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.     

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.     

Uncovering the pharmacological mechanism of motherwort (Leonurus japonicus Houtt.) for treating menstrual disorders: A systems pharmacology approach

Leonurus japonicus (motherwort) is a traditional Chinese medicine that is widely used to treat menstrual disorders (MDs). However, the pharmacological mechanisms that underlie its clinical application remain unclear. In this study, a network pharmacology-based approach was used that integrated drug-likeness evaluation, oral bioavailability prediction, target exploration, network construction, bioinformatic annotation and molecular docking to investigate the mechanisms that underlie motherwort treatment for MDs. In total, 29 bioactive compounds were collected from 51 compounds in motherwort, which shared 17 common MDs-related targets. Network analysis indicated that motherwort played a therapeutic role in MDs treatment through multiple components that acted on multiple targets. Pathway enrichment analysis showed that the putative targets of motherwort were primarily involved in various pathways associated with the endocrine system, cancers, vascular system, and anti-inflammation process. Notably, five targets (i.e., AKT1, PTGS2, ESR1, AR and PPARG) were screened as hub genes based on a degree algorithm. Moreover, most of the bioactive components in motherwort had good binding ability with these genes, implying that motherwort could regulate their biological function. Collectively, this study elucidated the molecular mechanisms that underlay the efficiency of motherwort against MDs and demonstrated the potential of network pharmacology as an approach to uncover the action mechanism of herbal medicines.     

Effects of Sargassum thunbergii Extract on Skin Whitening and Anti-Wrinkling through Inhibition of TRP-1 and MMPs

Sargassum thunbergii has been traditionally used as an edible and medicinal material in oriental countries. However, the skin-whitening and anti-wrinkling effects of S. thunbergii have not yet been investigated. This study was conducted to establish optimal extraction conditions for the production of bioactive compounds with antioxidant activity as well as skin-whitening and anti-wrinkle effects using ultrasound-assisted extraction (UAE) in S. thunbergii. The extraction time (5.30~18.7 min), extraction temperature (22.4~79.6 °C), and ethanol concentration (0.0~99.5%), which are the main variables of the UAE, were optimized using a central composite design. Quadratic regression equations were derived based on experimental data and showed a high coefficient of determination (R² > 0.85), demonstrating suitability for prediction. The optimal UAE condition for maximizing all dependent variables, including radical scavenging activity (RSA), tyrosinase inhibitory activity (TIA), and collagenase inhibitory activity (CIA), was identified as an extraction time of 12.0 min, an extraction temperature of 65.2 °C, and ethanol of 53.5%. Under these conditions, the RSA, TIA, and CIA of S. thunbergii extract were 86.5%, 88.3%, and 91.4%, respectively. We also confirmed S. thunbergii extract had inhibitory effects on the mRNA expression of tyrosinase-related protein-1, matrix metalloproteinase-1, and matrix metalloproteinase-9, which are the main genes of melanin synthesis and collagen hydrolysis. Liquid chromatography-tandem mass spectrometry was used to identify the main phenolic compounds in S. thunbergii extract, and caffeic acid was identified as a major peak, demonstrating that high value-added ingredients with skin-whitening and anti-wrinkling effects can be produced from S. thunbergii and used for developing cosmetic materials.     

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.     

A novel method for investigating the mechanism of the anti-rheumatoid arthritis activity of Angelicae pubescentis radix by integrating UHPLC–QTOF/MS and network pharmacology

The study aimed to establish a strategy to elucidate the in vivo constituents of Angelicae Pubescentis Radix (APR, also known as Duhuo) and reveal the probable mechanisms underlying its anti-rheumatoid arthritis activity. First recorded by Shennong Bencao Jing, APR is mainly used to treat Bi syndrome. Eleven absorbed components of APR were successfully identified using the rheumatoid arthritis (RA) rat model and the UHPLC–QTOF/MS technique. Two active ingredients (osthole and columbianadin) and five corresponding targets (PTGS1, PTGS2, RXRA, CCNA2 and ACHE) were found to construct a compound–protein interaction network in RA. In addition, a non-alcoholic fatty liver disease pathway, which was related to anti-RA activity, was eventually identified by KEGG analysis. Subsequently, molecular docking was performed by establishing a mixed matrix network, including the absorbed component, corresponding target and signaling pathway with two key compounds (osthole and columbianadin) and two important targets (PTGS2 and PTGS1). The result of molecular docking is in agreement with the network pharmacology.     

Investigating ego modules involved in TGFβ3-induced chondrogenesis in mesenchymal stem cells based on ego network

ObjectiveThis paper aimed to investigate ego modules for TGFβ3-induced chondrogenesis in mesenchymal stem cells (MSCs) using ego network algorithm.MethodsThe ego network algorithm comprised three parts, extracting differential expression network (DEN) based on gene expression data and protein-protein interaction (PPI) data; exploring ego genes by reweighting DEN; and searching ego modules by ego gene expansions. Subsequently, permutation test was carried out to evaluate the statistical significance of the ego modules. Finally, pathway enrichment analysis was conducted to investigate ego pathways enriched by the ego modules.ResultsA total of 15 ego genes were obtained from the DEN, such as PSMA4, HNRNPM and WDR77. Starting with each ego genes, 15 candidate modules were gained. When setting the thresholds of the area under the receiver operating characteristics curve (AUC) ≥0.9 and gene size ≥4, three ego modules (Module 3, Module 8 and Module 14) were identified, and all of them had statistical significances between normal and TGFβ3-induced chondrogenesis in MSCs. By mapping module genes to confirmed pathway database, their ego pathways were detected, Cdc20:Phospho-APC/C mediated degradation of Cyclin A for Module 3, Mitotic G1-G1/S phases for Module 8, and mRNA Splicing for Module 14.ConclusionsWe have successfully identified three ego modules, evaluated their statistical significances and investigated their functional enriched ego pathways. The findings might provide potential biomarkers and give great insights to reveal molecular mechanism underlying this process.     

Uncovering the anticancer mechanism of petroleum extracts of Farfarae Flos against Lewis lung cancer by metabolomics and network pharmacology analysis

Lung cancer shows the highest incidence rate in the world. Thus, it has become increasingly important to find therapeutic drugs to treat lung cancer. Farfarae Flos (FF) has been used in traditional Chinese medicine to treat pulmonary diseases such as cough, bronchitis and asthmatic disorders. In this study, the anti-proliferation effects of petroleum extracts of FF (PEFF) on Lewis lung cancer cells and the corresponding mechanisms were studied using cell metabolomics. Fifteen differential metabolites in the cell extracts and the corresponding medium related to the anti-proliferation effect of PEFF were identified, which were probably involved in pyruvate metabolism and glycine, serine and threonine metabolism. For the cellular uptake compounds in PEFF, six metabolites derived from two prototype compounds were also tentatively identified by UHPLC-Q-Orbitrap high-resolution MS. Network pharmacology analysis demonstrated that the anti-proliferation mechanism of PEFF was also probably related to the target genes, including, Aurora-A, glutathione S-transferase Mu 1 (GSTM1), glutathione S-transferase P 1 (GSTP1), progesterone receptor and heme oxygenase-1 (HO-1), and further associated with the proteoglycans and PI3K/Akt signaling pathway. Cell metabolomics and network pharmacology analysis provided a holistic method to investigate the anti-proliferation mechanisms of PEFF. However, further studies were still needed to validate the potential target genes, pathways and active compounds in PEFF.     

Network Pharmacology-Based Study to Uncover Potential Pharmacological Mechanisms of Korean Thistle (Cirsium japonicum var. maackii (Maxim.) Matsum.) Flower against Cancer

Cirsium japonicum var. maackii (Maxim.) Matsum. or Korean thistle flower is a herbal plant used to treat tumors in Korean folk remedies, but its essential bioactives and pharmacological mechanisms against cancer have remained unexplored. This study identified the main compounds(s) and mechanism(s) of the C. maackii flower against cancer via network pharmacology. The bioactives from the C. maackii flower were revealed by gas chromatography-mass spectrum (GC-MS), and SwissADME evaluated their physicochemical properties. Next, target(s) associated with the obtained bioactives or cancer-related targets were retrieved by public databases, and the Venn diagram selected the overlapping targets. The networks between overlapping targets and bioactives were visualized, constructed, and analyzed by RPackage. Finally, we implemented a molecular docking test (MDT) to explore key target(s) and compound(s) on AutoDockVina and LigPlot+. GC-MS detected a total of 34 bioactives and all were accepted by Lipinski’s rules and therefore classified as drug-like compounds (DLCs). A total of 597 bioactive-related targets and 4245 cancer-related targets were identified from public databases. The final 51 overlapping targets were selected between the bioactive targets network and cancer-related targets. With Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, a total of 20 signaling pathways were manifested, and a hub signaling pathway (PI3K-Akt signaling pathway), a key target (Akt1), and a key compound (Urs-12-en-24-oic acid, 3-oxo, methyl ester) were selected among the 20 signaling pathways via MDT. Overall, Urs-12-en-24-oic acid, 3-oxo, methyl ester from the C. maackii flower has potent anti-cancer efficacy by inactivating Akt1 on the PI3K-Akt signaling pathway.     

Characterization and identification of steroidal alkaloids in Fritillaria species using liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry

Liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (LC/ESI-QTOF-MS/MS) was performed to study the fragmentation behaviors of steroidal alkaloids from Fritillaria species, the antitussive and expectorant herbs widely used in traditional Chinese medicine. We propose, herein, a strategy that combining key diagnostic fragment ions and the relative abundances and amounts of major fragment ions (the ions exceeding 10% in abundance) to distinguish different sub-classes of Fritillaria alkaloids (FAs). It was found that hydrogen rearrangement and induction effects result in ring cleavage of the basic skeletons occurred in the MS/MS process and produced characteristic fragment ions, which are useful for structural elucidation. This method was finally used to investigate the primary steroidal alkaloids in the extracts of eight major Fritillaria species. As a result, 41 steroidal alkaloids (29 cevanine type, 1 jervine type, 6 veratramine type and 5 secosolanidine type alkaloids) were selectively identified in these Fritillaria species. Twenty-six compounds were unambiguously identified by comparing with the reference compounds and 15 compounds were tentatively identified or deduced according to their MS/MS data. Logical fragmentation pathways for different types of FAs have been proposed and are useful for the identification of these types of steroidal alkaloids in natural products especially when there are no reference compounds available.     

The protective effect of icariin on glucocorticoid-damaged BMECs explored by microfluidic organ chip

Osteonecrosis of the femoral head(ONFH) is a devastating musculoskeletal disease characterized by the impaired circulation of bone. The purpose of this study was to explore the underlying mechanisms of the protective effect of icariin on the glucocorticoid-induced injury of bone microvascular endothelial cells(BMECs). Normal BMECs were extracted from the femoral heads by enzymatic isolation and magneticactivated cell sorting methods. Dexamethasone and icariin were used to intervene BMECs in micr...     

Investigating dysregulated pathways in Staphylococcus aureus (SA) exposed macrophages based on pathway interaction network

ObjectiveThis work aimed to identify dysregulated pathways for Staphylococcus aureus (SA) exposed macrophages based on pathway interaction network (PIN).MethodsThe inference of dysregulated pathways was comprised of four steps: preparing gene expression data, protein–protein interaction (PPI) data and pathway data; constructing a PIN dependent on the data and Pearson correlation coefficient (PCC); selecting seed pathway from PIN by computing activity score for each pathway according to principal component analysis (PCA) method; and investigating dysregulated pathways in a minimum set of pathways (MSP) utilizing seed pathway and the area under the receiver operating characteristics curve (AUC) index implemented in support vector machines (SVM) model.ResultsA total of 20,545 genes, 449,833 interactions and 1189 pathways were obtained in the gene expression data, PPI data and pathway data, respectively. The PIN was consisted of 8388 interactions and 1189 nodes, and Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins was identified as the seed pathway. Finally, 15 dysregulated pathways in MSP (AUC = 0.999) were obtained for SA infected samples, such as Respiratory electron transport and DNA Replication.ConclusionsWe have identified 15 dysregulated pathways for SA infected macrophages based on PIN. The findings might provide potential biomarkers for early detection and therapy of SA infection, and give insights to reveal the molecular mechanism underlying SA infections. However, how these dysregulated pathways worked together still needs to be studied.     

Down regulation of lactotransferrin enhanced radio-sensitivity of nasopharyngeal carcinoma

IntroductionIt is reported that LTF had a radiation resistance effect, and its expression in nasopharyngeal carcinoma (NPC) was significantly down-regulated. However, the mechanism of down-regulated LTF affecting the sensitivity of radiotherapy has remained elusive.MethodsWe re-analyzed the microarray data GSE36972 and GSE48503 to find differentially expressed genes (DEGs) in NPC cell line 5−8 F transfected with LTF or vector control, and the DEGs between radio-resistant and radio-sensitive NPC cell lines. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and protein-protein interaction network (PPI) analysis of DEGs were performed to obtain the node genes. The target genes of miR-214 were also predicted to complement the mechanism associated with radiotherapy resistance because it could directly target LTF.ResultsThis study identified 1190 and 1279 DEGs, respectively. GO and KEGG analysis showed that apoptotic process and proliferation, PI3K-Akt signaling pathway were significantly enriched pathways. Four nodes (DUSP1, PPARGC1A, FOS and SMARCA1) associated with LTF were screened. And 42 target genes of miR-214 were cross-linked to radiotherapy sensitivity.ConclusionsThe present study demonstrates the possible molecular mechanism that the down-regulated LTF enhances the radiosensitivity of NPC cells through interaction with DUSP1, PPARGC1A, FOS and SMARCA1, and miR-214 as its superior negative regulator may play a role in regulating the radiotherapy effect.     

Network-Based Identification of Novel Connections Among Apoptotic Signaling Pathways in Cancer

MicroRNAs (miRNAs), highly conserved, non-coding endogenous RNA and nearly ~22 nucleotides (nt) in length, are well-known to regulate several apoptotic pathways in cancer. In this study, we computationally constructed the initial human apoptotic PPI network by several online databases, and further integrated these high-throughput datasets into a Na?ve Bayesian model to predict protein functional connections. Based on the modified apoptotic network, we identified several apoptotic hub proteins such as TP53, SRC, M3K3/5/8, cyclin-dependent kinase2/6, TNFR16/19, and TGF-?? receptor 1/2. Subsequently, we identified some microRNAs that could target the aforementioned apoptotic hub proteins by using TargetScan, PicTar, and Diana-MicroH. In conclusion, these results demonstrate the PPI network-based identification of new connections amongst apoptotic pathways in cancer, which may shed new light on the intricate relationships between core apoptotic pathways and some targeted miRNAs in human cancers.     

Identification of Novel Influenza Polymerase PB2 Inhibitors Using a Cascade Docking Virtual Screening Approach

To discover novel inhibitors that target the influenza polymerase basic protein 2 (PB2) cap-binding domain (CBD), commercial ChemBridge compound libraries containing 384,796 compounds were screened using a cascade docking of LibDock–LigandFit–GOLD, and 60 compounds were selected for testing with cytopathic effect (CPE) inhibition assays and surface plasmon resonance (SPR) assay. Ten compounds were identified to rescue cells from H1N1 virus-mediated death at non-cytotoxic concentrations with EC₅₀ values ranging from 0.30 to 67.65 μM and could bind to the PB2 CBD of H1N1 with Kd values ranging from 0.21 to 6.77 μM. Among these, four compounds (11D4, 12C5, 21A5, and 21B1) showed inhibition of a broad spectrum of influenza virus strains, including oseltamivir-resistant ones, the PR/8-R292K mutant (H1N1, recombinant oseltamivir-resistant strain), the PR/8-I38T mutant (H1N1, recombinant baloxavir-resistant strain), and the influenza B/Lee/40 virus strain. These compounds have novel chemical scaffolds and relatively small molecular weights and are suitable for optimization as lead compounds. Based on sequence and structure comparisons of PB2 CBDs of various influenza virus subtypes, we propose that the Phe323/Gln325, Asn429/Ser431, and Arg355/Gly357 mutations, particularly the Arg355/Gly357 mutation, have a marked impact on the selectivities of PB2 CBD-targeted inhibitors of influenza A and influenza B.     

Recent research progress on small molecule compounds and its derivatives of antiparasitic drugs

Neglected tropical diseases (NTDs) refer to infectious diseases caused by multiple pathogens that are prevalent in hot, humid climates in tropical areas. With the global economic growth and the improvement of public health status, eliminating neglected tropical diseases will be of great significance to the healthy development of human beings. However, the number of drugs and vaccines for NTDs treatment is extremely limited, so it is urgent to develop new drugs. Since most NTDs are caused by parasites, this paper selected parasitic diseases with high morbidity and mortality, and focused on new effective therapeutic targets and excellent lead compounds for these diseases. Schistosomiasis, human African trypanosomiasis (HAT), Chagas disease, leishmaniasis, filariasis and toxoplasmosis correspond to a series targets such as smHDAC8, thioredoxin glutathione reductase (TGR), T. cruzi glucokinase (TcGlcK), phosphofructokinase (PFK), type IB topoisomerase, cell division cycle-2-related Kinase, sterolmethyl transferase, calumenin, dihydrofolate reductase (DHFR) and Toxoplasma gondii farnesyl-diphosphate synthase (TgFPPs). In this paper, the pharmacological effects of typical lead compounds corresponding to each disease, the structural characteristics of the mother nucleus and the pharmacological activities of the substituent. In addition, the binding patterns of some involved targets (such as smHDAC8) with corresponding lead compounds (such as compound 13) and the signaling pathways associated with gluconeogenesis, glycolysis, and pentose phosphate pathways are analyzed in detail. In this paper, the interaction mechanism between the lead compounds and the target were thoroughly discussed, in order to provide the research ideas of potential anti-parasite compounds, and further improve the understanding and prevention ability of such diseases of NTDs.     

Identification of Casiopeina II-gly secondary targets through a systems pharmacology approach

Casiopeinas are a group of copper-based compounds designed to be used as less toxic, more efficient chemotherapeutic agents. In this study, we analyzed the in vitro effects of Casiopeina II-gly on the expression of canonical biological pathways. Using microarray data from HeLa cell lines treated with Casiopeina II-gly, we identified biological pathways that are perturbed after treatment. We present a novel approach integrating pathway analysis and network theory: The Pathway Crosstalk Network. We constructed a network with deregulated pathways, featuring links between those pathways that crosstalk with each other. We identified modules grouping deregulated pathways that are functionally related. Through this approach, we were able to identify three features of Casiopeina treatment: (a) Perturbation of signaling pathways, related to induction of apoptosis; (b) perturbation of metabolic pathways, and (c) activation of immune responses. These findings can be useful to drive new experimental exploration on their role in adverse effects and efficacy of Casiopeinas.