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Flavonoid compound of red fruit papua and its derivatives against sars-cov-2 mpro: An in silico approach

Ananto et al., Journal of Applied Pharmaceutical Science, doi:10.7324/JAPS.2024.177392
Nov 2024  
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Quercetin for COVID-19
24th treatment shown to reduce risk in July 2021, now with p = 0.002 from 12 studies.
Lower risk for ICU, hospitalization, recovery, cases, and viral clearance.
No treatment is 100% effective. Protocols combine treatments.
5,200+ studies for 112 treatments. c19early.org
In Silico study showing that flavonoid compounds from red fruit, especially quercetin 3'-glucoside derivatives, may inhibit SARS-CoV-2 main protease (Mpro). Authors used molecular docking to identify quercetin 3'-glucoside as the best binding flavonoid to Mpro, interacting with key residues Asn142 and Cys145. They then designed 225 derivatives, with the top compound SR133 showing improved binding energy over the parent compound and antiviral drugs remdesivir and paxlovid in docking studies. Molecular dynamics simulations confirmed the stability of SR133 binding to Mpro.
73 preclinical studies support the efficacy of quercetin for COVID-19:
45 In Silico studies1-45
22 In Vitro studies1,2,5,15,19,21,25,42,46-59
6 In Vivo animal studies5,19,52,55,60,61
In Silico studies predict inhibition of SARS-CoV-2, or minimization of side effects, with quercetin or metabolites via binding to the spikeA,2,3,9,10,22,24,25,27,30,38,39,41,42,62, MproB,2,3,7,9,11,13,15,17,18,20,23,24,27,30,34,36-38,42-45, RNA-dependent RNA polymeraseC,1-3,9,32, PLproD,3,37,45, ACE2E,22,23,27,28,37,41, TMPRSS2F,22, nucleocapsidG,3, helicaseH,3,29,34, endoribonucleaseI,39, NSP16/10J,6, cathepsin LK,26, Wnt-3L,22, FZDM,22, LRP6N,22, ezrinO,40, ADRPP,38, NRP1Q,41, EP300R,16, PTGS2S,23, HSP90AA1T,16,23, matrix metalloproteinase 9U,31, IL-6V,21,35, IL-10W,21, VEGFAX,35, and RELAY,35 proteins. In Vitro studies demonstrate inhibition of the MproB,15,46,51,59 protein, and inhibition of spike-ACE2 interactionZ,47. In Vitro studies demonstrate efficacy in Calu-3AA,50, A549AB,21, HEK293-ACE2+AC,58, Huh-7AD,25, Caco-2AE,49, Vero E6AF,19,42,49, mTECAG,52, and RAW264.7AH,52 cells. Animal studies demonstrate efficacy in K18-hACE2 miceAI,55, db/db miceAJ,52,61, BALB/c miceAK,60, and rats19. Quercetin reduced proinflammatory cytokines and protected lung and kidney tissue against LPS-induced damage in mice60, inhibits LPS-induced cytokine storm by modulating key inflammatory and antioxidant pathways in macrophages5, and inhibits SARS-CoV-2 ORF3a ion channel activity, which contributes to viral pathogenicity and cytotoxicity54.
Important missing comments or errors? Let us know.
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 Mpro, also known as 3CLpro or nsp5, is a cysteine protease that cleaves viral polyproteins into functional units needed for replication. Inhibiting Mpro 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 nucleocapsid (N) protein binds and encapsulates the viral genome by coating the viral RNA. N enables formation and release of infectious virions and plays additional roles in viral replication and pathogenesis. N is also an immunodominant antigen used in diagnostic assays.
h. 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.
i. 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.
j. The NSP16/10 complex consists of non-structural proteins 16 and 10, forming a 2'-O-methyltransferase that modifies the viral RNA cap structure. This modification helps the virus evade host immune detection by mimicking host mRNA, making NSP16/10 a promising antiviral target.
k. 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.
l. Wingless-related integration site (Wnt) ligand 3 is a host signaling molecule that activates the Wnt signaling pathway, which is important in development, cell growth, and tissue repair. Some studies suggest that SARS-CoV-2 infection may interfere with the Wnt signaling pathway, and that Wnt3a is involved in SARS-CoV-2 entry.
m. 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.
n. 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.
o. 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.
p. 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.
q. 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.
r. 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.
s. 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.
t. 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.
u. 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.
v. 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.
w. 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.
x. 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.
y. 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.
z. 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.
aa. 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.
ab. 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.
ac. HEK293-ACE2+ is a human embryonic kidney cell line engineered for high ACE2 expression and SARS-CoV-2 susceptibility.
ad. Huh-7 cells were derived from a liver tumor (hepatoma).
ae. 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.
af. 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.
ag. mTEC is a mouse tubular epithelial cell line.
ah. RAW264.7 is a mouse macrophage cell line.
ai. A mouse model expressing the human ACE2 receptor under the control of the K18 promoter.
aj. 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.
ak. A mouse model commonly used in infectious disease and cancer research due to higher immune response and susceptibility to infection.
Ananto et al., 5 Nov 2024, Indonesia, peer-reviewed, 4 authors. Contact: harnodp@ugm.ac.id.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperQuercetinAll
Flavonoid compound of red fruit papua and its derivatives against sars-cov-2 mpro: An in silico approach
Agus Dwi Ananto, Harno Dwi Pranowo, Winarto Haryadi, Niko Prasetyo
Journal of Applied Pharmaceutical Science, doi:10.7324/japs.2024.177392
In the past years, the world has experienced a profound impact due to the abrupt appearance of a new virus , presenting a significant threat to human health. Currently, there exists no widely established treatment for COVID-19 that proves consistently effective, but many studies have implemented drug repurposing and the use of herbal medicines. The potential of antiviral compounds from natural products can be predicted through in silico approach. This study aimed to determine and design flavonoid compounds from red fruits and their derivatives that have the potential to suppress the SARS-CoV-2 Mpro, ensuring a stable molecular framework and adhering to a standard pharmacokinetic profile. The study started with molecular docking using a lead compound followed by Molecular dynamics (MD) simulation up to 100 ns and pharmacokinetic prediction. The analysis of docking outcomes reveals that among flavonoid compounds, quercetin 3'-glucoside exhibits the most favorable binding energy value. Furthermore, the identification of hydrogen bonds with amino acid residues Asn142 and Cys145 provides additional rationale for selecting this compound as a pivotal candidate in the design of novel derivatives. The molecular docking procedure and subsequent MD simulations were conducted utilizing the Yasara-structure software. Furthermore, the evaluation of the pharmacokinetic profile was performed utilizing pkCSM ADMET to gain insights into the compound's absorption, distribution, metabolism, excretion, and toxicity characteristics. According to the docking outcomes, among the 225 newly designed compounds, the ligand with code SR133 demonstrated the most favorable binding energy of -8.0950 Kcal/mol, surpassing the reference compound. Subsequent MD simulation analysis indicates that this ligand demonstrates good stability. The presence of hydrogen bonds in the active site of SARS-CoV-2Mpro involving the main amino acid residues Asn142 and Cys145 further clarifies that this new compound has excellent inhibitory potential. The pharmacokinetic prediction of SR133 shows that this compound has a good pharmacokinetic profile and is worth proposing as a new drug candidate.
All authors made substantial contributions to The authors report no financial or any other conflicts This study does not involve experiments on animals All the data is available with the authors and shall be The authors declares that they have not used artificial AUTHOR CONTRIBUTIONS and design, acquisition of data, or analysis interpretation of data; took part in drafting the article or revising it critically for important intellectual content; agreed to submit to the current journal; gave final approval of the version to be published; and agree to be accountable for all aspects of the work. All the authors are eligible to be an author as per the the international CONFLICTS OF INTEREST of interest in this work. ETHICAL APPROVALS or human subjects. DATA AVAILABILITY provided upon request. USE OF ARTIFICIAL INTELLIGENCE (AI)-ASSISTED TECHNOLOGY intelligence (AI)-tools for writing and editing of the manuscript, and no images were manipulated using AI. PUBLISHER'S NOTE This journal remains neutral with regard to jurisdictional claims in published institutional affiliation. committee of medical journal editors (ICMJE) requirements/ guidelines.
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