{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T16:01:13Z","timestamp":1790092873265,"version":"4.0.1"},"reference-count":46,"publisher":"American Chemical Society (ACS)","issue":"37","license":[{"start":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T00:00:00Z","timestamp":1788307200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009888","name":"Regione Toscana","doi-asserted-by":"publisher","award":["Bando Ricerca Salute 435, 2018"],"award-info":[{"award-number":["Bando Ricerca Salute 435, 2018"]}],"id":[{"id":"10.13039\/501100009888","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has challenged the durability of vaccine-mediated protection, reinforcing the need for broad-spectrum antiviral agents. Herein, we performed a structure- and dynamics-driven virtual screening to identify novel small-molecule inhibitors of SARS-CoV-2 cell entry by targeting a conserved pocket within the S2 subunit of the spike glycoprotein domain. Extensive molecular dynamics simulations of the S2 domain revealed a druggable binding pocket close to the fusion peptide site. Consensus pharmacophore-guided virtual screening of \u223c900,000 compounds yielded 11 candidates selected for biological evaluation. The selected compounds reduced SARS-CoV-2 infection in vitro at nanomolar concentrations against different variants with an increased selectivity index. Moreover, viral-cell entry and mechanistic experiments support the selective inhibition of the early steps of viral fusion. Finally, in silico evolutionary analyses showed good conservation of the pharmacophore region among different SARS-related coronaviruses. Our results provide a basis for further optimization studies on novel antifusion SARS-CoV-2 inhibitors with potential cross-clade antiviral activity.<\/jats:p>","DOI":"10.1021\/acsomega.6c04313","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T18:20:10Z","timestamp":1788459610000},"page":"55486-55498","source":"Crossref","is-referenced-by-count":0,"title":["Structure- and\nDynamics-Driven Discovery of Small\nMolecule Inhibitors Targeting a Conserved Pocket near the Fusion Peptide\nin the Prefusion SARS-CoV-2 S2 Glycoprotein Subunit"],"prefix":"10.1021","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6527-2571","authenticated-orcid":true,"given":"Marco","family":"Leusciatti","sequence":"first","affiliation":[{"name":"Giulio Natta Institute of Chemical Sciences and Technologies (CNR-SCITEC) , , Via Mario Bianco, 9 , , ,","place":["Milan, Milano, Italy, 20131"]},{"name":"University of Pavia , , Viale Taramelli, 12 , , ,","place":["Pavia, Pavia, Italy, 27100"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1088-7253","authenticated-orcid":true,"given":"Silvia","family":"Rinaldi","sequence":"additional","affiliation":[{"name":"Institute of Chemistry of Organometallic Compounds (CNR-ICCOM) , , Via Madonna del Piano, 10 , , ,","place":["Sesto Fiorentino, Firenze, Italy, 50019"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosaria","family":"Arvia","sequence":"additional","affiliation":[{"name":"University of Florence , , ,","place":["Florence, Italy, 50134"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1124-1788","authenticated-orcid":true,"given":"Andrea","family":"Catte","sequence":"additional","affiliation":[{"name":"Institute of Chemistry of Organometallic Compounds (CNR-ICCOM) , , Via Madonna del Piano, 10 , , ,","place":["Sesto Fiorentino, Firenze, Italy, 50019"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9681-7845","authenticated-orcid":true,"given":"Giulia","family":"Morra","sequence":"additional","affiliation":[{"name":"Giulio Natta Institute of Chemical Sciences and Technologies (CNR-SCITEC) , , Via Mario Bianco, 9 , , ,","place":["Milan, Milano, Italy, 20131"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3374-7621","authenticated-orcid":true,"given":"Simone","family":"Giannecchini","sequence":"additional","affiliation":[{"name":"University of Florence , , ,","place":["Florence, Italy, 50134"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,2]]},"reference":[{"key":"2026092210565565600_cit1","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1056\/NEJMoa2001017","article-title":"China novel coronavirus\nInvestigating and research team. A novel coronavirus from patients\nwith pneumonia in China, 2019","volume":"382","author":"Zhu","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"2026092210565565600_cit2","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1038\/s41579-025-01255-x","article-title":"SARS-CoV-2 variants:\nbiology, pathogenicity, immunity and control","volume":"24","author":"Uraki","year":"2026","journal-title":"Nat. Rev. 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Microbiol."},{"key":"2026092210565565600_cit9","doi-asserted-by":"publisher","first-page":"115923","DOI":"10.1016\/j.ejmech.2023.115923","article-title":"Targeting SARS-CoV-2\nentry processes: The promising potential and future of host-targeted\nsmall-molecule inhibitors","volume":"263","author":"Wu","year":"2024","journal-title":"Eur. J. Med. Chem."},{"issue":"8","key":"2026092210565565600_cit10","doi-asserted-by":"publisher","first-page":"14","DOI":"10.3390\/v14081816","article-title":"Stabilisation\nof Viral Membrane Fusion\nProteins in Prefusion Conformation by Structure-Based Design for Structure\nDetermination and Vaccine Development","volume":"14","author":"Ebel","year":"2022","journal-title":"Viruses"},{"key":"2026092210565565600_cit11","doi-asserted-by":"publisher","first-page":"902","DOI":"10.3390\/v15040902","article-title":"Molecular\nmodeling of viral type I fusion proteins: inhibitors of Influenza\nvirus hemagglutinin and the Spike protein of Coronavirus","volume":"15","author":"Borisevich","year":"2023","journal-title":"Viruses"},{"key":"2026092210565565600_cit12","doi-asserted-by":"publisher","first-page":"1335","DOI":"10.1038\/s41467-024-45480-z","article-title":"A general\ncomputational design strategy\nfor stabilizing viral class I fusion proteins","volume":"15","author":"Gonzalez","year":"2024","journal-title":"Nat. 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Virol"},{"key":"2026092210565565600_cit19","doi-asserted-by":"publisher","first-page":"7411","DOI":"10.1128\/JVI.00079-09","article-title":"Characterization\nof a highly conserved domain within the severe acute respiratory syndrome\ncoronavirus spike protein S2 domain with characteristics of a viral\nfusion peptide","volume":"83","author":"Madu","year":"2009","journal-title":"J. Virol"},{"key":"2026092210565565600_cit20","doi-asserted-by":"publisher","first-page":"166946","DOI":"10.1016\/j.jmb.2021.166946","article-title":"SARS-CoV-2 Fusion\npeptide has a greater membrane perturbating\npffect than SARS-CoV with highly specific dependence on Ca2","volume":"433","author":"Lai","year":"2021","journal-title":"J. Mol. Biol."},{"key":"2026092210565565600_cit21","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(24)00769-2","article-title":"Targeting\nthe SARS-CoV-2 reservoir in long COVID","volume":"25","author":"Proal","year":"2025","journal-title":"Lancet\nInfect. 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Commun."},{"key":"2026092210565565600_cit26","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202417534","article-title":"Dual-Locking\nthe SARS-CoV-2 Spike trimer: an amphipathic molecular \u201cBolt\u201d\nstabilizes conserved druggable interfaces for Coronavirus inhibition","volume":"12","author":"Li","year":"2025","journal-title":"Adv. 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Rep."},{"key":"2026092210565565600_cit30","doi-asserted-by":"publisher","first-page":"1267","DOI":"10.1021\/acsmedchemlett.1c00263","article-title":"Discovery\nof small molecule entry inhibitors targeting the fusion peptide of\nSARS-CoV-2 Spike protein","volume":"12","author":"Hu","year":"2021","journal-title":"ACS Med. Chem. Lett."},{"key":"2026092210565565600_cit31","doi-asserted-by":"publisher","first-page":"1295","DOI":"10.3390\/v14061295","article-title":"Borneol ester derivatives as entry inhibitors of a\nwide spectrum of SARS-CoV-2 viruses","volume":"14","author":"Yarovaya","year":"2022","journal-title":"Viruses"},{"key":"2026092210565565600_cit32","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1002\/(SICI)1521-3773(19990115)38:1\/2&lt;236::AID-ANIE236&gt;3.0.CO;2-M","article-title":"Peptide folding:\nwhen simulation meets experiment","volume":"38","author":"Daura","year":"1999","journal-title":"Angew. Chem.,\nInt. Ed."},{"key":"2026092210565565600_cit33","doi-asserted-by":"publisher","first-page":"199170","DOI":"10.1016\/j.virusres.2023.199170","article-title":"SARS-CoV-2 inhibitory activity of a short peptide derived\nfrom internal fusion peptide of S2 subunit of spike glycoprotein","volume":"334","author":"Stincarelli","year":"2023","journal-title":"Virus Res."},{"key":"2026092210565565600_cit34","doi-asserted-by":"publisher","first-page":"110383","DOI":"10.1016\/j.virol.2024.110383","article-title":"Architects of infection: A structural\noverview of SARS-related coronavirus spike glycoproteins","volume":"604","author":"Hills","year":"2025","journal-title":"Virology"},{"key":"2026092210565565600_cit35","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1038\/s41586-022-04466-x","article-title":"Memory B cell repertoire\nfrom triple vaccinees against diverse SARS-CoV-2\nvariants","volume":"603","author":"Wang","year":"2022","journal-title":"Nature"},{"key":"2026092210565565600_cit36","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/nmeth.4067","article-title":"CHARMM36m: an improved force field\nfor folded and intrinsically\ndisordered proteins","volume":"14","author":"Huang","year":"2017","journal-title":"Nat. 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Comput.-Aided Mol.\nDes."},{"key":"2026092210565565600_cit43","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1021\/ci049714+","article-title":"ZINC\u2013a free database of commercially available\ncompounds for virtual screening","volume":"45","author":"Irwin","year":"2005","journal-title":"J. Chem. Inf.\nModel"},{"issue":"2","key":"2026092210565565600_cit44","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1007\/s00705-021-05343-0","article-title":"Trypsin enhances SARS-CoV-2\ninfection\nby facilitating viral entry","volume":"167","author":"Kim","year":"2022","journal-title":"Arch. Virol"},{"key":"2026092210565565600_cit45","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1099\/vir.0.81187-0","article-title":"Comparison\nof in vitro replication features of H7N3\ninfluenza viruses from wild ducks and turkeys: potential implications\nfor interspecies transmission","volume":"87","author":"Giannecchini","year":"2006","journal-title":"J. Gen. 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