Investigation of the potential mechanism of the Shugan Xiaozhi decoction for the treatment of nonalcoholic fatty liver disease based on network pharmacology, molecular docking and molecular dynamics simulation.

Nonalcoholic fatty liver disease (NAFLD) is a metabolic disease, the incidence of which increases annually. Shugan Xiaozhi (SGXZ) decoction, a composite traditional Chinese medicinal prescription, has been demonstrated to exert a therapeutic effect on NAFLD. In this study, the potential bioactive ingredients and mechanism of SGXZ decoction against NAFLD were explored via network pharmacology, molecular docking, and molecular dynamics simulation. Compounds in SGXZ decoction were identified and collected from the literature, and the corresponding targets were predicted through the Similarity Ensemble Approach database. Potential targets related to NAFLD were searched on DisGeNET and GeneCards databases. The compound-target-disease and protein-protein interaction (PPI) networks were constructed to recognize key compounds and targets. Functional enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed on the targets. Molecular docking was used to further screen the potent active compounds in SGXZ. Finally, molecular dynamics (MD) simulation was applied to verify and validate the binding between the most potent compound and targets. A total of 31 active compounds and 220 corresponding targets in SGXZ decoction were collected. Moreover, 1,544 targets of NAFLD were obtained, of which 78 targets intersected with the targets of SGXZ decoction. Key compounds and targets were recognized through the compound-target-disease and PPI network. Multiple biological pathways were annotated, including PI3K-Akt, MAPK, insulin resistance, HIF-1, and tryptophan metabolism. Molecular docking showed that gallic acid, chlorogenic acid and isochlorogenic acid A could combine with the key targets. Molecular dynamics simulations suggested that isochlorogenic acid A might potentially bind directly with RELA, IL-6, VEGFA, and MMP9 in the regulation of PI3K-Akt signaling pathway. This study investigated the active substances and key targets of SGXZ decoction in the regulation of multiple-pathways based on network pharmacology and computational approaches, providing a theoretical basis for further pharmacological research into the potential mechanism of SGXZ in NAFLD.

Yang R ，Yang H ，Jiang D ，Xu L ，Feng L ，Xing Y ... -  《PeerJ》

An herbal formulation "Shugan Xiaozhi decoction" ameliorates methionine/choline deficiency-induced nonalcoholic steatohepatitis through regulating inflammation and apoptosis-related pathways.

Shugan Xiaozhi (SGXZ) decoction is a traditional Chinese medicine used for treating nonalcoholic steatohepatitis (NASH). It has been used clinically for over 20 years and proved to be effective; however, the molecular mechanism underlying the effects of SGXZ decoction remains unclear. We analyzed the chemical components, core targets, and molecular mechanisms of SGXZ decoction to improve NASH through network pharmacology and in vivo experiments. The chemical components, core targets, and related signaling pathways of SGXZ decoction intervention in NASH were predicted using network pharmacology. Molecular docking was performed to verify chemical components and their core targets. The results were validated in the NASH model treated with SGXZ decoction. Mouse liver function was assessed by measuring ALT and AST levels. TC and TG levels were determined to evaluate lipid metabolism, and lipid deposition was assessed via oil red O staining. Mouse liver damage was determined via microscopy following hematoxylin and eosin staining. Liver fibrosis was assessed via Masson staining. Western blot (WB) and immunohistochemical (IHC) analyses were performed to detect inflammation and the expression of apoptosis-related proteins, including IL-1β, IL-6, IL-18, TNF-α, MCP1, p53, FAS, Caspase-8, Caspase-3, Caspase-9, Bax, Bid, Cytochrome c, Bcl-2, and Bcl-XL. In addition, WB and IHC were used to assess protein expression associated with the TLR4/MyD88/NF-κB pathway. Quercetin, luteolin, kaempferol, naringenin, and nobiletin in SGXZ decoction were effective chemical components in improving NASH, and TNF-α, IL-6, and IL-1β were the major core targets. Molecular docking indicated that these chemical components and major core targets might interact. KEGG pathway analysis showed that the pathways affected by SGXZ decoction, primarily including apoptosis and TLR4/NF-κB signaling pathways, interfere with NASH. In vivo experiments indicated that SGXZ decoction considerably ameliorated liver damage, fibrosis, and lipid metabolism disorder in MCD-induced NASH mouse models. In addition, WB and IHC verified the underlying molecular mechanisms of SGXZ decoction as predicted via network pharmacology. SGXZ decoction inhibited the activation of apoptosis-related pathways in MCD-induced NASH mice. Moreover, SGXZ decoction suppressed the activation of TLR4/MyD88/NF-κB pathway in MCD-induced NASH mice. SGXZ decoction can treat NASH through multiple targets and pathways. These findings provide new insights into the effective treatment of NASH using SGXZ decoction.

Wang S ，Chen B ，Du R ，Zhong M ，Zhang C ，Jin X ，Cui X ，Zhou Y ，Kang Q ，Xu H ，Li Y ，Wu Q ，Tong G ，Luo L ... -  《-》

Network Pharmacology and Molecular Docking Integrated with Molecular Dynamics Simulations Investigate the Pharmacological Mechanism of Yinchenhao Decoction in the Treatment of Non-alcoholic Fatty Liver Disease.

Non-Alcoholic Fatty Liver Disease (NAFLD) has become a significant health and economic burden globally. Yinchenhao decoction (YCHD) is a traditional Chinese medicine formula that has been validated to exert therapeutic effects on NAFLD. The current study aimed to explore the pharmacological mechanisms of YCHD on NAFLD and further identify the potential active compounds acting on the main targets. Compounds in YCHD were screened and collected from TCMSP and published studies, and their corresponding targets were obtained from the SWISS and SEA databases. NAFLD-related targets were searched in the GeneCards and DisGeNet databases. The "compound- intersection target" network was constructed to recognize the key compounds. Moreover, a PPI network was constructed to identify potential targets. GO and KEGG analyses were performed to enrich the functional information of the intersection targets. Then, molecular docking was used to identify the most promising compounds and targets. Finally, molecular dynamics (MD) simulations were performed to verify the binding affinity of the most potential compounds with the key targets. A total of 53 compounds and 556 corresponding drug targets were collected. Moreover, 2684 NAFLD-related targets were obtained, and 201 intersection targets were identified. Biological processes, including the apoptotic process, inflammatory response, xenobiotic metabolic process, and regulation of MAP kinase activity, were closely related to the treatment of NAFLD. Metabolic pathways, non-alcoholic fatty liver disease, the MAPK signaling pathway, and the PI3K-Akt signaling pathway were found to be the key pathways. Molecular docking showed that quercetin and isorhamnetin were the potential active compounds, while AKT1, IL1B, and PPARG were the most promising targets. MD simulations further verified that the binding of PPARG-isorhamnetin (-35.96 ± 1.64 kcal/mol) and AKT1-quercetin (-31.47 ± 1.49 kcal/mol) was due to their lowest binding free energy. This study demonstrated that YCHD exerts therapeutic effects for the treatment of NAFLD through multiple targets and pathways, providing a theoretical basis for further pharmacological research on the potential mechanisms of YCHD in NAFLD.

Yang R ，Jiang D ，Xu H ，Yang H ，Feng L ，Wu Q ，Xing Y ... -  《-》

Molecular mechanism of Fufang Zhenzhu Tiaozhi capsule in the treatment of type 2 diabetes mellitus with nonalcoholic fatty liver disease based on network pharmacology and validation in minipigs.

Fufang Zhenzhu Tiaozhi formula (FTZ) of which a patented preparation of Chinese herbal medicine has been well documented with significant clinical curative effect for hyperglycemia and hyperlipidemia. Because of the complexity of the chemical constituents of Chinese herbal formulas, the holistic pharmacological mechanism of FTZ acting on type 2 diabetes mellitus (T2DM) and nonalcoholic fatty liver disease (NAFLD) remains unclear. To investigate the pharmacological efficacy and mechanism of FTZ in the treatment of T2DM accompanied by NAFLD. Network pharmacology and validation in minipigs were used in this study. First, potential bioactive compounds of FTZ were identified by the traditional Chinese medicine system pharmacology technology platform (TCMSP). Then, targets of compounds were gathered using DrugBank, SwissTargetPrediction and TCMSP, while targets for T2DM and NAFLD were collected from CTD (compounds-targets-diseases network) and GeneCards. Common targets were defined as direct therapeutic targets acting on T2DM with NAFLD. In addition, crucial targets were chosen by the protein-protein interaction (PPI) network and contribution to compound-therapeutic targets in T2DM with the NAFLD network. Furthermore, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the metabolism-related signaling pathways affected by FTZ. Candidate patterns selected by network pharmacology were tested in the minipigs model of T2DM with NAFLD. Measurements of triglycerides (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), fasting insulin (FINS) and fasting blood glucose (FBG) in the blood and the expression levels of proteins, including PI3K-AKT and HIF-1α, in the livers of the minipigs were followed by the administration of FTZ. A total of 116 active compounds and 82 potential targets related to T2DM and NAFLD were found. Pathway and functional enrichment analysis showed that FTZ mainly regulates metabolism-related pathways, including PI3K-AKT, HIF-1α, TNFα and MAPK. Animal experiments showed that FTZ treatment significantly reduced the serum levels of TG, TC, LDL-C and FBG, increased serum levels of HDL-C, ameliorated systemic insulin resistance (IR), and attenuated liver damage in minipigs with T2DM and NAFLD. FTZ treatment has an obviously favorable influence on hepatic steatosis and liver lipid accumulation in the histopathologic features of HE, Oil red O staining, and electron microscopy. Mechanistically, FTZ improved liver metabolism by increasing the phosphorylation of PI3K-AKT and decreasing the expression of HIF-1α. Network pharmacology was supported by experimental studies, which indicated that FTZ has demonstrated therapeutic benefits in T2DM and NAFLD by regulating the PI3K-AKT and HIF-1α signaling pathways.

Wang H ，Tan H ，Zhan W ，Song L ，Zhang D ，Chen X ，Lin Z ，Wang W ，Yang Y ，Wang L ，Bei W ，Guo J ... -  《-》

Integration of Network Pharmacology and Molecular Docking Technology Reveals the Mechanism of the Therapeutic Effect of Xixin Decoction on Alzheimer's Disease.

So far, only a few researchers have systematically analyzed the constituents of the traditional Chinese medicine prescription Xixin Decoction (XXD) and its potential mechanism of action in treating Alzheimer's disease (AD). This study aimed to explore the potential mechanism of XXD in the treatment of AD using network pharmacology and molecular docking. The compounds of XXD were searched within the Traditional Chinese Medicine System Pharmacology Database (TCMSP) and the Traditional Chinese Medicine Integrated Database (TCMID) databases. Overlapping AD-related targets obtained from the two databases and the predicted targets of XXD obtained from SwissTargetPrediction platform were imported into the STRING database to build PPI networks including hub targets; Cytoscape software was used to construct the herb-compound-target network while its plug-in CytoNCA was used to screen the main active compounds of XXD. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses explored the core biological mechanism and pathways via the Metascape platform. In addition, we used AutoDock Vina and PyMOL software to investigate the molecular docking of main compounds to hub targets. We determined 114 active compounds, 973 drug targets, and 973 disease targets. However, intersection analysis screened out 208 shared targets.Protein-protein interaction (PPI) network identified 9 hub targets. The hub targets were found to be majorly enriched in several biological processes (positive regulation of kinase activity, positive regulation of cell death, regulation of MAPK cascade, trans-synaptic signaling, synaptic signaling, etc.) and the relevant pathways of Alzheimer's disease, including neuroactive ligand-receptor interaction, dopaminergic synapse, serotonergic synapse, and the MAPK signaling pathway, etc. The pathway-target-compound network of XXD for treating AD was then constructed. 8 hub targets exhibited good binding activity with 9 main active compounds of XXD in molecular docking. In this study, we found multi-compound-multi-target-multi-pathway regulation to reveal the mechanism of XXD for treating AD based on network pharmacology and molecular docking. XXD may play a therapeutic role through regulating the Alzheimer's disease pathway, its downstream PI3K/Akt signaling pathway or the MAPK signaling pathway, thereby treating AD. This provides new insights for further experiments on the pharmacological effects of XXD.

Zhang Z ，Xu J ，Ma S ，Lin N ，Hou M ，Wei M ，Li T ，Shi J ... -  《-》