A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-Wei-Di-Huang pill as a case study

Biological network comparison identifies a novel synergistic mechanism of Ginseng Radix-Astragali Radix herb pair in cancer-related fatigue

ETHNOPHARMACOLOGICAL RELEVANCE

Ginseng Radix and Astragali Radix are commonly combined to tonify Qi and alleviate fatigue. Previous studies have employed biological networks to investigate the mechanisms of herb pairs in treating different diseases. However, these studies have only elucidated a single network for each herb pair, without emphasizing the superiority of the herb combination over individual herbs.

AIM OF THE STUDY

This study proposes an approach of comparing biological networks to highlight the synergistic effect of the pair in treating cancer-related fatigue (CRF).

METHODS

The compounds and targets of Ginseng Radix, Astragali Radix, and CRF diseases were collected and predicted using different databases. Subsequently, the overlapping targets between herbs and disease were imported into the STRING and DAVID tools to build protein-protein interaction (PPI) networks and analyze enriched KEGG pathways. The biological networks of Ginseng Radix and Astragali Radix were compared separately or together using the DyNet application. Molecular docking was used to verify the predicted results. Further, in vitro experiments were conducted to validate the synergistic pathways identified in in silico studies.

RESULTS

In the PPI network comparison, the combination created 89 new interactions and an increased average degree (11.260) when compared to single herbs (10.296 and 9.394). The new interactions concentrated on HRAS, STAT3, JUN, and IL6. The topological analysis identified 20 core targets of the combination, including three Ginseng Radix-specific targets, three Astragali Radix-specific targets, and 14 shared targets. In KEGG enrichment analysis, the combination regulated additional signaling pathways (152) more than Ginseng Radix (146) and Astragali Radix (134) alone. The targets of the herb pair synergistically regulated cancer pathways, specifically hypoxia-inducible factor 1 (HIF-1) signaling pathway. In vitro experiments including enzyme-linked immunosorbent assay and Western blot demonstrated that two herbs combination could up-regulate HIF-1α signaling pathway at different combined concentrations compared to either single herb alone.

CONCLUSION

The herb pair increased protein interactions and adjusted metabolic pathways more than single herbs. This study provides insights into the combination of Ginseng Radix and Astragali Radix in clinical practice.

Advances in Parkinson's disease research - A computational network pharmacological approach

Parkinson's disease (PD), the second most prevalent neurodegenerative disorder, is projected to see a significant rise in incidence over the next three decades. The precise treatment of PD remains a formidable challenge, prompting ongoing research into early diagnostic methodologies. Network pharmacology, a burgeoning field grounded in systems biology, examines the intricate networks of biological systems to identify critical signal nodes, facilitating the development of multi-target therapeutic molecules. This approach systematically maps the components of Parkinson's disease, thereby reducing its complexity. In this review, we explore the application of network pharmacology workflows in PD, discuss the techniques employed in this field, and evaluate the current advancements and status of network pharmacology in the context of Parkinson's disease. The comprehensive insights will pave newer paths to explore early disease biomarkers and to develop diagnosis with a holistic in silico, in vitro, in vivo and clinical studies.

Evaluation of Cordyceps militaris steroids as anti-inflammatory agents to combat the Covid-19 cytokine storm: a bioinformatics and structure-based drug designing approach

Since the SARS-CoV-2 epidemic, researchers have been working on figuring out ways to tackle multi-organ failure and hyperinflation, which are brought on by a cytokine storm. Angiotensin-converting enzyme 2 (ACE2), a SARS-CoV-2 spike glycoprotein's cellular receptor, is involved in complicated molecular processes that result in hyperinflammation. Cordyceps militaris is one of the traditional Chinese medicines that is used as an immune booster, and it has exhibited efficacy in lowering blood glucose levels, seminal emissions, and infertility. In the current study, we explored the potential of Cordyceps militaris steroids as key agents in managing the anger of cytokine storm in Covid-19 using network ethnopharmacological techniques and structure-based drug designing approaches. The steroids present in Cordyceps militaris were initially screened against the targets involved in inflammatory pathways. The results revealed that out of 16 steroids, 5 may be effective against 17 inflammatory pathways by targeting 11 pathological proteins. Among the five steroids, beta-sitosterol, Cholest-5-en-3β-ol, 3β, and 7α-Dihydroxycholest-5-ene were found to interact with thrombin (F2), an important protein reported to reduce the severity of inflammatory mediators and Cholest-4-en-3-one was found to target Glucocorticoid receptor (NR3C1). The top docked steroid displayed key interactions with both targets, which retained key interactions throughout the 100 ns simulation period. These compounds were also shown high binding free energy scores in water swap studies. Based on obtained results the current study suggests the use of Cordyceps militaris as an add-on therapy that may reduce the progression of inflammatory co-morbidities among patients infected with SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

The Efficacy of Ganoderma lucidum Extracts on Treating Endometrial Cancer: A Network Pharmacology Approach

Ganoderma lucidum (GL) is a prominent medicinal mushroom in traditional Chinese medicine, known for its potent antitumor properties. This study aimed to illustrate the efficacy of GL extracts (GLE) on treating endometrial cancer (EC) and explore the underlying mechanisms via network pharmacology and experimental validation. Network pharmacological analysis was conducted to explore the therapeutic efficacy and mechanisms of GL on EC. In vitro experimental validation was performed on human endometrial cancer cell lines HEC-1-A and KLE. Network pharmacology revealed that key targets of GL against EC were primarily associated with the Rap1 signaling pathway. In in vitro experiments, GLE or GGTI-298 (a GTPase inhibitor) treatment inhibited cell proliferation and migration, promoted cell apoptosis, increased caspase-3 level, and arrested cell cycle in G1 phase in HEC-1-A and KLE cells. GLE increased the protein expression of Rap1-GTP, p-AKT, and p-ERK2 in HEC-1-A and KLE cells. Moreover, GGTI-298 enhanced the effects of GLE on suppressing the malignant progression of EC cells and on activating Rap1 signaling pathway. GLE inhibited the malignant progression of EC cells probably via activating the Rap1 signaling pathway.

Advances in traditional herbal formulation based nano-vaccine for cancer immunotherapy: Unraveling the enigma of complex tumor environment and multidrug resistance

Cancer is attributed to uncontrolled cell growth and is among the leading causes of death with no known effective treatment while complex tumor microenvironment (TME) and multidrug resistance (MDR) are major challenges for developing an effective therapeutic strategy. Advancement in cancer immunotherapy has been limited by the over-activation of the host immune response that ultimately affects healthy tissues or organs and leads to a feeble response of the patient's immune system against tumor cells. Besides, traditional herbal medicines (THM) have been well-known for their essential role in the treatment of cancer and are considered relatively safe due to their compatibility with the human body. Yet, poor solubility, low bio-availability, and lack of understanding about their pathophysiological mechanism halt their clinical application. Moreover, considering the complex TME and drug resistance, the most precarious and least discussed concerns for developing THM-based nano-vaccination, are identification of specific biomarkers for drug inhibitory protein and targeted delivery of bioactive ingredients of THM on the specific sites in tumor cells. The concept of THM-based nano-vaccination indicates immunomodulation of TME by THM-based bioactive adjuvants, exerting immunomodulatory effects, via targeted inhibition of key proteins involved in the metastasis of cancer. However, this concept is at its nascent stage and very few preclinical studies provided the evidence to support clinical translation. Therefore, we attempted to capsulize previously reported studies highlighting the role of THM-based nano-medicine in reducing the risk of MDR and combating complex tumor environments to provide a reference for future study design by discussing the challenges and opportunities for developing an effective and safe therapeutic strategy against cancer.

Long COVID-19 gastrointestinal related disorders and traditional Chinese medicine: A network target-based approach

The significant number of individuals impacted by the pandemic makes prolonged symptoms after COVID-19 a matter of considerable concern. These are numerous and affect multiple organ systems. According to the World Health Organization (WHO), prolonged gastrointestinal issues are a crucial part of post-COVID-19 syndrome. The resulting disruption of homeostasis underscores the need for a therapeutic approach based on compounds that can simultaneously affect more than one target/node. The present review aimed to check for nutraceuticals possessing multiple molecular mechanisms helpful in relieving Long COVID-19-specific gastrointestinal symptoms. Specific plants used in Keywords Chinese Medicine (TCM) expected to be included in the WHO Global Medical Compendium were selected based on the following criteria: (1) they are widely used in the Western world as natural remedies and complementary medicine adjuvants; (2) their import and trade are regulated by specific laws that ensure quality and safety (3) have the potential to be beneficial in alleviating intestinal issues associated with Long COVID-19. Searches were performed in PubMed, Elsevier, Google Scholar, Scopus, Science Direct, and ResearchGate up to 2023. Cinnamomum cassia, Glycyrrhiza uralensis, Magnolia officinalis, Poria cocos, Salvia miltiorrhiza, Scutellaria baicalensis, and Zingiber officinalis were identified as the most promising for their potential impact on inflammation and oxidative stress. Based on the molecular mechanisms of the phytocomplexes and isolated compounds of the considered plants, their clinical use may lead to benefits in gastrointestinal diseases associated with Long COVID-19, thanks to a multiorgan and multitarget approach.

A systematic strategy for investigating the pharmacological effects and mechanism of traditional Chinese medicinal formula: Guilin Xiguashuang as a case

BACKGROUND

Traditional Chinese medicinal formula (TCMF) has specific advantages in treating diseases. However, the pharmacological effects and mechanism of TCMF composed of traditional Chinese medicines (TCM) with unclear active components or targets have not yet been fully elucidated.

OBJECTIVES

This research proposed a strategy for elucidating the pharmacological effects and mechanism to address this issue systematically.

METHODS

With Guilin Xiguashuang (GLXGS) taken as a case, this study newly provided the multi-level assays, which decomposes TCMF into components, TCM, and TCMF levels. The main pharmacological effects were acquired through a comprehensive analysis based on the active components, pharmacological effects of TCM, and clinical efficacy of TCMF, respectively. The core targets and pathways were further identified and verified to elucidate the mechanism.

RESULTS

The main pharmacological effects of GLXGS were anti-inflammatory, analgesic, antibacterial, immunoregulatory, and wound healing. Moreover, the mechanism analysis demonstrated that GLXGS was involved in the regulation of NF-κB and VEGF signaling pathways and core targets, such as IL-6 and TNF-α. Finally, unproven immunomodulatory and anti-inflammatory mechanism were verified using RAW264.7 and THP-1 cells. GLXGS was verified to down-regulate IL-6, IL-1β, TNF-α, and CD86 in lipopolysaccharides-stimulated RAW264.7 cells, while enhancing polarization in both RAW264.7 and THP-1 cells, which were consistent with analysis results.

CONCLUSION

The present research provides a systematic strategy for the pharmacological effect prediction and mechanism analysis of TCMF, which is of great significance for studying complex TCMF.

The mechanism of Chebulae Fructus Immaturus promote diabetic wound healing based on network pharmacology and experimental verification

ETHNOPHARMACOLOGICAL RELEVANCE

Diabetic ulcers (DUs) are commonly seen in the lower limbs, especially the feet. Long-term hyperglycaemia in diabetic patients may cause peripheral microvascular damage, which affects local blood flow reconstruction when the skin is ruptured. This results in delayed or even non-healing of skin wounds. Chebulae Fructus Immaturus (CFI) is a traditional Chinese medicine. According to traditional Chinese medicine theory, CFI belongs to the lung channel and large intestine channel. Clinical data confirm a significant clinical effect of CFI in the treatment of skin diseases. CFI can be safely used to treat wounds due to its natural active ingredients.

AIM OF THE STUDY

This study utilised HPLC-ESI-QTOF-MS/MS combined with network pharmacology to investigate the mechanism of Chebulae Fructus Immaturus extract (CFIE) in the treatment of DU. Moreover, the efficacy of CFIE on DU was verified in vitro and in vivo by constructing cell models and mouse models.

MATERIALS AND METHODS

The main ingredients of CFIE were identified by HPLC-ESI-QTOF-MS/MS. The targets of these ingredients were predicted by database analysis and intersected with the DU targets. Gene ontology (GO) was used for functional enrichment of differential genes, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for enrichment of signalling pathways related to the differential genes. The network pharmacology findings were validated in vivo and in vitro, and the affinity of key targets and active components was assessed using molecular docking.

RESULTS

Twenty-nine compounds of CFIE were identified by HPLC-ESI-QTOF-MS/MS, and their potential targets were predicted. Among these, 41 targets were associated with DU. KEGG enrichment analysis showed that the PI3K/AKT and HIF-1α signalling pathways were significantly enriched, which may be related to the promotion of wound angiogenesis. In vitro cell experiments showed that CFIE promoted the proliferation, migration and angiogenesis of HUVECs, and also affected the expression of pathway-related proteins. In vivo experiments showed that CFIE increased the expression of pathway-related proteins in wound tissue and promoted the formation of blood vessels.

CONCLUSIONS

In summary, this study systematically demonstrated the possible therapeutic effects and mechanisms of CFIE on DU through network pharmacology analysis and experimental verification. The results revealed that CFIE can accelerate the angiogenesis of diabetic wounds through the PI3K/AKT and HIF-1α signalling pathways, ultimately promoting the healing of diabetic wounds.

TCMNPAS: a comprehensive analysis platform integrating network formulaology and network pharmacology for exploring traditional Chinese medicine

The application of network formulaology and network pharmacology has significantly advanced the scientific understanding of traditional Chinese medicine (TCM) treatment mechanisms in disease. The field of herbal biology is experiencing a surge in data generation. However, researchers are encountering challenges due to the fragmented nature of the data and the reliance on programming tools for data analysis. We have developed TCMNPAS, a comprehensive analysis platform that integrates network formularology and network pharmacology. This platform is designed to investigate in-depth the compatibility characteristics of TCM formulas and their potential molecular mechanisms. TCMNPAS incorporates multiple resources and offers a range of functions designed for automated analysis implementation, including prescription mining, molecular docking, network pharmacology analysis, and visualization. These functions enable researchers to analyze and obtain core herbs and core formulas from herbal prescription data through prescription mining. Additionally, TCMNPAS facilitates virtual screening of active compounds in TCM and its formulas through batch molecular docking, allowing for the rapid construction and analysis of networks associated with "herb-compound-target-pathway" and disease targets. Built upon the integrated analysis concept of network formulaology and network pharmacology, TCMNPAS enables quick point-and-click completion of network-based association analysis, spanning from core formula mining from clinical data to the exploration of therapeutic targets for disease treatment. TCMNPAS serves as a powerful platform for uncovering the combinatorial rules and mechanism of TCM formulas holistically. We distribute TCMNPAS within an open-source R package at GitHub ( https://github.com/yangpluszhu/tcmnpas ), and the project is freely available at http://54.223.75.62:3838/ .

Network Pharmacology with Metabolomics Study to Reveal the Mechanisms of Bushen Huoxue Formula in Intervertebral Disc Degeneration Treatment

Background

Intervertebral disc degeneration (IVDD) is a pathophysiological process that leads to severe back pain or neurological deficits. The Bushen Huoxue Formula (BSHXF) is a traditional herbal remedy widely used to treat diseases related to IVDD. However, its pharmacological mechanism needs further exploration.

Objective

This study aimed to elucidate the mechanisms through which BSHXF treats IVDD-related diseases by integrating metabolomics with network pharmacology.

Methods

Network pharmacology was utilized to identify potential targets of BSHXF against IVDD. Additionally, an animal model of needle puncture-induced disc degeneration was established to assess the effect of BSHXF. Mice were randomly assigned to the sham group, model group, and BSHXF group. Various techniques, including PCR, CCK-8 assay, MRI, histological examinations, and immunohistochemical analyses, were employed to evaluate degenerative and oxidative stress conditions in mouse disc tissue and cultured nucleus pulposus (NP) cells. UHPLC-HRMS/MS was used to differential distinct metabolites in the disc tissue from different groups, and MetaboAnalyst 5.0 was employed to enrich the metabolic pathways.

Results

Through network pharmacology, 15 core proteins were identified through protein-protein interaction (PPI) network construction. Functional enrichment analysis highlighted the critical role of BSHXF in addressing IVDD by influencing the response to oxidative stress. Furthermore, experimental evidence demonstrated that BSHXF significantly improved the pathological progression of IVDD and increased oxidative stress markers SOD-1 and GPX1, both in the disc degeneration model and cultured NP cells. Metabolomics identified differential metabolites among the three groups, revealing 15 metabolic pathways between the sham and model groups, and 13 metabolic pathways enriched between the model and BSHXF groups.

Conclusion

This study, integrating network pharmacology and metabolomics, suggests that BSHXF can alleviate IVDD progression by modulating oxidative stress. Key metabolic pathways associated with BSHXF-mediated reduction of oxidative stress include the citrate cycle, cysteine and methionine metabolism, alanine, aspartate and glutamate metabolism, glycine, serine and threonine metabolism, D-glutamine and D-glutamate metabolism, glutathione metabolism, and tryptophan metabolism. While this research demonstrates the therapeutic potential of BSHXF in reducing oxidative stress levels in IVDD, further research is needed to thoroughly understand its underlying mechanisms.

Protective effect of Baoyuan Jieyu formula on long-term spaceflight composite stress-induced depressive-like behavior and memory deficits through regulation of Ca2+ channel currents

Long-term spaceflight composite stress (LSCS) can cause adverse effects on human systems, especially the central nervous system. This study aimed to identify the underlying mechanisms of the protective effect of Baoyuan Jieyu Formula (BYJYF) on LSCS-induced depressive-like behavior and memory deficits. In this experiment, we simulated the real space station environment for a period of 42 days. Novel object recognition test and forced swimming test were used to assess the memory abilities and depression level of rats as well as test the therapeutic effects of BYJYF treatment. Results showed LSCS could induce depressive-like behavior and damage short-term memory in the behavioral level, and BYJYF could enhance the ability to resist LSCS. Meanwhile, LSCS increased the levels of CRH, ACTH, and CORT and induced HPA axis hyperactivity, which can be relieved by BYJYF. Further, we predicted and verified the potential signaling pathways of BYJYF. Results showed BYJYF may reverse the inhibition of LSCS on Ca2+ channel currents. And we also found that BYJYF may exert its medicinal effects via four main active components including saikosaponin A. Overall, BYJYF exhibited protective effects against LSCS-induced depressive-like behavior and memory deficits, which might be ascribed to the regulation of Ca2+ channel currents and four active components. And it might become a promising candidate medicine for diseases induced by LSCS.

Study of Herbs Cortex Moutan, Poria cocos, and Alisma orientale and Periodontitis

INTRODUCTION

The Chinese traditional herbs Cortex Moutan, Poria cocos, and Alisma orientale are considered to have potential to ameliorate periodontitis, although the possible underlying mechanisms remain mostly unknown. Due to the complex formulation of Chinese herbs, it is important to understand the mechanisms of pharmacologic effects of traditional herbs for better application in modern medical treatment.

METHODS

Network pharmacology was applied to explore the mechanism of Cortex Moutan, Poria cocos, and Alisma orientale. First we analysed their chemical ingredients using the Traditional Chinese Medicine Systems Pharmacology database and identified 20 active ingredients. Then we analysed the target genes of these 20 active ingredients as well as genes associated with periodontitis and found 74 co-target genes. We further analysed the protein-protein interaction network of these 74 co-target genes using the STRING database and enriched the pathways using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis.

RESULTS

The top 10 core targets elicited were vascular endothelial growth factor A (VEGFA), interlukin-6 (IL-6), tumour necrosis factor (TNF), matrix metalloproteinase-2 (MMP2), matrix metalloproteinase-9 (MMP9), AKT serine/threonine kinase 1 (AKT1), prostaglandin-endoperoxide synthase 2 (PTGS2), kinase insert domain receptor (KDR), fibroblast growth factor 2 (FGF2), and serpin family E member 1 (SERPINE1). Using these a network of "herbs-ingredients-targetgenes-KEGG pathways." was constructed.

CONCLUSIONS

The target and bioprocess network suggested that the pharmacologic effects of Cortex Moutan, Poria cocos, and Alisma orientale may be mainly dependent on their anti-inflammatory potential. Further work is required to eucidate their detailed mechanisms of activity.

Network pharmacology analysis of the active ingredients of Corydalis hendersonii Hemsl. and their effects on eliminating neuroinflammation and improving motor functions in MPTP-intoxicated mice

ETHNOPHARMACOLOGICAL RELEVANCE

Corydalis hendersonii Hemsl. (CH), is a traditional Tibetan medicine used in highland areas for the treatment of alpine polycythemia, ulcers and various inflammatory diseases. Its antioxidant and anti-inflammatory effects have been demonstrated in experimental mice. Loss of dopaminergic neurons due to oxidative damage is thought to be an important factor in the development of PD, the potential antioxidant, anti-inflammatory effects of CH could potentially be used for PD treatment.

AIM OF THE STUDY

To identify potential targets of CH using network pharmacology and to investigate the neuroprotective effects in cultured cell models and in MPTP-intoxicated mice.

MATERIALS AND METHODS

The main chemical components of CH were analyzed by UPLC-MS/MS and their potential targets of action or signaling pathways were analyzed using network pharmacology. MPP + or LPS was added to SH-SY5Y or BV2 cells, respectively, to establish cellular models. MPTP was administered to C57BL/6J mice to induce inflammation and dopaminergic neuron loss as well as dyskinesia, followed by behavioral analysis to determine the role of CH in eliminating inflammation, avoiding neuron loss, and improving dyskinesia.

RESULTS

CH contains 241 alkaloids, 213 flavonoids, 177 terpenoids and 114 phenolic compounds. The targets crossover between CH and PD yielded 210 potential therapeutic targets, especially growth factors and inflammatory pathway-related genes, such as BDNF, NF-κB, as potential key targets. In cultured cells, CHE eliminated MPP + -induced impairment of cell viability as well as LPS-induced inflammation, respectively. In mice, CHE ameliorated MPTP-induced dyskinesia and rescued the loss of dopaminergic neurons in the substantia nigra and striatum. Mechanistically, CHE effectively maintained the activity of the BDNF-TrkB/Akt signaling pathway, accordingly, inhibited inflammatory signaling pathways such as HIF-1α/PKM2 and Notch/NF-kB.

CONCLUSIONS

CH performed well in eliminating inflammation and improving locomotor deficits in mice, and its potent active ingredients are worthy of subsequent research and development.

The Potential Mechanisms of Qufeng Zhitong Capsule against Rheumatoid Arthritis Based on Network Pharmacology and In Vitro Experiments

Qufeng Zhitong capsule (QFZTC) is a traditional Chinese herbal formula with potential therapeutic efficacy in rheumatoid arthritis (RA). This study seeks to clarify the potential effects and mechanisms of QFZTC against RA. Active compounds and targets of QFZTC were retrieved from the Herbal Ingredients' Targets (HIT), Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), and Traditional Chinese Medicine Integrated Database (TCMID) databases. RA-related targets were searched on GeneCards and DisGeNET databases. Protein-protein interaction (PPI) network was established using the STRING database. Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) enrichment analyses were performed on hub targets. Molecular docking was conducted on hub targets and active compounds. High-performance liquid chromatography (HPLC) was applied to characterize the active compounds in QFZTC. RA-fibroblast like synoviocytes (RA-FLSs) were cultured and treated by QFZTC-containing serum, in which proinflammatory cytokines and hub targets were detected. Cell viability was determined by cell counting kit-8 (CCK-8) assay. A total of 360 active compounds and 445 potential targets are identified for QFZTC against RA. Protein-protein interaction (PPI) network determined five hub targets, interleukin 6 (IL6), IL1B, VEGFA, JUN, and tumor necrosis factor (TNF). GO and KEGG analyses revealed that the MAPK pathway may be a critical signaling in QFZTC treating RA. Molecular docking showed that luteolin, kaempferol, and myricetin has good affinity with TNF, and they were identified by HPLC. In vitro experiments confirmed that QFZTC restrained the cell viability and inflammation in RA. This study revealed the active compounds and molecular targets for QFZTC treating RA. QFZTC is a promising drug and ameliorates RA by inhibiting inflammatory response.

Exploring the Potential Mechanisms of Action of Gentiana Veitchiorum Hemsl. Extract in the Treatment of Cholestasis using UPLC-MS/MS, Systematic Network Pharmacology, and Molecular Docking

INTRODUCTION

Gentiana veitchiorum Hemsl. (GV) has a long history in Tibetan medicine for treating hepatobiliary disease cholestasis. However, the mechanisms mediating its efficacy in treating cholestasis have yet to be determined.

AIM

To elucidate the mechanisms of action of GV in the treatment of cholestasis, an integrated approach combining ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis with network pharmacology was established.

MATERIALS AND METHODS

A comprehensive analysis of the chemical composition of GV was achieved by UPLC-MS/MS. Subsequently, a network pharmacology method that integrated target prediction, a protein-protein interaction (PPI) network, gene set enrichment analysis, and a component- target-pathway network was established, and finally, molecular docking and experiments in vitro were conducted to verify the predicted results.

RESULTS

Twenty compounds that were extracted from GV were identified by UPLC-MS/MS analysis. Core proteins such as AKT1, TNF, and IL6 were obtained through screening in the Network pharmacology PPI network. The Kyoto Encyclopedia of the Genome (KEGG) pathway predicted that GV could treat cholestasis by acting on signaling pathways such as TNF/IL-17 / PI3K-Akt. Network pharmacology suggested that GV might exert a therapeutic effect on cholestasis by regulating the expression levels of inflammatory mediators, and the results were further confirmed by the subsequent construction of an LPS-induced RAW 264.7 cell model.

CONCLUSIONS

In this study, UPLC-MS/MS analysis, network pharmacology, and experiment validation were used to explore potential mechanisms of action of GV in the treatment of cholestasis.

Role of Network Pharmacology in Prediction of Mechanism of Neuroprotective Compounds

Network pharmacology is an emerging pioneering approach in the drug discovery process, which is used to predict the therapeutic mechanism of compounds using various bioinformatic tools and databases. Emerging studies have indicated the use of network pharmacological approaches in various research fields, particularly in the identification of possible mechanisms of herbal compounds/ayurvedic formulations in the management of various diseases. These techniques could also play an important role in the prediction of the possible mechanisms of neuroprotective compounds. The first part of the chapter includes an introduction on neuroprotective compounds based on literature. Further, network pharmacological approaches are briefly discussed. The use of network pharmacology in the prediction of the neuroprotective mechanism of compounds is discussed in detail with suitable examples. Finally, the chapter concludes with the current challenges and future prospectives.

Mechanisms of Nelumbinis folium targeting PPARγ for weight management: A molecular docking and molecular dynamics simulations study

The lotus leaf, Nelumbinis folium (NF), has frequently appeared in obesity clinical trials as an intervention to promote weight loss and improve metabolic profiles. However, the molecular mechanisms by which it interacts with important obesity targets and pathways, such as the peroxisome proliferator-activated receptor gamma (PPARγ) within the PPAR signalling pathway, were not well understood. This study aims to screen for candidate compounds from NF with desirable pharmacokinetic properties and examine their binding feasibility at the PPARγ ligand-binding domain (LBD). Ligand- and structure-based screening of NF compounds were performed, and a consensus approach has been applied to identify druggable candidates. By examining the pharmacokinetic profiles, a large proportion of NF compounds exhibited favourable drug-likeness and oral bioavailability properties. Furthermore, the binding affinity scores and poses provided new insights on the distinctive binding behaviours of NF compounds at the LBD of PPARγ in its inactive form. Several NF compounds could bind strongly to PPARγ at sub-pockets where partial agonists and antagonists were found to bind and may induce conformational changes that influence co-repressor binding, trans-repression, and gene expression inhibition. Subsequent molecular dynamics simulations of a candidate compound (NF129 narcissin) bound to PPARγ revealed conformational stability, residue fluctuation, and binding behaviours comparable to that of the known inhibitor, SR1664. Therefore, it can be proposed that narcissin exhibits characteristics of a PPARγ antagonist. Further experimental validation to support the development of NF129 as a future anti-obesity agent is warranted.

Exploring the mechanism of Liuwei Dihuang formula for promoting melanin synthesis in juvenile zebrafish based on network pharmacology and molecular docking

Background

Vitiligo stands as a challenging skin disorder with limited treatment options available. LiuWei DiHuang formula (LDF), a renowned Traditional Chinese medicine, has exhibited promising results in treating vitiligo over an extended period. However, the precise underlying mechanism of its action remains elusive.

Methods

Employing a comprehensive network pharmacology approach, this study identified active compounds and their corresponding targets within LDF, while also pinpointing vitiligo-associated targets sourced from the TCMSP database, OMIM, DisGenNET, and Genecards. A network was established to illustrate the connections between active compounds and targets, alongside a protein-protein interaction network. Further analyses, encompassing Gene Ontology (GO) function and KEGG pathway enrichment, were conducted using the DAVID platform. Molecular docking simulations were performed utilizing AutoDockTools and AutoDockVina software. To validate the outcomes of the systematic pharmacological investigation, experiments were conducted using juvenile zebrafish.

Results

The collective effort of the network pharmacology approach yielded a compilation of 41 compounds and 192 targets. Molecular docking simulations notably revealed the lowest binding energies for CAT-quercetin and CAT-Kaempferol interactions. The utilization of juvenile zebrafish experiments highlighted a significant increase in melanocyte count following methoxsalen and LDF treatment. Notably, LDF prominently augmented the expression levels of proteins related to melanogenesis. Additionally, LDF showcased the capacity to enhance CAT and SOD levels while concurrently reducing ROS and MDA activity. In contrast to the model group, substantial increases in protein and mRNA levels of Nrf2 and HO-1 were observed in response to LDF treatment (P < 0.05).

Conclusion

Through a meticulous network pharmacology approach, this study successfully predicted active components and potential targets associated with LDF's application in vitiligo treatment. The therapeutic effectiveness of LDF against vitiligo is postulated to stem from its regulation of oxidative stress factors and the Nrf2/HO-1 pathway.

Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes

Background: Herbal medicines traditionally target organs for treatment based on medicinal properties, and this theory is widely used for prescriptions. However, the scientific evidence explaining how herbs act on specific organs by biological methods has been still limited. This study used bioinformatic tools to identify the target organ locations of Radix Achyranthis Bidentatae (RAB), a blood-activating herb that nourishes the liver and kidney, strengthens bones, and directs prescription to the lower body. Methods: RAB's active compounds and targets were collected and predicted using databases such as TCMSP, HIT2.0, and BATMAN-TCM. Next, the RAB's target list was analyzed based on two approaches to obtain target organ locations. DAVID and Gene ORGANizer enrichment-based approaches were used to enrich an entire gene list, and the BioGPS and HPA gene expression-based approaches were used to analyze the expression of core genes. Results: RAB's targets were found to be involved in whole blood, blood components, and lymphatic organs across all four tools. Each tool indicated a particular aspect of RAB's target organ locations: DAVID-enriched genes showed a predominance in blood, liver, and kidneys; Gene ORGANizer showed the effect on low body parts as well as bones and joints; BioGPS and HPA showed high gene expression in bone marrow, lymphoid tissue, and smooth muscle. Conclusion: Our bioinformatics-based target organ location prediction can serve as a modern interpretation tool for the target organ location theory of traditional medicine. Future studies should predict therapeutic target organ locations in complex prescriptions rather than single herbs and conduct experiments to verify predictions.

Combining network pharmacology, molecular docking, molecular dynamics simulation, and experimental verification to examine the efficacy and immunoregulation mechanism of FHB granules on vitiligo

Background

Fufang Honghua Buji (FHB) granules, have proven efficacy against vitiligo in long-term clinical practice. However, its major active chemical components and molecular mechanisms of action remain unknown. The purpose of this study was to confirm the molecular mechanism of FHB's therapeutic effect on vitiligo utilizing network pharmacology, molecular docking, and molecular dynamics simulation prediction, as well as experimental verification.

Methods

Traditional Chinese Medicine Systems Pharmacology (TCMSP) and HERB databases were used to obtain the chemical composition and action targets of FHB. Online Mendelian Inheritance in Man (OMIM), DrugBank, DisGeNET, GeneCards, and Therapeutic Target Database (TTD) databases were applied to screen for vitiligo-related targets. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed through the Matascape database. Molecular docking and dynamics simulation methods were for the analysis of the binding sites and binding energies between the FHB's active components and the targets. Finally, a vitiligo mouse model was created, and the therapeutic effect and molecular mechanism of action of FHB were validated using enzyme linked immunosorbent assay (ELISA), western blot (WB), and quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Additionally, hematoxylin-eosin staining (HE) and blood biochemical assays were conducted to assess the biosafety of FHB.

Result

The screening of chemical composition and targets suggested that 94 genetic targets of FHB were associated with vitiligo. The bioinformatics analysis suggested that luteolin, quercetin, and wogonin may be major active components, and nuclear factor-kappa B p65 subunit (RELA), signal transducer, and activator of transcription (STAT) 3 and RAC-alpha serine/threonine-protein kinase (AKT) 1 may be potential targets of FHB-vitiligo therapy. Molecular docking and dynamics simulation further demonstrated that luteolin, quercetin, and wogonin all bound best to STAT3. Through experimental verification, FHB has been demonstrated to alleviate the pathogenic characteristics of vitiligo mice, suppress the JAK-STAT signaling pathway, reduce inflammation, and increase melanogenesis. The in vivo safety evaluation experiments also demonstrated the non-toxicity of FHB.

Conclusions

FHB exerts anti-inflammatory and melanogenesis-promoting effects via the effect of multi-component on multi-target, among which the JAK-STAT pathway is a validated FHB-vitiligo target, providing new ideas and clues for the development of vitiligo therapy.

Uncovering the mechanisms of Yi Qi Tong Qiao Pill in the treatment of allergic rhinitis based on Network target analysis

OBJECTIVE

The purpose of this study is to reveal the mechanism of action of Yi Qi Tong Qiao Pill (YQTQP) in the treatment of allergic rhinitis (AR), as well as establish a paradigm for the researches on traditional Chinese medicine (TCM) from systematic perspective.

METHODS

Based on the data collected from TCM-related and disease-related databases, target profiles of compounds in YQTQP were calculated through network-based algorithms and holistic targets of TQTQP was constructed. Network target analysis was performed to explore the potential mechanisms of YQTQP in the treatment of AR and the mechanisms were classified into different modules according to their biological functions. Besides, animal and clinical experiments were conducted to validate our findings inferred from Network target analysis.

RESULTS

Network target analysis showed that YQTQP targeted 12 main pathways or biological processes related to AR, represented by those related to IL-4, IFN-γ, TNF-α and IL-13. These results could be classified into 3 biological modules, including regulation of immune and inflammation, epithelial barrier disorder and cell adhesion. Finally, a series of experiments composed of animal and clinical experiments, proved our findings and confirmed that YQTQP could improve related symptoms of AR, like permeability of nasal mucosa epithelium.

CONCLUSION

A combination of Network target analysis and the experimental validation indicated that YQTQP was effective in the treatment of AR and might provide a new insight on revealing the mechanism of TCM against diseases. Trial registration Name of the registry: Chinese Clinical Trial Registry: Trial registration number: ChiCTR-TRC-13,003,137: Date of registration: Registered 29 March 2013 - Retrospectively registered: URL of trial registry record: https://www.chictr.org.cn/showproj.html?proj=6422 .

Repositioning of clinically approved drug Bazi Bushen capsule for treatment of Aizheimer's disease using network pharmacology approach and in vitro experimental validation

Aims

To explore the new indications and key mechanism of Bazi Bushen capsule (BZBS) by network pharmacology and in vitro experiment.

Methods

The ingredients library of BZBS was constructed by retrieving multiple TCM databases. The potential target profiles of the components were predicted by target prediction algorithms based on different principles, and validated by using known activity data. The target spectrum of BZBS with high reliability was screened by considering the source of the targets and the node degree in compound-target (C-T) network. Subsequently, new indications for BZBS were predicted by disease ontology (DO) enrichment analysis and initially validated by GO and KEGG pathway enrichment analysis. Furthermore, the target sets of BZBS acting on AD signaling pathway were identified by intersection analysis. Based on STRING database, the PPI network of target was constructed and their node degree was calculated. Two Alzheimer's disease (AD) cell models, BV-2 and SH-SY5Y, were used to preliminarily verify the anti-AD efficacy and mechanism of BZBS in vitro.

Results

In total, 1499 non-repeated ingredients were obtained from 16 herbs in BZBS formula, and 1320 BZBS targets with high confidence were predicted. Disease enrichment results strongly suggested that BZBS formula has the potential to be used in the treatment of AD. GO and KEGG enrichment results provide a preliminary verification of this point. Among them, 113 functional targets of BZBS belong to AD pathway. A PPI network containing 113 functional targets and 1051 edges for the treatment of AD was constructed. In vitro experiments showed that BZBS could significantly reduce the release of TNF-α and IL-6 and the expression of COX-2 and PSEN1 in Aβ_25-35-induced BV-2 cells, which may be related to the regulation of ERK_1/2/NF-κB signaling pathway. BZBS reduced the apoptosis rate of Aβ_25-35 induced SH-SY5Y cells, significantly increased mitochondrial membrane potential, reduced the expression of Caspase3 active fragment and PSEN1, and increased the expression of IDE. This may be related to the regulation of GSK-3β/β-catenin signaling pathway.

Conclusions

BZBS formula has a potential use in the treatment of AD, which is achieved through regulation of ERK_1/2, NF-κB signaling pathways, and GSK-3β/β-catenin signaling pathway. Furthermore, the network pharmacology technology is a feasible drug repurposing strategy to reposition new clinical use of approved TCM and explore the mechanism of action. The study lays a foundation for the subsequent in-depth study of BZBS in the treatment of AD and provides a basis for its application in the clinical treatment of AD.

Herb-drug interactions between Panax notoginseng or its biologically active compounds and therapeutic drugs: A comprehensive pharmacodynamic and pharmacokinetic review

ETHNOPHARMACOLOGICAL RELEVANCE

Herbs, along with the use of herb-drug interactions (HDIs) to combat diseases, are increasing in popularity worldwide. HDIs have two effects: favorable interactions that tend to improve therapeutic outcomes and/or minimize the toxic effects of drugs, and unfavorable interactions aggravating the condition of patients. Panax notoginseng (Burk.) F.H. Chen is a medicinal plant that has long been commonly used in traditional Chinese medicine to reduce swelling, relieve pain, clear blood stasis, and stop bleeding. Numerous studies have demonstrated the existence of intricate pharmacodynamic (PD) and pharmacokinetic (PK) interactions between P. notoginseng and conventional drugs. However, these HDIs have not been systematically summarized.

AIM OF THE REVIEW

To collect the available literature on the combined applications of P. notoginseng and drugs published from 2005 to 2022 and summarize the molecular mechanisms of interactions to circumvent the potential risks of combination therapy.

MATERIALS AND METHODS

This work was conducted by searching PubMed, Scopus, Web of Science, and CNKI databases. The search terms included "notoginseng", "Sanqi", "drug interaction," "synergy/synergistic", "combination/combine", "enzyme", "CYP", and "transporter".

RESULTS

P. notoginseng and its bioactive ingredients interact synergistically with numerous drugs, including anticancer, antiplatelet, and antimicrobial agents, to surmount drug resistance and side effects. This review elaborates on the molecular mechanisms of the PD processed involved. P. notoginseng shapes the PK processes of the absorption, distribution, metabolism, and excretion of other drugs by regulating metabolic enzymes and transporters, mainly cytochrome P450 enzymes and P-glycoprotein. This effect is a red flag for drugs with a narrow therapeutic window. Notably, amphipathic saponins in P. notoginseng act as auxiliary materials in drug delivery systems to enhance drug solubility and absorption and represent a new entry point for studying interactions.

CONCLUSION

This article provides a comprehensive overview of HDIs by analyzing the results of the in vivo and in vitro studies on P. notoginseng and its bioactive components. The knowledge presented here offers a scientific guideline for investigating the clinical importance of combination therapies. Physicians and patients need information on possible interactions between P. notoginseng and other drugs, and this review can help them make scientific predictions regarding the consequences of combination treatments.

Prospects for the application of traditional Chinese medicine network pharmacology in food science research

There has always been a particular difficulty with in-depth research on the mechanisms of food nutrition and bioactivity. The main function of food is to meet the nutritional needs of the human body, rather than to exert a therapeutic effect. Its relatively modest biological activity makes it difficult to study from the perspective of general pharmacological models. With the popularity of functional foods and the concept of dietary therapy, and the development of information and multi-omics technology in food research, research into these mechanisms is moving towards a more microscopic future. Network pharmacology has accumulated nearly 20 years of research experience in traditional Chinese medicine (TCM), and there has been no shortage of work from this perspective on the medicinal functions of food. Given the similarity between the concept of 'multi-component-multi-target' properties of food and TCM, we think that network pharmacology is applicable to the study of the complex mechanisms of food. Here we review the development of network pharmacology, summarize its application to 'medicine and food homology', and propose a methodology based on food characteristics for the first time, demonstrating its feasibility for food research. © 2023 Society of Chemical Industry.

Integration of pharmacodynamics, network pharmacology and metabolomics to elucidate effect and mechanism of Artemisia capillaris Thunb. in the treatment of jaundice

ETHNOPHARMACOLOGICAL RELEVANCE

As one of the most commonly used herbs, Artemisia capillaris Thunb. (ACT) display favorable effect in the treatment of jaundice. However, mechanism of ACT in the treatment of jaundice remains unclear at present, which limits its development and application.

AIM OF THE STUDY

To investigate effect and mechanism of Artemisia capillaris Thunb. (ACT) in the treatment of jaundice using pharmacodynamics, network pharmacology and metabolomics.

METHODS

Effect of ACT in treating jaundice was evaluated by biochemical assays and pathological observation using the α-naphthyl isothiocyanate (ANIT)-induced mice. Jaundice-relieving mechanism of ACT was investigated by integration of network pharmacology and metabolomics.

RESULTS

After the mice with jaundice were administrated ACT extract for 9 days, compared to that of the model group, serum D-BIL, T-BIL and ALP levels of the mice in the low, medium, high dose of ACT group decreased by 39.81%, 15.30% and 16.92%; 48.06%, 42.54% and 36.91%; 26.90%, 12.34% and 16.90%, respectively. The pathologic study indicated that ACT improved the symptoms of liver injury of the mice with jaundice. The network of herb (i.e., ACT)-components-targets-disease (i.e., jaundice) was established, which consisted of 17 components classified in flavonoids, chromones, organic acids, terpenoids, and 234 targets related to treatment of jaundice. Metabolomics analysis showed that, compared to that in the model group, level of 8 differential metabolites were upregulated and level of 29 differential metabolites were downregulated in the mice liver in the ACT group, respectively. The main metabolic pathways involved in treatment of jaundice by ACT were pantothenate and CoA biosynthesis, glutathione metabolism, biosynthesis of unsaturated fatty acids, primary bile acid biosynthesis in the liver, respectively. The integrated analysis of network pharmacology and metabolomics showed that 3α,7α,12α a-Trihydroxy-5β-cholanate, glycocholate, taurocholate, pantetheine 4'-phosphate, and d-4'-phosphopantothenate were the potential biomarkers for treatment of jaundice, and AKR1C4, ALDH2 and HSD11B were the potential drug targets in the treatment of jaundice by ACT.

CONCLUSION

The study based on metabolomics and network pharmacology indicated that ACT can display favorable jaundice-relieving effect by its multiple components regulating multiple biomarkers, multiple targets and multiple pathways, and may be a rational therapy for the treatment of jaundice.

Exploring the effect of Weifuchun capsule on the toll-like receptor pathway mediated HES6 and immune regulation against chronic atrophic gastritis

ETHNOPHARMACOLOGICAL RELEVANCE

Weifuchun capsule (WFC) is a traditional Chinese patent medicine for chronic atrophic gastritis (CAG) in clinic. However, the mechanism of action of WFC for CAG still remains unclear due to its complex composition.

AIM OF THE STUDY

The study was projected to uncover the mechanism of action of WFC and the corresponding pharmacodynamic substance of WFC against CAG as well as providing a standard example for the research of traditional Chinese medicine (TCM) from the perspective of the network and the system.

MATERIALS AND METHODS

We identified the compounds of WFC through LC-MS/MS analysis and performed a systematic network targets analysis for WFC in the treatment of CAG which thoroughly described the mechanism of action of WFC for CAG. Based on analysis integrating omics data and algorithms, we focused on the specific immune regulatory role of WFC in the treatment of CAG, especially on a hub pathway, Toll-like receptor signaling pathway and thus deciphered the role of WFC in immune regulation, anti-inflammation and mediation of HES6. In experiments part, MNNG-GES-1-cell line and rat models were used to validate our findings.

RESULTS

In this study, compounds of WFC are identified through LC‒MS/MS and network target analysis is performed to dissect the specific immunoregulatory effect as well as mediation of HES6, a newly discovered biomolecule related to gastritis carcinoma progression, of WFC on CAG through the Toll-like receptor signaling pathway. Based on cell line and rat models, we verify the mechanism of action of WFC for CAG in inhibiting inflammatory cytokines, regulating immune cells like T cells and macrophages, related genes including TLR2 and CD14. It is also validated that WFC inhibits the expression of HES6 (P < 0.05).

CONCLUSION

Based on the combination of computational strategy and experiments, our study offers a comprehensive analysis to reveal the role of WFC in regulating immune response, inhibiting inflammation in the treatment of CAG, and provides a standard example for the research of TCM from the perspective of the network and the system.

Fuzheng Xiaoai Decoction 1 ameliorated cancer cachexia-induced muscle atrophy via Akt-mTOR pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Fuzheng Xiaoai Decoction 1 (FZXAD1) is a clinical experience prescription for the treatment of cancer patients at an advanced stage. FZXAD1 has been used for more than 10 years in the clinic and can effectively improve the deficiency syndrome of cancer patients. However, its mechanisms need further clarification.

AIM OF THE STUDY

To check the effects of FZXAD1 in colon 26 (C26) cancer cachexia mice and try to clarify the mechanisms of FZXAD1 in ameliorating cancer cachexia symptoms.

MATERIALS AND METHODS

An animal model of cancer cachexia was constructed with male BALB/c mice bearing C26 tumor cells. Food intake, body weight and tumor size were measured daily during the animal experiment. Tissue samples in different groups including tumor and gastrocnemius muscle, were dissected and weighed at the end of the assay. Serum biochemical indicators such as total protein (TP), glucose (GLU) and alkaline phosphatase (ALP) were also detected. Network pharmacology-based analysis predicted the possible targets and signaling pathways involved in the effects of FZXAD1 on cancer cachexia therapy. Western blotting assays of the gastrocnemius muscle tissues from C26 tumor-bearing mice were then used to confirm the predicted possible targets of FZXAD1.

RESULTS

The results of animal experiments showed that FZXAD1 could ameliorate cancer cachexia by alleviating the muscle wasting as well as kidney atrophy and increasing the body weight of cancer cachexia mice. AKT1, MTOR, MAPK3, HIF1A and MAPK1 were predicted as the core targets of FZXAD1. Western blotting confirmed the prediction that FZXAD1 increased the expression levels of phosphorylated Akt and mTOR in the muscle tissues. In addition, FZXAD1 treatment obviously ameliorated the increased levels of HIF-1α and phosphorylated Erk1/2 in C26 tumor-bearing mice.

CONCLUSION

FZXAD1 effectively ameliorated cancer cachexia in an animal model of mice, which is consistent with its efficacy in the treatment of cancer patients. The mechanisms of FZXAD1 might be mainly based on its alleviating effects on muscle atrophy by activating the Akt-mTOR pathway and thus helping to maintain body weight.

An in silico and in vitro integrated analysis method to reveal the curative mechanisms and pharmacodynamic substances of Bufei granule on chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a common respiratory disease with high disability and mortality. Clinical studies have shown that the Traditional Chinese Medicine Bufei Granule (BFG) has conspicuous effects on relieving cough and improving lung function in patients with COPD and has a reliable effect on the treatment of COPD, whereas the therapeutic mechanism is vague. In the present study, the latent bronchodilators and mechanism of BFG in the treatment of COPD were discussed through the method of network pharmacology. Then, the molecular docking and molecular dynamics simulation were performed to calculate the binding efficacy of corresponding compounds in BFG to muscarinic receptor. Finally, the effects of BFG on bronchial smooth muscle were validated by in vitro experiments. The network pharmacology results manifested the anti-COPD effect of BFG was mainly realized via restraining airway smooth muscle contraction, activating cAMP pathways and relieving oxidative stress. The results of molecular docking and molecular dynamics simulation showed alpinetin could bind to cholinergic receptor muscarinic 3. The in vitro experiment verified both BFG and alpinetin could inhibit the levels of CHRM3 and acetylcholine and could be potential bronchodilators for treating COPD. This study provides an integrating network pharmacology method for understanding the therapeutic mechanisms of traditional Chinese medicine, as well as a new strategy for developing natural medicines for treating COPD.

Exploring the molecular mechanism of Gan Shuang granules for the treatment of non-alcoholic steatohepatitis using network pharmacology, molecular docking, and experimental verification

Background: With the gradual increase in prevalence in recent years, non-alcoholic steatohepatitis (NASH) has become one of the significant health problems that urgently needs to be addressed worldwide. GanShuang Granules (GSG) is derived from the classical Chinese formula Xiaoyao San and mainly used in the clinical treatment of chronic liver diseases. Objective: In this study, we aim to gain a deeper insight into the inhibiting effects of GSG on non-alcoholic fatty liver disease (NAFLD) rats and preliminarily elucidate the underlying intervention mechanisms. Methods: First, High performance liquid chromatography (UHPLC-Q/Orbitrap-MS/MS) was used for the active compounds prediction in GSG. Then the data was mapped to mzCloud database. The targets corresponding to GSG compounds were collected from public databases, along with disease genes for NAFLD. The core targets and molecular mechanisms of GSG for NAFLD treatment were predicted by protein-protein interaction (PPI) network, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses. Molecular docking of the core target-component interactions was simulated using AutoDock Vina software. The effect of GSG on NASH rats was evaluated by pathological staining and analysis of various index results. Finally, the candidate targets were further validated by ELISA and western blot (WB) analyses. Results: Combining UHPLC-Q/Orbitrap-MS/MS data analysis and public database data, a total of 346 cross-targets were obtained, corresponding to 81 compounds. The subnetwork with an MCODE score of 53.623 is a potential core target group for this study. GO and KEGG enrichment analyses showed that the targets of GSG in NAFLD were mostly related to oxidative stress, the NF-κB signaling pathway, and the apoptosis signaling pathway. By integrating the results of network pharmacology analysis, the core objectives of this study mainly include AKT1, CASP9, TNF, and CASP8. The core ingredients are related to resveratrol and fisetin. The molecular docking results indicated key binding activity between AKT1-fisetin, AKT1-Resveratrol, and CASP8-fisetin. Moreover, GSG could improve the inflammatory status and restore the abnormal lipid accumulation of NAFLD/NASH liver, and these levels are further verified by pathological staining and detection of related indicators. Mechanistically, GSG could regulate protein expression levels in the liver for P65, p-P65, IKB, p-IKB, IKK, caspase-3, -8, -9, and cytochrome C, etc. It reflects the inhibitory effect of GSG on the NF-κB/IκB signaling pathway. Conclusion: Our results suggested that GSG demonstrated therapeutic effects on NAFLD/NASH rats, and these may be mainly reflected in the inhibitory effects on the NF-κB/IκB signaling pathway and its downstream inflammation and apoptosis signals.

Exploring the comorbidity mechanisms between asthma and idiopathic pulmonary fibrosis and the pharmacological mechanisms of Bu-Shen-Yi-Qi decoction therapy via network pharmacology

Backgrounds

Asthma and idiopathic pulmonary fibrosis (IPF) are common chronic diseases of the respiratory system in clinical practice. However, the relationship and molecular links remain unclear, and the current treatment’s efficacy is disappointing. Bu-Shen-Yi-Qi (BSYQ) decoction has proven effective in treating various chronic airway inflammatory diseases, including asthma and IPF. But the underlying pharmacological mechanisms are still to be elucidated.

Methods

This study searched the proteins related to asthma and IPF via TTD, CTD, and DisGeNET databases and then submitted to the STRING to establish the protein–protein interaction (PPI) network. The co-bioinformatics analysis was conducted by Metascape. The active ingredients of BSYQ decoction were screened from TCMSP, ETCM, BATMAN-TCM databases, and HPLC/MS experiment. The corresponding targets were predicted based on TCMSP, ETCM, and BATMAN-TCM databases. The shared targets for asthma and IPF treatment were recognized, and further GO and KEGG analyses were conducted with the DAVID platform. Finally, molecule docking via Autodock Vina was employed to predict the potential binding mode between core potential compounds and targets.

Results

Finally, 1333 asthma-related targets and 404 IPF-related proteins were retrieved, 120 were overlapped between them, and many of the asthma-related proteins fall into the same statistically significant GO terms with IPF. Moreover, 116 active ingredients of BSYQ decoction were acquired, and 1535 corresponding targets were retrieved. Eighty-three potential compounds and 56 potential targets were recognized for both asthma and IPF treatment. GO and KEGG analysis indicated that the inflammation response, cytokine production, leukocyte differentiation, oxygen level response, etc., were the common pathological processes in asthma and IPF, which were regulated by BSYQ decoction. Molecule docking further predicted the potential binding modes between the core potential compounds and targets.

Conclusion

The current study successfully clarified the complex molecule links between asthma and IPF and found the potential common targets. Then we demonstrated the efficacy of BSYQ decoction for asthma and IPF treatment from the angle of network pharmacology, which may provide valuable references for further studies and clinical use.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12906-022-03637-7.

Network pharmacology and in vivo experiments reveal the pharmacological effects and molecular mechanisms of Simiao Powder in prevention and treatment for gout

Background

Gout is a common disease with high incidence due to unhealthy diet and living habits. Simiao Powder, as a classic formula consisted of four common herbs, has been widely used in clinical practice since ancient times to prevent and treat gout. However, the pharmacological mechanism of Simiao Powder is still unclear.

Methods

Based on network pharmacology, Simiao Powder active compounds were identified in TCMSP, ETCM and BATMAN database, used to establish a network of interaction between potential targets of Simiao Powder and known therapeutic targets of gout. Subsequently, the key potential targets are being used for protein–protein interaction, GO enrichment analysis and KEGG pathway enrichment analysis through several authoritative open databases. Molecular docking through AutoDockTools software can verify interaction between molecules. Finally, to validate the predicted results, in vivo experiments based on hyperuricemic-gout mice model were designed and treated with Simiao powder and allopurinol. Serum levels of uric acid (UA), creatinine (Cr), blood urea nitrogen (BUN) and xanthine oxidase (XOD) were determined using a customized assay kit while the expression of PPAR-γ, PTGS1, IL-6 and Bcl2 mRNA were analyzed through qRT-PCR.

Results

Disease-target-compound network was visualized basing on the 20 bioactive compounds and the 19 potential targets using Cytoscape software. The results of PPI analysis, GO enrichment and KEGG pathway enrichment analysis indicate that the potential mechanism of Simiao Powder in treating gout may be achieved by regulating immune and inflammatory reactions, improving metabolism and endocrine. The results of molecular docking show that most of the targets and components have good binding activity. In vivo experiments revealed that Simiao powder can decreased serum UA and XOD levels in hyperuricemic-gout mice, and improved renal function. Furthermore, Simiao powder certainly regulates the expression of PPAR-γ, PTGS1, IL-6 and Bcl2 mRNA in ankle tissue in hyperuricemic-gout mice.

Conclusion

Collectively, this research predicted a multiple compounds, targets, and pathways model mechanism of Simiao Powder in the prevention and treatment of gout, providing new ideas and methods for in-depth research, via vivo experiments.

Uncovering the characteristics of the gut microbiota in patients with acute ischemic stroke and phlegm-heat syndrome

Growing evidence has indicated that the characteristics of gut microbiota are associated with acute ischemic stroke (AIS). Phlegm-heat syndrome (PHS), a specific pathological state of the AIS, is one of the common traditional Chinese syndromes of stroke. The long duration of PHS in patients with AIS could lead to poor clinical outcomes. Gut microbiota characteristics in patients with both AIS and PHS, and their relationship remains unknown. This study was designed to investigate the alterations in gut microbiota in patients with AIS and PHS through a cross-sectional study. Fecal samples were collected from 10 patients with AIS and non-PHS (ntAIS), 7 patients with AIS and PHS (tAIS), and 10 healthy controls (HC). Samples were profiled via Illumina sequencing of the 16S rRNA V3-V4. Stroke severity was assessed at admission by the National Institutes of Health Stroke Scale (NIHSS) and modified Rankin scale (mRS); their correlation with gut microbiota was investigated. The alpha-diversity of the bacterial communities was significantly higher in the fecal samples of patients with tAIS than in patients with ntAIS (Shannon index, P = 0.037). In addition, the combined tAIS and ntAIS group (tntAIS) exhibited higher microbiotic diversity when compared with HC (chao1, P = 0.019). The structure of intestinal microbiota was effectively distinguished between the tAIS and ntAIS group (ANOSIM, r = 0.337, P = 0.007). Additionally, the gut microbiota structure was significantly different between the tntAIS and HC groups (ANOSIM, r = 0.217, P = 0.005). The genera, Ruminococcaceae_ UCG_002 and Christensenellaceae_R-7_group, were implicated in the discrimination of PHS from non-PHS. The order Lactobacillales and family Lachnospiraceae were significantly negatively correlated with NIHSS and mRS at admission (P < 0.05). By contrast, the order Desulfovibrionales, families Christensenellaceae and Desulfovibrionaceae, and genera Ruminococcaceae UCG-014 and Ruminococcaceae UCG-002 were significantly positively correlated with NIHSS and mRS at admission (P < 0.05). This study is the first to profile the characteristics of gut microbiota in patients with AIS and PHS, compared with those with non-PHS. The genera, Ruminococcaceae_ UCG_002 and Christensenellaceae_R-7_group, may be objective indicators of this traditional Chinese medicine (TCM) syndrome in AIS. Furthermore, it provides a microbe-inspired biological basis for TCM syndrome differentiation.

Weipiling decoction alleviates N-methyl-N-nitro-N′-nitrosoguanidine-induced gastric precancerous lesions via NF-κB signalling pathway inhibition

Aim of the study

We aimed to explore how weipiling (WPL) decoction WPL alleviates gastric precancerous lesions (GPLs) and uncover its anti-inflammatory roles in GPL treatment.

Materials and methods

The anti-GPL action mechanisms of WPL were analysed using a network pharmacological method. The WPL extract was prepared in a traditional way and evaluated for its major components using high-performance liquid chromatography with tandem mass spectrometry (HPLC–MS/MS). BALB/c mice were exposed to N-methyl-N-nitro-N-nitrosoguanidine (MNNG) (150 μg/mL) for 6 weeks to induce GPLs. GPL mice were administered WPL (3.75 g/kg/day and 15 g/kg/day) for an additional 8 weeks. Haematoxylin and eosin (H&E) staining was used to investigate histological alterations in gastric tissues. Expression of the T helper 1 (Th1) cell markers CD4⁺ and interferon-gamma (INF-γ) were tested using immunohistochemistry (IHC). Inflammatory protein and mRNA levels in the nuclear factor kappa B (NF-κB) pathway were detected using western blotting and a quantitative reverse transcription polymerase chain reaction (RT-qPCR), respectively.

Results

We identified and selected 110 active compounds and 146 targets from public databases and references. Four representative components of WPL were established and quantified by HPLC–MS/MS analysis. WPL attenuated MNNG-induced GPLs, including epithelial shedding, cavity fusion, basement membranes with asymmetrical thickness, intestinal metaplasia, dysplasia, pro-inflammatory Th1-cell infiltration, and INF-γ production, indicating that WPL prevents inflammation in the gastric mucosa. Furthermore, WPL reversed MNNG-induced activation of the IκB/NF-κB signalling pathway and subsequently attenuated the upregulation of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), and nicotinamide adenine dinucleotide phosphate oxidase (NADPH oxidase (NOX)) family members NOX2 and NOX4.

Conclusion

WPL attenuated GPLs by controlling the generation of pro-inflammatory elements and inhibiting the NF-κB signalling pathway in vivo.

Network Pharmacology and Molecular Docking-Based Mechanism Study to Reveal Antihypertensive Effect of Gedan Jiangya Decoction

Primary hypertension is understood as a disease with diverse etiology, a complicated pathological mechanism, and progressive changes. Gedan Jiangya Decoction (GJD), with the patent publication number CN114246896A, was designed to treat primary hypertension. It contains six botanical drugs; however, the underlying mechanism is uncertain. We utilized network pharmacology to predict the active components, targets, and signaling pathways of GJD in the treatment of primary hypertension. We also investigated the potential molecular mechanism using molecular docking and animal experiments. The Traditional Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP), the Protein Database (UniProt), and a literature review were used to identify the active components and related targets of GJD's pharmacological effects. The GeneCards, Online Mendelian Inheritance in Man (OMIM), Therapeutic Target Database (TTD), and DrugBank databases were utilized to identify hypertension-related targets. Based on a Venn diagram of designed intersection targets, 214 intersection targets were obtained and 35 key targets for the treatment of hypertension were determined using the STRING data platform and Cytoscape software. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of key targets revealed that the relevant molecular action pathways of GJD in the treatment of hypertension include the Toll-like receptor, MAPK, PI3K-Akt, and renin-angiotensin signaling pathways. A GJD active ingredient-key target-pathway connection diagram was created using Cytoscape software, and 11 essential active components were selected. Molecular docking was then used to verify the binding activity of key targets and key active ingredients in GJD to treat primary hypertension. The results of this study indicate that AGTR1, AKT1 with puerarin, EDNRA with tanshinone IIA, MAPK14 with daidzein, MAPK8 with ursolic acid, and CHRM2 with cryptotanshinone had high binding activity to the targets with active components, whereas AGTR1 was selected as target genes verified by our experiment. HPLC was utilized to identify the five active ingredients. Experiments in high-salt rats demonstrated that GJD might decrease the expression of AGTR1 in the kidney and thoracic aorta while increasing the expression of eNOS by preventing the activation of the renin-angiotensin pathway, thereby reducing lowering systolic and diastolic blood pressure.

A precise efficacy determination strategy of traditional Chinese herbs based on Q-markers: Anticancer efficacy of Astragali radix as a case

BACKGROUND

As a "multi-components and multi-efficacy" complex system, traditional Chinese herbs are universally distributed and applied in treating clinical diseases. However, the efficacy deviation and ambiguous clinical location are affected by different effects and content of components caused by uncertain factors in the production process. It further restricts resource allocation and clinical medication and hinders modernization and globalization. In this study, a precise efficacy determination strategy was innovatively proposed, aiming to quantitatively predict the efficacy of herbs and obtain precise medicinal materials. Quality-markers (Q-markers) characterizing the efficacy are conducive to achieving precise efficacy determination.

PURPOSE

With the anticancer efficacy of Astragali radix (AR) as a case, the present study was designed to establish a methodology for precise efficacy determination based on Q-markers characterizing specific efficacy.

METHODS

Guided by the basic principles of Q-markers, the potential Q-markers characterizing the anticancer efficacy of AR were screened through molecular simulation and network pharmacology. The activity of Q-markers was evaluated on MDA-MB-231 cells, and the content of Q-markers was determined by HPLC. A quantitative efficacy prediction model of the relationship between the influencing factors and anticancer efficacy was further constructed through the effect-constituents index (ECI) and machine learning and verified by biotechnology, which can be directly applied to predict the efficacy in numerous samples.

RESULTS

Astragaloside I, astragaloside II, and astragaloside III inhibited the proliferation of MDA-MB-231 cells and were successfully quantified in AR samples, reflecting the effectiveness and measurability of Q-markers. Gradient Boost Regression showed the best performance in the quantitative efficacy prediction model with EV_test= 0.815, R²_test= 0.802. The results of precise efficacy determination indicated that 1-2-3 (Wuzhai, Shanxi, two years, C segment) sample performed best in 54 batches of AR samples with biased anticancer efficacy. Furthermore, AR samples with higher ECI had higher anticancer efficacy and vice versa.

CONCLUSION

The precise efficacy determination strategy established in the present study is reliable and proved in the AR case, which is expected to support resource allocation optimization, efficacy stability improvement, and precise clinical medication achievement.

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

Objective

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

Methods

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

Results

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

Conclusion

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

Miltirone Attenuates Reactive Oxygen Species-Dependent Neuronal Apoptosis in MPP+-Induced Cell Model of Parkinson's Disease Through Regulating the PI3K/Akt Pathway

Miltirone is a phenanthrene-quinone derived from Salvia miltiorrhiza Bunge with anti-inflammatory and anti-oxidant effects. Our study aimed to explore the protective effect of miltirone on 1-methyl-4-phenylpyridinium (MPP⁺)-induced cell model of Parkinson's disease (PD). PharmMapper database was employed to predict the targets of miltirone. PD-related genes were identified using GeneCards database. The overlapping genes between miltirone and PD were screened out using Venn diagram. KEGG analysis was performed using DAVID and KOBAS databases. Cell viability, reactive oxygen species (ROS) generation, apoptosis, and caspase-3 activity were detected by CCK-8 assay, a ROS assay kit, TUNEL, and caspase-3 activity assay, respectively. Effect of miltirone on the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) pathway was explored by western blot analysis. A total of 214 targets of miltirone and 372 targets related to PD were attained, including 29 overlapping targets. KEGG analysis demonstrated that the 29 overlapping targets were both significantly enriched in the PI3K/Akt pathway. MPP⁺ stimulation reduced the cell viability in SH-SY5Y cells and neuronal primary cultures derived from human brain. Miltirone or N-acetylcysteine (NAC) attenuated MPP⁺-induced reduction in cell viability, ROS production, SOD activity reduction, apoptosis, and increase of caspase-3 activity. Additionally, miltirone recuperated MPP⁺-induced inactivation of the PI3K/Akt pathway. Moreover, treatment with LY294002, an inhibitor of the PI3K/Akt pathway, reversed the inhibitory effect of miltirone on MPP⁺-induced ROS generation and apoptosis in SH-SY5Y cells and neuronal primary cultures. In conclusion, miltirone attenuated ROS-dependent apoptosis in MPP⁺-induced cellular model of PD through activating the PI3K/Akt pathway.

Exploration of the Molecular Mechanism of Danzhi Xiaoyao Powder in Endometrial Cancer through Network Pharmacology

Endometrial cancer (EC) is a common malignant tumor of the female reproductive system. Current treatments such as surgery and long-term hormone therapy are ineffective and have side effects. Danzhi Xiaoyao powder (DXP) can inhibit the growth of EC cells and induce apoptosis, but the pharmacological and molecular mechanisms of anticancer effects are still unclear. In this study, active components and potential targets of DXP were obtained from public databases. Protein effects and regulatory pathways of common targets were analyzed by protein-protein interaction (PPI), GO and KEGG. The results of network pharmacology showed that there are 87 common targets between EC and DXP. GO enrichment analysis showed that these targets were associated with response to oxidative stress, response to nutrient levels, hormone receptor binding and nuclear hormone receptor binding, etc. The results of KEGG analysis indicated that IL-17, TNF, PI3K/AKT, and RAS/RAF/MEK/ERK (ERK) signaling pathway were enriched in the anti-EC of DXP. Additionally, we cultured HEC-1B and KLE cells for validate experiments. DXP showed an inhibition of proliferation, migration, and cell cycle of both cells. Moreover, the expression of RAS, p-RAF, p-MEK, ERK, and p-ERK related proteins were downregulated. In conclusion, DXP might inhibit the proliferation of EC cells via apoptosis. Furthermore, DXP-induced inhibition of EC development might involve RAS/RAF/MEK/ERK pathway.

Bibliometric Analysis of Network Pharmacology in Traditional Chinese Medicine

Aim

We evaluated the developmental process, research status, and existing challenges of network pharmacology. Moreover, we elucidated the corresponding solutions to improve and develop network pharmacology.

Methods

Research data for the current study were retrieved from the Web of Science. The developmental process of network pharmacology was analyzed using HisCite, whereas cooccurrence analysis of countries, institutions, keywords, and references in literature was conducted using CiteSpace.

Results

In literature, there was a trend of annual increase of studies on network pharmacology and China was found to be the country with the most published literature on network pharmacology. The main publishing research institutions were universities of traditional Chinese medicine (TCM). The keywords with more research frequency were TCM, mechanisms, molecular docking, and quercetin, among others.

Conclusion

Currently, studies on network pharmacology are mainly associated with the exploration of action mechanisms of TCM. The main active ingredient in many Chinese medicines is quercetin. This ingredient may lead to deviation of research results, inability to truly analyze active ingredients, and even mislead the research direction of TCM. Such deviation may be because the database fails to reflect the content and composition changes of Chinese medicinal components. The database does not account for interactions among components, targets, and diseases, and it ignores the different pathological states of the disease. Therefore, network pharmacology should be improved from the databases and research methods.

Network Pharmacology Approach for Medicinal Plants: Review and Assessment

Natural products have played a critical role in medicine due to their ability to bind and modulate cellular targets involved in disease. Medicinal plants hold a variety of bioactive scaffolds for the treatment of multiple disorders. The less adverse effects, affordability, and easy accessibility highlight their potential in traditional remedies. Identifying pharmacological targets from active ingredients of medicinal plants has become a hot topic for biomedical research to generate innovative therapies. By developing an unprecedented opportunity for the systematic investigation of traditional medicines, network pharmacology is evolving as a systematic paradigm and becoming a frontier research field of drug discovery and development. The advancement of network pharmacology has opened up new avenues for understanding the complex bioactive components found in various medicinal plants. This study is attributed to a comprehensive summary of network pharmacology based on current research, highlighting various active ingredients, related techniques/tools/databases, and drug discovery and development applications. Moreover, this study would serve as a protocol for discovering novel compounds to explore the full range of biological potential of traditionally used plants. We have attempted to cover this vast topic in the review form. We hope it will serve as a significant pioneer for researchers working with medicinal plants by employing network pharmacology approaches.

Network Pharmacology Analysis of Huangqi Jianzhong Tang Targets in Gastric Cancer

Background: The Chinese medicine, Huangqi Jianzhong Tang (HJT), is widely used to treat gastric cancer (GC). In this study, network pharmacological methods were used to analyze the potential therapeutic targets and pharmacological mechanisms of HJT in GC.

Methods: Bioactive components and targets of HJT and GC-related targets were identified using public databases. The protein-protein interaction network of potential targets of HJT in GC was constructed using the Cytoscape plug-in (v3.8.0), CytoHubba. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed, in addition to molecular docking and animal experiments to verify the results of network pharmacology analysis.

Results: A total of 538 GC-related targets were identified. The bioactive components of HJT were selected for drug-likeness evaluation and binomial statistical model screening, which revealed 63 bioactive components and 72 targets. Based on GO enrichment analysis, all targets in the protein-protein interaction network were mainly involved in the response to oxidative stress and neuronal death. Further, KEGG enrichment analysis suggested that the treatment of GC with HJT mainly involved the Wnt signaling pathway, PI3K-Akt signaling pathway, TGF-β signaling pathway, and MAPK signaling pathway, thereby providing insights into the mechanism of the effects of HJT on GC.

Conclusion: This study revealed the potential bioactive components and molecular mechanisms of HJT, which may be useful for the treatment of GC, and provided insights into the development of new drugs for GC.

Network pharmacology analysis and molecular docking to unveil the potential mechanisms of San-Huang-Chai-Zhu formula treating cholestasis

Objective

Chinese medicine formulae possess the potential for cholestasis treatment. This study aimed to explore the underlying mechanisms of San-Huang-Chai-Zhu formula (SHCZF) against cholestasis.

Methods

The major chemical compounds of SHCZF were identified by high-performance liquid chromatography. The bioactive compounds and targets of SHCZF, and cholestasis-related targets were obtained from public databases. Intersected targets of SHCZF and cholestasis were visualized by Venn diagram. The protein-protein interaction and compound-target networks were established by Cytoscape according to the STRING database. The biological functions and pathways of potential targets were characterized by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. The biological process-target-pathway network was constructed by Cytoscape. Finally, the interactions between biological compounds and hub target proteins were validated via molecular docking.

Results

There 7 major chemical compounds in SHCZF. A total of 141 bioactive compounds and 83 potential targets were screened for SHCZF against cholestasis. The process of SHCZF against cholestasis was mainly involved in AGE-RAGE signaling pathway in diabetic complications, fluid shear stress and atherosclerosis, and drug metabolism-cytochrome P450. ALB, IL6, AKT1, TP53, TNF, MAPK3, APOE, IL1B, PPARG, and PPARA were the top 10 hub targets. Molecular docking showed that bioactive compounds of SHCZF had a good binding affinity with hub targets.

Conclusions

This study predicted that the mechanisms of SHCZF against cholestasis mainly involved in AGE-RAGE signaling pathway in diabetic complications, fluid shear stress and atherosclerosis, and drug metabolism-cytochrome P450. Moreover, APOE, AKT1, and TP53 were the critical hub targets for bioactive compounds of SHCZF.

Integrating network pharmacology deciphers the action mechanism of Zuojin capsule in suppressing colorectal cancer

BACKGROUND AND PURPOSE

Zuojin capsule (ZJC), a classical prescription, is outstanding in improving the conditions of patients with gastrointestinal diseases and colorectal cancer (CRC). Although ZJC has multi-ingredient and multi-target characteristics, its pharmacological effect on colorectal cancer and the underlying mechanism remain unclear.

METHOD

Here, the activity of ZJC against CRC was evaluated by the experiments with CRC cells and HCT-116 xenografted mice. The key genes of CRC were obtained from the cancer genome atlas (TCGA). The genes potentially targeted by ZJC were collected from traditional Chinese medicine systems pharmacology (TCMSP) database. The underlying pathways related to selected targets were analyzed through gene ontology (GO) and pathway enrichment analyses. Western blot (WB), cellular thermal shift assay (CETSA), molecular docking and quantitative real-time PCR (QRT-PCR) were carried out to confirm the validity of the targets.

RESULTS

In vitro and in vivo results indicated that ZJC may inhibit CRC cells and tumor growth. The network pharmacological analysis indicated that 22 compounds, 51 targets and 20 pathways were involved in the compound-target-pathway network. Our results confirmed that ZJC inhibited cycle progression, migration and induced apoptosis by targeting candidate genes (CDKN1A, Bcl2, E2F1, PRKCB, MYC, CDK2, and MMP9). We found that ZJC could directly change the protein level by regulating the protein stability and transcriptional activity of the target.

CONCLUSIONS

In summary, combined network pharmacology and biological experiments proved that the main ingredients of ZJC such as quercetin, (R)-Canadine, palmatine, rutaecarpine, evodiamine, beta-sitosterol and berberine can target CDKN1A, Bcl2, E2F1, PRKCB, MYC, CDK2 and MMP9 to combat colorectal cancer. The results of this study provide a basic theory for the clinical trials of Zuojin Capsules against colorectal cancer.

Synthesis, biological evaluation, pharmacokinetic studies and molecular docking of 4'''-acetyl-delicaflavone as antitumor agents

Structural modification of natural products is the effective option to improve their pharmacological effects and drug properties. DLF is a lead compound of antitumor drug, which is a broad-spectrum, low toxic and high-efficient component isolated from Selaginella doederleinii Hieron by our research group. Here, we report the structural modification method of this component, and find that the acetylated product of C4'''- OH (C4'''-acetyl-delicaflavone, 4'''ADLF) has better inhibitory effect on the selected cancer cell lines, including, lung, liver, colon and cervical cancer cell lines. Since the increased water solubility of 4'''ADLF may lead to higher absorption rate and activity, we evaluate the pharmacodynamics in vitro and in vivo, and the pharmacokinetic of 4'''ADLF. It shows that 4'''ADLF inhibit the proliferation and induce cycle arrest in tumor cells, and had better anticancer activity and bioavailability than DLF.

Network pharmacology to unveil the mechanism of Moluodan in the treatment of chronic atrophic gastritis

BACKGROUND

Moluodan (MLD) is a traditional Chinese patent medicine for the treatment of chronic atrophic gastritis (CAG). However, the mechanism of action (MoA) of MLD for treating CAG still remain unclear.

PURPOSE

Elucidate the MoA of MLD for treating CAG based on network pharmacology.

STUDY DESIGN

Integrate computational prediction and experimental validation based on network pharmacology.

METHODS

Computationally, compounds of MLD were scanned by LC-MS/MS and the target profiles of compounds were identified based on network-based target prediction method. Compounds in MLD were compared with western drugs used for gastritis by hierarchical clustering of target profile. Key biological functional modules of MLD were analyzed, and herb-biological functional module network was constructed to elucidate combinatorial rules of MLD herbs for CAG. Experimentally, MLD's effect on different biological functional modules were validated from both phenotypic level and molecular level in 1- Methyl-3-nitro-1-nitrosoguanidine (MNNG)-induced GES-1 cells.

RESULTS

Computational results show that the target profiles of compounds in MLD can cover most of the biomolecules reported in literature. The MoA of MLD can cover most types of MoA of western drugs for CAG. The treatment of CAG by MLD involved the regulation of various biological functional modules, e.g., inflammation/immune, cell proliferation, cell apoptosis, cell differentiation, digestion and metabolism. Experimental results show that MLD can inhibit cell proliferation, promote cell apoptosis and differentiation, reduce the inflammation level and promote lipid droplet accumulation in MNNG-induced GES-1 cells.

CONCLUSION

The network pharmacology framework integrating computational prediction and experimental validation provides a novel way for exploring the MoA of MLD.

Review of the correlation between Chinese medicine and intestinal microbiota on the efficacy of diabetes mellitus

Diabetes mellitus is a serious metabolic disorder that can lead to a number of life-threatening complications. Studies have shown that intestinal microbiota is closely related to the development of diabetes, making it a potential target for the treatment of diabetes. In recent years, research on the active ingredients of traditional Chinese medicine (TCM), TCM compounds, and prepared Chinese medicines to regulate intestinal microbiota and improve the symptoms of diabetes mellitus is very extensive. We focus on the research progress of TCM active ingredients, herbal compounds, and prepared Chinese medicines in the treatment of diabetes mellitus in this paper. When diabetes occurs, changes in the abundance and function of the intestinal microbiota disrupt the intestinal environment by disrupting the intestinal barrier and fermentation. TCM and its components can increase the abundance of beneficial bacteria while decreasing the abundance of harmful bacteria, regulate the concentration of microbial metabolites, improve insulin sensitivity, regulate lipid metabolism and blood glucose, and reduce inflammation. TCM can be converted into active substances with pharmacological effects by intestinal microbiota, and these active substances can reverse intestinal microecological disorders and improve diabetes symptoms. This can be used as a reference for diabetes prevention and treatment.

The Challenges of Ethical Review in Clinical Research of Traditional Chinese Medicine

The ethical review of TCM (traditional Chinese medicine) clinical research in China is highly consistent with that of Western medicine, but it lacks the characteristics and culture of TCM. Compared with modern medicine, TCM has its own characteristics, such as the theory of Yin-Yang and the five elements, the treatment of syndrome differentiation, and the compatibility of prescriptions. These characteristics determine the ethical particularity of TCM clinical research. This article discusses the challenges in the ethical review of TCM clinical research, such as scientific design, efficacy evaluation, risk assessment, informed consent, and placebo use. We propose opportunities and difficulties in the ethical review of TCM clinical research and provide some relevant suggestions.

Nutraceuticals in mental diseases - Bridging the gap between traditional use and modern pharmacology

In evidence-based pharmacotherapy, the complexity of etiopathogenesis and pathophysiology of mental diseases has attracted comparably little consideration so far. The choice of currently available pharmacotherapies is predominantly guided by specific clinical phenotypes and is limited by low response rates and clinically relevant side effects. Nutraceuticals typically represent multicomponent compounds and may offer high therapeutic potential, by simultaneously addressing multiple aspects in mental disease pathogenesis with rather little side effects. Here, recent pharmacological research on natural products is assessed with focus on a multitarget therapeutic concept, based on shared molecular mechanisms, and in particular, on how far nutraceuticals might address such multitargets. Overcoming deficits regarding clearly defined compositions, concentration-dependent and causative structure-activity-response relationships, evaluation of bioavailability, metabolic fate, and long-term safety are crucial for translating potential plant-based drug candidates into proof-of-concept clinical studies.

Exploring the synergistic mechanism of Gegen Qinlian Decoction on the Wnt signaling pathway using an integrated strategy of network pharmacology and RNA-seq

ETHNOPHARMACOLOGICAL RELEVANCE

Gegen Qinlian Decoction (GQD) (including: Puerariae lobatae (Willd.) Ohwi, radix; (short for Gengen) Glycyrrhiza uralensis Fisch., root and rhizome (short for Gancao), honeyed; Coptis chinensis Franch., rhizome (short for Huanglian); Scutellaria baicalensis Georgi, radix, boiled (short for S. baicalensis) has been widely used to treat inflammatory bowel disease (IBD) and colorectal cancer (CRC). To explore compatibility mechanism of GQD could be of advantage to investigate the complex principle of TCM, which might be conducive to the exploration of the modernization of TCM.

AIM OF REVIEW

In this study, a strategy based on system pharmacology was constructed to uncover the multi-target regulation and compatibility mechanism of GQD on the Wnt signaling pathways.

MATERIAL AND METHODS

The pharmacological network of GQD was constructed by TCMSP, DAVID, Uniprote database. The cell growth inhibitory effects of puerarin (PUE), wogonin (WOG), berberine (BER), and glycyrrhetinic acid (GLY) on SW480 cells were assessed using CCK-8 assay. The multi-target regulation and compatibility mechanism of combination PUE with GLY were examined by RNA-seq, HPLC-QQQ/MS, qRT- PCR and Western blot analysis.

RESULTS

Network pharmacology analysis indicated that PUE, WOG, BER and GLY were the active components in GQD and had a synergistic effect on the targets of the Wnt signaling pathway. Additionally, pharmacological experiments revealed that WOG, BER, and GLY inhibited activity of colorectal cancer (CRC) cell lines SW480 cells, and that PUE only exhibited effective antitumour activity when combined with GLY. CTNNB1, CCND1 and SMAD4 were identified as synergistic targets inhibited by PUE-GLY. Moreover, PUE-GLY could influence the Wnt signaling pathway by upregulating GSK3B and downregulating CTNNB1 synergistically. It also showed that GLY could effectively increase the intracellular content of PUE based on HPLC-QQQ/MS analysis, and this process was achieved by influencing the targets of the membrane's pathway, such as cell adhesion molecules, focal adhesion, and tight junctions.

CONCLUSION

GLY was revealed a multi-target mechanism, which could downregulate CTNNB1 as the active component and intervene in membrane proteins (CDH1, CADM1, ITGB2, ICAM1, ITGA1) as 'guide' in the formulae. Moreover, the mechanism of synergistic antitumour action of PUE (the active component of Monarch drug) and GLY (the active component of Guide drug) on the Wnt signaling pathway was explored systematically. It was a promising breakthrough for elucidating the scientific connotation of the compatibility of TCM formulae and provide a valuable and practicable methodology for clarifying the mechanisms of TCM.