Exploring the bioactive compounds of Feiduqing formula for the prevention and management of COVID-19 through network pharmacology and molecular docking

Qin et al., Medical Data Mining, doi:10.53388/MDM202407003

Nov 2023

Source PDF All Studies Meta AnalysisMeta

In Silico study of components of Feiduqing finding that quercetin, among other compounds, has significant binding affinity to PTGS2, HSP90AA1, SARS-CoV-2 M^pro, and ACE2, suggesting that quercetin may have therapeutic potential for COVID-19. PTGS2 (prostaglandin-endoperoxide synthase 2), also known as COX-2, is an enzyme involved in prostaglandin biosynthesis and inflammation and is a target for anti-inflammatory drugs. HSP90AA1 is a heat shock protein that helps fold and stabilize proteins and has been shown to be important for replication of some RNA viruses.

32 preclinical studies support the efficacy of quercetin for COVID-19:

18 In Silico studies Alavi, Azmi, Chellasamy, Corbo, Ibeh, Kandeil, Mandal, Moschovou, Nguyen, Pan, Qin, Sai Ramesh, Sekiou, Singh, Thapa, Wang, Yang, Şimşek

11 In Vitro studies Aguado, Bahun, DiGuilio, Goc, Kandeil, Munafò, Pan, Singh (B), Wu, Xu, Zhang

3 In Vivo animal studies Aguado, Wu, Wu (B)

Important missing comments or errors? Let us know.

1. Aguado et al., Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology, bioRxiv, doi:10.1101/2023.01.17.524329.biorxiv.org, doi.org.

2. Alavi et al., Interaction of Epigallocatechin Gallate and Quercetin with Spike Glycoprotein (S-Glycoprotein) of SARS-CoV-2: In Silico Study, Biomedicines, doi:10.3390/biomedicines10123074.mdpi.com, doi.org.

3. Azmi et al., Utilization of quercetin flavonoid compounds in onion (Allium cepa L.) as an inhibitor of SARS-CoV-2 spike protein against ACE2 receptors, 11th International Seminar on New Paradigm and Innovation on Natural Sciences and its Application, doi:10.1063/5.0140285.scitation.org, doi.org.

4. Bahun et al., Inhibition of the SARS-CoV-2 3CLpro main protease by plant polyphenols, Food Chemistry, doi:10.1016/j.foodchem.2021.131594.sciencedirect.com, doi.org.

5. Chellasamy et al., Docking and molecular dynamics studies of human ezrin protein with a modelled SARS-CoV-2 endodomain and their interaction with potential invasion inhibitors, Journal of King Saud University - Science, doi:10.1016/j.jksus.2022.102277.sciencedirect.com, doi.org.

6. Corbo et al., Inhibitory potential of phytochemicals on five SARS-CoV-2 proteins: in silico evaluation of endemic plants of Bosnia and Herzegovina, Biotechnology & Biotechnological Equipment, doi:10.1080/13102818.2023.2222196.tandfonline.com, doi.org.

7. DiGuilio et al., Quercetin improves and protects Calu-3 airway epithelial barrier function, Frontiers in Cell and Developmental Biology, doi:10.3389/fcell.2023.1271201.frontiersin.org, doi.org.

8. Goc et al., Inhibitory effects of specific combination of natural compounds against SARS-CoV-2 and its Alpha, Beta, Gamma, Delta, Kappa, and Mu variants, European Journal of Microbiology and Immunology, doi:10.1556/1886.2021.00022.akjournals.com, doi.org.

9. Ibeh et al., Computational studies of potential antiviral compounds from some selected Nigerian medicinal plants against SARS-CoV-2 proteins, Informatics in Medicine Unlocked, doi:10.1016/j.imu.2023.101230.sciencedirect.com, doi.org.

10. Kandeil et al., Bioactive Polyphenolic Compounds Showing Strong Antiviral Activities against Severe Acute Respiratory Syndrome Coronavirus 2, Pathogens, doi:10.3390/pathogens10060758.mdpi.com, doi.org.

11. Mandal et al., In silico anti-viral assessment of phytoconstituents in a traditional (Siddha Medicine) polyherbal formulation – Targeting Mpro and pan-coronavirus post-fusion Spike protein, Journal of Traditional and Complementary Medicine, doi:10.1016/j.jtcme.2023.07.004.sciencedirect.com, doi.org.

12. Moschovou et al., Exploring the Binding Effects of Natural Products and Antihypertensive Drugs on SARS-CoV-2: An In Silico Investigation of Main Protease and Spike Protein, International Journal of Molecular Sciences, doi:10.3390/ijms242115894.mdpi.com, doi.org.

13. Munafò et al., Quercetin and Luteolin Are Single-digit Micromolar Inhibitors of the SARS-CoV-2 RNA-dependent RNA Polymerase, Research Square, doi:10.21203/rs.3.rs-1149846/v1.researchsquare.com, doi.org.

14. Nguyen et al., The Potential of Ameliorating COVID-19 and Sequelae From Andrographis paniculata via Bioinformatics, Bioinformatics and Biology Insights, doi:10.1177/11779322221149622.sagepub.com, doi.org.

15. Pan et al., Quercetin: A promising drug candidate against the potential SARS-CoV-2-Spike mutants with high viral infectivity, Computational and Structural Biotechnology Journal, doi:10.1016/j.csbj.2023.10.029.sciencedirect.com, doi.org.

16. Qin et al., Exploring the bioactive compounds of Feiduqing formula for the prevention and management of COVID-19 through network pharmacology and molecular docking, Medical Data Mining, doi:10.53388/MDM202407003.tmrjournals.com, doi.org.

17. Sai Ramesh et al., Computational analysis of the phytocompounds of Mimusops elengi against spike protein of SARS CoV2 – An Insilico model, International Journal of Biological Macromolecules, doi:10.1016/j.ijbiomac.2023.125553.sciencedirect.com, doi.org.

18. Sekiou et al., In-Silico Identification of Potent Inhibitors of COVID-19 Main Protease (Mpro) and Angiotensin Converting Enzyme 2 (ACE2) from Natural Products: Quercetin, Hispidulin, and Cirsimaritin Exhibited Better Potential Inhibition than Hydroxy-Chloroquine Against COVID-19 Main Protease Active Site and ACE2, ChemRxiv, doi:10.26434/chemrxiv.12181404.v1.chemrxiv.org, doi.org.

19. Şimşek et al., In silico identification of SARS-CoV-2 cell entry inhibitors from selected natural antivirals, Journal of Molecular Graphics and Modelling, doi:10.1016/j.jmgm.2021.108038.sciencedirect.com, doi.org.

20. Singh et al., Flavonoids as Potent Inhibitor of SARS-CoV-2 Nsp13 Helicase: Grid Based Docking Approach, Middle East Research Journal of Pharmaceutical Sciences, doi:10.36348/merjps.2023.v03i04.001.kspublisher.com, doi.org.

21. Singh (B) et al., The spike protein of SARS-CoV-2 virus induces heme oxygenase-1: Pathophysiologic implications, Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, doi:10.1016/j.bbadis.2021.166322.sciencedirect.com, doi.org.

22. Thapa et al., In-silico Approach for Predicting the Inhibitory Effect of Home Remedies on Severe Acute Respiratory Syndrome Coronavirus-2, Makara Journal of Science, doi:10.7454/mss.v27i3.1609.ac.id, doi.org.

23. Wang et al., Computational Analysis of Lianhua Qingwen as an Adjuvant Treatment in Patients with COVID-19, Society of Toxicology Conference, 2023, www.researchgate.net/publication/370491709_Y_Wang_A_E_Tan_O_Chew_A_Hsueh_and_D_E_Johnson_2023_Computational_Analysis_of_Lianhua_Qingwen_as_an_Adjuvant_Treatment_in_Patients_with_COVID-19_Toxicologist_1921_507.researchgate.net.

24. Wu et al., SARS-CoV-2 N protein induced acute kidney injury in diabetic db/db mice is associated with a Mincle-dependent M1 macrophage activation, Frontiers in Immunology, doi:10.3389/fimmu.2023.1264447.frontiersin.org, doi.org.

25. Wu (B) et al., Treatment with Quercetin inhibits SARS-CoV-2 N protein-induced acute kidney injury by blocking Smad3-dependent G1 cell cycle arrest, Molecular Therapy, doi:10.1016/j.ymthe.2022.12.002.sciencedirect.com, doi.org.

26. Xu et al., Bioactive compounds from Huashi Baidu decoction possess both antiviral and anti-inflammatory effects against COVID-19, Proceedings of the National Academy of Sciences, doi:10.1073/pnas.2301775120.pnas.org, doi.org.

27. Yang et al., In silico evidence implicating novel mechanisms of Prunella vulgaris L. as a potential botanical drug against COVID-19-associated acute kidney injury, Frontiers in Pharmacology, doi:10.3389/fphar.2023.1188086.frontiersin.org, doi.org.

28. Zhang et al., Discovery of the covalent SARS‐CoV‐2 M^pro inhibitors from antiviral herbs via integrating target‐based high‐throughput screening and chemoproteomic approaches, Journal of Medical Virology, doi:10.1002/jmv.29208.wiley.com, doi.org.

Qin et al., 11 Nov 2023, China, peer-reviewed, 8 authors.

Contact: epuswei@gmail.com, 874643370@qq.com.

In Silico studies are an important part of preclinical research, however results may be very different in vivo.

All Studies Meta Analysis Submit Updates or Corrections

This Paper Quercetin All

Exploring the bioactive compounds of Feiduqing formula for the prevention and management of COVID-19 through network pharmacology and molecular docking

Shuang-Lin Qin, Hui Yao, Ting Huang, Hong-Fei Yang, Ting-Ting Ge, Jie-Qiong Wang, Wei-Wu Wang, Qing Min

Medical Data Mining, doi:10.53388/mdm202407003

Background: To explore the effective chemical constituents of Feiduqing formula for prevention and treatment of coronavirus disease 2019 . Methods: The compounds and action targets of twelve herbal medicines in Feiduqing formula were collected via Traditional Chinese Medicine Systems Pharmacology Database and Analytic Platform. The genes corresponding to the targets were queried through the UniProt database. The "herbal medicine-ingredient-target" network was established by Cytoscape software. The Gene Ontology function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed by Database for Annotation, Visualization and Integrated Discovery. Molecular docking was used to analyze the binding force of core active compounds of Feiduqing formula with PTGS2, HSP90AA1, SARS-CoV-2 3CL hydrolase and angiotensin converting enzyme II (ACE2). Results: The "herbal medicine-ingredient-target" network included 434 nodes and 1948 edges, including 222 components such as quercetin, kaempferol, luteolin, etc. The key targets are PTGS2, HSP90AA1, PTGS1, ESR1, AR, NOS2, etc. Gene Ontology function enrichment analysis revealed 2530 items, including RNA polymerase II-specific, response to oxidative stress, transcription factor activity, etc. Kyoto Encyclopedia of Genes and Genomes pathway enrichment screened 169 signal pathways, including Human cytomegalovirus infection, Kaposi sarcoma-associated herpesvirus infection, Hepatitis B, Hepatitis C, IL-17, TNF, etc. The results of molecular docking showed that quercetin, luteolin, β-sitosterol, stigmasterol and other core active compounds have a certain degree of affinity with PTGS2, HSP90AA1, SARS-CoV-2 3CL hydrolase and ACE2. Conclusion: The active compounds of Feiduqing formula may have a therapeutic effect on COVID-19 pneumonia through the action on PTGS2, HSP90AA1, SARS-CoV-2 3CL hydrolase and ACE2, and regulating many signaling pathways.

Competing interests The authors declare no conflicts of interest.

References

Ahmed, Ramakrishnan, Systems biological approach of molecular descriptors connectivity: optimal descriptors for oral bioavailability prediction, PLoS One, doi:10.1371/journal.pone.0040654

Ai, Wu, Qi, Study on the Mechanisms of Active Compounds in Traditional Chinese Medicine for the Treatment of Influenza Virus by Virtual Screening, Interdiscip Sci, doi:10.1007/s12539-018-0289-0

Bai, Qin, Zhao, Wang, Wang, Integrated innovation of Chinese and western medicine: Target-combined Holistic Treatment, Chin Sci Bull, doi:10.1360/TB-2021-0867

Chen, Wang, Lu, Uncovering potential anti-neuroinflammatory components of Modified Wuziyanzong Prescription through a target-directed molecular docking fingerprint strategy, J Pharm Biomed Anal, doi:10.1016/j.jpba.2018.05.001

Cui, Li, Guo, Traditional Chinese medicine for treatment of coronavirus disease 2019: a review, Tradit Chin Med, doi:10.53388/TMR20200222165

Han, Zhao, Shi, Application of integrated traditional Chinese and Western medicine in the treatment of novel coronavirus pneumonia, Chin Tradit Herb Drugs

Health, Of, Prc, New Diagnostic and treatment protocol for coronavirus pneumonia (trial version 9)

Hopkins, Network pharmacology: the next paradigm in drug discovery, Nat Chem Biol, doi:10.1038/nchembio.118

Hsin, Ghosh, Kitano, Combining machine learning systems and multiple docking simulation packages to improve docking prediction reliability for network pharmacology, PLoS One, doi:10.1371/journal.pone.0083922

Huang, Sherman, Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat Protoc, doi:10.1038/nprot.2008.211

Kim, Thiessen, Bolton, PubChem Substance and Compound databases, Nucleic Acids Res, doi:10.1093/nar/gkv951

Li, Wang, Guo, Li, Efficacy and safety of traditional Chinese medicine for the treatment of influenza A (H1N1): A meta-analysis, J Chin Med Assoc, doi:10.1016/j.jcma.2015.10.009

Niu, Wang, Xiao, Rapid establishment of traditional Chinese medicine prevention and treatment of 2019-nCoV based on clinical experience and molecular docking, China J Chin Mater Med, doi:10.19540/j.cnki.cjcmm.20200206.501

Ru, Li, Wang, TCMSP: a database of systems pharmacology for drug discovery from herbal medicines, J Cheminform, doi:10.1186/1758-2946-6-13

Su, Morris, Demchak, Bader, Biological Network Exploration with Cytoscape 3, Curr Protoc Bioinformatics, doi:10.1002/0471250953.bi0813s47

Sun, Sun, Yan, Li, Xin, Data mining and systematic pharmacology to reveal the mechanisms of traditional Chinese medicine in Mycoplasma pneumoniae pneumonia treatment, Biomed Pharmacother, doi:10.1016/j.biopha.2020.109900

Ursu, Rayan, Goldblum, Oprea, Understanding drug-likeness, WIREs Comput Mol Sci, doi:10.1002/wcms.52

Wang, Horby, Hayden, Gao, A novel coronavirus outbreak of global health concern, Lancet, doi:10.1016/S0140-6736(20)30185-9

Wang, Liu, Chen, The establishment of reference sequence for SARS-CoV-2 and variation analysis, J Med Virol, doi:10.1002/jmv.25762

Wang, Qu, To understand the etiology of new coronavirus pneumonia from the point of view of traditional Chinese medicine, J Pract Tradit Chin Internal Med, doi:10.13729/j.issn.1671-7813.Z20220328

Wei, Zhong, Sun, Proteomic and mechanistic study of Qingxuan Tongluo formula and curcumin in the treatment of Mycoplasma pneumoniae pneumonia, Biomed Pharmacother, doi:10.1016/j.biopha.2020.110998

Xie, Gao, Li, Research progress and application strategy on network pharmacology in Chinese materia medica, Chin Tradit Herb Drugs, doi:10.7501/j.issn.0253-2670.2019.10.001

Xing, Lyu, Chai, Zhu, Advances in the mechanism of traditional Chinese medicine by network pharma-cology method, J Pharm Pract, doi:10.3969/j.issn.1006-0111.2018.02.001

Yang, Cheng, Yan, A cell-based high-throughput protocol to screen entry inhibitors of highly pathogenic viruses with Traditional Chinese Medicines, J Med Virol, doi:10.1002/jmv.24705

Yang, Hu, Can Yin-Chai-Xiao-Du decoction be useful of COVID-19? The mechanism research based on network pharmacology, Tradit Chin Med, doi:10.53388/TMR20200601185

Yang, Li, Chao, Thinking on Etiology and pathogenesis of novel coronavirus pneumonia in traditional Chinese medicine, J Tradit Chin Med, doi:10.13288/j.11-2166/r.2020.07.002

Yang, Yt, Miao, Network pharmacology studies on the effect of Chai-Ling decoction in coronavirus disease, Tradit Med Res, doi:10.53388/TMR20200324170

Zhang, Cui, Zhang, Efficacy of Xuebijing injection for the treatment of coronavirus disease 2019 via network pharmacology, Tradit Chin Med, doi:10.53388/TMR20200507178

Zhang, Effect of integrated traditional Chinese and Western medicine on SARS: A review of clinical evidence, World J Gastroenterol, doi:10.3748/wjg.v10.i23.3500

Download Image

Please send us corrections, updates, or comments. c19early involves the extraction of over 100,000 datapoints from thousands of papers. Community updates help ensure high accuracy. Vaccines and treatments are complementary. All practical, effective, and safe means should be used based on risk/benefit analysis. No treatment, vaccine, or intervention is 100% available and effective for all current and future variants. We do not provide medical advice. Before taking any medication, consult a qualified physician who can provide personalized advice and details of risks and benefits based on your medical history and situation. FLCCC and WCH provide treatment protocols.

Submit

@CovidAnalysis

FAQ

Public domain CC0 1.0