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.

BACKGROUND: 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. OBJECT: 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. METHODS: 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. RESULTS: 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. CONCLUSION: 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.

Identification of Potential TMPRSS2 Inhibitors for COVID-19 Treatment in Chinese Medicine by Computational Approaches and Surface Plasmon Resonance Technology.

BACKGROUND: Coronavirus disease-19 (COVID-19) pneumonia continues to spread in the entire globe with limited medication available. In this study, the active compounds in Chinese medicine (CM) recipes targeting the transmembrane serine protease 2 (TMPRSS2) protein for the treatment of COVID-19 were explored. METHODS: The conformational structure of TMPRSS2 protein (TMPS2) was built through homology modeling. A training set covering TMPS2 inhibitors and decoy molecules was docked to TMPS2, and their docking poses were re-scored with scoring schemes. A receiver operating characteristic (ROC) curve was applied to select the best scoring function. Virtual screening of the candidate compounds (CCDs) in the six highly effective CM recipes against TMPS2 was conducted based on the validated docking protocol. The potential CCDs after docking were subject to molecular dynamics (MD) simulations and surface plasmon resonance (SPR) experiment. RESULTS: A training set of 65 molecules were docked with modeled TMPS2 and LigScore2 with the highest area under the curve, AUC, value (0.886) after ROC analysis selected to best differentiate inhibitors from decoys. A total of 421 CCDs in the six recipes were successfully docked into TMPS2, and the top 16 CCDs with LigScore2 higher than the cutoff (4.995) were screened out. MD simulations revealed a stable binding between these CCDs and TMPS2 due to the negative binding free energy. Lastly, SPR experiments validated the direct combination of narirutin, saikosaponin B1, and rutin with TMPS2. CONCLUSIONS: Specific active compounds including narirutin, saikosaponin B1, and rutin in CM recipes potentially target and inhibit TMPS2, probably exerting a therapeutic effect on COVID-19.

Efficacy and safety of acetyl-CoA carboxylase (ACC) inhibitors in the treatment of nonalcoholic steatohepatitis (NASH): A protocol for systematic review.

BACKGROUND: The pathological mechanism of nonalcoholic steatohepatitis (NASH) is closely related to abnormal lipid regulation in hepatocytes. Patients with NASH generally have a significant increase in de novo lipogenesis, which acetyl-CoA carboxylase (ACC) catalyzes the first committed step. However, the treatment with ACC inhibitors remains controversial. Thus, our study will systematically evaluate the efficacy and safety of ACC inhibitors for the treatment of NASH. METHODS: We plan to search PubMed, Cochrane Library, Web of Science, EMBASE, Google Scholar, ClinicalTrials.gov, China Science and Technology Journal Database, Chinese Biomedical Literature Database, Wan-fang Database and China National Knowledge Infrastructure to obtain literatures from January 2015 to January 2030 under the inclusion and exclusion criteria, and include randomized controlled trials containing intervention of ACC inhibitors for NASH. The proportion of patients with reduction in ballooning, inflammation and fibrosis will be accepted as the main outcome. RoB 2 will be used for the risk of bias, as well as Egger's test and funnel plot for reporting bias. We will adopt Review Manager 5.4.1 for data synthesis, subgroup analysis, meta-regression analysis and sensitivity analysis, and conduct trial sequential analysis and quality of evidence evaluation using trial sequential analysis 0.9.5.10 Beta software and GRADE Profiler 3.6.1 software respectively. RESULTS: This systematic review will assess the proportion of patients with reduction of ballooning, inflammation and fibrosis, changes in hepatic steatosis, levels of liver enzymes and liver injury markers, metabolic parameters, safety and tolerability to measure the clinical benefits of ACC inhibitors for NASH. CONCLUSION: The conclusion of this systematic review will achieve convincing evidence to evaluate the efficacy and safety of ACC inhibitors for NASH.

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.

Background: 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. Methods: 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. Results: 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. Conclusion: 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.

Intervention of Shugan Xiaozhi Decoction on Nonalcoholic Fatty Liver Disease via Mediating Gut-Liver Axis.

Nonalcoholic fatty liver disease (NAFLD) is a chronic liver disease with an increasing incidence rate but few therapies. Shugan Xiaozhi decoction (SX) has demonstrated beneficial effects in treating NAFLD with an unclear mechanism. This study was aimed at investigating the therapeutic mechanism of SX on high-fat diet-induced NAFLD rats via the gut-liver axis. Hepatic steatosis and integrity of intestinal mucosa in NAFLD rats were assessed by histopathological staining. The level of lipid and inflammation were estimated by enzyme-linked immunosorbent assay. Western Blotting was used to detect apolipoprotein (apo) B48 expression. 16S rRNA analysis was used to measure the changes of gut microbial composition after SX treatment. The expressions of zona occludens 1 protein (ZO-1), occludin, and secretory immunoglobulin A (sIgA) in the colon were detected by immunostaining to investigate the intestinal barrier function. Our study found that SX reduced hepatic steatosis, the levels of alanine aminotransferase, aspartate aminotransferase, total cholesterol, and triglyceride and apoB48 expression but increased peroxisome proliferator activated receptor α (PPARα) level. Moreover, SX altered the diversity of gut microbiota, upregulating the relative abundance of f_Prevotellaceae, while downregulating f_Bacteroidales_ S24-7, f_Lachnospiraceae, f_Ruminococcaceae, f_Erysipelotrichaceae, and f_Desulfovibrionaceae. By increasing the expression of ZO-1 and occludin and decreasing the level of proinflammatory factors, including sIgA, lipopolysaccharide, tumor necrosis factor-α, interleukin-1ß, monocyte chemotactic protein-1, and transforming growth factor-ß1, SX improved intestinal mucosal integrity and barrier function. Our study illustrated that the gut-liver axis was a potential way for SX to ameliorate NAFLD, that is, by regulating the expression of PPARα, apoB48, and modulating gut microbiota to protect the intestinal barrier function, and thus alleviate lipid deposition and inflammatory response in the liver.