{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T21:40:30Z","timestamp":1780522830262,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.ppat.1011065","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,1,6]],"date-time":"2023-01-06T00:00:00Z","timestamp":1672963200000}}],"reference-count":74,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2022,12,22]],"date-time":"2022-12-22T00:00:00Z","timestamp":1671667200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"name":"Emergent Ventures through the Thistledown Foundation","award":["#2161"],"award-info":[{"award-number":["#2161"]}]},{"name":"Emergent Ventures through the Thistledown Foundation","award":["#2189"],"award-info":[{"award-number":["#2189"]}]},{"name":"National Institute of Health","award":["P01AI120943, R01AI123926 and R01AI161374"],"award-info":[{"award-number":["P01AI120943, R01AI123926 and R01AI161374"]}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["OV3-170346"],"award-info":[{"award-number":["OV3-170346"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["#OV3-170649"],"award-info":[{"award-number":["#OV3-170649"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018693","name":"HORIZON EUROPE","doi-asserted-by":"crossref","award":["952373"],"award-info":[{"award-number":["952373"]}],"id":[{"id":"10.13039\/100018693","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has made it clear that combating coronavirus outbreaks benefits from a combination of vaccines and therapeutics. A promising drug target common to all coronaviruses\u2014including SARS-CoV, MERS-CoV, and SARS-CoV-2\u2014is the papain-like protease (PLpro). PLpro cleaves part of the viral replicase polyproteins into non-structural protein subunits, which are essential to the viral replication cycle. Additionally, PLpro can cleave both ubiquitin and the ubiquitin-like protein ISG15 from host cell substrates as a mechanism to evade innate immune responses during infection. These roles make PLpro an attractive antiviral drug target. Here we demonstrate that ubiquitin variants (UbVs) can be selected from a phage-displayed library and used to specifically and potently block SARS-CoV-2 PLpro activity. A crystal structure of SARS-CoV-2 PLpro in complex with a representative UbV reveals a dimeric UbV bound to PLpro at a site distal to the catalytic site. Yet, the UbV inhibits the essential cleavage activities of the protease <jats:italic>in vitro<\/jats:italic> and in cells, and it reduces viral replication in cell culture by almost five orders of magnitude.<\/jats:p>","DOI":"10.1371\/journal.ppat.1011065","type":"journal-article","created":{"date-parts":[[2022,12,22]],"date-time":"2022-12-22T18:51:45Z","timestamp":1671735105000},"page":"e1011065","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":32,"title":["Ubiquitin variants potently inhibit SARS-CoV-2 PLpro and viral replication via a novel site distal to the protease active site"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0401-3055","authenticated-orcid":true,"given":"Vera J. 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Couzin-Frankel","year":"2021","journal-title":"Science"},{"issue":"6575","key":"ppat.1011065.ref040","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1126\/science.abl4784","article-title":"An oral SARS-CoV-2 Mpro inhibitor clinical candidate for the treatment of COVID-19","volume":"374","author":"DR Owen","year":"2021","journal-title":"Science"},{"issue":"5","key":"ppat.1011065.ref041","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1007\/s40265-022-01692-5","article-title":"Nirmatrelvir Plus Ritonavir: First Approval.","volume":"82","author":"YN Lamb","year":"2022","journal-title":"Drugs"},{"issue":"7","key":"ppat.1011065.ref042","doi-asserted-by":"crossref","first-page":"3507","DOI":"10.3390\/ijms23073507","article-title":"Potential Resistance of SARS-CoV-2 Main Protease (Mpro) against Protease Inhibitors: Lessons Learned from HIV-1 Protease.","volume":"23","author":"JA M\u00f3ty\u00e1n","year":"2022","journal-title":"International journal of molecular sciences"},{"issue":"42","key":"ppat.1011065.ref043","doi-asserted-by":"crossref","first-page":"16119","DOI":"10.1073\/pnas.0805240105","article-title":"A noncovalent class of papain-like protease\/deubiquitinase inhibitors blocks SARS virus replication","volume":"105","author":"K Ratia","year":"2008","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"6","key":"ppat.1011065.ref044","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1016\/j.chembiol.2021.04.020","article-title":"Development of potent and selective inhibitors targeting the papain-like protease of SARS-CoV-2","volume":"28","author":"H Shan","year":"2021","journal-title":"Cell Chem Biol"},{"issue":"18","key":"ppat.1011065.ref045","doi-asserted-by":"crossref","first-page":"e106275","DOI":"10.15252\/embj.2020106275","article-title":"Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2","volume":"39","author":"T Klemm","year":"2020","journal-title":"The EMBO Journal"},{"issue":"2","key":"ppat.1011065.ref046","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1021\/acsptsci.1c00240","article-title":"Validation and Invalidation of SARS-CoV-2 Papain-like Protease Inhibitors.","volume":"5","author":"C Ma","year":"2022","journal-title":"ACS Pharmacol Transl Sci."},{"key":"ppat.1011065.ref047","article-title":"Targeting SARS-CoV-2 Proteases for COVID-19 Antiviral Development.","volume":"9","author":"Z Lv","year":"2022","journal-title":"Front Chem"},{"issue":"12","key":"ppat.1011065.ref048","doi-asserted-by":"crossref","first-page":"3594","DOI":"10.3390\/ph3123594","article-title":"Cell-Penetrating Penta-Peptides (CPP5s): Measurement of Cell Entry and Protein-Transduction Activity.","volume":"3","author":"JA Gomez","year":"2010","journal-title":"Pharmaceuticals (Basel)."},{"issue":"4","key":"ppat.1011065.ref049","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1016\/j.addr.2004.10.009","article-title":"Membrane-permeable arginine-rich peptides and the translocation mechanisms","volume":"57","author":"S. 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