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Zhang M, Zhang X, Pei J, Guo B, Zhang G, Li M, Huang L. Identification of phytochemical compounds of Fagopyrum dibotrys and their targets by metabolomics, network pharmacology and molecular docking studies. Heliyon 2023; 9:e14029. [PMID: 36911881 PMCID: PMC9977108 DOI: 10.1016/j.heliyon.2023.e14029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 01/30/2023] [Accepted: 02/19/2023] [Indexed: 03/05/2023] Open
Abstract
Acute lung injury (ALI) is a clinically severe lung illness with high incidence rate and mortality. Especially, coronavirus disease 2019 (COVID-19) poses a serious threat to world wide governmental fitness. It has distributed to almost from corner to corner of the universe, and the situation in the prevention and control of COVID-19 remains grave. Traditional Chinese medicine plays a vital role in the precaution and therapy of sicknesses. At present, there is a lack of drugs for treating these diseases, so it is necessary to develop drugs for treating COVID-19 related ALI. Fagopyrum dibotrys (D. Don) Hara is an annual plant of the Polygonaceae family and one of the long-history used traditional medicine in China. In recent years, its rhizomes (medicinal parts) have attracted the attention of scholars at home and abroad due to their significant anti-inflammatory, antibacterial and anticancer activities. It can work on SARS-COV-2 with numerous components, targets, and pathways, and has a certain effect on coronavirus disease 2019 (COVID-19) related acute lung injury (ALI). However, there are few systematic studies on its aerial parts (including stems and leaves) and its potential therapeutic mechanism has not been studied. The phytochemical constituents of rhizome of F. dibotrys were collected using TCMSP database. And metabolites of F. dibotrys' s aerial parts were detected by metabonomics. The phytochemical targets of F. dibotrys were predicted by the PharmMapper website tool. COVID-19 and ALI-related genes were retrieved from GeneCards. Cross targets and active phytochemicals of COVID-19 and ALI related genes in F. dibotrys were enriched by gene ontology (GO) and KEGG by metscape bioinformatics tools. The interplay network entre active phytochemicals and anti COVID-19 and ALI targets was established and broke down using Cytoscape software. Discovery Studio (version 2019) was used to perform molecular docking of crux active plant chemicals with anti COVID-19 and ALI targets. We identified 1136 chemicals from the aerial parts of F. dibotrys, among which 47 were active flavonoids and phenolic chemicals. A total of 61 chemicals were searched from the rhizome of F. dibotrys, and 15 of them were active chemicals. So there are 6 commonly key active chemicals at the aerial parts and the rhizome of F. dibotrys, 89 these phytochemicals's potential targets, and 211 COVID-19 and ALI related genes. GO enrichment bespoken that F. dibotrys might be involved in influencing gene targets contained numerous biological processes, for instance, negative regulation of megakaryocyte differentiation, regulation of DNA metabolic process, which could be put down to its anti COVID-19 associated ALI effects. KEGG pathway indicated that viral carcinogenesis, spliceosome, salmonella infection, coronavirus disease - COVID-19, legionellosis and human immunodeficiency virus 1 infection pathway are the primary pathways obsessed in the anti COVID-19 associated ALI effects of F. dibotrys. Molecular docking confirmed that the 6 critical active phytochemicals of F. dibotrys, such as luteolin, (+) -epicatechin, quercetin, isorhamnetin, (+) -catechin, and (-) -catechin gallate, can combine with kernel therapeutic targets NEDD8, SRPK1, DCUN1D1, and PARP1. In vitro activity experiments showed that the total antioxidant capacity of the aerial parts and rhizomes of F. dibotrys increased with the increase of concentration in a certain range. In addition, as a whole, the antioxidant capacity of the aerial part of F. dibotrys was stronger than that of the rhizome. Our research afford cues for farther exploration of the anti COVID-19 associated ALI chemical compositions and mechanisms of F. dibotrys and afford scientific foundation for progressing modern anti COVID-19 associated ALI drugs based on phytochemicals in F. dibotrys. We also fully developed the medicinal value of F. dibotrys' s aerial parts, which can effectively avoid the waste of resources. Meanwhile, our work provides a new strategy for integrating metabonomics, network pharmacology, and molecular docking techniques which was an efficient way for recognizing effective constituents and mechanisms valid to the pharmacologic actions of traditional Chinese medicine.
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Key Words
- ARDS, acute respiratory distress syndrome
- BC, BetweennessCentrality
- CC, ClosenessCentrality
- CHM, Chinese herbal medicines
- COVID-19 related ALI, Coronavirus disease 2019 related acute lung injury
- Coronavirus disease 2019 related acute lung injury
- DL, drug-like properties
- Fagopyrum dibotrys
- GO, Gene Ontology
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LC-MS, liquid chromatography-mass spectrometry
- Metabolomics
- Molecular docking
- NC, NeighborhoodConnectivity
- NSCLC, Non-small cell lung carcinoma
- Network pharmacology
- OB, oral bioavailability
- PARP-1, Poly(ADP-ribose)polymerase-1
- PDB, Protein Data Bank database
- PPI network, protein-protein interaction network
- RMSD, Root mean square deviation
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- TCM, traditional Chinese medicine
- TCMSP, traditional Chinese medicine systems pharmacology database and analysis platform
- WTM, widely targeted metabolome
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Affiliation(s)
- Min Zhang
- A Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- College of Pharmacy, Baotou Medical College, Baotou, 014040, China
- Inner Mongolia Autonomous Region Hospital of Traditional Chinese Medicine, Hohhot, 010020, China
- Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, 010010, China
| | - Xinke Zhang
- A Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Baolin Guo
- A Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Guoshuai Zhang
- A Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Minhui Li
- College of Pharmacy, Baotou Medical College, Baotou, 014040, China
- Inner Mongolia Autonomous Region Hospital of Traditional Chinese Medicine, Hohhot, 010020, China
- Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, 010010, China
- Corresponding author. College of Pharmacy, Baotou Medical College, Baotou, 014040, China.
| | - Linfang Huang
- A Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- Corresponding author.
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Zhuang Z, Wen J, Zhang L, Zhang M, Zhong X, Chen H, Luo C. Can network pharmacology identify the anti-virus and anti- inflammatory activities of Shuanghuanglian oral liquid used in Chinese medicine for respiratory tract infection? Eur J Integr Med 2020; 37:101139. [PMID: 32501408 PMCID: PMC7255237 DOI: 10.1016/j.eujim.2020.101139] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/09/2020] [Accepted: 05/09/2020] [Indexed: 02/06/2023]
Abstract
Introduction Shuanghuanglian (SHL) oral liquid is a well-known traditional Chinese medicine preparation administered for respiratory tract infections in China. However, the underlying pharmacological mechanisms remain unclear. The present study aims to determine the potential pharmacological mechanisms of SHL oral liquid based on network pharmacology. Methods A network pharmacology-based strategy including collection and analysis of putative compounds and target genes, network construction, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and Gene Ontology (GO) enrichment, identification of key compounds and target genes, and molecule docking was performed in this study. Results A total of 82 bioactive compounds and 226 putative target genes of SHL oral liquid were collected. Of note, 28 hub target genes including 4 major hub target genes: estrogen receptor 1 (ESR1), nuclear receptor coactivator 2 (NCOA2), nuclear receptor coactivator 1 (NCOA1), androgen receptor (AR) and 5 key compounds (quercetin, luteolin, baicalein, kaempferol and wogonin) were identified based on network analysis. The hub target genes mainly enriched in pathways including PI3K-Akt signaling pathway, human cytomegalovirus infection, and human papillomavirus infection, which could be the underlying pharmacological mechanisms of SHL oral liquid for treating diseases. Moreover, the key compounds had great molecule docking binding affinity with the major hub target genes. Conclusion Using network pharmacology analysis, SHL oral liquid was found to contain anti-virus, anti-inflammatory, and “multi-compounds and multi-targets” with therapeutic actions. These findings may provide a valuable direction for further clinical application and research.
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Key Words
- AM, alveolar macrophages
- AR, androgen receptor
- CAS, Chemical abstracts service number
- CFDA, The China Food and Drug Administration
- COX, cyclooxygenases
- COX-2, cyclooxygenase
- DL, drug-likeness
- ESR1, estrogen receptor 1
- Flos Lonicerae
- Fructus Forsythiae
- GO, Gene Ontology
- HCMV, Human cytomegalovirus
- HCV, human cytomegalovirus
- HPV, Human papillomavirus
- HQ, Huangqin, Radix Scutellariae
- JYH, Jinyinhua, Flos Lonicerae
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LQ, Lianqiao, Fructus Forsythiae
- MCP, monocyte chemoattractant protein
- NCOA1, nuclear receptor coactivator 1
- NCOA2, nuclear receptor coactivator 2
- NO, nitric oxide
- Network pharmacology
- OB, oral bioavailability
- PG, prostaglandin
- Pharmacological mechanism
- ROS, reactive oxygen species
- RSV, respiratory syncytial virus
- Radix Scutellariae
- Respiratory tract infection
- SARS-CoV, severe acute respiratory syndrome coronavirus
- SHL oral liquid, Shuanghuanglian oral liquid
- SMILES, Simplified molecular input line entry specification
- Shuanghuanglian oral liquid
- TCM, traditional Chinese medicine
- TCMSP, Traditional Chinese Medicine Systems Pharmacology database
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Affiliation(s)
- Zhenjie Zhuang
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Junmao Wen
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lu Zhang
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Mingjia Zhang
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoying Zhong
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huiqi Chen
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chuanjin Luo
- The First Affiliated Hospital of Guangdong University of Chinese Medicine, No.12, Airport Road, Baiyun District, Guangzhou 510405, China
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