A network-based pharmacology study of active compounds and targets of Fritillaria thunbergii against influenza

Seasonal and pandemic influenza infections are serious threats to public health and the global economy. Since antigenic drift reduces the effectiveness of conventional therapies against the virus, herbal medicine has been proposed as an alternative. Fritillaria thunbergii (FT) have been traditionally used to treat airway inflammatory diseases such as coughs, bronchitis, pneumonia, and fever-based illnesses. Herein, we used a network pharmacology-based strategy to predict potential compounds from Fritillaria thunbergii (FT), target genes, and cellular pathways to better combat influenza and influenza-associated diseases. We identified five compounds, and 47 target genes using a compound-target network (C-T). Two compounds (beta-sitosterol and pelargonidin) and nine target genes (BCL2, CASP3, HSP90AA1, ICAM1, JUN, NOS2, PPARG, PTGS1, PTGS2) were identified using a compound-influenza disease target network (C-D). Protein-protein interaction (PPI) network was constructed and we identified eight proteins from nine target genes formed a network. The compound-disease-pathway network (C-D-P) revealed three classes of pathways linked to influenza: cancer, viral diseases, and inflammation. Taken together, our systems biology data from C-T, C-D, PPI and C-D-P networks predicted potent compounds from FT and new therapeutic targets and pathways involved in influenza.     

Homotherapy for heteropathy active components and mechanisms of Qiang-Huo-Sheng-Shi decoction for treatment of rheumatoid arthritis and osteoarthritis

Qiang-Huo-Sheng-Shi decoction (QHSSD), a classic traditional Chinese herbal formula, which has been reported to be effective in rheumatoid arthritis (RA) and osteoarthritis (OA). However, the concurrent targeting mechanism of how the aforementioned formula is valid in the two distinct diseases OA and RA, which represents the homotherapy-for-heteropathy principle in traditional Chinese medicine (TCM), have not yet been clarified. In the present study, network pharmacology was adopted to analyze the potential molecular mechanism, and therapeutic effective components of QHSSD on both OA and RA. A total of 153 active ingredients in QHSSD were identified, 142 of which associated with 59 potential targets for the two diseases were identified. By constructing the protein-protein interaction network and the compound-target-disease network, 72 compounds and 10 proteins were obtained as the hub targets of QHSSD against OA and RA. The hub genes of ESR1, PTGS2, PPARG, IL1B, TNF, MMP2, IL6, CYP3A4, MAPK8, and ALB were mainly involved in osteoclast differentiation, the NF-κB and TNF signaling pathways. Moreover, molecular docking results showed that the screened active compounds had a high affinity for the hub genes. This study provides new insight into the molecular mechanisms behind how QHSSD presents homotherapy-for-heteropathy therapeutic efficacy in both OA and RA. For the first time, a two-disease model was linked with a TCM formula using network pharmacology to identify the key active components and understand the common mechanisms of its multi-pathway regulation. This study will inspire more innovative and important studies on the modern research of TCM formulas.     

Exploring the mechanism of action Xianlingubao Prescription in the treatment of osteoporosis by network pharmacology

In this study, the network pharmacology analysis method was used to explore the bioactive components and targets of Xianlinggubao (XLGB) and further elucidate its potential biological mechanisms of action in the treatment of osteoporosis (OP). The bioactive compounds and predictive targets of XLGB were collected from the traditional Chinese medicine systems pharmacology databases and analysis platform(TCMSP), the Encyclopeida of traditional Chinese medicine (ETCM), traditional Chinese medicine Databse@Taiwan, ChEMBL, STITCH, and SymMap database. The targets corresponding to OP were obtained by using Online Mendelian Inheritance in Man® (OMIM), GeneCards, the National Center for Biotechnology Information-Gene database. The XLGB-OP targets were obtained by intersecting with the targets of XLGB and OP. Protien-Protien interaciton (PPI) network was constructed using STRING online database and analyzed using Cytoscape 3.7.0 software to screen out hub genes. Gene ontology (GO) and KEGG enrichment analysis of the target in the PPI network was conducted using the ClusterProfiler package in R with adjusted p-value<0.05. A total of 65 XLGB bioactive compounds were screened corresponding to 776 XLGB targets and 2556 OP targets. The GO analysis and KEGG enrichment analyses suggested XLGB played a therapeutic roles in OP treatment via the interleukin-17 signaling pathway, hypoxia-inducible factor-1 signaling pathway, insulin resistance, Th-17 signaling pathway, etc. Five hub genes (AKT1, MAPK1, MAPK8, TP53, and STAT3) were screened using the degree algorithm, and molecular docking stimulation results showed that most bioactive compounds of XLGB had strong binding efficiency with hub genes. Overall, this study laid the foundation for further in vivo and in vitro experimental research and expanded the clinical applications of XLGB.     

Anti-inflammatory or anti-SARS-CoV-2 ingredients in Huashi Baidu Decoction and their corresponding targets: Target screening and molecular docking study

Coronavirus disease 2019 (COVID-19) is a rapidly emerging infectious disease caused by SARS-CoV-2. Inflammatory factors may play essential roles in COVID-19 progression. Huashi Baidu Decoction (HSBD) is a traditional Chinese medicine (TCM) formula that can expel cold, dispel dampness, and reduce inflammation. HSBD has been widely used for the treatment of COVID-19. However, the active ingredients and potential targets for HSBD to exert anti-inflammatory or anti-SARS-CoV-2 effects remain unclear. In this paper, the active ingredients with anti-inflammatory or anti-viral effects in HSBD and their potential targets were screened using the Discovery Studio 2020 software. By overlapping the targets of HSBD and COVID-19, 8 common targets (FYN, SFTPD, P53, RBP4, IL1RN, TTR, SRPK1, and AKT1) were identified. We determined 2 key targets (P53 and AKT1) by network pharmacology. The main active ingredients in HSBD were evaluated using the key targets as receptor proteins for molecular docking. The results suggested that the best active ingredients Kaempferol2 and Kaempferol3 have the potential as supplements for the treatment of COVID-19.     

中药补气与活血分子作用机理的计算机模拟

采用分子相似性分析、分子对接和生物网络技术等计算机模拟方法对治疗冠心病的中药活血与补气的分子作用机理进行研究. 结果表明, 计算机模拟方法可以体现化合物的结构差异, 并提示中药中化学成分与相关靶标相互作用的分子机理, 而生物网络的构建和分析可以将化学成分的聚类、差异, 以及有效成分与相关靶标的复杂分子作用机理可视化.     

Exploring the mechanism of Cremastra Appendiculata (SUANPANQI) against breast cancer by network pharmacology and molecular docking

BackgroundSUANPANQI, the pseudo phosphorous stem of Cremastra appendiculata, is one of the most well-known traditional Chinese medicine, which has been shown to inhibit tumorigenesis in various human cancers. However, the underlying mechanism of SUANPANQI treatment against breast cancer (BRCA) remains unclear. In this study. we aim to investigate the bioactive compounds and mechanisms of SUANPANQI in the treatment of BRCA based on network pharmacology and molecular docking.MethodsThe compounds were collected from previous research. SwissADME was used to screen bioactive compounds. The targets corresponding to SUANPANQI and BRCA were obtained using MalaCards and SwissTargetPrediction. SUANPANQI-related and BRCA-related targets were found and then overlapped to get intersections, which represented potential anti-BRCA targets of SUANPANQI. The Cytoscape software was used to construct bioactive compounds targeting the BRCA network. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the targets was extracted from the metascape database, then conducted using the Cluster Profiler package in R software. Protein-Protein interaction (PPI) network was constructed using the STRING online database and analyzed using Cytoscape software. Pivotal genes were screened using the topological analysis, survival analysis, and pathological stage analysis. Molecular docking analysis was used to verify whether the bioactive compounds had a definite affinity with the pivotal targets.ResultsSixty-five bioactive compounds of SUANPANQI were involved with 225 predicted BRCA targets. Then, a compound-target network and a PPI network were constructed. The GO analysis and KEGG enrichment analysis suggested that SUANPANQI worked against BRCA via PI3K-Akt, Ras, FoxO, Rap1, and ErbB signaling pathways, etc. After topological analysis, survival analysis, and pathological stage analysis of the SUANPANQI potential targets against BRCA, 6 pivotal target genes (AR, HSP90AA1, MMP9, PGR, PTGS2, TNF) that were highly responsible for the therapeutic effects of SUANPANQI against BRCA were obtained. Molecular docking results showed that 6 bioactive compounds of SUANPANQI had strong binding efficiency with the 6 pivotal genes.ConclusionsThe present study clarifies the mechanism of SUANPANQI against BRCA through multiple targets and pathways, and provides evidence to support its clinical use.     

A comprehensive application: Molecular docking and network pharmacology for the prediction of bioactive constituents and elucidation of mechanisms of action in component-based Chinese medicine

Traditional Chinese medicine (TCM) has been used for more than 2000 years in China. TCM has received wide attention recently due to its unique charm. At the same time, its main obstacles have attracted wide attention, including vagueness of drug composition and treatment mechanism. With the development of virtual screening technology, more and more Chinese medicine compounds have been studied to discover the potential active components and mechanisms of action. Molecular docking is a computer technology based on structural design. Network pharmacology establishes powerful and comprehensive databases to understand the relationship between TCM and disease network. In this review, emergent uses and applications of two techniques and further superiorities of the two techniques when embarked to boil down into a tidy system were illustrated. A combination of the two provides a theoretical basis and technical support for the construction of modern TCM based on the compatibility of components and accelerates the realization of two basic elements as well, including the clearness of the pharmacodynamic substances and explanation of the effect of TCM.     

Network pharmacology analysis of Chaihu Lizhong Tang treating non-alcoholic fatty liver disease

BackgroundIn this study, the network pharmacological methods were used to predict the target of active components of Chaihu Lizhong Tang (CHLZT) in the treatment of non-alcoholic fatty liver disease (NAFLD).MethodThe active components of "CHLZT", their targets, and NAFLD related targets were screened by multiple databases, and the potential targets of "CHLZT" in the treatment of NAFLD were predicted. The active component-target network of "CHLZT" was constructed by Cytoscape software. The potential target of "CHLZT" for the treatment of NAFLD constructed protein-protein interaction (PPI) network in the Search Tool for the Retrieval of Interacting Genes Database (STRING). The hub genes of “CHLZT” in the treatment of NAFLD were screened by network topological parameters, and the results were verified by molecular docking. "ClusterProfiler" in R was used for Gene Ontology (GO) analysis and KEGG pathway enrichment analysis.ResultsOB ≥ 30 % and DL ≥ 0.18 were selected as the screening criteria of active components. A total of 83 active components and 456 targets were selected. Based on the evaluation of topological parameters of degree network, five hub genes for interaction with "CHLZT" therapy for NAFLD were screened, that is, AKT1, ALB, IL6, EGFR, and CASP3. The results of molecular docking showed that the active components in "CHLZT" had a good binding ability with the key targets. The enrichment analysis results showed that the treatment of NAFLD with "CHLZT" mainly involved in cofactor binding, protease binding, AGE-RAGE signaling pathway in diabetic complications, and IL-17 signaling pathway, which mediated the potential mechanism of "CHLZT" intervention in NAFLD.ConclusionThe molecular mechanism of "CHLZT" in the treatment of NAFLD indicated the synergistic features of multi-component, multi-target, and multi-pathway of traditional Chinese medicine, which provided an important scientific basis for further elucidating the mechanism of "CHLZT" in the treatment of NAFLD.     

复方心可舒治疗冠心病多靶点作用的分子对接

心可舒为治疗冠心病的常用中药复方,临床疗效确切,但是其效应物质基础和作用机制一直没有得到明确的解释.本文以从心可舒中直接鉴定出的51个化学成分和过氧化物酶体增生物激活受体γ(PPAR-γ),血管紧张素I转化酶(ACE),羟甲基戊二酰辅酶A还原酶(HMGR),环氧合酶2(COX-2)以及凝血酶(thrombin)等5个冠心病相关靶点为研究对象,采用LibDock和AutoDock2种分子对接程序联合对接的方法对以上化学成分和靶点的相互作用进行探讨.首先用均方根偏差(RMSD)和富集因子(EF)考察了2种程序对于5个靶点受体配体结合体系的适用性,进而发现当2种程序联合使用时,各靶点的富集因子较程序单独使用时有明显的提高,因而最终使用LibDock和AutoDock联合进行筛选.计算结果表明心可舒中的葛根苷A、葛根苷B、丹酚酸A和丹酚酸C4个化合物可能作用于2个或者2个以上的靶点,另外还有8个化合物能够分别作用于5个靶点的其中1个靶点.本研究初步阐释了心可舒多靶点作用的分子机制,为心可舒的后期开发提供了一定的参考.     

Computational screening for active compounds targeting protein sequences: methodology and experimental validation

The three-dimensional (3D) structures of most protein targets have not been determined so far, with many of them not even having a known ligand, a truly general method to predict ligand-protein interactions in the absence of three-dimensional information would be of great potential value in drug discovery. Using the support vector machine (SVM) approach, we constructed a model for predicting ligand-protein interaction based only on the primary sequence of proteins and the structural features of small molecules. The model, trained by using 15,000 ligand-protein interactions between 626 proteins and over 10,000 active compounds, was successfully used in discovering nine novel active compounds for four pharmacologically important targets (i.e., GPR40, SIRT1, p38, and GSK-3β). To our knowledge, this is the first example of a successful sequence-based virtual screening campaign, demonstrating that our approach has the potential to discover, with a single model, active ligands for any protein.     

以人血清白蛋白为固定相的分子生物色谱分析几种中药活性成分的研究

提出用人血清白蛋白分子生物色谱分析中药活性成分的方法,分别比较了当归等4种单味中药的分离结果,考察了提取当归的3种溶剂及提取时间对活性物质提取量的影响,同时建立了当归中阿魏酸与藁本内酯的定量分析方法.     

Screening of Potential Anti-Thrombotic Ingredients from Salvia miltiorrhiza in Zebrafish and by Molecular Docking

Background: Danshen (DS), the dry root of Salvia miltiorrhiza Bge., has been used in traditional Chinese medicine (TCM) for many years to promote blood circulation and to inhibit thrombosis. However, the active ingredients responsible for the anti-thrombotic effect and the underlying mechanisms are yet to be fully elucidated. Methods: Molecular docking was used to predict the active ingredients in DS and their potential targets by calculating the scores of docking between DS ingredients and thrombosis-related proteins. Then, a chemical-induced zebrafish thrombosis model was applied to confirm their anti-thrombotic effects. Result: The molecular docking results indicated that compared to the control ligand, higher docking scores were observed for several compounds in DS, among which salvianolic acid B (SAB), lithospermic acid (LA), rosmarinic acid (MA), and luteolin-7-O-β-d-glucoside (LG) could attenuate zebrafish caudal vein thrombosis and recover the decrease in heart red blood cells (RBCs) in a dose-dependent manner. Conclusions: Our study showed that it is possible to screen the potential active components in natural products by combining the molecular docking method and zebrafish in vivo model.     

Network pharmacology-based approach of novel traditional Chinese medicine formula for treatment of acute skin inflammation in silico

Matrix metalloproteinase-9 (MMP-9) appears to play an important role in acute skin inflammation. Subantimicrobial dose of tetracycline has been demonstrated to inhibit the activity of MMP-9 protein. However, long-term use tetracycline will induce side effect. The catalytic site of MMP-9 is located at zinc-binding amino acids, His401, His405 and His411. We attempted to search novel medicine formula as MMP-9 inhibitors from traditional Chinese medicine (TCM) database by using in silico studies. We utilized high-throughput virtual screening to find which natural compounds could bind to the zinc-binding site. The quantitative structure-activity relationship (QSAR) models, which constructed by scaffold of MMP-9 inhibitors and its activities, were employed to predict the bio-activity of the natural compounds for MMP-9. The results showed that Celacinnine, Lobelanidine and Celallocinnine were qualified to interact with zinc-binding site and displayed well predictive activity. We found that celallocinnine was the best TCM compound for zinc binging sites of MMP-9 because the stable interactions were observed under dynamic condition. In addition, Celacinnine and Lobelanidine could interact with MMP-9 related protein that identified by drug-target interaction network analysis. Thus, we suggested the herbs Hypericum patulum, Sedum acre, and Tripterygium wilfordii that containing Celallocinnine, Celacinnine and Lobelanidine might be a novel medicine formula to avoid the side effect of tetracycline and increase the efficacy of treatment.     

利用网络药理学方法研究热毒宁注射液抗流感病毒的分子作用机制

采用分子对接、网络分析预测热毒宁注射液抗流感病毒的分子作用机制, 并通过已建立的体外流感病毒神经氨酸酶筛选模型对网络预测结果验证. 结果表明, 热毒宁注射液所含化合物在化学空间上具有类药性质; 网络分析揭示出热毒宁注射液是通过与流感病毒吸附、脱壳、复制以及释放等环节的多个蛋白相互作用发挥抗流感病毒作用的; 对于预测的15 个活性分子而言, 实验结果初步证实, 对A型流感病毒, 木犀草素呈现较强的抑制作用, 槲皮素则呈现较弱的抑制作用, 这也初步证实了预测结果.     

Roles of paeoniflorin and senkyunolide I in SiWu decoction on antiplatelet and anticoagulation activities

Traditional Chinese medicine (TCM) is a complex system, which consists of numerous compounds with related mechanisms to maximize therapeutic efficacy with minimal adverse effects. Some new methods disclosing the contribution of these constituents as well as their relationship in the formula are necessary for elucidating the bio‐active constituents and the working mechanisms of TCM. In this study, depletion of target components using preparative HPLC followed by antiplatelet and anticoagulation activities evaluation was first applied to investigate the roles of paeoniflorin and senkyunolide I in a well‐known formula, SiWu decoction. The results showed that both paeoniflorin and senkyunolide I not only directly brought about some bio‐activities, but also indirectly made the contribution to the total bio‐activity reflection of SiWu decoction, especially the latter should deserve to be drawn attention to the research of complicated bio‐active constituents of TCM or its formula. So, the significant and effective approach will be very useful for the elucidation of the contribution of each different chemical constituent to the bio‐activity of a TCM formula. Furthermore, this study demonstrated the potential utilization of preparative HPLC in the research of TCM.