{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T01:17:00Z","timestamp":1793409420533,"version":"4.5.0"},"reference-count":66,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,5,15]],"date-time":"2025-05-15T00:00:00Z","timestamp":1747267200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006502","name":"Defense Sciences Office, DARPA","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006502","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020392","name":"Good Ventures Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020392","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016528","name":"Hansj\u00f6rg Wyss Institute for Biologically Inspired Engineering, Harvard University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016528","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000879","name":"Alfred P. Sloan Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000879","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Mol. Biosci."],"abstract":"<jats:p>\n                    Development of oral, broad-spectrum therapeutics targeting SARS-CoV-2, its variants, and related coronaviruses could curb the spread of COVID-19 and avert future pandemics. We created a novel computational discovery pipeline that employed molecular dynamics simulation (MDS), artificial intelligence (AI)-based docking predictions, and medicinal chemistry to design viral entry inhibitors that target a conserved region in the SARS-CoV-2 spike (S) protein that mediates membrane fusion. DrugBank library screening identified the orally available, FDA-approved AXL kinase inhibitor bemcentinib as binding this site and we demonstrated that it inhibits viral entry in a kinase-independent manner. Novel analogs predicted to bind to the same region and disrupt S protein conformational changes were designed using MDS and medicinal chemistry. These compounds significantly suppressed SARS-CoV-2 infection and blocked the entry of S protein-bearing pseudotyped \u03b1,\u03b2,\u03b3,\u03b4,\n                    <jats:italic>\u03bf<\/jats:italic>\n                    variants as well as SARS CoV and MERS-CoV in human ACE2-expressing or DPP4-expressing cells more effectively than bemcentinib. When administered orally, the optimized lead compound also significantly inhibited SARS-CoV2 infection in mice. This computational design strategy may accelerate drug discovery for a broad range of applications.\n                  <\/jats:p>","DOI":"10.3389\/fmolb.2025.1575747","type":"journal-article","created":{"date-parts":[[2025,5,15]],"date-time":"2025-05-15T00:11:50Z","timestamp":1747267910000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Broad-spectrum coronavirus inhibitors discovered by modeling viral fusion dynamics"],"prefix":"10.3389","volume":"12","author":[{"given":"Charles B.","family":"Reilly","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel","family":"Moore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanda","family":"Lightbown","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Austin","family":"Paul","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvie G.","family":"Bernier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth E.","family":"Carlson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donald E.","family":"Ingber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,5,15]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"B2","doi-asserted-by":"publisher","first-page":"W537","DOI":"10.1093\/nar\/gks375","article-title":"H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations","volume":"40","author":"Anandakrishnan","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"B3","doi-asserted-by":"publisher","first-page":"W344","DOI":"10.1093\/nar\/gkw408","article-title":"ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules","volume":"44","author":"Ashkenazy","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B4","doi-asserted-by":"publisher","first-page":"e2114397119","DOI":"10.1073\/pnas.2114397119","article-title":"A tethered ligand assay to probe SARS-CoV-2:ACE2 interactions","volume":"119","author":"Bauer","year":"2022","journal-title":"Proc. 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