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A study on the effect of natural products against the transmission of B.1.1.529 Omicron

Alkafaas et al., Virology Journal, doi:10.1186/s12985-023-02160-6
Aug 2023  
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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.
No treatment is 100% effective. Protocols combine treatments.
5,100+ studies for 109 treatments. c19early.org
Review of natural products for SARS-CoV-2 omicron including an In Silico study showing quercetin, curcumin, ascorbic acid, nigellidine, and chloroquine among many compounds docked to the ACE2 metallopeptidase domain. Quercetin, curcumin, and ascorbic acid bound ACE2 with energy scores of -16.51, -13.5, and -12.55 kcal/mol. Nigellidine and chloroquine bound with lower affinity (-11.73 and -10.33 kcal/mol). The results suggest these compounds may have potential to inhibit SARS-CoV-2 infection by binding the ACE2 receptor.
68 preclinical studies support the efficacy of quercetin for COVID-19:
In Silico studies predict inhibition of SARS-CoV-2, or minimization of side effects, with quercetin or metabolites via binding to the spikeA,6,7,19,21,22,27,35,36,38,39,59,60, MproB,4,6,8,10,12,14,15,17,20,21,27,31,33-35,39,40,42,60,61, RNA-dependent RNA polymeraseC,6,29, PLproD,34,42, ACE2E,19,20,25,34,38,60, TMPRSS2F,19, helicaseG,26,31, endoribonucleaseH,36, NSP16/10I,3, cathepsin LJ,23, Wnt-3K,19, FZDL,19, LRP6M,19, ezrinN,37, ADRPO,35, NRP1P,38, EP300Q,13, PTGS2R,20, HSP90AA1S,13,20, matrix metalloproteinase 9T,28, IL-6U,18,32, IL-10V,18, VEGFAW,32, and RELAX,32 proteins. In Vitro studies demonstrate inhibition of the MproB,12,43,48,56 protein, and inhibition of spike-ACE2 interactionY,44. In Vitro studies demonstrate efficacy in Calu-3Z,47, A549AA,18, HEK293-ACE2+AB,55, Huh-7AC,22, Caco-2AD,46, Vero E6AE,16,39,46, mTECAF,49, and RAW264.7AG,49 cells. Animal studies demonstrate efficacy in K18-hACE2 miceAH,52, db/db miceAI,49,58, BALB/c miceAJ,57, and rats62. Quercetin reduced proinflammatory cytokines and protected lung and kidney tissue against LPS-induced damage in mice57, inhibits LPS-induced cytokine storm by modulating key inflammatory and antioxidant pathways in macrophages2, and inhibits SARS-CoV-2 ORF3a ion channel activity, which contributes to viral pathogenicity and cytotoxicity51.
Study covers quercetin, curcumin, nigella sativa, vitamin C, and HCQ.
Alkafaas et al., 25 Aug 2023, peer-reviewed, 12 authors. Contact: samar.alkafas@science.tanta.edu.eg, samarsamy2017@yahoo.com, ghoshs@ufs.ac.za, soumyaghosh@yahoo.com, h.onyeaka@bham.ac.uk.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperQuercetinAll
A study on the effect of natural products against the transmission of B.1.1.529 Omicron
Samar Sami Alkafaas, Abanoub Mosaad Abdallah, Aya Misbah Hussien, Heba Bedair, Mahmoud Abdo, Soumya Ghosh, Sara Samy Elkafas, Wilgince Apollon, Morteza Saki, Samah A Loutfy, Helen Onyeaka, Mohamed Hessien
Virology Journal, doi:10.1186/s12985-023-02160-6
Background The recent outbreak of the Coronavirus pandemic resulted in a successful vaccination program launched by the World Health Organization. However, a large population is still unvaccinated, leading to the emergence of mutated strains like alpha, beta, delta, and B.1.1.529 (Omicron). Recent reports from the World Health Organization raised concerns about the Omicron variant, which emerged in South Africa during a surge in COVID-19 cases in November 2021. Vaccines are not proven completely effective or safe against Omicron, leading to clinical trials for combating infection by the mutated virus. The absence of suitable pharmaceuticals has led scientists and clinicians to search for alternative and supplementary therapies, including dietary patterns, to reduce the effect of mutated strains. Main body This review analyzed Coronavirus aetiology, epidemiology, and natural products for combating Omicron. Although the literature search did not include keywords related to in silico or computational research, in silico investigations were emphasized in this study. Molecular docking was implemented to compare the interaction between natural products and Chloroquine with the ACE2 receptor protein amino acid residues of Omicron. The global Omicron infection proceeding SARS-CoV-2 vaccination was also elucidated. The docking results suggest that DGCG may bind to the ACE2 receptor three times more effectively than standard chloroquine. Conclusion The emergence of the Omicron variant has highlighted the need for alternative therapies to reduce the impact of mutated strains. The current review suggests that natural products such as DGCG may be effective in binding to the ACE2 receptor and combating the Omicron variant, however, further research is required to validate the results of this study and explore the potential of natural products to mitigate COVID-19. Highlights • There are 32 mutations in the spike of the Omicron variant. • Non-SARS-COV-2 vaccinated individuals accelerate transmission of Omicron variant.
Declarations Ethics approval and consent to participate Not applicable. Consent for publication All the authors read and agreed to publish this article. Competing interests The authors declare that they have no competing interests. Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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However, a large ' 'population is still unvaccinated, leading to the emergence of mutated strains like alpha, ' 'beta, delta, and B.1.1.529 (Omicron). Recent reports from the World Health Organization ' 'raised concerns about the Omicron variant, which emerged in South Africa during a surge in ' 'COVID-19 cases in November 2021. Vaccines are not proven completely effective or safe against ' 'Omicron, leading to clinical trials for combating infection by the mutated virus. The absence ' 'of suitable pharmaceuticals has led scientists and clinicians to search for alternative and ' 'supplementary therapies, including dietary patterns, to reduce the effect of mutated ' 'strains.</jats:p>\n' ' </jats:sec><jats:sec>\n' ' <jats:title>Main body</jats:title>\n' ' <jats:p>This review analyzed Coronavirus aetiology, epidemiology, and natural ' 'products for combating Omicron. Although the literature search did not include keywords ' 'related to in silico or computational research, in silico investigations were emphasized in ' 'this study. Molecular docking was implemented to compare the interaction between natural ' 'products and Chloroquine with the ACE2 receptor protein amino acid residues of Omicron. The ' 'global Omicron infection proceeding SARS-CoV-2 vaccination was also elucidated. The docking ' 'results suggest that DGCG may bind to the ACE2 receptor three times more effectively than ' 'standard chloroquine.</jats:p>\n' ' </jats:sec><jats:sec>\n' ' <jats:title>Conclusion</jats:title>\n' ' <jats:p>The emergence of the Omicron variant has highlighted the need for ' 'alternative therapies to reduce the impact of mutated strains. The current review suggests ' 'that natural products such as DGCG may be effective in binding to the ACE2 receptor and ' 'combating the Omicron variant, however, further research is required to validate the results ' 'of this study and explore the potential of natural products to mitigate COVID-19.</jats:p>\n' ' </jats:sec><jats:sec>\n' ' <jats:title>Graphical abstract</jats:title>\n' ' \n' ' </jats:sec>', 'DOI': '10.1186/s12985-023-02160-6', 'type': 'journal-article', 'created': {'date-parts': [[2023, 8, 25]], 'date-time': '2023-08-25T06:02:14Z', 'timestamp': 1692943334000}, 'update-policy': 'http://dx.doi.org/10.1007/springer_crossmark_policy', 'source': 'Crossref', 'is-referenced-by-count': 3, 'title': 'A study on the effect of natural products against the transmission of B.1.1.529 Omicron', 'prefix': '10.1186', 'volume': '20', 'author': [ {'given': 'Samar Sami', 'family': 'Alkafaas', 'sequence': 'first', 'affiliation': []}, {'given': 'Abanoub Mosaad', 'family': 'Abdallah', 'sequence': 'additional', 'affiliation': []}, {'given': 'Aya Misbah', 'family': 'Hussien', 'sequence': 'additional', 'affiliation': []}, {'given': 'Heba', 'family': 'Bedair', 'sequence': 'additional', 'affiliation': []}, {'given': 'Mahmoud', 'family': 'Abdo', 'sequence': 'additional', 'affiliation': []}, {'given': 'Soumya', 'family': 'Ghosh', 'sequence': 'additional', 'affiliation': []}, {'given': 'Sara Samy', 'family': 'Elkafas', 'sequence': 'additional', 'affiliation': []}, {'given': 'Wilgince', 'family': 'Apollon', 'sequence': 'additional', 'affiliation': []}, {'given': 'Morteza', 'family': 'Saki', 'sequence': 'additional', 'affiliation': []}, {'given': 'Samah A.', 'family': 'Loutfy', 'sequence': 'additional', 'affiliation': []}, {'given': 'Helen', 'family': 'Onyeaka', 'sequence': 'additional', 'affiliation': []}, {'given': 'Mohamed', 'family': 'Hessien', 'sequence': 'additional', 'affiliation': []}], 'member': '297', 'published-online': {'date-parts': [[2023, 8, 25]]}, 'reference': [ { 'key': '2160_CR1', 'doi-asserted-by': 'crossref', 'first-page': '1', 'DOI': '10.12998/wjcc.v10.i1.1', 'volume': '10', 'author': 'S-Y Ren', 'year': '2022', 'unstructured': 'Ren S-Y, Wang W-B, Gao R-D, Zhou A-M. 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' 'Binding of a natural anthocyanin inhibitor to influenza neuraminidase by ' 'mass spectrometry. Anal Bioanal Chem. 2013;405:6563–72.', 'journal-title': 'Anal Bioanal Chem'}], 'container-title': 'Virology Journal', 'original-title': [], 'language': 'en', 'link': [ { 'URL': 'https://link.springer.com/content/pdf/10.1186/s12985-023-02160-6.pdf', 'content-type': 'application/pdf', 'content-version': 'vor', 'intended-application': 'text-mining'}, { 'URL': 'https://link.springer.com/article/10.1186/s12985-023-02160-6/fulltext.html', 'content-type': 'text/html', 'content-version': 'vor', 'intended-application': 'text-mining'}, { 'URL': 'https://link.springer.com/content/pdf/10.1186/s12985-023-02160-6.pdf', 'content-type': 'application/pdf', 'content-version': 'vor', 'intended-application': 'similarity-checking'}], 'deposited': { 'date-parts': [[2023, 11, 18]], 'date-time': '2023-11-18T22:18:41Z', 'timestamp': 1700345921000}, 'score': 1, 'resource': {'primary': {'URL': 'https://virologyj.biomedcentral.com/articles/10.1186/s12985-023-02160-6'}}, 'subtitle': [], 'short-title': [], 'issued': {'date-parts': [[2023, 8, 25]]}, 'references-count': 221, 'journal-issue': {'issue': '1', 'published-online': {'date-parts': [[2023, 12]]}}, 'alternative-id': ['2160'], 'URL': 'http://dx.doi.org/10.1186/s12985-023-02160-6', 'relation': {}, 'ISSN': ['1743-422X'], 'subject': ['Infectious Diseases', 'Virology'], 'container-title-short': 'Virol J', 'published': {'date-parts': [[2023, 8, 25]]}, 'assertion': [ { 'value': '29 March 2023', 'order': 1, 'name': 'received', 'label': 'Received', 'group': {'name': 'ArticleHistory', 'label': 'Article History'}}, { 'value': '15 August 2023', 'order': 2, 'name': 'accepted', 'label': 'Accepted', 'group': {'name': 'ArticleHistory', 'label': 'Article History'}}, { 'value': '25 August 2023', 'order': 3, 'name': 'first_online', 'label': 'First Online', 'group': {'name': 'ArticleHistory', 'label': 'Article History'}}, {'order': 1, 'name': 'Ethics', 'group': {'name': 'EthicsHeading', 'label': 'Declarations'}}, { 'value': 'Not applicable.', 'order': 2, 'name': 'Ethics', 'group': {'name': 'EthicsHeading', 'label': 'Ethics approval and consent to participate'}}, { 'value': 'All the authors read and agreed to publish this article.', 'order': 3, 'name': 'Ethics', 'group': {'name': 'EthicsHeading', 'label': 'Consent for publication'}}, { 'value': 'The authors declare that they have no competing interests.', 'order': 4, 'name': 'Ethics', 'group': {'name': 'EthicsHeading', 'label': 'Competing interests'}}], 'article-number': '191'}
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