Liver Injury Caused by Psoraleae Fructus： A Review / 中国实验方剂学杂志

Psoraleae Fructus （PF） is a non-toxic Chinese herbal medicine， while the liver injury caused by PF has aroused wide concern in recent years. At present， animal experiments and in vitro studies have been carried out to explore the mechanism， targets， and toxic components of PF in inducing liver injury， which， however， have differences compared with the actual conditions in clinical practice， and there are still some potential hepatotoxic components and targets of PF that have not been discovered. With the continuous progress in systems biology， establishing the drug-induced liver injury model and the liver injury prediction model based on network toxicology can reduce the cost of animal experiments， improve the toxicity prediction efficiency， and provide new tools for predicting toxic components and targets. To systematically explain the characteristics of liver injury in the application of PF and explore the potential hepatotoxic components and targets of PF， we reviewed the related articles published by China National Knowledge Infrastructure （CNKI）， Wanfang Data， VIP， and PubMed from 1962 to 2021 and analyzed the characteristics and influencing factors of liver injury caused by PF in the patients. Furthermore， we summarized the chemical components of PF and the components entering blood. By reviewing the mechanism， targets， and components of PF in inducing liver injury that were discovered by in vivo and in vitro experiments， we summarized the known compounds in PF that may cause liver injury. Finally， the current methods for building the prediction model of PF-induced liver injury were summarized， and the predicted toxic components and targets were introduced. The possible factors of PF in causing liver injury were explained from three aspects： clinical characteristics， preclinical studies， and computer-assisted network prediction， which provide a reference for predicting the risk of PF-induced liver injury.

Mechanism of Sophorae tonkinensis radix et rhizome-induced nephrotoxicity in rats based on network toxicology and experimental validation / 中国药理学通报

Aim To investigate the mechanism of Sophorae tonkinensis radix et rhizome (ST) induced nephrotoxicity based on network toxicology and experimental verification. Methods Through network toxicology the target of toxic components of ST was predicted, nephrotoxicity-related target genes were located, the intersection of targets was taken, the STRING platform was imported to map the target protein interactions, MetaScape database was used for GO and KEGG analysis, BioGPS database for screening the key expressed genes in rat nephrotoxicity and the component-target-pathway network was constructed. The mechanism of ST induced nephrotoxicity was verified through animal experiments, and qRT-PCR was applied to detect mRNA expression level of key genes in kidney tissue. Results Twenty toxic components of ST were screened from network toxicology, mainly including matrine, sophoridine, maackiain. A total of 135 targets were involved, and HSP90AA1, SRC, MAPK1, MAPK3, AKT1 were the main targets. A total of 169 related signaling pathways were yielded by KEGG analysis, and the mechanism of nephrotoxicity might be related to cancer pathway, PI3K-Akt signaling pathway, HIF-1 signaling pathway, MAPK signaling pathway. PPARA, RAF1, MAP2K1, SRC, AKT1 and MAPK3 were screened from BioGPS database. The results of animal experiments showed that BUN and SCr level increased (P <0. 01) in rats with high-dose group, and the kidney tissue was significantly damaged. qRT-PCR results indicated that the expression of PPARA, RAF1, MAP2K1, MAPK3 mRNA increased, the expression of AKT1 mRNA decreased in the high-dose group of ST (P <0. 05). Conclusions The mechanism of Sophorae tonkinensis radix et rhizome induced nephrotoxicity is found to be related to the combined action of multiple components, multiple targets and multiple pathways, which also provides a theoretical basis for the in-depth exploration of the toxicology.

Toxicity mechanism of Rhododendri Mollis Flos: based on serum metabolomics and network toxicology / 中国中药杂志

This study aims to explore the toxicity mechanism of Rhododendri Mollis Flos(RMF) based on serum metabolomics and network toxicology. The toxic effect of RMF on normal rats was evaluated according to the symptoms, serum biochemical indexes, and histopathology. Serum metabolomics was combined with multivariate statistical analysis to search endogenous differential metabolites and related metabolic pathways. The toxic components, targets, and signaling pathways of RMF were screened by network toxicology technique, and the component-target-metabolite-metabolic pathway network was established with the help of serum metabolomics. The result suggested the neurotoxicity, hepatotoxicity, and cardiotoxicity of RMF. A total of 31 differential metabolites and 10 main metabolic pathways were identified by serum metabolomics, and 11 toxic components, 332 related target genes and 141 main signaling pathways were screened out by network toxicology. Further analysis yielded 7 key toxic components: grayanotoxin Ⅲ,grayanotoxinⅠ, rhodojaponin Ⅱ, rhodojaponin Ⅴ, rhodojaponin Ⅵ, rhodojaponin Ⅶ, and kalmanol, which acted on the following 12 key targets: androgen receptor(AR), albumin(ALB), estrogen receptor β(ESR2), sex-hormone binding globulin(SHBG), type 11 hydroxysteroid(17-beta) dehydrogenase(HSD17 B11), estrogen receptor α(ESR1), retinoic X receptor-gamma(RXRG), lactate dehydrogenase type C(LDHC), Aldo-keto reductase(AKR) 1 C family member 3(AKR1 C3), ATP binding cassette subfamily B member 1(ABCB1), UDP-glucuronosyltransferase 2 B7(UGT2 B7), and glutamate-ammonia ligase(GLUL). These targets interfered with the metabolism of gamma-aminobutyric acid, estriol, testosterone, retinoic acid, 2-oxobutyric acid, and affected 4 key metabolic pathways of alanine, aspartate and glutamate metabolism, cysteine and methionine metabolism, steroid hormone biosynthesis, and retinol metabolism. RMF exerts toxic effect on multiple systems through multiple components, targets, and pathways. Through the analysis of key toxic components, target genes, metabolites, and metabolic pathways, this study unveiled the mechanism of potential neurotoxicity, cardiotoxicity, and hepatotoxicity of RMF, which is expected to provide a clue for the basic research on toxic Chinese medicinals.

Mechanism of hepatotoxicity induced by ethanol extract of Dysosma versipellis based on "quantity-weight-evidence" network toxicology / 中国中药杂志

In this study, the toxicological/pharmacological research method of "quantity-weight-evidence" network was first proposed and practiced to supplement the existing methodology of network toxicology. We transformed the traditional qualitative network into a quantitative network in this study by attributing weights to toxic component content and target frequency, which improved the reliability of data and provided a research idea for the systematic safety evaluation and toxicological research of Chinese medicinal herbs. Firstly, 50% ethanol extract of Dysosma versipellis(DV) was administrated to rats via gavage and the potential hepatotoxic components were identified by serum pharmacochemistry. Then, the component targets were obtained from SwissTargetPrediction, PharmMapper and other online databases, and the target weights were given according to the relative content of components and target fishing frequency. Meanwhile, the targets of hepatotoxicity were predicted from online databases such as Comparative Toxicology Database(CTD) and GeneCards. Subsequently, protein-protein interaction analysis and KEGG pathway enrichment were performed with the STRING database. Finally, the quantitative network of "toxic components-weighted targets-pathways" was constructed. Eleven potential toxic compounds were predicted, including podophyllotoxin, podophyllotoxone, deoxypodophyllotoxin, and 6-methoxypodophyllotoxin. A total of 106 hepatotoxic targets and 65 weighted targets(e.g., Cdk2, Egfr, and Cyp2 c9) were identified. The results of Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment showed that these targets could act on PI3 K-AKT, MAPK, and Ras signaling pathways to play a role in inflammatory response and oxidative stress. However, traditional network toxicology showed that 51 targets such as AKT1, Alb, and Stat3 may lead to hepatotoxicity by mediating inflammation and cell proliferation. In conclusion, we proposed "quantity-weight-evidence" network toxicology in this study and used it to study the mechanism of DV-induced hepatotoxicity in rats. This study confirms the feasibility of this new methodology in toxicological evaluation and further improves the systematic evaluation of the safety of Chinese medicinal herbs.

Potential hepatotoxic compounds and mechanisms of Epimedii Folium based on network toxicology and cell experimental validation / 中国中药杂志

To probe the potential hepatotoxic components of Epimedii Folium and investigate its mechanism based on network toxicology and cell experimental validation. According to the previous results of component measurement and cytotoxicity evaluation, 11 active compounds related to hepatotoxicity in Epimedii Folium were chosen as research object in this study. Through SwissTargetPrediction database and GeneCards database, the potentially hepatotoxic targets of Epimedii Folium were obtained. Subsequently, the protein-target interaction network and active compounds-hepatotoxic targets network were established to analyze the core targets and screen the key hepatotoxic compounds in Epimedii Folium. Meanwhile, the signaling pathways and molecular mechanisms were inferred with GO functional enrichment analysis and KEGG pathway enrichment analysis on the core targets. At last, the effect of icaritin as the chief hepatotoxic compound on the indexes related to hepatotoxicity in HL-7702 cells and HepG2 cells was investigated to validate the hepatotoxicity mechanism of Epimedii Folium. Through the network toxicology analysis, 190 action targets and 991 hepatotoxic targets were collected, then 64 potentially hepatotoxic targets of Epimedii Folium including AKT1, EGFR, MAPK3, TNF and so on were obtained, and icaritin was screened as the key hepatotoxic compound. GO functional enrichment analysis indicated 160 biological process terms such as protein phosphorylation and negative regulation of apoptotic process, 41 molecular function terms such as protein binding and ATP binding, and 32 cellular component terms such as cytosol and cell surface. KEGG pathway enrichment analysis inferred 75 signaling pathways involving PI3 K-Akt and HIF-1. After comprehensive analysis, it was inferred that the hepatotoxicity mechanism of Epimedii Folium was related with regulating oxidative stress and apoptosis. The results of cell biology experiments showed that icaritin could significantly increase the level of aspartate aminotransferase and lactate dehydrogenase, reduce the level of glutathione, improve the quality of reactive oxygen species and reduce mitochondrial membrane potential, indicating that it could cause hepatotoxicity by destroying cell membrane structure, inhibiting antioxidant enzyme activity, activating oxidative stress and inducing apoptosis. These results proved the reliability of results of network pharmacology. This study preliminarily clarified the material base and the mechanism of potential hepatotoxicity of Epimedii Folium, which provided important information for further research and safe application.

Investigation of the mechanism of hepatotxicity induced by Fructus Psoraleae combined with UPLC-QTOF-MS and network toxicology technology / 国际药学研究杂志

Objective: To analyze and identify the chemical constituents from Fructus Psraleae(FP)in the rat liver after intragastric FP administration, and explore the potential mechanism of FP- induced hepatotoxicity via the network toxicology study. Methods: UPLC-QTOF-MS and UNIFI data screening platform were used to quickly identify the chemical constituents from FP in the rat liver afte intragastric FP administration, and multiple databases were used to search for information about chemical component targets, hepatotoxic targets, component hepatotoxic common targets and indirect targets. The construction of protein protein interaction (PPI)network and the enrichment analysis of gene ontology(GO)biological function and Kyoto Encycolpenia of Genes and Genomes (KEGG)pathway were carried out on the searched targets by using the String database and Cytoscape 3.6.1 software to explore the key targets and potential mechanism of hepatotoxicity induced by constituents from FP. Results: Eleven prototypic components of FP were identified in the rat liver. The network toxicology studies showed that there were a total of 52 potential targets and 23 pathways for the FP hepatotoxicity, among which ALB, HOMX1, GSR, GSTM3 and CYP2C9 targets, as well as the thyroid synthesis pathway and the glutathione metabolism pathway had a strong correlation with the FP hepatotoxicity. Conclusion: By UPLC-QTOF-MS combined with the UNIFI platform, the 11 chemical constituents from FP could be quickly identified in the liver of rats that were intragastrically administered FP, and the network toxicology study has predicted potential molecular mechanism of the hepatotoxicity induced by FP. The present results provide a reference for further study the hepatotoxicity of FP.

Mechanism of renal injury in rats induced by Phytolaccae Radix based on network toxicology / 中草药

Objective: Based on the strategy of network toxicology, the potential mechanism of renal injury in rats induced by Phytolaccae Radix was preliminarily explored. Methods: Firstly, by consulting the online database and mining the text, the chemical composition library of Phytolaccae Radix was established. The reverse molecular docking technology based on pharmacophores was performed to predict the relevant targets of chemical components and the target of nephrotoxicity induced by Phytolaccae Radix was obtained by intersecting with the target of nephrotoxicity. Potential substance basis of nephrotoxicity induced by Phytolaccae Radix was obtained by reverse analysis. Secondly, a large-scale protein-protein interactions were used to screen key targets, and key pathways for nephrotoxicity were analyzed by GO and KEGG biological annotation. Finally, a rat model of nephrotoxicity induced by esculentoside A was constructed and molecular biology methods were used to detect the expression of important targets in related pathways. Results: A total of 56 chemical components and 148 potential targets were obtained through literatures and related databases. Among them, 38 components, 34 targets, and 93 pathways were closely related to the generation of nephrotoxicity, mainly involving TNF signaling pathway, calcium signaling pathway, NF-κB signaling pathway, and VEGF signaling, thus participating in the beginning and end of nephrotoxicity events. Pathological results showed that the kidney tissues of rats were damaged to varying degrees after 7 d of treatment with esculentoside A. Western blot showed that the expression of IκBα was down-regulated (P < 0.01) and the expression of p-IκBα was up-regulated (P < 0.05). Quantitative detection of TNF-α and IL-1β by ELISA showed that both expressions were up-regulated (P < 0.05). Conclusion: Network toxicology can be used to preliminarily screen potential toxic substances. Esculentoside A based on network toxicology screening can induce nephrotoxicity in rats. Its molecular mechanism is related to activation of NF-κB signaling pathway and overexpression of inflammatory factors.

Prediction of quality markers of traditional Chinese medicines based on network pharmacology / 中草药·英文版

Network pharmacology is a powerful tool to reflect the pharmacologically active effects, mechanism of action and toxic activity of traditional Chinese medicines (TCMs). The ingredients of TCMs, associated with quality control of TCM products, are those fundamental chemicals that exhibit biological activities. A great amount of effort has been made by scientists in that field in order to improve the quality of TCMs, though the approaches to determine their quality and the TCM theory and compatibility rules remain ambiguous. Now some methods and technologies must be applied to predict and explore the quality marker (Q-marker) for quality control, as well as to clarify the factors affecting the quality of TCM, which may give new insight into rational ground of establishment of appropriate quality control and assessment system. In this review paper, authors focus on the prediction of quality markers of TCMs by network pharmacology based on three aspects: (1) from network medicine to network pharmacology, (2) complex network system of traditional Chinese medicine, and (3) predicting TCM quality markers based on network pharmacology. Authors proposed the research pattern on network pharmacology based on biological and medical networks, and further TCM network pharmacology based on substantial basis of TCM formulae, and the idea of “effect-ingredient-target-fingerprint” to predict and recognize the TCM Q-marker was the ultimate goal. In addition, authors yet noted how to make full use of the advantages of network toxicology to provide new ideas for the toxicity study of complex TCM systems and the prediction of TCM toxicity markers.

Network toxicology and LC-MS-based metabolomics: New approaches for mechanism of action of toxic components in traditional Chinese medicines / 中草药·英文版

Network toxicology combined with metabonomics is of great significance for the study of the toxic mechanism and prediction of toxicity of traditional Chinese medicines (TCMs). In this study, we reviewed the application of network toxicology based on LC-MS metabolomics, mainly in the study of toxic components and the toxicity mechanism of TCMs, which provides new ideas and methods for the further study of the toxicity mechanism of TCMs.

Toxicology of Asari Radix et Rhizoma Based on Network Analysis / 中国实验方剂学杂志

Objective:To analyze the known mechanism of toxicology and predict the unknown toxicity in Asari Radix et Rhizoma sinensis by establishing the network relationship of compound, protein, gene and toxicant reaction. Method:After comparing the Asari Radix et Rhizoma candidate compounds obtained from the traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP) database and the toxicological information obtained from the Comparative Toxicogenomics Database(CTD) database, we screened out 13 toxic components from Asari Radix et Rhizoma. And use the Pharm Mapper Server website to find the detailed information of target proteins of the 13 components. The network structure of these 13 chemical components and their corresponding target proteins were drawn by using Cytospace software, and several target proteins with the highest degree of association were found. ClueGO+CluePedia plug-in of Cytospace software was applied in gene ontology(GO) enrichment analysis of genes and kyoto encyclopedia of genes and genomes(KEGG) pathway enrichment analysis, so as to determine the pathways through which toxic substances in Asari Radix et Rhizoma might be harmful to human body. Result:The toxic substances in Asari Radix et Rhizoma may induce tumor and cancer formation through p53 signaling pathway, interleukin(IL)-17 signaling pathway, nuclear factor(NF)-kappa B signaling pathway, tumor necrosis factor(TNF)-signaling pathway. Asari Radix et Rhizoma could inhibit the central nervous system by regulating apoptosis pathways and neurons, and may also cause other autoimmune diseases by IL-17, TNF-α pathway and apoptosis regulation. Conclusion:This study preliminarily explores related mechanisms of toxicity of Asari Radix et Rhizoma,this method can be used to predict toxicity and explain toxicity mechanism of traditional Chinese medicine.

Cardiotoxicity of Aconiti Kusnezoffii Radix Based on Network Toxicology / 中国实验方剂学杂志

Objective:The mechanism of action of cardiac toxicity of Radix Aconiti Agrestis was explored by establishing the active components-targets network of Radix Aconiti Agrestis, protein interaction network, the biological function and pathway network of targets, and using molecular docking technology. Methods:The Traditional Chinese Medicine Systems Pharmacology(TCMSP) database and the Comparative Toxicogenomics Database(CTD) were used to filtrate the toxic candidates of Radix Aconiti Agrestis. Predicting the functional targets of toxic candidates of Radix Aconiti Agrestis by PharmMapper and compared with the cardiac related gene proteins found in the human gene database (GeneCards), and the overlapping proteins were selected as potential cardiac toxicity targets of Radix Aconiti Agrestis. The Cytoscape software was used to construct the network between toxic candidate components and targets. The protein interaction network was mapped by the String database combined with Cytoscape software. The biological functions of the targets and the involved pathways were analyzed with the DAVID platform.The binding of the key proteins with certain toxic candidate components of Radix Aconiti Agrestis was verified by Discover Studio software finally. Results:There were six candidates for toxic ingredients, which involving 27 cardiac toxicity targets. Network analysis results show that the targets were mainly by participating in the heart of phosphorus metabolism, regulation and other related phosphorus metabolism and regulation of phosphorylation and FKBP1A,TGF4-β2, INSR targets to have an important impact on the metabolism,development and form of the heart,and further to have cardiac toxicity. Conclusion:Based on the characteristics of the multi-component, multi-target and multi-pathway of traditional Chinese medicine, the mechanism of cardiac toxicity of Radix Aconiti Agrestis was explored and its possible toxicity was predicted, which provided a new idea and method for further research on the mechanism of cardiac toxicity of Radix Aconiti Agrestis.

Research and application of hepatotoxicity evaluation technique of traditional Chinese medicine / 中国中药杂志

The safety of traditional Chinese medicine (TCM) has received the widespread attention in recent years. Hepatotoxicity of TCM is one of the key problems of the safety of TCM. This article summarized research progress and application prospect in the mechanism of TCM hepatotoxicity, biomarkers, toxic omics database, prevention of hepatotoxicity of the liver cell lines, subcellular fraction, three-dimensional cultivation models, the model animals, aiming to provide theoretical basis for TCM toxicity evaluation and technical guidelines, thus promoting the development of TCM toxicity studies. Hope for Chinese medicine liver toxicity evaluation method provides the theoretical foundation and technical guidelines, promote the development and improvement of TCM liver toxicity research system.

Development and Application of Network Toxicology in Safety Research of Chinese Materia Medica / 中草药·英文版

Network toxicology that is an important branch of the network pharmacology emerges on the basis of network biology. It refers to study on the toxicological features of a constructed network model which is used to analyze toxic substances and their interaction and regulation in biological systems, particularly investigate the toxic effects of drugs and/or compatibility of medicines on body, and clarify the mechanism of toxicity. Network toxicology currently develops rapidly in safety prediction of Chinese materia medica (CMM). The application of network toxicology to safety and toxicology study on CMM is extremely beneficial to identify the toxic components and potential incompatibility of CMM. Since CMM is a complex system with multi-components, multi-targets, and multi-interactions, the network toxicology in safety prediction of CMM faces three great challenges, including integration studies of bioinformatics, innovation of methods, and tools and risk assessment in future development of the network toxicology in CMM research. In this paper, relevant database, approaches and tools that network toxicology utilized in the safety study of CMM were carefully reviewed. Based on the progress made, the scientific development and modernization of CMM will be greatly enhanced.

Network Pharmacology for Traditional Chinese Medicine Research: Methodologies and Applications / 中草药·英文版

The inception of network pharmacology comes from the advance in "multi-target, multi-drug" paradigm and opens up a new field for pharmaceutical science. Traditional Chinese medicine (TCM) is well-known for its use of medicinal herb combinations to treat the functional disorders induced by diseases through a holistic view, which naturally followed the principal of network pharmacology. In this review, the methodologies of network pharmacology in TCM studies were summarized. Specifically, the methodologies for network construction and network analysis were discussed in detail by following several TCM study cases. The perspectives for TCM network pharmacology were also provided.