Identification of the Active Constituents and Significant Pathways of Shen-qi-Yi-zhu Decoction on Antigastric Cancer: A Network Pharmacology Research and Experimental Validation

Shen-qi-Yi-zhu decoction (SQYZD) is an empirical prescription with antigastric cancer (GC) property created by Xu Jing-fan, a National Chinese Medical Master. However, its underlying mechanisms are still unclear. Based on network pharmacology and experimental verification, this study puts forward a systematic method to clarify the anti-GC mechanism of SQYZD. The active ingredients of SQYZD and their potential targets were acquired from the TCMSP database. The target genes related to GC gathered from GeneCards, DisGeNET, OMIM, TTD, and DrugBank databases were imported to establish protein-protein interaction (PPI) networks in GeneMANIA. Cytoscape was used to establish the drug-ingredients-targets-disease network. The hub target genes collected from the SQYZD and GC were parsed via GO and KEGG analysis. Our findings from network pharmacology were successfully validated using an in vitro HGC27 cell model experiment. In a word, this study proves that the combination of network pharmacology and in vitro experiments is effective in clarifying the potential molecular mechanism of traditional Chinese medicine (TCM).

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Identifying Active Compounds and Mechanism of Camellia nitidissima Chi on Anti-Colon Cancer by Network Pharmacology and Experimental Validation

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/7169211 ◽

2021 ◽

Vol 2021 ◽

pp. 1-15

Author(s):

Yiwei Chen ◽

Erwei Hao ◽

Fan Zhang ◽

Zhengcai Du ◽

Jinling Xie ◽

...

Keyword(s):

Colon Cancer ◽

Experimental Validation ◽

Molecular Mechanisms ◽

Target Genes ◽

Cell Model ◽

Hct116 Cell ◽

Network Pharmacology ◽

Kegg Analysis ◽

Camellia Nitidissima

Camellia nitidissima Chi (CNC) is a traditional Chinese medicine (TCM) with anticancer property. However, its underlying mechanisms of anti-colon cancer (CC) remain unknown. Therefore, a systematic approach is proposed in the present study to elucidate the anticancer mechanisms of CNC based on network pharmacology and experimental validation. Initially, the potential active ingredients of CNC were verified via the TCMSP database based on the oral bioavailability (OB) and drug-likeness (DL) terms. Hub targets of CNC were acquired from SwissTarget prediction and TCMSP databases, and target genes related to CC were gathered from GeneCards and OMIM databases. Cytoscape was used to establish the compound-target networks. Next, the hub target genes collected from the CNC and CC were parsed via GO and KEGG analysis. Results of GO and KEGG analysis reveal that quercetin and luteolin in CNC, VEGFA and AKT1 targets, and PI3K-Akt pathway were associated with the suppression of CC. Besides, the result of molecular docking unveils that VEGFA demonstrates the most powerful binding affinity among the binding outcomes. This finding was successfully validated using in vitro HCT116 cell model experiment. In conclusion, this study proved the usefulness of integrating network pharmacology with in vitro experiments in the elucidation of underlying molecular mechanisms of TCM.

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Elucidation of the Mechanisms and Molecular Targets of Lianhuaqingwen for Treatment of COVID-19 Based on Network Pharmacology

Asian Journal of Complementary and Alternative Medicine ◽

10.53043/2347-3894.acam90020 ◽

2021 ◽

Vol 9 (4) ◽

pp. 111-122

Author(s):

Yan Luo ◽

Si-ting Gao ◽

Jun-xiong Cheng ◽

Wei-jian Xiong ◽

Wen-Fu Cao

Keyword(s):

Target Genes ◽

Molecular Targets ◽

Core Gene ◽

Mechanisms Of Action ◽

Network Pharmacology ◽

Pathway Network ◽

Functional Annotations ◽

Gene Pathway ◽

Protein Protein Interaction ◽

Ppi Networks

Lianhuaqingwen (LH) is the widely used in the treatment of Coronavirus disease 2019 (COVID-19). However, its mechanisms of action and molecular targets for treatment of COVID-19 are not clear. The active compounds of LH were collected and their targets were identified through the network pharmacology. The mechanism of compound multi components and multi targets and its relationship with disease are analyzed. COVID-19 targets were obtained by analyzing with TCMSP. In total, 282 active ingredients and 510 targets of LH were identified. Twenty-one target genes associated with LH and COVID-19. Protein-protein interaction (PPI) data were then obtained and PPI networks of LH putative targets and COVID-19-related targets were visualized and merged to identify the candidate targets for LH against COVID-19. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis were carried out. The gene-pathway network was constructed to screen the crucial target genes. The functional annotations of target genes were found to be related to immune regulation, host defense, inflammatory reaction and autoimmune diseases and so on. Twenty pathways including immunology, cancer, and cell processing were significantly enriched. Quercetin and luteolin might be the crucial ingredients. IL6 was the core gene and other several genes including IL1B, STAT1, IFNGR1, and NCF1 were the key genes in the gene-pathway network of LH for treatment of COVID-19. The results indicated that LH’s effects against COVID-19 might relate to regulation of immunological function through the specific biological processes and the related pathways. This study demonstrates the application of network pharmacology in evaluating mechanisms of action and molecular targets of complex herbal formulations.

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Uncovering Quercetin’s Effects against Influenza A Virus Using Network Pharmacology and Molecular Docking

Processes ◽

10.3390/pr9091627 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1627

Author(s):

Minjee Kim ◽

Young Bong Kim

Keyword(s):

Molecular Docking ◽

Influenza A ◽

Target Genes ◽

Network Pharmacology ◽

Binding Affinities ◽

Anticancer Activities ◽

Biological Targets ◽

Protein Protein Interaction ◽

Ppi Networks ◽

Docking Method

(1) Background: Re-emerging influenza threats continue to challenge medical and public health systems. Quercetin is a ubiquitous flavonoid found in food and is recognized to possess antioxidant, anti-inflammatory, antiviral, and anticancer activities. (2) Methods: To elucidate the targets and mechanisms underlying the action of quercetin as a therapeutic agent for influenza, network pharmacology and molecular docking were employed. Biological targets of quercetin and target genes associated with influenza were retrieved from public databases. Compound–disease target (C-D) networks were constructed, and targets were further analyzed using KEGG pathway analysis. Potent target genes were retrieved from the compound–disease–pathway (C-D-P) and protein–protein interaction (PPI) networks. The binding affinities between quercetin and the targets were identified using molecular docking. (3) Results: The pathway study revealed that quercetin-associated influenza targets were mainly involved in viral diseases, inflammation-associated pathways, and cancer. Four targets, MAPK1, NFKB1, RELA, and TP53, were identified to be involved in the inhibitory effects of quercetin on influenza. Using the molecular docking method, we evaluated the binding affinity of each ligand (quercetin)–target and discovered that quercetin and MAPK1 showed the strongest calculated binding energy among the four ligand–target complexes. (4) Conclusion: These findings identified potential targets of quercetin and suggest quercetin as a potential drug for influenza treatment.

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Therapeutic Effects of Naringin in Rheumatoid Arthritis: Network Pharmacology and Experimental Validation

Frontiers in Pharmacology ◽

10.3389/fphar.2021.672054 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yirixiati Aihaiti ◽

Yong Song Cai ◽

Xiadiye Tuerhong ◽

Yan Ni Yang ◽

Yao Ma ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Target Genes ◽

Topological Analysis ◽

Osteoclast Differentiation ◽

Critical Factor ◽

Network Pharmacology ◽

Therapeutic Effects ◽

Dependent Manner ◽

Ppi Networks

Rheumatoid arthritis is a chronic autoimmune disease characterized by persistent hyperplasia of the synovial membrane and progressive erosion of articular cartilage. Disequilibrium between the proliferation and death of RA fibroblast-like synoviocytes (RA-FLSs) is the critical factor in progression of RA. Naringin has been reported to exert anti-inflammatory and antioxidant effect in acute and chronic animal models of RA. However, the therapeutic effect and underlying mechanisms of naringin in human RA-FLS remain unclear. Based on network pharmacology, the corresponding targets of naringin were identified using SwissTargetPrediction database, STITCH database, and Comparative Toxicogenomics Database. Deferentially expressed genes (DEGs) in RA were obtained from the GEO database. The protein–protein interaction (PPI) networks of intersected targets were constructed using the STRING database and visualized using Cytoscape. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed, and the pathways directly related to pathogenesis of RA were integrated manually. Further, in vitro studies were carried out based on network pharmacology. 99 target genes were intersected between targets of naringin and DEGs. The PPI network and topological analysis indicated that IL-6, MAPK8, MMP-9, TNF, and MAPK1 shared the highest centrality among all. GO analysis and KEGG analysis indicated that target genes were mostly enriched in (hsa05200) pathways in cancer, (hsa05161) hepatitis B, (hsa04380) osteoclast differentiation, (hsa04151) PI3K-Akt signaling pathway, and (hsa05142) Chagas disease (American trypanosomiasis). In vitro studies revealed that naringin exposure was found to promote apoptosis of RA-FLS, increased the activation of caspase-3, and increased the ratio of Bax/Bcl-2 in a dose-dependent manner. Furthermore, treatment of naringin attenuated the production of inflammatory cytokines and matrix metalloproteinases (MMPs) in TNF-ɑ–induced RA-FLS. Moreover, treatment of naringin inhibited the phosphorylation of Akt and ERK in RA-FLS. Network pharmacology provides a predicative strategy to investigate the therapeutic effects and mechanisms of herbs and compounds. Naringin inhibits inflammation and MMPs production and promotes apoptosis in RA-FLS via PI3K/Akt and MAPK/ERK signaling pathways.

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Identification and Classification of Hubs in microRNA Target Gene Networks in Human Neural Stem/Progenitor Cells following Japanese Encephalitis Virus Infection

mSphere ◽

10.1128/msphere.00588-19 ◽

2019 ◽

Vol 4 (5) ◽

Author(s):

Sriparna Mukherjee ◽

Irshad Akbar ◽

Reshma Bhagat ◽

Bibhabasu Hazra ◽

Arindam Bhattacharyya ◽

...

Keyword(s):

Progenitor Cells ◽

Gene Networks ◽

Mirna Target ◽

Target Gene ◽

Target Genes ◽

Hub Genes ◽

Protein Protein Interaction ◽

Ppi Networks ◽

Neural Stem Progenitor Cells

ABSTRACT RNA viruses are known to modulate host microRNA (miRNA) machinery for their own benefit. Japanese encephalitis virus (JEV), a neurotropic RNA virus, has been reported to manipulate several miRNAs in neurons or microglia. However, no report indicates a complete sketch of the miRNA profile of neural stem/progenitor cells (NSPCs), hence the focus of our current study. We used an miRNA array of 84 miRNAs in uninfected and JEV-infected human neuronal progenitor cells and primary neural precursor cells isolated from aborted fetuses. Severalfold downregulation of hsa-miR-9-5p, hsa-miR-22-3p, hsa-miR-124-3p, and hsa-miR-132-3p was found postinfection in both of the cell types compared to the uninfected cells. Subsequently, we screened for the target genes of these miRNAs and looked for the biological pathways that were significantly regulated by the genes. The target genes involved in two or more pathways were sorted out. Protein-protein interaction (PPI) networks of the miRNA target genes were formed based on their interaction patterns. A binary adjacency matrix for each gene network was prepared. Different modules or communities were identified in those networks by community detection algorithms. Mathematically, we identified the hub genes by analyzing their degree centrality and participation coefficient in the network. The hub genes were classified as either provincial (P < 0.4) or connector (P > 0.4) hubs. We validated the expression of hub genes in both cell line and primary cells through qRT-PCR after JEV infection and respective miR mimic transfection. Taken together, our findings highlight the importance of specific target gene networks of miRNAs affected by JEV infection in NSPCs. IMPORTANCE JEV damages the neural stem/progenitor cell population of the mammalian brain. However, JEV-induced alteration in the miRNA expression pattern of the cell population remains an open question, hence warranting our present study. In this study, we specifically address the downregulation of four miRNAs, and we prepared a protein-protein interaction network of miRNA target genes. We identified two types of hub genes in the PPI network, namely, connector hubs and provincial hubs. These two types of miRNA target hub genes critically influence the participation strength in the networks and thereby significantly impact up- and downregulation in several key biological pathways. Computational analysis of the PPI networks identifies key protein interactions and hubs in those modules, which opens up the possibility of precise identification and classification of host factors for viral infection in NSPCs.

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A Network Pharmacology Approach to Predict the Proangiogenesis Mechanism of Huangqi-Honghua Herb Pair after Cerebral Ischemia

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/9834856 ◽

2021 ◽

Vol 2021 ◽

pp. 1-13

Author(s):

Jinyi Cao ◽

Lu Lei ◽

Kai Wang ◽

Jing Sun ◽

Yi Qiao ◽

...

Keyword(s):

Cerebral Ischemia ◽

Signaling Pathway ◽

Target Genes ◽

Blood Stasis ◽

Blood Stasis Syndrome ◽

Network Pharmacology ◽

Western Blot Assay ◽

Medicinal Value ◽

Pharmacological Method

Objective. Huangqi-Honghua herb pair is known for its medicinal value to treat Qi deficiency and blood stasis syndrome with a long history in clinical practice. To understand its possible mechanism in a systematic study, a network pharmacological method was addressed. Methods. Detailed information on the HH compounds was obtained from two public databases, and oral bioavailability (OB) and drug-like (DL) of the compounds were evaluated. A correlation between HH compounds, its potential targets, and known targets was extrapolated, and the herb-compound-target-disease (H-C-T-D) network was established. Next, the pathway enrichment and essential genes were analyzed. Then, three key genes (VEGFA, VEGFR2, and eNOS), highly associated with angiogenesis, were screened and verified through western blot assay. Results. Out of 276 compounds, 21 HH compounds and 78 target genes regulating the major pathways associated with CI in the network are analyzed. The bioactive compounds in HH were active in various signal transduction pathways such as the toll-like receptor signaling pathway, VEGF signaling pathway, TNF signaling pathway, and HIF-1 signaling pathway are important pathways that may regulate anti-inflammatory, antiapoptotic, immune correlation, and antioxidative effects. The core genes are PTGS2, TNF, NOS2, IL6, BCL2, IL1B, SOD2, NOS3, SOD1, MMP9, and VEGFA. The in vitro results suggested that HH treatment could significantly elevate the expression of proangiogenic genes such as VEGFA, VEGFR2, and eNOS compared with OGD groups. Conclusions. Our results predict that HH may regulate the expression of VEGFA, VEGFR2, and eNOS via the VEGF and HIF-1 signaling pathway to promote angiogenesis and alleviate cerebral ischemia injury.

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The Mechanism Study of Xiao-Xian-Xiong Decoction in the Treatment of Atherosclerosis with Network Pharmacology

10.21203/rs.3.rs-73640/v1 ◽

2020 ◽

Author(s):

Liucheng Xiao ◽

Zonghuan Li ◽

Chongyuan Fan ◽

Chenggong Zhu ◽

Xingyu Ma ◽

...

Keyword(s):

Cell Proliferation ◽

Signaling Pathway ◽

Mapk Pathway ◽

Enrichment Analysis ◽

Foam Cells ◽

Functional Enrichment ◽

Network Pharmacology ◽

Mechanism Study ◽

Ppi Networks

Abstract Background: Xiao-Xian-Xiong decoction is a useful formula in the treatment of atherosclerosis in traditional Chinese medicine. In this study, we aimed to investigate the function of Xiao-Xian-Xiong decoction in the treatment of atherosclerosis. Methods: In this study, we conducted the method of network pharmacology and molecular docking to discover the mechanism of Xiao-Xian-Xiong decoction against atherosclerosis. Then, we validated the function of Xiao-Xian-Xiong decoction in atherosclerosis in vitro. We investigated the function and mechanism of Xiao-Xian-Xiong decoction in RAW264.7 macrophage-derived foam cells.Results: We identified 213 targets of Xiao-Xian-Xiong decoction and 331 targets of atherosclerosis. The PPI networks of Xiao-Xian-Xiong decoction and atherosclerosis were constructed. Furthermore, the two PPI networks were merged and the core PPI network was obtained. Then, functional enrichment analysis was conducted with GO and KEGG signaling pathway analysis. KEGG analysis indicated Xiao-Xian-Xiong decoction was correlated with ubiquitin mediated proteolysis pathway, PI3K-AKT pathway, MAPK pathway, Notch signaling pathway, and TGF-β signaling pathway. At last, we validated the function of Xiao-Xian-Xiong decoction with atherosclerosis in vitro. Xiao-Xian-Xiong decoction reduced lipid accumulation and promoted the outflow of cholesterol in RAW264.7-derived foam cells. Xiao-Xian-Xiong decoction increased the expression of ABCA1 and ABCG1 protein in foam cells. ABCA1 and ABCG1 were related with regulation of the inflammatory pathway and cell proliferation in atherosclerosis.Conclusions: Combined the mechanism of available treatments of atherosclerosis, we inferred Xiao-Xian-Xiong decoction could alleviate atherosclerosis by inhibiting inflammatory response and cell proliferation.

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Identifying Active Compounds and Targets of Fritillariae thunbergii against Influenza-Associated Inflammation by Network Pharmacology Analysis and Molecular Docking

Molecules ◽

10.3390/molecules25173853 ◽

2020 ◽

Vol 25 (17) ◽

pp. 3853 ◽

Cited By ~ 1

Author(s):

Minjee Kim ◽

Ki Hoon Park ◽

Young Bong Kim

Keyword(s):

Molecular Docking ◽

Binding Affinity ◽

Target Genes ◽

Inflammatory Diseases ◽

Network Pharmacology ◽

Pharmacokinetic Parameters ◽

Active Compounds ◽

Biological Targets ◽

Underlying Mechanisms ◽

Cox 1

Complications due to influenza are often associated with inflammation with excessive release of cytokines. The bulbs of Fritillariae thunbergii (FT) have been traditionally used to control airway inflammatory diseases, such as bronchitis and pneumonia. To elucidate active compounds, the targets, and underlying mechanisms of FT for the treatment of influenza-induced inflammation, systems biology was employed. Active compounds of FT were identified through the TCMSP database according to oral bioavailability (OB) and drug-likeness (DL) criteria. Other pharmacokinetic parameters, Caco-2 permeability (Caco-2), and drug half-life (HL) were also identified. Biological targets of FT were retrieved from DrugBank and STITCH databases, and target genes associated with influenza, lung, and spleen inflammation were collected from DisGeNET and NCBI databases. Compound-disease-target (C-D-T) networks were constructed and merged using Cytoscape. Target genes retrieved from the C-D-T network were further analyzed with GO enrichment and KEGG pathway analysis. In our network, GO and KEGG results yielded two compounds (beta-sitosterol (BS) and pelargonidin (PG)), targets (PTGS1 (COX-1) and PTGS2 (COX-2)), and pathways (nitric oxide, TNF) were involved in the inhibitory effects of FT on influenza-associated inflammation. We retrieved the binding affinity of each ligand-target, and found that PG and COX-1 showed the strongest binding affinity among four binding results using a molecular docking method. We identified the potential compounds and targets of FT against influenza and suggest that FT is an immunomodulatory therapy for influenza-associated inflammation.

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ROS-Induced GATA4 and GATA6 Downregulation Inhibits StAR Expression in LPS-Treated Porcine Granulosa-Lutein Cells

Oxidative Medicine and Cellular Longevity ◽

10.1155/2019/5432792 ◽

2019 ◽

Vol 2019 ◽

pp. 1-14 ◽

Cited By ~ 3

Author(s):

Xiaolu Qu ◽

Leyan Yan ◽

Rihong Guo ◽

Hui Li ◽

Zhendan Shi

Keyword(s):

Molecular Mechanisms ◽

Cell Model ◽

Animal Husbandry ◽

Dependent Manner ◽

Progesterone Production ◽

Progesterone Synthesis ◽

Porcine Granulosa Cell ◽

Underlying Mechanisms ◽

Dose Dependent

LPS is a major endotoxin produced by gram-negative bacteria, and exposure to it commonly occurs in animal husbandry. Previous studies have shown that LPS infection disturbs steroidogenesis, including progesterone production, and subsequently decreases animal reproductive performance. However, little information about the underlying mechanisms is available thus far. In the present study, an in vitro-luteinized porcine granulosa cell model was used to study the underlying molecular mechanisms of LPS treatment. We found that LPS significantly inhibits progesterone production and downregulates the expressions of progesterone synthesis-associated genes (StAR, CYP11A1, and 3β-HSD). Furthermore, the levels of ROS were significantly increased in an LPS dose-dependent manner. Moreover, transcriptional factors GATA4 and GATA6, but not NR5A1, were significantly downregulated. Elimination of LPS-stimulated ROS by melatonin or vitamin C could restore the expressions of GATA4, GATA6, and StAR. In parallel, StAR expression was also inhibited by the knockdown of GATA4 and GATA6. Based on these data, we conclude that LPS impairs StAR expression via the ROS-induced downregulation of GATA4 and GATA6. Collectively, these findings provide new insights into the understanding of reproductive losses in animals suffering from bacterial infection and LPS exposure.

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Potential Molecular Target Prediction and Docking Verification of Hua-Feng-Dan in Stroke Based on Network Pharmacology

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/8872593 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12

Author(s):

Ping Yang ◽

Haifeng He ◽

Shangfu Xu ◽

Ping Liu ◽

Xinyu Bai

Keyword(s):

Molecular Docking ◽

Signaling Pathways ◽

Target Genes ◽

Target Prediction ◽

Interaction Network ◽

Network Pharmacology ◽

Core Network ◽

Active Ingredients ◽

Protein Protein Interaction ◽

Highly Correlated

Objective. Hua-Feng-Dan (HFD) is a Chinese medicine for stroke. This study is to predict and verify potential molecular targets and pathways of HFD against stroke using network pharmacology. Methods. The TCMSP database and TCMID were used to search for the active ingredients of HFD, and GeneCards and DrugBank databases were used to search for stroke-related target genes to construct the “component-target-disease” by Cytoscape 3.7.1, which was further filtered by MCODE to build a core network. The STRING database was used to obtain interrelationships by topology and to construct a protein-protein interaction network. GO and KEGG were carried out through DAVID Bioinformatics. Autodock 4.2 was used for molecular docking. BaseSpace was used to correlate target genes with the GEO database. Results. Based on OB ≥ 30% and DL ≥ 0.18, 42 active ingredients were extracted from HFD, and 107 associated targets were obtained. PPI network and Cytoscape analysis identified 22 key targets. GO analysis suggested 51 cellular biological processes, and KEGG suggested that 60 pathways were related to the antistroke mechanism of HFD, with p53, PI3K-Akt, and apoptosis signaling pathways being most important for HFD effects. Molecular docking verified interactions between the core target (CASP8, CASP9, MDM2, CYCS, RELA, and CCND1) and the active ingredients (beta-sitosterol, luteolin, baicalein, and wogonin). The identified gene targets were highly correlated with the GEO biosets, and the stroke-protection effects of Xuesaitong in the database were verified by identified targets. Conclusion. HFD could regulate the symptoms of stroke through signaling pathways with core targets. This work provided a bioinformatic method to clarify the antistroke mechanism of HFD, and the identified core targets could be valuable to evaluate the antistroke effects of traditional Chinese medicines.

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