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ObjectiveTo mine the compatibility rules of patented traditional Chinese medicine (TCM) compound prescriptions for treating chronic atrophic gastritis (CAG) by systems pharmacology and molecular docking methods, and predict the targets and molecular mechanisms of Chinese medicinals with different efficacy in the treatment of CAG. MethodThe TCM compound prescriptions for treating CAG were extracted from the patent system of the China National Intellectual Property Administration. The active components and targets of the prescriptions were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), Traditional Chinese Medicine Integrative Database (TCMID), and UniProt. The candidate targets and pathways of CAG were obtained from GeneCards, DisGeNet, Online Mendelian Inheritance in Man (OMIM), MalaCards, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome. The gene ontology (GO) functional annotation and KEGG pathway enrichment were realized by R Studio 4.1.2. STRING11.0 was employed to build the protein-protein interaction (PPI) network, and AutoDock Vina 4.2.6 was used for the docking between key targets and components. ResultA total of 228 TCM compound prescriptions for treating CAG were extracted. The medicinals used in these prescriptions mainly had warm or cold nature, bitter or sweet taste, tropism to the spleen, stomach, and liver meridians, and the efficacy of tonifying Qi, regulating Qi movement, clearing heat, and activating and toniying blood. The prescriptions mainly treated CAG via p53, mitogen-activated protein kinase (MAPK), phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt), forkhead box protein O (FoxO), vascular endothelial growth factor (VEGF), and hypoxia-inducible factor-1 (HIF-1) signaling pathways. Molecular docking results confirmed that the active components in the prescriptions had docking activities with key receptor proteins. ConclusionThis study preliminarily analyzed the compatibility rules of TCM compound prescriptions in the treatment of CAG. The medicinals with different efficacy treat CAG by regulating cell proliferation, apoptosis, and oxidative stress response, preventing carcinogen production, promoting gastric acid secretion, and improving local microcirculation in a multi-target, multi-pathway, multi-link manner. The findings facilitate the research on the TCM treatment of CAG.
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ObjectiveTo explore the mechanism of Tangbikang granules （TBK） against diabetic peripheral neuropathy （DPN） based on network pharmacology and in-vivo experiment. MethodThe active components in medicinals of TBK and their target genes were searched from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform （TCMSP）. The active components of the medicinals which are not included in TCMSP were searched from previous research. After the analysis of drug-likeness by SwissADME， the target genes of them were predicted with SwissTargetPrediction. DPN-related target genes were retrieved from GeneCards. The common targets of the disease and the prescription were the hub genes of TBK against DPN， which were uploaded to Metascape for Gene Ontology （GO） term enrichment and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analysis. High-sugar and high-fat diet and low-dose streptozotocin （STZ， ip） were employed to induce diabetes in rats， and then the model rats were respectively treated with low-dose （0.625 g·kg-1）， medium-dose （1.25 g·kg-1）， and high-dose （2.5 g·kg-1） TBK for 12 weeks. Sensory nerve conduction velocity （SNCV） was evaluated. After hematoxylin and eosin （HE） staining， the sciatic nerve was observed under light microscope to examine the nerve damage. Real-time PCR was performed to detect the gene expression of adenosine monophosphate-activated protein kinase （AMPK） pathway-related targets in rat sciatic nerve， and Western blot to measure the protein expression of AMPK and phosphorylated （p）-AMPK in rat sciatic nerve. ResultThe main active components of TBK， such as quercetin， kaempferol， β-sitosterol， leech pteridine A， stigmasterol， and baicalein were screened out， mainly acting on interleukin-6 （IL-6）， tumor necrosis factor （TNF）， protein kinase B （Akt）， JUN， and HSP90AA1 and signaling pathways such as AMPK， nuclear factor-κB （NF-κB）， and Janus kinase/signal transducer and activator of transcription （JAK/STAT）. Molecular docking results showed that β-sitosterol and stigmasterol had high binding affinity with IL-6， TNF， JUN， and HSP90AA1. As for the animal experiment， compared with the normal group， model group had low SNCV of sciatic nerve （P<0.01）， disordered and loose myelinated nerve fibers with axonotmesis and demyelinization， low mRNA expression of AMPKα， AMPKβ， peroxisome proliferator-activated receptor γ coactivator-1α （PGC-1α）， Sirtuin 3 （SirT3）， mitochondrial transcription factor A （TFAM）， and low p-AMPK/AMPK ratio in sciatic nerve （P<0.05， P<0.01）. Compared with the model group， TBK of the three doses raised the SNCV （P<0.01）， restored nerve morphology and nerve compactness， and increased the mRNA expression of AMPKα， AMPKβ， PGC-1α， SirT3， and TFAM （P<0.05， P<0.01）. The ratio of p-AMPK/AMPK in the high-dose and medium-dose TBK groups was higher than that in the model group （P<0.01）， while the protein expression in the low-dose TBK group was insignificantly different from that in the model group. ConclusionTBK exerts therapeutic effect on DPN through multiple pathways and targets. The mechanism is that it activates and regulates AMPK/PGC-1α/SirT3 signaling， which lays a basis for further study of TBK in the treatment of DPN.
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Quantitative systems pharmacology (QSP) modeling is an emerging computational medicine approach with growing applications and significance in modern drug development. QSP models are generally formulated based on multiscale disease mechanisms and drug-target interactions, which makes them capable of integrating multimodal data from the preclinical and clinical space. This also enables them to generate quantitative characterization of the dynamic disease progression as well as high-throughput predictions of drug-induced efficacy and toxicity signals. Therefore, QSP modeling and model-based virtual clinical trials have been widely implemented to guide drug development, in scenarios such as target identification and assessment, clinical trial design, evaluation of combination therapy and biomarkers, and personalized medicine. In US and Europe, QSP modeling has been developing rapidly in the past 10 years and is now an integral part of the model-informed drug development paradigm; however, in China it is still a nascent field. Here we will present a comprehensive review of the recent advancements of QSP and its impact in modern drug development through a number of case studies. This review will provide guidance for the future drug development efforts and the growth of QSP practice in China.
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The high mortality of tumor is one of the most urgent problems to be solved. However, the current clinical trials provide limited quantitative descriptions on dynamic changes of drug efficacy, which restrict the selection of dosing regimens. Quantitative systems pharmacology (QSP) is a new approach for precise treatment of tumors. It quantifies the network relationship between drug action and diseases by integrating the tumor growth and molecules, cells in vivo, thereby predicting the efficacy, toxicity, and mechanism of antitumor drugs as well as identifying predictive biomarkers. In this review, we provide an overview of definition of QSP, current approaches and typical applications in research of antitumor drugs to enhance our understanding of QSP.
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ObjectiveTo explore the effective components， targets， and mechanism of Houttuynia cordata against lung cancer by means of systems pharmacology and further to provide a reference for the further development and clinical application of this medicinal. MethodChemical components of H. cordata were retrieved from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform （TCMSP） and the active components were screened based on oral bioavailability （OB） and drug-likeness （DL）. Then the potential targets were predicted， followed by enrichment analysis. Finally， sodium houttuyfonate （SH） was selected for verifying the anti-tumor mechanism. Cell counting kit-8 （CCK-8） assay was used to evaluate the effect of SH on the in vitro proliferation of two lung cancer cell lines： A549 and LLC， and the regulation of tumor-related proteins by SH was verified by Western blot. ResultA total of 7 active compounds and 352 targets of the active components were screened out. According to the enrichment analysis of targets， H. cordata had potential therapeutic effects on cancer. SH had inhibitory effect on both A549 and LLC. Western blot results showed that G1/S-specific Cyclin D1， E1 and cyclin-dependent kinase （CDK）2， CDK4 all tended to be down-regulated， and Janus kinase 2 （JAK2）/signal transducer and activator of transcription 3 （STAT3） also changed significantly. ConclusionH. cordata has the potential anti-tumor effects by arresting the tumor cells in the G1 phase through the JAK2/STAT3 pathway.
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Objective: Osteoporosis has become the biggest cause of non-fatal health issue. Currently, the limitations of traditional anti-osteoporosis drugs such as long-term ill-effects and drug resistance, have raised concerns toward complementary and alternative therapies, particularly herbal medicines and their natural active compounds. Thus, this study aimed to provide an integrative analysis of active chemicals, drug targets and interacting pathways of the herbs for osteoporosis treatment. Methods: Here, we introduced a systematic pharmacology model, combining the absorption, distribution, metabolism, and excretion (ADME) screening model, drug targeting and network pharmacology, to probe into the therapeutic mechanisms of herbs in osteoporosis. Results: We obtained 86 natural compounds with favorable pharmacokinetic profiles and their 58 targets from seven osteoporosis-related herbs. Network analysis revealed that they probably synergistically work through multiple mechanisms, such as suppressing inflammatory response, maintaining bone metabolism or improving organism immunity, to benefit patients with osteoporosis. Furthermore, experimental results showed that all the five compounds (calycosin, asperosaponin VI, hederagenin, betulinic acid and luteolin) enhanced osteoblast proliferation and differentiation in vitro, which corroborated the validity of this system pharmacology approach. Notably, gentisin and aureusidin among the identified compounds were first predicted to be associated with osteoporosis. Conclusion: Herbs and their natural compounds, being characterized as the classical combination therapies, might be engaged in multiple mechanisms to coordinately improve the osteoporosis symptoms. This work may contribute to offer novel strategies and clues for the therapy and drug discovery of osteoporosis and other complex diseases.
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Holistic medicine is an interdisciplinary field that integrates all types of biological information (proteins, small molecules, tissues, organs, external environmental signals, etc.) to provide predictable and operational models for healthcare and disease treatment. Despite the global and integrative character of this discipline, scientific evidences to clarify the mechanism of holistic medicine is still lacking. Systems pharmacology, as a newly developed discipline based on the interdisciplinary and integration of classical pharmacology, computer technology, bioinformatics, and network pharmacology, has systematically studied the interaction between drugs and the human body, as well as its law and nature at the molecular, cellular, organ and network levels. Since its birth in 2011, this discipline has been widely used in the research of the promotion of holistic medicine, compound analysis, the development of new drugs, and interpretation of basic theories of traditional Chinese medicine (TCM). In this paper, in order to provide new methods and ideas for the modernization of holistic medicine, the authors introduce the research ideas of systems pharmacology of TCM in detail, and the mechanism of holistic medicine in the treatment of complex diseases is explained by sorting out the researches of systems pharmacology on multi-component, multi-target, multi-pathway, multi-function, compatibility of TCM, etc.
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Objective: To explore the pharmacological mechanism of traditional Chinese medicine (TCM) Magnoliae Officinalis Cortex by systems pharmacology (SP). Methods: A database of magnolia components was established by using the database of TCM ingredients and a large number of literature search. After that, ADME was used to screen the active compounds of magnolia, and these ingredients and an in silico software were used to identify targets. Finally, the pharmacological mechanism of magnolia was analyzed by SP methods network analysis and pathway analysis. Results: The most comprehensive database of magnolia ingredients to date have been established, containing a total of 144 magnolia compounds. After screening, we obtained seven magnolia active compounds which meet the conditions and identified 54 interacting targets. The network analysis showed that these targets were mainly related to intestinal motility, inflammation, diabetes and thrombus. Through pathway analysis, we found that a total of 152 biological pathways were involved in the targets of magnolia, and these pathways were involved in cancer-related mechanisms in addition to the above diseases. Conclusion: This study not only uses SP to reveal the pharmacological mechanisms of magnolia on intestinal motility, inflammation, diabetes, thrombus and cancer, but also reflects the typical “multi-component, multi-target, multi-channel” TCM characteristics of magnolia and provides a new SP technology to explore the pharmacological mechanism of TCM.
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italic>Cichorium glandulosum has been used to treat non-alcoholic fatty liver disease (NAFLD) and type 2 diabetes mellitus (T2DM) in Uyghur folk medicine. The mechanism of Cichorium glandulosum (CG)on type 2 diabetes mellitus accompanied with non-alcoholic fatty liver disease (T2DM-NAFLD) remains unclear. The effect of CGextraction on T2DM-NAFLD was determined in animal experiments here (all the experiments here were approved by the Animal Care Committee of the First Affiliated Hospital of the Medical College, Shihezi University). The mechanism of CG for treatment of T2DM-NAFLD was predicted and verified based on systems pharmacology. Based on the active compounds of CGon T2DM-NAFLD, T2DM and NAFLD-related targets, pathways and diseases were screened and predicted. Active compounds-targets, compounds-targets-pathways and compounds-targets-diseases were constructed and analyzed. The results of animal experiments showed that CGextractioncan reduce the levels of blood glucose and blood lipid in T2DM-NAFLD rats. In addition, it can improve the glucose tolerance and relieve liver injury. Total 29 active compounds and 198 targets were screened by systems pharmacology, of which 106 targets were involved in T2DM, 88 were involved in NAFLD, and 56 targets were common between T2DM and NAFLD, mainly related to insulin resistance and inflammation. These 198 targets include those in metabolic pathways, calcium pathway, PI3K/Akt pathway, cAMP pathway, and MAPK pathway. Our study confirmed that CG can be potential phytomedicine for treatment of T2DM-NAFLD. This work provides a reference for studying the treatment of multiple diseases using multiple-targets phytomedicine in systems pharmacology.
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Liver injury remains a significant global health problem and has a variety of causes, including oxidative stress (OS), inflammation, and apoptosis of liver cells. There is currently no curative therapy for this disorder. Sanwei Ganjiang Prescription (SWGJP), derived from traditional Chinese medicine (TCM), has shown its effectiveness in long-term liver damage therapy, although the underlying molecular mechanisms are still not fully understood. To explore the underlining mechanisms of action for SWGJP in liver injury from a holistic view, in the present study, a systems pharmacology approach was developed, which involved drug target identification and multilevel data integration analysis. Using a comprehensive systems approach, we identified 43 candidate compounds in SWGJP and 408 corresponding potential targets. We further deciphered the mechanisms of SWGJP in treating liver injury, including compound-target network analysis, target-function network analysis, and integrated pathways analysis. We deduced that SWGJP may protect hepatocytes through several functional modules involved in liver injury integrated-pathway, such as Nrf2-dependent anti-oxidative stress module. Notably, systems pharmacology provides an alternative way to investigate the complex action mode of TCM.
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Humains , Médicaments issus de plantes chinoises , Chimie , Expression des gènes , Hépatocytes , Métabolisme , Foie , Plaies et blessures , Métabolisme , Maladies du foie , Traitement médicamenteux , Génétique , Métabolisme , Stress oxydatif , PharmacologieRÉSUMÉ
Guanxinshutong capsule (GXSTC) is an effective and safe traditional Chinese medicine used in the treatment of cardiovascular diseases (CVDs) for many years. However, the targets of this herbal formula and the underlying molecular mechanisms of action involved in the treatment of CVDs are still unclear. In the present study, we used a systems pharmacology approach to identify the active ingredients of GXSTC and their corresponding targets in the calcium signaling pathway with respect to the treatment of CVDs. This method integrated chromatographic techniques, prediction of absorption, distribution, metabolism, and excretion, analysis using Kyoto Encyclopedia of Genes and Genomes, network construction, and pharmacological experiments. 12 active compounds and 33 targets were found to have a role in the treatment of CVDs, and four main active ingredients, including protocatechuic acid, cryptotanshinone, eugenol, and borneol were selected to verify the effect of (GXSTC) on calcium signaling system in cardiomyocyte injury induced by hypoxia and reoxygenation. The results from the present study revealed the active components and targets of GXSTC in the treatment of CVDs, providing a new perspective to enhance the understanding of the role of the calcium signaling pathway in the therapeutic effect of GXSTC.
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Animaux , Rats , Animaux nouveau-nés , Camphanes , Chimie , Cardiotoniques , Chimie , Pharmacologie , Cellules cultivées , Médicaments issus de plantes chinoises , Chimie , Pharmacologie , Eugénol , Chimie , Expression des gènes , Hydroxybenzoates , Chimie , Spectrométrie de masse , Modèles biologiques , Myocytes cardiaques , Nitric oxide synthase type III , Génétique , Phénanthrènes , Chimie , Rat Sprague-Dawley , Récepteur de type PAR-1 , Génétique , Biologie des systèmesRÉSUMÉ
Liver injury remains a significant global health problem and has a variety of causes, including oxidative stress (OS), inflammation, and apoptosis of liver cells. There is currently no curative therapy for this disorder. Sanwei Ganjiang Prescription (SWGJP), derived from traditional Chinese medicine (TCM), has shown its effectiveness in long-term liver damage therapy, although the underlying molecular mechanisms are still not fully understood. To explore the underlining mechanisms of action for SWGJP in liver injury from a holistic view, in the present study, a systems pharmacology approach was developed, which involved drug target identification and multilevel data integration analysis. Using a comprehensive systems approach, we identified 43 candidate compounds in SWGJP and 408 corresponding potential targets. We further deciphered the mechanisms of SWGJP in treating liver injury, including compound-target network analysis, target-function network analysis, and integrated pathways analysis. We deduced that SWGJP may protect hepatocytes through several functional modules involved in liver injury integrated-pathway, such as Nrf2-dependent anti-oxidative stress module. Notably, systems pharmacology provides an alternative way to investigate the complex action mode of TCM.
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Humains , Médicaments issus de plantes chinoises , Chimie , Expression des gènes , Hépatocytes , Métabolisme , Foie , Plaies et blessures , Métabolisme , Maladies du foie , Traitement médicamenteux , Génétique , Métabolisme , Stress oxydatif , PharmacologieRÉSUMÉ
Guanxinshutong capsule (GXSTC) is an effective and safe traditional Chinese medicine used in the treatment of cardiovascular diseases (CVDs) for many years. However, the targets of this herbal formula and the underlying molecular mechanisms of action involved in the treatment of CVDs are still unclear. In the present study, we used a systems pharmacology approach to identify the active ingredients of GXSTC and their corresponding targets in the calcium signaling pathway with respect to the treatment of CVDs. This method integrated chromatographic techniques, prediction of absorption, distribution, metabolism, and excretion, analysis using Kyoto Encyclopedia of Genes and Genomes, network construction, and pharmacological experiments. 12 active compounds and 33 targets were found to have a role in the treatment of CVDs, and four main active ingredients, including protocatechuic acid, cryptotanshinone, eugenol, and borneol were selected to verify the effect of (GXSTC) on calcium signaling system in cardiomyocyte injury induced by hypoxia and reoxygenation. The results from the present study revealed the active components and targets of GXSTC in the treatment of CVDs, providing a new perspective to enhance the understanding of the role of the calcium signaling pathway in the therapeutic effect of GXSTC.
Sujet(s)
Animaux , Rats , Animaux nouveau-nés , Camphanes , Chimie , Cardiotoniques , Chimie , Pharmacologie , Cellules cultivées , Médicaments issus de plantes chinoises , Chimie , Pharmacologie , Eugénol , Chimie , Expression des gènes , Hydroxybenzoates , Chimie , Spectrométrie de masse , Modèles biologiques , Myocytes cardiaques , Nitric oxide synthase type III , Génétique , Phénanthrènes , Chimie , Rat Sprague-Dawley , Récepteur de type PAR-1 , Génétique , Biologie des systèmesRÉSUMÉ
OBJECTIVE:To investigate the possible mechanism of Artemisia capillaries,and to provide reference for further development and utilization of it. METHODS:The effective components and related target protein of A. capillaries were screened by Traditional Chinese Medicine Systems Pharmacology (TCMSP) analysis platform database. The effective compound-target protein visual network of A. capillaries was established by using Cytoscape 3.5.1 software,topology analysis was also performed. The protein-protein interaction (PPI) network was constructed and analyzed by STRING database. KEGG pathway enrichment of target protein coding gene was analyzed by DAVID bioinformatics resource database. RESULTS:A total of 13 kinds of effective compounds,189 target proteins and 34 enrichment pathways were selected. Quercetin,β-glutamol,isorhamnetin and artepillin C were main effective compounds. Prostaglandin G/H sythase 2(PTGS 2),heat shock protein 90(HSP 90),dipeptidyl peptidase Ⅳ, protein kinase A catalytic subunit Cα were main target proteins. Transcription factor AP-1 and cell tumor antigen p53 played a key role in PPI network. The target protein coding gene was rich in TNF-α signaling pathway,HIF-1 signaling pathway,Toll-like receptor signaling pathway,PI3K/Akt signaling pathway,T cell receptor signaling pathway,thyroid hormone signaling pathway, apoptotic signaling pathway,etc. CONCLUSIONS:Quercetin,β-glutamol and isorhamnetin of A. capillaries play an effect on PTGS2,HSP90,transcription factor AP-1 and other target proteins through TNF-α signaling pathway,HIF-1 signaling pathway and PI3K/Akt signaling pathway,so as to play anti-inflammatory and antitumor effect.
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Toutongning capsule (TTNC) is a traditional Chinese medicine(TCM) with good effect for treating migraine in clinical application. In this paper, a systems pharmacology method was carried out to study the TNF mechanism of the TTNC on the migraine. First, the ingredients for TTNC were collected from TCM databases, and ADME properties prediction was firstly applied to screen out the active compounds of TTNC. Then, the target searching and identification was performed by using CSDT model, and the targets were mapped to the migraine disease to determine the active targets through some common databases like TTD. To obtain the targets related with TNF signaling pathway, KEGG pathway analysis was performed by DAVID online analysis tool. Finally, the "herbs-compounds-targets" network was built by Cytoscape software. According to the results of degree and betweenness in the network, the key active compounds and targets were determined to explore the TNF mechanism for TTNC. Results showed that 19 active compounds and 8 targets played a crucial role in the treatment of migraine by TNF pathway for TTNC. This work provided a new perspective to deepen the understanding of the TNF signaling pathway mechanism in migraine treatment by TTNC, and may provide a necessary theoretical basis for the determination of effective markers and the clinical research of this medicine.
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To explore the pharmacological mechanism of glycyrrhizin with series methods of systems pharmacology, main diseases related to glycyrrhizin were obtained by text mining tool; and the target proteins of glycyrrhizin were obtained via the database of Polysearch and PubChem. Then, the target proteins interaction network of glycyrrhizin was built using the software called Cytoscape. Next, the protein groups related to glycyrrhizin were analyzed by using Gene Ontology (GO) tool, and the action pathway of its target proteins was analyzed by using enrichment method. Text mining results showed that the related diseases of glycyrrhizin included chronic hepatitis C, chronic hepatitis, hepatitis, HIV virus, liver cancer and so on. Gene ontology analysis indicated that glycyrrhizin played a role mainly through modification of proteins and chromatin. The signaling pathway enrichment results showed that the main action proteins of glycyrrhizin were related to MAPK signaling pathway, toll-like receptor signaling pathway, neurotrophic factor signaling pathway, cancer and apoptosis pathways. So we can conclude that glycyrrhizin may exert its biological functions primarily by regulating multiple pathways such as MAPK signaling pathway and Toll-like receptors signaling pathway. The pharmacological action of a drug can be rapidly and comprehensively analyzed by the ways of systems pharmacology.
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OBJECTIVE: To explore the molecular mechanism and targets with"Relieving the Depressed Liver" effectofemotional diseases treatment by Radix Bupleuri. METHOD: Systems pharmacology methodwas employed to exploring the ingredients, targets and diseases information which was related "Relieving the Depressed Liver" effect in Radix Bupleuri. Next, the "disease-target" network and "drug-target" network were built by Cytoscape 3.2.1 and we analyzed the network by using network topological analysis method and systems pharmacological data. RESULT: Twenty-five targets were found to be associated with emotional diseases. Eight core ingredients from 118 ingredients in Radix Bupleuri were directly related to these targets. The molecular mechanism of Radix Bupleuri treatment of emotional diseases is produced by the interactions between the 118 ingredients and 25 potential targets, and eight core compounds may play a central role in the process of this treatment mechanism. CONCLUSION: Through the construction of systems pharmacology models, the molecular mechanism of "Relieving the Depressed Liver" effect of Radix Bupleuri from the system level is we interpreted. Our study provides a theoretical foundation for the explanation of TCM treating mechanism and "treat different diseases with same Chinese medicine" phenomenon.