{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T20:58:24Z","timestamp":1790888304166,"version":"4.1.0"},"reference-count":59,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2021,4,12]],"date-time":"2021-04-12T00:00:00Z","timestamp":1618185600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004442","name":"Narodowym Centrum Nauki","doi-asserted-by":"publisher","award":["#2020\/01\/0\/NZ7\/00244"],"award-info":[{"award-number":["#2020\/01\/0\/NZ7\/00244"]}],"id":[{"id":"10.13039\/501100004442","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes the papain-like protease (PLpro). The protein not only plays an essential role in viral replication but also cleaves ubiquitin and ubiquitin-like interferon-stimulated gene 15 protein (ISG15) from host proteins, making it an important target for developing new antiviral drugs. In this study, we searched for novel, noncovalent potential PLpro inhibitors by employing a multistep in silico screening of a 15 million compound library. The selectivity of the best-scored compounds was evaluated by checking their binding affinity to the human ubiquitin carboxy-terminal hydrolase L1 (UCH-L1), which, as a deubiquitylating enzyme, exhibits structural and functional similarities to the PLpro. As a result, we identified 387 potential, selective PLpro inhibitors, from which we retrieved the 20 best compounds according to their IC50 values toward PLpro estimated by a multiple linear regression model. The selected candidates display potential activity against the protein with IC50 values in the nanomolar range from approximately 159 to 505 nM and mostly adopt a similar binding mode to the known, noncovalent SARS-CoV-2 PLpro inhibitors. We further propose the six most promising compounds for future in vitro evaluation. The results for the top potential PLpro inhibitors are deposited in the database prepared to facilitate research on anti-SARS-CoV-2 drugs.<\/jats:p>","DOI":"10.3390\/ijms22083957","type":"journal-article","created":{"date-parts":[[2021,4,12]],"date-time":"2021-04-12T03:04:06Z","timestamp":1618196646000},"page":"3957","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["SARS-CoV-2 Papain-Like Protease Potential Inhibitors\u2014In Silico Quantitative Assessment"],"prefix":"10.3390","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3346-5579","authenticated-orcid":false,"given":"Adam","family":"Stasiulewicz","sequence":"first","affiliation":[{"name":"Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland"},{"name":"Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6377-321X","authenticated-orcid":false,"given":"Alicja W.","family":"Maksymiuk","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland"},{"name":"School of the Biological Sciences, University of Cambridge, 17 Mill Lane, Cambridge CB2 1RX, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8117-0391","authenticated-orcid":false,"given":"Mai Lan","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland"},{"name":"Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0066-446X","authenticated-orcid":false,"given":"Barbara","family":"Be\u0142za","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland"},{"name":"College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2452-0724","authenticated-orcid":false,"given":"Joanna I.","family":"Sulkowska","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,4,12]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization WHO Director-General\u2019s Opening Remarks at the Media Briefing on COVID-19\u201411 March 2020, World Health Organization. Available online: https:\/\/www.who.int\/director-general\/speeches\/detail\/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19---11-march-2020."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1056\/NEJMoa2001017","article-title":"A novel Coronavirus from Patients with Pneumonia in China, 2019","volume":"382","author":"Zhu","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1016\/S0140-6736(20)30211-7","article-title":"Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study","volume":"395","author":"Chen","year":"2020","journal-title":"Lancet"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/S1473-3099(20)30120-1","article-title":"An interactive web-based dashboard to track COVID-19 in real time","volume":"20","author":"Dong","year":"2020","journal-title":"Lancet Infect. Dis."},{"key":"ref_5","unstructured":"Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU) (2021, March 02). COVID-19 Dashboard. Available online: https:\/\/www.arcgis.com\/apps\/opsdashboard\/index.html#\/bda7594740fd40299423467b48e9ecf6."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4939-2438-7_1","article-title":"Coronaviruses: An overview of their replication and pathogenesis","volume":"Volume 1282","author":"Fehr","year":"2015","journal-title":"Coronaviruses. Methods in Molecular Biology"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2099","DOI":"10.1021\/acsinfecdis.0c00168","article-title":"Characterization and Noncovalent Inhibition of the Deubiquitinase and deISGylase Activity of SARS-CoV-2 Papain-Like Protease","volume":"6","author":"Freitas","year":"2020","journal-title":"ACS Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2305","DOI":"10.1099\/vir.0.19424-0","article-title":"Mechanisms and enzymes involved in SARS coronavirus genome expression","volume":"84","author":"Thiel","year":"2003","journal-title":"J. Gen. Virol."},{"key":"ref_9","first-page":"1","article-title":"SARS-CoV-2: The many pros of targeting PLpro","volume":"5","author":"McClain","year":"2020","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"127377","DOI":"10.1016\/j.bmcl.2020.127377","article-title":"The SARS-CoV-2 main protease as drug target","volume":"30","author":"Ullrich","year":"2020","journal-title":"Bioorganic Med. Chem. Lett."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1038\/s41586-020-2601-5","article-title":"Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity","volume":"587","author":"Shin","year":"2020","journal-title":"Nature"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Fischer, A., Sellner, M., Neranjan, S., Smie\u0161ko, M., and Lill, M.A. (2020). Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds. Int. J. Mol. Sci., 21.","DOI":"10.26434\/chemrxiv.11923239"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"3021","DOI":"10.1021\/jm201278q","article-title":"Discovery of novel urea-based hepatitis C protease inhibitors with high potency against protease-inhibitor-resistant mutants","volume":"55","author":"Kazmierski","year":"2012","journal-title":"J. Med. Chem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"4203","DOI":"10.1016\/j.jmb.2019.03.013","article-title":"ISG15: It\u2019s Complicated","volume":"431","author":"Dzimianski","year":"2019","journal-title":"J. Mol. Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"15189","DOI":"10.1128\/JVI.79.24.15189-15198.2005","article-title":"The papain-like protease of severe acute respiratory syndrome coronavirus has deubiquitinating activity","volume":"79","author":"Barretto","year":"2005","journal-title":"J. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"4550","DOI":"10.1128\/JVI.79.7.4550-4551.2005","article-title":"Deubiquitination, a new function of the severe acute respiratory syndrome coronavirus papain-like protease?","volume":"79","author":"Sulea","year":"2005","journal-title":"J. Virol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"170016","DOI":"10.1098\/rsob.170016","article-title":"Deubiquitylation of deubiquitylases","volume":"7","author":"Haq","year":"2017","journal-title":"Open Biol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1002\/acn3.298","article-title":"Absence of UCHL 1 function leads to selective motor neuropathy","volume":"3","author":"Jara","year":"2016","journal-title":"Ann. Clin. Transl. Neurol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1016\/j.cell.2006.06.046","article-title":"Ubiquitin hydrolase Uch-L1 rescues \u03b2-amyloid-induced decreases in synaptic function and contextual memory","volume":"126","author":"Gong","year":"2006","journal-title":"Cell"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1042\/BST20170087","article-title":"Regulation of the cell cycle and centrosome biology by deubiquitylases","volume":"45","author":"Darling","year":"2017","journal-title":"Biochem. Soc. Trans."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1016\/j.chembiol.2003.08.010","article-title":"Discovery of inhibitors that elucidate the role of UCH-L1 activity in the H1299 lung cancer cell line","volume":"10","author":"Liu","year":"2003","journal-title":"Chem. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Virnau, P., Mirny, L.A., and Kardar, M. (2006). Intricate knots in proteins: Function and evolution. PLoS Comput. Biol., 2.","DOI":"10.1371\/journal.pcbi.0020122"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.sbi.2020.01.007","article-title":"On folding of entangled proteins: Knots, lassos, links and \u03b8-curves","volume":"60","author":"Sulkowska","year":"2020","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1038\/s41467-021-21060-3","article-title":"Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors","volume":"12","author":"Osipiuk","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.apsb.2020.08.014","article-title":"Crystal structure of SARS-CoV-2 papain-like protease","volume":"11","author":"Gao","year":"2021","journal-title":"Acta Pharm. Sin. B"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1038\/s41467-020-20718-8","article-title":"The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery","volume":"12","author":"Fu","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_27","first-page":"1","article-title":"SARS-CoV-2 proteases PLpro and 3CLpro cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): Implications for disease presentation across species","volume":"10","author":"Moustaqil","year":"2020","journal-title":"Emerg. Microbes Infect."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1581","DOI":"10.1002\/jmv.26497","article-title":"The emerging SARS-CoV-2 papain-like protease: Its relationship with recent coronavirus epidemics","volume":"93","author":"Kandeel","year":"2021","journal-title":"J. Med Virol."},{"key":"ref_29","first-page":"1","article-title":"Structure-Activity Relationships of Benzamides and Isoindolines Designed as SARS-CoV Protease Inhibitors Effective against SARS-CoV-2","volume":"15","author":"Welker","year":"2020","journal-title":"ChemMedChem"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"eabd4596","DOI":"10.1126\/sciadv.abd4596","article-title":"Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti\u2013COVID-19 drug design","volume":"6","author":"Rut","year":"2020","journal-title":"Sci. Adv."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Zmudzinski, M., Rut, W., Olech, K., Granda, J., Giurg, M., Burda-Grabowska, M., Zhang, L., Sun, X., Lv, Z., and Nayak, D. (2020). Ebselen derivatives are very potent dual inhibitors of SARS-CoV-2 proteases-PLpro and Mpro in in vitro studies. bioRxiv.","DOI":"10.1101\/2020.08.30.273979"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1021\/jm990412m","article-title":"Protease inhibitors: Current status and future prospects","volume":"43","author":"Leung","year":"2000","journal-title":"J. Med. Chem."},{"key":"ref_33","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":"Ratia","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"949","DOI":"10.4155\/fmc.10.21","article-title":"Strategies for discovering and derisking covalent, irreversible enzyme inhibitors","volume":"2","author":"Johnson","year":"2010","journal-title":"Future Med. Chem."},{"key":"ref_35","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":"Klemm","year":"2020","journal-title":"EMBO J."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Shen, Z., Ratia, K., Cooper, L., Kong, D., Lee, H., Kwon, Y., Li, Y., Alqarni, S., Huang, F., and Dubrovskyi, O. (2021). Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures. bioRxiv.","DOI":"10.1101\/2021.02.13.431008"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Weglarz-Tomczak, E., Tomczak, J.M., Talma, M., and Brul, S. (2020). Ebselen as a highly active inhibitor of PLProCoV2. bioRxiv.","DOI":"10.1101\/2020.05.17.100768"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"9904","DOI":"10.1039\/D0SC02646H","article-title":"Multi-targeting of functional cysteines in multiple conserved SARS-CoV-2 domains by clinically safe Zn-ejectors","volume":"11","author":"Sargsyan","year":"2020","journal-title":"Chem. Sci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3900","DOI":"10.1016\/j.bmcl.2012.04.124","article-title":"The crystal structure of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) with a tripeptide fluoromethyl ketone (Z-VAE (OMe)-FMK)","volume":"22","author":"Davies","year":"2012","journal-title":"Bioorganic Med. Chem. Lett."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"9117","DOI":"10.1073\/pnas.0910870107","article-title":"Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation","volume":"107","author":"Boudreaux","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"4675","DOI":"10.1073\/pnas.0510403103","article-title":"Structural basis for conformational plasticity of the Parkinson\u2019s disease-associated ubiquitin hydrolase UCH-L1","volume":"103","author":"Das","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/S0092-8674(02)01012-7","article-title":"The UCH-L1 gene encodes two opposing enzymatic activities that affect \u03b1-synuclein degradation and Parkinson\u2019s disease susceptibility","volume":"111","author":"Liu","year":"2002","journal-title":"Cell"},{"key":"ref_43","first-page":"E1715","article-title":"Conservation of complex knotting and slipknotting patterns in proteins","volume":"109","author":"Rawdon","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"D306","DOI":"10.1093\/nar\/gku1059","article-title":"KnotProt: A database of proteins with knots and slipknots","volume":"43","author":"Jamroz","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"6735","DOI":"10.1021\/bi960099f","article-title":"Substrate binding and catalysis by ubiquitin C-terminal hydrolases: Identification of two active site residues","volume":"35","author":"Larsen","year":"1996","journal-title":"Biochemistry"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"3787","DOI":"10.1093\/emboj\/16.13.3787","article-title":"Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 \u00e5 resolution","volume":"16","author":"Johnston","year":"1997","journal-title":"EMBO J."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"6058","DOI":"10.1039\/D0SC01347A","article-title":"Engineered unnatural ubiquitin for optimal detection of deubiquitinating enzymes","volume":"11","author":"Rut","year":"2020","journal-title":"Chem. Sci."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1021\/ci049885e","article-title":"LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters","volume":"45","author":"Wolber","year":"2005","journal-title":"J. Chem. Inf. Model."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2393","DOI":"10.1021\/jm401712t","article-title":"X-ray structural and biological evaluation of a series of potent and highly selective inhibitors of human coronavirus papain-like proteases","volume":"57","author":"Barraza","year":"2014","journal-title":"J. Med. Chem."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1549","DOI":"10.1002\/jcc.10306","article-title":"Detailed analysis of grid-based molecular docking: A case study of CDOCKER\u2014A CHARMm-based MD docking algorithm","volume":"24","author":"Wu","year":"2003","journal-title":"J. Comput. Chem."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1021\/jm0306430","article-title":"Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy","volume":"47","author":"Friesner","year":"2004","journal-title":"J. Med. Chem."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1002\/wcms.1240","article-title":"In silico toxicology: Computational methods for the prediction of chemical toxicity","volume":"6","author":"Raies","year":"2016","journal-title":"Wiley Interdiscip. Rev. Comput. Mol. Sci."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0169-409X(96)00423-1","article-title":"Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings","volume":"23","author":"Lipinski","year":"1997","journal-title":"Adv. Drug Deliv. Rev."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2615","DOI":"10.1021\/jm020017n","article-title":"Molecular properties that influence the oral bioavailability of drug candidates","volume":"45","author":"Veber","year":"2002","journal-title":"J. Med. Chem."},{"key":"ref_55","unstructured":"(2020). LigandScout 4.4.5, Inte:Ligand GmbH."},{"key":"ref_56","unstructured":"(2020). BIOVIA Discovery Studio v20.1.0.19295, BIOVIA, Dassault Syst\u00e8mes."},{"key":"ref_57","unstructured":"(2016). Statistica 13.1, TIBCO Software Inc."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"(2017). Schr\u00f6dinger Release 2017-1, Maestro, Schr\u00f6dinger, LLC.","DOI":"10.2307\/j.ctvcm4h07.63"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"2348","DOI":"10.1093\/bioinformatics\/btm341","article-title":"ChemDB update\u2014Full-text search and virtual chemical space","volume":"23","author":"Chen","year":"2007","journal-title":"Bioinformatics"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/8\/3957\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T14:12:22Z","timestamp":1760364742000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/8\/3957"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4,12]]},"references-count":59,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2021,4]]}},"alternative-id":["ijms22083957"],"URL":"https:\/\/doi.org\/10.3390\/ijms22083957","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,4,12]]}}}