Prediction of potential cancer-related molecular targets of North African plants constituents using network pharmacology-based analysis

Recent advances in the area of plant-based anti-cancer drug discovery using computational approaches

Phytocompounds are a well-established source of drug discovery due to their unique chemical and functional diversities. In the area of cancer therapeutics, several phytocompounds have been used till date to design and develop new drugs. One of the desired interests of pharmaceutical companies and researchers globally is that new anti-cancer leads are discovered, for which phytocompounds can be considered a valuable source. Simultaneously, in recent years, the growth of computational approaches like virtual screening (VS), molecular dynamics (MD), pharmacophore modelling, Quantitative structure-activity relationship (QSAR), Absorption Distribution Metabolism Excretion and Toxicity (ADMET), network biology, and machine learning (ML) has gained importance due to their efficiency, reduced time-consuming nature, and cost-effectiveness. Therefore, the present review amalgamates the information on plant-based molecules identified for cancer lead discovery from in silico approaches. The mandate of this review is to discuss studies published in the last 5-6 years that aim to identify the phytomolecules as leads against cancer with the help of traditional computational approaches as well as newer techniques like network pharmacology and ML. This review also lists the databases and webservers available in the public domain for phytocompounds related information that can be harnessed for drug discovery. It is expected that the present review would be useful to pharmacologists, medicinal chemists, molecular biologists, and other researchers involved in the development of natural products (NPs) into clinically effective lead molecules.

An integrated network pharmacology approach to discover therapeutic mechanisms of Commiphora wightii for the treatment of Bell's palsy

Bell's palsy (BP) can result in facial paralysis. Inflammation or injury to the cranial nerves that regulate the facial muscles is primarily responsible for that disease. Commiphora wightii remains recognized as a cure for a few human ailments. This study focused on therapeutic phenomena of C. wightii for the treatment of Bell's palsy, utilizing the network drug discovery and molecular docking techniques. Active biological constituents of C. wightii were retrieved from literature and independent databases. Potential therapeutic targets (431) of 13 bioactive phytochemicals were fetched via SwissTargetPrediction tool. Putative intersecting targets (855) of Bell's palsy were computed through the DisGeNET and GeneCards datasets. Subsequently, by the analysis of potential shared targets (87) of C. wightii and Bell's palsy, a Venn diagram was drawn. DAVID database was used to evaluate gene functional annotations and enriched pathways that are involved in Bell's palsy. STRING database was used for generating the protein-protein relationship complex. Visual presentations of the interactions of potential targets to active chemical constituents were done by the Cytoscape. Whereas, the conformational research sorted out 10 key targets through the protein-protein interactions network. Moreover, the capacity of therapeutic ingredients to interact with a target inhibiting Bell's palsy was confirmed by molecular docking, which might ratify the findings of network pharmacology. In the molecular complex of AKT1-cholesterol, a 100-ns simulation unveiled a graceful stability, with a minimal 0.167 Å ligand shift and resilient hydrogen bonds (ASN54 and SER205). The final 20 ns showcased a P1 motif pirouette, gracefully forming aromatic bonds with H165 and W186, underscoring the complex's dynamic finesse. This study evaluated compound-target interactions and their impact on disease-related genes. It revealed that five genes (AKT1, TNF, MAPK3, EGFR and SRC) of C. wightii might be useful therapeutic targets for the treatment of Bell's palsy, as well as helping in lowering down the blood pressure.Communicated by Ramaswamy H. Sarma.

Systems pharmacology and multi-scale mechanism of Enicostema axillare bioactives in treating Alzheimer disease

As a progressive neurological disease with increased morbidity and mortality, Alzheimer Disease (AD) is characterized by neuron damage that controls memory and mental functions. Enicostema axillare (EA), an herb with a history of combativeness and effectiveness in treating Rheumatoid Arthritis, Cancer, and Diabetes, is used in Indian folk medicine from a holistic point of view. Though the herb is used for many illnesses, the molecular mechanism of its bioactive on AD has not been deciphered by intricate research. A unique pharmacology approach based on ADME drug screening and targeting, pathway enrichment (GO and KEGG), and network pharmacology, was established to explore the molecular mechanisms of E. axillare (EA) bioactive compounds for the treatment of AD. In brief, we bring to light the three active compounds of EA and seven potential molecular targets of AD, which are mainly implicated in four signaling pathways, i.e., MAPK, Apoptosis, neurodegeneration, and the TNF pathway. Moreover, the network analysis of the active compounds, molecular targets, and their pathways reveals the pharmacological nature of the compounds. Further, molecular docking studies were carried out to explore the interactions between the EA bioactive compounds and the targets and examine the binding affinity. The outcome of the work reflects the potential therapeutic effects of the compounds for treating AD through the modulation of the key proteins, which further corroborates the reliability of our network pharmacology analysis. This study not only helps in understanding the molecular mechanism of the drugs but also helps in finding and sorting new drugs for the treatment of AD, and other complex diseases through modern medicine.

Unravelling the Molecular Mechanisms of a Quercetin Nanocrystal for Treating Potential Parkinson's Disease in a Rotenone Model: Supporting Evidence of Network Pharmacology and In Silico Data Analysis

The prevalence of Parkinson's disease places a significant burden on society; therefore, there is an urgent need to develop more effective drugs. However, the development of these drugs is both expensive and risky. Quercetin (QUE) has potent pharmacological effects on neurodegenerative diseases, but its low solubility in water and poor bioavailability limit its use in pharmaceutical applications. In this study, Quercetin nanocrystals (QNC) were synthesized and compared to standard QUE. A network-pharmacology-based methodology was applied, including target prediction, network construction, a gene ontology (GO) analysis, a KEGG pathway enrichment analysis, and molecular docking. This study aimed to identify the targets of QUE relevant to the treatment of Parkinson's disease and investigate the associated pharmacological mechanisms. Most of the predicted targets are involved in dopamine uptake during synaptic transmission. QUE regulates the key targets DRD2 and DRD4, which significantly affect dopaminergic synapses. The molecular docking results showed that QUE had a better binding affinity than the standard drug l-Dopa. From these experiments, it can be concluded that QNC effectively reduced the adverse effects caused by rotenone-induced oxidative stress in biochemical, neurochemical, and histopathological alterations. Therefore, QNC can potentially treat Parkinson's disease, and its effectiveness should be assessed in future clinical trials.

Advanced network pharmacology study reveals multi-pathway and multi-gene regulatory molecular mechanism of Bacopa monnieri in liver cancer based on data mining, molecular modeling, and microarray data analysis

Liver cancer is a malignant tumor that grows on the surface or inside the liver. The leading cause is a viral infection with hepatitis B or C virus. Natural products and their structural analogues have historically made a major contribution to pharmacotherapy, especially for cancer. A list of studies evidences the therapeutic efficacy of Bacopa monnieri against liver cancer, but the precise molecular mechanism is yet to be discovered. This study combines data mining, network pharmacology, and molecular docking analysis to potentially revolutionize liver cancer treatment by identifying effective phytochemicals. Initially, the information on active constituents of B. monnieri and target genes of both liver cancer and B. monnieri were retrieved from literature as well as from publicly available databases. Based on the matching results between B. monnieri potential targets and liver cancer targets, the protein-protein interaction (PPI) network was constructed using the STRING database and imported into Cytoscape for screening of hub genes based on their degree of connectivity. Later, the interactions network between compounds and overlapping genes was constructed using Cytoscape software to analyze the network pharmacological prospective effects of B. monnieri on liver cancer. Gene Ontology (GO) and KEGG pathway analysis of hub genes revealed that these genes are involved in the cancer-related pathway. Lastly, the expression level of core targets was analyzed using microarray data (GSE39791, GSE76427, GSE22058, GSE87630, and GSE112790). Further, the GEPIA server and PyRx software were used for survival and molecular docking analysis, respectively. In summary, we proposed that quercetin, luteolin, apigenin, catechin, epicatechin, stigmasterol, beta-sitosterol, celastrol, and betulic acid inhibit tumor growth by affecting tumor protein 53 (TP53), interleukin 6 (IL6), RAC-alpha serine/threonine protein kinases 1 (AKT1), caspase-3 (CASP3), tumor necrosis factor (TNF), jun proto-oncogene (JUN), heat shot protein 90 AA1 (HSP90AA1), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), and SRC proto-oncogene (SRC). Through, microarray data analysis, the expression level of JUN and IL6 were found to be upregulated while the expression level of HSP90AA1 was found to be downregulated. Kaplan-Meier survival analysis indicated that HSP90AA1 and JUN are promising candidate genes that can serve as diagnostic and prognostic biomarkers for liver cancer. Moreover, the molecular docking and molecular dynamic simulation of 60ns well complemented the binding affinity of the compound and revealed strong stability of predicted compounds at the docked site. Calculation of binding free energies using MMPBSA and MMGBSA validated the strong binding affinity between the compound and binding pockets of HSP90AA1 and JUN. Despite that, in vivo and in vitro studies are mandatory to unveil pharmacokinetics and biosafety profiles to completely track the candidature status of B. monnieri in liver cancer.

Efficacies and side effects of medicinal plants used by patients with cancer in Morocco: A retrospective treatment-outcome study

ETHNOPHARMACOLOGICAL RELEVANCE

Medicinal plants have long been used as traditional medicines in Morocco. Patients with cancer frequently use medicinal plants, with a frequency ranging from 11% to 39%. No studies have evaluated these patients in the Beni Mellal-Khenifra region.

AIM OF STUDY

We investigated the beneficial and adverse effects of medicinal plants used by patients with cancer in this region.

METHODS

We conducted a retrospective study of the outcomes of traditional treatment with medicinal plants (retrospective treatment-outcome study: RTO) in 194 patients with cancer at the regional oncology centre of Béni Mellal.

RESULTS

Beneficial effects were reported by 39% of patients. All users of the seeds of Prunus armeniaca L. reported beneficial effects (100%), followed by Curcuma longa L. (50%). We did not observe any significant difference in efficacies between the most commonly used plants (P > 0.05). Patients with cancer who had a low socioeconomic level experienced greater benefits from herbal medicines (p < 0.05). The prevalence of adverse effects was 16%. Juniperus oxycedrus L. was perceived as the most toxic plant (13 patients), as it induced significantly greater toxicity than the other plants (P < 0.05). Patients with a cancer duration of more than 12 months reported more adverse effects (p = 0.05).

CONCLUSIONS

The frequency of beneficial effects was higher than that of adverse effects. Health professionals should be aware of these effects in the process of therapeutic education. Preclinical and clinical research are considered necessary for the in-depth evaluation of the efficacies and toxicities of certain plants that have shown toxic or therapeutic potential.

Virtual Screening and Network Pharmacology-Based Study to Explore the Pharmacological Mechanism of Clerodendrum Species for Anticancer Treatment

BACKGROUND

Cancer is a second leading cause of death in the world, killing approximately 3500 per million people each year. Therefore, the drugs with multitarget pharmacology based on biological networks are crucial to investigate the molecular mechanisms of cancer drugs and repurpose the existing drugs to reduce adverse effects. Clerodendrum is a diversified genus with a wide range of economic and pharmacological properties. Limited studies were conducted on the genus's putative anticancer properties and the mechanisms of action based on biological networks remains unknown. This study was aimed to construct the possible compound/target/pathway biological networks for anticancer effect of Clerodendrum sp. using docking weighted network pharmacological approach and to investigate its potential mechanism of action.

METHODS

A total of 194 natural Clerodendrum sp. Compounds were retrieved from public databases and screened using eight molecular descriptors. The cancer-associated gene targets were retrieved from databases and the function of the target genes with related pathways were examined. Cytoscape v3.7.2 was used to build three major networks: compound-target network, target-target pathway network, and compound-target-pathway network.

RESULTS

Our finding indicates that the anticancer activity of Clerodendrum sp. involves 6 compounds, 9 targets, and 63 signaling pathways, resulting in multicompounds, multitargets, and multipathways networks. Additionally, molecular dynamics (MD) simulations were used to estimate the binding affinity of the best hit protein-ligand complexes. Conclusion. This study suggests the potential anticancer activity of Clerodendrum sp. which could further contribute to scavenger novel compounds for the development of new alternative anticancer drugs.

An In-Silico Identification of Potential Flavonoids against Kidney Fibrosis Targeting TGFβR-1

Fibrosis is a hallmark of progressive kidney diseases. The overexpression of profibrotic cytokine, namely transforming growth factor β (TGF-β) due to excessive inflammation and tissue damage, induces kidney fibrosis. The inhibition of TGF-β signaling is markedly limited in experimental disease models. Targeting TGF-β signaling, therefore, offers a prospective strategy for the management of kidney fibrosis. Presently, the marketed drugs have numerous side effects, but plant-derived compounds are relatively safer and more cost-effective. In this study, TGFβR-1 was targeted to identify the lead compounds among flavonoids using various computational approaches, such as ADME/T (absorption, distribution, metabolism, and excretion/toxicity) analysis, molecular docking, and molecular dynamics simulation. ADME/T screening identified a total of 31 flavonoids with drug-like properties of 31 compounds, a total of 5 compounds showed a higher binding affinity to TGFβR-1, with Epicatechin, Fisetin, and Luteolin ranking at the top three (-13.58, -13.17, and -10.50 kcal/mol, respectively), which are comparable to the control drug linagliptin (-9.074 kcal/mol). The compounds also exhibited outstanding protein-ligand interactions. The molecular dynamic simulations revealed a stable interaction of these compounds with the binding site of TGFβR-1. These findings indicate that flavonoids, particularly Epicatechin, Fisetin, and Luteolin, may compete with the ligand-binding site of TGFβR-1, suggesting that these compounds can be further evaluated for the development of potential therapeutics against kidney fibrosis. Further, in-vitro and in-vivo studies are recommended to support the current findings.

In Vitro Study of the Potential Role of Olive Oil Oleuropein in Modulating the 5-FU Cytotoxic Efficacy against the Tongue Squamous Cell Carcinoma

BACKGROUND: 5-fluorouracil (5-FU) is an anticancer drug used to inhibit the proliferation of many different tumor cells. Since severe side effects are associated with this drug, its combination with different natural compounds would allow the use of a significantly lower dose of 5-FU. Oleuropein (OLEU), has been shown to have inhibitory effects on various types of cancers. AIM: The main objective of the current study was to assess the cytotoxic effect of OLEU and the chemotherapeutic drug 5-FU on Human Tongue Carcinoma Cancer Cell Line (HNO-97) and Human Normal Oral Epithelial Cell Line (OEC) either independently or combinatory effect. MATERIALS AND METHODS: 3-(4,5- dimethylthiazol-2-Yl)-2,5-diphenyltetrazolium bromide (MTT) assay for cell viability, and half-maximal inhibitory concentration (IC50) was calculated. Flowcytometry for cell cycle analysis was performed. Also, in vitro scratch assay was done to assess the inhibitory effects of OLEU on the migration of cells.RESULTS: MTT assay study demonstrated that OLEU and 5-FU alone or in combinations have produced a significant inhibitory effect on both normal and cancer cell lines with a favorable impact for OLEU on cancer cell lines rather than the normal one. A significant increase in the cell inhibitory % was reported between the single and the combinations treated groups as compared to the non-treated control group. Cell cycle analysis via flowcytometry showed that OLEU had induced cell cycle arrest at G0/1 phase, decreased S phase and G2/M phase either independently or in combination for 24h and 48h when compared with a non-treated control group. A Scratch assay test showed that OLEU could induce delayed wound healing. CONCLUSIONS: The findings of the present study suggest that OLEU can exert an anti-cancer effect on HNO-97 and may have the potential for potentiation of 5-FU cytotoxic effects and reduction of its adverse effects. In addition, OLEU could inhibit cancer progression and expansion from the initial tumor.

Network Pharmacology and Bioinformatics Approach Reveals the Multi-Target Pharmacological Mechanism of Fumaria indica in the Treatment of Liver Cancer

Liver cancer (LC), a frequently occurring cancer, has become the fourth leading cause of cancer mortality. The small number of reported data and diverse spectra of pathophysiological mechanisms of liver cancer make it a challenging task and a serious economic burden in health care management. Fumaria indica is a herbaceous annual plant used in various regions of Asia to treat a variety of ailments, including liver cancer. Several in vitro investigations have revealed the effectiveness of F. indica in the treatment of liver cancer; however, the exact molecular mechanism is still unrevealed. In this study, the network pharmacology technique was utilized to characterize the mechanism of F. indica on liver cancer. Furthermore, we analyzed the active ingredient-target-pathway network and uncovered that Fumaridine, Lastourvilline, N-feruloyl tyramine, and Cryptopine conclusively contributed to the development of liver cancer by affecting the MTOR, MAPK3, PIK3R1, and EGFR gene. Afterward, molecular docking was used to verify the effective activity of the active ingredients against the prospective targets. The results of molecular docking predicted that several key targets of liver cancer (along with MTOR, EGFR, MAPK3, and PIK3R1) bind stably with the corresponding active ingredient of F. indica. We concluded through network pharmacology methods that multiple biological processes and signaling pathways involved in F. indica exerted a preventing effect in the treatment of liver cancer. The molecular docking results also provide us with sound direction for further experiments. In the framework of this study, network pharmacology integrated with docking analysis revealed that F. indica exerted a promising preventive effect on liver cancer by acting on liver cancer-associated signaling pathways. This enables us to understand the biological mechanism of the anti liver cancer activity of F. indica.

Bio-Active Compounds from Teucrium Plants Used in the Traditional Medicine of Kurdistan Region, Iraq

Herbal medicine is still widely practiced in the Kurdistan Region, Iraq, especially by people living in villages in mountainous regions. Seven taxa belonging to the genus Teucrium (family Lamiaceae) are commonly employed in the Kurdish traditional medicine, especially to treat jaundice, stomachache and abdominal problems. We report, in this paper, a comprehensive account about the chemical structures and bioactivities of most representative specialized metabolites isolated from these plants. These findings indicate that Teucrium plants used in the folk medicine of Iraqi Kurdistan are natural sources of specialized metabolites that are potentially beneficial to human health.

An exploratory study on the mechanism of Huangqi Guizhi Wuwu Decoction in the treatment of neuropathic pain

Huangqi Guizhi Wuwu Decoction (HGWD) has a definite effect on neuropathic pain (NP), whereas the specific mechanism has not been elucidated. The components and targets in HGWD were collected and identified through System Pharmacology Database (Traditional Chinese Medicine Database and Analysis Platform). Genecards and Online Mendelian Inheritance in Man databases were used to search for NP-related genes. The Venn diagram was drawn to get the intersection target. Cytoscape 3.8.0 software was used to construct the compound-disease-target-pathway networks. STRING database was applied to analyze protein-protein interaction of potential targets. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were used to identify the function of genes related to NP. Finally, molecular docking was performed to visualize the binding mode and affinity between proteins and active ingredients. According to the intersection target of the Venn diagram, the network graph is constructed by Cytoscape and the results show the five compounds, β-sitosterol, (+)-catechin, quercetin, Stigmasterol, kaempferol, and 15 genes (CASP3, FOS, GSK3B, HSP90AA1, IKBKB, IL6, MAPK8, RELA, ICAM1, SELE, ELK1, HSPB1, PRKACA, PRKCA, RAF1) were highly correlated with NP. KEGG and GO of 15 genes results that TNF, IL-17 and MAPK signaling pathway were Significantly related to the pathological mechanism of NP. Molecular docking showed that core genes in this network were IL-6 (TNF and IL-17 signaling pathways), ICAM1 (TNF signaling pathway), and CASP3 (three signal pathways). This study found that the five active compounds, three core genes, and three signaling pathways may be the key to the treatment of NP by HGWD.

Phytochemical-based nanodrug delivery in cancer therapy

There are estimated to be 13.1 million cancer deaths by 2030, with 7.6 million deaths occurring each year. Phytochemicals have long been used in traditional medicine to cure cancer. However, conventional therapy for metastatic illness may fail if cancer cells become resistant to multiple anticancer drugs. Phytochemicals encapsulated in nano-based medication delivery devices were studied for their cancer- and chemo-preventive properties. Nanocarriers containing phytoconstituents have been studied in terms of loading efficiency, nanocarrier size, the release profile of the drug, and cell inhibition and treatment tests.

Mechanism of Action of Flavonoids of Oxytropis falcata on the Alleviation of Myocardial Ischemia–Reperfusion Injury

Oxytropis falcata Bunge is a plant used in traditional Tibetan medicine, with reported anti-inflammatory and antioxidants effects and alleviation of myocardial ischemia reperfusion injury (MIRI). However, the underlying mechanism against MIRI and the phytochemical composition of O. falcata are vague. One fraction named OFF1 with anti-MIRI activity was obtained from O. falcata, and the chemical constituents were identified by ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC–MS). The potential targets and signaling pathways involved in the action of O. falcata against MIRI were predicted by network pharmacology analysis, and its molecular mechanism on MIRI was determined by in vitro assays. The results revealed that flavonoids are the dominant constituents of OFF1. A total of 92 flavonoids reported in O. falcata targeted 213 potential MIRI-associated factors, including tumor necrosis factor (TNF), prostaglandin-endoperoxide synthase 2 (PTGS2), and the NF-κB signaling pathway. The in vitro assay on H9c2 cardiomyocytes subjected to hypoxia/reoxygenation injury confirmed that the flavonoids in OFF1 reduced myocardial marker levels, apoptotic rate, and the inflammatory response triggered by oxidative stress. Moreover, OFF1 attenuated MIRI by downregulating the ROS-mediated JNK/p38MAPK/NF-κB pathway. Collectively, these findings provide novel insights into the molecular mechanism of O. falcata in alleviating MIRI, being a potential therapeutic candidate.

Exploration of hanshi zufei prescription for treatment of COVID-19 based on network pharmacology

Objective

Network pharmacology combines drug and disease targets with biological information networks based on the integrity and systematicness of the interactions between drugs and disease targets. This study aims to explore the molecular basis of Hanshi Zufei formula for treatment of COVID-19 based on network pharmacology and molecular docking techniques.

Methods

Using TCMSP, the chemical constituents and molecular targets of Atractylodis Rhizoma, Citri Reticulatae Pericarpium, Magnoliae Officinalis Cortex, Pogostemonis Herba, Tsaoko Fructus, Ephedrae Herba, Notopterygii Rhizoma et Radix, Zingiberis Rhizoma Recens, and Arecae Semen were investigated. The predicted targets of novel coronavirus were screened using the NCBI and GeneCards databases. To further screen the drug-disease core targets network, the corresponding target proteins were queried using multiple databases (Biogrid, DIP, and HPRD), a protein interaction network graph was constructed, and the network topology was analyzed. The molecular docking studies were also performed between the network’s top 15 compounds and the coronavirus (SARS-CoV-2) 3CL hydrolytic enzyme and angiotensin conversion enzyme II (ACE2).

Results

The herb-active ingredient-target network contained nine drugs, 86 compounds, and 49 drug-disease targets. Gene ontology (GO) enrichment analysis resulted in 1566 GO items (P < 0.05), among which 1438 were biological process items, 35 were cell composition items, and 93 were molecular function items. Fourteen signal pathways were obtained by enrichment screening of the KEGG pathway database (P < 0.05). The molecular docking results showed that the affinity of the core active compounds with the SARS-CoV-2 3CL hydrolase was better than for the other compounds.

Conclusion

Several core compounds can regulate multiple signaling pathways by binding with 3CL hydrolase and ACE2, which might contribute to the treatment of COVID-19.

Wenfei Buqi Tongluo Formula Against Bleomycin-Induced Pulmonary Fibrosis by Inhibiting TGF-β/Smad3 Pathway

Pulmonary fibrosis (PF) is the end stage of various chronic and progressive interstitial lung diseases. TGF-β, a profibrotic cytokine, can promote epithelial–mesenchymal transition (EMT), extracellular matrix (ECM) accumulation, and fibroblast proliferation, which contribute to progressive lung remodeling in PF. The Wenfei Buqi Tongluo (WBT) formula has been certified to be effective in the prevention and treatment of PF in clinical practice and has inhibitory effects on EMT, inflammation, and profibrotic factors. However, the pharmacological mechanisms of WBT against PF need to be further explored. In this study, we first analyzed the chemical components of the WBT formula using the UHPLC/Q-TOF-MS analysis. The potential targets of the identified compounds from WBT were predicted by the network pharmacology, which was confirmed by in vivo and in vitro study. After screening by the PubChem database, we first identified the 36 compounds of WBT and predicted the TGF-β signaling pathway, with ECM degradation as potential mechanism of WBT against PF by the network pharmacology. Furthermore, WBT treatment inhibited the levels of TGF-β and Smad3 phosphorylation and subsequently alleviated EMT and ECM accumulation in the bleomycin-induced mouse model and TGF-β1–induced cell model. These findings indicate that WBT can block the progressive process of PF by inhibiting EMT and promoting ECM degradation via the TGF-β/Smad3 pathway. This study may provide new insights into the molecular mechanism of WBT for the prevention and treatment of PF in the clinical application.

Implementation of System Pharmacology and Molecular Docking Approaches to Explore Active Compounds and Mechanism of Ocimum Sanctum against Tuberculosis

Worldwide, Tuberculosis (TB) is caused by Mycobacterium tuberculosis bacteria. Ocimum sanctum, commonly known as holy basil (Tulsi), is an herbaceous perennial that belongs to the family Lamiaceae and is considered one of the most important sources of medicine and drugs for the treatment of various diseases. The presented study aims to discover the potential phenomenon of Ocimum sanctum in the medicament of tuberculosis using a network pharmacology approach. Active ingredients of Ocimum sanctum were fetched through two different databases and from literature review and then targets of these compounds were harvested by SwissTargetPrediction. Potential targets of TB were downloaded from GeneCards and DisGNet databases. After screening of mutual targets, enrichment analysis through DAVID was performed. Protein–protein interaction was performed using the String database and visualized by Cytoscape. Then the target-compound-pathway network was constructed with Cytoscape. In the end, molecular docking was performed to get the potential active ingredients against tuberculosis. Eight active ingredients with 776 potential therapeutic targets were obtained from O. sanctum, 632 intersected targets from two databases were found in TB, 72 common potential targets were found from TB and O. sanctum. The topological analysis exposes those ten targets that formed the core PPI network. Furthermore, molecular docking analysis reveals that active compounds have the greater binding ability with the potential target to suppress TB.

A review of the phytochemistry, ethnopharmacology and biological activities of Teucrium genus (Germander)

Teucrium L (Lamiaceae) is mainly distributed in the Mediterranean area. A comprehensive survey in the electronic databases (during 2000-2020 years) with keywords of 'Teucrium' and 'Germander' showed that chemical analyses are available for 27 species, with sesquiterpenoids, iridoids, di and triterpenoids, and phenolic compounds as identified structures. The neo-clerodane diterpenoids as potential chemotaxonomic markers were the main compounds of this genus. As a result, Italy and Turkey have good attempts at phytochemical analysis. The pharmacological activities of different species including antioxidant, cytotoxic activity, antidiabetic, antimicrobial, anti-inflammatory and anti-insect have been summarized. Teucrium polium and Teucrium chamaedrys mainly have been used in digestive problems and diabetes in traditional medicine. Evidence-based clinical trials are needed to confirm the therapeutic properties of this genus. As well to the popularity of Asian and Anatolian species as ingredients in contemporary medicines and products, further research is required in comparison to European species.

Utilizing Network Pharmacology and Molecular Docking Integrated Surface Plasmon Resonance Technology to Investigate the Potential Targets and Mechanisms of Tripterygium wilfordii against Pulmonary Artery Hypertension

BACKGROUND

Pulmonary artery hypertension (PAH) is a rare, life-limiting cardiopulmonary disorder characterized by the progressive and remodeling of pulmonary vasculature. Although the development of the technology brings us many approaches for the treatment of PAH, the effect of treatment is unsatisfactory. Tripterygium wilfordii (TW), as a traditional Chinese medicine (TCM), has been widely used in anti-inflammation, anticancer, and other fields. However, the potential of TW in treating PAH is currently unclear.

METHODS

Active ingredients and their corresponding genes were harvested from the Traditional Chinese Medicine Database and Analysis Platform (TCMSP), CTD, and STITCH. Meanwhile, genes associated with PAH were adopted from OMIM and GeneCards databases. Through Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses, potential targeting KEGG pathways and functions were further collected. Then, STRING was used to generate the protein-protein interaction (PPI) network. The "ingredients-targets-pathway" network was built by Cystoscope. Finally, the binding between active ingredients of TW and corresponding targets of PAH was identified via molecular docking technology and surface plasmon resonance (SPR) experiments.

RESULTS

The network pharmacology analysis revealed 36 active ingredients in TW and 150 potential targets related to the treatment of PAH with TW. Moreover, GO enrichment analysis showed that the key function in molecular function (MF) was related to enzyme binding, the key function in biological process (BP) was related to cellular response to organic substance, and the key function in cellular component (CC) was related to KEGG enrichment analysis and found that it was closely related to the IL-17 signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, and apoptosis. At last, molecular docking results revealed that the main active ingredients of TW had a strong binding ability with the PAH target protein. In addition, the SPR experiment revealed that kaempferol was combined with the CASP3 protein rather than PARP1, while triptolide was combined with PARP1 rather than the CASP3 protein.

CONCLUSION

TW may have therapeutic effects on PAH through multitargets and multimethods, which provide a scientific basis for further elaborating the mechanism of Tripterygium wilfordii in the treatment of PAH.

A combined network pharmacology and molecular biology approach to investigate the active ingredients and potential mechanisms of mulberry (Morus alba L.) leaf on obesity

BACKGROUND

As one of traditional Chinese medicine, mulberry leaf is abundant in diverse active ingredients and widely used for the treatment of metabolic disease and its complications. However, there are a few of reports on its application in the prevention and treatment of obesity. And the molecular mechanism on the anti-obesity of mulberry leaf are unknown till now.

PURPOSE

The present study aimed to evaluate the potential ingredients and targets of mulberry leaf and uncover the anti-obesity mechanisms by using the network pharmacology tactics and verify its effect by biological experiments.

STUDY DESIGN

Active ingredients and key targets of mulberry leaf, genes related to obesity were screened through public database. Based on the results of network pharmacology, the flavonoids-enriched fraction of mulberry leaf (MLF) was extracted and composition of this fraction was identified. After that, HepG2 cells model of lipid accumulation was established for verifying the effect of MLF and related mechanisms.

RESULTS

A total of 37 active ingredients in mulberry leaf, 192 predicted biological targets and 8813 obesity-related targets were determined, of which 180 overlapping targets might have obvious curative effects on obesity. The networks showed that mulberry leaf might play a role through key targets, such as AKT, MAPK and IL-6, and regulated PI3K-Akt signaling pathway. Based on HPLC-ESI-QQQ-MS analysis, 13 constituents of MLF were identified, including 9 flavonoids. Furthermore, HepG2 cells model of lipid accumulation was established. The results indicated that MLF treatment could down-regulate the secretion of inflammatory cytokines, as well as clearly inhibited lipid droplets formation and alleviated TC, TG, HDL-C and LDL-C levels. Positive effect was observed on hypolipidemic efficacy due to the regulation of PI3K/Akt/Bcl-xl pathway, as indicated by the amelioration of PI3K, Akt and Bcl-xl gene and protein expression.

CONCLUSION

This study firstly systematically disclose the multi-ingredients, multi-targets mechanisms of mulberry leaf on obesity by using network pharmacology approach, and validate in HepG2 cells that the protective effect of MLF against obesity involved both inflammation response and lipid metabolism involving PI3K/Akt/Bcl-xl signaling pathway. It provides indications for further mechanistic research of mulberry leaf and also for the development as a potential candidate for the therapy for obese patients.

Elucidating the Effects of Curcumin against Influenza Using In Silico and In Vitro Approaches

The influenza virus is a constantly evolving pathogen that challenges medical and public health systems. Traditionally, curcumin has been used to treat airway inflammatory diseases, such as bronchitis and pneumonia. To elucidate common targets of curcumin and influenza infection and underlying mechanisms, we employed network pharmacology and molecular docking approaches and confirmed results using in vitro experiments. Biological targets of curcumin and influenza were collected, and potential targets were identified by constructing compound–disease target (C-D) and protein–protein interaction (PPI) networks. The ligand–target interaction was determined using the molecular docking method, and in vitro antiviral experiments and target confirmation were conducted to evaluate curcumin’s effects on influenza. Our network and pathway analyses implicated the four targets of AKT1, RELA, MAPK1, and TP53 that could be involved in the inhibitory effects of curcumin on influenza. The binding energy calculations of each ligand–target interaction in the molecular docking showed that curcumin bound to AKT1 with the highest affinity among the four targets. In vitro experiments, in which influenza virus-infected MDCK cells were pre-, co-, or post-treated with curcumin, confirmed curcumin’s prophylactic and therapeutic effects. Influenza virus induction increased the level of mRNA expression of AKT in MDCK cells, and the level was attenuated by curcumin treatment. Collectively, our findings identified potential targets of curcumin against influenza and suggest curcumin as a potential therapy for influenza infection.

A preliminary study on the neurotoxic mechanism of harmine in Caenorhabditis elegans

Harmine is a beta-carboline and harmala alkaloid with extensive bioactivities. However, its toxicity, especially in neural system, is not systematically assessed and the toxic mechanism is not yet clear. Using Caenorhabditis elegans (C. elegans) as a model system, we found that harmine exhibited dosage dependent (0, 5, 10, 20, 40, 80, 160, and 320 μmol/L) toxic effect, such as growth inhibition, egg laying defects, shortened life span and increased mortality. Although harmine did not result in obvious structural alterations in neurite or death of neurons, it did show direct acetylcholinesterase inhibition activity. Further, we found that harmine treatment decreased worm pharyngeal pump rate and lowered the content of nitric oxide (NO) in worm body, implying foraging disorders, which is an indicator of acetylcholinergic neuron activity inhibition. Besides, network pharmacology and molecular docking reveals that acetylcholinesterase is one of the major neural toxicity targets as well. Above all, harmine can directly inhibit the activity of acetylcholinesterase, leading to excessive accumulation of acetylcholine, which may be one of the harmine neurotoxicity mechanisms.

Uncovering the pharmacological mechanisms of Xijiao Dihuang decoction combined with Yinqiao powder in treating influenza viral pneumonia by an integrative pharmacology strategy

Xijiao Dihuang decoction combined with Yinqiao powder (XDD-YQP) is a classical combination formula; however, its therapeutic effects in treating influenza viral pneumonia and the pharmacological mechanisms remain unclear. The therapeutic effect of XDD-YQP in influenza viral pneumonia was evaluated in mice. Subsequently, an everted gut sac model coupled with UPLC/Q-TOF MS were used to screen and identify the active compounds of XDD-YQP. Furthermore, network pharmacological analysis was adopted to probe the mechanisms of the active compounds. Lastly, we verified the targets predicted from network pharmacological analysis by differential bioinformatics analysis. Animal experiments showed that XDD-YQP has a therapeutic effect on influenza viral pneumonia. Moreover, 113 active compounds were identified from intestinal absorbed solutions of XDD-YQP. Using network pharmacological analysis, 90 major targets were selected as critical in the treatment of influenza viral pneumonia through 12 relevant pathways. Importantly, the MAPK signaling pathway was found to be closely associated with the other 11 pathways. Moreover, seven key targets, EGFR, FOS, MAPK1, MAP2K1, HRAS, NRAS, and RELA, which are common targets in the MAPK signaling pathway, were investigated. These seven key targets were identified as differentially expressed genes (DEGs) between influenza virus-infected and uninfected individuals. Hence, the seven key targets in the MAPK signaling pathway may play a vital role in the treatment of influenza viral pneumonia with XDD-YQP. This research may offer an integrative pharmacology strategy to clarify the pharmacological mechanisms of traditional Chinese medicines. The results provide a theoretical basis for a broader clinical application of XDD-YQP.

Therapeutic targets and biological mechanisms of action of curcumin against Zika virus: In silico and in vitro analyses

Zika virus (ZIKV) is a mosquito-borne flavivirus, that could cause congenital Zika syndrome (CZS), characterized by microcephaly, neurological complications and fetal deaths. No specific treatments for ZIKV are currently available, highlighting the urgent global need to identify and develop therapeutic agents. Drug repositioning of approved natural compounds can provide effective alternative solutions for novel antiviral development. The current study focused on curcumin, a component of turmeric known to exert diverse antiviral effects. We integrated in silico information from publicly available databases to predict interactions between curcumin and potential targets of ZIKV. In our network analysis, we identified four targets, TP53, AKT1, PTEN, and TNF, which were identified as potential targets associated with ZIKV. Based on retrieved targets, we performed molecular docking study and identified curcumin-TNF showed the strongest binding among four targets. The anti-Zika effects of curcumin were validated in vitro with the aid of antiviral and plaque reduction assay. Curcumin at concentrations ranging from 12.5 to 50 μM displayed significant antiviral activity in a dose-dependent manner (p < 0.05). In view of its natural abundance and prevalence in the human diet, curcumin holds significant promise for treatment of ZIKV infections.

Identification of phytochemicals from North African plants for treating Alzheimer's diseases and of their molecular targets by in silico network pharmacology approach

BACKGROUND

The global social expenses of Alzheimer's disease (AD) have been increased to US$1 trillion due to high cost, side-effects, and low efficiency of the current AD-therapies. Another reason is the lack of preventive drugs and the low-income situation of Asian and African countries. Accordingly, patients rather prefer traditional herbal remedies. Network-pharmacology has been a well-established method for the visualization and the construction of disorder target protein-drug framework. This could aid in the identification of drugs molecular-mechanisms.

AIM

The aim of this study is to investigate the phytochemical constituents that could target Alzheimer's disease from the North African plants. This could be done by exploring their possible mechanisms of action through molecular network pharmacology-based approach.

EXPERIMENTAL PROCEDURE

The Phytochemical-compounds of North-African plants (NAP) have been accessed from open-databank. ADME-screening has been conducted for filtering of the NAP phytochemical-constituents utilizing Qikprop-software. The open STITCH databank has been utilized for the prediction of the phytochemical-constituents target-proteins; UniProt and TDD-DB databanks have been utilized for distinguishing AD-related proteins. Phytochemical constituent-target protein (C-T) and plant-phytochemical constituent-target protein (P-C-T) frameworks have been assembled utilizing Cytoscape to interpret the anti-Alzheimer's disease mechanism of action of the targeted phytochemical constituents.

RESULTS

The NAP 6842 phytochemical-constituents (from more than 1000 plants) have been exposed to ADME and CNS modulating filtration, generating 94 phytochemical-constituents which have been subjected to target-prediction investigation. The 94 phytochemical-constituents and the 4 AD-identified targets have been associated through 155 edges which formed the main pathways related to AD. Cuparene, alpha-selinene, beta-sesquiphellandrene, calamenene, 2-4-dimethylheptane, undecane, n-tetradecane, hexadecane, nonadecane, n-eicosane, and heneicosane have had C-T network highest combined-score, whilst the proteins MAO-B, HMG-CoA, BACE1, and GCR have been the most enriched ones by comprising the uppermost combined-scores of C-T. Hypericum perforatum, Piper nigrum, Juniperus communis, Levisticum officinale, Origanum vulgare acquired the uppermost number of P-C-Target interactions.

CONCLUSION

The phytochemical-targets prediction of NAP utilizing molecular-network pharmacology-based investigation has paved the way for networking multi-target, multi-constituent, and multi-pathway mechanisms. This may introduce potential future targets for the regulation and the management of Alzheimer's disease.

TAXONOMY CLASSIFICATION BY EVISE

Alzheimer's disease, Network pharmacology, In-silico computer based approach.

Study on Network Pharmacological Analysis and Preliminary Validation to Understand the Mechanisms of Plantaginis Semen in Treatment of Gouty Nephropathy

Plantaginis Semen (PS) has been used to promote diuresis and clear away dampness. Recent reports have shown that PS can be used to treat gouty nephropathy (GN). However, the action and mechanism of PS have not been well defined in treating GN. The present study aimed to define the molecular mechanisms of PS as a potential therapeutic approach to treat GN. A combination of network pharmacology and validation experiments in GN is used to understand the potential mechanism. Information on pharmaceutically active compounds in PS and gene information related to GN was obtained from public databases. The compound target network and protein-protein interaction network were constructed to study the mechanism of action of PS in the treatment of GN. The mechanism of action of PS in the treatment of GN was analyzed via Gene Ontology (GO) biological process annotation and Kyoto Gene and Genomics Encyclopedia (KEGG) pathway enrichment. Validation experiments were performed to verify the core targets. The GN rat model was prepared by the method of combining yeast and adenine. Hematoxylin-eosin (HE) staining was used to observe the morphology of renal tissue in rats. ELISA was applied to detect TGF-β1, TNF-α, and IL-1β levels in renal tissue. The expressions of TGF-β1, TNF-α, and IL-1β were determined using immunohistochemistry. Through the results of network pharmacology, we obtained 9 active components, 118 predicted targets, and 149 GN targets from the public database. Based on the protein-protein interaction (PPI), 26 hub genes for interaction with PS treating for GN were screened, including MMP9, TNF, IL1β, and IL6. The enrichment analysis results showed that the treatment of GN with PS was mainly involved in the TGF-β1 signaling pathway, MAPK signaling pathway, TNF signaling pathway, NF-κB signaling pathway, and PI3K Akt signaling pathway. Validation experiment results showed that PS could reduce the content of urinary protein and UA and deregulate the expression of TGF-β1, TNF-α, and IL-1β in the treatment of GN. The molecular mechanism of PS in the treatment of GN indicated the synergistic features of multicomponent, multitarget, and multipathway of traditional Chinese medicine, which provided an essential scientific basis for further elucidating the mechanism of PS in the treatment of GN.

Network pharmacology-based therapeutic mechanism of Kuanxiong aerosol for angina pectoris

ETHNOPHARMACOLOGICAL RELEVANCE

Kuanxiong aerosol has been reported to be an effective and safe clinical treatment for angina pectoris (AP).

AIM OF THE STUDY

To explore the potential pharmacological mechanism of Kuanxiong aerosol by combined methods of network pharmacology prediction and experimental verification.

MATERIALS AND METHODS

Networks of Kuanxiong aerosol-associated targets and AP-related genes were constructed through STRING database. Potential targets and pathway enrichment analysis related to the therapeutic efficacy of Kuanxiong aerosol were identified using Cytoscape and Database for Annotation, Visualization and Integrated Discovery (DAVID). To explore the mechanism of action of Kuanxiong aerosol, its in vitro effects on myocardial hypoxia, inflammatory cytokines, and oxidative injury, and its in vivo pharmacological effects on myocardial ischemia and cardiac fibrosis were studied in rat models.

RESULTS

Network pharmacology analysis revealed that the potential targets mainly include the Fas ligand (FASLG), interleukin 4 (IL4), and catalase (CAT), which mediated the processes of apoptosis, and cellular responses to hypoxia, lipopolysaccharide (LPS), reactive oxygen species (ROS), and mechanical stimulus. Multiple pathways, such as the hypoxia-inducible factor 1 (HIF1) and tumor necrosis factor (TNF) pathways were found to be closely related to the pharmacological protective mechanism of Kuanxiong aerosol against AP. In addition, Kuanxiong aerosol suppressed the hypoxia, LPS, and hydrogen peroxide (H₂O₂)-induced injuries of H9c2 cardiomyocytes through the regulation of HIF1A, suppressed expression of IL6 and TNF, and antioxidant property. In the rat model of myocardial ischemia, Kuanxiong aerosol was found to lower the creatine kinase (CK), creatine kinase-myocardial band (CK-MB), and lactate dehydrogenase (LDH) levels, without altering the hemodynamic function. Kuanxiong aerosol was capable of attenuating cardiac fibrosis and improving cardiac function in a cardiac fibrosis rat model.

CONCLUSIONS

This study revealed that the pharmacological mechanisms of Kuanxiong aerosol for AP therapy were related to anti-myocardial ischemia, anti-inflammation, and anti-oxidation via a non-hemodynamic manner, indicating that Kuanxiong aerosol is a preferable drug clinically for AP treatment due to its both preventive and protective effects.

Integrated Network Pharmacology Analysis and Experimental Validation to Reveal the Mechanism of Anti-Insulin Resistance Effects of Moringa oleifera Seeds

Background and Purpose

Insulin resistance (IR) is one of the factors that results in metabolic syndrome, type 2 diabetes mellitus and different aspects of cardiovascular diseases. Moringa oleifera seeds (MOS), traditionally used as an antidiabetic food and traditional medicine in tropical Asia and Africa, have exhibited potential effects in improving IR. To systematically explore the pharmacological mechanism of the anti-IR effects of MOS, we adopted a network pharmacology approach at the molecular level.

Methods

By incorporating compound screening and target prediction, a feasible compound-target-pathway network pharmacology model was established to systematically predict the potential active components and mechanisms of the anti-IR effects of MOS. Biological methods were then used to verify the results of the network pharmacology analysis.

Results

Our comprehensive systematic approach successfully identified 32 bioactive compounds in MOS and 44 potential targets of these compounds related to IR, as well as 37 potential pathways related to IR. Moreover, the network pharmacology analysis revealed that glycosidic isothiocyanates and glycosidic benzylamines were the major active components that improved IR by acting on key targets, such as SRC, PTPN1, and CASP3, which were involved in inflammatory responses and insulin-related pathways. Further biological research demonstrated that the anti-IR effects of MOS were mediated by increasing glucose uptake and modulating the expression of SRC and PTPN1.

Conclusion

Our study successfully predicts the active ingredients and potential targets of MOS for improving IR and helps to illustrate mechanism of action at a systemic level. This study not only provides new insights into the chemical basis and pharmacology of MOS but also demonstrates a feasible method for discovering potential drugs from traditional medicines.

Network pharmacology based virtual screening of active constituents of Prunella vulgaris L. and the molecular mechanism against breast cancer

Prunella vulgaris L, a perennial herb widely used in Asia in the treatment of various diseases including cancer. In vitro studies have demonstrated the therapeutic effect of Prunella vulgaris L. against breast cancer through multiple pathways. However, the nature of the biological mechanisms remains unclear. In this study, a Network pharmacology based approach was used to explore active constituents and potential molecular mechanisms of Prunella vulgaris L. for the treatment of breast cancer. The methods adopted included active constituents prescreening, target prediction, GO and KEGG pathway enrichment analysis. Molecular docking experiments were used to further validate network pharmacology results. The predicted results showed that there were 19 active ingredients in Prunella vulgaris L. and 31 potential gene targets including AKT1, EGFR, MYC, and VEGFA. Further, analysis of the potential biological mechanisms of Prunella vulgaris L. against breast cancer was performed by investigating the relationship between the active constituents, target genes and pathways. Network analysis showed that Prunella vulgaris L. exerted a promising preventive effect on breast cancer by acting on tumor-associated signaling pathways. This provides a basis to understand the mechanism of the anti-breast cancer activity of Prunella vulgaris L.

Pharmacological Effects of Agastache rugosa against Gastritis Using a Network Pharmacology Approach

Agastache rugosa is used as a Korean traditional medicine to treat gastric diseases. However, the active ingredients and pharmacological targets of A. rugosa are unknown. In this study, we aimed to reveal the pharmacological effects of A. rugosa on gastritis by combining a mice model and a network pharmacology method. The macrophage and gastritis-induced models were used to evaluate the pharmacological effects of A. rugosa. The results show that A. rugosa relieved mucosal damage induced by HCl/EtOH in vivo. Network analysis identified 99 components in A. rugosa; six components were selected through systematic screening, and five components were linked to 45 gastritis-related genes. The main components were acacetin and luteolin, and the identified core genes were AKT serine/threonine kinase 1 (AKT1), nuclear factor kappa B inhibitor alpha (NFKBIA), and mitogen-activated protein kinase-3 (MAPK3) etc. in this network. The network of components, target genes, protein–protein interactions, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was closely connected with chemokines and with phosphoinositide 3-kinase-Akt (PI3K/AKT), tumor-necrosis-factor alpha (TNFα), mitogen-activated protein kinase, nuclear factor kappa B, and Toll-like receptor (TLR) pathways. In conclusion, A. rugosa exerts gastro-protective effects through a multi-compound and multi-pathway regulatory network and holds potential for treating inflammatory gastric diseases.

Identifying Active Compounds and Targets of Fritillariae thunbergii against Influenza-Associated Inflammation by Network Pharmacology Analysis and Molecular Docking

Complications due to influenza are often associated with inflammation with excessive release of cytokines. The bulbs of Fritillariae thunbergii (FT) have been traditionally used to control airway inflammatory diseases, such as bronchitis and pneumonia. To elucidate active compounds, the targets, and underlying mechanisms of FT for the treatment of influenza-induced inflammation, systems biology was employed. Active compounds of FT were identified through the TCMSP database according to oral bioavailability (OB) and drug-likeness (DL) criteria. Other pharmacokinetic parameters, Caco-2 permeability (Caco-2), and drug half-life (HL) were also identified. Biological targets of FT were retrieved from DrugBank and STITCH databases, and target genes associated with influenza, lung, and spleen inflammation were collected from DisGeNET and NCBI databases. Compound-disease-target (C-D-T) networks were constructed and merged using Cytoscape. Target genes retrieved from the C-D-T network were further analyzed with GO enrichment and KEGG pathway analysis. In our network, GO and KEGG results yielded two compounds (beta-sitosterol (BS) and pelargonidin (PG)), targets (PTGS1 (COX-1) and PTGS2 (COX-2)), and pathways (nitric oxide, TNF) were involved in the inhibitory effects of FT on influenza-associated inflammation. We retrieved the binding affinity of each ligand-target, and found that PG and COX-1 showed the strongest binding affinity among four binding results using a molecular docking method. We identified the potential compounds and targets of FT against influenza and suggest that FT is an immunomodulatory therapy for influenza-associated inflammation.

Natural tyrosine kinase inhibitors acting on the epidermal growth factor receptor: Their relevance for cancer therapy

Epidermal growth factor receptor (EGFR), also known as ErbB-1/HER-1, plays a key role in the regulation of the cell proliferation, migration, differentiation, and survival. Since the constitutive activation or overexpression of EGFR is nearly found in various cancers, the applications focused on EGFR are the most widely used in the clinical level, including the therapeutic drugs of targeting EGFR, monoclonal antibodies (mAbs) and tyrosine kinase inhibitors (TKIs).Over the past decades, the compounds from natural sources have been a productive source of novel drugs, especially in both discovery and development of anti-tumor drugs by targeting the EGFR pathways as the TKIs. This work presents a review of the compounds from natural sources as potential EGFR-TKIs involved in the regulation of cancer. Moreover, high-throughput drug screening of EGFR-TKIs from the natural compounds has also been summarized.

Marrubium vulgare L.: A Phytochemical and Pharmacological Overview

Marrubium vulgare is a plant with high bioactive potential. It contains marrubiin, a labdane diterpene that is characteristic for this genus, as well as a complex mixture of phenolic compounds. According to numerous studies, M. vulgare acts as a good antioxidant agent, and due to this, it could potentially be useful in treatments of cancer, diabetes mellitus, and liver diseases. In addition, its anti-inflammatory, wound-healing, antihypertensive, hypolipidemic, and sedative potential are discussed. Apart from that, its antimicrobial activity, especially against Gram+ bacteria, fungi, herpes simplex virus, and parasites such as Toxoplasma gondii, Trichomonas vaginalis, and Plasmodium berghei-berghei was recorded. Additionally, it could be used as a chicken lice repellent, herbicide, and natural insecticide against mosquito larvae and natural molluscicide. In veterinary medicine, M. vulgare can be used as an anthelmintic against the eggs and larvae of bovine strongyles parasites, and as an antibiotic against bovine mastitis caused by resistant bacterial strains. Due to the mentioned benefits, there is a tendency for the cultivation of M. vulgare in order to ensure high-quality raw material, but more firm scientific evidence and well-designed clinical trials are necessary for the well-established use of M. vulgare herb and its preparations.

A novel artificial intelligence protocol for finding potential inhibitors of acute myeloid leukemia

There is currently no effective treatment for acute myeloid leukemia, and surgery is also ineffective as an important treatment for most tumors. Rapidly developing artificial intelligence technology can be applied to different aspects of drug development, and it plays a key role in drug discovery. Based on network pharmacology and virtual screening, candidates were selected from the molecular database. Nine artificial intelligence algorithm models were used to further verify the candidates' potential. The 350 training results of the deep learning model showed higher credibility, and the R-square of the training set and test set of the optimal model reached 0.89 and 0.84, respectively. The random forest model has an R-square of 0.91 and a mean square error of only 0.003. The R-square of the Adaptive Boosting model and the Bagging model reached 0.92 and 0.88, respectively. Molecular dynamics simulation evaluated the stability of the ligand-protein complex and achieved good results. Artificial intelligence models had unearthed the promising candidates for STAT3 inhibitors, and the good performance of most models showed that they still had practical value on small data sets.

A bioinformatics investigation into the pharmacological mechanisms of the effect of the Yinchenhao decoction on hepatitis C based on network pharmacology

Background

Globally, more than 170 million people are infected with hepatitis C virus, a major cause of cirrhosis and hepatocellular carcinoma. The Yinchenhao Decoction (YCHD) is a classic formula comprising three herbal medicines. This decoction have long been used in China for clinically treating acute and chronic infectious hepatitis and other liver and gallbladder damp heat-accumulation disorders.

Methods

In this study, we identified 32 active ingredients and 200 hepatitis C proteins and established a compound-predicted target network and a hepatitis C protein–protein interaction network by using Cytoscape 3.6.1. Then, we systematically analyzed the potential targets of the YCHD for the treatment of hepatitis C. Finally, molecular docking was applied to verify the key targets. In addition, we analyzed the mechanism of action of the predicted targets by the Kyoto Encyclopedia of Genes and Genomes and gene ontology analyses.

Results

This study adopted a network pharmacology approach, mainly comprising target prediction, network construction, module detection, functional enrichment analysis, and molecular docking to systematically investigate the mechanisms of action of the YCHD in hepatitis C. The targets of the YCHD in the treatment of hepatitis C mainly involved PIK3CG, CASP3, BCL2, CASP8, and MMP1. The module and pathway enrichment analyses showed that the YCHD had the potential to influence varieties of biological pathways, including the TNF signaling pathway, Ras signaling pathway, PI3K-Akt signaling pathway, FoxO signaling pathway, and pathways in cancer, that play an important role in the pathogenesis of hepatitis C.

Conclusion

The results of this study preliminarily verified the basic pharmacological effects and related mechanisms of the YCHD in the treatment of hepatitis C.

Network pharmacology-based study on the mechanism of Yiganling capsule in hepatitis B treatment

Background

Yiganling (YGL) capsule is a traditional Chinese medicine preparation consisting of eight herbs that has been clinically proven to have a favorable treatment effect on Hepatitis B (HB). However, due to its multiple targets and multi-pharmacological effects, the mechanisms of YGL capsule in the treatment of HB are unknown.

Methods

First, the chemical constituents of YGL capsules were obtained from the Chinese medicine database, and YGL capsules were constructed. Second, active compounds were screened by the ADME model. The target fishing model was used to screen the corresponding targets of active compounds and to construct a compounds and compound targets network. Using human disease databases and literature mining, we systematically identified genes associated with HB, constructed disease-specific protein-protein interaction networks, and performed clustering and enrichment analyses of these networks. These networks were then merged to obtain a compound-disease target network, and cluster and enrichment analyses were performed on the compound-disease target network to acquire a compounds-disease targets-mechanism network and a clustering network.

Results

We successfully built eight pharmacological network diagrams, including four primary networks and other network maps. The four dominating network maps included a HB disease-associated protein-protein interaction network, a YGL capsule compounds-target network, a YGL capsule ingredient target-HB disease target network, and a YGL-HB disease mechanism network. Other networks included a pathway of HB disease targets, the HB disease protein-protein interaction cluster analysis network, and the YGL-HB target clustering network.

Conclusion

This study successfully forecasted, illuminated, and confirmed the synergistic effects of HB disease molecules and discovered the potential of HB relevant targets, clusters, and target-related biological processes and signaling pathways. Our research not only provides theoretical support for the molecular and pharmacological mechanisms of YGL capsule in HB treatment, but also provides new research methods for the study of the other traditional Chinese medicinal compounds.

A network pharmacology approach to explore the potential targets underlying the effect of sinomenine on rheumatoid arthritis

OBJECTIVE

To explore the potential targets underlying the effect of sinomenine (SIN) on rheumatoid arthritis (RA) by utilizing a network pharmacology approach.

METHODS

SIN and its drug targets were identified using network analysis followed by experimental validation. First, the Pharmmapper, UniProt and GeneCards databases were mined for information relevant to the prediction of SIN targets and RA-related targets. Second, the SIN-target gene and SIN-RA target gene networks were created in Cytoscape software followed by the collection of the candidate targets of each component by R software. Eventually, the key targets and enriched pathways were examined by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis.

RESULTS

Sixty-seven potential targets of SIN and 3797 related targets involved in RA were subjected to network analysis, and the 20 intersection targets indicated the principal pathways linked to RA. Additionally, 16 key targets, which were linked to more than three genes, were determined to be crucial genes. GO analysis showed that 14 biological processes, 5 cellular components and 2 molecular functions were identified, when corrected by a P value ≤ 0.01. Seven related signaling pathways were identified by KEGG analysis, when corrected according to a Bonferroni P value ≤ 0.05.

CONCLUSION

The present study explored the potential targets and signaling pathways of SIN during the treatment of RA, which may help to illustrate the mechanism (s) involved in the action of SIN and may provide a better understanding of its anti-rheumatoid arthritis effects in terms of inhibiting angiogenesis, synovial hyperplasia, and bone destruction.

Mechanism of action of celastrol against rheumatoid arthritis: A network pharmacology analysis

Network pharmacology uses bioinformatics to broaden our understanding of drug actions and thereby to advance drug discovery. Here we apply network pharmacology to generate testable hypotheses about the multi-target mechanism of celastrol against rheumatoid arthritis. We reconstructed drug-target pathways and networks to predict the likely protein targets of celastrol and the main interactions between those targets and the drug. Then we validated our predictions of four candidate targets (IKK-β, JNK, COX-2, MEK1) by performing docking studies with celastrol. The results suggest that celastrol acts against rheumatoid arthritis by regulating the function of several signaling proteins, including MMP-9, COX-2, c-Myc, TGF-β, c-JUN, JAK-1, JAK-3, IKK-β, SYK, MMP-3, JNK and MEK1, which regulate the functions of Th1 and Th2 cells, macrophages, fibroblasts and endothelial cells in rheumatoid arthritis. Celastrol is predicted to affect networks involved mainly in cancer, connective tissue disorders, organismal injury and abnormalities, tissue development, cell death and survival. This network pharmacology strategy may be useful for discovery of multi-target drugs against complex diseases.