{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T10:07:49Z","timestamp":1785146869859,"version":"3.55.0"},"reference-count":52,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T00:00:00Z","timestamp":1784851200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>The SARS-CoV-2 JN.1 subvariant has attracted attention due to the accumulation of mutations in the Spike (S) glycoprotein, particularly within the receptor-binding domain (RBD), contributing to the structural heterogeneity of the Spike protein. However, the extent to which conformational dynamics influence ligand-recognition patterns across functional Spike states remains insufficiently characterized. In this study, we applied a hierarchical computational framework combining homology modeling, molecular dynamics simulations, and molecular docking to determine whether conformational sampling modifies the location, accessibility, and recurrence of ligand-interaction regions in the JN.1 Spike protein. Closed, semi-closed, and open conformations were modeled and subjected to triplicate simulations, including an initial 100 ns phase followed by extended 200 ns simulations. Representative conformations were obtained by trajectory clustering and used for docking analyses. Two flavonoids, hesperitin-7-O-rutinoside (H7R) and flavanone-7-O-glucoside (F7G), were employed as structural probes to assess how ligand interaction patterns vary across conformational states. Comparative analyses revealed that conformational sampling modifies the location, accessibility and spatial distribution of ligand-interaction regions while generating distinct docking poses and recurrent interaction patterns not fully captured by static structural models. These findings highlight the importance of dynamics-informed structural ensembles for docking analyses in flexible viral proteins. Rather than predicting absolute binding affinities, this study provides an exploratory computational framework for evaluating ligand-recognition behavior in structurally dynamic viral systems.<\/jats:p>","DOI":"10.3390\/ijms27156624","type":"journal-article","created":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T09:47:41Z","timestamp":1785145661000},"page":"6624","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Flavonoids as Structural Probes Reveal Conformationally Dependent Ligand Recognition in the SARS-CoV-2 JN.1 Spike Protein"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-5775-8107","authenticated-orcid":false,"given":"Susana R.","family":"Castro-Jim\u00e9nez","sequence":"first","affiliation":[{"name":"Departamento de Biotecnolog\u00eda, Universidad Aut\u00f3noma Metropolitana-Iztapalapa, Ciudad de M\u00e9xico 09340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Armando","family":"Mej\u00eda","sequence":"additional","affiliation":[{"name":"Departamento de Biotecnolog\u00eda, Universidad Aut\u00f3noma Metropolitana-Iztapalapa, Ciudad de M\u00e9xico 09340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos","family":"Cabello","sequence":"additional","affiliation":[{"name":"Departamento de Virolog\u00eda e Investigaci\u00f3n en Micolog\u00eda, Instituto Nacional de Enfermedades Respiratorias, Ciudad de M\u00e9xico 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela","family":"L\u00e9on-Gutierrez","sequence":"additional","affiliation":[{"name":"Inmolecule International Limited, 16 Great Queen Street, Covent Garden, London WC2B 5AH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5180-6504","authenticated-orcid":false,"given":"Cesar","family":"Mill\u00e1n-Pacheco","sequence":"additional","affiliation":[{"name":"Facultad de Farmacia, Universidad Aut\u00f3noma del Estado de Morelos, Av. Universidad No. 1001, Col Chamilpa, Cuernavaca 62209, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41579-021-00573-0","article-title":"SARS-CoV-2 variants, spike mutations and immune escape","volume":"19","author":"Harvey","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1038\/s41576-021-00408-x","article-title":"The biological and clinical significance of emerging SARS-CoV-2 variants","volume":"22","author":"Tao","year":"2021","journal-title":"Nat. Rev. Genet."},{"key":"ref_3","unstructured":"World Health Organization (WHO) (2023, November 10). Updated Working Definitions and Primary Actions for SARS-CoV-2 Variants. 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