A crowdsourcing open platform for literature curation in UniProt

Wang, Yuqi; Wang, Qinghua; Huang, Hongzhan; Huang, Wei; Chen, Yongxing; McGarvey, Peter B.; Wu, Cathy H.; Arighi, Cecilia N.

doi:10.1371/journal.pbio.3001464

Cited by 102 publications

(69 citation statements)

References 8 publications

(9 reference statements)

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“…Mogroside V-linked targets were identified using the Swiss Target Prediction, PharmMapper, and Batman databases. Targets of drug action were screened after review (Swiss-Prot) for target correction using the UniProt database ( 19 ). GeneCards, DrugBank, Online Mendelian Inheritance in Man (OMIM) ( 20 ), and therapeutic target databases searched for COVID-19 and ovarian cancer-related targets.…”

Section: Methodsmentioning

confidence: 99%

Preclinical In Silico Evidence Indicates the Pharmacological Targets and Mechanisms of Mogroside V in Patients With Ovarian Cancer and Coronavirus Disease 2019

Chen

Wei

et al. 2022

Front. Endocrinol.

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The borderless transmission of coronavirus remains uncontrolled globally. The uncharted severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant reduces the therapeutic efficacy of vaccines against coronavirus disease 2019 (COVID-19). Clinical observations suggest that tumour cases are highly infected with coronavirus, possibly due to immunologic injury, causing a higher COVID-19-related death toll. Presently, screening of candidate medication against coronavirus is in progress. Mogroside V, a bioactive ingredient of Siraitia grosvenorii, has been reported in China to have lung-protective and anticancer effects. The current study used network pharmacology and molecular docking to unlock the potential drug targets and remedial mechanisms of mogroside V against patients with ovarian cancer with COVID-19. We identified 24 related targets of mogroside V in patients with ovarian cancer and COVID-19 and characterised another 10 core targets of mogroside V against COVID-19 ovarian cancer, including Jun, IL2, HSP90AA1, AR, PRKCB, VEGFA, TLR9, TLR7, STAT3, and PRKCA. The core targets’ biological processes and signalling pathways were revealed by enrichment analysis. Molecular docking suggested favourable docking between core target protein and mogroside V, including vascular endothelial growth factor A (VEGFA). These findings indicated that mogroside V might be a potential therapeutic agent in the mitigation of COVID-19 ovarian cancer.

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Section: Methodsmentioning

confidence: 99%

Preclinical In Silico Evidence Indicates the Pharmacological Targets and Mechanisms of Mogroside V in Patients With Ovarian Cancer and Coronavirus Disease 2019

Chen

Wei

et al. 2022

Front. Endocrinol.

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“…3D structures of HIV proteins (gp120 and integrase) were also retrieved from RCSB Protein Data Bank [30] . From the uniport database [36] annotations (accessed on: 21/06/22), we found that the surface protein gp120 is a part of envelope glycoprotein gp160 (PDB id: 3J70). So, we considered the sequence range corresponding to gp120 (33–511) for further analysis.…”

Section: Methodsmentioning

confidence: 99%

Virus-host interaction analysis in colorectal cancer identifies core virus network signature and small molecules

AVS

Sinha²,

Donakonda³

2022

Computational and Structural Biotechnology Journal

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“…UniProt ( https://www.uniprot.org ) provides information on chemical substances and biological activities. We make a decision to eliminate some chemicals after the replicated data is deleted due to the lack of accurate structural information of the targets of the compounds, which is unable to be forecasted successfully [ 35 , 36 ] ( Figure 1 ).…”

Section: Methodsmentioning

confidence: 99%

Reveal the Mechanisms of Yi-Fei-Jian-Pi-Tang on Covid-19 through Network Pharmacology Approach

Lang

Yang

Cai

et al. 2022

Computational Intelligence and Neuroscience

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Objectives. The Traditional Chinese Medicine (TCM) formula Yi-Fei-Jian-Pi-Tang (YFJPT) has been demonstrated effective against Corona Virus Disease 2019 (Covid-19). The aim of this article is to make a thorough inquiry about its active constituent as well as mechanisms against Covid-19 via TCM network pharmacology. Methods. All the ingredients of YFJPT are obtained from the pharmacology database of the TCM system. The genes which are associated with the targets are obtained by utilizing UniProt. The herb-target network is built up by utilizing Cytoscape. The target protein-protein interaction network is built by utilizing the STRING database and Cytoscape. The critical targets of YFJPT are explored by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Results. The outcomes show that YFJPT might has 33 therapeutic targets on Covid-19, namely, interleukin 2 (IL2), heme oxygenase 1 (HMOX1), interleukin 4 (IL4), interferon gamma (FNG), α nuclear factor of kappa light polypeptide gene enhancer in Bcells inhibitor, alpha (NFKBIA), nuclear factor-k-gene binding (NFKB), nitric oxide synthase 3 (NOS3), intercellular adhesion molecule 1 (ICAM1), hypoxia inducible factor 1 subunit alpha (HIF1A), mitogen-activated protein kinase 3 (MAPK3), epidermal growth factor receptor (EGFR), interleukin 10 (IL10), jun proto-oncogene (JUN), C-C motif chemokine ligand 2 (CCL2), C-X-C motif chemokine ligand 8 (CXCL8), tumor protein p53 (TP53), interleukin 1 beta (IL1B), AKT serine/threonine kinase 1 (AKT1), tumor necrosis factor (TNF), interleukin 6 (IL6), erb-b2 receptor tyrosine kinase 2 (ERBB2), RELA proto-oncogene (RELA), NF-κB subunit, caspase 8 (CASP8), peroxisome proliferator activated receptor alpha (PPARA), TIMP metallopeptidase inhibitor 1 (TIMP1), transforming growth factor beta 1 (TGFB1), interleukin 1 alpha (IL1A), signal transducer and activator of transcription 1 (STAT1), mitogen-activated protein kinase 8 (MAPK8), myeloperoxidase (MPO), matrix metallopeptidase 3 (MMP3), matrix metallopeptidase 1 (MMP1), and NFE2 like bZIP transcription factor 2 (NFE2L2). The gene enrichment analysis prompts that YFJPT most likely contributes to patients related to Covid-19 by regulating the pathways of cancers. Conclusions. That will lay a foundation for the clinical rational application and further experimental research of YFJPT.

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A crowdsourcing open platform for literature curation in UniProt

Cited by 102 publications

References 8 publications

Preclinical In Silico Evidence Indicates the Pharmacological Targets and Mechanisms of Mogroside V in Patients With Ovarian Cancer and Coronavirus Disease 2019

Preclinical In Silico Evidence Indicates the Pharmacological Targets and Mechanisms of Mogroside V in Patients With Ovarian Cancer and Coronavirus Disease 2019

Virus-host interaction analysis in colorectal cancer identifies core virus network signature and small molecules

Reveal the Mechanisms of Yi-Fei-Jian-Pi-Tang on Covid-19 through Network Pharmacology Approach

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