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Zou H, Niu Z, Tang Z, Cheng P, Yin Y, Luo G, Huang S. The Mechanism of Action of the Active Ingredients of Coptidis rhizoma against Porcine Epidemic Diarrhea Was Investigated Using Network Pharmacology and Molecular Docking Technology. Viruses 2024; 16:1229. [PMID: 39205203 PMCID: PMC11360715 DOI: 10.3390/v16081229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
The objective of this study was to elucidate the mechanism of action of the active components of Coptidis rhizoma against porcine epidemic diarrhea and to provide a theoretical foundation for further development of novel anti-PED therapeutic agents based on Coptidis rhizoma. The potential targets of Coptidis rhizoma against PEDV were identified through a comprehensive literature review and analysis using the TCMSP pharmacological database, SwissDrugDesign database, GeneCards database, and UniProt database. Subsequently, the STRING database and Cytoscape 3.7.1 software were employed to construct a protein-protein interaction (PPI) network and screen key targets. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted on the identified targets. Molecular docking studies were performed using AutoDock 1.5.7 software to analyze the binding energy and modes of interaction between the active components of Coptidis rhizoma and the target proteins. The PyMOL 2.5.0a0 software was employed to visualize the docking results. Through comprehensive analysis, 74 specific targets of active components of Coptidis rhizoma against PEDV were identified. The core gene targets were screened, and an interaction network diagram was subsequently generated. Ultimately, 14 core targets were identified, with STAT3, ESR1, CASP3, and SRC exhibiting the most significant interactions. GO enrichment analysis revealed a total of 215 molecular items, including 48 biological function items, 139 biological process items, and 28 cellular component items. KEGG enrichment analysis identified 140 signaling pathways. Molecular docking analysis demonstrated that epiberberine and palmatine exhibited high binding affinity with STAT3 protein, worenine showed high binding affinity with ESR1 protein, obacunone exhibited high binding affinity with CASP3 protein, and epiberberine, obacunone, berberine, and berberruine exhibited high binding affinity with SRC protein. A network pharmacology and molecular docking technology approach was employed to screen six important active components of Coptidis rhizoma and four important potential targets against PEDV infection. The findings indicated that the active components of Coptidis rhizoma could serve as promising pharmaceutical agents for the prevention and control of PEDV, with significant potential for clinical application.
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Affiliation(s)
- Hong Zou
- College of Animal Science & Technology, Chongqing Three Gouges Vocational College, Chongqing 404100, China; (H.Z.); (Y.Y.)
| | - Zheng Niu
- College of Veterinary Medicine, Northwest A & F University, Xianyang 712000, China;
| | - Zhangchen Tang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 402460, China;
| | - Peng Cheng
- Wanzhou Center for Animal Husbandry Industry Development of Chongqing, Chongqing 404100, China;
| | - Yanling Yin
- College of Animal Science & Technology, Chongqing Three Gouges Vocational College, Chongqing 404100, China; (H.Z.); (Y.Y.)
| | - Gan Luo
- Wanzhou Center for Animal Husbandry Industry Development of Chongqing, Chongqing 404100, China;
| | - Shilei Huang
- College of Animal Science & Technology, Chongqing Three Gouges Vocational College, Chongqing 404100, China; (H.Z.); (Y.Y.)
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Butt DQ, Harun MH, Che Jalil NA, Shamsuddin SH, Jaafar S, Ahmad B. Protumorigenic Interferon-Stimulated Genes in Cancer: A Comprehensive Review. Cureus 2024; 16:e63216. [PMID: 39070493 PMCID: PMC11279184 DOI: 10.7759/cureus.63216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2024] [Indexed: 07/30/2024] Open
Abstract
Interferon-stimulated genes (ISGs), whose production is triggered by interferons, are known to defend the host from pathogenic and cancer-specific antigens, one of which is by inducing apoptosis in infected or mutated cells. It has been reported recently that specific ISGs aid cancer cells in evading immunosurveillance and inflammatory cells by inhibiting the apoptosis process. This report reviewed four apoptosis-regulating ISG proteins: interferon-stimulated gene 15 (ISG15), interferon alpha-inducible protein 27 (IFI27), interferon alpha-inducible protein 6 (IFI6), and radical S-adenosyl methionine domain containing 2 (RSAD2), demonstrating anti-apoptosis function, and considered them protumorigenic.
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Affiliation(s)
- Danial Qasim Butt
- Oral Medicine and Oral Pathology Unit, School of Dental Sciences, Universiti Sains Malaysia, Kubang Kerian, MYS
| | - Masitah Hayati Harun
- Oral Medicine and Oral Pathology Unit, School of Dental Sciences, Universiti Sains Malaysia, Kubang Kerian, MYS
| | - Nur Asyilla Che Jalil
- Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, MYS
| | | | - Saidi Jaafar
- Basic Sciences Unit, School of Dental Sciences, Universiti Sains Malaysia, Kubang Kerian, MYS
| | - Basaruddin Ahmad
- Biostatistics Unit, School of Dental Sciences, Universiti Sains Malaysia, Kubang Kerian, MYS
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Xu X, Ma M, Shi X, Yan Y, Liu Y, Yang N, Wang Q, Zhang S, Zhang Q. The novel Nsp9-interacting host factor H2BE promotes PEDV replication by inhibiting endoplasmic reticulum stress-mediated apoptosis. Vet Res 2023; 54:27. [PMID: 36949543 PMCID: PMC10035214 DOI: 10.1186/s13567-023-01158-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/15/2023] [Indexed: 03/24/2023] Open
Abstract
Porcine epidemic diarrhoea (PED) caused by porcine epidemic diarrhoea virus (PEDV) has led to significant economic losses in the swine industry worldwide. Histone Cluster 2, H2BE (HIST2H2BE), the main protein component in chromatin, has been proposed to play a key role in apoptosis. However, the relationship between H2BE and PEDV remains unclear. In this study, H2BE was shown to bind and interact with PEDV nonstructural protein 9 (Nsp9) via immunoprecipitation-mass spectrometry (IP-MS). Next, we verified the interaction of Nsp9 with H2BE by immunoprecipitation and immunofluorescence. H2BE colocalized with Nsp9 in the cytoplasm and nuclei. PEDV Nsp9 upregulated the expression of H2BE by inhibiting the expression of IRX1. We demonstrated that overexpression of H2BE significantly promoted PEDV replication, whereas knockdown of H2BE by small interfering RNA (siRNA) inhibited PEDV replication. Overexpression of H2BE led to significantly inhibited GRP78 expression, phosphorylated PERK (p-PERK), phosphorylated eIF2 (p-eIF2), phosphorylated IRE1 (p-IRE1), and phosphorylated JNK (p-JNK); negatively regulated CHOP and Bax expression and caspase-9 and caspase-3 cleavage; and promoted Bcl-2 production. Knocking down H2BE exerted the opposite effects. Furthermore, we found that after deletion of amino acids 1-28, H2BE did not promote PEDV replication. In conclusion, these studies revealed the mechanism by which H2BE is associated with ER stress-mediated apoptosis to regulate PEDV replication. Nsp9 upregulates H2BE. H2BE plays a role in inhibiting apoptosis and thus facilitating viral replication, which depends on the N-terminal region of H2BE (amino acids 1-28). These findings provide a reference for host-PEDV interactions and offer the possibility for developing strategies for PEDV decontamination and prevention.
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Affiliation(s)
- Xingang Xu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mingrui Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaojie Shi
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yuchao Yan
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yi Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Naling Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Quanqiong Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuxia Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Qi Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Shi X, Zhang Q, Wang J, Zhang Y, Yan Y, Liu Y, Yang N, Wang Q, Xu X. Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection. BMC Genomics 2022; 23:586. [PMID: 35964002 PMCID: PMC9375197 DOI: 10.1186/s12864-022-08805-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 07/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Porcine Epidemic Diarrhea Virus (PEDV) is a coronavirus that seriously affects the swine industry. MicroRNAs and long noncoding RNAs are two relevant non-coding RNAs (ncRNAs) class and play crucial roles in a variety of physiological processes. Increased evidence indicates a complex interaction between mRNA and ncRNA. However, our understanding of the function of ncRNA involved in host-PEDV interaction is limited. RESULTS A total of 1,197 mRNA transcripts, 539 lncRNA transcripts, and 208 miRNA transcripts were differentially regulated at 24 h and 48 h post-infection. Gene ontology (GO) and KEGG pathway enrichment analysis showed that DE mRNAs and DE lncRNAs were mainly involved in biosynthesis, innate immunity, and lipid metabolism. Moreover, we constructed a miRNA-mRNA-pathway network using bioinformatics, including 12 DE mRNAs, 120 DE miRNAs, and 11 pathways. Finally, the target genes of DE miRNAs were screened by bioinformatics, and we constructed immune-related lncRNA-miRNA-mRNA ceRNA networks. Then, the selected DE genes were validated by qRT-PCR, which were consistent with the results from RNA-Seq data. CONCLUSIONS This study provides the comprehensive analysis of the expression profiles of mRNAs, lncRNAs, and miRNAs during PEDV infection. We characterize the ceRNA networks which can provide new insights into the pathogenesis of PEDV.
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Affiliation(s)
- Xiaojie Shi
- College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Qi Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Jingjing Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Yuting Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Yuchao Yan
- College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Yi Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Naling Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Quanqiong Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Xingang Xu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China.
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