Network pharmacology-based prediction of the active ingredients and potential targets of Chinese herbal Radix Curcumae formula for application to cardiovascular disease

Bushen Huoxue Recipe inhibits endometrial epithelial-mesenchymal transition through the transforming growth factor-β/nuclear factor kappa-B pathway to improve polycystic ovary syndrome-mediated infertility

OBJECTIVE

To investigate the target and mechanism of action of Bushen Huoxue Recipe (BSHX) for the treatment of infertility in polycystic ovary syndrome (PCOS), to provide a basis for the development and clinical application of herbal compounds.

METHODS

Prediction and validation of active ingredients and targets of BSHX for the treatment of PCOS by using network pharmacology-molecular docking technology. In an animal experiment, the rats were randomly divided into four groups (control group, model group, BSHX group, metformin group, n = 16 in each group), and letrozole combined with high-fat emulsion gavage was used to establish a PCOS rat model. Body weight, vaginal smears, and number of embryos were recorded for each group of rats. Hematoxylin-eosin (HE) staining was used to observe the morphological changes of ovarian and endometrial tissues, and an enzyme-linked immunosorbent assay (ELISA) was used to detect the serum inflammatory factor levels. Expression levels of transforming growth factor-β (TGF-β), transforming growth factor beta activated kinase 1 (TAK1), nuclear factor kappa-B (NF-κB), Vimentin, and E-cadherin proteins were measured by western blot (WB).

RESULTS

Ninety active pharmaceutical ingredients were obtained from BSHX, involving 201 protein targets, of which 160 were potential therapeutic targets. The active ingredients of BSHX exhibited lower binding energy with tumor necrosis factor-α (TNF-α), TGF-β, TAK1, and NF-κB protein receptors (< -5.0 kcal/mol). BSHX significantly reduced serum TNF-α levels in PCOS rats (p < .01), effectively regulated the estrous cycle, restored the pathological changes in the ovary and endometrium, improved the pregnancy rate, and increased the number of embryos. The results of WB suggested that BSHX can down-regulate protein expression levels of TGF-β and NF-κB in endometrial tissue (p < .05), promote the expression level of E-cadherin protein (p < .001), intervene in the endometrial epithelial-mesenchymal transition (EMT) process.

CONCLUSIONS

TGF-β, TAK1, NF-κB, and TNF-α are important targets of BSHX for treating infertility in PCOS. BSHX improves the inflammatory state of PCOS, intervenes in the endometrial EMT process through the TGF-β/NF-κB pathway, and restores endometrial pathological changes, further improving the pregnancy outcome in PCOS.

JinLiDa granules alleviates cardiac hypertrophy and inflammation in diabetic cardiomyopathy by regulating TP53

BACKGROUND

JinLiDa granules (JLD) is a traditional Chinese medicine (TCM) used to treat type 2 diabetes mellitus with Qi and Yin deficiency. Clinical evidence has shown that JLD can alleviate diabetic cardiomyopathy, but the exact mechanism is not yet clear.

PURPOSE

The purpose of this study was to examine the potential role and mechanism of JLD in the treatment of diabetic cardiomyopathy through network pharmacological analysis and basic experiments.

METHODS

The targets of JLD associated with diabetic cardiomyopathy were examined by network pharmacology. Protein interaction analysis was performed on the targets, and the associated pathways were searched by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Diabetic mice were treated with low or high doses of JLD by gavage, and AC16 and H9C2 cardiomyocytes exposed to high-glucose conditions were treated with JLD. The analysis results were verified by various experimental techniques to examine molecular mechanisms.

RESULTS

Network pharmacological analysis revealed that JLD acted on the tumor suppressor p53 (TP53) during inflammation and fibrosis associated with diabetic cardiomyopathy. The results of basic experiments showed that after JLD treatment, ventricular wall thickening in diabetic mouse hearts was attenuated, cardiac hypertrophy and myocardial inflammation were alleviated, and the expression of cardiac hypertrophy- and inflammation-related factors in cardiomyocytes exposed to a high-glucose environment was decreased. Cardiomyocyte morphology also improved after JLD treatment. TP53 expression and the tumor necrosis factor (TNF) and transforming growth factor beta-1 (TGFβ1) signaling pathways were significantly altered, and inhibiting TP53 expression effectively alleviated the activation of the TNF and TGFβ1 signaling pathways under high glucose conditions. Overexpression of TP53 activated these signaling pathways.

CONCLUSIONS

JLD acted on TP53 to regulate the TNF and TGFβ1 signaling pathways, effectively alleviating cardiomyocyte hypertrophy and inflammation in high glucose and diabetic conditions. Our study provides a solid foundation for the future treatment of diabetic cardiomyopathy with JLD.

Explore the active ingredients and potential mechanism of action on Actinidia arguta leaves against T2DM by integration of serum pharmacochemistry and network pharmacology

BACKGROUND

Actinidia arguta leaves (AAL) are traditionally consumed as a vegetable and as tea in folk China and Korea. Previous studies have reported the anti-diabetic effect of AAL, but its bioactive components and mechanism of action are still unclear.

AIM OF THE STUDY

This study aims to identify the hypoglycemic active components of AAL by combining serum pharmacochemistry and network pharmacology and to elucidate its possible mechanism of action.

METHODS

Firstly, the effective components in mice serum samples were characterized by UPLC-Q/TOF-MSE. Furthermore, based on these active ingredients, network pharmacology analysis was performed to establish an "H-C-T-P-D" interaction network and reveal possible biological mechanisms. Finally, the affinity between serum AAL components and the main proteins in the important pathways above was investigated through molecular docking analysis.

RESULTS

Serum pharmacochemistry analysis showed that 69 compounds in the serum samples were identified, including 23 prototypes and 46 metabolites. The metabolic reactions mainly included deglycosylation, dehydration, hydrogenation, methylation, acetylation, glucuronidation, and sulfation. Network pharmacology analysis showed that the key components quercetin, pinoresinol diglucoside, and 5-O-trans-p-coumaroyl quinic acid butyl ester mainly acted on the core targets PTGS2, HRAS, RELA, PRKCA, and BCL2 targets and through the PI3K-Akt signaling pathway, endocrine resistance, and MAPK signaling pathway to exert a hypoglycemic effect. Likewise, molecular docking results showed that the three potential active ingredients had good binding effects on the five key targets.

CONCLUSION

This study provides a basis for elucidating the pharmacodynamic substance basis of AA against T2DM and further exploring the mechanism of action.

Deciphering the pharmacological mechanisms of Shenlingbaizhu formula in antibiotic-associated diarrhea treatment: Network pharmacological analysis and experimental validation

ETHNOPHARMACOLOGICAL RELEVANCE

Shenlingbaizhu (SLBZ) formula, a classical traditional Chinese medicinal (TCM) formula, has been widely used for treating antibiotic-associated diarrhea (AAD). However, the underlying pharmacological mechanisms have not yet been investigated thoroughly.

AIM OF THE STUDY

To explore the remission mechanism of SLBZ in the treatment of AAD, we conducted network pharmacological analysis and experimental validation in vitro and in vivo.

MATERIALS AND METHODS

In this study, the main compounds of SLBZ were identified by ultra-high-performance liquid chromatography-mass spectroscopy (UHPLC-MS) and online databases. The targets of the active components and AAD-related targets were predicted by network pharmacology, and the potential targets of SLBZ against AAD were obtained. Then the core targets were recognized after Protein-Protein Interaction (PPI) analysis. Based on these, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analyses were conducted, and the key pathway was screened. Subsequently, molecular docking was performed using Auto Dock Vina to find the key components that played a crucial role in that pathway. Molecular dynamics simulation was performed by Gromacs software to detect the binding mode. Finally, the results were confirmed by in vitro and in vivo experiments.

RESULTS

A total of 66 active ingredients of SLBZ were detected by UHPLC-MS, and 128 active ingredients were screened out by network pharmacological analysis. Additionally, 935 drug targets and 1686 AAD-related targets were obtained. Seventy-eight intersected genes were selected as potential therapeutic targets and 19 genes were excavated as core targets. Enrichment analysis revealed PI3K-AKT signaling pathway was the key pathway in SLBZ against AAD. Topological analysis further revealed that JAK2, MTOR, TLR4, and SYK were the key targets affected by SLBZ on the PI3K-AKT pathway, and 52 components of SLBZ were associated with them. Molecular docking and dynamics simulation revealed strong binding affinities between MTOR and diosgenin. Subsequently, after SLBZ treatment, the expression levels of JAK2, MTOR, TLR4, and SYK were found significantly upregulated in the AAD model rats (p < 0.05). The cell experiment further validated the good binding ability between MTOR and diosgenin.

CONCLUSION

We demonstrate that the therapeutic effect of SLBZ on AAD was achieved in part by inhibiting the PI3K-AKT pathway.

Utilizing network pharmacology, molecular docking, and animal models to explore the therapeutic potential of the WenYang FuYuan recipe for cerebral ischemia-reperfusion injury through AGE-RAGE and NF-κB/p38MAPK signaling pathway modulation

BACKGROUND

Stroke is a debilitating condition with high morbidity, disability, and mortality that significantly affects the quality of life of patients. In China, the WenYang FuYuan recipe is widely used to treat ischemic stroke. However, the underlying mechanism remains unknown, so exploring the potential mechanism of action of this formula is of great practical significance for stroke treatment.

OBJECTIVE

This study employed network pharmacology, molecular docking, and in vivo experiments to clarify the active ingredients, potential targets, and molecular mechanisms of the WenYang FuYuan recipe in cerebral ischemia-reperfusion injury, with a view to providing a solid scientific foundation for the subsequent study of this recipe.

MATERIALS AND METHODS

Active ingredients of the WenYang FuYuan recipe were screened using the traditional Chinese medicine systems pharmacology database and analysis platform. Network pharmacology approaches were used to explore the potential targets and mechanisms of action of the WenYang FuYuan recipe for the treatment of cerebral ischemia-reperfusion injury. The Middle Cerebral Artery Occlusion/Reperfusion 2 h Sprague Dawley rat model was prepared, and TTC staining and modified neurological severity score were applied to examine the neurological deficits in rats. HE staining and Nissl staining were applied to examine the pathological changes in rats. Immunofluorescence labeling and Elisa assay were applied to examine the expression levels of certain proteins and associated factors, while qRT-PCR and Western blotting were applied to examine the expression levels of linked proteins and mRNAs in disease-related signaling pathways.

RESULTS

We identified 62 key active ingredients in the WenYang FuYuan recipe, with 222 highly significant I/R targets, forming 138 pairs of medication components and component-targets, with the top five being Quercetin, Kaempferol, Luteolin, β-sitosterol, and Stigmasterol. The key targets included TP53, RELA, TNF, STAT1, and MAPK14 (p38MAPK). Targets related to cerebral ischemia-reperfusion injury were enriched in chemical responses, enzyme binding, endomembrane system, while enriched pathways included lipid and atherosclerosis, fluid shear stress and atherosclerosis, AGE-RAGE signaling in diabetic complications. In addition, the main five active ingredients and targets in the WenYang FuYuan recipe showed high binding affinity (e.g. Stigmasterol and MAPK14, total energy <-10.5 Kcal/mol). In animal experiments, the WenYang FuYuan recipe reduced brain tissue damage, increased the number of surviving neurons, and down-regulated S100β and RAGE protein expression. Moreover, the relative expression levels of key targets such as TP53, RELA and p38MAPK mRNA were significantly down-regulated in the WenYang FuYuan recipe group, and serum IL-6 and TNF-a factor levels were reduced. After WenYang FuYuan recipe treatment, the AGE-RAGE signaling pathway and downstream NF-kB/p38MAPK signaling pathway-related proteins were significantly modulated.

CONCLUSION

This study utilized network pharmacology, molecular docking, and animal experiments to identify the potential mechanism of the WenYang FuYuan recipe, which may be associated with the regulation of the AGE-RAGE signaling pathway and the inhibition of target proteins and mRNAs in the downstream NF-kB/p38MAPK pathway.

Traditional Chinese medicine and mitophagy: A novel approach for cardiovascular disease management

BACKGROUND

Cardiovascular disease (CVD) remains the leading cause of morbidity and mortality worldwide, imposing an enormous economic burden on individuals and human society. Laboratory studies have identified several drugs that target mitophagy for the prevention and treatment of CVD. Only a few of these drugs have been successful in clinical trials, and most studies have been limited to animal and cellular models. Furthermore, conventional drugs used to treat CVD, such as antiplatelet agents, statins, and diuretics, often result in adverse effects on patients' cardiovascular, metabolic, and respiratory systems. In contrast, traditional Chinese medicine (TCM) has gained significant attention for its unique theoretical basis and clinical efficacy in treating CVD.

PURPOSE

This paper systematically summarizes all the herbal compounds, extracts, and active monomers used to target mitophagy for the treatment of CVD in the last five years. It provides valuable information for researchers in the field of basic cardiovascular research, pharmacologists, and clinicians developing herbal medicines with fewer side effects, as well as a useful reference for future mitophagy research.

METHODS

The search terms "cardiovascular disease," "mitophagy," "herbal preparations," "active monomers," and "cardiac disease pathogenesis" in combination with "natural products" and "diseases" were used to search for studies published in the past five years until January 2024.

RESULTS

Studies have shown that mitophagy plays a significant role in the progression and development of CVD, such as atherosclerosis (AS), heart failure (HF), myocardial infarction (MI), myocardial ischemia/reperfusion injury (MI/RI), cardiac hypertrophy, cardiomyopathy, and arrhythmia. Herbal compound preparations, crude extracts, and active monomers have shown potential as effective treatments for these conditions. These substances protect cardiomyocytes by inducing mitophagy, scavenging damaged mitochondria, and maintaining mitochondrial homeostasis. They display notable efficacy in combating CVD.

CONCLUSION

TCM (including herbal compound preparations, extracts, and active monomers) can treat CVD through various pharmacological mechanisms and signaling pathways by inducing mitophagy. They represent a hotspot for future cardiovascular basic research and a promising candidate for the development of future cardiovascular drugs with fewer side effects and better therapeutic efficacy.

Discovery and validation of COX2 as a target of flavonoids in Apocyni Veneti Folium: Implications for the treatment of liver injury

ETHNOPHARMACOLOGICAL RELEVANCE

Apocyni Veneti Folium (AVF), a popular traditional Chinese medicine (TCM), is known for its effects in soothing the liver and nerves and eliminating heat and water. It is relevant from an ethnopharmacological perspective. Pharmacological research has confirmed its benefits on antihypertension, antihyperlipidemia, antidepression, liver protection, immune system boosting, antiaging, and diabetic vascular lesions. Previous studies have shown that flavonoids, the active ingredients, have a hepatoprotective effect. However, the exact mechanism has not been clarified.

AIM OF THE STUDY

This study aimed to identify the active flavonoids in AVF and their corresponding targets for liver injury. Multiple methods were introduced to confirm the targets.

MATERIAL AND METHODS

AVF compounds were analyzed using liquid chromatography-mass spectrometry (LC-MS). Then, network pharmacology was utilized to screen potential hepatoprotection targets of the compounds. An enzyme activity assay was performed to determine the effect of the compounds on the targets. Biolayer interferometry (BLI) was applied to confirm the direct interaction between the compounds and the targets.

RESULTS

A total of 71 compounds were identified by LC-MS and 19 compounds and 112 shared targets were screened using network pharmacology. These common targets were primarily involved in the TNF signaling pathway, cancer pathways, hepatitis B, drug responses, and negative regulation of the apoptotic process. Flavonoids were the primary pharmacological substance basis of AVF. The cyclooxygenase 2 (COX2) protein was one of the direct targets of flavonoids in AVF. The enzyme activity assay and BLI-based intermolecular interactions demonstrated that the compounds astragalin, isoquercitrin, and hyperoside exhibited stronger inhibition of enzyme activity and a higher affinity with COX2 compared to epigallocatechin, quercetin, and catechin.

CONCLUSIONS

COX2 was preliminarily identified as a target of flavonoids, and the mechanism of the hepatoprotective effect of AVF might be linked to flavonoids inhibiting the activity of COX2. The findings can establish the foundation for future research on the traditional hepatoprotective effect of AVF on the liver and for clinical studies on liver disorders.

Anti-papillary thyroid carcinoma effects of dioscorea bulbifera L. through ferroptosis and the PI3K/AKT pathway based on network pharmacology and experimental validation

ETHNOPHARMACOLOGICAL RELEVANCE

Papillary thyroid carcinoma (PTC) is the predominant form of thyroid cancer with a rising global incidence. Despite favorable prognoses, a significant recurrence rate persists. Dioscorea bulbifera L. (DBL), a traditional Chinese medicine, has been historically used for thyroid-related disorders. However, its therapeutic effects and mechanisms of action on PTC remain unclear.

AIM OF THE STUDY

To explore the potential therapeutic effects, principal active components, and molecular mechanisms of DBL in the treatment of PTC through network pharmacology and molecular docking, with experimental validation conducted to corroborate these findings.

MATERIALS AND METHODS

The Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) was utilized as a systematic tool for collecting and screening the phytochemical components of DBL, and for establishing associations between these components and molecular targets. Based on this, network data was visually processed using Cytoscape software (version 3.8.0). Concurrently, precise molecular docking studies of the principal active components of DBL and their corresponding targets were conducted using Autodock software. Additionally, PTC-related genes were selected through the GeneCards and GEO databases. We further employed the DAVID bioinformatics resources to conduct comprehensive Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses on the intersecting genes between DBL and PTC. These analyses aid in predicting the potential therapeutic actions of DBL on PTC and its mechanisms of action. To validate these findings, corresponding in vitro experimental studies were also conducted.

RESULTS

In this investigation, 14 bioactive compounds of DBL and 195 corresponding molecular targets were identified, with 127 common targets shared between DBL and PTC. Molecular docking revealed strong binding affinities between major bioactive compounds and target proteins. GO enrichment analysis unveiled key processes involved in DBL's action. KEGG analysis highlighted DBL's modulation of the PI3K/AKT signaling pathway. Experimental outcomes demonstrated DBL's potential in inhibiting PTC cell proliferation and migration, suppressing PI3K/AKT pathway activation, and promoting ferroptosis.

CONCLUSION

In conclusion, DBL offers a multifaceted therapeutic approach for PTC, targeting multiple molecular entities and influencing diverse biological pathways. Network pharmacology and molecular docking shed light on DBL's potential utility in PTC treatment, substantiated by experimental validation. This study contributes valuable insights into using DBL as a promising therapeutic agent for PTC management.

Network pharmacology and molecular docking: combined computational approaches to explore the antihypertensive potential of Fabaceae species

Hypertension is a major global public health issue, affecting quarter of adults worldwide. Numerous synthetic drugs are available for treating hypertension; however, they often come with a higher risk of side effects and long-term therapy. Modern formulations with active phytoconstituents are gaining popularity, addressing some of these issues. This study aims to discover novel antihypertensive compounds in Cassia fistula, Senna alexandrina, and Cassia occidentalis from family Fabaceae and understand their interaction mechanism with hypertension targeted genes, using network pharmacology and molecular docking. Total 414 compounds were identified; initial screening was conducted based on their pharmacokinetic and ADMET properties, with a particular emphasis on adherence to Lipinski's rules. 6 compounds, namely Germichrysone, Benzeneacetic acid, Flavan-3-ol, 5,7,3',4'-Tetrahydroxy-6, 8-dimethoxyflavon, Dihydrokaempferol, and Epiafzelechin, were identified as effective agents. Most of the compounds found non-toxic against various indicators with greater bioactivity score. 161 common targets were obtained against these compounds and hypertension followed by compound-target network construction and protein-protein interaction, which showed their role in diverse biological system. Top hub genes identified were TLR4, MMP9, MAPK14, AKT1, VEGFA and HSP90AA1 with their respective associates. Higher binding affinities was found with three compounds Dihydrokaempferol, Flavan-3-ol and Germichrysone, -7.1, -9.0 and -8.0 kcal/mol, respectively. The MD simulation results validate the structural flexibility of two complexes Flavan-MMP9 and Germich-TLR4 based on no. of hydrogen bonds, root mean square deviations and interaction energies. This study concluded that C. fistula (Dihydrokaempferol, Flavan-3-ol) and C. occidentalis (Germichrysone) have potential therapeutic active constituents to treat hypertension and in future novel drug formulation.

Network Pharmacology and Experimental Validation to Explore the Potential Mechanism of Nigella sativa for the Treatment of Breast Cancer

Breast cancer is a prevalent and potentially life-threatening disease that affects women worldwide. Natural products have gained attention as potential anticancer agents due to their fewer side effects, low toxicity, and cost effectiveness compared to traditional chemotherapy drugs. In the current study, the network pharmacology approach was used following a molecular docking study to evaluate the therapeutic potential of N. sativa-derived phytochemicals against breast cancer. Specifically, the study aimed to identify potential anticancer agents targeting key proteins implicated in breast cancer progression. Five proteins (i.e., EGFR, MAPK3, ESR1, MAPK1, and PTGS2) associated with breast cancer were selected as receptor proteins. Fourteen phytochemicals from N. sativa were prioritized based on drug-likeness (DL) and oral bioavailability (OB) parameters (with criteria set at DL > 0.18 and OB > 30%, respectively). Subsequent analysis of gene targets identified 283 overlapping genes primarily related to breast cancer pathogenesis. Ten hub genes were identified through topological analysis based on their significance in the KEGG pathway and GO annotations. Molecular docking revealed strong binding affinities between folic acid, betulinic acid, stigmasterol, and selected receptor proteins. These phytochemicals also demonstrated druggability potential. In vitro experiments in the MDA-MB-231 breast cancer cell line revealed that betulinic acid and stigmasterol significantly reduced cell viability after 24 h of treatment, confirming their anticancer activity. Furthermore, in vivo evaluation using a DMBA-induced rat model showed that betulinic acid and stigmasterol contributed to the significant recovery of cancer markers. This study aimed to explore the mechanisms underlying the anticancer potential of N. sativa phytochemicals against breast cancer, with the ultimate goal of identifying novel therapeutic candidates for future drug development. Overall, these results highlight betulinic acid and stigmasterol as promising candidates to develop novel anticancer agents against breast cancer. The comprehensive approach of this study, which integrates network pharmacology and molecular docking study and its experimental validation, strengthens the evidence supporting the therapeutic benefits of N. sativa-derived phytochemicals in breast cancer treatment, making them promising candidates for the development of novel anticancer agents against breast cancer.

Network toxicology, molecular docking technology, and experimental verification revealed the mechanism of cantharidin-induced testicular injury in mice

As a protein kinase inhibitor, cantharidin (CTD) exhibits antitumor activities. However, CTD is highly toxic, thereby limiting clinical applications. Moreover, relatively few studies have investigated CTD-induced reproductive toxicity, thus the underlying mechanism remains unclear. In this study, the toxic effects of CTD on mouse testis were confirmed in vivo and the potential mechanism was predicted by network toxicology (NT) and molecular docking technology. Proteins involved in the signaling pathways and core targets were verified. The results showed that different concentrations of CTD induced weight loss increased the testicular coefficient, and caused obvious pathological damage to testicular cells. The NT results showed that the main targets of CTD-induced testicular injury (TI) included AKT1, Caspase 3, Bcl-2, and Bax. The results of pathway enrichment analysis showed that CTD-induced TI was closely related to apoptosis and the PI3K/AKT and HIF-1 signaling pathways. Molecular docking methods confirmed high affinity between CTD and key targets. Western blot analysis showed that CTD inhibited expression of PI3K, AKT, and the anti-apoptotic protein Bcl-2, while promoting expression of the pro-apoptotic proteins Bax and Caspase 3. These results suggest that CTD-induced TI involves multiple targets and pathways, and the underlying mechanism was associated with inhibition of the apoptosis-related PI3K/AKT signaling pathway.

A novel mechanism for regulating lung immune homeostasis: Zukamu granules alleviated acute lung injury in mice by inhibiting NLRP3 inflammasome activation and regulating Th17/Treg cytokine balance

ETHNOPHARMACOLOGICAL RELEVANCE

Acute lung injury (ALI) is a severely acute lung inflammation with high morbidity and mortality. Zukamu granules (ZKMG) is one of the Uygur patent drugs commonly used in clinic, which is included in the National Essential Drugs List (2018 edition). Clinical studies have shown that ZKMG has a significant effect on acute upper respiratory tract infection, and has better anti-inflammatory and antipyretic effects. However, the immunomodulatory mechanism of ZKMG on ALI is still not clear.

AIM OF THE STUDY

The aim of this study is to investigate the lung protective effect and immunomodulatory mechanism of ZKMG on lipopolysaccharide (LPS) -induced ALI mice, and to provide an important basis for the treatment strategy and theoretical basis of ALI.

MATERIALS AND METHODS

First, network pharmacology was used to predict the potential signaling pathways and biological processes of ZKMG related to immunology. Molecular docking technique was used to predict the possibility between the core components of ZKMG acting on NLRP3 protein. In addition, protein levels of F4/80 in lung tissues were assessed by Immunohistochemistry (IHC). The contents of IL-1β, IL-18, IL-17A and IL-10 in the lung tissue and serum, MPO in the lung tissue were detected by enzyme-linked immunosorbent assay (ELISA). Real-time quantitative PCR analysis (RT-qPCR) was used to detect NLRP3 mRNA in lung tissue. Protein levels of NLRP3, Caspase-1, Cleaved caspase-1 p20, ASC, and GSDMD were detected by Western blot (WB).

RESULTS

The results of network pharmacology showed that the immune pathways of ZKMG were mainly Th17 signaling pathway, IL-17 signaling pathway, NOD-like receptor signaling pathway, etc. Molecular docking results showed that the core components of ZKMG had good binding ability to NLRP3 protein. The verification experiments showed that ZKMG can reduce the degree of lung injury, and reduce the level of inflammatory infiltration of neutrophils and macrophages by reducing the content of MPO and F4/80. In addition, ZKMG can reduce NLRP3 mRNA, inhibit the expression of NLRP3/Caspase-1/GSDMD and other related pathway proteins, and reduce inflammatory factors such as IL-1β and IL-18. It can also reduce the content of pro-inflammatory cytokine IL-17A, increase the content of anti-inflammatory cytokine IL-10 in lung tissue.

CONCLUSION

ZKMG can reduce the degree of lung tissue injury in ALI by inhibiting NLRP3/Caspase-1/GSDMD signaling pathway and restoring the IL-17A/IL-10 cytokine balance, and its protective mechanism may be related to the regulation of lung immune homeostasis. It will provide a new strategy for studying the regulation of lung immune homeostasis.

Interpreting the Mechanism of Active Ingredients in Polygonati Rhizoma in Treating Depression by Combining Systemic Pharmacology and In Vitro Experiments

Polygonati Rhizoma (PR) has certain neuroprotective effects as a homology of medicine and food. In this study, systematic pharmacology, molecular docking, and in vitro experiments were integrated to verify the antidepressant active ingredients in PR and their mechanisms. A total of seven compounds in PR were found to be associated with 45 targets of depression. Preliminarily, DFV docking with cyclooxygenase 2 (COX2) showed good affinity. In vitro, DFV inhibited lipopolysaccharide (LPS)-induced inflammation of BV-2 cells, reversed amoeba-like morphological changes, and increased mitochondrial membrane potential. DFV reversed the malondialdehyde (MDA) overexpression and superoxide dismutase (SOD) expression inhibition in LPS-induced BV-2 cells and decreased interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and IL-6 mRNA expression levels in a dose-dependent manner. DFV inhibited both mRNA and protein expression levels of COX2 induced by LPS, and the activation of NACHT, LRR, and PYD domains-containing protein 3 (NLRP3) and caspase1 was suppressed, thus exerting an antidepressant effect. This study proves that DFV may be an important component basis for PR to play an antidepressant role.

Carbon Dots Derived from Curcumae Radix and Their Heartprotective Effect

Background

Acute myocardial infarction (AMI) is a common cardiovascular disease in clinic. Currently, there is no specific treatment for AMI. Carbon dots (CDs) have been reported to show excellent biological activities, which hold promise for the development of novel nanomedicines for the treatment of cardiovascular diseases.

Methods

In this study, we firstly prepared CDs from the natural herb Curcumae Radix Carbonisata (CRC-CDs) by a green, simple calcination method. The aim of this study is to investigate the cardioprotective effect and mechanism of CRC-CDs on isoproterenol (ISO) -induced myocardial infarction (MI) in rats.

Results

The results showed that pretreatment with CRC-CDs significantly reduced serum levels of cardiac enzymes (CK-MB, LDH, AST) and lipids (TC, TG, LDL) and reduced st-segment elevation and myocardial infarct size on the ECG in AMI rats. Importantly, cardiac ejection fraction (EF) and shortening fraction (FS) were markedly elevated, as was ATPase activity. In addition, CRC-CDs could significantly increase the levels of superoxide dismutase (SOD), reduced glutathione (GSH), catalase (CAT), and reduce the levels of malondialdehyde (MDA) and reactive oxygen species (ROS) in myocardial tissue, thereby exerting cardioprotective effect by enhancing the antioxidant capacity of myocardial tissue. Moreover, the TUNEL staining image showed that positive apoptotic cells were markedly declined after CRC-CDs treatment, which indicate that CRC-CDs could inhibit cardiomyocyte apoptosis. Importantly, The protective effect of CRC-CDs on H2O2 -pretreated H9c2 cells was also verified in vitro.

Conclusion

Taken together, CRC-CDs has the potential for clinical application as an anti-myocardial ischemia drug candidate, which not only provides evidence for further broadening the biological application of cardiovascular diseases, but also offers potential hope for the application of nanomedicine to treat intractable diseases.

Tibetan medicine Ruyi Zhenbao Pill ameliorates neuropathic pain by inhibiting the CXCL10-CXCR3 pathway in spinal cord of spinal nerve ligation model

ETHNOPHARMACOLOGICAL RELEVANCE

Ruyi Zhenbao Pill (RYZBP) is a traditional Tibetan medicine that has been used for over 300 years in China to treat neurological diseases, specifically neuropathic pain (NP). However, its characteristics and mechanism of action in treating NP remains unclear.

AIM OF THE STUDY

Based on animal experiments and transcriptomics to evaluate the characteristics and mechanism of RYZBP in treating NP.

METHODS

Mice were divided into six groups using random assignment: sham-operation group, spinal nerve ligation (SNL) group, RYZBP low (0.65 g kg-1), medium (1.30 g kg-1), high (2.60 g kg-1) doses groups, and positive drug pregabalin (PGB, 0.05 g kg-1) group. Mice received intragastrical administered for 14 consecutive days. SNL and intrathecal injection models were employed. The analgesic effects were assessed using the Von Frey test, Acetone test, and Hot Plate test. L5 spinal dorsal horns were collected for transcriptomics on day 15. The potential signaling pathways and Hub genes of RYZBP to ameliorate NP were obtained through transcriptomics and network pharmacology. Molecular docking was utilized to evaluate the binding ability of candidate active ingredients with the Hub genes. Finally, western blot (WB) and immunofluorescence (IF) were used to validate the predicted targets.

RESULTS

RYZBP demonstrated a dose-dependent alleviation of mechanical allodynia, cold and heat stimulus-induced pain in SNL mice. Transcriptomics analysis identified 24 differentially expressed genes, and pathway enrichment analysis revealed that the CXCL10-CXCR3 signal axis may be the primary biological pathway through which RYZBP relieve NP. Molecular docking test indicated that the active ingredient in RYZBP exhibit a strong affinity for the target protein CXCL10. WB and IF tests showed that RYZBP can significantly inhibit CXCL10 and CXCR3 and its downstream molecules expression in the spinal dorsal horn of SNL mice. Additionally, intrathecal injection of rmCXCL10 worsened pain hypersensitivity, while RYZBP was able to suppress the pain hypersensitivity response induced by rmCXCL10 and reduce the expression levels of CXCL10 and CXCR3 and its downstream molecules.

CONCLUSION

RYZBP had a significant analgesic effect on NP model, and this effect may be related to inhibiting the CXCL10-CXCR3 pathway in the spinal dorsal horn.

An integrated network pharmacology approach to discover therapeutic mechanisms of Commiphora wightii for the treatment of Bell's palsy

Bell's palsy (BP) can result in facial paralysis. Inflammation or injury to the cranial nerves that regulate the facial muscles is primarily responsible for that disease. Commiphora wightii remains recognized as a cure for a few human ailments. This study focused on therapeutic phenomena of C. wightii for the treatment of Bell's palsy, utilizing the network drug discovery and molecular docking techniques. Active biological constituents of C. wightii were retrieved from literature and independent databases. Potential therapeutic targets (431) of 13 bioactive phytochemicals were fetched via SwissTargetPrediction tool. Putative intersecting targets (855) of Bell's palsy were computed through the DisGeNET and GeneCards datasets. Subsequently, by the analysis of potential shared targets (87) of C. wightii and Bell's palsy, a Venn diagram was drawn. DAVID database was used to evaluate gene functional annotations and enriched pathways that are involved in Bell's palsy. STRING database was used for generating the protein-protein relationship complex. Visual presentations of the interactions of potential targets to active chemical constituents were done by the Cytoscape. Whereas, the conformational research sorted out 10 key targets through the protein-protein interactions network. Moreover, the capacity of therapeutic ingredients to interact with a target inhibiting Bell's palsy was confirmed by molecular docking, which might ratify the findings of network pharmacology. In the molecular complex of AKT1-cholesterol, a 100-ns simulation unveiled a graceful stability, with a minimal 0.167 Å ligand shift and resilient hydrogen bonds (ASN54 and SER205). The final 20 ns showcased a P1 motif pirouette, gracefully forming aromatic bonds with H165 and W186, underscoring the complex's dynamic finesse. This study evaluated compound-target interactions and their impact on disease-related genes. It revealed that five genes (AKT1, TNF, MAPK3, EGFR and SRC) of C. wightii might be useful therapeutic targets for the treatment of Bell's palsy, as well as helping in lowering down the blood pressure.Communicated by Ramaswamy H. Sarma.

Chinese Herbal Medicines for Coronary Heart Disease: Clinical Evidence, Pharmacological Mechanisms, and the Interaction with Gut Microbiota

Coronary heart disease (CHD) is a common type of cardiovascular disease (CVD) that has been on the rise in terms of both incidence and mortality worldwide, presenting a significant threat to human health. An increasing body of studies has shown that traditional Chinese medicine (TCM), particularly Chinese herbal medicines (CHMs), can serve as an effective adjunctive therapy to enhance the efficacy of Western drugs in treating CHD due to their multiple targets and multiple pathways. In this article, we critically review data available on the potential therapeutic strategies of CHMs in the intervention of CHD from three perspectives: clinical evidence, pharmacological mechanisms, and the interaction with gut microbiota. We identified 20 CHMs used in clinical practice and it has been found that the total clinical effective rate of CHD patients improved on average by 17.78% with the intervention of these CHMs. Subsequently, six signaling pathways commonly used in treating CHD have been identified through an overview of potential pharmacological mechanisms of these 20 CHMs and the eight representative individual herbs selected from them. CHMs could also act on gut microbiota to intervene in CHD by modulating the composition of gut microbiota, reducing trimethylamine-N-oxide (TMAO) levels, increasing short-chain fatty acids (SCFAs), and maintaining appropriate bile acids (BAs). Thus, the therapeutic potential of CHMs for CHD is worthy of further study in view of the outcomes found in existing studies.

Calycosin ameliorates osteoarthritis by regulating the imbalance between chondrocyte synthesis and catabolism

Osteoarthritis (OA) is a severe chronic inflammatory disease. As the main active component of Astragalus mongholicus Bunge, a classic traditional ethnic herb, calycosin exhibits anti-inflammatory action and its mechanism of exact targets for OA have yet to be determined. In this study, we established an anterior cruciate ligament transection (ACLT) mouse model. Mice were randomized to sham, OA, and calycosin groups. Cartilage synthesis markers type II collagen (Col-2) and SRY-Box Transcription Factor 9 (Sox-9) increased significantly after calycosin gavage. While cartilage matrix degradation index cyclooxygenase-2 (COX-2), phosphor-epidermal growth factor receptor (p-EGFR), and matrix metalloproteinase-9 (MMP9) expression were decreased. With the help of network pharmacology and molecular docking, these results were confirmed in chondrocyte ADTC5 cells. Our results indicated that the calycosin treatment significantly improved cartilage damage, this was probably attributed to reversing the imbalance between chondrocyte synthesis and catabolism.

Huzhangqingmaiyin protected vascular endothelial cells against cerebral small vessel disease through inhibiting inflammation

ETHNOPHARMACOLOGICAL RELEVANCE

Huzhangqingmaiyin (HZQMY) is a Chinese medicine formula used to treat small vessel disease, but the mechanism is unclear.

AIM OF THE STUDY

This study aimed to reveal the protective effects of HZQMY on human brain microvascular endothelial cells (HBMECs) and explore the potential targets and mechanistic pathways using network pharmacology on treating cerebral small vessel disease (CSVD).

MATERIALS AND METHODS

HBMECs were cultured in vitro and an endothelial cell injury model was constructed by hypoxia for 12 h followed by reoxygenation for 8 h (H/R). Cell viability was measured by CCK-8 assay, migration ability of cells was detected by scratch assay, angiogenesis ability of endothelial cells was detected by tubulogenesis assay. Meanwhile, JC-1 staining was employed to determine the alteration of mitochondrial membrane potential, and finally, cell apoptosis was assessed by flow cytometry. To further explore the mechanism of action of HZQMY, the target proteins of a candidate active compound was first collected from the traditional Chinese medicine systems pharmacology database with analytical platform and Swiss target prediction database (www.swisstargetprediction.ch) by HPLC/MS determination of its main active components. CSVD associated targets were retrieved from four disease associated targets databases, OMIM, DisGenNET, GeneCards and GeneCLip, respectively. Using the website String, the genes overlapped between HZQMY and CSVD were imported into the database, PPI network plots were drawn using Cytoscape software. GO and KEGG analyses were performed to explore the possible pathways and targets of HZQMY. Its most probable targets were further explored with molecular docking and verified.

RESULTS

HZQMY at 0.5-2 μg/mL concentration range could promote cell proliferation, cell migration, angiogenesis, reduce mitochondrial membrane potential damage as well as inhibit apoptosis. Besides that, 29 active compounds were detected from HZQMY, including key components such as quercetin, polydatin, kaempferol, isorhamnetin and resveratrol. Core targets that might include IL-1β、ICAM-1、VCAM-1 and VEGF and so on.

CONCLUSIONS

HZQMY could regulate the levels of key targets such as IL-1β、ICAM-1、VCAM-1 and VEGF, so as to achieve the purpose of treating CSVD.

Toxicological safety evaluation of zengye granule through acute and 30-day toxicity studies in rats

ETHNOPHARMACOLOGICAL RELEVANCE

Zengye granule (ZYG), a traditional Chinese medicine formula composed of Radix Scrophulariae, Radix Ophiopogonis, and Radix Rehmanniae in the ratio of 1.0:0.8:0.8, is listed in the Chinese Pharmacopoeia for treating diseases associated with yin deficiency, such as inner heat, dry mouth and pharynx, and dry bound stool. However, little information is available on its toxicological safety.

AIM OF THE STUDY

To evaluate the acute and subacute toxicity of ZYG after oral administration in rats.

MATERIALS AND METHODS

In the acute toxicity study, ZYG was orally administered to rats at a single dose of 10 g/kg/day. In the subacute toxicity study, ZYG was administered orally to rats at repeated daily doses of 2.5, 5.0, or 10 g/kg/day for 30 days. The toxicological effects were evaluated by assessing the rats' general behavior, body weight, food intake, water consumption, blood biochemical and hematological parameters, organ coefficients, and organ histopathology.

RESULTS

No obvious adverse reactions were found in the rats in the acute toxicity study, indicating that ZYG was non-toxic. In the subacute toxicity study, ZYG had no toxic effect on the rats at a dose of 2.5 g/kg/day but showed slight toxicity in the kidneys, and spleens of the rats at doses of 5 and 10 g/kg/day. Significant drug toxicity was observed in male and female rats at 5 and 10/kg/day; however, elevated WBCs counts, ALT, and LYMs levels were found in female rats.

CONCLUSIONS

The oral administration of ZYG at a dose of less than 10 g/kg/day for 1 day or 2.5 g/kg/day for 30 consecutive days can be considered safe, as these doses showed no distinct toxicity or side effects in the rats in this study. Therefore, the dosage should be set according to the clinically recommended dosage to ensure its safety.

Yiqi Huayu Jiedu Decoction inhibits liver metastasis of colorectal cancer via enhancing natural killer cells function

ETHNOPHARMACOLOGICAL RELEVANCE

Complementary treatment with valuable efficacy and less toxic or side effect is in urgent need for colorectal cancer (CRC) therapy. Yiqi Huayu Jiedu Decoction (YHJD) is a polyherbal formulation which has been applied in clinic to treat CRC for a long period of time. Nevertheless, the potential active ingredients and molecular mechanism remains to be further explored.

AIM OF THE STUDY

To probe the effective compounds of YHJD and its underlying pharmacological effects. Moreover, the influence on liver metastasis of CRC as well as function of natural killer (NK) cells results from YHJD was investigated.

MATERIALS AND METHODS

The active ingredients and target genes of YHJD was examined through TCMSP databases. Compound-compound target network was performed by applying Cytoscape3.9.1 software. The CRC-related disease targets were explored via DisGeNET database. Venn database was used to find the common genes between CRC and YHJD. Protein-protein interaction network was established by STRING database. Biological process and signaling pathways potentially regulated by YHJD were evaluated by DAVID database. Western blot assay was then conducted to further investigate the effect of YHJD on PI3K-AKT signaling. The association between NK cells content and TNM or pathological stages of CRC was studied through TCGA database. The killing efficiency of NK cells was researched by CCK8 experiment. In vivo assay and HE staining were performed to assess the anti-liver metastasis effect of YHJD. The variation of NK cells content was authenticated by applying flow cytometry analysis.

RESULTS

We firstly found 176 active ingredients and 268 target genes of YHJD. Compound-compound target network was then established consisted of 455 nodes and 3989 edges. Then 707 disease targets associated with CRC were discovered and 42 common genes between CRC and YHJD were identified. Protein-protein interaction network was further constructed, among which 5 vital genes including TP53, AKT1, TNF, MYC and CCND1 were recognized. GO and KEGG analysis was performed to explore probable biological process and signaling pathways regulated by YHJD. Particularly, the ratio of p-PI3K/PI3K and p-AKT/AKT at protein level representing the activation of PI3K-AKT signaling could be suppressed by YHJD. In addition, bioinformatic analysis detected reduced NK cells content in CRC tissues, which gave rise to more advanced node, metastasis and pathological stages. We next presented that YHJD can improve the killing effect of NK cells on CRC. At meantime, YHJD was capable of suppressing liver metastasis of CRC in vivo as well as promoting the content of NK cells, while the improving effect was partially neutralized by anti-ASGM1.

CONCLUSIONS

Our research indicates that YHJD can prohibit liver metastasis of CRC in vivo. The therapeutic effectiveness is linked to regulation of multiple targets and effector process, especially PI3K-AKT signaling as well as immune response dominated by NK cells.

Network pharmacology prediction and molecular docking-based strategy to explore the potential mechanism of Radix Astragali against hypopharyngeal carcinoma

To explore the anti-tumor effects of Radix Astragali on hypopharyngeal carcinoma and its mechanism. We have bioinformatically analyzed the potential targets of Radix Astragali and predicted the molecular mechanism of Radix Astragali treating of hypopharyngeal carcinoma. The binding process of the hub targets that could prolong the survival time of hypopharyngeal cancer patients with Radix Astragali was simulated by molecular docking. The results showed that 17 out of 36 hub targets could effectively improve the 5-year survival rate of hypopharyngeal cancer patients. Radix Astragali acts on hypopharyngeal carcinoma by regulating a signaling network formed by hub targets connecting multiple signaling pathways and is expected to become a drug for treating and prolonging hypopharyngeal carcinoma patients' survival time.

Screening of the key response component groups and mechanism verification of Huangqi-Guizhi-Wuwu-Decoction in treating rheumatoid arthritis based on a novel computational pharmacological model

BACKGROUND

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by the destruction of synovial tissue and articular cartilage. Huangqi-Guizhi-Wuwu-Decoction (HGWD), a formula of Traditional Chinese Medicine (TCM), has shown promising clinical efficacy in the treatment of RA. However, the synergistic effects of key response components group (KRCG) in the treatment of RA have not been well studied.

METHODS

The components and potential targets of HGWD were extracted from published databases. A novel node influence calculation model that considers both the node control force and node bridging force was designed to construct the core response space (CRS) and obtain key effector proteins. An increasing coverage coefficient (ICC) model was employed to select the KRCG. The effectiveness and potential mechanism of action of KRCG were confirmed using CCK-8, qPCR, and western blotting.

RESULTS

A total of 796 key effector proteins were identified in CRS. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses confirmed their effectiveness and reliability. In addition, 59 components were defined as KRCG, which contributed to 85.05% of the target coverage of effective proteins. Of these, 677 targets were considered key reaction proteins, and their enriched KEGG pathways accounted for 84.89% of the pathogenic genes and 87.94% of the target genes. Finally, four components (moupinamide, 6-Paradol, hydrocinnamic acid, and protocatechuic acid) were shown to inhibit the inflammatory response in RA by synergistically targeting the cAMP, PI3K-Akt, and HIF-1α pathways.

CONCLUSIONS

We have introduced a novel model that aims to optimize and analyze the mechanisms behind herbal formulas. The model revealed the KRCG of HGWD for the treatment of RA and proposed that KRCG inhibits the inflammatory response by synergistically targeting cAMP, PI3K-Akt, and HIF-1α pathways. Overall, the novel model is plausible and reliable, offering a valuable reference for the secondary development of herbal formulas.

Mechanistic insights into the anti-depressant effect of curcumin based on network pharmacology and experimental validation

Curcumin (CUR) exhibits a definite curative effect in the treatment of depression. To identify potential antidepressant targets and mechanisms of action of CUR. This study used network pharmacology to explore the signaling pathways and CUR-related targets in depression. C57BL/6 J mice (male,12-14 weeks old) were randomly divided into four groups (n = 8): saline-treated (control mice), lipopolysaccharide (LPS, 2 mg/kg/day, intraperitoneally), LPS + CUR (50 mg/kg/day, intragastrically), and LPS + CUR + LY294002 (7.5 mg/kg/day, intraperitoneally). After 1 week, behavioral tests were performed. Then, neuronal damage in the prefrontal cortex of mice was evaluated by hematoxylin-eosin (HE) staining. We uncovered the main active mechanism of CUR against depression using Western blotting and enzyme-linked immunosorbent assay (ELISA). Gene set enrichment analysis (GSEA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that the most significantly enriched pathway in CUR against depression was the PI3K-Akt pathway. Moreover, 52 targets were significantly correlated with the PI3K-Akt signaling pathway and CUR-related targets. In addition, among the top 50 targets ranked by degree in the protein-protein interaction (PPI) network, there were 23 targets involved in the 52 intersection targets. Administration of LPS alone extended immobility time in the open field test (OFT) and tail suspension test (TST) and decreased sucrose consumption in the sucrose preference test (SPT). Pretreatment with CUR relieved LPS-induced changes in the behavioral tests, activity of the PI3K-Akt signaling pathway, neuronal damage in the prefrontal cortex (PFC), and inflammatory response. Moreover, inhibition of the PI3K-Akt signaling pathway by LY294002 blocked the therapeutic effects of CUR. Our study indicates that CUR may be an effective antidepressant agent in an LPS-induced mouse model, partly because of its anti-inflammatory action through the PI3K-Akt signaling pathway.

A novel strategy for the study on molecular mechanism of prostate injury induced by 4,4'-sulfonyldiphenol based on network toxicology analysis

The study aimed to investigate the underlying molecular mechanisms of prostate injury induced by 4,4'-sulfonyldiphenol (BPS) exposure and propose a novel research strategy to systematically explore the molecular mechanisms of toxicant-induced adverse health effects. By utilizing the ChEMBL, STITCH, and GeneCards databases, a total of 208 potential targets associated with BPS exposure and prostate injury were identified. Through screening the potential target network in the STRING database and Cytoscape software, we determined 21 core targets including AKT1, EGFR, and MAPK3. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses conducted through the DAVID database illustrated that the potential targets of BPS in prostatic toxicity were primarily enriched in cancer signaling pathways and calcium signaling pathways. These findings suggest that BPS may actively participate in the occurrence and development of prostate inflammation, prostatic hyperplasia, prostate cancer, and other aspects of prostate injury by regulating prostate cancer cell apoptosis and proliferation, activating inflammatory signaling pathways, and modulating prostate adipocytes and fibroblasts. This research provides a theoretical basis for understanding the molecular mechanism of underlying BPS-induced prostatic toxicity and establishes a foundation for the prevention and treatment of prostatic diseases associated with exposure to plastic products containing BPS and certain BPS-overwhelmed environments.

Exploring the Mechanism of Si-miao-yong-an Decoction in the Treatment of Coronary Heart Disease based on Network Pharmacology and Experimental Verification

BACKGROUND

To investigate the active ingredients and the mechanisms of Si-miaoyong- an Decoction (SMYA) in the treatment of coronary heart disease (CHD) by using network pharmacology, molecular docking technology, and in vitro validation.

METHODS

Through the Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP), Uniprot database, GeneCards database, and DAVID database, we explored the core compounds, core targets and signal pathways of the effective compounds of SMYA in the treatment of CHD. Molecular docking technology was applied to evaluate the interactions between active compounds and key targets. The hypoxia-reoxygenation H9C2 cell model was applied to carry out in vitro verification experiments. A total of 109 active ingredients and 242 potential targets were screened from SMYA. A total of 1491 CHD-related targets were retrieved through the Gene- Cards database and 155 overlapping CHD-related SMYA targets were obtained. PPI network topology analysis indicated that the core targets of SMYA in the treatment of CHD include interleukin- 6 (IL-6), tumor suppressor gene (TP53), tumor necrosis factor (TNF), vascular endothelial growth factor A (VEGFA), phosphorylated protein kinase (AKT1) and mitogen-activated protein kinase (MAPK). KEGG enrichment analysis demonstrated that SMYA could regulate Pathways in cancer, phosphatidylinositol 3 kinase/protein kinase B (PI3K/Akt) signaling pathway, hypoxiainducible factor-1(HIF-1) signaling pathway, VEGF signaling pathway, etc. Results: Molecular docking showed that quercetin had a significant binding activity with VEGFA and AKT1. In vitro studies verified that quercetin, the major effective component of SMYA, has a protective effect on the cell injury model of cardiomyocytes, partially by up-regulating expressions of phosphorylated AKT1 and VEGFA.

CONCLUSION

SMYA has multiple components and treats CHD by acting on multiple targets. Quercetin is one of its key ingredients and may protect against CHD by regulating AKT/VEGFA pathway.

Deciphering Multi-target Pharmacological Mechanism of Cucurbita pepo Seeds against Kidney Stones: Network Pharmacology and Molecular Docking Approach

BACKGROUND

Urolithiasis is a prevalent condition with significant morbidity and economic implications. The economic burden associated with urolithiasis primarily stems from medical expenses. Previous literature suggests that herbal plants, including Cucurbita pepo, have lithotriptic capabilities. C. pepo is an annual, herbaceous, widely grown, and monoecious vegetative plant known for its antioxidants, fibers, and fatty acids. Recent studies on C. pepo seeds have shown therapeutic potential in reducing bladder stones and urodynamic illnesses, like kidney stones. However, the precise molecular and pharmacological mechanisms are unclear.

OBJECTIVE

In this research, we employed network pharmacology and molecular docking to examine the active compounds and biological mechanisms of Cucurbita pepo against kidney stones.

METHODS

Active constituents were obtained from previous studies and the IMPPAT database, with their targets predicted using Swiss target prediction. Kidney stone-associated genes were collected from DisGeNET and GeneCards. The active constituent-target-pathway network was constructed using Cytoscape, and the target protein-protein interaction network was generated using the STRING database. Gene enrichment analysis of C. pepo core targets was conducted using DAVID. Molecular docking was performed to identify potential kidney stone-fighting agents.

RESULTS

The findings revealed that Cucurbita pepo contains 18 active components and has 192 potential gene targets, including AR, EGFR, ESR1, AKT1, MAPK3, SRC, and MTOR. Network analysis demonstrated that C. pepo seeds may prevent kidney stones by influencing disease-related signaling pathways. Molecular docking indicated that key kidney stone targets (mTOR, EGFR, AR, and ESR1) effectively bind with active constituents of C. pepo.

CONCLUSION

These findings provide insight into the anti-kidney stone effects of Cucurbita pepo at a molecular level. In conclusion, this study contributes to understanding the potential of Cucurbita pepo in combating kidney stones and lays the foundation for further research.

Identification of formononetin as the active compound of CR-SR in hepatocellular carcinoma treatment: An integrated approach combining network pharmacology and weighted gene co-expression networks

Hepatocellular carcinoma (HCC) is a life-threatening disease for which there is no cure. Traditional Chinese medicine is a treasure trove of Medicinals that has been used for thousands of years. In China, the traditional herb pair, Curcumae Rhizoma and Sparganii Rhizoma (CR-SR) represent a classic herbal combination used for the treatment of HCC. However, the drug targets and pharmacological mechanism of action of CR-SR in the treatment of HCC are unclear. To address this, we screened the active components and drug targets of CR-SR from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and a high-throughput experiment- and reference-guided database of traditional Chinese medicines (HERB database). Combined with the weighted co-expression network analysis of dataset GSE76427, we constructed an active component-target-disease regulatory network. It was found that CR-SR's active components for HCC treatment included trans-gondoic acid, beta-sitosterol, stigmasterol, hederagenin, and formononetin. These compounds specifically targeted the genes Estrogen Receptor 1 (ESR1), Cyclin A2 (CCNA2), Checkpoint Kinase 1 (CHEK1), and Nuclear Receptor Coactivator 2 (NCOA2). ESR1, CCNA2, and CHEK1 genes showed significant differences in survival prognosis, expression levels, and statistical significance during the pathological stage. Moreover, their high affinity for formononetin was determined through molecular docking analysis. Cell assays and high-throughput sequencing were performed to reveal that the inhibitory effect of formononetin on HepG2 cell proliferation was related to hepatocyte metabolism and cell cycle regulation-related pathways. This study provides insights into potential HCC treatments.

Potential Mechanisms Underlying the Therapeutic Roles of Gancao fuzi Decoction in Cold-dampness Obstruction Syndrome-type Knee Osteoarthritis

BACKGROUND

The key active components and potential molecular mechanism of Gancao Fuzi decoction (GFD) in the treatment of cold-dampness obstruction-type knee osteoarthritis (KOA) remain unclear.

OBJECTIVES

To explore the mechanism of GFD in the treatment of cold-dampness obstruction syndrome-type KOA by network pharmacology.

METHODS

The potential active components and targets of the four herbs in GFD (Fuzi, Guizhi, Baizhu, and Gancao) were screened using the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. The targets of KOA were obtained with the Comparative Toxicogenomics Database (CTD), the GeneCards database, and the DisGeNET database, and the common targets of the drugs and disease were ultimately obtained. Cytoscape (v.3.7.1) was used to draw the active component-target network, and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) (v.11.0) database was used to construct the protein interaction network. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used for the Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the intersecting targets.

RESULTS

A total of 102 potential active components and 208 targets of GFD in the treatment of cold-dampness obstruction syndrome-type KOA were screened. GFD treatment was found to be closely related to many inflammatory signalling pathways in the treatment of KOA.

CONCLUSION

The effect of GFD on cold-dampness obstruction syndrome-type KOA is mediated by multicomponent, multitarget, and multichannel mechanisms, which provides the basis for further experimental study of its pharmacodynamic material basis and mechanism.

Underlying Mechanism of Traditional Herbal Formula Chuang-Ling-Ye in the Treatment of Diabetic Foot Ulcer through Network Pharmacology and Molecular Docking

BACKGROUND

Chuang-Ling-Ye (CLY) has been clinically proven to be an effective Chinese medicine for the treatment of diabetic foot ulcers (DFU).

OBJECTIVES

This study aimed to investigate the possible mechanism of CLY in relation to DFU using network pharmacology and molecular docking.

MATERIALS AND METHODS

Firstly, relevant targets of CLY against DFU were obtained from TCMSP, Swiss Target Prediction database and GEO database. Then, topological analysis was employed by Cytoscape to screen the top 6 core active ingredients and the top 8 hub targets. Furthermore, the OmicShare Tools were applied for gene ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analysis. Finally, the results of network pharmacology were verified by molecular docking method.

RESULTS

CLY has 61 active compounds and 361 targets after de-duplication, and the top 8 hub targets were EGFR, TP53, CCND1, IL-1B, CREBBP, AR, PTGS2 and PGR. GO enrichment analysis is mainly related to signal transducer activity, receptor activity, and molecular transducer activity. KEGG pathway analysis indicated that these shared targets were primarily focused on AGE-RAGE signaling pathway in diabetic complications, HIF-1 signaling pathway, IL-17 signaling pathway, and JAK-STAT signaling pathway. Molecular docking results showed that physciondiglucoside, 2-cinnamoyl-glucose and kinobeon A were well bound with EGFR, IL-1B, AR and PTGS2.

CONCLUSION

This study demonstrated that CLY has anti-oxidative stress and anti-inflammatory effects in the treatment of DFU through various constituents, multiple targets, and multiple pathways, which provides a valuable point of reference for future investigations on CLY.

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.

Efficient analysis of toxicity and mechanisms of environmental pollutants with network toxicology and molecular docking strategy: Acetyl tributyl citrate as an example

The study aims to promote network toxicology strategy to efficiently investigate the putative toxicity and underlying molecular mechanisms of environmental pollutants through an example of exploring brain injury induced by ATBC exposure. By utilizing ChEMBL, STITCH, GeneCards, and OMIM databases, we identified 213 potential targets associated with ATBC exposure and brain injury. Further refinements via STRING and Cytoscape software highlight 23 core targets, including AKT1, CASP3, and HSP90AA1. GO and KEGG pathway analysis conducted through DAVID and FUMA databases reveal that core targets of ATBC-induced brain toxicity are predominantly enriched in cancer signaling and neuroactive ligand receptor interaction pathways. Molecular docking was performed with Autodock, which confirmed robust binding between ATBC and core targets. Together, these findings suggest that ATBC may impact the occurrence and development of brain cancer and brain related inflammation, whereas pose risks for cognitive impairment and neurodegeneration, by modulating the apoptosis and proliferation of brain cancer cells, activating inflammatory signaling pathways, and regulating neuroplasticity. This research provides a theoretical basis for understanding the molecular mechanism of ATBC-induced brain toxicity, as well as establishing a foundation for the prevention and treatment of prostatic diseases associated with exposure to plastic products containing ATBC and certain ATBC-overwhelmed environments. Moreover, our network toxicology approach also expedites the elucidation of toxicity pathways for uncharacterized environmental chemicals.

Integrated bioinformatics and network pharmacology to explore the therapeutic target and molecular mechanisms of Bailing capsule on polycystic ovary syndrome

BACKGROUND

Polycystic ovary syndrome (PCOS) is a complex endocrine and metabolic disorder that is common in women of reproductive age. The clinical features of PCOS include hyperandrogenemia and polycystic ovarian changes. Bailing capsule (BL), a proprietary Chinese medicine that contains fermented Cordyceps sinensis powder, has been applied to treat PCOS. However, the specific active ingredients of BL and its mechanisms of action are yet to be elucidated.

METHODS

Initially, the effectiveness of BL on PCOS model mice was evaluated. Subsequently, the active ingredients of BL were searched in the TCMSP and TCM Systems Pharmacology databases, and their targets were predicted using Swiss Target Prediction and SEA databases. Furthermore, the GEO gene database was used to screen for differentially expressed genes (DEGs) related to PCOS. Data from Gene Card, OMIM, DDT, and Drugbank databases were then combined to establish a PCOS disease gene library. Cross targets were imported into the STRING database to construct a protein-protein interaction network. In addition, GO and KEGG pathway enrichment analyses were performed using Metascape and DAVID databases and visualized using Cytoscape software and R 4.2.3. The core targets were docked with SYBYL-X software, and their expressions in PCOS mice were further verified using qPCR.

RESULTS

The core active ingredients of BL were identified to be linoleyl acetate, cholesteryl palmitate, arachidonic acid, among others. Microarray data sets from four groups containing disease and normal samples were obtained from the GEO database. A total of 491 DEGs and 106 drug-disease cross genes were selected. Estrous cycle and ovarian lesions were found to be improved in PCOS model mice following BL treatment. While the levels of testosterone, progesterone, and prolactin decreased, that of estradiol increased. qPCR findings indicated that the expressions of JAK2, PPARG, PI3K, and AKT1 were upregulated, whereas those of ESR1 and IRS1 were downregulated in PCOS model mice. After the administration of BL, the expressions of associated genes were regulated. This study demonstrated that BL exerted anti-PCOS effects via PIK3CA, ESR1, AKT, PPARG, and IRS1 targets affecting PI3K-Akt signaling pathways.

DISCUSSION

This research clarified the multicomponent, multitarget, and multichannel action of BL and provided a theoretical reference for further investigations on its pharmacological basis and molecular mechanisms against PCOS.

Research into the anti-pulmonary fibrosis mechanism of Renshen Pingfei formula based on network pharmacology, metabolomics, and verification of AMPK/PPAR-γ pathway of active ingredients

ETHNOPHARMACOLOGICAL RELEVANCE

Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive disease with limited therapy. Renshen Pingfei Formula (RPFF), a classic Chinese medicine derivative formula, has been shown to exert therapeutic effects on IPF.

AIM OF THE STUDY

The study aimed to explore the anti-pulmonary fibrosis mechanism of RPFF through network pharmacology, clinical plasma metabolomics, and in vitro experiment.

METHODS

Network pharmacology was used to study the holistic pharmacological mechanism of RPFF in the treatment of IPF. The differential plasma metabolites for RPFF in the treatment of IPF were identified by untargeted metabolomics analysis. By integrated analysis of metabolomics and network pharmacology, the therapeutic target of RPFF for IPF and the corresponding herbal ingredients were identified. In addition, the effects of the main components of the formula, kaempferol and luteolin, which regulate the adenosine monophosphate (AMP)-activated protein kinase (AMPK)/peroxisome proliferator-activated receptor γ (PPAR-γ) pathway were observed in vitro according to the orthogonal design.

RESULTS

A total of 92 potential targets for RPFF in the treatment of IPF were obtained. The Drug-Ingredients-Disease Target network showed that PTGS2, ESR1, SCN5A, PPAR-γ, and PRSS1 were associated with more herbal ingredients. The protein-protein interaction (PPI) network identified the key targets of RPFF in IPF treatment, including IL6, VEGFA, PTGS2, PPAR-γ, and STAT3. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis acquired the main enriched pathways, and PPAR-γ involved in multiple signaling pathways, including the AMPK signaling pathway. Untargeted clinical metabolomics analysis revealed plasma metabolite variations in patients with IPF versus controls and before versus after RPFF treatment for patients with IPF. Six differential metabolites were explored as differential plasma metabolites for RPFF in IPF treatment. Combined with network pharmacology, a therapeutic target PPAR-γ of RPFF in IPF treatment and the corresponding herbal components were identified. Based on the orthogonal experimental design, the experiments showed that kaempferol and luteolin can decrease the mRNA and protein expression of α-smooth muscle actin (α-SMA), and the combination of lower dose can inhibit α-SMA mRNA and protein expression by promoting the AMPK/PPAR-γ pathway in transforming growth factor beta 1 (TGF-β1)-treated MRC-5 cells.

CONCLUSIONS

This study revealed that the therapeutic effects of RPFF are due to multiple ingredients and have multiple targets and pathways, and PPAR-γ is one of therapeutic targets for RPPF in IPF and involved in the AMPK signaling pathway. Two ingredients of RPFF, kaempferol and luteolin, can inhibit fibroblast proliferation and the myofibroblast differentiation of TGF-β1, and exert a synergistic effect through AMPK/PPAR-γ pathway activation.

Mechanism of Rhodiola rosea-Euonymus alatus drug pair against rheumatoid arthritis: Network pharmacology and experimental validation

PURPOSE

The present study aimed to explore the potential components and mechanisms of Rhodiola rosea-Euonymus alatus drug pair (TY) that ameliorate rheumatoid arthritis (RA).

METHODS

The main active components, core targets, and important pathways of TY against RA were predicted by network pharmacology analysis. The binding activity between the main active components and the core targets was verified by the molecular docking technique. Collagen-induced arthritis (CIA) rat model and tumor necrosis factor (TNF)-α-induced fibroblast-like synovial cells in human RA (HFLS-RA) model were established, respectively. The core targets were verified by cell counting kit-8 assay, hematoxylin eosin, enzyme-linked immunosorbent assay, real-time polymerase chain reaction, and Western blot analysis, and the therapeutic effect of TY was evaluated.

RESULTS

A total of 18 possible components and 34 core targets were obtained by network pharmacology, among which inflammatory response, phosphatidylinositide 3-kinases (PI3K)-AKT and MAPK pathways were involved in the therapeutic effect of TY on RA. The results of molecular docking showed that kaempferol and quercetin had high binding affinity to interleukin (IL)-1β, IL-6, matrix metalloproteinase (MMP)9, and TNF-α. In vivo and in vitro experiments showed that TY dose-dependently inhibited the proliferation of HFLS-RA cells induced by TNF-α, and significantly reduced the paw swelling and arthritis scores in CIA rats. At the same time, TY inhibited the production of inflammatory factors in CIA rat serum and TNF-α-induced HFLS-RA cells. It also decreased the expression of PI3K, phospho-protein kinase B, MMP1, MMP3, MMP9, and increased the protein and mRNA levels of tissue inhibitors of MMPs (TIMP)1 in synovial tissue.

CONCLUSION

TY can inhibit the PI3K/AKT signaling pathway and regulate the balance between MMPs and TIMP, thus playing a therapeutic role in RA.

Integrated metabolomics and network pharmacology to reveal antioxidant mechanisms and potential pharmacological ingredients of citrus herbs

The benefits of citrus herbs are strongly associated with their secondary metabolites. In the study, we conducted widely-targeted metabolomics and ultra-high performance liquid chromatography (UPLC) to compare the variability of ingredients in four citrus herbs. In total, we discovered 1126 secondary metabolites, primarily comprising flavonoids, phenolic acids, lignans and coumarins, and alkaloids. Differential metabolites of citrus herbs were searched by multivariate statistical analysis. Notably, Citri Reticulatae Pericarpium contained higher levels of flavonoids, while Zhique and Huajuhong demonstrated a greater abundance of coumarins. Among the flavonoids determined by UPLC, Guangchenpi demonstrated significantly elevated levels of polymethoxyflavones (tangeretin and nobiletin) compared to other citrus herbs. Additionally, we determined their antioxidant capacity (Chenpi > Guangchenpi > Huajuhong > Zhique) using in vitro assays. Finally, we utilized network pharmacology to explore the antioxidant mechanisms and potential pharmacological ingredients, providing a basis for future preventive and therapeutic applications of these metabolites.

Screening study on significant Chinese herb for anti-idiopathic pulmonary fibrosis by combining clinical experience prescriptions and molecular dynamics simulation technologies

Various techniques such as data mining, network pharmacology, molecular docking and molecular dynamics simulation were used in this study to screen and validate effective herbal medicines for the treatment of idiopathic pulmonary fibrosis (IPF) and to reveal their mechanisms of action at the molecular level. The use of this approach will provide new tools and ideas for future drug screening, especially for the application of herbal medicines in the treatment of complex diseases. Among them, the five identified core targets, including IL6, TP53, AKT1, VEGFA, and TNF, as well as a series of major active compounds, will be important references for future anti-IPF drug development. This information will accelerate the discovery and development of relevant drugs. Meanwhile, this study further confirmed the potential value of four Chinese herbal medicines, including Gancao, Danshen, Huangqin, and Sanqi, in the treatment of IPF. This will promote more clinical trials and practices to confirm and optimise the application of these herbs. Finally, this study is an important theoretical guide to enhance the advantages of Chinese herbal medicines in the prevention and treatment of major and difficult diseases, as well as to understand and utilise the potential efficacy of Chinese herbal medicines. This will further promote the scientific research and clinical application of herbal medicines and provide more possibilities for future disease treatmentCommunicated by Ramaswamy H. Sarma.

Study on the Alleviating Effect and Potential Mechanism of Ethanolic Extract of Limonium aureum (L.) Hill. on Lipopolysaccharide-Induced Inflammatory Responses in Macrophages

Inflammation is the host response of immune cells during infection and traumatic tissue injury. An uncontrolled inflammatory response leads to inflammatory cascade, which in turn triggers a variety of diseases threatening human and animal health. The use of existing inflammatory therapeutic drugs is constrained by their high cost and susceptibility to systemic side effects, and therefore new therapeutic candidates for inflammatory diseases need to be urgently developed. Natural products are characterized by wide sources and rich pharmacological activities, which are valuable resources for the development of new drugs. This study aimed to uncover the alleviating effect and potential mechanism of natural product Limonium aureum (LAH) on LPS-induced inflammatory responses in macrophages. The experimental results showed that the optimized conditions for LAH ultrasound-assisted extraction via response surface methodology were an ethanol concentration of 72%, a material-to-solvent ratio of 1:37 g/mL, an extraction temperature of 73 °C, and an extraction power of 70 W, and the average extraction rate of LAH total flavonoids was 0.3776%. Then, data of 1666 components in LAH ethanol extracts were obtained through quasi-targeted metabolomics analysis. The ELISA showed that LAH significantly inhibited the production of pro-inflammatory cytokines while promoting the secretion of anti-inflammatory cytokines. Finally, combined with the results of network pharmacology analysis and protein expression validation of hub genes, it was speculated that LAH may alleviate LPS-induced inflammatory responses of macrophages through the AKT1/RELA/PTGS2 signaling pathway and the MAPK3/JUN signaling pathway. This study preliminarily revealed the anti-inflammatory activity of LAH and the molecular mechanism of its anti-inflammatory action, and provided a theoretical basis for the development of LAH as a new natural anti-inflammatory drug.

System pharmacology-based determination of the functional components and mechanisms in chronic heart failure treatment: an example of Zhenwu decoction

Chronic heart failure (CHF) is the primary cause of death among patients with cardiovascular diseases, representing the advanced stage in the development of several cardiovascular conditions. Zhenwu decoction (ZWD) has gained widespread recognition as an efficacious remedy for CHF due to its potent therapeutic properties and absence of adverse effects. Nevertheless, the precise molecular mechanisms underlying its actions remain elusive. This study endeavors to unravel the intricate pharmacological underpinnings of five herbs within ZWD concerning CHF through an integrated approach. Initially, pertinent data regarding ZWD and CHF were compiled from established databases, forming the foundation for constructing an intricate network of active component-target interactions. Subsequently, a pioneering method for evaluating node significance was formulated, culminating in the creation of core functional association space (CFAS). To discern vital components, a novel dynamic programming algorithm was devised and used to determine the core component group (CCG) within the CFAS. Enrichment analysis of the CCG targets unveiled the potential coordinated molecular mechanisms of ZWD, illuminating its capacity to ameliorate CHF by modulating genes and related signaling pathways involved in pathological remodeling. Notable pathways encompass PI3K-Akt, diabetic cardiomyopathy, cAMP and MAPK signaling. Concluding the computational analyses, in vitro experiments were executed to assess the effects of vanillic acid, paradol, 10-gingerol and methyl cinnamate. Remarkably, these compounds demonstrated efficacy in reducing the production of ANP and BNP within isoprenaline-induced AC 16 cells, further validating their potential therapeutic utility. This investigation underscores the efficacy of the proposed model in enhancing the precision and reliability of CCG selection within ZWD, thereby presenting a novel avenue for mechanistic inquiries, compound refinement and the secondary development of TCM herbs.

Study on the mechanism of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen in sedation and tranquillising mind

This study analysed the pharmacological mechanism of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen in sedation and tranquillising mind using network pharmacology methods. The findings of this study aimed to serve as a reference for the development of novel drugs and the clinical expansion and application of traditional Chinese medicine formulas. The chemical constituents and therapeutic targets of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen were acquired from TCMSP, HERB, and ETCM databases. Active components were identified using ADME criteria, while the primary targets associated with sedation and mental tranquillity were obtained from GENECARDS, OMIM, and DRUGBANK databases. A protein-protein interaction (PPI) network analysis was conducted using the STRING platform to investigate potential functional protein modules by the network. The METASCAPE platform was employed for the study of the "component-target" and its associated biological processes and pathways. Subsequently, the "component-target" network was constructed using Cytoscape 3.9.1 software. Finally, the validation of molecular docking was conducted through AUTODOCK. The findings revealed that Quercetin, Atropine, Dauricine, (S)-Coclaurine, and other active ingredients were identified as the core constituents of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen. Additionally, PTGS2, PTGS1, MAOB, GABRA1, SLC6A2, ADRB2, CHRM1, HTR2A, and other targets were identified as the core targets. The results of the molecular docking analysis demonstrated that Quercetin, Atropine, Dauricine, and (S)-Coclaurine exhibited binding solid affinity towards PTGS2 and PTGS1. The predominant biological pathways associated with sedation and tranquilisation primarily involved Neuroactive ligand-receptor interaction and activation of receptors involved in chemical carcinogenesis. This study provided initial findings on the multi-component, multi-target, and multi-pathway mechanism underlying the sedative and tranquillising effects of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen. These findings had the potential to serve as a foundation for the future development and utilisation of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen.

Salvia miltiorrhiza and Tanshinone IIA reduce endothelial inflammation and atherosclerotic plaque formation through inhibiting COX-2

The mechanisms of Salvia miltiorrhiza (SM) and Tanshinone IIA (Tan IIA) in the treatment of atherosclerosis was examined by combining network pharmacology and molecular biology experiments. The TCMSP and BATMAN-TCM databases provided 104 SM candidate ingredients and 813 target genes, while GEO and GeneCards databases identified 35 overlapping targets between SM and coronary artery disease (CAD). From these data, we constructed a CAD-target-active ingredient network, and using Gene Ontology (GO) and KEGG pathway analysis, 211 GO terms and 43 pathways were identified, which facilitated the construction of a key active ingredient-target-pathway network. We then constructed a protein-protein interaction (PPI) network and performed molecular docking simulations between Tan IIA and 10 key target proteins to analyze the interactions between the molecule and the protein. SM was found to alleviate CAD by reducing the expression of key pro-inflammatory factors, such as COX-2 (PTGS2), MMP9, ICAM1, TNF-α, and NF-κB. Tan IIA was identified as the primary effective component of SM in treating CAD, with TNF and PTGS2 being its main targets. We further validated these findings using in vitro/in vivo experiments. The results showed that both SM and Tan IIA attenuated the buildup of plaque and the accumulation of lipids in ApoE-/- mice. In addition, SM and Tan IIA reduced vascular inflammatory factors expression in ApoE-/- mice and ox-LDL-cultured HUVECs. Furthermore, our findings showed that Tan IIA reduced vascular endothelial inflammation and prevented plaque formation via COX-2/TNF-a/NF-κB signaling pathway. We have demonstrated for the first time that Tan IIA plays a vital role in attenuating atherosclerosis by downregulating COX-2 expression.

Anti-inflammation is an important way that Qingre-Huazhuo-Jiangsuan recipe treats acute gouty arthritis

Background: Acute gouty arthritis (AGA) significantly impairs patients' quality of life. Currently, existing therapeutic agents exhibit definite efficacy but also lead to serious adverse reactions. Therefore, it is essential to develop highly efficient therapeutic agents with minimal adverse reactions, especially within traditional Chinese medicine (TCM). Additionally, food polyphenols have shown potential in treating various inflammatory diseases. The Qingre-Huazhuo-Jiangsuan-Recipe (QHJR), a modification of Si-Miao-San (SMS), has emerged as a TCM remedy for AGA with no reported side effects. Recent research has also highlighted a strong genetic link to gout. Methods: The TCM System Pharmacology (TCMSP) database was used to collect the main chemical components of QHJR and AGA-related targets for predicting the metabolites in QHJR. HPLC-Q-Orbitrap-MS was employed to identify the ingredients of QHJR. The collected metabolites were then used to construct a Drugs-Targets Network in Cytoscape software, ranked based on their "Degree" of significance. Differentially expressed genes (DEGs) were screened in the Gene Expression Omnibus (GEO) database using GEO2R online analysis. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. The DEGs were utilized to construct a Protein-Protein Interaction (PPI) Network via the STRING database. In vivo experimental validation was conducted using colchicine, QHJR, rapamycin (RAPA), and 3-methyladenine (3-MA) as controls to observe QHJR's efficacy in AGA. Synovial tissues from rats were collected, and qRT-PCR and Western blot assays were employed to investigate Ampk-related factors (Ampk, mTOR, ULK1), autophagy-related factors (Atg5, Atg7, LC3, p62), and inflammatory-related factors (NLRP3). ELISA assays were performed to measure inflammatory-related factor levels (IL-6, IL-1β, TNF-α), and H&E staining was used to examine tissue histology. Results: Network analysis screened out a total of 94 metabolites in QHJR for AGA. HPLC-Q-Orbitrap-MS analysis identified 27 of these metabolites. Notably, five metabolites (Neochlorogenic acid, Caffeic acid, Berberine, Isoliquiritigenin, Formononetin) were not associated with any individual herbal component of QHJR in TCMSP database, while six metabolites (quercetin, luteolin, formononetin, naringenin, taxifolin, diosgenin) overlapped with the predicted results from the previous network analysis. Further network analysis highlighted key components, such as Caffeic acid, cis-resveratrol, Apigenin, and Isoliquiritigenin. Other studies have found that their treatment of AGA is achieved through reducing inflammation, consistent with this study, laying the foundation for the mechanism study of QHJR against AGA. PPI analysis identified TNF, IL-6, and IL-1β as hub genes. GO and KEGG analyses indicated that anti-inflammation was a key mechanism in AGA treatment. All methods demonstrated that inflammatory expression increased in the Model group but was reversed by QHJR. Additionally, autophagy-related expression increased following QHJR treatment. The study suggested that AMPKα and p-AMPKα1 proteins were insensitive to 3 MA and RAPA, implying that AMPK may not activate autophagy directly but through ULK1 and mTOR. Conclusion: In conclusion, this study confirms the effectiveness of QHJR, a modified formulation of SMS (a classic traditional Chinese medicine prescription for treating gout), against AGA. QHJR, as a TCM formula, offers advantages such as minimal safety concerns and potential long-term use. The study suggests that the mechanism by which QHJR treats AGA may involve the activation of the AMPK/mTOR/ULK1 pathway, thereby regulating autophagy levels, reducing inflammation, and alleviating AGA. These findings provide new therapeutic approaches and ideas for the clinical treatment of AGA.

Identification of Artemisia Argyi (AA) Therapy in Alzheimer's Disease (AD) Using Network Pharmacology and Molecular Docking

This study aims to investigate the molecular mechanism of Artemisia argyi (AA) in the treatment of cognitive impairment of Alzheimer's disease (AD) and the docking activity of AA on potential therapeutic targets using network pharmacology and molecular docking techniques. Bioinformatic analysis showed that neuroactive ligand-receptor interaction, the pathway of cancer, calcium signaling, neurodegeneration-multiple disease, and chemical carcinogenesis-receptor activation might be the related signal pathway in AA-AD. Moreover, the binding energy of AA active compounds to potential targets are ≦-4.16 kJ mol-1 with 10 patterns ≦-10 kJ mol-1 . The results of molecular docking showed that there would be a stable binding ability between the active components of AA and potential target genes. Among them, 24-methylenecyloartanone, beta-sitosterol, and Stigmasterol are active components with potential oral bioavailability (OB), drug-likeness (DL), and blood-brain-barrier(BBB) are screened out with the stable binding ability to target genes, which may be potential components of AA treatment for AD. This study laid an important foundation for further study of the molecular mechanism of AA treatment for AD.

Drug candidates and potential targets of Curculigo spp. compounds for treating diabetes mellitus based on network pharmacology, molecular docking and molecular dynamics simulation

Curculigo spp. is a herb that is commonly used in Indonesia to treat diabetes mellitus (DM) . The main active components of Curculigo spp. were identified through our previous metabolomic study and online database platform. However, the biological mechanisms underlying Curculigo spp. activity in treating DM remain unclear. Therefore, in this study, a network pharmacology was used to explore the active compounds of Curculigo spp. and their potential molecular mechanisms for treating DM. Oral bioavailability and drug-likeness from the compounds of Curculigo spp. were screened using Lipinski's rule of five, BBB, HIA + and Caco-2 permeability criteria. A network of compound-target-disease-pathway was then constructed using Cytoscape. The highest degree compounds and targets were then confirmed by molecular docking and molecular dynamics (MD) simulations. The human body can absorb 33 compounds derived from Curculigo spp. In addition, 58 nodes and 62 edges generated a network analysis with the DM target. The highest degree of the compound-target-disease pathway was for orcinol glucoside, AKR1B1, autoimmune diabetes, bile acid and bile salt metabolism. Furthermore, the computational docking method on Curculigo spp. compounds with the highest degree revealed that orcinol glucoside interacted with PTPN1 through a hydrogen bond and resulted in a binding energy of -7.2 kcal mol-1. Through hydrogen bonds, orcinol glucoside in PTPN1 regulates multiple signaling pathways via the adherens junction pathway, which may play a therapeutic role in DM (type 2 diabetes: obesity). In addition, MD simulation confirmed that orcinol glucoside, is suitable for DM treatment by interacting with PTPN1.Communicated by Ramaswamy H. Sarma.

Integrating network pharmacology with molecular docking for elucidation of molecular biological mechanisms of Jiedu Qingjin formula for non-small cell lung cancer

Traditional Chinese medicine is an important part of complementary alternative medicine. Jiedu Qingjin formula (JDQJF) is an effective national invention patent for the treatment of non-small cell lung cancer (NSCLC). We investigated the molecular biological mechanisms based on network pharmacology, molecular docking, and molecular dynamics simulations. Compounds of JDQJF were screened through the TCMSP, ETCM, and literature. Targets were searched by DrugBank and predicted by SwissTargetPrediction. GEO database was applied for screening differentially expressed genes between cancerous tissues and healthy tissues of NSCLC. Subsequently, the protein-protein interaction between JDQJF and NSCLC were obtained by Cytoscape. Visual analyses were carried out to extract candidate genes, then subjected to Metascape for enrichment analyses. Finally, molecular docking was performed by AutoDock, and the best complexes were subjected to molecular dynamics simulation and binding energy calculations by MMPBSA. A total of 273 compounds, 390 targets, 3146 GO terms, and 174 KEGG pathways were obtained. Five potential compounds (quercetin, adenosine, apigenin, heptadecanoic acid, and luteolin) were notably modulated by key targets AKT1, MAPK3, and RAF1. Enrichment results included cell cycle process, growth transduction factor, immune response-activating transduction, and involved PI3K/AKT, MAPK, NF-κB and VEGF pathway. RAF1-quercetin showed the highest binding affinity (-9.1 kcal/mol), revealed stable interactions during the simulation, and the highest estimated relative binding energy of the RAF1-Heptadecanoic was -184.277 kcal/mol. This study suggested that EMT-related, inflammation-related, immune-related, and angiogenesis-related pathways may be associated with JDQJF, and involved in the advancement of NSCLC, which points out the research direction for subsequent utility mechanism validation.Communicated by Ramaswamy H. Sarma.

The preliminary development and clinical verification of the positive index score scale of "Heart Arthralgia Syndrome"

BACKGROUND

In recent years, the age of onset for coronary heart disease (CHD) has become one of the leading causes of death worldwide. The medical treatments occasionally cause side effects; therefore, there is still an urgent need to develop new therapeutic modalities for CHD in clinical practice. "Heart Arthralgia Syndrome (HAS)" is a general term for CHD with arthralgia symptoms proposed by our team based on clinical experience. At present, there is little in-depth research on the treatment of HAS by TCM. Pick Complex Therapy (PCT) is an innovative and developed theory of collateral acupuncture therapy for HAS.

METHODS

We collected data from 276 patients who met the criteria for (coronary heart disease with numbness of neck, shoulder, waist, and leg). We selected 24 diagnostic criteria for HAS by means of multiple methods, including Cronbach's α coefficient, retest reliability, subjective evaluation, discrete trend, Pearson's rank correlation coefficient and factor analysis method. We thereafter evaluated the reliability, validity and responsiveness of the scale. In the clinical validation phase, we verified whether the preliminary developed positive index (PI) scale can guide clinical practice. Forty (40) patients with HAS were selected in the study. SPSS23.0 statistical software was used for statistical processing and analysis.

RESULTS

Assessment results of the initial PI scale for HAS: the average time to complete the scale was 7.47 ± 3.59 minutes. Cronbach's α coefficient for the initial table was 0.711, the retest reliability was 0.897, the Kaiser-Meyer-Olkin test result was 0.844, and the Bartlett test result was 2502.300. Following maximum variance rotation analysis, the cumulative variance contribution rate was determined to be 66.605%. In the clinical validation phase of the PI scale, we tested 40 patients before and after the PCT treatments. After 3 measurements, the correlation between the PI scale for HAS and the angina pectoris grading scoring method table decreased gradually. The last 2 measurement results of study indicated that there was a significant correlation between the PI scale and thrombin time, while physical and chemical examination showed no significant changes.

CONCLUSION

The PI scale for HAS can be widely used in the clinic as a preliminary evaluation tool for guiding PCT.

Homotherapy for heteropathy of Alzheimer's disease and anemia through reducing the expression of toll-like receptor and TNF by steamed Panax notoginseng

BACKGROUND

One of the effects of Steamed Panax notoginsen (SPN) is to replenish blood, which is mostly used to treat anemia in clinic. SPN has the effect of treating anemia and Alzheimer's disease (AD) in clinical and basic research. In traditional Chinese medicine, anemia and AD have the same characteristics, and their symptoms are qi and blood deficiency.

METHODS

First, data analysis was carried out through network pharmacology to predict the action targets of SPN homotherapy in the treatment of AD and anemia. Specifically, TCMSP and relevant literature were used to screen the main active ingredients of Panax notoginseng, and SuperPred was used to predict the action targets of the active ingredients. Disease targets related to AD and anemia were collected through Genecards database, and STRING and protein interaction (PPI) was used for enrichment analysis, Analyze the characteristics of the active ingredient target network on the Cytascape 3.9.0 platform, and use Metascape to enrich the gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes Pathway Enrichment (KEGG pathway). Then Drosophila was used as the AD animal model, and the effects of SPN on the climbing ability, olfactory memory and brain Aβ, with rats as anemia animal models, the improvement effect of SPN on blood routine and organ index of rats with blood deficiency induced by CTX and APH was analyzed to further explain the therapeutic effect of SPN on these two diseases. Finally, the regulatory effect of SPN on the key active target of allotherapy for AD and anemia was verified by PCR.

RESULTS

After the screening, 17 active components and 92 action targets of SPN were obtained. The degree values of components and the first 15 targets are NFKB1, IL10, PIK3CA, PTGS2, SRC, ECFR, CASP3, MTOR, IL1B, ESR1, AKT1, HSP90AA1, IL6, TNF, and Toll-like receptor, it is mainly related to inflammatory response, immune regulation and antioxidation. SPN improved the climbing ability, olfactory memory ability, and Aβ42 content in the brain of Aβ flies, and significantly reduced the expression of TNF and Toll-like receptor in the brain after treatment. SPN can significantly improve the blood routine index and organ index of anemia rats, and also significantly reduce the expression of TNF and Toll-like receptor in the brain after treatment.

CONCLUSION

SPN can regulate the expression of TNF and Toll-like receptor to achieve the same treatment of AD and anemia.

Molecular Docking Integrated with Network Pharmacology Explores the Therapeutic Mechanism of Cannabis sativa against Type 2 Diabetes

The incidence of type 2 diabetes (T2D) is rising, and finding new treatments is important. C. sativa is a plant suggested as a potential treatment for T2D, but how it works needs to be clarified. This study explored the pharmacological mechanism of C. sativa in treating T2D. We identified the active compounds in C. sativa and their targets. From there, we examined the genes associated with T2D and found overlapping genes. We conducted an enrichment analysis and created a protein-protein and target-compound interactions network. We confirmed the binding activities of the hub proteins and compounds with molecular docking. We identified thirteen active compounds from C. sativa, which have 150 therapeutic targets in T2D. The enrichment analysis showed that these proteins are involved in the hormone, lipid, and stress responses. They bind transcription factors and metals and participate in the insulin, PI3K/Akt, HIF-1, and FoxO signaling pathways. We found four hub proteins (EGFR, ESR1, HSP90AA1, and SRC) that bind to the thirteen bioactive compounds. This was verified using molecular docking. Our findings suggest that C. sativa's antidiabetic action is carried out through the insulin signaling pathway, with the participation of HIF-1 and FoxO.

Underlying Mechanisms of Bergenia spp. to Treat Hepatocellular Carcinoma Using an Integrated Network Pharmacology and Molecular Docking Approach

Hepatocellular carcinoma (HCC) is the fifth most common and fatal cancer reported, representing 72.5% of malignancies around the world. The majority of HCC incidents have been associated with infections caused by hepatitis B and C viruses. Many first- and second-line conventional drugs, e.g., sorafenib, cabozantinib, or ramucirumab, have been used for the management of HCC. Despite different combinational therapies, there are still no defined biomarkers for an early stage diagnosis of HCC. The current study evaluated the potential of Bergenia stracheyi, Bergenia ciliata, Bergenia pacumbis, and Bergenia purpurascens, which belong to the family Saxifragaceae, to treat HCC using an integrated network pharmacology and molecular docking approach. Four active phytochemicals were selected based on oral bioavailability (OB) and drug likeness (DL) parameters. The criteria of phytochemical selection were set to OB > 30% and DL > 0.18. Similarly, the gene targets related to Bergenia spp. and the genes related to HCC were retrieved from different databases. The integration of these genes revealed 98 most common overlapping genes, which were mainly interrelated with HCC pathogenesis. Ultimately, the 98 Bergenia-HCC associated genes were used for protein-protein interaction (PPI), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and Gene Ontology (GO) enrichment analyses. Finally, the topological analysis revealed the top ten hub genes with maximum degree rank. From the top ten genes, STAT3, MAPK3, and SRC were selected due to their involvement in GO annotation and KEGG pathway. To confirm the network pharmacology results, molecular docking analysis was performed to target STAT3, MAPK3, and SRC receptor proteins. The phytochemical (+)-catechin 3-gallate exhibited a maximum binding score and strong residue interactions with the active amino acids of MAPK3-binding pockets (S-score: -10.2 kcal/mol), SRC (S-score: -8.9 kcal/mol), and STAT3 (S-score: -8.9 kcal/mol) as receptor proteins. (+)-Catechin 3-gallate and β-sitosterol induced a significant reduction in cell viability in HepG2 after 24 h of treatment in a dose-dependent manner. The results of this study explore the potential of (+)-catechin 3-gallate and β-sitosterol, which can be used in the future as potential drug candidates to suppress HCC.

Mechanism of baixiangdan capsules on anti-neuroinflammation: combining dry and wet experiments

Neuroinflammation plays an important role in the pathogenesis of neurological disorders, and despite intensive research, treatment of neuroinflammation remains limited. BaiXiangDan capsule (BXD) is widely used in clinical practice. However, systematic studies on the direct role and mechanisms of BXD in neuroinflammation are still lacking. We systematically evaluated the potential pharmacological mechanisms of BXD on neuroinflammation using network pharmacological analysis combined with experimental validation. Multiple databases are used to mine potential targets for bioactive ingredients, drug targets and neuroinflammation. GO and KEGG pathway analysis was also performed. Interactions between active ingredients and pivotal targets were confirmed by molecular docking. An experimental model of neuroinflammation was used to evaluate possible therapeutic mechanisms for BXD. Network pharmacological analysis revealed that Chrysoeriol, Kaempferol and Luteolin in BXD exerted their anti-neuroinflammatory effects mainly by acting on targets such as NCOA2, PIK3CA and PTGS2. Molecular docking results showed that their average affinity was less than -5 kcal/mol, with an average affinity of -8.286 kcal/mol. Pathways in cancer was found to be a potentially important pathway, with involvement of PI3K/AKT signaling pathways. In addition, in vivo experiments showed that BXD treatment ameliorated neural damage and reduced neuronal cell death. Western blotting, RT-qPCR and ELISA analysis showed that BXD inhibited not only the expression of IL-1β, TNF-α and NO, but also NF-κB, MMP9 and PI3K/AKT signaling pathways. This study applied network pharmacology and in vivo experiments to explore the possible mechanisms of BXD against neuroinflammation, providing insight into the treatment of neuroinflammation.