Based on Network Pharmacology and Molecular Docking to Explore the Underlying Mechanism of Huangqi Gegen Decoction for Treating Diabetic Nephropathy

The synergistic effect of Huangqi Gegen decoction on thrombosis relates to the astragalus polysaccharide-improved oral delivery of puerarin

ETHNO-PHARMACOLOGICAL RELEVANCE

Huangqi Gegen decoction (HGD), which comprises Astragali Radix (AR) and Puerariae Radix (PR), is widely used to treat thrombosis in China. However, the mechanism underlying its synergistic effect in thrombosis treatment remains unclear.

AIM OF THE STUDY

Following PR administration, low plasma exposure was reported for its primary ingredients. In this regard, this study examined the effect of AR on PR's antithrombotic efficacy with respect to the impact of Astragalus Polysaccharide (APS) on the oral delivery of Puerarin (PUE).

MATERIALS AND METHODS

To evaluate the synergistic effect of HGD, a thrombus mice model was established via intraperitoneal injection of carrageenan. After treatment, histopathological observations were made, and the proportion of thrombus length in the tail, as well as the plasma APTT, PT, INR, and FIB levels, were detected. Molecular docking was employed to assess the PR ingredients that could inhibit the HMGB1/NF-κB/NLRP3 pathway. The Pharmacokinetics of PR ingredients in rats were also compared between the PR and HGD groups. Moreover, the effect of APS on the solubility, intestinal absorption, and pharmacokinetics of PUE was evaluated. Furthermore, the impact of APS on the antithrombotic efficacy of PUE was assessed.

RESULTS

In mice, AR enhanced the antithrombotic effect of PR. This improved PR effect was associated with isoflavones-induced downregulation of the HMGB1/NF-κB/NLRP3 pathway. The synergistic effect resulting from the compatibility of HGD components was primarily achieved by improving the plasma exposure of PR isoflavones. Specifically, APS enhanced PUE's water solubility through the formation of self-assembly Nanoparticles, increasing its intestinal absorption and oral bioavailability, which, in turn, suppressed the HMGB1/NF-κB/NLRP3 pathway, thus improving its antithrombotic effect.

CONCLUSIONS

Our findings revealed that APS improved PUE's plasma exposure, enhancing its inhibitory effect on the HMGB1/NF-κB/NLRP3 pathway. This mechanism presents a key aspect of the synergistic effect of HGD compatibility in thrombosis treatment.

Protective effects of Huang-Qi-Ge-Gen decoction against diabetic liver injury through regulating PI3K/AKT/Nrf2 pathway and metabolic profiling

ETHNOPHARMACOLOGICAL RELEVANCE

Huang-Qi-Ge-Gen decoction (HGD) is a traditional Chinese medicine prescription that has been used for centuries to treat "Xiaoke" (the name of diabetes mellitus in ancient China). However, the ameliorating effects of HGD on diabetic liver injury (DLI) and its mechanisms are not yet fully understood.

AIM OF THE STUDY

To elucidate the ameliorative effect of HGD on DLI and explore its material basis and potential hepatoprotective mechanism.

MATERIALS AND METHODS

A diabetic mice model was induced by feeding a high-fat diet and injecting intraperitoneally with streptozotocin (40 mg kg-1) for five days. After the animals were in confirmed diabetic condition, they were given HGD (3 or 12 g kg-1, i. g.) for 14 weeks. The effectiveness of HGD in treating DLI mice was evaluated by monitoring blood glucose and blood lipid levels, liver function, and pathological conditions. Furthermore, UPLC-MS/MS was used to identify the chemical component profile in HGD and absorption components in HGD-treated plasma. Network pharmacology and molecular docking were performed to predict the potential pathway of HGD intervention in DLI. Then, the results of network pharmacology were validated by examining biochemical parameters and using western blotting. Lastly, urine metabolites were analyzed by metabolomics strategy to explore the effect of HGD on the metabolic profile of DLI mice.

RESULTS

HGD exerted therapeutic potential against the disorders of glucose metabolism and lipid metabolism, liver dysfunction, liver steatosis, and fibrosis in a DLI model mice induced by HFD/STZ. A total of 108 chemical components in HGD and 18 absorption components in HGD-treated plasma were preliminarily identified. Network pharmacology and molecular docking results of the absorbed components in plasma indicated PI3K/AKT as a potential pathway for HGD to intervene in DLI mice. Further experiments verified that HGD markedly reduced liver oxidative stress in DLI mice by modulating the PI3K/AKT/Nrf2 signaling pathway. Moreover, 19 differential metabolites between normal and DLI mice were detected in urine, and seven metabolites could be significantly modulated back by HGD.

CONCLUSIONS

HGD could ameliorate diabetic liver injury by modulating the PI3K/AKT/Nrf2 signaling pathway and urinary metabolic profile.

Exploration of the possible mechanisms of Ling Gui Zhu Gan decoction in nephrotic syndrome based on network pharmacology, molecular docking and molecular dynamics simulation

This study aimed to explore the possible mechanisms of Ling Gui Zhu Gan decoction (LGZGD) in the treatment of nephrotic syndrome (NS) using network pharmacology combined with molecular docking and molecular dynamics simulation. The active ingredients of LGZGD and their targets were retrieved from Traditional Chinese Medicine Systems Pharmacology Database and Swiss Target Prediction database. The NS targets were retrieved from Genecards, OMIM and Drugbank databases. Next, the intersecting targets of drug and disease were imported into the String database for protein-protein interaction network analysis, and the core targets were identified through topological analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed in the Metascape platform. Finally, molecular docking and molecular dynamics simulation were performed for further validation. The network analysis showed that 109 active ingredients of LGZGD were associated with 105 targets in NS. The key active ingredients (quercetin, kaempferol, naringenin, licochalcone A, formononetin, beta-sitosterol) and the core targets (IL6, AKT1, TNF, VEGFA, TP53, JUN, IL1B, CASP3, EGFR, and STAT3) were further identified. Enrichment analysis indicated that multiple biological processes and pathways, including AGE-RAGE, PI3K-Akt, JAK-STAT, and HIF-1 signaling pathways, might be regulated by LGZGD in the treatment of NS. Molecular docking and molecular dynamics simulation results further indicated that the key active ingredients of LGZGD could stably bind to the core targets through hydrogen bonding and hydrophobic interaction. This study demonstrates that the active ingredients of LGZGD may regulate multiple targets, biological processes and signaling pathways in NS. Our findings may provide a theoretical basis for further studies on LGZGD in the treatment of NS.

Rapid identification of chemical components in Xuelian granule by UHPLC-Q-orbitrap-HRMS based on enzyme activity in vitro

BACKGROUND

Xuelian granule (XL), a traditional Chinese medicine (TCM) formula, has been used for the treatment of diabetic nephropathy for a long time as a hospital preparation. Because the active ingredients in the XL that can help to treat diabetic nephropathy are still unclear, which limits the interpretation for its pharmacological mechanism, further development and subsequent study on the material basis of its efficacy.

METHODS

In this study, a screening method based on inhibition activity against aldose reductase (AR) was employed for activity-directed chemical analysis of XL using ultra-high performance liquid chromatography combined with quadrupole-orbitrap high resolution mass spectrometry (UHPLC-Q-orbitrap-HRMS) technique.

RESULTS

A total of 178 compounds, including 46 terpenes, 47 organic acids, 25 flavonoids, 29 phenylethanoid glycosides, and 31 other types, were tentatively identified from XL which might responsible for its AR inhibition activity.

CONCLUSION

This is the first study for a systematic, rapid, and accurate qualitative analysis of XL. This research provides a scientific and experimental basis for further researches on pharmacodynamics material basis and quality control of XL.

Exploring the mechanism of action of Hedyotis diffusa Willd on acne using network analysis

In this study, we used a network pharmacological method to explore the active ingredients of Hedyotis diffusa Willd (HDW) in the treatment of acne and elucidated the physiological mechanisms in the human body in which they are involved. We identified the active compounds of HDW that are expected to act effectively in the human body using the Traditional Chinese Medicine Systems Pharmacology database and analysis platform and extracted potential interacting proteins for each active compound using the Swiss Target Prediction platform. Next, we analyzed the potential mechanisms of action of the protein targets shared by HDW and each standard drug on acne and assessed the possibility of spontaneous occurrence of the binding between proteins and active compounds through the molecular docking process. Seven active compounds were selected according to the oral bioavailability and drug-likeness criteria of the Traditional Chinese Medicine Systems Pharmacology database and analysis platform. Subsequently, 300 protein targets were collected from the Swiss Target Prediction. Using the Search Tool for the Retrieval of Interacting Genes/Proteins database, a protein-protein interaction network was constructed by analyzing the relationship between HDW, acne, and each standard drug. By analyzing the gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathway, the "positive regulation of lipid metabolic process" was found to be the most involved pathway shared by HDW, acne, and isotretinoin. An analysis of the protein targets shared by the antibiotic agents with HDW and acne found that "cholesterol storage" in tetracycline, "icosacoid transport" in azithromycin, "steroid hydroxylase activity" in erythromycin, "positive regulation of leukocyte tethering or rolling" in clindamycin, "response to UV-A" in minocycline, "steroid 11-beta-monooxygenase activity" in doxycycline, and "neutrophil-mediated immunity" in trimethoprim were the most involved. Virtual molecular docking analysis showed that all proteins spontaneously bound to their corresponding active compounds. Our analysis suggests that HDW can, directly and indirectly, suppress sebum secretion and exert antiinflammatory effects on acne. Further, HDW may regulate free radicals and suppress apoptosis. Therefore, HDW can be used as an alternative or supplement to standard drugs for acne treatment in patients who cannot use standard treatments due to side effects.

Combining lipidomics and efficacy-oriented compatibility revealed that Qi Ge decoction compatibility improved lipid metabolism in hyperlipidemic rats

The mechanism underlying traditional Chinese medicine (TCM) compatibility is difficult to understand. This study combined lipidomics and efficacy-oriented compatibility to explore underlying compatibility mechanisms of Qi Ge decoction (QG) for improving lipid metabolism in hyperlipidemic rats. The QG was divided into three groups according to the efficacy group strategy: the Huangqi-Gegen (HG), Chenpi (CP), and QG groups. Hyperlipidemic rats were treated with QG, HG, CP, or atorvastatin for 3 weeks. The mass spectral data of widely targeted lipidomics were used to evaluate lipid changes. Principal component analysis and orthogonal partial least squares discriminant analysis were used to assess the lipidomic differences between the groups. MetaboAnalyst 5.0 was used to explore metabolic pathways. Compared with the model group, serum cholesterol, triglyceride, and hepatic steatosis were significantly reduced by QG, whereas HG and CP had no significant effects on these indexes. Lipidomics showed that QG, HG, and CP back-regulated 60, 11, and 14 lipids, respectively. Compared with HG and CP, QG had more metabolic targets in diglycerides, triglycerides, ceramides, and phosphatidylethanolamines. Pathway analysis indicated that QG mainly regulated glycerophospholipid and glycerolipid metabolism. This study provided a new method of combining lipidomics and efficacy-oriented compatibility for exploring the scientific connotation of TCM compatibility.

Integrated Bioinformatics and Clinical Correlation Analysis of Key Genes, Pathways, and Potential Therapeutic Agents Related to Diabetic Nephropathy

Background

Diabetic nephropathy (DN) is a common microvascular complication of diabetes and a major cause of end-stage renal disease, resulting in a substantial socioeconomic burden around the world. Some unknown biomarkers, mechanisms, and potential novel agents regarding DN are yet to be identified.

Methods

GSE30528 and GSE1009 were downloaded as training datasets to identify differentially expressed genes (DEGs) of DN. Common DEGs were selected for further analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of DEGs were performed to explore molecular mechanisms and pathways. Protein-protein interaction (PPI) network of DEGs was used to identify the top 10 hub genes of DN. Expression profiles of the hub genes were validated in GSE96804 and GSE47183 datasets. The clinical correlation analyses were conducted to confirm the association between key genes and clinical characteristics in the Nephroseq v5 database. The Drug Gene Interaction Database was used to predict potential targeted drugs.

Results

345 and 1228 DEGs were identified in GSE30528 and GSE1009, respectively; and 120 common DEGs were found. The biological process of DEGs was significantly enriched in kidney development. PI3K-Akt signaling pathway, focal adhesion, complement and coagulation cascades were significantly enriched KEGG pathways. The identified top10 hub genes were VEGFA, NPHS1, WT1, TJP1, CTGF, FYN, SYNPO, PODXL, TNNT2, and BMP2. VEGFA, NPHS1, WT1, CTGF, SYNPO, PODXL, and TNNT2 were significantly downregulated in DN. VEGFA, NPHS1, WT1, CTGF, SYNPO, and PODXL were positively correlated with glomerular filtration rate. The targeted drugs or molecular compounds were enalapril, sildenafil, and fenofibrate target for VEGFA; losartan target for NPHS1; halofuginone, deferoxamine, curcumin, and sirolimus target for WT1; and purpurogallin target for TNNT2.

Conclusions

VEGFA, NPHS1, WT1, CTGF, SYNPO, and PODXL are promising biomarkers for diagnosing and evaluating the progression of DN. The drug-gene interaction analyses provide a list of candidate drugs for the precise treatment of DN.

Identification of the active compounds and their mechanisms of medicinal and edible Shanzha based on network pharmacology and molecular docking

Shanzha (Crataegus pinnatifida Bunge), an edible traditional Chinese medicine (TCM), has an effect on dyspepsia. However, the investigations of the pharmacological effects have not been carried out. This study aimed to identify the potential targets and pharmacological mechanisms of Shanzha in the treatment of dyspepsia by network pharmacology and molecular docking. Five active compounds and 13 key targets were obtained by a set of bioinformatics assays. Vitexin 7-glucoside, suchilactone, and 20-hexadecanoylingenol were the main compounds acting on dyspepsia. The key targets were prostaglandin-endoperoxide synthase 2 (PTGS2), serine/threonine-protein kinase mTOR (MTOR), heat shock protein HSP 90-alpha (HSP90AA1), mitogen-activated protein kinase 1 (MAPK1), MAPK3, E3 ubiquitin-protein ligase Mdm2 (MDM2), receptor tyrosine-protein kinase erbB-2 (ERBB2), caspase-3 (CASP3), matrix metalloproteinase-9 (MMP9), estrogen receptor (ESR1), tumor necrosis factor (TNF), phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (PIK3CA), and peroxisome proliferator-activated receptor gamma (PPARG), which played the vital roles in TNF, prostate cancer, thyroid hormone, hepatitis B and estrogen signaling pathway. The molecular mechanisms of Shanzha regulating dyspepsia were mainly related to reduction of inflammatory response, controlling cell proliferation and survival, increasing intestinal moisture, and promoting intestinal motility. PRACTICAL APPLICATIONS: Shanzha has been used as an edible TCM to improve digestion for a long time. However, the ingredients and mechanisms of Shanzha in the treatment of dyspepsia are not clear. In this research, network pharmacological analysis integrated with molecular docking was conducted to investigate the molecular mechanism. The results suggested that the core targets alleviated dyspepsia by reducing the intestinal inflammatory response, increasing intestinal movement, controlling cell physiological activities, and reducing constipation. In summary, this study demonstrated the multiple compounds, targets, and pathways characteristics of Shanzha in the treatment of dyspepsia, which may provide guidance and foundations for further application of edible medicine.

Systems pharmacology to reveal multi-scale mechanisms of traditional Chinese medicine for gastric cancer

Because of the complex etiology, the treatment of gastric cancer is a formidable challenge for contemporary medical. The current treatment method focuses on traditional surgical procedures, supplemented by other treatments. Among these other treatments, Traditional Chinese Medicine (TCM) plays an important role. Here, we used the systems pharmacology approach to reveal the potential molecular mechanism of PRGRC on gastric cancer which composes of Pinellia ternata(Thunb.) Breit., Rheum palmatumL., Gentiana scabraBunge, Radix Aucklandiae and Citrus aurantium L. This approach combines pharmacokinetics analysis with pharmacodynamics evaluation for the active compounds screening, targets prediction and pathways assessing. Firstly, through pharmacokinetic evaluation and target prediction models, 83 potential compounds and 184 gastric cancer-related targets were screened out. Then, the results of network analysis suggested that the targets of PRGRC were mainly involved two aspects: apoptosis and inflammation. Finally, we verified the reliability of the above analysis at the cellular level by using naringenin and luteolin with good pharmacokinetic activity as representative compounds. Overall, we found that PRGRC could influence the development of gastric cancer from a multi-scale perspective. This study provided a new direction for analyzing the mechanism of TCM.