Network pharmacology study on the mechanism of traditional Chinese medicine for upper respiratory tract infection

A structural similarity networking assisted collision cross-section prediction interval filtering strategy for multi-compound identification of complex matrix by ion-mobility mass spectrometry

Ion mobility coupled with mass spectrometry (IM-MS), an emerging technology for analysis of complex matrix, has been facing challenges due to the complexities of chemical structures and original data, as well as low-efficiency and error-proneness of manual operations. In this study, we developed a structural similarity networking assisted collision cross-section prediction interval filtering (SSN-CCSPIF) strategy. We first carried out a structural similarity networking (SSN) based on Tanimoto similarities among Morgan fingerprints to classify the authentic compounds potentially existing in complex matrix. By performing automatic regressive prediction statistics on mass-to-charge ratios (m/z) and collision cross-sections (CCS) with a self-built Python software, we explored the IM-MS feature trendlines, established filtering intervals and filtered potential compounds for each SSN classification. Chemical structures of all filtered compounds were further characterized by interpreting their multidimensional IM-MS data. To evaluate the applicability of SSN-CCSPIF, we selected Ginkgo biloba extract and dripping pills. The SSN-CCSPIF subtracted more background interferences (43.24%∼43.92%) than other similar strategies with conventional ClassyFire criteria (10.71%∼12.13%) or without compound classification (35.73%∼36.63%). Totally, 229 compounds, including eight potential new compounds, were characterized. Among them, seven isomeric pairs were discriminated with the integration of IM-separation. Using SSN-CCSPIF, we can achieve high-efficient analysis of complex IM-MS data and comprehensive chemical profiling of complex matrix to reveal their material basis.

Chemical profiling and mechanistic studies of Zhi-Shang-Feng granules against influenza virus by high-performance liquid chromatography coupled with Q exactive focus hybrid quadrupole orbitrap high-resolution mass spectrometry in combination with network pharmacology analysis

Zhi-Shang-Feng Granules are used in the clinical treatment of influenza to relieve headaches, chills and fever, bronchitis, nasal congestion, neuralgia and other symptoms. To decipher the components responsible for therapeutic effects of Zhi-Shang-Feng g ranules against influenza virus, an analytical method based on high-performance liquid chromatography coupled with Q exactive focus hybrid quadrupole orbitrap high resolution mass spectrometry was developed and the chemical profile of Zhi-Shang-Feng granules was characterized. Then, the identified components were used to conduct network pharmacological analysis and determine the potential mechanism of Zhi-Shang-Feng Granules. As a result, 177 compounds were putatively identified through comprehensive analysis by liquid chromatography coupled with high-resolution mass spectrometry, of which 23 compounds were unambiguously confirmed with reference standards. Components in Zhi-Shang-Feng Granules were found to specifically act on different enzymes, G-protein-coupled receptors, ion channels and transporters in the immune, endocrine, nervous, and circulatory systems. The potential mechanism was related to several biological processes, including cell growth and death, pattern recognition receptor signalling, signalling by interleukins, and lipid metabolism. The combination of chemical profile characterization and network construction provided useful insight into the overall chemical composition of Zhi-Shang-Feng granules and revealed their potential anti-infection, anti-inflammatory and immunoregulatory mechanisms against influenza virus infected disease.

Combination of bioaffinity ultrafiltration-UFLC-ESI-Q/TOF-MS/MS, in silico docking and multiple complex networks to explore antitumor mechanism of topoisomerase I inhibitors from Artemisiae Scopariae Herba

BACKGROUND

Artemisiae Scopariae Herba (ASH) has been widely used as plant medicine in East Asia with remarkable antitumor activity. However, the underlying mechanisms have not been fully elucidated.

METHODS

This study aimed to construct a multi-disciplinary approach to screen topoisomerase I (topo I) inhibitors from ASH extract, and explore the antitumor mechanisms. Bioaffinity ultrafiltration-UFLC-ESI-Q/TOF-MS/MS was used to identify chemical constitution of ASH extract as well as the topo I inhibitors, and in silico docking coupled with multiple complex networks was applied to interpret the molecular mechanisms.

RESULTS

Crude ASH extract exhibited toxicogenetic and antiproliferative activities on A549 cells. A series of 34 ingredients were identified from the extract, and 6 compounds were screened as potential topo I inhibitors. Docking results showed that the formation of hydrogen bond and π-π stacking contributed most to their binding with topo I. Interrelationships among the 6 compounds, related targets and pathways were analyzed by multiple complex networks model. These networks displayed power-law degree distribution and small-world property. Statistical analysis indicated that isorhamnetin and quercetin were main active ingredients, and that chemical carcinogenesis-reactive oxygen species was the critical pathway. Electrophoretic results showed a therapeutic effect of ASH extract on the conversion of supercoiled DNA to relaxed forms, as well as potential synergistic effect of isorhamnetin and quercetin.

CONCLUSIONS

The results improved current understanding of Artemisiae Scopariae Herba on the treatment of tumor. Moreover, the combination of multi-disciplinary methods provided a new strategy for the study of bioactive constituents in medicinal plants.

Metabolomics analyses of traditional Chinese medicine formula Shuang Huang Lian by UHPLC-QTOF-MS/MS

Background

Shuang Huang Lian (SHL) is a traditional Chinese medicine (TCM) formula made from Lonicerae Japonicae Flos, Forsythiae Fructus, and Scutellariae Radix. Despite the widespread use of SHL in clinical practice for treating upper respiratory tract infections (URTIs), the complete component fingerprint and the pharmacologically active components in the SHL formula remain unclear. The objective of this study was to develop an untargeted metabolomics method for component identification, quantitation, pattern recognition, and cross-comparison of various SHL preparation forms (i.e., granule, oral liquid, and tablet).

Methods

Ultra-high-performance liquid chromatography and quadrupole time-of-flight tandem mass spectrometry (UHPLC-QTOF-MS/MS) together with bioinformatics were used for chemical profiling, identification, and quantitation of SHL. Multivariate data analyses such as principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were performed to assess the correlations among the three SHL preparation forms and the reproducibility of the technical and biological replicates.

Results

A UHPLC-QTOF-MS/MS-based untargeted metabolomics method was developed and applied to analyze three SHL preparation forms, consisting of 178 to 216 molecular features. Among the 95 common molecular features from the three SHL preparation forms, quantitative analysis was performed using a single exogenous reference internal standard. Forty-seven of the 95 common molecular features have been identified using various databases. Among the 47 common components, there were 17 flavonoids, 7 oligopeptides, 5 terpenoids, 2 glycosides, 2 cyclohexanecarboxylic acids, 2 spiro compounds, 2 lipids, 2 glycosylglycerol derivatives, and 8 various compounds such as alkyl caffeate ester, aromatic ketone, benzaldehyde, benzodioxole, benzofuran, chalcone, hydroxycoumarin, and purine nucleoside. Five of the 47 common components were designated by the Chinese Pharmacopoeia as the quality markers of medicinal plants of SHL, and 15 were previously reported to have pharmacological activities. Distinct patterns of the three SHL preparation forms were observed in the PCA and PLS-DA plots.

Conclusions

The developed method is reliable and reproducible, which is useful for the profiling, component identification, quantitation, quality assessment of various SHL preparation forms and may apply to the analysis of other TCM formulas.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13020-022-00610-x.

A network pharmacology study to investigate bioactive compounds and signaling pathways of garlic (Allium sativum L.) husk against type 2 diabetes mellitus

During garlic harvest, much husk has been generated, nearly all husk is discarded as unnecessary by-products. However, in Korean folk remedies, Allium sativum L. husk (ASLH) extracts have been used as a reliever against type 2 diabetes mellitus (T2DM). Currently, its significant mechanisms against T2DM remain unclear. Thus, the aim of this study is to investigate the characteristics of its key signaling pathways, targets, and compounds. The compounds in ASLH were analyzed by gas chromatography-mass spectrum (GC-MS) and confirmed drug-like compounds (DLCs) in silico. Then, protein-protein interaction (PPI) networks and signaling pathways, targets, compounds are constructed, visualized by using RStudio. Finally, we performed a molecular docking test (MDT) to identify the key mechanism(s), target(s), and compound(s) of ASLH on T2DM. A total of 23 compounds in ASLH were identified by GC-MS, and all compounds were accepted by Lipinski's rule. The 23 compounds were associated with 521 targets and retrieved 4,736 T2DM-related targets by Online Mendelian Inheritance in Man (OMIM) and DisGeNET. The final overlapping 87 targets were obtained between compounds-targets and T2DM-related targets. The number of 13 signaling pathways, 33 targets, and 19 compounds of ASLH were associated with T2DM. In parallel, MDT revealed four potential compounds: (1) 9-hexacosene, (2) 2-(([2-ethylhexyl]oxy)carbonyl)benzoic acid, (3) clionasterol, (4) 4-methyl-2-phenylpyrimidine on PPAR signaling pathway. Overall, the four compounds from ASLH might show an anti-T2DM synergistic effect by activating the PPAR signaling pathway or inactivating the phospholipase D signaling pathway. In this study, we suggest that ASLH might be considered a health-promising resource from both nutraceutical and pharmaceutical perspectives. PRACTICAL APPLICATIONS: Allium sativum L. husk (ASLH) has been regarded as wastes that come from garlic (Allium sativum L.). During the harvesting period of garlic, a considerable amount of ASLH is a severe problem in farm communities. Particularly, garlic bioactive compounds are well documented including organosulfur compounds. Conversely, at present, no information is available on chemical compounds of ASLH to use in health industries. Taking this matter into consideration, our analysis approach was to select drug-like compounds (DLCs) from ASLH via GC-MS, thereby we can explore the compounds with high cell permeability. The screened compounds can be used as nutraceutical or medicinal or even cosmetical resources. In this study, we described the significant compounds via the network pharmacology concept to uncover the pharmaceutical mechanism(s) of ASLH against T2DM. Eventually, this work provides nutraceutical or medicinal value of ASLH and suggests that ASLH might be used as an upcycling resource to relieve T2DM.

Bioactivity assessment of essential oils of Cymbopogon species using a network pharmacology approach

Essential oils of Cymbopogon species have wide commercial applications in fragrance, perfumery, and pharmaceuticals as they exhibit a horizon of bioactivities. Here, essential oils of C. flexuosus and C. martinii were analysed to identify bioactive constituents and bioactivities using a network pharmacology approach. Essential oils were isolated using hydro-distillation in a mini Clevenger apparatus. Analysis of essential oils by GC-MS revealed 20 and 15 chemical constituents in C. flexuosus and C. martinii, respectively. An ingredient-target protein-pathway network was constructed comprising 10 oil constituents (citral, geraniol, geranyl acetate, limonene, linalool, α-terpineol, borneol, α-pinene, myrcene, and n-decanol), 14 target proteins, 51 related pathways, and 108 connections. Analyses of the network showed geraniol, geranyl acetate, limonene, linalool, and citral as major active constituents. A core sub-network constructed from the ingredient-target protein-pathway network revealed bioactivities including anti-cancer, anti-inflammatory and neuroprotective. The protein association network pointed out the major target proteins viz., THRB, FXR, ALOX15, and TSHR and pathways like metabolic, and neuroactive ligand-receptor interaction pathways of essential oil constituents. The target proteins and pathways provided insights into the mechanism of action of bioactive constituents. Based on the results of the study, geraniol was correlated with neuroprotective, citral to chemo-preventive, and limonene to anti-inflammatory activities. Thus, the study offers a new way for the assessment of the bioactivities of Cymbopogon species essential oils leading to the development of new biomedicines.

Study on the Mechanism of Liuwei Dihuang Pills in Treating Parkinson's Disease Based on Network Pharmacology

Background

Parkinson's disease (PD) is a common neurodegenerative disease in middle-aged and elderly people. Liuwei Dihuang (LWDH) pills have a good effect on PD, but its mechanism remains unclear. Network pharmacology is the result of integrating basic theories and research methods of medicine, biology, computer science, bioinformatics, and other disciplines, which can systematically and comprehensively reflect the mechanism of drug intervention in disease networks.

Methods

The main components and targets of herbs in LWDH pills were obtained through Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Its active components were screened based on absorption, distribution, metabolism, and excretion (ADME); the PD-related targets were obtained from the Genecards, OMIM, TTD, and DRUGBANK databases. We used R to take the intersection of LWDH- and PD-related targets and Cytoscape software to construct the drug-component-target network. Moreover, STRING and Cytoscape software was used to analyze protein-protein interactions (PPI), construct a PPI network, and explore potential protein functional modules in the network. The Metascape platform was used to perform KEGG pathway and GO function enrichment analyses. Finally, molecular docking was performed to verify whether the compound and target have good binding activity.

Results

After screening and deduplication, 210 effective active ingredients, 204 drug targets, 4333 disease targets, and 162 drug-disease targets were obtained. We consequently constructed a drug-component-targets network and a PPI-drug-disease-targets network. The results showed that the hub components of LWDH pills were quercetin, stigmasterol, kaempferol, and beta-sitosterol; the hub targets were AKT1, VEGFA, and IL6. GO and KEGG enrichment analyses showed that these targets are involved in neuronal death, G protein-coupled amine receptor activity, reactive oxygen species metabolic processes, membrane rafts, MAPK signaling pathways, cellular senescence, and other biological processes. Molecular docking showed that the hub components were in good agreement with the hub targets.

Conclusion

LWDH pills have implications for the treatment of PD since they contain several active components, target multiple ligands, and activate various pathways. The hub components possibly include quercetin, stigmasterol, kaempferol, and beta-sitosterol and act through pairing with hub targets, such as AKT1, VEGFA, and IL6, to regulate neuronal death, G protein-coupled amine receptor activity, reactive oxygen species metabolic process, membrane raft, MAPK signaling pathway, and cellular senescence for the treatment of PD.

Phytomolecules Repurposed as Covid-19 Inhibitors: Opportunity and Challenges

The SARS-CoV-2 virus has spread worldwide to cause a full blown pandemic since 2020. To date, several promising synthetic therapeutics are repurposed and vaccines through different stages of clinical trials were approved and being administered, but still the efficacy of the drugs and vaccines are yet to be decoded. This article highlights the importance of traditional medicinal plants and the phytomolecules derived from them, which possess in vitro antiviral and anti-CoV properties and further explores their potential as inhibitors to molecular targets of SARS-CoV-2 that were evaluated by in silico approaches. Botanicals in traditional medicinal systems have been investigated for anti-SARS-CoV-2 activity through in silico and in vitro studies. However, information linking structure of phytomolecules to their antiviral activity is limited. Most phytomolecules with anti-CoV activity were studied for inhibition of the human ACE2 receptor through which the virus enters host cells, and non-structural proteins 3CLpro and PLpro. Although the proteases are ideal anti-CoV targets, information on plant-based inhibitors for the CoV structural proteins, e.g., spike, envelope, membrane, nucleocapsid required further investigations. In absence of scientific evaluations through in vitro and biocompatibility studies, plant-based antivirals fall short as treatment options. Plant-based anti-SARS-CoV-2 therapeutics can be promising alternatives to their synthetic counterparts as they are economical and bear fewer chances of toxicity, side effects, and viral resistance. Our review could provide a systematic overview of the potential phytomolecules which can be repurposed and subjected to further modes of experimental evaluation to qualify for use in treatment and prophylaxis of SARS-CoV-2 infections.

In Silico Molecular Docking and Interaction Analysis of Traditional Chinese Medicines Against SARS-CoV-2 Receptor

The novel coronavirus, 2019-nCoV, has led to a major pandemic in 2020 and is responsible for more than 2.9 million officially recorded deaths worldwide. As well as synthetic anti-viral drugs, there is also a need to explore natural herbal remedies. The Traditional Chinese Medicines (TCMs) system has been used for thousands of years for the prevention, diagnosis, and treatment of several chronic diseases. In this paper, we performed an in silico molecular docking and interaction analysis of TCMs against SARS-CoV-2 receptor RNA-dependent RNA polymerase (RdRp). We obtained the 5 most effective plant compounds which had a better binding affinity towards the target receptor protein. These compounds areforsythoside A, rutin, ginkgolide C, icariside II, and nolinospiroside E. The top-ranked compound, based on docking score, was nolinospiroside, a glycoside found in Ophiopogon japonicas that has antioxidant properties. Protein-ligand interaction analysis discerned that nolinospiroside formed a strong bond between ARG 349 of the protein receptor and the carboxylate group of the ligand, forming a stable complex. Hence, nolinospiroside could be deployed as a lead compound against SARS-CoV-2 infection that can be further investigated for its potential benefits in curbing the viral infection.

Assessing the Anti-inflammatory Mechanism of Reduning Injection by Network Pharmacology

Reduning Injection (RDNI) is a traditional Chinese medicine formula indicated for the treatment of inflammatory diseases. However, the molecular mechanism of RDNI is unclear. The information of RDNI ingredients was collected from previous studies. Targets of them were obtained by data mining and molecular docking. The information of targets and related pathways was collected in UniProt and KEGG. Networks were constructed and analyzed by Cytoscape to identify key compounds, targets, and pathways. Data mining and molecular docking identified 11 compounds, 84 targets, and 201 pathways that are related to the anti-inflammatory activity of RDNI. Network analysis identified two key compounds (caffeic acid and ferulic acid), five key targets (Bcl-2, eNOS, PTGS2, PPARA, and MMPs), and four key pathways (estrogen signaling pathway, PI3K-AKT signaling pathway, cGMP-PKG signaling pathway, and calcium signaling pathway) which would play critical roles in the treatment of inflammatory diseases by RDNI. The cross-talks among pathways provided a deeper understanding of anti-inflammatory effect of RDNI. RDNI is capable of regulating multiple biological processes and treating inflammation at a systems level. Network pharmacology is a practical approach to explore the therapeutic mechanism of TCM for complex disease.

Effects and safety of tanreqing injection on viral pneumonia: A protocol for systematic review and meta-analysis

BACKGROUND

Viral pneumonia is a common respiratory disease that leads to high mortality around the world. Tanreqing (TRQ) injection has been widely used to treat viral pneumonia in China. However, the efficiency and safety of TRQ injection for viral pneumonia have not been scientifically and methodically evaluated up to now. Thus, this protocol describes a plan of performing a systematic review and meta-analysis to evaluate the efficacy and safety of TRQ injection on patients with viral pneumonia.

METHODS

Only randomized controlled trials will be enrolled in our study, and we will search eligible studies in the following electronic databases: PubMed, Embase, Cochrane Central Register of Controlled Trials, Clinical Trials, China National Knowledge Infrastructure, the Wanfang database, the Chinese Scientific Journal Database, and the Sinomed. The total effective rate of clinical efficacy will be used as primary outcome. Time to relieve symptoms, incidence of adverse reactions, and the laboratory parameters will be used as secondary outcomes. Any side effects and adverse events will be recorded and assessed as safety outcomes. Study inclusion, data extraction, and quality assessment will be performed independently by 2 reviewers, and any disagreement will be resolved by a third reviewer. After that, data synthesis and subgroup analysis will be conducted with the Review Manager V.5.3.3 software.

RESULTS

This review will provide a high-quality synthesis to assess the effectiveness and safety of TRQ injection for viral pneumonia patients.

CONCLUSION

Our study will provide comprehensive evidence to decide whether TRQ injection is effective and safe for viral pneumonia patients.

PROSPERO REGISTRATION NUMBER

PROSPERO CRD42020164164.

The Role of Periplaneta americana (Blattodea: Blattidae) in Modern Versus Traditional Chinese Medicine

The purpose of this review is to elaborate the role of Periplaneta (P.) americana L. in modern and traditional Chinese medicine (TCM) and compare the use of the species in these two forms of medical treatments. From searches on Google Scholar, PubMed, and Web of Science databases, studies were identified involving TCMs with P. americana, which have a history of use over several thousand years, and demonstrate how extracts from this insect play a role in the treatment of diseases through antibacterial, antiviral, antitumor activity, and enhancement of immune function. Extracts from P. americana have not been fully developed for clinical use because the active components have not been completely purified or their molecular mechanisms thoroughly understood. The development of extraction technology in modern Chinese medicine has revealed that many extracts from P. americana are able to play an important role in the control of diseases such as cancer. Drugs such as 'Kangfuxin Solution' and 'Xinmailong Injection' are now widely used for gastrointestinal ulcers and chronic heart failure, having achieved beneficial curative effects in clinical studies. Based on this, the information from studies of P. americana in TCM and modern medicine should be combined and their respective advantages applied. This review provides an overview of the role of P. americana in modern and TCM and thus contributes to identification of further applications and area requiring drug development.

A systematic analysis of natural α-glucosidase inhibitors from flavonoids of Radix scutellariae using ultrafiltration UPLC-TripleTOF-MS/MS and network pharmacology

BACKGROUND

Flavonoids from plant medicines are supposed to be viable alternatives for the treatment of type 2 diabetes (T2D) as less toxicity and side effects. Radix scutellariae (RS) is a widely used traditional medicine in Asia. It has shown great potential in the research of T2D. However, the pharmacological actions remain obscured due to the complex chemical nature of plant medicines.

METHODS

In the present study, a systematic method combining ultrafiltration UPLC-TripleTOF-MS/MS and network pharmacology was developed to screen α-glucosidase inhibitors from flavonoids of RS, and explore the underlying mechanism for the treatment of T2D.

RESULTS

The n-butanol part of ethanol extract from RS showed a strong α-glucosidase inhibition activity (90.55%, IC50 0.551 mg/mL) against positive control acarbose (90.59%, IC50 1.079 mg/mL). A total of 32 kinds of flavonoids were identified from the extract, and their ESI-MS/MS behaviors were elucidated. Thirteen compounds were screened as α-glucosidase inhibitors, including viscidulin III, 2',3,5,6',7-pentahydroxyflavanone, and so on. A compound-target-pathway (CTP) network was constructed by integrating these α-glucosidase inhibitors, target proteins, and related pathways. This network exhibited an uneven distribution and approximate scale-free property. Chrysin (k = 87), 5,8,2'-trihydroxy-7-methoxyflavone (k = 21) and wogonin (k = 20) were selected as the main active constituents with much higher degree values. A protein-protein interaction (PPI) weighted network was built for target proteins of these α-glucosidase inhibitors and drug targets of T2D. PPARG (Cd = 0.165, Cb = 0.232, Cc = 0.401), ACACB (Cd = 0.155, Cb = 0.184, Cc = 0.318), NFKB1 (Cd = 0.233, Cb = 0.161, Cc = 0.431), and PGH2 (Cd = 0.194, Cb = 0.157, Cc = 0.427) exhibited as key targets with the highest scores of centrality indices. Furthermore, a core subnetwork was extracted from the CTP and PPI weighted network. Type II diabetes mellitus (hsa04930) and PPAR signaling pathway (hsa03320) were confirmed as the critical pathways.

CONCLUSIONS

These results improved current understanding of natural flavonoids on the treatment of T2D. The combination of ultrafiltration UPLC-TripleTOF-MS/MS and network pharmacology provides a novel strategy for the research of plant medicines and complex diseases.

Omics strategies decipher therapeutic discoveries of traditional Chinese medicine against different diseases at multiple layers molecular-level

Traditional Chinese medicine (TCM) has been broadly used for the personalized treatment of many diseases in China for thousands of years. In the past century, TCM was also introduced to other Asian countries and even the Western world. Increasing evidence has shown that TCM has the capacity to treat numerous complex diseases in the clinic, such as cardiovascular diseases (CVDs), infectious diseases, metabolic diseases, and neurodegenerative diseases. However, the earlier lack of analytical strategies to annotate the chemical complexity has severely impeded the modern study and translational application of TCM. This critical review aims to explore and exploit applications of systems biology-driven omics methods in TCM against a diversity of diseases, toward the specific use of TCM to treat patients with different diseases. Such effort shall enhance the applicability of systems biology-driven omics strategies in deciphering the mechanisms by which TCM treats different diseases and may lead to the discovery of new therapeutic directions. In addition, we proposed the possible strategies to innovate the applicable pattern of omics technologies in TCM niches, such as precision-modification metabolomics and chinmedomics methods, allowing to unveil the complexity of TCM, which must enable TCM to serve better for the population-health. Taken together, this review eventually shall highlight the core value of omics technologies in innovating TCM to combat the diseases in a new horizon.

Network Pharmacology Reveals the Molecular Mechanism of Cuyuxunxi Prescription in Promoting Wound Healing in Patients with Anal Fistula

Background

The healing process of the surgical wound of anal fistulotomy is much slower because of the presence of stool within the wound. Cuyuxunxi (CYXX) prescription is a Chinese herbal fumigant that is being used to wash surgical wound after anal fistulotomy. This study aimed at investigating the molecular mechanism of CYXX prescription using a network pharmacology-based strategy.

Materials and Methods

The active compounds in each herbal medicine were retrieved from the traditional Chinese medicine systems pharmacology (TCMSP) database and in Traditional Chinese Medicine Integrated Database (TCMID) analysis platform based on the criteria of oral bioavailability ≥40% and drug-likeness ≥0.2. The disease-related target genes were extracted from the Comparative Toxicogenomics Database. Protein-protein interaction network was built for the overlapped genes as well as functional enrichment analysis. Finally, an ingredient-target genes-pathway network was built by integrating all information.

Results

A total of 375 chemical ingredients of the 5 main herbal medicines in CYXX prescription were retrieved from TCMSP database and TCMID. Among the 375 chemical ingredients, 59 were active compounds. Besides, 325 target genes for 16 active compounds in 3 herbal medicines were obtained. Functional enrichment analysis revealed that these overlapped genes were significantly related with immune response, biosynthesis of antibiotics, and complement and coagulation cascades. A comprehensive network which contains 133 nodes (8 disease nodes, 3 drug nodes, 8 ingredients, 103 target gene nodes, 7 GO nodes, and 4 pathway nodes) was built.

Conclusion

The network built in this study might aid in understanding the action mechanism of CYXX prescription at molecular level to pathway level.

Network pharmacology-based analysis on bioactive anti-diabetic compounds in Potentilla discolor bunge

ETHNOPHARMACOLOGICAL RELEVANCE

Potentilla discolor Bunge (PDB) is a commonly used herbal for alleviating diabetes mellitus and its complications. Although accumulating evidences show the anti-diabetic efficacy of PDB, the vital anti-diabetic compounds and their functional targets remain elusive.

AIM OF THE STUDY

To investigate the anti-diabetic ingredients and their functional mechanisms in PDB, gas chromatograph-mass spectrometry analysis was performed on PDB extract and 21 were testified as anti-diabetic compounds.

MATERIALS AND METHODS

Subsequently their potential protein targets were also identified. The bioinformatics analysis was implemented by network pharmacology-based approaches. STRING analysis was performed to reveal enrichment of these target proteins, protein-protein interactions, pathways and related diseases. Cytoscape was used to determine the potential protein targets for these components in PDB, indicating that 21 anti-diabetic compounds in PDB regulate 33 diabetes-related proteins in 28 signal pathways and involve 21 kinds of diabetes-related diseases. Among the 21 potential anti-diabetic components predicted by network analysis, tricetin was firstly experimentally validated at the molecular and cellular level.

RESULTS

Results indicated that this active small-molecule compound may have beneficial effects on improving glucose uptake.

CONCLUSIONS

We envisage that network analysis will be useful in screening bioactive compounds of medicinal plants.

A network pharmacology study on the triterpene saponins from Medicago sativa L. for the treatment of Neurodegenerative diseases

Neurodegenerative diseases (NDDs) are characterized by progressive and irreversible, is a kind of complex illnesses, and the long-term therapy which is frequently associated with adverse side effects. Medicago sativa L., widely consumed as a vegetable, has the effects of improving memory and relieving central nervous system diseases. However, there are less studies on its specific mechanism for NDDs. In this investigation, we applied a method of network pharmacology, which combined molecular docking and network analysis to decipher the mechanisms of M. sativa in NDDs. The pharmacological system generated 55 triterpene saponins from M. sativa, and predicted 27 potential targets with 100 pathways in the treatment of NDDs. As a result, 13 compounds, 10 target proteins, and 6 signaling pathways were found to play important roles in the treatment of NDDs. In addition, in vitro experiments of isolates confirmed activities for NDDs, which were consistent with the results of network pharmacology prediction. PRACTICAL APPLICATIONS: Medicago sativa L. has been widely consumed as a vegetable, which possesses many nutritional components. As a functional food stuff, M. sativa can improve human health, such as memory improving activities, relieving central nervous system diseases, immunomodulatory, antioxidant, anticancer, and anti-inflammatory. In this article, the mechanism of triterpene saponins from M. sativa against NDDs was successfully predicted by network pharmacology method. The results will serve as a reference of M. sativa against NDDs.

Qualitative and quantitative analysis of Porana sinensis Hemsl by UHPLC-Q-Exactive MS, TLC autographic method and DART-MS

INTRODUCTION

Erycibe obtusifolia and E. schmidtii are widely used in traditional Chinese medicine (TCM) to treat joint pain and rheumatoid arthritis. With the reduction of wild E. obtusifolia and E. schmidtii resources, Porana sinensis has been widely used as a substitute. However, few studies have been conducted on the chemical composition and quality control of P. sinensis.

OBJECTIVE

To clarify the chemical composition and improve the quality control of P. sinensis.

METHODOLOGY

We developed an ultra-high performance liquid chromatography electrospray ionisation Q-Exactive Focus tandem mass spectrometry (UHPLC-ESI-Q-Exactive Focus-MS/MS) method to characterise the chemical constituents of P. sinensis. A strategy based on a combination of high-performance thin-layer chromatography (HPTLC) and direct analysis in real-time (DART) ion source was proposed for the identification of alkaloid components in P. sinensis. Thin-layer chromatography (TLC) autography for 2,2'-diphenyl-1-picrylhydrazyl free radical (DPPH˙) and TLC bioautography for xanthine oxidase were used to rapidly screen marker compounds for high-performance liquid chromatography (HPLC) determination of P. sinensis. Based on the selected marker compounds, a HPLC method for the quantitative determination of eight marker compounds in P. sinensis was developed.

RESULTS

Eighteen compounds in P. sinensis were identified by UHPLC-Q-Exactive MS. Taken together with the results of TLC autography and TLC bioautography, eight compounds were chosen as marker compounds for HPLC determination of P. sinensis. The alkaloid components in P. sinensis were identified as Baogongteng A and Baogongteng C by DART-MS.

CONCLUSION

We systematically clarified the chemical composition of P. sinensis for the first time, and potentially improved its quality control. These results should promote the application of P. sinensis as a new resource for Caulis Erycibes.

Chinese herbal medicine for acute upper respiratory tract infections and reproductive safety: A systematic review

Acute upper respiratory tract infections (AURTIs) are common and self-limited in people with normal immunity but sometimes lead to poor clinical outcomes under specific conditions such as pregnancy if not treated appropriately. Chinese herbal medicines (CHM), which are widely used to treat AURTIs, have proven to be effective in preclinical and clinical studies. This review focuses on the bioactivities of typical CHM and the adverse reactions they cause, and especially issues with reproductive safety when treating AURTIs. The main mechanisms for clinical efficacy may include anti-viral, anti-bacterial, anti-inflammatory, antipyretic, and immunomodulatory action as indicated by preclinical evidence. Most clinical trials indicate that CHM shortens the natural course of AURTIs and that it relieves related symptoms such as a fever, headaches, coughing, myalgia, a cold, sore throat, and a nasal obstruction. However, some CHM have a range of adverse effects and potentially affect reproduction from endocrinal secretion to embryo development while others do not. Therefore, clinical adverse reactions and preclinical studies on the toxicity of CHM are discussed. More reliable evidence is required to conclude that CHM are efficacious and safe for pregnant women with AURTIs. This review should help to promote advances in the research on and development of CHM as alternative treatments for AURTIs and offer insight into strategies to manage the safety of CHM during clinical use.

Screening and analysis of key active constituents in Guanxinshutong capsule using mass spectrum and integrative network pharmacology

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.

New Contributions to Asarum Powder on Immunology Related Toxicity Effects in Lung

Objective. Asarum is widely used in clinical practice of Chinese medicine in the treatment of respiratory diseases. Many toxic ingredients (safrole, etc.) had been found in Asarum that show multiple visceral toxicities. In this study, we performed systematic investigation of expression profiles of genes to take a new insight into unclear mechanism of Asarum toxicities in lung. Methods. mRNAs were extracted from lungs of rats after intragastric administration with/without Asarum powders, and microarray assays were applied to investigate gene expression profiles. Differentially expressed genes with significance were selected to carry out GO analysis. Subsequently, quantitative PCRs were performed to verify the differential expression of Tmprss6, Prkag3, Nptx2, Antxr11, Klk11, Rag2, Olr77, Cd7, Il20, LOC69, C6, Ccl20, LOC68, and Cd163 in lung. Changes of Ampk, Bcl2, Caspase 3, Il1, Il20, Matriptase2, Nfκb, Nptx2, and Rag2 in the lung on protein level were verified by western blotting and immunohistochemistry. Results. Compared with control group, the estimated organ coefficients were relatively increased in Asarum group. Results of GO analysis showed that a group of immune related genes in lung were expressed abnormally. The result of PCRs showed that Ccl20 was downregulated rather than other upregulated genes in the Asarum group. Western blotting and immunohistochemistry images showed that Asarum can upregulate the expression of Ampk, Caspase 3, Il1, Il20, Matriptase2, Nfκb, and Rag2 and downregulate the expression of Bcl2 in lung. Conclusion. Our data suggest that expressions of immune related genes in lung were selectively altered by Asarum. Therefore, inflammatory response was active, by regulating Caspase 3, Il1, Il20, Matriptase2, Nfκb, Rag2, Tmprss6, Prkag3, Nptx2, Antxr1, Klk11, Olr77, Cd7, LOC69, C6, LOC68, Cd163, Ampk, Bcl2, and Ccl20. Our study indicated that inflammatory factors take effect in lung toxicity caused by Asarum, which provides a new insight into molecular mechanism of Asarum toxicities in lung.

Simultaneous determination of seven flavonoids, two phenolic acids and two cholesterines in Tanreqing injection by UHPLC-MS/MS

A new ultra-high performance liquid chromatography combined with triple quadrupole mass spectrometry was developed to evaluate the quality of Tanreqing injection. Seven flavonoids (Rutin, Baicalin, Scutellarin, Chrysin-7-O-Beta-d-glucoronide, Oroxylin A-7-O-β-d-glucoronide, Wogonin, Luteolin-7-O-glucoside), two phenolic acids (Chlorogenic acid, Caffeic acid) and two cholesterines (Ursodeoxycholic acid, Chenodeoxycholic acid) in Tanreqing injection could be measured simultaneously. For the determination of the eleven compounds, the conditions were set as follows: The mobile phase was a gradient of 0.1% aqueous formic acid solution (A) and acetonitrile (B); the flow rate was 0.2 mL min^-1, the column was Acquity UPLC HSS T3 column (2.1 mm × 100 mm, 1.8 μm); and the multiple-reaction monitoring (MRM) with a negative electro spray ionization interface (ESI-) was selected. Within the test ranges, all the standard regression curves showed excellent linear regression (r > 0.99). In terms of (relative standard deviation) RSDs, the precision, repeatability and stability of the eleven compounds were all lower than 3%. The recovery rates of Tanreqing injection and the RSD were 97.8-103.7% and 0.4%-2.0%, respectively. The RSD value was in accordance with the requirements of less than 3.0%. This method has been successfully used in the analysis of Tanreqing injection. In summary, a fast, accurate and reliable UPLC-ESI^--MS/MS method was successfully developed for the simultaneous detection of the eleven major active ingredients with different chemical structures in Tanreqing injection, and can be used for the quality control of Tanreqing injection as well.

Systems Pharmacology-Based Approach of Connecting Disease Genes in Genome-Wide Association Studies with Traditional Chinese Medicine

Traditional Chinese medicine (TCM) originated in ancient China has been practiced over thousands of years for treating various symptoms and diseases. However, the molecular mechanisms of TCM in treating these diseases remain unknown. In this study, we employ a systems pharmacology-based approach for connecting GWAS diseases with TCM for potential drug repurposing and repositioning. We studied 102 TCM components and their target genes by analyzing microarray gene expression experiments. We constructed disease-gene networks from 2558 GWAS studies. We applied a systems pharmacology approach to prioritize disease-target genes. Using this bioinformatics approach, we analyzed 14,713 GWAS disease-TCM-target gene pairs and identified 115 disease-gene pairs with q value < 0.2. We validated several of these GWAS disease-TCM-target gene pairs with literature evidence, demonstrating that this computational approach could reveal novel indications for TCM. We also develop TCM-Disease web application to facilitate the traditional Chinese medicine drug repurposing efforts. Systems pharmacology is a promising approach for connecting GWAS diseases with TCM for potential drug repurposing and repositioning. The computational approaches described in this study could be easily expandable to other disease-gene network analysis.

Approaches in studying the pharmacology of Chinese Medicine formulas: bottom-up, top-down-and meeting in the middle

Investigating the pharmacology is key to the modernization of Chinese Medicine (CM) formulas. However, identifying which are the active compound(s) of CM formulas, which biological entities they target, and through which signaling pathway(s) they act to modify disease symptoms, are still difficult tasks for researchers, even when equipped with an arsenal of advanced modern technologies. Multiple approaches, including network pharmacology, pharmaco-genomics, -proteomics, and -metabolomics, have been developed to study the pharmacology of CM formulas. They fall into two general categories in terms of how they tackle a problem: bottom-up and top-down. In this article, we compared these two different approaches in several dimensions by using the case of MaZiRenWan (MZRW, also known as Hemp Seed Pill), a CM herbal formula for functional constipation. Multiple hypotheses are easy to be proposed in the bottom-up approach (e.g. network pharmacology); but these hypotheses are usually false positives and hard to be tested. In contrast, it is hard to suggest hypotheses in the top-down approach (e.g. pharmacometabolomics); however, once a hypothesis is proposed, it is much easier to be tested. Merging of these two approaches could results in a powerful approach, which could be the new paradigm for the pharmacological study of CM formulas.

Analysis of the main active ingredients and bioactivities of essential oil from Osmanthus fragrans Var. thunbergii using a complex network approach

BACKGROUND

Osmanthus fragrans has been used as folk medicine for thousands of years. The extracts of Osmanthus fragrans flowers were reported to have various bioactivities including free radical scavenging, anti-inflammation, neuroprotection and antitumor effects. However, there is still lack of knowledge about its essential oil.

METHODS

In this work, we analyzed the chemical composition of the essential oil from Osmanthus fragrans var. thunbergii by GC-MS. A complex network approach was applied to investigate the interrelationships between the ingredients, target proteins, and related pathways for the essential oil. Statistical characteristics of the networks were further studied to explore the main active ingredients and potential bioactivities of O. fragrans var. thunbergii essential oil.

RESULTS

A total of 44 ingredients were selected from the chemical composition of O. fragrans var. thunbergii essential oil, and that 191 potential target proteins together with 70 pathways were collected for these compounds. An ingredient-target-pathway network was constructed based on these data and showed scale-free property as well as power-law degree distribution. Eugenol and geraniol were screened as main active ingredients with much higher degree values. Potential neuroprotective and anti-tumor effect of the essential oil were also found. A core subnetwork was extracted from the ingredient-target-pathway network, and indicated that eugenol and geraniol contributed most to the neuroprotection of this essential oil. Furthermore, a pathway-based protein association network was built and exhibited small-world property. MAPK1 and MAPK3 were considered as key proteins with highest scores of centrality indices, which might play an important role in the anti-tumor effect of the essential oil.

CONCLUSIONS

This work predicted the main active ingredients and bioactivities of O. fragrans var. thunbergii essential oil, which would benefit the development and utilization of Osmanthus fragrans flowers. The application of complex network theory was proved to be effective in bioactivities studies of essential oil. Moreover, it provides a novel strategy for exploring the molecular mechanisms of traditional medicines.

Guanxin Danshen Formulation Protects against Myocardial Ischemia Reperfusion Injury-Induced Left Ventricular Remodeling by Upregulating Estrogen Receptor β

Background: Guanxin Danshen formulation (GXDSF) is a traditional Chinese herbal recipe recorded in the Chinese Pharmacopeia since 1995 edition, which consists of Salviae miltiorrhizae Radix et Rhizoma, Notoginseng Radix et Rhizoma and Dalbergiae odoriferae Lignum. Our previous research suggested GXDSF had positive effect on cardiovascular disease. Therefore, the aim of this study was to elucidate the effects of GXDSF on myocardial ischemia reperfusion injury-induced left ventricular remodelling (MIRI-LVR). Methods: The effects of GXDSF on cardiac function were detected by haemodynamics and echocardiograms. The effects of GXDSF on biochemical parameters (AST, LDH and CK-MB) were analyzed. Histopathologic examinations were performed to evaluate the effect of GXDSF on cardiac structure. In addition, the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database was used to predict the main target of GXDSF. Target validation was conducted by using western blots and immunofluorescent double staining assays. Results: We found that +dp/dt and LVSP were significantly elevated in the GXDSF-treated groups compared with the MIRI-LVR model group. Left ventricular ejection fraction (LVEF) and left ventricular fractional shortening (LVFS) were increased in the GXDSF-treated groups compared with the model group. All biochemical parameters (AST, LDH and CK-MB) were considerably decreased in the GXDSF-treated groups compared with the model group. Fibrosis parameters (collagen I and III, α-SMA, and left ventricular fibrosis percentage) were decreased to different degrees in the GXDSF-treated groups compared with the model group, and the collagen III/I ratio was elevated by the same treatments. TCMSP database prediction and western blot results indicated that estrogen receptor β (ERβ) could be the main target of GXDSF. PHTPP, a selective antagonist of ERβ, could inhibit the expression of ERβ and the phosphorylation of PI3K and Akt in myocardial tissue induced by GXDSF, and partly normalize the improving effects of GXDSF on +dp/dt, LVEF, LVFS, LDH, CK-MB, α-SMA and myocardial fibrosis. Conclusion: Collectively, GXDSF showed therapeutic potential for use in the prevention and treatment of myocardial ischemia reperfusion injury-induced ventricular remodeling by upregulating ERβ via PI3K/Akt signaling. Moreover, these findings may be valuable in understand the mechanism of disease and provide a potential therapy of MIRI-IVR.

Comparison of plasma pharmacokinetics of Tanreqing solution between intratracheal aerosolization and intravenous injection in rats

A rapid ultra high performance liquid chromatography tandem mass spectrometry method was developed for the simultaneous analysis of baicalin, oroxylin A-7-O-β-d-glucoronide and chlorogenic acid in rats plasma, and applied to comparison of pharmacokinetics of Tanreqing solution between intratracheal aerosolization and intravenous injection. Results of the analytical method validation assay showed high sensitivity, accuracy and suitable recovery. Results of pharmacokinetics showed similar decline phases for baicalin, oroxylin A-7-O-β-d-glucoronide and chlorogenic acid in two different delivery routes. The half-lives of intratracheal aerosolization and intravenous injection were 0.90 and 1.22 h for baicalin, 0.47 and 0.17 h for oroxylin A-7-O-β-d-glucoronide and 0.22 and 0.13 h for chlorogenic acid, and this implies that compounds were retained in the lung for a relatively short time. This study was the first to provide important pharmacokinetics information for traditional Chinese medicine delivery to the lung.

Anti-inflammatory effects of Shufengjiedu capsule for upper respiratory infection via the ERK pathway

BACKGROUND

Shufengjiedu Capsule (SFJD) is a type of Chinese traditional medicine compound for the treatment of acute upper respiratory tract infection. The present work aims to decipher the mechanism of SFJD.

METHODS

In this study, we used target prediction and RNA sequence (RNA-Seq) based on transcriptome analysis to clarify the inflammation-eliminating mechanism of SFJD. Firstly, Pseudomonas aeruginosa (PAK) was used to induce acute lung injury in KM mice. After being treated by SFJD, the differently expressed genes were analyzed by RNA-Seq. Secondly, the chemical constituents of SFJD were identified by ultra-performance liquid chromatography quadrupole/time of flight mass spectrometry (UPLC/Q-TOF-MS) and submitted to PharmMapper to predict targets. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and String 9.1 websites were employed to establish the interaction network of inflammation of these targets.

RESULTS

The results indicated that SFJD alleviated PAK induced lung injury in KM mice. We infer that the mechanism is a complex network containing 15 pathways related to inflammation regulated by 16 types of components from six types of herbs via 29 proteins. The ERK signaling pathway was a key pathway among them, which was predicted to be regulated by 14 types of components in SFJD. Phillyrin, emodin, and verbenalin were screened out by binding capacity, and the synergistic effect of them was further confirmed.

CONCLUSIONS

Various components of SFJD ameliorated PAK induced upper respiratory tract infection via multiple targets, of which ERK phosphorylation might be the key event regulated specifically by verbenalin, phillyrin and emodin.

Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective

With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level. Finally, a computational workflow for the network-based TCM study, derived from our previous successful applications, was proposed.

Network Pharmacology Studies on the Bioactive Compounds and Action Mechanisms of Natural Products for the Treatment of Diabetes Mellitus: A Review

Diabetes mellitus (DM) is a kind of chronic and metabolic disease, which can cause a number of diseases and severe complications. Network pharmacology approach is introduced to study DM, which can combine the drugs, target proteins and disease and form drug-target-disease networks. Network pharmacology has been widely used in the studies of the bioactive compounds and action mechanisms of natural products for the treatment of DM due to the multi-components, multi-targets, and lower side effects. This review provides a balanced and comprehensive summary on network pharmacology from current studies, highlighting different bioactive constituents, related databases and applications in the investigations on the treatment of DM especially type 2. The mechanisms related to type 2 DM, including α-amylase and α-glucosidase inhibitory, targeting β cell dysfunction, AMPK signal pathway and PI3K/Akt signal pathway are summarized and critiqued. It suggests that the network pharmacology approach cannot only provide a new research paradigm for natural products, but also improve the current antidiabetic drug discovery strategies. Furthermore, we put forward the perspectives on the reasonable applications of network pharmacology for the therapy of DM and related drug discovery.

Network pharmacology-based virtual screening of natural products from Clerodendrum species for identification of novel anti-cancer therapeutics

In the present work, latest network pharmacological approach has been used for the screening of natural anticancer compounds from Clerodendrum species.

Toxic Constituents Index: A Toxicity-Calibrated Quantitative Evaluation Approach for the Precise Toxicity Prediction of the Hypertoxic Phytomedicine-Aconite

Complex chemical composition is an important reason for restricting herbal quality evaluation. Despite the multi-components determination method significantly promoted the progress of herbal quality evaluation, however, which mainly concerned the total amount of multiple components and ignored the activity variation between each one, and did not accurately reflect the biological activity of botanical medicines. In this manuscript, we proposed a toxicity calibrated contents determination method for hyper toxic aconite, called toxic constituents index (TCI). Initially, we determined the minimum lethal dose value of mesaconitine (MA), aconitine (AC), and hypaconitine (HA), and established the equation TCI = 100 × (0.3387 ×X_MA + 0.4778 ×X_AC + 0.1835 ×X_HA). Then, 10 batches of aconite were selected and their evaluation results of toxic potency (TP), diester diterpenoid alkaloids (DDAs), and TCI were compared. Linear regression analysis result suggested that the relevance between TCI and TP was the highest and the correlation coefficient R was 0.954. Prediction error values study also indicated that the evaluation results of TCI was highly consistent with that of TP. Moreover, TCI and DDAs were both applied to evaluate 14 batches of aconite samples oriented different origins; from the different evaluation results, we found when the proportion of HA was reached 25% in DDAs, the pharmacopeia method could generate false positive results. All these results testified the accuracy and universality of TCI method. We believe that this study method is rather accurate, simple, and easy operation and it will be of great utility in studies of other foods and herbs.

Drug target identification using network analysis: Taking active components in Sini decoction as an example

Identifying the molecular targets for the beneficial effects of active small-molecule compounds simultaneously is an important and currently unmet challenge. In this study, we firstly proposed network analysis by integrating data from network pharmacology and metabolomics to identify targets of active components in sini decoction (SND) simultaneously against heart failure. To begin with, 48 potential active components in SND against heart failure were predicted by serum pharmacochemistry, text mining and similarity match. Then, we employed network pharmacology including text mining and molecular docking to identify the potential targets of these components. The key enriched processes, pathways and related diseases of these target proteins were analyzed by STRING database. At last, network analysis was conducted to identify most possible targets of components in SND. Among the 25 targets predicted by network analysis, tumor necrosis factor α (TNF-α) was firstly experimentally validated in molecular and cellular level. Results indicated that hypaconitine, mesaconitine, higenamine and quercetin in SND can directly bind to TNF-α, reduce the TNF-α-mediated cytotoxicity on L929 cells and exert anti-myocardial cell apoptosis effects. We envisage that network analysis will also be useful in target identification of a bioactive compound.

Systems psychopharmacology: A network approach to developing novel therapies

The multifactorial origin of most chronic disorders of the brain, including schizophrenia, has been well accepted. Consequently, pharmacotherapy would require multi-targeted strategies. This contrasts to the majority of drug therapies used until now, addressing more or less specifically only one target molecule. Nevertheless, quite some searches for multiple molecular targets specific for mental disorders have been undertaken. For example, genome-wide association studies have been conducted to discover new target genes of disease. Unfortunately, these attempts have not fulfilled the great hopes they have started with. Polypharmacology and network pharmacology approaches of drug treatment endeavor to abandon the one-drug one-target thinking. To this end, most approaches set out to investigate network topologies searching for modules, endowed with "important" nodes, such as "hubs" or "bottlenecks", encompassing features of disease networks, and being useful as tentative targets of drug therapies. This kind of research appears to be very promising. However, blocking or inhibiting "important" targets may easily result in destruction of network integrity. Therefore, it is suggested here to study functions of nodes with lower centrality for more subtle impact on network behavior. Targeting multiple nodes with low impact on network integrity by drugs with multiple activities ("dirty drugs") or by several drugs, simultaneously, avoids to disrupt network integrity and may reset deviant dynamics of disease. Natural products typically display multi target functions and therefore could help to identify useful biological targets. Hence, future efforts should consider to combine drug-target networks with target-disease networks using mathematical (graph theoretical) tools, which could help to develop new therapeutic strategies in long-term psychiatric disorders.

Influences of Re Du Ning Injection, a traditional Chinese medicine injection, on the CYP450 activities in rats using a cocktail method

ETHNOPHARMACOLOGICAL RELEVANCE

Re Du Ning Injection (RDN), a traditional Chinese medicine injection, is made from the extracts of Lonicerae japonicae flos (LJF), Artemisiae annuae herba (AAH) and Gardeniae fructus (GF). Since last decade, RDN has been widely used in China for the treatment of fever, inflammation, allergy and viral infection.

AIM OF THE STUDY

To elucidate the potential influences of RDN on the activities of four cytochrome P450 (CYP) isozymes in rats (CYP1A2, CYP2C11, CYP2D1 and CYP3A1/2) by "cocktail method".

MATERIALS AND METHODS

A sensitive and specific LC-MS method capable of simultaneous quantification of four substrates and their metabolites in rat plasma was developed and validated. Relative activity estimation of four isozymes was carried out by comparing plasma pharmacokinetics of substrates and their metabolites (phenacetin/ paracetamol for CYP1A2, tolbutamide/4-hydroxytolbutamide for CYP2C11, dextromethorphan/ dextrorphan for CYP2D1 and dapsone/N-acetyl dapsone for CYP3A1/2) between control and RDN treatment groups.

RESULTS

Compared with control group, RDN at different levels could increase the total amount of tolbutamide, dextromethorphan and dapsone absorbed into blood, while decrease the total amount of phenacetin absorbed into blood at low and medium dosage and increase it at high dosage.

CONCLUSIONS

RDN could inhibit the activities of CYP2C11, CYP2D1 and CYP3A1/2, induce the activity of CYP1A2 at low and medium dosage but inhibit it at high dosage. The results indicated that drug co-administrated with RDN may need dose adjustment.

Insight into the molecular mechanism of a herbal injection by integrating network pharmacology and in vitro

Chinese medical herbs could treat complex diseases through the synergistic effect of multi-components, multi-targets and multi-channels. However, it was difficult to systematically investigate the pharmacological mechanisms of action due to the complex chemical composition and the lack of an effective research approach. Fortunately, network pharmacology as an integrated approach was proposed to systematically investigate and explain the underlying molecular mechanisms of Chinese medical herbs. Reduning injection (RDN) is one of the herbal injections for treatment of upper respiratory tract infections (URTIs). Previous studies revealed the molecular mechanism of RDN on URTIs through network pharmacology. In this work, the mechanism of RDN was verified by enzyme linked immunosorbent assay (ELISA), Western Blot, immunofluorescence assay and electrophoretic mobility shift assay (EMSA) in lipopolysaccharide (LPS)-induced RAW264.7 cells and enzyme assay. RDN dose-dependently suppressed the production of nitric oxide (NO), prostaglandin E2 (PGE2), interleukin-6 (IL-6) and interleukin-1β (IL-1β), and reduced the protein expression of inducible NO synthetase (iNOS) and cyclooxygenase-2 (COX-2), which could be related to its suppression on the phosphorylations of mitogen-activated protein (MAP) kinases, including extracellular signal-regulated kinase (ERK), c-jun NH2-terminal kinase(JNK) and p38, as well as the activation and translocation of nuclear factor-κB (NF-κB). In addition, the activity of RDN on PGE2 was also partly attributed to the inhibition of COX-2 enzyme. Therefore, it can be concluded that RDN inhibited the production of inflammatory mediators and the macrophage activation to treat URTIs via down-regulating the activation of MAPK and NF-κB signaling pathways, which might pave a way to illustrate the molecular mechanism of herbs.

Research on the change of chemical composition in productive process of Re Du Ning injection by HPLC/Q-TOF MS

A high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HPLC/Q-TOF MS) was developed for the analysis of chemical composition change in the production process of Re Du Ning injection, a Chinese medicine preparation with a combination of Lonicera japonica Thunb., Gardenia jasminoides Ellis and Artemisia annua L. A total of 90 compounds from raw materials-intermediates-Re Du Ning injection were detected; among them, 55 compounds were identified or tentatively characterized, and the characteristic ions of different types of compounds were described. Based on these studies, the different types of compounds in the various process routes were analyzed. A total of 28 compounds, including seven iridoid glycosides and six monoterpenes from G. jasminoides Ellis, five iridoid glycosides, nine phenolic acids and one unknown compound from L. japonica Thunb., were transferred to Re Du Ning injection, and two unknown compounds were generated in the production process of Re Du Ning injection. The results indicated that the Chinese Medicine Pharmaceutical process control is very important. This method could provide some reference for other Chinese medicine preparations.

Quantitative modeling of dose-response and drug combination based on pathway network

Background

Quantitative description of dose–response of a drug for complex systems is essential for treatment of diseases and drug discovery. Given the growth of large-scale biological data obtained by multi-level assays, computational modeling has become an important approach to understand the mechanism of drug action. However, due to complicated interactions between drugs and cellular targets, the prediction of drug efficacy is a challenge, especially for complex systems. And the biological systems can be regarded as networks, where nodes represent molecular entities (DNA, RNA, protein and small compound) and processes, edges represent the relationships between nodes. Thus we combine biological pathway-based network modeling and molecular docking to evaluate drug efficacy.

Results

Network efficiency (NE) and network flux (NF) are both global measures of the network connectivity. In this work, we used NE and NF to quantitatively evaluate the inhibitory effects of compounds against the lipopolysaccharide-induced production of prostaglandin E2. The edge values of the pathway network of this biological process were reset according to the Michaelis-Menten equation, which used the binding constant and drug concentration to determine the degree of inhibition of the target protein in the pathway. The combination of NE and NF was adopted to evaluate the inhibitory effects. The dose–response curve was sigmoid and the EC50 values of 5 compounds were in good agreement with experimental results (R² = 0.93). Moreover, we found that 2 drugs produced maximal synergism when they were combined according to the ratio between each EC50.

Conclusions

This quantitative model has the ability to predict the dose–response relationships of single drug and drug combination in the context of the pathway network of biological process. These findings are valuable for the evaluation of drug efficacy and thus provide an effective approach for pathway network-based drug discovery.

Multiscale Modeling of Drug-induced Effects of ReDuNing Injection on Human Disease: From Drug Molecules to Clinical Symptoms of Disease

ReDuNing injection (RDN) is a patented traditional Chinese medicine, and the components of it were proven to have antiviral and important anti-inflammatory activities. Several reports showed that RDN had potential effects in the treatment of influenza and pneumonia. Though there were several experimental reports about RDN, the experimental results were not enough and complete due to that it was difficult to predict and verify the effect of RDN for a large number of human diseases. Here we employed multiscale model by integrating molecular docking, network pharmacology and the clinical symptoms information of diseases and explored the interaction mechanism of RDN on human diseases. Meanwhile, we analyzed the relation among the drug molecules, target proteins, biological pathways, human diseases and the clinical symptoms about it. Then we predicted potential active ingredients of RDN, the potential target proteins, the key pathways and related diseases. These attempts may offer several new insights to understand the pharmacological properties of RDN and provide benefit for its new clinical applications and research.

Predicting and verifying outcome of Tripterygium wilfordii Hook F. based therapy in rheumatoid arthritis: from open to double-blinded randomized trial

Tripterygium wilfordii Hook F. (TwHF) based therapy has been proved as effective in treating rheumatoid arthritis (RA), yet the predictors to its response remains unclear. A two-stage trial was designed to identify and verify the baseline symptomatic predictors of this therapy. 167 patients with active RA were enrolled with a 24-week TwHF based therapy treatment and the symptomatic predictors were identified in an open trial; then in a randomized clinical trial (RCT) for verification, 218 RA patients were enrolled and classified into predictor positive (P+) and predictor negative (P−) group, and were randomly assigned to accept the TwHF based therapy and Methotrexate and Sulfasalazine combination therapy (M&S) for 24 weeks, respectively. Five predictors were identified (diuresis, excessive sweating, night sweats for positive; and yellow tongue-coating, thermalgia in the joints for negative). In the RCT, The ACR 20 responses were 82.61% in TwHF/P+ group, significantly higher than that in TwHF/P− group (P = 0.0001) and in M&S/P+ group (P < 0.05), but not higher than in M&S/P− group. Similar results were yielded in ACR 50 yet not in ACR 70 response. No significant differences were detected in safety profiles among groups. The identified predictors enable the TwHF based therapy more efficiently in treating RA subpopulations.

Investigation of the therapeutic effectiveness of active components in Sini decoction by a comprehensive GC/LC-MS based metabolomics and network pharmacology approaches

As a classical formula, Sini decoction (SND) has been fully proved to be clinically effective in treating doxorubicin (DOX)-induced cardiomyopathy. Current chemomics and pharmacology proved that the total alkaloids (TA), total gingerols (TG), total flavones and total saponins (TFS) are the major active ingredients of Aconitum carmichaelii, Zingiber officinale and Glycyrrhiza uralensis in SND respectively. Our animal experiments in this study demonstrated that the above active ingredients (TAGFS) were more effective than formulas formed by any one or two of the three individual components and nearly the same as SND. However, very little is known about the action mechanisms of TAGFS. Thus, this study aimed to use for the first time the combination of GC/LC-MS based metabolomics and network pharmacology for solving this problem. By metabolomics, it was found that TAGFS worked by regulating six primary pathways. Then, network pharmacology was applied to search for specific targets. 17 potential cardiovascular related targets were found through molecular docking, 11 of which were identified by references, which demonstrated the therapeutic effectiveness of TAGFS using network pharmacology. Among these targets, four targets, including phosphoinositide 3-kinase gamma, insulin receptor, ornithine aminotransferase and glucokinase, were involved in the TAGFS regulated pathways. Moreover, phosphoinositide 3-kinase gamma, insulin receptor and glucokinase were proved to be targets of active components in SND. In addition, our data indicated TA as the principal ingredient in the SND formula, whereas TG and TFS served as adjuvant ingredients. We therefore suggest that dissecting the mode of action of clinically effective formulae with the combination use of metabolomics and network pharmacology may be a good strategy.

System-level study on synergism and antagonism of active ingredients in traditional Chinese medicine by using molecular imprinting technology

In this work, synergism and antagonism among active ingredients of traditional Chinese medicine (TCM) were studied at system-level by using molecular imprinting technology. Reduning Injection (RDNI), a TCM injection, was widely used to relieve fever caused by viral infection diseases in China. Molecularly imprinted polymers (MIPs) synthesized by sol-gel method were used to separate caffeic acid (CA) and analogues from RDNI without affecting other compounds. It can realize the preparative scale separation. The inhibitory effects of separated samples of RDNI and sample combinations in prostaglandin E2 biosynthesis in lipopolysaccharide-induced RAW264.7 cells were studied. The combination index was calculated to evaluate the synergism and antagonism. We found that components which had different scaffolds can produce synergistic anti-inflammatory effect inside and outside the RDNI. Components which had similar scaffolds exhibited the antagonistic effect, and the antagonistic effects among components could be reduced to some extent in RDNI system. The results indicated MIPs with the characteristics of specific adsorption ability and large scale preparation can be an effective approach to study the interaction mechanism among active ingredients of complex system such as TCM at system-level. And this work would provide a new idea to study the interactions among active ingredients of TCM.