scholarly journals Investigating the Mechanism of Scutellariae barbata Herba in the Treatment of Colorectal Cancer by Network Pharmacology and Molecular Docking

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Xiangjun Qi ◽  
Hongbin Xu ◽  
Peng Zhang ◽  
Guoming Chen ◽  
Zhiqiang Chen ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Molecular Docking ◽  
Differentially Expressed Gene ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Active Constituent ◽  
Active Constituents ◽  
Go Analysis ◽  
Protein Protein Interaction ◽  
Mitogen Activated Protein

Background. Colorectal cancer (CRC) is one of the most common gastrointestinal tumors, which accounts for approximately 10% of all diagnosed cancers and cancer deaths worldwide per year. Scutellariae barbatae Herba (SBH) is one of the most frequently used traditional Chinese medicine (TCM) in the treatment of CRC. Although many experiments have been carried out to explain the mechanisms of SBH, the mechanisms of SBH have not been illuminated fully. Thus, we constructed a network pharmacology and molecular docking to investigate the mechanisms of SBH. Methods. We adopted active constituent prescreening, target predicting, protein-protein interaction (PPI) analysis, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, differentially expressed gene analysis, and molecular docking to establish a system pharmacology database of SBH against CRC. Results. A total of 64 active constituents of SBH were obtained and 377 targets were predicted, and the result indicated that quercetin, luteolin, wogonin, and apigenin were the main active constituents of SBH. Glucocorticoid receptor (NR3C1), pPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (PIK3CA), cellular tumor antigen p53 (TP53), transcription factor AP-1 (JUN), mitogen-activated protein kinase 1 (MAPK1), Myc protooncogene protein (MYC), cyclin-dependent kinase 1 (CDK1), and broad substrate specificity ATP-binding cassette transporter ABCG2 (ABCG2) were the major targets of SBH in the treatment of CRC. GO analysis illustrated that the core biological process regulated by SBH was the regulation of the cell cycle. Thirty pathways were presented and 8 pathways related to CRC were involved. Molecular docking presented the binding details of 3 key targets with 6 active constituents. Conclusions. The mechanisms of SBH against CRC depend on the synergistic effect of multiple active constituents, multiple targets, and multiple pathways.

scholarly journals Investigating the Multitarget Mechanism of Traditional Chinese Medicine Prescription for Cancer-Related Pain by Using Network Pharmacology and Molecular Docking Approach

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Jinyuan Chang ◽  
Lixing Liu ◽  
Yaohan Wang ◽  
Yutong Sui ◽  
Hao Li ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Transient Receptor Potential ◽  
Trp Channels ◽  
Receptor Potential ◽  
Binding Activity ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Transient Receptor Potential Vanilloid ◽  
Mitogen Activated Protein ◽  
Transient Receptor

Gu-tong formula (GTF) has achieved good curative effects in the treatment of cancer-related pain. However, its potential mechanisms have not been explored. We used network pharmacology and molecular docking to investigate the molecular mechanism and the effective compounds of the prescription. Through the analysis and research in this paper, we obtained 74 effective compounds and 125 drug-disease intersection targets to construct a network, indicating that quercetin, kaempferol, and β-sitosterol were possibly the most important compounds in GTF. The key targets of GTF for cancer-related pain were Jun proto-oncogene (JUN), mitogen-activated protein kinase 1 (MAPK1), and RELA proto-oncogene (RELA). 2204 GO entries and 148 pathways were obtained by GO and KEGG enrichment, respectively, which proved that chemokine, MAPK, and transient receptor potential (TRP) channels can be regulated by GTF. The results of molecular docking showed that stigmasterol had strong binding activity with arginine vasopressin receptor 2 (AVPR2) and C-X3-C motif chemokine ligand 1 (CX3CL1) and cholesterol was more stable with p38 MAPK, prostaglandin-endoperoxide synthase 2 (PTGS2), and transient receptor potential vanilloid-1 (TRPV1). In conclusion, the therapeutic effect of GTF on cancer-related pain is based on the comprehensive pharmacological effect of multicomponent, multitarget, and multichannel pathways. This study provides a theoretical basis for further experimental research in the future.

scholarly journals Medical Significance of Uterine Corpus Endometrial Carcinoma Patients Infected With SARS-CoV-2 and Pharmacological Characteristics of Plumbagin

2021 ◽  
Vol 12 ◽  
Author(s):  
Yongming Li ◽  
Songzuo Yu ◽  
Yu Li ◽  
Xiao Liang ◽  
Min Su ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Endometrial Carcinoma ◽  
In Silico ◽  
Prognostic Index ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Molecular Pathways ◽  
Uterine Corpus ◽  
Mitogen Activated Protein ◽  
Pharmacologically Active

BackgroundClinically, evidence shows that uterine corpus endometrial carcinoma (UCEC) patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may have a higher death-rate. However, current anti-UCEC/coronavirus disease 2019 (COVID-19) treatment is lacking. Plumbagin (PLB), a pharmacologically active alkaloid, is an emerging anti-cancer inhibitor. Accordingly, the current report was designed to identify and characterize the anti-UCEC function and mechanism of PLB in the treatment of patients infected with SARS-CoV-2 via integrated in silico analysis.MethodsThe clinical analyses of UCEC and COVID-19 in patients were conducted using online-accessible tools. Meanwhile, in silico methods including network pharmacology and biological molecular docking aimed to screen and characterize the anti-UCEC/COVID-19 functions, bio targets, and mechanisms of the action of PLB.ResultsThe bioinformatics data uncovered the clinical characteristics of UCEC patients infected with SARS-CoV-2, including specific genes, health risk, survival rate, and prognostic index. Network pharmacology findings disclosed that PLB-exerted anti-UCEC/COVID-19 effects were achieved through anti-proliferation, inducing cytotoxicity and apoptosis, anti-inflammation, immunomodulation, and modulation of some of the key molecular pathways associated with anti-inflammatory and immunomodulating actions. Following molecular docking analysis, in silico investigation helped identify the anti-UCEC/COVID-19 pharmacological bio targets of PLB, including mitogen-activated protein kinase 3 (MAPK3), tumor necrosis factor (TNF), and urokinase-type plasminogen activator (PLAU).ConclusionsBased on the present bioinformatic and in silico findings, the clinical characterization of UCEC/COVID-19 patients was revealed. The candidate, core bio targets, and molecular pathways of PLB action in the potential treatment of UCEC/COVID-19 were identified accordingly.

scholarly journals Network Pharmacology to Explore the Molecular Mechanisms of Prunella vulgaris for Treating Hashimoto’s Thyroiditis

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiao-xiong Gan ◽  
Lin-kun Zhong ◽  
Fei Shen ◽  
Jian-hua Feng ◽  
Ya-yi Li ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Protein Kinase ◽  
Traditional Chinese Medicine ◽  
Signaling Pathway ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Ppi Network ◽  
Prunella Vulgaris ◽  
Mitogen Activated Protein

Purpose:Prunella vulgaris (PV), a traditional Chinese medicine, has been used to treat patients with thyroid disease for centuries in China. The purpose of the present study was to investigate its bioactive ingredients and mechanisms against Hashimoto’s thyroiditis (HT) using network pharmacology and molecular docking technology to provide some basis for experimental research.Methods: Ingredients of the PV formula were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Additionally, HT-related genes were retrieved from the UniProt and GeneCards databases. Cytoscape constructed networks for visualization. A protein–protein interaction (PPI) network analysis was constructed, and a PPI network was built using the Search Tool for the Retrieval of Interacting Genes (STRING) database. These key targets of PV were enriched and analyzed by molecular docking verification, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment.Results: The compound–target network included 11 compounds and 66 target genes. Key targets contained Jun proto-oncogene (JUN), hsp90aa1.1 (AKI), mitogen-activated protein kinase 1 (MAPK1), and tumor protein p53 (TP53). The main pathways included the AGE-RAGE signaling pathway, the TNF signaling pathway, the PI3K–Akt signaling pathway, and the mitogen-activated protein kinase signaling pathway. The molecular docking results revealed that the main compound identified in the Prunella vulgaris was luteolin, followed by kaempferol, which had a strong affinity for HT.Conclusion: Molecular docking studies indicated that luteolin and kaempferol were bioactive compounds of PV and might play an essential role in treating HT by regulating multiple signaling pathways.

scholarly journals Network Pharmacology Integrated Molecular Docking Analysis of Potential Common Mechanisms of Shu-Feng-Jie-Du Capsule in the Treatment of SARS, MERS, and COVID-19

2020 ◽  
Vol 15 (11) ◽  
pp. 1934578X2097291
Author(s):  
Ying Zhang ◽  
Yi Xie ◽  
Bing Yu ◽  
Chong Yuan ◽  
Zixin Yuan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Protein Kinase ◽  
Signaling Pathways ◽  
Interaction Network ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Active Components ◽  
Discovery Studio ◽  
Mitogen Activated Protein ◽  
Coronavirus Infection

Shu-Feng-Jie-Du Capsules (SFJDCs) have been clinically proven to have a good therapeutic effect on COVID-19 in China. This study aimed to analyze the common mechanisms of SFJDC in the treatment of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and COVID-19 via network pharmacology and molecular docking. We further explored the potential application value of SFJDC in the treatment of coronavirus infection. All components of SFJDC were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. The viral associated targets of the active components were forecast using the Pharmmapper database and GeneCards. The Database for Annotation, Visualization, and Integrated Discovery and KOBAS 3.0 system were used for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of SFJDC’s core targets. Further, the protein–protein interaction network was built using STRING database. The herb–component network and component–target–pathway network were constructed using Cytoscape 3.7.2. The core active components of SFJDC were docked with core targets and COVID-19 coronavirus 3 Cl hydrolase and angiotensin-converting enzyme 2 (ACE2) via Discovery Studio 2016 software. A total of 110 active components were filtered from SFJDC, with 47 core targets, including epidermal growth factor receptor, mitogen-activated protein kinase 1, mitogen-activated protein kinase 3, and interleukin 6. There were 416 GO items in the GO enrichment analysis ( P < .05) and 57 signaling pathways ( P < .05) in KEGG, mainly including pathways in cancer, pancreatic cancer, colorectal cancer, apoptosis, and neurotrophin signaling pathway, among others. The results of molecular docking showed that luteolin and rhein had a higher docking score with 3 Cl, ACE2, and core targets of SFJDC for antiviral effect. SFJDC is characterized by multicomponent, multitarget, and multisignaling pathways for the treatment of coronavirus infection. The mechanism of action of SFJDC in the treatment of MERS, SARS, and COVID-19 may be associated with the regulation of genes coexpressed with ACE2 and immune- related signaling pathways.

scholarly journals Elucidating the Mechanisms of Action of Lianhua Qingwen decoction for the Treatment of COVID-19 via Systems Pharmacology Approaches

2021 ◽  
Author(s):  
Xiting Wang ◽  
Tao Lu
Keyword(s):  
Molecular Docking ◽  
Blood Circulation ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Detection Algorithm ◽  
Network Pharmacology ◽  
Systems Pharmacology ◽  
Protein Protein Interaction ◽  
Further Development ◽  
Protein Protein Interaction Network

Abstract Due to the severity of the COVID-19 epidemic, to identify a proper treatment for COVID-19 is of great significance. Traditional Chinese Medicine (TCM) has shown its great potential in the prevention and treatment of COVID-19. One of TCM decoction, Lianhua Qingwen decoction displayed promising treating efficacy. Nevertheless, the underlying molecular mechanism has not been explored for further development and treatment. Through systems pharmacology and network pharmacology approaches, we explored the potential mechanisms of Lianhua Qingwen treating COVID-19 and acting ingredients of Lianhua Qingwen decoction for COVID-19 treatment. Through this way, we generated an ingredients-targets database. We also used molecular docking to screen possible active ingredients. Also, we applied the protein-protein interaction network and detection algorithm to identify relevant protein groupings of Lianhua Qingwen. Totally, 605 ingredients and 1,089 targets were obtained. Molecular Docking analyses revealed that 35 components may be the promising acting ingredients, 7 of which were underlined according to the comprehensive analysis. Our enrichment analysis of the 7 highlighted ingredients showed relevant significant pathways that could be highly related to their potential mechanisms, e.g. oxidative stress response, inflammation, and blood circulation. In summary, this study suggests the promising mechanism of the Lianhua Qingwen decoction for COVID-19 treatment. Further experimental and clinical verifications are still needed.

scholarly journals MOLECULAR DOCKING TERPINEN-4-OL SEBAGAI ANTIINFLAMASI PADA ATEROSKLEROSIS SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
pp. 221
Author(s):  
N. M. P. Susanti ◽  
N. P. L. Laksmiani ◽  
N. K. M. Noviyanti ◽  
K. M. Arianti ◽  
I K. Duantara
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Endothelial Dysfunction ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Inflammatory Process ◽  
Mapk Pathway ◽  
Chronic Inflammatory Disease ◽  
Mitogen Activated Protein Kinase ◽  
Mitogen Activated Protein

Atherosclerosis is a chronic inflammatory disease that begins with endothelial dysfunction, it caused fat accumulation and plaque growth in the inner arteries walls. Endothelial dysfunction will activate the Mitogen Activated Protein Kinase (MAPK) pathway involving ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins, as well as the Nuclear Factor Kappa B (NF-kB) pathway involving IKK proteins. Terpinen-4-ol is constituent found in the bangle rhizome. The purpose of this study were to determine the affinity and mechanisms of terpinen-4-ol against ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins as anti-inflammatory in atherosclerosis performed using molecular docking method. The study was conducted exploratively with several steps such as preparation and optimization of terpinen-4-ol structure, preparation of 3D ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins, validation method of molecular docking, and docking terpinen-4-ol in these proteins. The docking result are assessed from the binding energy and hydrogen bonds formed between terpinen-4-ol and proteins. The smaller value of binding energy terpinen-4-ol with target proteins showed the complex that form more stable. The result showed that terpinen-4-ol and has activity in inhibiting the inflammatory process because it is able to disturb ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins with respective bond energy values -5,12; -5,24; -5,08; -5,88; and -4,99 Kcal/mol. The molecular mechanism in inhibiting the activity of ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins is through the formation of hydrogen bonds in these proteins. These results show that terpinen-4-ol have the potential to inhibit inflammatory process and the formation of atherosclerotic plaque can be obstructed. Keywords : atherosclerosis, terpinen-4-ol, molecular docking, in silico

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