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Network pharmacology and molecular docking reveal the mechanisms of action of Panax notoginseng against post-COVID-19 thromboembolism

Yuan et al., Review of Clinical Pharmacology and Pharmacokinetics - International Edition, doi:10.61873/DTFA3974

May 2024

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Quercetin for COVID-19

24th treatment shown to reduce risk in July 2021

^*, now with p = 0.0031 from 11 studies.

Lower risk for ICU admission, hospitalization, recovery, cases, and viral clearance.

No treatment is 100% effective. Protocols combine treatments. ^* >10% efficacy, ≥3 studies.

4,800+ studies for 102 treatments. c19early.org

In Silico study showing potential benefits of quercetin and ginsenosides from Panax notoginseng (PNGS) for post-COVID-19 thromboembolism. Authors used network pharmacology and molecular docking to analyze PNGS mechanisms against COVID-19-associated thromboembolism. Quercetin and ginsenosides were identified as top bioactive components in PNGS. Molecular docking revealed stable binding between quercetin and ginsenoside with key targets ACE, F3, IL-1β, MAPK1, and SERPINE1. Quercetin showed strong binding affinities to SERPINE1 (-8.7 kcal/mol), MAPK1 (-8.5 kcal/mol), and ACE (-8.3 kcal/mol). The study suggests PNGS may target COVID-19-induced thromboembolism through multiple pathways, including AGE/RAGE signaling, fluid shear stress and atherosclerosis, complement and coagulation cascades, and direct COVID-19 pathways.

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

40 In Silico studies1-40

18 In Vitro studies1,10,14,16,20,37,41-52

6 In Vivo animal studies1,14,46,48,53,54

In Silico studies predict inhibition of SARS-CoV-2, or minimization of side effects, with quercetin or metabolites via binding to the spikeA,4,5,17,19,20,25,33,34,36,37,55,56, M^proB,2,4,6,8,10,12,13,15,18,19,25,29,31-33,37,38,40,56,57, RNA-dependent RNA polymeraseC,4,27, PLproD,32,40, ACE2E,17,18,23,32,36,56, TMPRSS2F,17, helicaseG,24,29, endoribonucleaseH,34, cathepsin LI,21, Wnt-3J,17, FZDK,17, LRP6L,17, ezrinM,35, ADRPN,33, NRP1O,36, EP300P,11, PTGS2Q,18, HSP90AA1R,11,18, matrix metalloproteinase 9S,26, IL-6T,16,30, IL-10U,16, VEGFAV,30, and RELAW,30 proteins. In Vitro studies demonstrate inhibition of the M^proB,10,45,52 protein, and inhibition of spike-ACE2 interactionX,41. In Vitro studies demonstrate efficacy in Calu-3Y,44, A549Z,16, HEK293-ACE2+AA,51, Huh-7AB,20, Caco-2AC,43, Vero E6AD,14,37,43, mTECAE,46, and RAW264.7AF,46 cells. Animal studies demonstrate efficacy in K18-hACE2 miceAG,48, db/db miceAH,46,54, BALB/c miceAI,53, and rats58. Quercetin reduced proinflammatory cytokines and protected lung and kidney tissue against LPS-induced damage in mice53 and inhibits LPS-induced cytokine storm by modulating key inflammatory and antioxidant pathways in macrophages1.

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57. Sekiou (B) 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.

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a. The trimeric spike (S) protein is a glycoprotein that mediates viral entry by binding to the host ACE2 receptor, is critical for SARS-CoV-2's ability to infect host cells, and is a target of neutralizing antibodies. Inhibition of the spike protein prevents viral attachment, halting infection at the earliest stage.

b. The main protease or M^pro, also known as 3CL^pro or nsp5, is a cysteine protease that cleaves viral polyproteins into functional units needed for replication. Inhibiting M^pro disrupts the SARS-CoV-2 lifecycle within the host cell, preventing the creation of new copies.

c. RNA-dependent RNA polymerase (RdRp), also called nsp12, is the core enzyme of the viral replicase-transcriptase complex that copies the positive-sense viral RNA genome into negative-sense templates for progeny RNA synthesis. Inhibiting RdRp blocks viral genome replication and transcription.

d. The papain-like protease (PLpro) has multiple functions including cleaving viral polyproteins and suppressing the host immune response by deubiquitination and deISGylation of host proteins. Inhibiting PLpro may block viral replication and help restore normal immune responses.

e. The angiotensin converting enzyme 2 (ACE2) protein is a host cell transmembrane protein that serves as the cellular receptor for the SARS-CoV-2 spike protein. ACE2 is expressed on many cell types, including epithelial cells in the lungs, and allows the virus to enter and infect host cells. Inhibition may affect ACE2's physiological function in blood pressure control.

f. Transmembrane protease serine 2 (TMPRSS2) is a host cell protease that primes the spike protein, facilitating cellular entry. TMPRSS2 activity helps enable cleavage of the spike protein required for membrane fusion and virus entry. Inhibition may especially protect respiratory epithelial cells, buy may have physiological effects.

g. The helicase, or nsp13, protein unwinds the double-stranded viral RNA, a crucial step in replication and transcription. Inhibition may prevent viral genome replication and the creation of new virus components.

h. The endoribonuclease, also known as NendoU or nsp15, cleaves specific sequences in viral RNA which may help the virus evade detection by the host immune system. Inhibition may hinder the virus's ability to mask itself from the immune system, facilitating a stronger immune response.

i. Cathepsin L is a host lysosomal cysteine protease that can prime the spike protein through an alternative pathway when TMPRSS2 is unavailable. Dual targeting of cathepsin L and TMPRSS2 may maximize disruption of alternative pathways for virus entry.

k. The frizzled (FZD) receptor is a host transmembrane receptor that binds Wnt ligands, initiating the Wnt signaling cascade. FZD serves as a co-receptor, along with ACE2, in some proposed mechanisms of SARS-CoV-2 infection. The virus may take advantage of this pathway as an alternative entry route.

l. Low-density lipoprotein receptor-related protein 6 is a cell surface co-receptor essential for Wnt signaling. LRP6 acts in tandem with FZD for signal transduction and has been discussed as a potential co-receptor for SARS-CoV-2 entry.

m. The ezrin protein links the cell membrane to the cytoskeleton (the cell's internal support structure) and plays a role in cell shape, movement, adhesion, and signaling. Drugs that occupy the same spot on ezrin where the viral spike protein would bind may hindering viral attachment, and drug binding could further stabilize ezrin, strengthening its potential natural capacity to impede viral fusion and entry.

n. The Adipocyte Differentiation-Related Protein (ADRP, also known as Perilipin 2 or PLIN2) is a lipid droplet protein regulating the storage and breakdown of fats in cells. SARS-CoV-2 may hijack the lipid handling machinery of host cells and ADRP may play a role in this process. Disrupting ADRP's interaction with the virus may hinder the virus's ability to use lipids for replication and assembly.

o. Neuropilin-1 (NRP1) is a cell surface receptor with roles in blood vessel development, nerve cell guidance, and immune responses. NRP1 may function as a co-receptor for SARS-CoV-2, facilitating viral entry into cells. Blocking NRP1 may disrupt an alternative route of viral entry.

p. EP300 (E1A Binding Protein P300) is a transcriptional coactivator involved in several cellular processes, including growth, differentiation, and apoptosis, through its acetyltransferase activity that modifies histones and non-histone proteins. EP300 facilitates viral entry into cells and upregulates inflammatory cytokine production.

q. Prostaglandin G/H synthase 2 (PTGS2, also known as COX-2) is an enzyme crucial for the production of inflammatory molecules called prostaglandins. PTGS2 plays a role in the inflammatory response that can become severe in COVID-19 and inhibitors (like some NSAIDs) may have benefits in dampening harmful inflammation, but note that prostaglandins have diverse physiological functions.

r. Heat Shock Protein 90 Alpha Family Class A Member 1 (HSP90AA1) is a chaperone protein that helps other proteins fold correctly and maintains their stability. HSP90AA1 plays roles in cell signaling, survival, and immune responses. HSP90AA1 may interact with numerous viral proteins, but note that it has diverse physiological functions.

s. Matrix metalloproteinase 9 (MMP9), also called gelatinase B, is a zinc-dependent enzyme that breaks down collagen and other components of the extracellular matrix. MMP9 levels increase in severe COVID-19. Overactive MMP9 can damage lung tissue and worsen inflammation. Inhibition of MMP9 may prevent excessive tissue damage and help regulate the inflammatory response.

t. The interleukin-6 (IL-6) pro-inflammatory cytokine (signaling molecule) has a complex role in the immune response and may trigger and perpetuate inflammation. Elevated IL-6 levels are associated with severe COVID-19 cases and cytokine storm. Anti-IL-6 therapies may be beneficial in reducing excessive inflammation in severe COVID-19 cases.

u. The interleukin-10 (IL-10) anti-inflammatory cytokine helps regulate and dampen immune responses, preventing excessive inflammation. IL-10 levels can also be elevated in severe COVID-19. IL-10 could either help control harmful inflammation or potentially contribute to immune suppression.

v. Vascular Endothelial Growth Factor A (VEGFA) promotes the growth of new blood vessels (angiogenesis) and has roles in inflammation and immune responses. VEGFA may contribute to blood vessel leakiness and excessive inflammation associated with severe COVID-19.

w. RELA is a transcription factor subunit of NF-kB and is a key regulator of inflammation, driving pro-inflammatory gene expression. SARS-CoV-2 may hijack and modulate NF-kB pathways.

x. The interaction between the SARS-CoV-2 spike protein and the human ACE2 receptor is a primary method of viral entry, inhibiting this interaction can prevent the virus from attaching to and entering host cells, halting infection at an early stage.

y. Calu-3 is a human lung adenocarcinoma cell line with moderate ACE2 and TMPRSS2 expression and SARS-CoV-2 susceptibility. It provides a model of the human respiratory epithelium, but many not be ideal for modeling early stages of infection due to the moderate expression levels of ACE2 and TMPRSS2.

z. A549 is a human lung carcinoma cell line with low ACE2 expression and SARS-CoV-2 susceptibility. Viral entry/replication can be studied but the cells may not replicate all aspects of lung infection.

aa. HEK293-ACE2+ is a human embryonic kidney cell line engineered for high ACE2 expression and SARS-CoV-2 susceptibility.

ab. Huh-7 cells were derived from a liver tumor (hepatoma).

ac. Caco-2 cells come from a colorectal adenocarcinoma (cancer). They are valued for their ability to form a polarized cell layer with properties similar to the intestinal lining.

ad. Vero E6 is an African green monkey kidney cell line with low/no ACE2 expression and high SARS-CoV-2 susceptibility. The cell line is easy to maintain and supports robust viral replication, however the monkey origin may not accurately represent human responses.

ae. mTEC is a mouse tubular epithelial cell line.

af. RAW264.7 is a mouse macrophage cell line.

ag. A mouse model expressing the human ACE2 receptor under the control of the K18 promoter.

ah. A mouse model of obesity and severe insulin resistance leading to type 2 diabetes due to a mutation in the leptin receptor gene that impairs satiety signaling.

ai. A mouse model commonly used in infectious disease and cancer research due to higher immune response and susceptibility to infection.

Yuan et al., 5 May 2024, peer-reviewed, 15 authors. Contact: juliu@tcd.ie.

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

This Paper Quercetin All

Network pharmacology and molecular docking reveal the mechanisms of action of Panax notoginseng against post-COVID-19 thromboembolism

Shouli Yuan, Ismael Obaidi, Tao Zhang, Maria Pigott, Shibo Jiang, Helen Sheridan, Junying Liu

Review of Clinical Pharmacology and Pharmacokinetics - International Edition, doi:10.61873/dtfa3974

Panax notoginseng (PNGS) is a potent folk therapy for blood-related diseases. However, further research is required to fully elucidate the mechanisms of its pharmacological activities and to explore its therapeutic potential for treating thromboembolism (TE) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed at analysing the molecular mechanisms of PNGS and at clarifying their potential role in treating TE induced by COVID-19, by employing network pharmacology and molecular docking. To this end, a network pharmacological approach was combined with expression profiling by high-throughput sequencing of GSE156701 so as to elucidate the compound constituents of PNGS for treating TE caused by SARS-CoV-2 at a systemic level. Protein-protein interaction network, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analyses were employed in order to decipher the associated drug-target interactions. The integration of these results suggested that five targets, including the angiotensin-converting enzyme (ACE), the coagulation factor III (F3), interleukin-1 beta (IL-1β), the mitogenactivated protein kinase 1 (MAPK1), and the plasminogen activator inhibitor-1 (SERPINE1), represent major genes involved in thromboembolism. The data suggest that PNGS exerts collective therapeutic effects against TE caused by SARS-CoV-2, and provides a theoretical basis for further laboratory study of the active drug-like ingredients and the potential mechanisms of PNGS in TE treatment.

CONFLICT OF INTEREST STATEMENT The authors declare no conflicts of interest.

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Yi, Potential benefits of ginseng against COVID-19 by targeting inflammasomes, J. Ginseng Res, doi:10.1016/j.jgr.2022.03.008

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To this end, a network pharmacological ap¬proach was ' 'combined with expression profiling by high-throughput sequencing of GSE156701 so as to ' 'elucidate the compound constituents of PNGS for treating TE caused by SARS-CoV-2 at a ' 'systemic level. Protein-protein interac¬tion network, Gene Ontology, and Kyoto Encyclopedia ' 'of Genes and Genomes analyses were employed in order to decipher the associated drug-target ' 'interactions. The integration of these results suggested that five targets, including the ' 'angiotensin-converting enzyme (ACE), the coagulation factor III (F3), interleukin-1 beta ' '(IL-1β), the mitogen-activated protein kinase 1 (MAPK1), and the plasminogen activator ' 'inhibitor-1 (SERPINE1), represent major genes involved in thromboembolism. The data suggest ' 'that PNGS exerts collective therapeutic effects against TE caused by SARS-CoV-2, and provides ' 'a theoretical basis for further laboratory study of the active drug-like ingredients and the ' 'potential mechanisms of PNGS in TE treatment.', 'DOI': '10.61873/dtfa3974', 'type': 'journal-article', 'created': {'date-parts': [[2024, 5, 6]], 'date-time': '2024-05-06T18:28:05Z', 'timestamp': 1715020085000}, 'page': '181-184', 'source': 'Crossref', 'is-referenced-by-count': 0, 'title': 'Network pharmacology and molecular docking reveal the mechanisms of action of Panax notoginseng ' 'against post-COVID-19 thromboembolism', 'prefix': '10.61873', 'volume': '38', 'author': [ { 'ORCID': 'http://orcid.org/0000-0002-4733-9891', 'authenticated-orcid': False, 'given': 'Shouli', 'family': 'Yuan', 'sequence': 'first', 'affiliation': []}, { 'name': 'Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China', 'sequence': 'first', 'affiliation': []}, { 'ORCID': 'http://orcid.org/0000-0003-1204-955X', 'authenticated-orcid': False, 'given': 'Ismael', 'family': 'Obaidi', 'sequence': 'additional', 'affiliation': []}, { 'ORCID': 'http://orcid.org/0000-0003-1079-5364', 'authenticated-orcid': False, 'given': 'Tao', 'family': 'Zhang', 'sequence': 'additional', 'affiliation': []}, { 'ORCID': 'http://orcid.org/0009-0005-9502-9045', 'authenticated-orcid': False, 'given': 'Maria', 'family': 'Pigott', 'sequence': 'additional', 'affiliation': []}, { 'ORCID': 'http://orcid.org/0000-0003-1493-6523', 'authenticated-orcid': False, 'given': 'Shibo', 'family': 'Jiang', 'sequence': 'additional', 'affiliation': []}, { 'ORCID': 'http://orcid.org/0000-0002-9454-752X', 'authenticated-orcid': False, 'given': 'Helen', 'family': 'Sheridan', 'sequence': 'additional', 'affiliation': []}, { 'ORCID': 'http://orcid.org/0000-0002-6924-9432', 'authenticated-orcid': False, 'given': 'Junying', 'family': 'Liu', 'sequence': 'additional', 'affiliation': []}, { 'name': 'NatPro Centre for Natural Products Research, School of Pharmacy and Pharmaceutical ' 'Sciences, Trinity College Dublin, Dublin, Ireland', 'sequence': 'additional', 'affiliation': []}, { 'name': 'College of Pharmacy, University of Babylon, Hillah, Iraq', 'sequence': 'additional', 'affiliation': []}, { 'name': 'School of Food Science & Environmental Health, Technological University Dublin, ' 'Grangegorman, Dublin, Ireland', 'sequence': 'additional', 'affiliation': []}, { 'name': 'NatPro Centre for Natural Products Research, School of Pharmacy and Pharmaceutical ' 'Sciences, Trinity College Dublin, Dublin, Ireland', 'sequence': 'additional', 'affiliation': []}, { 'name': 'Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic ' 'Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan ' 'University, Shanghai, China', 'sequence': 'additional', 'affiliation': []}, { 'name': 'NatPro Centre for Natural Products Research, School of Pharmacy and Pharmaceutical ' 'Sciences, Trinity College Dublin, Dublin, Ireland', 'sequence': 'additional', 'affiliation': []}, { 'name': 'NatPro Centre for Natural Products Research, School of Pharmacy and Pharmaceutical ' 'Sciences, Trinity College Dublin, Dublin, Ireland', 'sequence': 'additional', 'affiliation': []}], 'member': '48040', 'published-online': {'date-parts': [[2024, 5, 5]]}, 'reference': [ { 'key': 'ref0', 'doi-asserted-by': 'publisher', 'unstructured': '1. Toufen Junior C., Pêgo-Fernandes P.M.: COVID-19: long-term ' 'respiratory consequences. Sao Paulo Med. J. 139(5): 421-423 (2021).', 'DOI': '10.1590/1516-3180.2021.139526052021'}, { 'key': 'ref1', 'doi-asserted-by': 'publisher', 'unstructured': '2. Arévalos V., Ortega-Paz L., Rodríguez-Arias J.J., Calvo López M., ' 'Castrillo-Golvano L., Salazar-Rodríguez A., et al.: Acute and chronic ' 'effects of COVID-19 on the cardiovascular system. J. Cardiovasc. Dev. ' 'Dis. 8(10): 128 (2021).', 'DOI': '10.3390/jcdd8100128'}, { 'key': 'ref2', 'doi-asserted-by': 'publisher', 'unstructured': '3. Xie W., Meng X., Zhai Y., Zhou P., Ye T., Wang Z., et al.: Panax ' 'notoginseng saponins: a review of its mechanisms of antidepressant or ' 'anxiolytic effects and network analysis on phytochemistry and ' 'pharmacology. Molecules 23(4): 940 (2018).', 'DOI': '10.3390/molecules23040940'}, { 'key': 'ref3', 'doi-asserted-by': 'publisher', 'unstructured': '4. Yi Y.S.: Potential benefits of ginseng against COVID-19 by targeting ' 'inflammasomes. J. Ginseng Res. 46(6): 722-730 (2022).', 'DOI': '10.1016/j.jgr.2022.03.008'}, { 'key': 'ref4', 'doi-asserted-by': 'publisher', 'unstructured': '5. Boozari M., Hosseinzadeh H.: Natural products for COVID-19 prevention ' 'and treatment regarding to previous coronavirus infections and novel ' 'studies. Phytother. Res. 35(2): 864-876 (2021).', 'DOI': '10.1002/ptr.6873'}, { 'key': 'ref5', 'doi-asserted-by': 'publisher', 'unstructured': '6. Ding Q., Zhu W., Diao Y., Xu G., Wang L., Qu S., et al.: Elucidation ' 'of the mechanism of action of ginseng against acute lung injury/acute ' 'respiratory distress syndrome by a network pharmacology-based strategy. ' 'Front. Pharmacol. 11: 611794 (2021).', 'DOI': '10.3389/fphar.2020.611794'}, { 'key': 'ref6', 'doi-asserted-by': 'publisher', 'unstructured': '7. Khan S.S.: The central role of PAI-1 in COVID-19: thrombosis and ' 'beyond. Am. J. Respir. Cell Mol. Biol. 65(3): 238-240 (2021).', 'DOI': '10.1165/rcmb.2021-0208ED'}, { 'key': 'ref7', 'unstructured': '8. Coutts R.T.: The Psychopharmacology of Herbal Medicine: Plant Drugs ' 'That Alter Mind, Brain and Behavior. J. Psychiatry Neurosci. 28(4): ' '300-301 (2003).'}, { 'key': 'ref8', 'doi-asserted-by': 'publisher', 'unstructured': '9. Hossain M.A., Kim J.H.: Possibility as role of ginseng and ' 'ginsenosides on inhibiting the heart disease of COVID-19: a systematic ' 'review. J. Ginseng Res. 46(3): 321-330 (2022).', 'DOI': '10.1016/j.jgr.2022.01.003'}, { 'key': 'ref9', 'doi-asserted-by': 'publisher', 'unstructured': '10. Khan A., Iqtadar S., Mumtaz S.U., Heinrich M., Pascual-Figal D.A., ' 'Livingstone S., et al.: Oral co-supplementation of curcumin, quercetin, ' 'and vitamin D3 as an adjuvant therapy for mild to moderate symptoms of ' 'COVID-19 -- results from a pilot open-label, randomized controlled ' 'trial. Front. 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