Exploring the possible molecular targeting mechanism of Saussurea involucrata in the treatment of COVID-19 based on bioinformatics and network pharmacology

Zhang, Dongdong; Wang, Zhaoye; Li, Jin; Zhu, Jianbo

doi:10.1016/j.compbiomed.2022.105549

Cited by 20 publications

(12 citation statements)

References 52 publications

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“…The YSM and chick’s extra-embryonic membranes models have been used in various researches, and there is a growing repository of data (e.g. anatomical, pharmaceutical, physiological and genetic) that continues to expand the model for toxicological studies ( Zhou et al, 2013 ; Deshpande et al, 2018 ; Khosravi et al, 2019 ; Fonseca et al, 2021 ; Zhang et al, 2022 ). The chick embryo has also proven to be a manageable and reliable model for evaluating antidiabetic agents ( Haselgrübler et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

“…Molecular dynamics (MD) simulations were done by Gromacs 5.4.1 and the amber force field ( Wang et al, 2004 ; Van Der Spoel et al, 2005 ). The GROMACS package was applied for molecular dynamics simulations by various researchers ( Jacob et al, 2017 ; Tavakkoli et al, 2021 ; Zhang et al, 2022 ). The docked structures of the EMP with Bax and Bcl-2 were placed inside a dodecahedron box and were solvated withTIP3P water molecules.…”

Section: Methodsmentioning

confidence: 99%

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Empagliflozin induces apoptotic-signaling pathway in embryonic vasculature: In vivo and in silico approaches via chick’s yolk sac membrane model

Mosallanejad

Mahmoodi²,

Tavakkoli³

et al. 2022

Front. Pharmacol.

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The present investigation was conducted to evaluate the vascular-toxicity of empagliflozin (EMP) in embryonic vasculature. Firstly, the vascular-toxicity of the drug as well as its interaction with apoptotic regulator proteins was predicted via in silico approach. In the next step, the apoptotic-signaling pathway in embryonic vasculature was evaluated using a chick’s YSM model. In silico simulation confirmed vascular-toxicity of EMP. There was also an accurate affinity between EMP, Bax and Bcl-2 (−7.9 kcal/mol). Molecular dynamics assay revealed complex stability in the human body conditions. Furthermore, EMP is suggested to alter Bcl-2 more than BAX. Morphometric quantification of the vessels showed that the apoptotic activity of EMP in embryonic vasculature was related to a marked reduction in vessel area, vessel diameter and mean capillary area. Based on the qPCR and immunohistochemistry assays, enhanced expression level of BAX and reduced expression level of Bcl-2 confirmed apoptotic responses in the vessels of the YSM. We observed that induction of an apoptotic signal can cause the embryonic defect of the vascular system following EMP treatment. The acquired data also raised suspicions that alteration in apoptotic genes and proteins in the vasculature are two critical pathways in vascular-toxicity of EMP.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Empagliflozin induces apoptotic-signaling pathway in embryonic vasculature: In vivo and in silico approaches via chick’s yolk sac membrane model

Mosallanejad

Mahmoodi²,

Tavakkoli³

et al. 2022

Front. Pharmacol.

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“…[95] With a better understanding of the disease, the interaction of adipocytokine signaling pathways with COVID-19 has received widespread attention, and enhanced ACE2 expression induced by adipocytokine dysregulation, preexisting endothelial dysfunction and a procoagulant state in the metabolic syndrome may play a crucial role in the development of severe COVID-19. [96] In addition, a number of potential pathways have been identified, such as neuroactive ligand-receptor interactions [97][98][99] and renin secretion. [100][101][102] However, we have identified some issues in the relevant literature.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics and systems biology approaches to identify the effects of COVID-19 on neurodegenerative diseases: A review

Guan

Wang

et al. 2022

Medicine

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease , has been devastated by COVID-19 in an increasing number of countries and health care systems around the world since its announcement of a global pandemic on 11 March 2020. During the pandemic, emerging novel viral mutant variants have caused multiple outbreaks of COVID-19 around the world and are prone to genetic evolution, causing serious damage to human health. As confirmed cases of COVID-19 spread rapidly, there is evidence that SARS-CoV-2 infection involves the central nervous system (CNS) and peripheral nervous system (PNS), directly or indirectly damaging neurons and further leading to neurodegenerative diseases (ND), but the molecular mechanisms of ND and CVOID-19 are unknown. We employed transcriptomic profiling to detect several major diseases of ND: Alzheimer 's disease (AD), Parkinson' s disease (PD), and multiple sclerosis (MS) common pathways and molecular biomarkers in association with COVID-19, helping to understand the link between ND and COVID-19. There were 14, 30 and 19 differentially expressed genes (DEGs) between COVID-19 and Alzheimer 's disease (AD), Parkinson' s disease (PD) and multiple sclerosis (MS), respectively; enrichment analysis showed that MAPK, IL-17, PI3K-Akt and other signaling pathways were significantly expressed; the hub genes (HGs) of DEGs between ND and COVID-19 were CRH, SST, TAC1, SLC32A1, GAD2, GAD1, VIP and SYP. Analysis of transcriptome data suggests multiple co-morbid mechanisms between COVID-19 and AD, PD, and MS, providing new ideas and therapeutic strategies for clinical prevention and treatment of COVID-19 and ND. Abbreviations: ACE2 = angiotensin-converting enzyme 2, AD = Alzheimer's disease, BBB = blood-brain barrier, CNS = central nervous system, COVID-19 = coronavirus disease, DEGs = differentially expressed genes, GO = gene ontology, GRN = gene regulatory network, HG = hub gene, KEGG = Kyoto Encyclopedia of Genes and Genomes, miRNA = micro RNA, MS = multiple sclerosis, ND = neurodegenerative diseases, PD = Parkinson's disease, PPI = protein-protein interaction network, SARS-CoV-2 = syndrome coronavirus 2, TFS = transcription factors.

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“…Currently, most countries' targeted vaccine research and development for COVID-19 have problems such as complex processes, relatively high market prices, and difficulty to find targets. These restrictions prevent routine vaccination for COVID-19 patients [8] . In addition, COVID-19 can cause multiple complications, leading to poor prognosis in COVID-19 patients [9] .…”

Section: Introductionmentioning

confidence: 99%

Identification and analysis of co-disease genes between COVID-19 and osteoarthritis

Zhang,

Liu,

et al. 2024

Preprint

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Background: The molecular mechanisms of corona virus disease 2019 (COVID-19) and osteoarthritis (OA) are unclear, and there is an urgent need to identify new biomarkers and explore their potential molecular mechanisms in COVID-19 and OA. Methods: The GSE57218, GSE157103 training sets and the GSE82107, GSE171110 validation sets were acquired via gene expression omnibus (GEO) database. First, differentially expressed genes (DEGs) between disease and normal samples in the GSE57218 and GSE157103 training sets were respectively sifted out by differential expression analysis. The modules with the highest correlation with OA and normal, COVID-19 and non COVID-19 were gained by weighted gene co-expression network analysis (WGCNA), individually. Then, OA-DEGs were intersected with the module genes that had significant correlation with OA, and COVID-19-DEGs were intersected with the module genes which were dramatically correlated with COVID-19 to yield OA-intersected genes and COVID-19 intersected genes, respectively. The OA-intersected genes and COVID-19 intersected genes were intersected to yield candidate genes, and they were analyzed for function enrichment analysis. Next, the seven algorithms (Closeness, MCC, Degree, MNC, Radality, Stress and EPC) were performed on candidate genes to sift out biomarkers. Finally, we constructed the competing endogenous RNA (ceRNA), transcription factor (TF)/miRNA-mRNA and drug-target regulatory networks. Results:There were 1135 OA-DEGs and 4336 COVID-19-DEGs between disease and normal samples in the GSE57218 and GSE157103 training sets, respectively. The pink, blue and brown modules had significant correlations with OA in the GSE57218 training set, while in the GSE157103 training set, the pink and brown modules were notably correlated with COVID-19. We finally yield 715 OA-intersected genes and 2282 COVID-19-intersected genes. After intersecting the above two intersected genes, we gained 106 candidate genes, and they were involved in ADP metabolic process, nucleoside diphosphate phosphorylation, etc.. The 7 biomarkers, namely AK1, APP, ENO1, TPI1, HSP90B1, HSPB1 and ESR1, were acquired based on seven algorithms. Finally, we successfully constructed the ceRNA, TF/miRNA-mRNA and drug-target networks. Conclusion: Through bioinformatic methods, we explored the biomarkers (AK1, APP, ENO1, TPI1, HSP90B1, HSPB1 and ESR1) of COVID-19 combined OA, providing new ideas for studies related to molecular mechanisms and treatment of comorbidity.

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Exploring the possible molecular targeting mechanism of Saussurea involucrata in the treatment of COVID-19 based on bioinformatics and network pharmacology

Cited by 20 publications

References 52 publications

Empagliflozin induces apoptotic-signaling pathway in embryonic vasculature: In vivo and in silico approaches via chick’s yolk sac membrane model

Empagliflozin induces apoptotic-signaling pathway in embryonic vasculature: In vivo and in silico approaches via chick’s yolk sac membrane model

Bioinformatics and systems biology approaches to identify the effects of COVID-19 on neurodegenerative diseases: A review

Identification and analysis of co-disease genes between COVID-19 and osteoarthritis

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