Network analysis, and human and animal studies disclose the anticystitis glandularis effects of vitamin C

Research progress of traditional Chinese medicine compound "Xiaochaihu Decoction" in the treatment of depression

Depression is a common psychiatric disorder under the category of depression syndrome in Traditional Chinese Medicine (TCM) theory. Meanwhile, Xiaochaihu Decoction is a classical TCM formulation regulating Qi, resolving and dissipating stagnation. Clinically, the formulation has long been adopted to treat Shaoyang stagnation syndrome for depression syndrome. In this review, potential targets of action and the corresponding pathways of Xiaochaihu Decoction are explored for depression treatment via network pharmacology. The article also systematically summarizes the active components and pharmacological mechanisms of seven Chinese herbal medicine components in Xiaochaihu Decoction and guides the future study direction of Xiaochaihu Decoction, which may serve a promising treatment for depression.

Network Pharmacologic Analysis of Dendrobium officinale Extract Inhibiting the Proliferation of Gastric Cancer Cells

Globally, gastric cancer (GC) is one of the three most deadly cancers. Dendrobium officinale (D. officinale) is a traditional Chinese medicine (TCM), and its extract can significantly inhibit the proliferation of gastric cancer cells. However, there are no unified conclusions on its potential active components and possible mechanisms of action. This paper aims at exploring the potential active components, targets, and cell pathways of D. officinale extract in inhibiting the proliferation of gastric cancer cells by using network pharmacology and cytology experiments. In this paper, UPLC-MS/MS was used to identify the main chemical components in the extracts of D. officinale, and the an ADME model was used to screen the potential active components. Network pharmacology methods such as target prediction, pathway identification, and network construction were used to determine the mechanism through which the D. officinale extract inhibited gastric cancer cell proliferation. MTT assays, fluorescence confocal microscopy, clone formation, and flow cytometry were used to verify the inhibitory activity of the D. officinale extract on gastric cancer cell proliferation in vitro. The UPLC-MS/MS analysis identified 178 chemical components from the D. officinale extract. Network pharmacology analysis showed that 13 chemical components had the potential to inhibit the proliferation of gastric cancer cells, with the possible involvement of 119 targets and 20 potential signaling pathways. In vitro experiments confirmed that the D. officinale extract could significantly inhibit the proliferation of gastric cancer cells. Therefore, we believe that the D. officinale extract can inhibit the proliferation of gastric cancer cells through effects on multiple components, multiple targets, and multiple pathways.

Mechanisms of Vitamin C Regulating Immune and Inflammation Associated with Neonatal Hypoxic-Ischemic Encephalopathy Based on Network Pharmacology and Molecular Simulation Technology

Background

There are still controversies about the curative effect of vitamin C in treating HIE, and its mechanism of action is not entirely clear. This study is designed to explore the potential molecular mechanism of vitamin C in treating neonatal hypoxic ischemic encephalopathy (HIE).

Methods

The effect targets of vitamin C and the pathogenic targets of neonatal HIE were obtained via retrieval of public databases to screen out the molecular targets of vitamin C acting on neonatal HIE. Gene Ontology (GO) functional annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed on the main targets. Vitamin C and the optimum target structural components are subjected to molecular docking and molecular dynamics simulation analysis via computer software so as to verify their binding activity and stability.

Result

Based on 16 overlapping targets of vitamin C and HIE, seven main targets were identified in this study. According to GO and KEGG analysis, molecular functions (top 25 items) and signal pathways (21 items) related to inflammatory reaction, immune response, and cell transcriptional control may be potential pathways for vitamin C to treat neonatal HIE. Molecular docking and molecular dynamics simulation were adopted to definitively determine the 4 optimum core target spots.

Conclusion

The efficacy of vitamin C on HIE is involved in the immunoregulation and inflammation-related functional processes and signal pathways. These molecular mechanisms, including core targets, will contribute to the clinical practice of neonatal HIE in the future.

Bioinformatics and In Silico Findings Uncover Bio-Targets of Calycosin Against Heart Failure and Diabetes Mellitus

BACKGROUND

Heart failure (HF) and diabetes mellitus (DM) are life-threatening diseases. However, existing clinical drugs to treat HF complicated with DM are relatively limited. In this study, we performed a viable bioinformatics strategy combining network pharmacology and molecular docking to identify potential anti-HF and -DM targets and therapeutic mechanisms of calycosin, a functional phytoestrogen.

METHODS

Web-based databases were used to collect candidate genes/targets of calycosin and HF/DM and then identify the hub bio-targets of calycosin against HF/DM. Using the online-available database, all functional processes and signaling pathways of calycosin against HF/DM were screened and identified before further visualization.

RESULTS

All potential bio-targets of calycosin and HF/DM were collected, and 20 hub targets of calycosin against HF/DM were identified. Interestingly, molecular docking findings indicated that mitogen-activated protein kinase-1 (MAPK1), β-arrestin 1 (ARRB1), and homologue-1 (ABL1) may be potent pharmacological targets of calycosin against HF/DM. In addition, all primary molecular functions of calycosin against HF/DM were identified, including regulating protein binding, ubiquitination, and the metabolic process. Furthermore, the top molecular pathways of calycosin against HF/DM were revealed, including cardiomyocyte and chemokine signaling pathways.

CONCLUSION

Our bioinformatics analysis uncovered the network targets and therapeutic mechanisms of calycosin against HF/DM. For the first time, the current in silico findings revealed that the identified hub targets may be used to screen and treat HF/DM.

Antioxidant Activity and the Potential Mechanism of the Fruit From Ailanthus altissima Swingle

The fruits of Ailanthus altissima Swingle (AS) possess a variety of pharmacological activities. Its antioxidant activity and the potential mode of action have not yet been investigated. In in vitro studies, AS revealed the strong reducing power and DPPH scavenging effect, but hydroxyl radical scavenging activity and ferrous ions-chelating ability were not strong. Meanwhile, the oxidative stress RAW264.7 cell injury model was established, the low and medium-doses of AS showed significant protective effects on the viability of H₂O₂-treated cells by CCK-8 method. Besides, three doses of AS all increased the activities of SOD, CAT, and GSH-Px and decreased the MDA level compared with the H₂O₂ group, suggesting it significantly relieved oxidative stress of cells. The active ingredients and related targets of AS were collected by HERB and Swiss Target Prediction database, the common targets of drugs and diseases database were conducted by GeneCards database platform and the Venny platform. We screened the core targets of AS like threonine kinase1 (AKT1), mitogen-activated protein kinase 1 (MAPK1), sirtuin-1 (SIRT1), mechanistic target of rapamycin kinase (MTOR) by STRING database, and the key pathways involved PI3K-AKT and FoxO signaling pathway by KEGG pathway enrichment analysis. Besides, qRT-PCR revealed AS preconditioning significantly up-regulated the expression level of AKT1, SIRT1, MAPK1, and MTOR in model cells, and the effect was related to the regulation of FoxO and PI3K/AKT signaling pathway. In summary, AS showed significant antioxidant activity and its potential mechanism was regulating FoxO and PI3K/AKT signaling pathway.

Bioinformatics and experimental findings reveal the therapeutic actions and targets of pachymic acid against cystitis glandularis

Pachymic acid (PA), a bioactive ingredient isolated from Poria cocos Wolf, is reported with potential benefits of anti-inflammatory, anti-oxidative actions. It is reasoned that PA may play the potential benefits against cystitis glandularis (CG), an inflammation of the bladder tissue. In this study, we aimed to apply the network pharmacology and molecular docking analyses to reveal concrete anti-CG targets and mechanisms of PA, and then the bioinformatic findings were verified by using clinical and animal samples. The methodological data from network pharmacology approach showed that 303 and 243 reporting targets of CG and PA, and other 31 shared targets of CG and PA were identified. Subsequently, all top targets of PA against CG were screened out, including cyclooxygenase-2, epidermal growth factor receptor, tumor antigen p53 (TP53), tumor necrosis factor-alpha (TNF), interleukin-1 (IL-1) beta, proto-oncogene c-jun. Molecular docking data demonstrated that PA exerted potent bonding capacities with TNF, TP53 proteins in CG. In human study, the findings suggested that overactivated TNF-α expression and suppressed TP53 activation were detected in CG samples. In animal study, PA-treated mice showed reduced intravesical IL-1, IL-6 levels, and lactate dehydrogenase content, downregulated TNF-α and upregulated TP53 proteins in bladder samples. Taken together, our bioinformatics and experimental findings identify the key anti-CG biotargets and mechanisms of PA. More markedly, these pivotal pharmacological targets of PA against CG have been screened out and verified by using computational and experimental analyses.

Clinical characterization and therapeutic targets of vitamin A in patients with hepatocholangiocarcinoma and coronavirus disease

Recent reports indicate that patients with hepatocholangiocarcinoma (CHOL) have a higher morbidity and mortality rate for coronavirus disease (COVID-19). Anti-CHOL/COVID-19 medicines are inexistent. Vitamin A (VA) refers to a potent nutrient with anti-cytotoxic and anti-inflammatory actions. Therefore, this study aimed to determine the potential functions and molecular mechanisms of VA as a potential treatment for patients with both CHOL and COVID-19 (CHOL/COVID-19). The transcriptome data of CHOL patients were obtained from the Cancer Genome Analysis database. Furthermore, the network pharmacology approach and bioinformatics analysis were used to identify and reveal the molecular functions, therapeutic biotargets, and signaling of VA against CHOL/COVID-19. First, clinical findings identified the medical characteristics of CHOL patients with COVID-19, such as susceptibility gene, prognosis, recurrence, and survival rate. Anti-viral and anti-inflammatory pathways, and immunopotentiation were found as potential targets of VA against CHOL/COVID-19. These findings illustrated that VA may contribute to the clinical management of CHOL/COVID-19 achieved by induction of cell repair, suppression of oxidative stress and inflammatory reaction, and amelioration of immunity. Nine vital therapeutic targets (BRD2, NOS2, GPT, MAPK1, CXCR3, ICAM1, CDK4, CAT, and TMPRSS13) of VA against CHOL/COVID-19 were identified. For the first time, the potential pharmacological biotargets, function, and mechanism of action of VA in CHOL/COVID-19 were elucidated.

Therapeutic targets and signaling mechanisms of vitamin C activity against sepsis: a bioinformatics study

Sepsis is a life-threatening complication of pneumonia, including coronavirus disease-2019 (COVID-19)-induced pneumonia. Evidence of the benefits of vitamin C (VC) for the treatment of sepsis is accumulating. However, data revealing the targets and molecular mechanisms of VC action against sepsis are limited. In this report, a bioinformatics analysis of network pharmacology was conducted to demonstrate screening targets, biological functions, and the signaling pathways of VC action against sepsis. As shown in network assays, 63 primary causal targets for the VC action against sepsis were identified from the data, and four optimal core targets for the VC action against sepsis were identified. These core targets were epidermal growth factor receptor (EGFR), mitogen-activated protein kinase-1 (MAPK1), proto-oncogene c (JUN), and signal transducer and activator of transcription-3 (STAT3). In addition, all biological processes (including a top 20) and signaling pathways (including a top 20) potentially involved in the VC action against sepsis were identified. The hub genes potentially involved in the VC action against sepsis and interlaced networks from the Kyoto Encyclopedia of Genes and Genomes Mapper assays were highlighted. Considering all the bioinformatic findings, we conclude that VC antisepsis effects are mechanistically and pharmacologically implicated with suppression of immune dysfunction-related and inflammation-associated functional processes and other signaling pathways. These primary predictive biotargets may potentially be used to treat sepsis in future clinical practice.

Network Pharmacology and bioinformatics analyses identify intersection genes of niacin and COVID-19 as potential therapeutic targets

OBJECTIVES

Patients with colorectal cancer (CRC) may be susceptible to the coronavirus disease-2019 (COVID-19). However, anti-CRC/COVID-19 treatment options are currently unavailable. Since niacin is a vitamin with cytoprotective and anti-inflammatory functions, this study aimed to evaluate the possible functional roles and underlying mechanisms of action of niacin as an anti-COVID-19 and -CRC therapy.

INTERVENTIONS

We used a series of network pharmacology-based and computational analyses to understand and characterize the binding capacity, biological functions, pharmacological targets and therapeutic mechanisms of niacin in CRC/COVID-19.

MEASUREMENTS AND MAIN RESULTS

We revealed the clinical characteristics of CRC patients and COVID-19 patients, including predisposing genes, survival rate and prognosis. Moreover, the results of molecular docking analysis indicated that niacin exerted effective binding capacity in COVID-19. Further, we disclosed the targets, biological functions and signaling pathways of niacin in CRC/COVID-19. The analysis indicated that niacin could help in treating CRC/COVID-19 through cytoprotection, enhancement of immunologic functions, inhibition of inflammatory reactions and regulation of cellular microenvironment. Furthermore, five core pharmacological targets of niacin in CRC/COVID-19 were also identified, including BCL2L1, PTGS2, IL1B, IFNG and SERPINE1.

CONCLUSIONS

This study, for the first time, revealed the niacin-associated molecular functions and pharmacological targets for treating CRC/COVID-19, as COVID-19 remains a serious pandemic. But the findings were not validated in actual CRC patients infected with COVID-19, so further investigation is needed to confirm the potential use of niacin for treating CRC/COVID-19.

Integrative pharmacological mechanism of vitamin C combined with glycyrrhizic acid against COVID-19: findings of bioinformatics analyses

OBJECTIVE

Coronavirus disease 2019 (COVID-19) is a fatal and fast-spreading viral infection. To date, the number of COVID-19 patients worldwide has crossed over six million with over three hundred and seventy thousand deaths (according to the data from World Health Organization; updated on 2 June 2020). Although COVID-19 can be rapidly diagnosed, efficient clinical treatment of COVID-19 remains unavailable, resulting in high fatality. Some clinical trials have identified vitamin C (VC) as a potent compound pneumonia management. In addition, glycyrrhizic acid (GA) is clinically as an anti-inflammatory medicine against pneumonia-induced inflammatory stress. We hypothesized that the combination of VC and GA is a potential option for treating COVID-19.

METHODS

The aim of this study was to determine pharmacological targets and molecular mechanisms of VC + GA treatment for COVID-19, using bioinformational network pharmacology.

RESULTS

We uncovered optimal targets, biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of VC + GA against COVID-19. Our findings suggested that combinatorial VC and GA treatment for COVID-19 was associated with elevation of immunity and suppression of inflammatory stress, including activation of the T cell receptor signaling pathway, regulation of Fc gamma R-mediated phagocytosis, ErbB signaling pathway and vascular endothelial growth factor signaling pathway. We also identified 17 core targets of VC + GA, which suggest as antimicrobial function.

CONCLUSIONS

For the first time, our study uncovered the pharmacological mechanism underlying combined VC and GA treatment for COVID-19. These results should benefit efforts to address the most pressing problem currently facing the world.

System biological investigations of hydroxychloroquine and azithromycin targets and their implications in QT interval prolongation

COVID-2019 pandemic is affecting people worldwide in the absence of an effective treatment strategy. Several suggestive therapeutic options through drug repurposing are recommended, but a complete consensus is not reached. A combination of Hydroxychloroquine (HCQ) and Azithromycin (AZM) has been widely tried and discussed but its administration has also led to potential adversities in patients. Studies are suggesting that most prominent adverse event with HCQ and AZM combination is QT interval prolongation. We studied interaction of HCQ with AZM and subsequent effect of this drug combination on QT interval prolongation. We performed system biological investigation of HCQ and AZM targets and screened important targets and pathways possibly involved in QT interval prolongation. The best core hub protein drug targets involved in QT interval prolongation were identified as HSP90AA1 exclusively associated with HCQ, while AKT1 exclusively associated with AZM on the basis of node degree value. It was found that PI3K/Akt, VEGF, ERBB2 pathways must be given consideration for understanding the role of HCQ and AZM in QT interval prolongation. Conclusion: Computational methods have certain limitations based on source database coverage and prediction algorithms and therefore this data needs experimental correlation to draw final conclusion, but current findings screen targets for QT interval prolongation associated with HCQ and AZM. These proteins and pathways may provide ways to reduce this major risk associated with this combination.

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Hydroxychloroquine and azithromycin is widely tried for recent pandemic.

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It is discussed to prolong QT interval causing severe adverse events.

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Potential drug targets involved in this process were screened using system biology.

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Pathways were also screened for drug combination mediated adverse events.

Revealing the targets and mechanisms of vitamin A in the treatment of COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), an epidemic disease characterized by rapid infection and a high death toll. The clinical diagnosis of patients with COVID-19 has risen sharply, especially in Western countries. Globally, an effective treatment for COVID-19 is still limited. Vitamin A (VA) exhibits pharmacological activity in the management of pneumonia. Thus, we reason that VA may potentially serve as an anti-SARS-CoV-2 regimen. In this study, bioinformatics analysis and computation assays using a network pharmacology method were conducted to explore and uncover the therapeutic targets and mechanisms of VA for treating COVID-19. We identified candidate targets, pharmacological functions, and therapeutic pathways of VA against SARS-CoV-2. Bioinformatics findings indicate that the mechanisms of action of VA against SARS-CoV-2 include enrichment of immunoreaction, inhibition of inflammatory reaction, and biological processes related to reactive oxygen species. Furthermore, seven core targets of VA against COVID-19, including MAPK1, IL10, EGFR, ICAM1, MAPK14, CAT, and PRKCB were identified. With this bioinformatics-based report, we reveal, for the first time, the anti-SARS-CoV-2 functions and mechanisms of VA and suggest that VA may act as a potent treatment option for COVID-19, a deadly global epidemic.

Therapeutic target and molecular mechanism of vitamin C-treated pneumonia: a systematic study of network pharmacology

Vitamin C (VC), a well-reported antioxidant, is found with beneficial actions of preventing and treating pneumonia.