Network Pharmacology and Molecular Docking Reveal the Multi-Target Anti-Osteoporosis Mechanism of Bushen Huoxue Decoction.

Breast cancer (BC) is by far seen as the most common malignancy globally, with 2.261 million patients newly diagnosed, accounting for 11.7% of all cancer patients, according to the Global Cancer Statistics Report (2020). The luminal A subtype accounts for at least half of all BC diagnoses. According to TCM theory, Bushen Huoxue Decoction (BSHXD) is a prescription used for cancer treatment that may influence luminal A subtype breast cancer (LASBC). To analyze the clinical efficacy and underlying mechanisms of BSHXD in LASBC. Network pharmacology and in vitro experiments were utilized to foresee the underlying mechanism of BSHXD for LASBC. According to the bioinformatics analysis, BSHXD induced several proliferation and apoptosis processes against LASBC, and the presumed targets of active components in BSHXD were mainly enriched in the HIF-1 and PI3K/AKT pathways. Flow cytometry assay and western blotting results revealed that the rate of apoptosis enhanced in a dose-dependent manner with BSHXD concentration increasing, respectively. BSHXD notably downregulated the expressions of HIF-1α, P-PI3K, PI3K, P-AKT and AKT proteins. However, adding an HIF-1α agonist restored those protein levels. The study proved that the mechanism of BSHXD in LASBC may be connected to suppressing proliferation by inhibiting the activity of the HIF-1α/PI3K/AKT signaling pathway and promoting apoptosis via the Caspase cascade in LASBC cells.

Network Pharmacology in Traditional Chinese Medicine

Mechanism of Sijunzi Decoction in the treatment of colorectal cancer based on network pharmacology and experimental validation

Houshiheisan modulates the NF-κB/MLCK signaling pathway to protect the endothelial barrier in cerebral small vessel disease.

Multi-omics and experimental validation reveal the mechanism of DanxiaTiaoban decoction in treating atherosclerosis.

Banxia Xiexin decoction (BXD) is a traditional prescription widely used to treat gastrointestinal conditions, including gastric cancer. Through network pharmacology, bioinformatics, and molecular docking analysis, this study aimed to investigate the potential mechanism of the antigastric cancer effect of BXD and pave the way for future research. The network pharmacology analysis used BXD index components to improve reliability and validity. Prognosis-related genes identified through Lasso and Cox regression analysis were considered potential BXD core targets for gastric cancer. Functional enrichment analysis was conducted to uncover the potential mechanism of action of BXD in gastric cancer. In addition, molecular docking of the index components of BXD and the core targets was used to validate the results. The present study obtained six index components of BXD and 155 corresponding antigastric cancer targets. ANXA5, CYP19A1, FGF1, and F2 in the prognostic signature model were identified as core targets of the index components of BXD. Protein-protein interaction networks and functional enrichment analysis indicated that proteoglycans in cancer, PI3K-Akt, and other pathways were involved. According to molecular docking results, six index components showed good-to-strong binding affinities to the core targets. The results indicated that the index components of BXD act on multiple pathways and targets of gastric cancer. Our study paved the way for further investigation of the antigastric cancer activity and mechanisms of BXD.

Object: Benzoinum is a traditional Chinese medicine used to treat ischemic stroke. However, the mechanism of action of benzoinum for treating ischemic stroke still remains unclear. This study aims to elucidate the mechanism of benzoinum for treating ischemic stroke based on network pharmacology and molecular docking, which will explore its key targets and provide a basis and new treatment ideas for its clinical application. Methods: Targets associated with ischemic stroke were retrieved from the Genecards database using the keywords "Ischemic stroke" and "Cerebral ischemia." Network pharmacology analysis was conducted, and a network diagram encompassing drugs, components, targets, and diseases was constructed. The analysis was performed using the Intelligent Network Pharmacology Platform Unique for Traditional Chinese Medicine (INPUT). PPI enrichment analysis was utilized to identify key target genes; GO and KEGG enrichment analyses were carried out to ascertain the primary biological processes, molecular functions, cellular components, and pathways involved. A target network diagram was generated to identify the most enriched targets. The interaction between compounds and targets was determined via molecular docking. Results: A total of 65 active ingredients from benzoinum were identified as potentially effective for the treatment of ischemic stroke. Potential active substances, oleanolic acid, 2,3,5,7- Tetrahydroxyflavone, naphthalene, eucalyptol, and benzoic acid were ranked according to their degree values. In addition, 226 targets were found to be involved in the process. The PPI topology analysis revealed that the core targets included TP53, JUN, STAT3, AKT1, PIK3CA, RELA, MAPK1, MAPK3, TNF, and CXCL8. GO enrichment analysis yielded 6807 entries, with 5589 entries in BP, 385 entries in CC, and 833 entries in MF. KEGG enrichment analysis resulted in 290 entries, primarily related to lipid and atherosclerosis, PI3K-Akt pathway, chemical carcinogenesis receptor activation, IL-17 pathway, and TNF pathway. Molecular docking also demonstrated the interactions between the principal compounds and their respective targets. Conclusion: Benzoinum appears to exert therapeutic effects on ischemic stroke through multiple components, targets, and pathways, with a primary association with its anti-inflammatory properties. However, further experimental validation is recommended to more accurately define its active constituents and mechanisms of action.

Background ZhiKe GanCao Decoction (ZKGCD) is a commonly used traditional Chinese medicine in the clinical treatment of intervertebral disc degeneration (IDD). However, its active ingredients and mechanism of action remain unclear. This study aims to propose the systematic mechanism of ZKGCD action on IDD based on network pharmacology, molecular docking, and enrichment analysis. Methods Firstly, the common target genes between ZKGCD and IDD were identified through relevant databases. Secondly, the protein-protein interaction (PPI) network of common genes was constructed and further analyzed to determine the core active ingredients and key genes. Thirdly, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of common genes were performed. Finally, the stability of the binding between core active ingredients and key genes was verified by molecular docking analysis. Results “Intersecting genes-active components” network consists of 154 active ingredients and 133 common genes. The ten key genes are AKT1, TNF, IL6, TP53, IL1B, JUN, CASP3, STAT3, MMP9, and MAPK3. Meanwhile, quercetin (Mol000098), luteolin (Mol000006), and kaempferol (Mol000422) are the most important core active ingredients. The main signal pathways selected by KEGG enrichment analysis includes AGE-RAGE signaling pathway in diabetic complications (hsa04933), TNF signaling pathway (hsa04668), IL-17 signaling pathway (hsa04657), cellular senescence (hsa04218), apoptosis (hsa04210), and PI3K-Akt signaling pathway (hsa04151), which are mainly involved in inflammation, apoptosis, senescence, and autophagy. Conclusion This study provides a basis for further elucidating the mechanism of action of ZKGCD in the treatment of IDD and offers a new perspective on the conversion of the active ingredient in ZKGCD into new drugs for treating IDD.

This study explores the potential mechanisms of Liujunzi Tang combined with Suanzaoren Tang in treating lung cancer with insomnia through network pharmacology and molecular docking methods. In the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, each single herb in the formula of Liujunzi Tang combined with Suanzaoren Tang was used as a search term, with repeated traditional Chinese medicines (TCMs) searched only once. Oral bioavailability (OB) ≥ 30% and drug-likeness (DL) ≥ 0.18 were set as screening criteria to obtain active components and targets of TCM. Disease-related targets for lung cancer with insomnia were obtained from the Gene Cards database, OMIM database, and PharmGKB database. The disease targets and drug effective component targets were intersected, and a disease-component intersection Venn diagram was drawn. The common intersection targets were imported into the DAVID database for Kyoto Encyclopedia of Genes and Genomics (KEGG) pathway and gene ontology (GO) function enrichment analysis, and molecular docking was performed to verify the affinity of active components with key targets. A total of 185 effective active components and 241 targets were obtained for Liujunzi Tang combined with Suanzaoren Tang. A total of 4290 disease targets were obtained from 3 disease databases. After removing 138 duplicate targets, a total of 4152 disease targets were obtained. The intersection of component targets and disease targets yielded 120 common targets. KEGG pathway enrichment was found in lipid and atherosclerosis, AGE-RAGE signaling pathway in diabetes complications, Kaposi sarcoma-related herpes virus infection, and other signaling pathways. Molecular docking showed that the core components naringenin had good binding activity with AKT1, quercetin and ginsenoside Rh2 with IL1B, and other targets. Through network pharmacology and molecular docking methods, it was explored that Liujunzi Tang combined with Suanzaoren Tang may treat lung cancer with insomnia through multiple components, multiple targets, and multiple pathways, regulating cancer pathways, lipid and atherosclerosis, and other signaling pathways, providing new ideas for the treatment of lung cancer with insomnia.

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

Insight into Shenqi Jiangtang Granule on the improved insulin sensitivity by integrating in silico and in vivo approaches

Xiaoqinglong Decoction (XQLD) is a traditional Chinese medicinal formula commonly used to treat chronic urticaria (CU). However, its underlying therapeutic mechanisms remain incompletely characterized. This study employed an integrated approach combining network pharmacology, bioinformatics, molecular docking, and molecular dynamics simulations to identify the active components, potential targets, and related signaling pathways involved in XQLD's therapeutic action against CU, thereby providing a mechanistic foundation for its clinical application. The active components of XQLD and their corresponding targets were identified using the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. CU-related targets were retrieved from the OMIM and GeneCards databases. Subsequently, core components and targets were determined via protein-protein interaction (PPI) network analysis and component-target-pathway network construction. Topological analyses were performed using Cytoscape software to prioritize core nodes within these networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted via the DAVID database to identify enriched biological processes and signaling pathways. Molecular docking was performed to evaluate binding interactions between key components and core targets, while molecular dynamics (MD) simulations were employed to assess the stability of the component-target complexes with the lowest binding energy. Finally, CU-related targets of XQLD were validated using datasets from the Gene Expression Omnibus (GEO) database. A total of 135 active components and 249 potential targets of XQLD were identified, alongside 1,711 CU-related targets. Core components, such as quercetin, kaempferol, beta-sitosterol, naringenin, stigmasterol, and luteolin, exhibited high degree values in the constructed networks. The core targets identified included AKT1, TNF, IL6, TP53, PTGS2, CASP3, BCL2, ESR1, PPARG, and MAPK3. GO and KEGG pathway enrichment analyses revealed the PI3K-Akt signaling pathway as a central regulatory mechanism. Molecular docking studies demonstrated strong binding affinities between active components and core targets, with the stigmasterol-AKT1 complex exhibiting the lowest binding energy (-11.4 kcal/mol) and high stability in MD simulations. Validation using GEO datasets identified 12 core genes shared between CU-related targets and XQLD-associated targets, including PTGS2 and IL6, which were also prioritized as core targets in the network pharmacology analyses. This study comprehensively integrates multidisciplinary approaches to clarify the potential molecular mechanisms of XQLD in treating CU, highlighting its multitarget and multipathway synergistic effects. Molecular docking and dynamics simulations confirm the stable interaction between stigmasterol and the core target AKT1. Additionally, GEO dataset analysis verifies the pathogenic relevance of targets such as PTGS2 and IL6, significantly enhancing the credibility of our findings. These results provide a modern scientific basis for the traditional therapeutic effects of XQLD on CU and have important implications for developing multitarget treatments for this condition. However, this study mainly relies on database mining and computational simulations. Further in vitro and in vivo experimental validations are needed to confirm the predicted component-target-pathway interactions. This study identifies the active components, potential targets, and pathways through which XQLD exerts therapeutic effects on CU. These findings provide a theoretical foundation for further mechanistic studies and support their clinical application in the treatment of CU.

Uveitis is a complex intraocular inflammatory disease and pathology results from the continuous production of proinflammatory cytokines in the optical axis. Qinghuo Rougan Formula (QHRGF), a traditional Chinese medicine (TCM) is now used to treat uveitis with desirable effect. However, the mechanism of action is still unclear. This study aimed to explore the potential diagnostic and therapeutic biomarkers for uveitis using systems biology methods, including network pharmacology and weighted gene co-expression network analysis (WGCNA). A molecular drug-compound-target-uveitis interaction network was established using network pharmacology. Functional enrichment analyses were performed to screen potential signaling pathways. The uveitis gene expression dataset from the Gene Expression Omnibus database was subjected to WGCNA to identify gene co-expression modules related to uveitis and explore the potential hub genes. The least absolute shrinkage and selection operator (LASSO) model was used to identify the hub genes. Additionally, molecular docking was performed to verify the accuracy and stability of the model. Finally, the suppressive effects of QHRGF on uveitis were experimentally verified in vivo. Network pharmacology and functional enrichment analysis showed that 18 targets and immune/inflammation-related pathways were associated with the QHRGF-targeted pathway network. The yellow module contained 120 genes had a strong correlation with uveitis using WGCNA. In total, 12 putative targets of QHRGF, differentially expressed genes, and yellow module genes were determined. Six hub genes were identified using LASSO model and the receiving operating characteristic curve analysis demonstrated the model can serve as biomarkers for uveitis. The advantages of these genes were approved using molecular docking. Finally, in vivo experiments provided evidence confirming that QHRGF was identified as the key target of the anti-inflammatory effect of uveitis. In conclusion, this research revealed that QHRGF can be used to treat uveitis through multiple components and targets. Meanwhile, the potential anti-inflammatory action of QHRGF in the treatment of uveitis was verified by combining network pharmacology and in vivo experiments, suggesting its potential as a quite prospective agent for the therapy of uveitis.

Diabetic nephropathy (DN), a leading cause of end-stage renal disease, is associated with high morbidity and mortality rates worldwide and the development of new drugs to treat DN is urgently required. Bu-Shen-Huo-Xue (BSHX) decoction is a traditional Chinese herbal formula, made according to traditional Chinese medicine (TCM) theory, and has been used clinically to treat DN. In the present study, we established a high-fat diet/streptozotocin-induced diabetic mouse model and treated the mice with BSHX decoction to verify its therapeutic effects in vivo. Ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) was applied to analyze the chemical composition and active compounds of BSHX decoction. Markers of podocyte epithelial-mesenchymal transition and the Rac1/PAK1/p38MAPK signaling pathway were evaluated to investigate the mechanism underlying function of BSHX decoction. BSHX decoction effectively alleviated diabetic symptoms, according to analysis of the renal function indicators, serum creatinine, blood urea nitrogen, serum uric acid, and urinary albumin excretion rate, as well as renal histopathology and ultrastructural pathology of DN mice. We identified 67 compounds, including 20 likely active compounds, in BSHX decoction. The podocyte markers, nephrin and podocin, were down-regulated, while the mesenchymal markers, α-SMA and FSP-1, were up-regulated in DN mouse kidney; however, the changes in these markers were reversed on treatment with BSHX decoction. GTP-Rac1 was markedly overexpressed in DN mice and its levels were significantly decreased in response to BSHX decoction. Similarly, levels of p-PAK1 and p-p38MAPK which indicate Rac1 activation, were reduced on treatment with BSHX decoction. Together, our data demonstrated that BSHX decoction ameliorated renal function and podocyte epithelial-mesenchymal transition via inhibiting Rac1/PAK1/p38MAPK signaling pathway in high-fat diet/streptozotocin-induced diabetic mice. Further, we generated a quality control standard and numerous potential active compounds from BSHX decoction for DN.

Glucocorticoid-induced osteoporosis (GIOP) is the most common form of secondary osteoporosis, which is caused by a disorder in bone metabolism due to excessive activation of osteoclasts. Bushen Huoxue decoction (BHD) is an herbal formula with multiple pharmacological effects, including anti-inflammatory, antioxidant activity and stem cell migration promotion. However, the effect of BHD on osteoclastogenesis has not been reported. In this study, we aimed to elucidate the effect of BHD on RANKL-stimulated osteoclastogenesis and explored its underlying mechanisms of action in vitro. Our results show that BHD had no effect on BMMs and RAW264.7 cells viability, but inhibited RANKL-induced osteoclast formation in vitro. Furthermore, BHD attenuated RANKL-induced NF-κB, ERK, and JNK signaling. The attenuation of NF-κB, ERK, and JNK activation were enough to impede downstream expression of c-fos and NFATc1 and related specific genes. Meanwhile, we investigated the therapeutic effect of BHD on glucocorticoid-induced osteoporosis (GIOP) mice. The result indicated that BHD prevents glucocorticoid-induced osteoporosis and preserves bone volume by repressing osteoclast activity. Collectively, BHD shows significant osteoclast inhibition and holds great promise in the treatment of osteoporosis.