INP-Guided Network Pharmacology Discloses Multi-Target Therapeutic Strategy Against Cytokine and IgE Storms in the SARS-CoV-2 NB.1.8.1 Variant

DOI record: { "DOI": "10.21203/rs.3.rs-6819274/v1", "URL": "http://dx.doi.org/10.21203/rs.3.rs-6819274/v1", "abstract": "<title>Abstract</title>\n <p>The continuous development of SARS-CoV-2 has given rise to the NB1.8.1 variant, which exhibits augmented pathogenicity, immune escape, and drug resistance against traditional therapeutics. The current study investigates a multi-layered systems pharmacology approach for identifying new therapeutic candidates that act on both viral entry and host-mediated inflammatory storms. By combining a seven-layer Intrinsic Network Pharmacology (INP) protocol with Network Pharmacology tools, we dissected the molecular failure network triggered by NB1.8.1, with emphasis on spike protein mutations that increase ACE2 binding, disrupt early interferon responses, and induce extreme cytokine and IgE storms. The HR1 and HR2 domain of the S2 fusion machinery was found to be a key weakness. We identified and confirmed a triterpenoid glycoside, ZINC000014930714, with high-affinity docking into the HR1 groove and strong pseudovirus fusion inhibition. Concurrently, we identified glycyrrhizin, a readily available natural saponin found in licorice, as a suitable surrogate with comparable fusion inhibition. Additional important modulators including camostat as an inhibitor of TMPRSS2, baricitinib targeting JAK and STAT signaling, sulforaphane as a Nrf2 activator, and metformin as an AMPK activator were incorporated into an inhalable nano-liposomal formulation strategy aimed at inhibiting viral propagation and resultant downstream immune storms. Network pharmacology modeling established that the indicated combination closes down several failure nodes in the INP layers. Our research offers a system-wide approach that not only reveals timely antiviral candidates against NB1.8.1 but also provides an adaptive platform for quick transition to emerging SARS-CoV-2 variants.</p>", "accepted": { "date-parts": [ [ 2025, 6, 4 ] ] }, "author": [ { "ORCID": "https://orcid.org/0000-0001-5181-6323", "affiliation": [ { "name": "North East Frontier Technical University" } ], "authenticated-orcid": false, "family": "Manikyam", "given": "Hemanth kumar", "sequence": "first" }, { "affiliation": [ { "name": "University of Miami" } ], "family": "Joshi", "given": "Sunil K", "sequence": "additional" } ], "container-title": [], "content-domain": { "crossmark-restriction": false, "domain": [] }, "created": { "date-parts": [ [ 2025, 6, 5 ] ], "date-time": "2025-06-05T04:55:12Z", "timestamp": 1749099312000 }, "deposited": { "date-parts": [ [ 2025, 6, 5 ] ], "date-time": "2025-06-05T04:55:14Z", "timestamp": 1749099314000 }, "group-title": "In Review", "indexed": { "date-parts": [ [ 2025, 6, 6 ] ], "date-time": "2025-06-06T04:02:38Z", "timestamp": 1749182558187, "version": "3.41.0" }, "institution": [ { "name": "Research Square" } ], "is-referenced-by-count": 0, "issued": { "date-parts": [ [ 2025, 6, 5 ] ] }, "license": [ { "URL": "https://creativecommons.org/licenses/by/4.0/", "content-version": "unspecified", "delay-in-days": 0, "start": { "date-parts": [ [ 2025, 6, 5 ] ], "date-time": "2025-06-05T00:00:00Z", "timestamp": 1749081600000 } } ], "link": [ { "URL": "https://www.researchsquare.com/article/rs-6819274/v1", "content-type": "text/html", "content-version": "vor", "intended-application": "text-mining" }, { "URL": "https://www.researchsquare.com/article/rs-6819274/v1.html", "content-type": "unspecified", "content-version": "vor", "intended-application": "similarity-checking" } ], "member": "297", "original-title": [], "posted": { "date-parts": [ [ 2025, 6, 5 ] ] }, "prefix": "10.21203", "published": { "date-parts": [ [ 2025, 6, 5 ] ] }, "publisher": "Springer Science and Business Media LLC", "reference": [ { "author": "Manikyam HK", "key": "ref1", "unstructured": "Manikyam HK, Joshi SK (2020) J Pharm Drug Res 3(2):341–361 Epub 2020 Mar 30. PMID: 32617527; PMCID: PMC7331973. Whole Genome Analysis and Targeted Drug Discovery Using Computational Methods and High Throughput Screening Tools for Emerged Novel Coronavirus (2019-nCoV)", "year": "2020" }, { "DOI": "10.3126/nje.v13i2.58243", "article-title": "Strengthening Healthcare through Academic and Industry Partnership Research", "author": "Sathian B", "doi-asserted-by": "crossref", "first-page": "1264", "issue": "2", "journal-title": "Nepal J Epidemiol", "key": "ref2", "unstructured": "Sathian B et al (2023) Strengthening Healthcare through Academic and Industry Partnership Research. Nepal J Epidemiol 13(2):1264", "volume": "13", "year": "2023" }, { "article-title": "Joshi. Computational methods to develop potential neutralizing antibody Fab region against SARS-CoV-2 as therapeutic and diagnostic tool. bioRxiv", "author": "Manikyam HK", "first-page": "2020", "key": "ref3", "unstructured": "Manikyam HK, Sunil K (2020) Joshi. Computational methods to develop potential neutralizing antibody Fab region against SARS-CoV-2 as therapeutic and diagnostic tool. bioRxiv : 2020–2005", "year": "2020" }, { "article-title": "Computational studies on Gene Ontology for Molecular functions, Cellular component and Biological process of SARS-CoV-2 targeted proteins", "author": "kumar Manikyam H", "key": "ref4", "unstructured": "kumar Manikyam H (2020) Computational studies on Gene Ontology for Molecular functions, Cellular component and Biological process of SARS-CoV-2 targeted proteins", "year": "2020" }, { "DOI": "10.1101/2025.04.30.651462", "doi-asserted-by": "crossref", "key": "ref5", "unstructured": "Antigenic and Virological Characteristics of SARS-CoV-2 Variant BA.3.2, XFG, and NB.1.8.1Caiwan Guo, Yuanling Yu, Jingyi Liu, Fanchong Jian, Sijie Yang, Weiliang Song, Lingling Yu, Fei Shao, Yunlong Cao bioRxiv 2025.04.30.651462; https://doi.org/10.1101/2025.04.30.651462" }, { "article-title": "Joshi. Nicotinamide, Folic Acid and Derivatives as Potent Inhibitors of Inflammatory Factors against Novel Corona Virus Infection", "author": "Manikyam H", "first-page": "2581", "issue": "5", "journal-title": "Acta Sci Pharm Sci (ISSN", "key": "ref6", "unstructured": "Manikyam H, Kumar, Sunil K (2020) Joshi. Nicotinamide, Folic Acid and Derivatives as Potent Inhibitors of Inflammatory Factors against Novel Corona Virus Infection. Acta Sci Pharm Sci (ISSN 4(5):2581–5423", "volume": "4", "year": "2020" }, { "author": "Acharya B", "first-page": "2699", "issue": "6", "journal-title": "Int J Pharm Sci Res", "key": "ref7", "unstructured": "Acharya B, Ghosh S, Hemanth Kumar M, NATURE'S RESPONSE TO INFLUENZA: A HIGH THROUGHPUT SCREENING STRATEGY OF AYURVEDIC MEDICINAL PHYTOCHEMICALS. (2016) Int J Pharm Sci Res 7(6):2699", "volume": "7", "year": "2016" }, { "article-title": "Joshi. Dammarane and Ergostane derivatives as prophylactic agents against SARS-CoV-2 host cell entry Inhibitors", "author": "Manikyam H", "first-page": "1211", "issue": "3", "journal-title": "J Pharmacogn Phytochem", "key": "ref8", "unstructured": "Manikyam H, Kumar, Sunil K (2020) Joshi. Dammarane and Ergostane derivatives as prophylactic agents against SARS-CoV-2 host cell entry Inhibitors. J Pharmacogn Phytochem 9(3):1211–1216", "volume": "9", "year": "2020" }, { "DOI": "10.9734/jpri/2024/v36i117599", "article-title": "High-Throughput Insilico Drug Screen against Mpox Targeted Proteins in Comparison with Repurposed Antiviral Drugs against Natural Compounds", "author": "Manikyam H", "doi-asserted-by": "crossref", "first-page": "41", "issue": "11", "journal-title": "J Pharm Res Int", "key": "ref9", "unstructured": "Manikyam H, Kumar et al (2024) High-Throughput Insilico Drug Screen against Mpox Targeted Proteins in Comparison with Repurposed Antiviral Drugs against Natural Compounds. J Pharm Res Int 36(11):41–52", "volume": "36", "year": "2024" }, { "author": "Manikyam HK", "key": "ref10", "unstructured": "Manikyam HK In Silico studies of Natural compounds that inhibit SARS-CoV-2 Nucleocapsid Nsp1/Nsp3 proteins mediated Viral Replication and Pathogenesis.", "volume-title": "In Silico studies of Natural compounds that inhibit SARS-CoV-2 Nucleocapsid Nsp1/Nsp3" }, { "DOI": "10.5138/09750185.2409", "article-title": "Ayurveda and Siddha systems polyherbal formulations to treat COVID-19 caused by SARS-CoV-2 and brief insight on application of Molecular Docking and SWISS Target prediction tools to study efficacy of active molecules", "author": "Manikyam HK", "doi-asserted-by": "publisher", "journal-title": "Int J Phytomedicine", "key": "ref11", "unstructured": "Manikyam HK, Joshi S, Noor A (2020) Ayurveda and Siddha systems polyherbal formulations to treat COVID-19 caused by SARS-CoV-2 and brief insight on application of Molecular Docking and SWISS Target prediction tools to study efficacy of active molecules. Int J Phytomedicine. 10.5138/09750185.2409", "year": "2020" }, { "DOI": "10.1186/s13020-024-01056-z", "author": "Zhai Y", "doi-asserted-by": "publisher", "key": "ref12", "unstructured": "Zhai Y et al (2025) Network Pharmacology: A Crucial Approach in Traditional Chinese Medicine Research. Chinese Medicine, vol. 20, no. 8. https://doi.org/10.1186/s13020-024-01056-z", "year": "2025" }, { "DOI": "10.3389/fphar.2022.952192", "article-title": "Network Pharmacology Reveals Multitarget Mechanism of Action of Drugs to Be Repurposed for COVID-19", "author": "Alegría-Arcos M", "doi-asserted-by": "publisher", "first-page": "952192", "journal-title": "Front Pharmacol", "key": "ref13", "unstructured": "Alegría-Arcos M et al (2022) Network Pharmacology Reveals Multitarget Mechanism of Action of Drugs to Be Repurposed for COVID-19. Front Pharmacol 13:952192. https://doi.org/10.3389/fphar.2022.952192", "volume": "13", "year": "2022" }, { "DOI": "10.3390/ph15050572", "author": "Noor F", "doi-asserted-by": "publisher", "key": "ref14", "unstructured": "Noor F et al (2022) Network Pharmacology Approach for Medicinal Plants: Review and Assessment. Pharmaceuticals, vol. 15, no. 5, article 572. https://doi.org/10.3390/ph15050572", "year": "2022" }, { "DOI": "10.3389/fphar.2024.1410942", "article-title": "Network Pharmacology: An Efficient but Underutilized Approach in Oral, Head and Neck Cancer Therapy—A Review", "author": "Muthuramalingam P", "doi-asserted-by": "publisher", "first-page": "1410942", "journal-title": "Front Pharmacol", "key": "ref15", "unstructured": "Muthuramalingam P et al (2024) Network Pharmacology: An Efficient but Underutilized Approach in Oral, Head and Neck Cancer Therapy—A Review. Front Pharmacol 15:1410942. https://doi.org/10.3389/fphar.2024.1410942", "volume": "15", "year": "2024" }, { "DOI": "10.1093/bib/bbaa373", "article-title": "Network Pharmacology and Bioinformatics Analyses Identify Intersection Genes of Niacin and COVID-19 as Potential Therapeutic Targets", "author": "Zhou Y", "doi-asserted-by": "publisher", "first-page": "1279", "issue": "2", "journal-title": "Brief Bioinform", "key": "ref16", "unstructured": "Zhou Y et al (2021) Network Pharmacology and Bioinformatics Analyses Identify Intersection Genes of Niacin and COVID-19 as Potential Therapeutic Targets. Brief Bioinform 22(2):1279–1290. https://doi.org/10.1093/bib/bbaa373", "volume": "22", "year": "2021" }, { "DOI": "10.1056/NEJMoa2031994", "article-title": "Baricitinib plus Remdesivir for Hospitalized Adults with Covid-19", "author": "Kalil AC", "doi-asserted-by": "publisher", "first-page": "795", "issue": "9", "journal-title": "N Engl J Med", "key": "ref17", "unstructured": "Kalil AC et al (2021) Baricitinib plus Remdesivir for Hospitalized Adults with Covid-19. N Engl J Med 384(9):795–807. https://doi.org/10.1056/NEJMoa2031994", "volume": "384", "year": "2021" }, { "DOI": "10.1056/NEJMoa2007764", "article-title": "Remdesivir for the Treatment of Covid-19 — Final Report", "author": "Beigel JH", "doi-asserted-by": "publisher", "first-page": "1813", "issue": "19", "journal-title": "N Engl J Med", "key": "ref18", "unstructured": "Beigel JH et al (2020) Remdesivir for the Treatment of Covid-19 — Final Report. N Engl J Med 383(19):1813–1826. https://doi.org/10.1056/NEJMoa2007764", "volume": "383", "year": "2020" }, { "DOI": "10.1016/j.cell.2020.06.043", "article-title": "Tracking Changes in SARS-CoV-2 Spike: Evidence That D614G Increases Infectivity of the COVID-19 Virus. Cell", "author": "Korber B", "doi-asserted-by": "publisher", "first-page": "812", "issue": "4", "key": "ref19", "unstructured": "Korber B et al (2020) Tracking Changes in SARS-CoV-2 Spike: Evidence That D614G Increases Infectivity of the COVID-19 Virus. Cell. 182(4):812–827e19. https://doi.org/10.1016/j.cell.2020.06.043", "volume": "182", "year": "2020" }, { "DOI": "10.1038/s41467-020-19808-4", "article-title": "SARS-CoV-2 Spike-Protein D614G Mutation Increases Virion Spike Density and Infectivity. Nature Communications", "author": "Zhang L", "doi-asserted-by": "publisher", "first-page": "6013", "key": "ref20", "unstructured": "Zhang L et al (2020), article no. SARS-CoV-2 Spike-Protein D614G Mutation Increases Virion Spike Density and Infectivity. Nature Communications. 11:6013. https://doi.org/10.1038/s41467-020-19808-4", "volume": "11", "year": "2020" }, { "DOI": "10.1038/s41586-021-03461-1", "article-title": "The N501Y Spike Substitution Enhances SARS-CoV-2 Infection and Transmission", "author": "Liu Y", "doi-asserted-by": "publisher", "first-page": "295", "journal-title": "Nature", "key": "ref21", "unstructured": "Liu Y et al (2021) The N501Y Spike Substitution Enhances SARS-CoV-2 Infection and Transmission. Nature 593:295–299. https://doi.org/10.1038/s41586-021-03461-1", "volume": "593", "year": "2021" }, { "DOI": "10.1056/NEJMc2100362", "article-title": "New SARS-CoV-2 Variants—Clinical, Public Health, and Vaccine Implications", "author": "Abdool Karim SS", "doi-asserted-by": "publisher", "first-page": "1866", "issue": "19", "journal-title": "N Engl J Med", "key": "ref22", "unstructured": "Abdool Karim SS (2021) New SARS-CoV-2 Variants—Clinical, Public Health, and Vaccine Implications. N Engl J Med 384(19):1866–1868. https://doi.org/10.1056/NEJMc2100362", "volume": "384", "year": "2021" }, { "DOI": "10.1016/j.cell.2020.02.052", "author": "Hoffmann M", "doi-asserted-by": "publisher", "key": "ref23", "unstructured": "Hoffmann M et al (2020) SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell, vol. 181, no. 2, pp. 271–280.e8. https://doi.org/10.1016/j.cell.2020.02.052", "year": "2020" }, { "DOI": "10.1016/j.bbrc.2020.10.109", "article-title": "Functional Importance of the D614G Mutation in the SARS-CoV-2 Spike Protein", "author": "Jackson CB", "doi-asserted-by": "publisher", "first-page": "108", "journal-title": "Biochem Biophys Res Commun", "key": "ref24", "unstructured": "Jackson CB et al (2021) Functional Importance of the D614G Mutation in the SARS-CoV-2 Spike Protein. Biochem Biophys Res Commun 538:108–115. https://doi.org/10.1016/j.bbrc.2020.10.109", "volume": "538", "year": "2021" }, { "DOI": "10.1038/s41586-020-2286-9", "article-title": "A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug Repurposing", "author": "Gordon DE", "doi-asserted-by": "publisher", "first-page": "459", "journal-title": "Nature", "key": "ref25", "unstructured": "Gordon DE et al (2020) A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug Repurposing. Nature 583:459–468. https://doi.org/10.1038/s41586-020-2286-9", "volume": "583", "year": "2020" }, { "DOI": "10.1126/science.abb2507", "article-title": "Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation", "author": "Wrapp D", "doi-asserted-by": "publisher", "first-page": "1260", "issue": "6483", "journal-title": "Science", "key": "ref26", "unstructured": "Wrapp D et al (2020) Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation. Science 367(6483):1260–1263. https://doi.org/10.1126/science.abb2507", "volume": "367", "year": "2020" }, { "DOI": "10.1038/s41586-020-2179-y", "article-title": "Structural Basis of Receptor Recognition by SARS-CoV-2", "author": "Shang J", "doi-asserted-by": "publisher", "first-page": "221", "journal-title": "Nature", "key": "ref27", "unstructured": "Shang J et al (2020) Structural Basis of Receptor Recognition by SARS-CoV-2. Nature 581:221–224. https://doi.org/10.1038/s41586-020-2179-y", "volume": "581", "year": "2020" }, { "DOI": "10.1016/j.cell.2020.02.058", "author": "Walls AC", "doi-asserted-by": "publisher", "key": "ref28", "unstructured": "Walls AC et al (2020) Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell, vol. 181, no. 2, pp. 281–292.e6. https://doi.org/10.1016/j.cell.2020.02.058", "year": "2020" }, { "DOI": "10.1038/s41586-020-2012-7", "article-title": "A Pneumonia Outbreak Associated with a New Coronavirus of Probable Bat Origin", "author": "Zhou P", "doi-asserted-by": "publisher", "first-page": "270", "journal-title": "Nature", "key": "ref29", "unstructured": "Zhou P et al (2020) A Pneumonia Outbreak Associated with a New Coronavirus of Probable Bat Origin. Nature 579:270–273. https://doi.org/10.1038/s41586-020-2012-7", "volume": "579", "year": "2020" }, { "DOI": "10.1038/s41541-020-00246-8", "article-title": "Experimental and in Silico Evidence Suggests Vaccines Are Unlikely to Be Affected by D614G Mutation in SARS-CoV-2 Spike Protein. npj Vaccines", "author": "McAuley AJ", "doi-asserted-by": "publisher", "first-page": "96", "key": "ref30", "unstructured": "McAuley AJ et al (2020), article no. Experimental and in Silico Evidence Suggests Vaccines Are Unlikely to Be Affected by D614G Mutation in SARS-CoV-2 Spike Protein. npj Vaccines. 5:96. https://doi.org/10.1038/s41541-020-00246-8", "volume": "5", "year": "2020" }, { "DOI": "10.1038/sj.clpt.6100052", "article-title": "Appropriate Phenotyping Procedures for Drug Metabolizing Enzymes and Transporters in Humans and Their Simultaneous Use in the 'Cocktail' Approach", "author": "Fuhr U", "doi-asserted-by": "publisher", "first-page": "270", "issue": "2", "journal-title": "Clin Pharmacol Ther", "key": "ref31", "unstructured": "Fuhr U et al (2007) Appropriate Phenotyping Procedures for Drug Metabolizing Enzymes and Transporters in Humans and Their Simultaneous Use in the 'Cocktail' Approach. Clin Pharmacol Ther 81(2):270–283. https://doi.org/10.1038/sj.clpt.6100052", "volume": "81", "year": "2007" }, { "DOI": "10.1038/s41579-021-00573-0", "article-title": "SARS-CoV-2 Variants, Spike Mutations and Immune Escape", "author": "Harvey WT", "doi-asserted-by": "publisher", "first-page": "409", "journal-title": "Nat Rev Microbiol", "key": "ref32", "unstructured": "Harvey WT et al (2021) SARS-CoV-2 Variants, Spike Mutations and Immune Escape. Nat Rev Microbiol 19:409–424. https://doi.org/10.1038/s41579-021-00573-0", "volume": "19", "year": "2021" }, { "DOI": "10.1038/s41467-022-29219-2", "article-title": "Spike Mutations in SARS-CoV-2 Omicron Variant Modulate Virus Entry and Sensitivity to Neutralizing Antibodies", "author": "Arora P", "doi-asserted-by": "publisher", "first-page": "1620", "journal-title": "Nat Commun", "key": "ref33", "unstructured": "Arora P et al (2022) Spike Mutations in SARS-CoV-2 Omicron Variant Modulate Virus Entry and Sensitivity to Neutralizing Antibodies. Nat Commun 13:1620. https://doi.org/10.1038/s41467-022-29219-2", "volume": "13", "year": "2022" }, { "DOI": "10.3389/fcimb.2021.777378", "article-title": "Emerging SARS-CoV-2 Variants and Their Impact on Spike Glycoprotein-Mediated Viral Entry and Immune Evasion", "author": "Tripathi AK", "doi-asserted-by": "publisher", "first-page": "777378", "journal-title": "Front Cell Infect Microbiol", "key": "ref34", "unstructured": "Tripathi AK et al (2021) Emerging SARS-CoV-2 Variants and Their Impact on Spike Glycoprotein-Mediated Viral Entry and Immune Evasion. Front Cell Infect Microbiol 11:777378. https://doi.org/10.3389/fcimb.2021.777378", "volume": "11", "year": "2021" }, { "DOI": "10.1016/j.cell.2020.12.045", "article-title": "A Systematic Review of Structural and Functional Impacts of SARS-CoV-2 Spike Mutations. Cell", "author": "Singh H", "doi-asserted-by": "publisher", "first-page": "444", "issue": "2", "key": "ref35", "unstructured": "Singh H et al (2021) A Systematic Review of Structural and Functional Impacts of SARS-CoV-2 Spike Mutations. Cell. 184(2):444–456. https://doi.org/10.1016/j.cell.2020.12.045. .e5", "volume": "184", "year": "2021" }, { "DOI": "10.1038/s41598-021-99791-y", "article-title": "The Antioxidant Nrf2 Activator, Sulforaphane, Suppresses SARS-CoV-2 Entry into Human Lung Epithelial Cells. Scientific Reports", "author": "Yamamoto M", "doi-asserted-by": "publisher", "first-page": "20532", "key": "ref36", "unstructured": "Yamamoto M et al (2021), article no. The Antioxidant Nrf2 Activator, Sulforaphane, Suppresses SARS-CoV-2 Entry into Human Lung Epithelial Cells. Scientific Reports. 11:20532. https://doi.org/10.1038/s41598-021-99791-y", "volume": "11", "year": "2021" } ], "reference-count": 36, "references-count": 36, "relation": {}, "resource": { "primary": { "URL": "https://www.researchsquare.com/article/rs-6819274/v1" } }, "score": 1, "short-title": [], "source": "Crossref", "subject": [], "subtitle": [], "subtype": "preprint", "title": "INP-Guided Network Pharmacology Discloses Multi-Target Therapeutic Strategy Against Cytokine and IgE Storms in the SARS-CoV-2 NB.1.8.1 Variant", "type": "posted-content" }