug research model". To advance the research of new tools, methods, and standards for TCM evaluation and to overcome fundamental, critical, and cutting-edge technical challenges in TCM regulation, this consensus aims to explore the characteristics, progress, challenges, applicable pathways, and specific applications of network pharmacology as a new theory, method, and tool in TCM drug development. The goal is to enhance the quality of TCM drug research and development and accelerate the efficiency of developing new TCM products.

Piceatannol-3'-O-β-D-glucopyranoside inhibits neuroexcitotoxicity and ferroptosis through NMDAR/NRF2/BACH1/ACSL4 pathway in acute ischemic stroke

BACKGROUND

Neuronal protection is a well-established method of acute ischemic stroke (AIS) treatment. The pharmacodynamic effect of Piceatannol-3'-O-β-D-glucopyranoside (Chinese name: Hartigan, QZZG) on AIS has been reported, but the molecular mechanism of this effect remains unknown.

PURPOSE

The purpose of this study is to elucidate the pharmacodynamic effects and mechanisms of QZZG in the treatment of AIS.

METHODS

A combined network pharmacology and metabolomics approach was used to predict the key targets and pathways of QZZG in the treatment of AIS and to elucidate the mechanism of QZZG through experimental validation.

RESULTS

In this study, QZZG improved histopathologic features and reduced infarct volume and neurologic deficit scores. Integrated network pharmacology and metabolomics revealed that QZZG may protect neurons by regulating glutamate and its receptors, and that glutamate is closely related to NMDAR1, NRF2, and Caspase-3. Pathway analysis results suggested that NMDAR-mediated Ca2+ inward flow is one of the critical pathways. In terms of neuroexcitotoxicity QZZG inhibited glutamate content, reduced Ca2+ inward flow, protected mitochondrial function, and reduced ROS, as well as being able to effectively inhibit the expression of NMDAR1, Caspase-3, Bax, and promote the expression of Bcl-2, NMDAR2A. In terms of ferroptosis QZZG promoted NRF2, HO-1, GPX4 and nuclear-NRF2, inhibited the expression of BACH1 and ACSL4, and suppressed Fe2+ accumulation and lipid peroxidation. Silencing of BACH1 resulted in elevated expression of NRF2 and decreased expression of ACSL4, which inhibited the sensitivity of neurons to ferroptosis. QZZG was able to further increase NRF2 expression under conditions of silencing BACH1. QZZG induced NRF2 and inhibited BACH1, ACSL4 was inhibited by ML385, and inhibition of NRF2 induced the expression of BACH1 and ACSL4, QZZG protects neurons in an NRF2-dependent manner.

CONCLUSION

In summary, QZZG inhibited neuroexcitotoxicity and ferroptosis by regulating the NMDAR/NRF2/BACH1/ACSL4 pathway. The study provided a relatively novel perspective on the mechanism of traditional Chinese medicine (TCM) treatment of the disease.

Revealing the molecular mechanism of baohuoside I for the treatment of breast cancer based on network pharmacology and molecular docking

ETHNOPHARMACOLOGICAL RELEVANCE

In Traditional Chinese Medicine (TCM), there are many prescriptions for treating breast cancer (BC) that utilize the herb Epimedium brevicornum Maxim, which warms and replenishes kidney yang. Baohuoside I (BI) is a flavonoid compound found in Epimedium brevicornum Maxim. As a single glycoside, it is not easily hydrolyzed in the intestine and is typically absorbed as a precursor. As a natural product with potential anti-cancer properties, studies have shown that BI possesses anti-cancer activity and can inhibit the invasion and migration of BC cells. However, its underlying mechanisms remain unclear, thus further research is needed to validate its modern mechanisms for traditional uses.

AIM OF THE STUDY

This study aimed to explore the regulatory mechanism of BI in the signaling pathways of BC cells through network pharmacology (NP), molecular docking (MD) techniques and cellular experiments.

METHODS

Potential targets were predicted using public databases, and a protein-protein interaction (PPI) network was constructed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Key signaling pathways were validated through MD techniques, cellular experiments, RNA interference and Western blot (WB) analysis.

RESULTS

Treatment-associated targets included SRC, MAPK1, HSP90AA1, PIK3CA, TP53, AKT1, and EGFR. GO enrichment, KEGG enrichment analyses, and MD results indicated that BI exerts its anti-breast cancer effects by inhibiting the tyrosine kinase activity of EGFR, as well as through downstream MAPK signaling pathway and PI3K-Akt signaling pathway pathways. In vitro experiments confirmed that BI primarily induce cell apoptosis through the EGFR-mediated MAPK signaling pathway and PI3K-Akt signaling pathway.

CONCLUSION

BI can inhibit EGFR activation and promote BC cell apoptosis through the MAPK signaling pathway and PI3K-Akt signaling pathway, thereby exerting therapeutic effects on BC. This study not only provides experimental evidence for the accuracy of NP but also offers an effective approach for rational utilization of Baohuoside I-like flavonoid compounds as anti-breast cancer drugs.

Screening of Anti-Hair Loss Plant Raw Materials Based on Reverse Network Pharmacology and Experimental Validation

Hair loss is one of the skin conditions that can affect people's mental health. Plant raw material extracts are of great interest due to their safety. In this study, we utilize reverse network pharmacology to screen for key targets of the Wnt/β-catenin signaling pathway and the TGFβ/BMP signaling pathway, as well as key differential lipids, for plant raw materials selection. The aim is to identify plant raw materials that may have anti-hair loss properties and to validate these findings through cell experiments. Licorice, salvia miltiorrhiza, mulberry leaf, ephedra and curcumae radix were found that may possess anti-hair loss effects. Licorice water extract (LWE), salvia miltiorrhiza water extract (SMWE), mulberry leaf water extract (MLWE), ephedra water extract (EWE) and curcumae radix water extract (CRWE) did not exhibit cytotoxicity on human dermal papilla cells (HDPCs). Through ALP staining, it was found that the expression of ALP in HDPCs treated with LWE, SMWE, MLWE, EWE and CRWE was enhanced. In addition, LWE, SMWE, MLWE, EWE and CRWE have reduced the expression of hair growth inhibitory factor TGF-β1 and inflammatory factor IL-6. Additionally, various water extracts can enhance the secretion of VEGF, with high concentrations of SMWE, EWE and CRWE exhibiting better efficacy. Furthermore, β-catenin, a key factor of the Wnt/β-catenin signaling pathway, was enhanced by LWE, SMWE, MLWE, EWE and CRWE treatment in cultured HDPCs. In conclusion, all five plant raw materials showed some anti-hair loss potential, providing theoretical support for their application in anti-hair loss products.

Network pharmacology: a crucial approach in traditional Chinese medicine research

Network pharmacology plays a pivotal role in systems biology, bridging the gap between traditional Chinese medicine (TCM) theory and contemporary pharmacological research. Network pharmacology enables researchers to construct multilayered networks that systematically elucidate TCM's multi-component, multi-target mechanisms of action. This review summarizes key databases commonly used in network pharmacology, including those focused on herbs, components, diseases, and dedicated platforms for network pharmacology analysis. Additionally, we explore the growing use of network pharmacology in TCM, citing literature from Web of Science, PubMed, and CNKI over the past two decades with keywords like "network pharmacology", "TCM network pharmacology", and "herb network pharmacology". The application of network pharmacology in TCM is widespread, covering areas such as identifying the material basis of TCM efficacy, unraveling mechanisms of action, and evaluating toxicity, safety, and novel drug development. However, challenges remain, such as the lack of standardized data collection across databases and insufficient consideration of processed herbs in research. Questions also persist regarding the reliability of study outcomes. This review aims to offer valuable insights and reference points to guide future research in precision TCM network pharmacology.

Unveiling the therapeutic mechanisms of taraxasterol from dandelion in endometriosis: Network pharmacology and cellular insights

AIMS

Endometriosis is a chronic inflammatory disease. The current treatment options in clinical practice mainly include hormonal therapy and surgical intervention. However, hormonal therapy is associated with serious side effects, and surgical treatment often leads to a high recurrence rate. Dandelion, a commonly used traditional Chinese medicine, has played a significant role in the treatment of endometriosis due to its notable efficacy and minimal side effects as a component of compound formulations. The purpose of this study is to investigate the molecular mechanisms of Taraxasterol, the main component of dandelion, in the treatment of endometriosis.

MATERIALS AND METHODS

This study employed network pharmacology to screen potential targets associated with Taraxasterol in the treatment of endometriosis. Subsequently, molecular docking was performed to preliminarily validate the core targets. Furthermore, GO and KEGG enrichment analyses were conducted to identify potential signaling pathways related to the treatment. The mechanisms underlying the therapeutic effects of Taraxasterol on endometriosis were further validated through in vitro cell experiments, including Western blotting, colony formation assays, scratch assays, and CCK-8 assays.

RESULTS

A total of 148 potential targets of Taraxasterol were selected through screening on a prediction website, along with 1180 disease targets and 71 overlapping targets. Subsequently, the overlapping targets were imported into the STRING database to construct a protein-protein interaction (PPI) network, which was visualized using Cytoscape 3.7. Ten key targets were identified from the network, and preliminary validation was performed through molecular docking of these ten targets. Additionally, GO and KEGG analyses were conducted on the overlapping targets, resulting in the identification of the top 10 enriched GO terms and the top 20 KEGG pathways, which were subsequently visualized. Finally, cellular experiments demonstrated that taraxasterol inhibits the proliferation and migration of ectopic endometrial cells through the PI3K/Akt/mTOR pathway, while promoting apoptosis.

CONCLUSIONS

Our study investigated the potential mechanisms underlying the therapeutic effects of Taraxacum officinale (dandelion) on endometriosis. Through network pharmacology and in vitro cellular experiments, we revealed that Taraxasterol, a bioactive compound present in dandelion, can inhibit the proliferation and migration of endometrial ectopic cells and promote apoptosis through the PI3K/Akt/mTOR pathway.

Oleanolic acid combined with aspirin plays antitumor roles in colorectal cancer via the Akt/NFκB/IκBα/COX2 pathway

Among the common malignancies, colorectal cancer (CRC) is often resistant to chemotherapy because of drug resistance and severe toxicity. Currently, aspirin is one of the most promising CRC chemopreventive drugs, both for primary prevention and for reducing the chance of recurrence and metastasis following radical surgery in patients with early-stage CRC. Oleanolic acid is a potential antineoplastic drug that has an antagonistic effect on many kinds of tumors. Network pharmacology, molecular docking, and in vitro experiments were performed to investigate whether OA combined with aspirin can enhance the anticancer effects of aspirin. As indicated by the network pharmacology results, oleanolic acid and aspirin can regulate multiple signaling pathways through multiple target proteins, including NFκB1\IκBα\PTGS2\MAPK3\PIK3CA. A series of cellular experiments demonstrated for the first time that oleanolic acid synergistically enhances aspirin to inhibit the proliferation and invasion of HCT116 and HT29 cells and induce S-phase arrest by regulating Akt/NFκB/IκBα/COX2 signaling pathway, thus synergistically enhancing the ability of aspirin to promote apoptosis of colorectal cancer cells. This study provides a novel approach to the use of fresh medications for the treatment of colorectal cancer and offers a theoretical foundation for the potential creation of aspirin derivatives based on oleanolic acid.

MitoQ enhances CYP19A1 expression to stimulate WNT/β-catenin signaling pathway for promoting hair growth in androgenetic alopecia

Increased sensitivity to androgens and androgen receptors is the underlying cause of androgenetic alopecia (AGA), a hereditary disease. Our study investigated the preventive effects of MitoQ on dihydrotestosterone (DHT)-induced mitochondrial dysfunction and subsequent hair loss from three perspectives: in vivo, in vitro, and network pharmacology. A mouse model of AGA was used to assess the effectiveness of MitoQ intervention. Seventy-five drug targets and 367 disease targets were identified through network pharmacology analysis. Molecular docking analysis revealed that the androgen receptor (AR) and CYP19A1, which are key targets of MitoQ, may play a role in AGA treatment. CYP19A1 expression was downregulated in lesions from patients with AGA compared to healthy scalp tissue, while AR expression was upregulated. Cellular tests of human dermal papilla cells (DPCs) treated with MitoQ revealed that the mRNA and protein expression of AR remained unchanged, but the mRNA expression of CYP19A1 was upregulated. Our experiments also confirmed that CYP19A1 overexpression prevented DHT-induced apoptosis and upregulated the expression levels of WNT3A and β-catenin, whereas increased apoptosis levels and the downregulation of WNT3A and β-catenin due to CYP19A1 knockdown were reduced by MitoQ. We verified that MitoQ enhanced hair growth in DHT-induced hair loss model mice and reversed DHT-induced apoptosis by enhancing the expression of CYP19A1 in DPCs and that MitoQ may act by mediating the WNT/β-catenin pathway. These findings indicate that MitoQ could be a promising intervention for AGA and that CYP19A1 may serve as a valuable therapeutic target for AGA.

Network pharmacology, experimental validation and pharmacokinetics integrated strategy to reveal pharmacological mechanism of goutengsan on methamphetamine dependence

Background

Goutengsan (GTS) is a traditional Chinese medicine formula that can improve multiple nervous system diseases, such as methamphetamine (MA) dependence. However, the mechanism how GTS treats MA dependence remains unclear. This study was aimed to investigate the action mechanism of GTS on MA dependence using network pharmacology, in vivo/in vitro experimental validation, pharmacokinetics, and tissue distribution in the brain.

Materials and Methods

The bioactive ingredients from GTS and possible targeted genes for treating MA dependence were predicted using network pharmacology. The binding of key components of GTS to the predicted proteins was studied using molecular docking, and the key components were verified by HPLC. The effects of GTS on an MA-induced model in rats and SH-SY5Y cells were studied. The regulatory effects of GTS on the expressions of predicted MAPK pathway-related proteins in rat brain tissues and SH-SY5Y cells were validated. Furthermore, the plasma exposure and brain tissue distribution of GTS ingredients for MA dependence treatment and MAPK pathway regulation were studied in mice.

Results

Network pharmacology screened 53 active ingredients, and 287 potential targets of GTS, and showed the MAPK pathway was among the most relevant pathways. Molecular docking showed that key active ingredients (e.g., 6-gingerol, liquiritin and rhynchophylline) bound strongly with MAPK core targets, such as MAPK3, and MAPK8. Five compounds of GTS were detected by HPLC, including 6-gingerol, chlorogenic acid, liquiritin, 5-o-methylviscumaboloside and hesperidin. GTS had a therapeutic effect on MA-dependent rats, and reduced hippocampal CA1 damage and relative expressions of p-MAPK3/MAPK3, p-MAPK8/MAPK8 in brain tissues induced by MA. GTS counteracted aberrant alterations in cAMP, 5-TH and cellular morphology induced by MA induction and exerts therapeutic effects on MA-induced SH-SY5Y cell models. GTS also can antagonize the high expressions of MAPK-related proteins in MA-induced SH-SY5Y cells. Pharmacokinetic experiment revealed the four ingredients of GTS (e.g., chlorogenic acid, 5-o-methylviscumaboloside, hesperidin and rhynchophylline) were exposed in the plasma and brain, which demonstrates its pharmacological effect on MA dependence.

Conclusion

GTS treats MA dependence by regulating the MAPK pathway via multiple bioactive ingredients. The network pharmacology, experimental validation and pharmacokinetics integrated strategy is efficient in discovering the key pharmacological mechanism of herbal formulae.

Investigation of the therapeutic effects and mechanisms of Houpo Mahuang Decoction on a mouse model of chronic obstructive pulmonary disease

Background

With a growing global population affected by Chronic Obstructive Pulmonary Disease (COPD), the traditional Chinese herbal formula Houpo Mahuang Decoction (HPMHD) has been used for centuries to address respiratory ailments. While studies have demonstrated the therapeutic benefits of HPMHD in COPD, the effective active ingredients, potential targets, and molecular mechanisms underlying its effectiveness remained unclear.

Methods

The mechanisms of action of certain HPMHD components, targets, and pathways for the treatment of COPD were predicted using a network pharmacology method. We induced a COPD mouse model using porcine pancreatic elastase and evaluated the pathological changes and healing processes through HE and Masson staining. Immunofluorescence was used to assess the levels of IL-6 and TNF-ɑ. RNA-Seq analysis was conducted to identify differentially expressed genes (DEGs) in the lungs of normal, control, and treated mice, revealing the biological pathways enriched by HPMHD in COPD treatment. Finally, the expression of DEGs was verified using Western blotting and RT-qPCR.

Results

HPMHD effectively alleviated pathological symptoms and improved COPD in mice by modulating the IL-17 signaling pathway. Treatment with HPMHD improved lung morphology and structure, reduced inflammatory cell infiltration, and inhibited IL-6 and TNF-ɑ levels. Network pharmacology and transcriptomics further revealed the mechanism, indicating that the IL-17 signaling pathway might been instrumental in the inhibitory effect of HPMHD on mouse model of COPD. Subsequent experiments, including protein blotting and RT-qPCR analysis, confirmed the activation of the IL-17 signaling pathway by HPMHD in the COPD mouse model, further supporting the initial findings.

Conclusion

HPMHD was shown to alleviate COPD and reduce lung inflammation in mice, potentially through the activation of the IL-17 signaling pathway. This study provides a novel direction for the development of COPD drugs.

Integrated network pharmacology and pharmacological investigations to discover the active compounds of Toona sinensis pericarps against diabetic nephropathy

ETHNOPHARMACOLOGICAL RELEVANCE

Toona sinensis (A. Juss.) Roem. Is a deciduous woody plant native to Eastern and Southeastern Asia. Different parts of this plant have a long history of being applied as traditional medicines to treat various diseases. The fruits have been used for antidiabetic, antidiabetic nephropathy (anti-DN), antioxidant, anti-inflammatory, and other activities.

AIM OF THE STUDY

The purpose of this study was to investigate the effects of EtOAc (PEAE) and n-BuOH extracts (PNBE) from T. sinensis pericarps (TSP) on kidney injury in high-fat and high-glucose diet (HFD)/streptozotocin (STZ)-induced DN mice by network pharmacology and pharmacological investigations, as well as to further discover active compounds that could ameliorate oxidative stress and inflammation, thereby delaying DN progression by regulating the Nrf2/NF-κB pathway in high glucose (HG)-induced glomerular mesangial cells (GMCs).

MATERIALS AND METHODS

The targets of TSP 1-16 with DN were analyzed by network pharmacology. HFD/STZ-induced DN mouse models were established to evaluate the effects of PEAE and PNBE. Six groups were divided into normal, model, PEAE100, PEAE400, PNBE100, and PNBE400 groups. Fasting blood glucose (FBG) levels, organ indices, plasma MDA, SOD, TNF-α, and IL-6 levels, as well as renal tissue Nrf2, HO-1, NF-κB, TNF-α, and TGF-β1 levels were determined, along with hematoxylin-eosin (H&E) and immunohistochemical (IHC) analysis of kidney sections. Furthermore, GMC activity screening combined with molecular docking was utilized to discover active compounds targeting HO-1, TNF-α, and IL-6. Moreover, western blotting assays were performed to validate the mechanism of Nrf2 and NF-κB in HG-induced GMCs.

RESULTS

Network pharmacology predicted that the main targets of PEAE and PNBE in the treatment of DN include IL-6, INS, TNF, ALB, GAPDH, IL-1β, TP53, EGFR, and CASP3. Additionally, major pathways include AGE-RAGE and IL-17. In vivo experiments, treatment with PEAE and PNBE effectively reduced FBG levels and organ indices, while plasma MDA, SOD, TNF-α, and IL-6 levels, renal tissue Nrf2, HO-1, NF-κB, TNF-α, and TGF-β1 levels, and renal function were significantly improved. PEAE and PNBE significantly improved glomerular and tubule injury, and inhibited the development of DN by regulating the levels of oxidative stress and inflammation-related factors. In vitro experiments, compound 11 strongly activated HO-1 and inhibited TNF-α and IL-6. The molecular docking results revealed that compound 11 exhibited a high binding affinity towards the targets HO-1, TNF-α, and IL-6 (<-6 kcal/mol). Western blotting results showed compound 11 effectively regulated Nrf2 and NF-κB p65 protein levels, and significantly improved oxidative stress damage and inflammatory responses in HG-induced GMCs.

CONCLUSION

PEAE, PNBE, and their compounds, especially compound 11, may have the potential to prevent and treat DN, and are promising natural nephroprotective agents.

Inhibition of M2 tumor-associated macrophages polarization by modulating the Wnt/β-catenin pathway as a possible liver cancer therapy method

The problem of liver cancer is becoming increasingly important due to the epidemic of metabolic diseases and persistent high alcohol consumption. This determines great attention to the development and improvement of methods for early diagnosis and treatment of liver cancer. Huang et al presented a study in the World Journal of Gastroenterology, in which they showed that the use of the traditional Chinese medicine Calculus bovis (CB) can suppress tumor growth in mice by inhibiting M2 tumor-associated macrophages (TAM) through modulating the activity of the Wnt/β-catenin pathway. The interaction of CB components with the Wnt/β-catenin pathway, M2 TAM polarization, and tumor dynamics were studied using network pharmacology, transcriptomics, and molecular docking. It is now generally accepted that the polarization of TAM and the differentiation of the functions of M1 and M2 phagocytes are of great importance for the progression of neoplasms. It is assumed that M2 TAM promote proliferation and migration of tumor cells. Attempts to medicinally influence the Wnt/β-catenin pathway in order to modulate phagocyte polarization now belong to one of the most promising areas of immunotherapy of oncological diseases. Undoubtedly, the work of the Chinese authors deserves attention and further development.

Recent strategies in target identification of natural products: Exploring applications in chronic inflammation and beyond

Natural products are a treasure trove for drug discovery, especially in the areas of infection, inflammation and cancer, due to their diverse bioactivities and complex, and varied structures. Chronic inflammation is closely related to many diseases, including complex diseases such as cancer and neurodegeneration. Improving target identification for natural products contributes to elucidating their mechanism of action and clinical progress. It also facilitates the discovery of novel druggable targets and the elimination of undesirable ones, thereby significantly enhancing the productivity of drug discovery and development. Moreover, the rise of polypharmacological strategies, considered promising for the treatment of complex diseases, will further increase the demand for target deconvolution. This review underscores strategies for identifying natural product targets (NPs) in the context of chronic inflammation over the past 5 years. These strategies encompass computational methodologies for early target discovery and the anticipation of compound binding sites, proteomics-driven approaches for target delineation and experimental biology techniques for target validation and comprehensive mechanistic exploration.

Cinnamaldehyde induces apoptosis and enhances anti-colorectal cancer activity via covalent binding to HSPD1

Colorectal cancer (CRC) is a common malignant tumor with high morbidity and mortality rates worldwide. Although surgical resection and adjuvant radiotherapy/chemotherapy are the mainstays of CRC treatment, the efficacy is unsatisfactory due to several limitations, including high drug resistance. Accordingly, there is a dire need for new drugs or a novel combination approach to treat this patient population. Herein, we found that cinnamaldehyde (CA) could exert an antitumor effect in HCT-116 cell lines. Target fishing, molecular imaging, and live-cell tracing using an alkynyl-CA probe revealed that the heat shock 60 kDa protein 1 (HSPD1) protein was the target of CA. The covalent binding of CA with HSPD1 altered its stability. Furthermore, our results demonstrated that CA could induce cell apoptosis by inhibiting the PI3K/Akt signaling pathway and enhanced anti-CRC activity both in vitro and in vivo. Meanwhile, CA combined with different chemotherapeutic agents was beneficial to patients resistant to anti-CRC drug therapy.

Cucurbitacin B and Its Derivatives: A Review of Progress in Biological Activities

The emergence of natural products has provided extremely valuable references for the treatment of various diseases. Cucurbitacin B, a tetracyclic triterpenoid compound isolated from cucurbitaceae and other plants, is the most abundant member of the cucurbitin family and exhibits a wide range of biological activities, including anti-inflammatory, anti-cancer, and even agricultural applications. Due to its high toxicity and narrow therapeutic window, structural modification and dosage form development are necessary to address these issues with cucurbitacin B. This paper reviews recent research progress in the pharmacological action, structural modification, and application of cucurbitacin B. This review aims to enhance understanding of advancements in this field and provide constructive suggestions for further research on cucurbitacin B.

Mechanism of Sophorae Flavescentis Radix against ovarian cancer via new pharmacology, molecular docking, and experimental verification

The study aims to elucidate the pharmacological mechanisms of Sophorae Flavescentis Radix (SFR, Kushen) against ovarian cancer (OV) by employing an integrated approach that encompasses network pharmacology, molecular docking, and experimental validation. The effective components and potential targets of SFR were identified through screening the Traditional Chinese Medicine Systems Pharmacology (TSMSP) public database using network pharmacology. Core anti-OV targets were pinpointed using protein-protein interaction (PPI) networks. Datasets from The Cancer Genome Atlas (TCGA), the Human Protein Atlas (HPA), and Gene Expression Profiling Interactive Analysis (GEPIA) were used to investigate the mRNA and protein expressions of critical target genes in both normal and cancerous ovarian tissues, alongside their relationship to overall ovarian survival. Functional and pathway enrichment assessments of putative targets were carried out with Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The assessment of stable binding effects was conducted through molecular docking with quercetin, luteolin, and formononetin, and validated by anti-OV cell activity. The investigation identified 22 active SFR components yielding 152 potential targets following the intersection with known OV targets. Analysis of PPI network highlighted 13 crucial target genes, including tumor necrosis factor (TNF) and interleukin-1A (IL-1A). GO enrichment analysis covered 703 biological activities, 72 cellular components, and 144 chemical functions. The KEGG enrichment analysis suggested that anti-cancer effects of SFR are mediated by the TNF, interleukin-17 (IL-17), and AGE-RAGE signaling pathways. Molecular docking demonstrated that TNF and IL-1A were stable and strong binding to quercetin, luteolin, and formononetin, indicating that these stable structures significantly inhibited A2780 OV cell viability. This study demonstrated the ability of TNF and IL-1A combined with quercetin, luteolin, and formononetin to decrease the activity of OV cells, suggesting potential therapeutic effect against OV.

The dual role of CCND1 in heterotopic ossification: A Non-canonical Pathway for Celecoxib treatment

Objective

To explore the effective targets of Celecoxib in the treatment of heterotopic ossification using network pharmacology methods.

Methods

Potential molecules related to heterotopic ossification were obtained by retrieving the GEO and CTD databases and intersecting them. Potential binding targets of Celecoxib were acquired from the STITCH database. A protein-protein interaction network was constructed between potential binding targets of Celecoxib and potential related molecules of heterotopic ossification using the STRING database. Molecules in the protein-protein interaction network were further analyzed using GO and KEGG enrichment analysis in R software, followed by enrichment analysis of active molecules in the Celecoxib-heterotopic ossification target dataset. Hub genes were selected based on the "degree" value and enrichment within the protein-protein interaction network. The binding affinity of hub genes to Celecoxib was observed using molecular docking techniques. Finally, in vitro experiments were conducted to validate the effectiveness of hub genes and explore their regulatory role in the progression of heterotopic ossification. Additionally, the therapeutic effect of Celecoxib, which modulates the expression of the hub genes, was investigated in the treatment of heterotopic ossification.

Results

568 potential molecules related to heterotopic ossification and 76 potential binding targets of Celecoxib were identified. After intersection, 13 potential functional molecules in Celecoxib's treatment of heterotopic ossification were obtained. KEGG analysis suggested pathways such as Rheumatoid arthritis, NF-kappa B signaling pathway, Pathways in cancer, Antifolate resistance, MicroRNAs in cancer play a role in the treatment of heterotopic ossification by Celecoxib. Further enrichment analysis of the 13 potential functional molecules identified 5 hub genes: IL6, CCND1, PTGS2, IGFBP3, CDH1. Molecular docking results indicated that Celecoxib displayed excellent binding affinity with CCND1 among the 5 hub genes. Experimental validation found that CCND1 is highly expressed in the progression of heterotopic ossification, promoting heterotopic ossification in the early stages and inhibiting it in the later stages, with Celecoxib's treatment of heterotopic ossification depending on CCND1.

Conclusion

In the process of treating heterotopic ossification with Celecoxib, immune and inflammatory signaling pathways play a significant role. The therapeutic effect of Celecoxib on heterotopic ossification depends on the hub gene CCND1, which plays different roles at different stages of the progression of heterotopic ossification, ultimately inhibiting the occurrence of heterotopic ossification.

The Discovery and Characterization of a Potent DPP-IV Inhibitory Peptide from Oysters for the Treatment of Type 2 Diabetes Based on Computational and Experimental Studies

The inhibition of dipeptidyl peptidase-IV (DPP-IV) is a promising approach for regulating the blood glucose levels in patients with type 2 diabetes (T2D). Oysters, rich in functional peptides, contain peptides capable of inhibiting DPP-IV activity. This study aims to identify the hypoglycemic peptides from oysters and investigate their potential anti-T2D targets and mechanisms. This research utilized virtual screening for the peptide selection, followed by in vitro DPP-IV activity assays to validate the chosen peptide. Network pharmacology was employed to identify the potential targets, GO terms, and KEGG pathways. Molecular docking and molecular dynamics simulations were used to provide virtual confirmation. The virtual screening identified LRGFGNPPT as the most promising peptide among the screened oyster peptides. The in vitro studies confirmed its inhibitory effect on DPP-IV activity. Network pharmacology revealed that LRGFGNPPT exerts an anti-T2D effect through multiple targets and signaling pathways. The key hub targets are AKT1, ACE, and REN. Additionally, the molecular docking results showed that LRGFGNPPT exhibited a strong binding affinity with targets like AKT1, ACE, and REN, which was further confirmed by the molecular dynamics simulations showcasing a stable peptide-target interaction. This study highlights the potential of LRGFGNPPT as a natural anti-T2D peptide, providing valuable insights for potential future pharmaceutical or dietary interventions in T2D management.

Uncovering the anti-breast cancer activity potential of east Kalimantan propolis by In vitro and bioinformatics analysis

Numerous side effects of breast cancer drugs have prompted researchers to explore more into new therapeutic approaches derived from natural substances. In this context, our study focused on uncovering the potential of East Kalimantan propolis from Trigona apicalis for breast cancer treatment including the underlying mechanisms through bioinformatics approached. We conducted integrated in vitro and bioinformatics analysis of network pharmacology, molecular docking, molecular dynamics and MM-GBSA analysis. Initially, in vitro cytotoxic assay demonstrated the anti-breast cancer activity potential of ethanol extract of East Kalimantan propolis, particularly its ethyl acetate fraction, which exhibited similar activity to doxorubicin, as indicated by their IC50 value. This study revealed eight propolis compounds, consisting of flavonoids and phenolic acids, in East Kalimantan propolis. By integrating microarray datasets (GSE29431, GSE36295, and GSE42568) analysis with potential targets derived from propolis compounds, 39 shared target genes were identified. Subsequently, GO and KEGG pathway, protein-protein interaction (PPI) network, core hub genes and gene expression analysis revealed three major targets, namely, PTGS2, CXCL2, and MMP9. Among them, only MMP9 was highly expressed in breast cancer than normal. Moreover, molecular docking revealed the six of propolis compounds which exhibited pronounced binding affinity towards MMP-9, better than marimastat as control drug. Dynamic simulation confirmed the stability of chrysin and quercetin as best compounds. Additionally, MM-GBSA analysis revealed a relative binding energy for chrysin (-25.6403 kcal/mol) that was comparable to marimastat (-27.3827 kcal/mol). In conclusion, this study reveals how East Kalimantan Propolis affect breast cancer and emphasizes MMP9 as a key target for future therapeutics.

Integrating network pharmacology and experimental models to investigate the efficacy and mechanism of Tiansha mixture on xerosis

Epidermal Growth Factor Receptor Inhibitors (EGFRIs) is a common cancer therapy, but they occasionally cause severe side effects such as xerosis. Tiansha mixture (TM), a traditional Chinese medicines formulation, is develpoed to treat xerosis. This study aims to understand mechanisms of TM on xerosis. Bio-active compounds were selected from databases (TCMSP, TCM-ID, HERB, ETCM) and removed for poor oral bioavailability and low drug likeness. Then a network-based approach filtered out potential active compounds against xerosis. KEGG enrichment analysis identified PI3K/AKT and ERK/MAPK pathways, which were further verified by molecular docking. Afterwards, the effect of TM on activation of PI3K/AKT and ERK/MAPK pathways was validated in gefitinib-induced xerosis rats, where AKT-activator SC79 and MAPK-activator CrPic were also applied. Skin damage was assessed by dorsal score and HE and Tunel stainings. the levels of inflammation factors IL-6 and TNF-α in serum and skin tissue were measured by ELISA. Western blot was used to detect protein levels in the pathways. Network pharmacology identified 111 bio-active compounds from TM and 14 potential targets. Docking simulation showed apigenin, luteolin, and quercetin bio-active compounds in TM bound to IKBKG, INSR, and RAF-1 proteins. In xerosis model rats, TM mitigated xerosis damage, decreased inflammation factors, and phosphorylation of PI3K/AKT and ERK/MAPK proteins. SC79 or CrPic or their combination reversed TM's effect. The current study identified potential targets and PI3K/AKT and ERK/MAPK pathways involved in the effect of TM on xerosis, thus providing a foundation for TM clinical application.

Network pharmacology and in silico approaches to uncover multitargeted mechanism of action of Zingiber zerumbet rhizomes for the treatment of idiopathic pulmonary fibrosis

Background

Idiopathic pulmonary fibrosis (IPF) is a disease with high mortality, and there are only two specific drugs available for therapeutic management with limitations. The study aims to identify comprehensive therapeutic mechanisms of Zingiber zerumbet rhizomes (ZZR) to treat IPF by using network pharmacology followed battery of in silico studies.

Methods

The protein-protein interaction network was developed using Cytoscape to obtain core disease targets involved in IPF and their interactive molecules of ZZR. Based on the pharmacophore properties of phytomolecules from ZZR, the drug targets in IPF were explored. Protein-protein interaction network was built in Cytoscape to screen potential targets and components of ZZR. Molecular docking and dynamics were conducted as an empirical study to investigate the mechanism explored through network pharmacology in relation to the hub targets.

Results

The network analysis conferred kaempferol derivatives that had demonstrated a promising therapeutic effect on the perturbed, robust network hubs of TGF-β1, EGFR, TNF-α, MMP2 & MMP9 reported to alter the biological process of mesenchymal transition, myofibroblast proliferation, and cellular matrix deposition in pulmonary fibrosis. The phytomolecules of ZZR act on two major significant pathways, namely the TGF-β-signaling pathway and the FOXO-signaling pathway, to inhibit IPF. Confirmational molecular docking and dynamics simulation studies possessed good stability and interactions of the protein-ligand complexes by RMSD, RMSF, rGyr, SASA, and principal component analysis (PCA). Validated molecular docking and dynamics simulations provided new insight into exploring the mechanism and multi-target effect of ZZR to treat pulmonary fibrosis by restoring the alveolar phenotype through cellular networking.

Conclusions

Network pharmacology and in silico studies confirm the multitargeted activity of ZZR in the treatment of IPF. Further in vitro and in vivo studies are to be conducted to validate these findings.

Phenotypic drug discovery: a case for thymosin alpha-1

Phenotypic drug discovery (PDD) involves screening compounds for their effects on cells, tissues, or whole organisms without necessarily understanding the underlying molecular targets. PDD differs from target-based strategies as it does not require knowledge of a specific drug target or its role in the disease. This approach can lead to the discovery of drugs with unexpected therapeutic effects or applications and allows for the identification of drugs based on their functional effects, rather than through a predefined target-based approach. Ultimately, disease definitions are mostly symptom-based rather than mechanism-based, and the therapeutics should be likewise. In recent years, there has been a renewed interest in PDD due to its potential to address the complexity of human diseases, including the holistic picture of multiple metabolites engaging with multiple targets constituting the central hub of the metabolic host-microbe interactions. Although PDD presents challenges such as hit validation and target deconvolution, significant achievements have been reached in the era of big data. This article explores the experiences of researchers testing the effect of a thymic peptide hormone, thymosin alpha-1, in preclinical and clinical settings and discuss how its therapeutic utility in the precision medicine era can be accommodated within the PDD framework.

Cinnamomi cortex extract mitigated monosodium urate-induced acute gouty arthritis in rats through nuclear factor-κB-NOD-like receptor thermal protein domain associated protein 3 signaling pathway

Cinnamomi cortex was applied to mitigate joint injury since ancient China. However, the effect of Cinnamomi cortex on gouty arthritis (GA) was rarely reported. This study aimed to explore the effect of Cinnamomi cortex on monosodium urate (MSU)-induced acute GA (AGA) in rats, and clarify the underlying mechanism. The results showed that Cinnamomi cortex extract (CE) containing rich polyphenols and flavonoids alleviated joint swelling and inflammation by reducing programmed cell death in MSU-induced AGA rats. Network pharmacology analysis showed that CE's predictive inflammatory pathways included nuclear factor-κB (NF-κB) and necroptosis pathways. CE reduced expression of pyroptosis-related regulators including Gasdermin D and Caspase 1 via regulating NF-κB/NOD-like receptor thermal protein domain associated protein 3 signaling pathway in AGA rats. In conclusion, this study provided a theoretical basis for Cinnamomi cortex applied as a new veterinary medicine to protect against GA.

DTKGIN: Predicting drug-target interactions based on knowledge graph and intent graph

Knowledge graph intent graph attention mechanism Predicting drug-target interactions (DTIs) plays a crucial role in drug discovery and drug development. Considering the high cost and risk of biological experiments, developing computational approaches to explore the interactions between drugs and targets can effectively reduce the time and cost of drug development. Recently, many methods have made significant progress in predicting DTIs. However, existing approaches still suffer from the high sparsity of DTI datasets and the cold start problem. In this paper, we develop a new model to predict drug-target interactions via a knowledge graph and intent graph named DTKGIN. Our method can effectively capture biological environment information for targets and drugs by mining their associated relations in the knowledge graph and considering drug-target interactions at a fine-grained level in the intent graph. DTKGIN learns the representation of drugs and targets from the knowledge graph and the intent graph. Then the probabilities of interactions between drugs and targets are obtained through the inner product of the representation of drugs and targets. Experimental results show that our proposed method outperforms other state-of-the-art methods in 10-fold cross-validation, especially in cold-start experimental settings. Furthermore, the case studies demonstrate the effectiveness of DTKGIN in predicting potential drug-target interactions. The code is available on GitHub: https://github.com/Royluoyi123/DTKGIN.

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

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

Identification of Erzhu Jiedu Recipe and its molecular mechanism underlying inhibited human hepatoma cells by UHPLC-Q-Exactive Orbitrap HRMS and network pharmacology

ETHNOPHARMACOLOGICAL RELEVANCE

Erzhu Jiedu Recipe (EZJDR) is a formula of traditional Chinese medicine (TCM) for treating hepatitis B virus-related hepatocellular carcinoma (HBV-HCC). However, its effective components and the mechanism of action remain unclear.

AIM OF THE STUDY

To explain how the active compounds of EZJDR suppress the growth of hepatoma cells.

METHODS

UHPLC-Q-Exactive Orbitrap HRMS was used to identify the chemical constituents of EZJDR and their distribution in the serum and liver of mice. Together with experimental investigations, network pharmacology unraveled the molecular mechanism of components of EZJDR underlying the inhibited Hep3B cells.

RESULTS

A total of 138 compounds which can be divided into 18 kinds of components (such as sesquiterpenoids, diterpenoids, anthraquinones, flavonoids and so on) were found in the aqueous extract of EZJDR. Of these components, the tricyclic-diterpenoids exhibited a highest exposure in the serum (74.5%) and liver (94.7%) of mice. The network pharmacology revealed that multiple components of EZJDR interacted with key node genes involved in apoptosis, proliferation, migration and metabolism through various signaling pathways, including ligand binding and protein phosphorylation. In vitro experiments demonstrated that 6 tricyclic-diterpenoids, 2 anthraquinones and 1 flavonoid inhibited the viability of Hep3B cells, with IC50 values ranging from 3.81 μM to 37.72 μM. Dihydrotanshinone I had the most potent bioactivity, arresting the S phase of cell cycle and inducing apoptosis. This compound changed the expression of proteins, including Bad, Bax, Bcl-2, Bal-x, caspase3 and catalase, which were associated with mitochondria-mediated apoptotic pathways. Moreover, dihydrotanshinone I increased the levels of p21 proteins, but decreased the phosphorylated p53, suggesting accumulation of p53 protein prevented cell cycle progression of Hep3B cells with damaged DNA.

CONCLUSIONS

These results suggested that multiple components of EZJDR-diterpenoid, anthraquinone and flavonoid-could be the effective material for the treatment of HBV-HCC. This research provided valuable insights into the molecular mechanism of action underlying the therapeutic effects of EZJDR.

Pharmacodynamic material basis and pharmacological mechanisms of Cortex Mori against diabetes mellitus

ETHNOPHARMACOLOGICAL RELEVANCE

The application of Cortex Mori (CM) in the treatment of diabetes mellitus (DM) has been extensively documented in traditional medicine. In recent years, the chemical composition of CM has been gradually unraveled, and its therapeutic mechanism in treating DM, diabetic nephropathy, diabetic cardiomyopathy, and other related conditions has been highlighted in successive reports. However, there is no systematic study on the treatment of DM based on the chemical composition of CM.

AIM OF THE STUDY

This study was conducted to systematically explore the hypoglycemic activity mechanism of CM based on its chemical composition.

METHODS

The material basis of Cortex Mori extract (CME) was investigated through qualitative analyses based on liquid chromatography-mass spectrometry (LC-MS). The possible acting mechanism was simulated using network pharmacology and validated in streptozotocin (STZ) + high fat diet (HFD)-induced diabetic rats and glucosamine-induced IR-HepG2 model with the assistance of molecular docking techniques.

RESULTS

A total of 39 compounds were identified in CME by the LC-MS-based qualitative analysis. In diabetic rats, it was demonstrated that CME significantly ameliorated insulin resistance, blood lipid levels, and liver injury. The network pharmacology analysis predicted five major targets, including AKT1, PI3K, FoxO1, Gsk-3β, and PPARγ. Additionally, three key compounds (resveratrol, protocatechuic acid, and kaempferol) were selected based on their predicted contributions. The experimental results revealed that CME, resveratrol, protocatechuic acid, and kaempferol could promote the expression of AKT1, PI3K, and PPARγ, while inhibiting the expression of FoxO1 and Gsk-3β. The molecular docking results indicated a strong binding affinity between resveratrol/kaempferol and their respective targets.

CONCLUSIONS

CME contains a substantial amount of prenylated flavonoids, which may be the focal point of research on the efficacy of CM in the treatment of DM. Besides, CME is effective in controlling blood glucose and insulin resistance, improving lipid levels, and mitigating liver injury in patients with DM. Relevant mechanisms may be associated with the activation of the PI3K/Akt pathway, the inhibition of the expression of FoxO1 and Gsk-3β, and the enhancement of PPARγ activity. This study represents the first report on the role of CME in the treatment of DM through regulating PPARγ, FoxO1, and Gsk-3β.

Network pharmacology and molecular docking-based strategy for predicting anti-tumour mechanism of linarin

The aim was to explore the anti-tumour mechanism of linarin (LIN) based on network pharmacology and molecular docking. PharmMapper database and GeneCards database were used to screen anti-tumour related targets of LIN. Enrichment analysis of GO and KEGG was conducted to predict the key targets and pathways. At last, LIN was docked with the key targets. ESR1, ESR2, EGFR, AR, TGFBR2, F2, MAPK10, MAPK14, CDK2 and HSP90AA1 were identified as the key targets. The key pathways included pathways in cancer, prostate cancer, pancreatic cancer and breast cancer. KEGG pathway maps indicated that the anti-tumour effect of LIN may be mainly achieved by intervening related targets in the following pathways: AR-HSP/AR-AR/PSA/proliferation and evading apoptosis;F2/GPCR/…/ROCK/tissue invasion and metastasis;F2/GPCR/…/Raf/MAPK signalling pathway/proliferation and sustained angiogenesis; EGFR/Grb2/…/Raf/MAPK signalling pathway/proliferation and sustained angiogenesis; ER/Oestrogen signalling pathway/proliferation;TGFBR2/Smad2/3/TGF-β signalling pathway/insensitivity to anti-growth signals; oxidative stress/KEAP1/NRF2/…/proliferation and evading apoptosis. LIN had strong binding activity with ESR2, EGFR, AR, CDK2 and HSP90AA1.

Revealing the active ingredients and mechanism of P. sibiricumm in non-small-cell lung cancer based on UPLC-Q-TOF-MS/MS, network pharmacology, and molecular docking

The alcohol extraction of P. sibiricum has exhibited significant inhibitory effects on the production of free radicals and the proliferation of non-small-cell lung carcinoma (NSCLC) A549 cells. Despite the diverse components found in alcohol extraction of P. sibiricum and its multiple targets, the active components and associated targets remain largely unidentified. Hence, there is a need for additional investigation into the pharmacodynamic elements and mechanisms of action. This study aimed to analyze and identify the components responsible for the anti-tumor activity of alcohol extraction from P. sibiricum using UPLC-Q-TOF-MS/MS for the first time. Subsequently, the targets of the active components were predicted using the SwissTargetPrediction database, whereas the targets for NSCLC were sourced from the Online Mendelian Inheritance in Man database (OMIM) and the GeneCards database. Next, the targets of chemical composition were integrated with disease targets via Venny online. GO and KEGG pathway enrichment analyses were performed utilizing DAVID. Subsequently, a network analysis of "components-targets-pathways" was established using Cytoscape 3.8.2 and assessed with the "network analyzer" plug-in. Molecular docking was conducted utilizing Autodock 1.5.6. The study aimed to examine the anti-proliferative impacts and underlying mechanisms of alcohol extraction from P. sibiricum on NSCLC through in vivo and in vitro investigations utilizing an animal model of transplanted tumor, CCK8 assay, cell scratch test, RT-qPCR, and western blotting. The study unveiled that 17 active components extracted from P. sibiricum alcohol demonstrated anti-non-small cell lung cancer (NSCLC) effects through the modulation of 191 targets and various significant signaling pathways. These pathways include Endocrine resistance, PI3K/AKT, Chemical carcinogenesis-receptor activation, Proteoglycans in cancer, EGFR tyrosine kinase inhibitor resistance, AMPK signaling pathway, and other related signaling pathways. Network analysis and molecular docking results indicated that specific compounds such as (25S)-26-O-(β-d-glucopyranosyl)-furost-5-en3β,22α,26-triol3-O-β-d-glucopyranosyl-(1→2)-β-d-glucopyranosyl-(1→4)-β-d-glucopyranoside, Timosaponin H1, Deapi-platycodin D3, (3R)-5,7-dihydroxy-6,8-dimethyl-3-(4'-hydroxybenzyl)-chroman-4-one, Disporopsin, Funkioside F, Kingianoside E, Parisyunnanoside H, and Sibiricoside B primarily targeted 17 key proteins (BCL2, EGFR, ESR1, ESR2, GRB2, IGF1R, JUN, MAP2K1, MAPK14, MAPK8, MDM2, MMP9, mTOR, PIK3CA, RAF1, RPS6KB1, and SRC) collectively. In conclusion, the alcohol extraction of P. sibiricum demonstrated inhibitory effects on cell proliferation, induction of apoptosis, and inhibition of metastasis through various pathways.

The anti-hyperlipidemia effect of Atractylodes macrocephala Rhizome increased HDL via reverse cholesterol transfer

Aim

Atractylodes macrocephala Rhizome (AM) has been used to treat hyperlipidemia for centuries, but its functional components and mechanisms are not clear. This research aimed to investigate the active components in AM and the mechanisms that underlie its anti-hyperlipidemia effect.

Methods

SD rats were fed a high-sucrose high-fat diet in conjunction with alcohol (HSHFDAC) along with different AM extracts (AMW, AMO, AME, and AMP) for 4 weeks. AM's active components were analyzed using multiple databases, and their mechanisms were explored through network pharmacology. The relationship between AM's effect of enhancing serum HDL-c and regulating the expression of reverse cholesterol transport (RCT)-related proteins (Apo-A1, LCAT, and SR-BI) was further validated in the HSHFDAC-induced hyperlipidemic rats. The kidney and liver functions of the rats were measured to evaluate the safety of AM.

Results

AMO, mainly comprised of volatile and liposoluble components, contributed the most significant anti-hyperlipidemia effect among the four extracts obtained from AM, significantly improving the blood lipid profile. Network pharmacology analysis also suggested that volatile and liposoluble components, comprise AM's main active components and they might act on signaling pathways associated with elevated HDL-c. Validation experiments found that AMO substantially and dose-dependently increased HDL-c levels, upregulated the expression of Apo-A1, SR-BI, and LCAT, improved the pathological changes in the kidney and liver, and significantly reduced the serum creatinine levels in rats with hyperlipidemia.

Conclusion

The main anti-hyperlipidemia active components of AM are its volatile and liposoluble components, which may enhance serum HDL-c by increasing the expression of the RCT-related proteins Apo-A1, LCAT, and SR-BI.

Palmatine alleviates cardiac fibrosis by inhibiting fibroblast activation through the STAT3 pathway

Cardiac fibrosis, the hallmark of cardiovascular disease, is characterized by excessive deposition of extracellular matrix in the heart. Emerging evidence indicates that cardiac fibroblasts (CFs) play pivotal roles in driving cardiac fibrosis. However, due to incomplete insights into CFs, there are limited effective approaches to prevent or reverse cardiac fibrosis currently. Palmatine, a protoberberine alkaloid extracted from traditional Chinese botanical remedies, possesses diverse biological effects. This study investigated the potential therapeutic value and mechanism of palmatine against cardiac fibrosis. Adult male C57BL/6 mice were treated with vehicle, isoproterenol (ISO), or ISO plus palmatine for one week. After echocardiography assessment, mice hearts were collected for histopathology, real-time polymerase chain reaction, and Western blot analyses. Primary rat CFs were utilized in vitro. Compared to control, ISO-treated mice exhibited cardiac hypertrophy and structural abnormalities; however, treatment with palmatine ameliorated these effects of ISO. Moreover, palmatine treatment mitigated ISO-induced cardiac fibrosis. Network pharmacology and molecular docking analysis showed that palmatine strongly binds the regulators of cardiac fibrosis including signal transducer and activator of transcription 3 (STAT3) and mammalian target of rapamycin. Furthermore, palmatine reduced the elevated fibrotic factor expressions and overactivated STAT3 induced by ISO, Transformed growth factor β1 (TGF-β1), or interleukin-6 both in vivo and in vitro. Additionally, blocking STAT3 suppressed the TGF-β1-induced CF activation. Collectively, these data demonstrated that palmatine attenuated cardiac fibrosis partly by inhibiting fibroblast activation through the STAT3 pathway. This provides an experimental basis for the clinical treatment of cardiac fibrosis with palmatine.

Protective effects of triptolide against oxidative stress in retinal pigment epithelium cells via the PI3K/AKT/Nrf2 pathway: a network pharmacological method and experimental validation

PURPOSE

Among aging adults, age-related macular degeneration (AMD), is a prevalent cause of blindness. Nevertheless, its progression may be halted by antioxidation in retinal pigment epithelium (RPE). The primary effective constituent of Tripterygium wilfordii Hook. F., triptolide (TP), has demonstrated anti-inflammatory, antiproliferative, and antioxidant properties. The mechanics of the protective effect of triptolide against the oxidative damage in retinal pigment epithelial (RPE) were assessed in this study.

METHODS

ARPE-19 cells were pretreated with TP, and then exposed to sodium iodate (SI). First, cell viability was assessed using CCK-8. Subsequently, we measured indicators for cell oxidation including reactive oxygen species (ROS), catalase (CAT), superoxide dismutase (SOD), and malondialdehyde (MDA). Then, we used network pharmacological analysis and molecular docking to explore the signaling pathway of TP. Last, we used western blot, ELISA, and immunofluorescence assays to clarify the potential mechanistic pathways.

RESULTS

The network pharmacology data suggested that TP may inhibit AMD by regulating the PI3K/Akt signaling pathway. Experimental results showed that the potential mechanism is that it regulates the PI3K/Akt pathway and promotes Nrf2 phosphorylation and activation, thereby raising the level of antioxidant factors (HO-1, NQO1) and reducing the generation of ROS, which inhibit oxidative damage.

CONCLUSION

Our findings suggested that the effect of TP on SI-exposed RPE cells principally relies on the regulation of oxidative stress through the PI3K/Akt/Nrf2 signaling pathway.

Scutellarin targets Wnt5a against zearalenone-induced apoptosis in mouse granulosa cells in vitro and in vivo

Zearalenone (ZEA) poses severe reproductive toxicity to both humans and animals. Scutellarin has been demonstrated to rescue ZEA-induced apoptosis in mouse ovarian granulosa cells (GCs), but its specific targets remain unclear. In the present study, the potential targets of scutellarin were determined to clarify the mechanisms of scutellarin against ZEA-induced ovarian damage. 287 targets of scutellarin in mouse ovarian GCs were obtained by magnetic nano-probe-based fishing assay and liquid chromatography-tandem mass spectrometry. Wnt5a had the lowest binding free energy with scutellarin at - 8.3 kcal/mol. QRT-PCR and western blot showed that scutellarin significantly increased the Wnt5a and β-catenin expression compared with the ZEA-treated group, and cleaved-caspase-3 expression was significantly increased in the scutellarin-treated group after interfering with the expression of Wnt5a. The affinity constant (KD) of Wnt5a and scutellarin was 1.7 × 10-5 M. The pull-down assay also demonstrated that scutellarin could specifically bind to Wnt5a protein. Molecular docking results showed that scutellarin could form hydrogen bonds with TRY52, GLN56, and SER90 on Wnt5a protein, and western blot assay confirmed SER90 was an important site for the binding. Scutellarin significantly increased Wnt5a and β-catenin expression and decreased cleaved-caspase-3 expression in ovarian tissues of mice. In conclusion, scutellarin exerted anti-apoptotic effects on ZEA-induced mouse ovarian GCs by targeting Wnt5a.

Targeting ferroptosis unveils a new era for traditional Chinese medicine: a scientific metrology study

In the past 11 years, there has been a surge in studies exploring the regulatory effect of Traditional Chinese Medicine (TCM) on ferroptosis. However, a significant gap persists in comprehensive scientometric analysis and scientific mapping research, especially in tracking the evolution, primary contributors, and emerging research focal points. This study aims to comprehensively update the advancements in targeting ferroptosis with various TCMs during the previous 11 years. The data, covering the period from 1 January 2012, to 30 November 2023, were retrieved from the Web of Science database. For in-depth scientometric and visualized analyses, a series of advanced analytical instruments were employed. The findings highlight China's predominant role, accounting for 71.99% of total publications and significantly shaping research in this domain. Noteworthy productivity was observed at various institutions, including Guangzhou University of Chinese Medicine, Chengdu University of Traditional Chinese Medicine, and Zhejiang University. Thomas Efferth emerged as the foremost author within this field, while Frontiers in Pharmacology boasted the highest publication count. This study pinpointed hepatocellular carcinoma, chemical and drug-induced liver injury, mitochondrial diseases, acute kidney injury, and liver failure as the most critical disorders addressed in this research realm. The research offers a comprehensive bibliometric evaluation, enhancing our understanding of the present status of TCM therapy in managing ferroptosis-related diseases. Consequently, it aids both seasoned researchers and newcomers by accelerating access to vital information and fostering innovative concept extraction within this specialized field.

YuPingFeng (YPF) upregulates caveolin-1 (CAV1) to alleviate pulmonary fibrosis through the TGF-β1/Smad2 pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Traditional Chinese medicine (TCM) is considered a valuable asset in China's medical tradition. YPF is a classic prescription that has been derived from the "Jiu Yuan Fang" formula and consists of three herbs: Huangqi (Astragalus membranaceus Bunge), Baizhu (Atractylodes rubra Dekker), and Fangfeng (Saposhnikovia divaricata (Turcz.) Schischk). This prescription is widely acclaimed for its exceptional pharmacological properties, including potent antioxidant effects, hormone regulation, and immune modulation effects.

AIM OF THE STUDY

Previous research provides evidence suggesting that YPF may have therapeutic effects on pulmonary fibrosis. Further exploration is essential to confirm its effectiveness and elucidate the fundamental processes.

MATERIALS AND METHODS

First, the active components and target genes of YPF were extracted from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Next, the GSE53845 dataset, which contains information on pulmonary fibrosis, was downloaded from the GEO database. Network informatics methods was then be utilized to identify target genes associated with pulmonary fibrosis. A YPF-based network of protein-protein interactions was constructed to pinpoint possible target genes for pulmonary fibrosis treatment. Additionally, an in vitro model of pulmonary fibrosis induced by bleomycin (BLM) was established to further investigate and validate the possible mechanisms underlying the effectiveness of YPF.

RESULTS

In this study, a total of 24 active ingredients of YPF, along with 178 target genes associated with the treatment, were identified. Additionally, 615 target genes related to pulmonary fibrosis were identified. Functional enrichment analysis revealed that 18 candidate genes (CGs) exhibited significant responses to tumor necrosis factor, NF-kB survival signaling, and positive regulation of apoptosis processes. Among these CGs, CAV1, VCAM1, and TP63 were identified as key target genes. Furthermore, cell experiments confirmed that the expression of CAV1 protein and RNA expression was increased in pulmonary fibrosis, but significantly decreased after treatment with YPF. Additionally, the expression of pSmad2, α-SMA, TGF-β1, and TNF-α was also decreased following YPF treatment.

CONCLUSIONS

Network pharmacology analysis revealed that YPF exhibits significant potential as a therapeutic intervention for pulmonary fibrosis by targeting various compounds and pathways. This study emphasizes that the efficacy of YPF in treating pulmonary fibrosis may be attributed to its ability to up-regulate CAV1 expression and inhibiting pulmonary fibrosis via modulation of the TGF-β1/Smad2 signaling pathway. These findings underscore the promising role of YPF and its ability to potentially alleviate pulmonary fibrosis.

Network pharmacology and in vivo evidence of the pharmacological mechanism of geniposide in the treatment of atherosclerosis

BACKGROUND

Atherosclerosis (AS) is a fundamental pathological state in various cardiovascular diseases. Geniposide, which is the main active component of Gardenia jasminides, is effective against AS. However, the underlying molecular mechanisms remain unclear. Here, we sought to elucidate them.

METHODS

The targets of AS and geniposide were collected from online public databases. The potential mechanism of Geniposide in treating AS was predicted by constructing a protein-protein interaction (PPI) network and conducting Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses. Hub proteins and core pathways were verified by molecular docking and in vivo experiments. Moreover, the effect of geniposide on AS was assessed by measuring the atherosclerotic plaque area in the thoracic aorta of mice. ApoE-/- mice were used to establish AS models and randomly divided into different groups. Two different doses of geniposide were administered to the mice. Hematoxylin and eosin (HE) staining was performed to evaluate the effects of geniposide on AS. Oil Red O and Sirius Red staining were used to evaluate plaque stability. The protein expression of key markers involved in the signalling pathways was examined using western blotting and immunofluorescence.

RESULTS

A total of 239 active targets, 3418 AS-related disease targets, and 129 overlapping targets were identified. Hub genes were detected, and molecular docking revealed that geniposide strongly interacted with hub proteins (AKT1, VEGFA, CTNNB1, MMP9, and EGFR). Moreover, 109 signalling pathways, including the Rap1 signalling pathway, were identified using enrichment analysis. The results of in vivo experiments demonstrated that geniposide reduced body weight and blood lipid levels, alleviated the formation of atherosclerotic plaques, enhanced plaque stability, and inhibited inflammation, at least partially, by activating the Rap1/PI3K/Akt signalling pathway in ApoE-/- mice.

CONCLUSION

Geniposide can alleviate AS and enhance the stability of atherosclerotic plaques by regulating the Rap1/PI3K/Akt signalling pathway.

Unraveling the mechanisms of Fenugreek seed for managing different gynecological disorders: steroidal saponins and isoflavones revealed as key bioactive metabolites

This study employed network pharmacology-based analysis and reverse molecular docking to investigate the molecular targets and pathways associated with gynecological disorders, particularly those related to steroidal hormones and their receptors, and the potential therapeutic effects of fenugreek (Trigonella foenum-graecum L.) constituents. The STITCH 5.0 database was utilized to identify potential molecular targets, and a compound-target network was constructed. The main targets associated with gynecological disorders included estrogen receptor beta (ESR2), estrogen-related receptor gamma (GPER1), oxytocin receptor (OXTR), progesterone receptor (PGR), prolactin receptor (PRLR), and several enzymes involved in sex hormone biosynthesis. Additionally, network topological analysis revealed that specific compounds, such as quercetin, luteolin, genistein, and vitexin, had significant interactions with the identified targets. Reverse molecular docking analysis confirmed the interactions between the identified compounds and target proteins where quercetin, luteolin, genistein, 4'-methylgenistein, trigoneoside IIB, diosgenin, and vitexin possessed the highest combined docking scores, indicating their multi-target nature. The results highlighted the potential of steroidal saponins, isoflavones, and flavones as active constituents of fenugreek with implications for lactation, reproductive processes, and estrogenic activity. The chemical profiling of saponin-enriched and flavonoid-enriched fractions using UPLC/MS/MS further supported the presence of these bioactive compounds. In an animal model study, the steroidal saponins-enriched fraction of fenugreek seed exhibited a significant increase in the body weight of lactating female rats and serum prolactin levels while the flavonoids-enriched fraction showed an increase in serum estradiol levels and improved the histological structure of ovaries.