Targeting asparagine and cysteine in SARS-CoV-2 variants and human pro-inflammatory mediators to alleviate COVID-19 severity; a cross-section and in-silico study

DOI record: { "DOI": "10.1038/s41598-025-19359-y", "ISSN": [ "2045-2322" ], "URL": "http://dx.doi.org/10.1038/s41598-025-19359-y", "abstract": "<jats:title>Abstract</jats:title>\n <jats:p>To date, COVID-19 continues to pose a global health challenge, with substantial morbidity, mortality, and long-term post-COVID-19 complications threatening public health resilience. During the early pandemic, the IL-6 inhibitor (tocilizumab) was the widely used approved immunotherapy for critically ill patients; however, a subset of ICU cases exhibited normal interleukin-6 (IL-6) levels and failed to respond. We hypothesized that interleukin-17 (IL-17), which acts synergistically with IL-6, contributes to cytokine storm progression and severe inflammation. Our study uniquely integrates a clinical cross-sectional analysis with advanced in-silico modelling, directly linking patient-derived biomarker, radiological, and statistical data to molecular-level mechanisms of COVID-19 severity. Serum IL-17 was significantly elevated in critical versus moderate COVID-19 cases, with a threshold of 187.9 ng/mL predicting poor outcomes by ROC analysis. Logistic regression identified age and monocytes as independent predictors of severity, supporting a combined biomarker approach for improving the prognosis and clinical outcomes. Radiological findings, including ground-glass opacities and consolidations, alongside hematological abnormalities, were more frequent in critical cases. Computational docking revealed key amino acid residues—particularly asparagine (Asn) and cysteine (Cys)—as structural determinants shared by SARS-CoV-2 spike protein and human inflammatory mediators (IL-17R, IL-6R, CD41/CD61, CD47/SIRP). Asparaginase (ASNase) targeted critical residues such as the invariant gate residue “Asn343” and Cys213 of spike protein, Asn240 of IL-17R, and Asn136 of IL-6R. Several phytochemicals, including phytic acid and amygdalin, as well as synthetic agents such as candesartan, remdesivir, and enalapril, were found to preferentially bind to cysteine (Cys) residues—and, to a lesser extent, asparagine (Asn) residues—within key binding interfaces, in addition to targeting B-cell epitopes. This conserved residue preference supports the rationale for a dual-action therapeutic strategy in which asparaginase (ASNase) is combined with selected plant-derived ligands to simultaneously disrupt viral entry mechanisms and attenuate the inflammatory signalling. This dual-perspective approach not only identified IL-17 and IL-6 as independent severity predictors but also revealed conserved Asn and Cys motifs as critical therapeutic targets, leading to novel strategies—such as ASNase, synthetic agents and phytochemical combinations—for simultaneously blocking viral entry and modulating hyperinflammatory pathways. These findings warrant rigorous experimental and clinical validation to facilitate translation into effective therapeutic interventions.</jats:p>", "alternative-id": [ "19359" ], "article-number": "38445", "assertion": [ { "group": { "label": "Article History", "name": "ArticleHistory" }, "label": "Received", "name": "received", "order": 1, "value": "1 May 2025" }, { "group": { "label": "Article History", "name": "ArticleHistory" }, "label": "Accepted", "name": "accepted", "order": 2, "value": "8 September 2025" }, { "group": { "label": "Article History", "name": "ArticleHistory" }, "label": "First Online", "name": "first_online", "order": 3, "value": "3 November 2025" }, { "group": { "label": "Declarations", "name": "EthicsHeading" }, "name": "Ethics", "order": 1 }, { "group": { "label": "Competing interests", "name": "EthicsHeading" }, "name": "Ethics", "order": 2, "value": "The authors declare no competing interests." }, { "group": { "label": "Ethics approval and consent to participate", "name": "EthicsHeading" }, "name": "Ethics", "order": 3, "value": "Informed consent was obtained from all subjects involved in our study." }, { "group": { "label": "Consent for publication", "name": "EthicsHeading" }, "name": "Ethics", "order": 4, "value": "The manuscript has been read and approved for submission by all the authors." } ], "author": [ { "ORCID": "https://orcid.org/0000-0002-6696-0405", "affiliation": [], "authenticated-orcid": false, "family": "Fadel", "given": "Hewida H.", "sequence": "first" }, { "ORCID": "https://orcid.org/0000-0003-3145-2416", "affiliation": [], "authenticated-orcid": false, "family": "EL-Esseily", "given": "Hadeer Adel", "sequence": "additional" }, { "ORCID": "https://orcid.org/0000-0001-6079-2984", "affiliation": [], "authenticated-orcid": false, "family": "Ahmed", "given": "Mohammed Abd EL-Rahman", "sequence": "additional" }, { "affiliation": [], "family": "Khamis Mohamed", "given": "Mohammed Ahmed", "sequence": "additional" }, { "ORCID": "https://orcid.org/0000-0002-3659-3616", "affiliation": [], "authenticated-orcid": false, "family": "Roushdy", "given": "Mohamed Nabil", "sequence": "additional" }, { "ORCID": "https://orcid.org/0000-0001-8087-0898", "affiliation": [], "authenticated-orcid": false, "family": "ElSherif", "given": "Amr", "sequence": "additional" }, { "ORCID": "https://orcid.org/0000-0001-5553-8842", "affiliation": [], "authenticated-orcid": false, "family": "Gharbeya", "given": "Kareem Mahamoud", "sequence": "additional" }, { "ORCID": "https://orcid.org/0000-0002-8107-9384", "affiliation": [], "authenticated-orcid": false, "family": "Abdelsalam", "given": "Hadeel Said", "sequence": "additional" } ], "container-title": "Scientific Reports", "container-title-short": "Sci Rep", "content-domain": { "crossmark-restriction": false, "domain": [ "link.springer.com" ] }, "created": { "date-parts": [ [ 2025, 11, 3 ] ], "date-time": "2025-11-03T15:13:57Z", "timestamp": 1762182837000 }, "deposited": { "date-parts": [ [ 2025, 11, 4 ] ], "date-time": "2025-11-04T04:45:16Z", "timestamp": 1762231516000 }, "funder": [ { "name": "Pharos University" } ], "indexed": { "date-parts": [ [ 2026, 1, 16 ] ], "date-time": "2026-01-16T10:56:32Z", "timestamp": 1768560992486, "version": "3.49.0" }, "is-referenced-by-count": 1, "issue": "1", "issued": { "date-parts": [ [ 2025, 11, 3 ] ] }, "journal-issue": { "issue": "1", "published-online": { "date-parts": [ [ 2025, 12 ] ] } }, "language": "en", "license": [ { "URL": "https://creativecommons.org/licenses/by/4.0", "content-version": "tdm", "delay-in-days": 0, "start": { "date-parts": [ [ 2025, 11, 3 ] ], "date-time": "2025-11-03T00:00:00Z", "timestamp": 1762128000000 } }, { "URL": "https://creativecommons.org/licenses/by/4.0", "content-version": "vor", "delay-in-days": 0, "start": { "date-parts": [ [ 2025, 11, 3 ] ], "date-time": "2025-11-03T00:00:00Z", "timestamp": 1762128000000 } } ], "link": [ { "URL": "https://www.nature.com/articles/s41598-025-19359-y.pdf", "content-type": "application/pdf", "content-version": "vor", "intended-application": "text-mining" }, { "URL": "https://www.nature.com/articles/s41598-025-19359-y", "content-type": "text/html", "content-version": "vor", "intended-application": "text-mining" }, { "URL": "https://www.nature.com/articles/s41598-025-19359-y.pdf", "content-type": "application/pdf", "content-version": "vor", "intended-application": "similarity-checking" } ], "member": "297", "original-title": [], "prefix": "10.1038", "published": { "date-parts": [ [ 2025, 11, 3 ] ] }, "published-online": { "date-parts": [ [ 2025, 11, 3 ] ] }, "publisher": "Springer Science and Business Media LLC", "reference": [ { "DOI": "10.1007/978-1-4939-9544-8_67-1", "author": "AS Monto", "doi-asserted-by": "publisher", "journal-title": "Viral Infect. 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