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The main protease of SARS-CoV-2 (Mpro) and the papain-like protease (PLpro) are essential for viral replication and are key targets for therapeutic development. In this work, we investigate the mechanisms of SARS-CoV-2 inhibition by diphenyl diselenide (PhSe)2 which is an archetypal model of diselenides and a renowned potential therapeutic agent. The in vitro inhibitory concentration of (PhSe)2 against SARS-CoV-2 in Vero E6 cells falls in the low micromolar range. Molecular dynamics (MD) simulations and density functional theory (DFT) calculations [level of theory: SMD-B3LYP-D3\u00ad(BJ)\/6-311G\u00ad(d,p), cc-pVTZ] are used to inspect non-covalent inhibition modes of both proteases via \u03c0-stacking and the mechanism of covalent (PhSe)2 + Mpro product formation involving the catalytic residue C145, respectively. The in vitro CC50 (24.61 \u03bcM) and EC50 (2.39 \u03bcM) data indicate that (PhSe)2 is a good inhibitor of the SARS-CoV-2 virus replication in a cell culture model. The in silico findings indicate potential mechanisms of proteases\u2019 inhibition by (PhSe)2; in particular, the results of the covalent inhibition here discussed for Mpro, whose thermodynamics is approximatively isoergonic, prompt further investigation in the design of antiviral organodiselenides.<\/jats:p>","DOI":"10.1021\/acs.jcim.3c00168","type":"journal-article","created":{"date-parts":[[2023,3,23]],"date-time":"2023-03-23T15:19:26Z","timestamp":1679584766000},"page":"2226-2239","source":"Crossref","is-referenced-by-count":29,"title":["Diphenyl Diselenide\nand SARS-CoV-2:\n                    <i>in silico<\/i>\n                    Exploration of the Mechanisms\nof Inhibition of Main Protease (Mpro) and Papain-like Protease\n(PLpro)"],"prefix":"10.1021","volume":"63","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9750-5034","authenticated-orcid":true,"given":"Folorunsho\nBright","family":"Omage","sequence":"first","affiliation":[{"name":"Universidade Federal de Santa Maria , , , ,","place":["Santa Maria, Rio Grande do Sul, Brazil, 97105-900"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0407-0263","authenticated-orcid":true,"given":"Andrea","family":"Madabeni","sequence":"additional","affiliation":[{"name":"Universita\u0300 Degli Studi di Padova , , Via Marzolo 1 , ,","place":["Padova, Italy, 35131"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8474-2973","authenticated-orcid":true,"given":"Amanda Resende","family":"Tucci","sequence":"additional","affiliation":[{"name":"Fundac\u0327a\u0303o Oswaldo Cruz , , , ,","place":["Manguinhos, Rio de Janeiro, Brazil, 21041-210"]},{"name":"Fundac\u0327a\u0303o Oswaldo Cruz , , , ,","place":["Manguinhos, Rio de Janeiro, Brazil, 21041-210"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9133-6102","authenticated-orcid":true,"given":"Pablo Andrei","family":"Nogara","sequence":"additional","affiliation":[{"name":"Universidade Federal de Santa Maria , , , ,","place":["Santa Maria, Rio Grande do Sul, Brazil, 97105-900"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5506-6347","authenticated-orcid":true,"given":"Marco","family":"Bortoli","sequence":"additional","affiliation":[{"name":"University of Girona , , C\/M. A. Capmany 69 , ,","place":["Girona, Spain, 17003"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1350-1301","authenticated-orcid":true,"given":"Alice dos Santos","family":"Rosa","sequence":"additional","affiliation":[{"name":"Fundac\u0327a\u0303o Oswaldo Cruz , , , ,","place":["Manguinhos, Rio de Janeiro, Brazil, 21041-210"]},{"name":"Fundac\u0327a\u0303o Oswaldo Cruz , , , ,","place":["Manguinhos, Rio de Janeiro, Brazil, 21041-210"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1712-2672","authenticated-orcid":true,"given":"Vivian","family":"Neuza dos Santos Ferreira","sequence":"additional","affiliation":[{"name":"Fundac\u0327a\u0303o Oswaldo Cruz , , , ,","place":["Manguinhos, Rio de Janeiro, Brazil, 21041-210"]},{"name":"Fundac\u0327a\u0303o Oswaldo Cruz , , , ,","place":["Manguinhos, Rio de Janeiro, Brazil, 21041-210"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3829-0595","authenticated-orcid":true,"given":"Joa\u0303o Batista","family":"Teixeira Rocha","sequence":"additional","affiliation":[{"name":"Universidade Federal de Santa Maria , , , ,","place":["Santa Maria, Rio Grande do Sul, Brazil, 97105-900"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0037-059X","authenticated-orcid":true,"given":"Milene Dias","family":"Miranda","sequence":"additional","affiliation":[{"name":"Fundac\u0327a\u0303o Oswaldo Cruz , , , ,","place":["Manguinhos, Rio de Janeiro, Brazil, 21041-210"]},{"name":"Fundac\u0327a\u0303o Oswaldo Cruz , , , ,","place":["Manguinhos, Rio de Janeiro, Brazil, 21041-210"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1673-5111","authenticated-orcid":true,"given":"Laura","family":"Orian","sequence":"additional","affiliation":[{"name":"Universita\u0300 Degli Studi di Padova , , Via Marzolo 1 , ,","place":["Padova, Italy, 35131"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2023,3,23]]},"reference":[{"key":"2026081804444993500_cit1","doi-asserted-by":"publisher","first-page":"7","DOI":"10.3389\/FCHEM.2021.622898","article-title":"Structural Basis of Potential Inhibitors\nTargeting SARS-CoV-2 Main Protease","volume":"9","author":"Mengist","year":"2021","journal-title":"Front. 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Transl.\nSci."},{"key":"2026081804444993500_cit9","doi-asserted-by":"publisher","DOI":"10.1101\/2020.05.20.107052","article-title":"Discovery of potent\ninhibitors of PLproCoV2 by screening a library\nof selenium-containing compounds","author":"We\u0328glarz-Tomczak","year":"2020","journal-title":"bioRxiv"},{"key":"2026081804444993500_cit10","doi-asserted-by":"publisher","DOI":"10.1101\/2020.05.17.100768","article-title":"Ebselen as a highly\nactive inhibitor of PLProCoV2","author":"We\u0328glarz-Tomczak","year":"2020","journal-title":"bioRxiv"},{"key":"2026081804444993500_cit11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-021-83229-6","article-title":"Identification of Ebselen and Its\nAnalogues as Potent Covalent Inhibitors of Papain-like Protease from\nSARS-CoV-2","volume":"11","author":"Weglarz-Tomczak","year":"2021","journal-title":"Sci. Reports"},{"key":"2026081804444993500_cit12","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1126\/SCIADV.ABD0345","article-title":"Molecular\nCharacterization of Ebselen Binding Activity to SARS-CoV-2 Main Protease","volume":"6","author":"Mene\u0301ndez","year":"2020","journal-title":"Sci. Adv."},{"key":"2026081804444993500_cit13","doi-asserted-by":"publisher","first-page":"2100028","DOI":"10.1002\/MINF.202100028","article-title":"In Silico Studies on the Interaction\nBetween Mpro and PLpro From SARS-CoV-2 and Ebselen, Its Metabolites\nand Derivatives","volume":"40","author":"Nogara","year":"2021","journal-title":"Mol. Inform."},{"key":"2026081804444993500_cit14","doi-asserted-by":"publisher","first-page":"12544","DOI":"10.1021\/ACSCATAL.0C03420\/SUPPL_FILE\/CS0C03420_SI_001.PDF","article-title":"Unraveling\nthe SARS-CoV-2 Main Protease Mechanism Using Multiscale Methods","volume":"10","author":"Ramos-Guzma\u0301n","year":"2020","journal-title":"ACS Catal."},{"key":"2026081804444993500_cit15","doi-asserted-by":"publisher","first-page":"5314","DOI":"10.1039\/D1CC01449H","article-title":"Influence\nof Charge Configuration on Substrate Binding\nto SARS-CoV-2 Main Protease","volume":"57","author":"Di\u0301az","year":"2021","journal-title":"Chem. Commun."},{"key":"2026081804444993500_cit16","doi-asserted-by":"publisher","first-page":"4195","DOI":"10.1021\/ACS.JPCLETT.1C00425\/SUPPL_FILE\/JZ1C00425_SI_001.PDF","article-title":"Tuning Proton Transfer\nThermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis\nand Inhibitor Design","volume":"12","author":"Zanetti-Polzi","year":"2021","journal-title":"J. Phys. Chem. Lett."},{"key":"2026081804444993500_cit17","doi-asserted-by":"publisher","first-page":"10626","DOI":"10.1039\/D0SC02823A","article-title":"Revealing the Molecular\nMechanisms of Proteolysis of\nSARS-CoV-2 Mpro by QM\/MM Computational Methods","volume":"11","author":"S\u0301widerek","year":"2020","journal-title":"Chem. Sci."},{"key":"2026081804444993500_cit18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-021-23313-7","article-title":"Inhibition\nMechanism of SARS-CoV-2 Main Protease by Ebselen and Its Derivatives","volume":"12","author":"Amporndanai","year":"2021","journal-title":"Nat. Commun."},{"key":"2026081804444993500_cit19","doi-asserted-by":"publisher","first-page":"1306","DOI":"10.1016\/J.CSBJ.2022.03.009","article-title":"Inhibition\nof the Main Protease of SARS-CoV-2 (Mpro) by Repurposing\/Designing\nDrug-like Substances and Utilizing Nature\u2019s Toolbox of Bioactive\nCompounds","volume":"20","author":"Antonopoulou","year":"2022","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"2026081804444993500_cit20","doi-asserted-by":"publisher","first-page":"3202","DOI":"10.1038\/s41467-020-16954-7","article-title":"Structural Plasticity of SARS-CoV-2\n3CL M Pro Active Site Cavity Revealed by Room Temperature X-Ray Crystallography","volume":"11","author":"Kneller","year":"2003","journal-title":"Nat. Struct. Biol."},{"key":"2026081804444993500_cit21","doi-asserted-by":"publisher","first-page":"2722","DOI":"10.1002\/jmv.26814","article-title":"Targeting SARS-CoV-2\nViral Proteases as a Therapeutic Strategy to Treat COVID-19","volume":"93","author":"Anirudhan","year":"2021","journal-title":"J. Med. Virol."},{"key":"2026081804444993500_cit22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-021-21060-3","article-title":"Structure\nof Papain-like Protease from SARS-CoV-2 and\nIts Complexes with Non-Covalent Inhibitors","volume":"12","author":"Osipiuk","year":"2021","journal-title":"Nat. Commun."},{"key":"2026081804444993500_cit23","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.1007\/S00204-021-03003-5","article-title":"Toxicology\nand Pharmacology of Synthetic\nOrganoselenium Compounds: An Update","volume":"95","author":"Nogueira","year":"2021","journal-title":"Arch. Toxicol."},{"key":"2026081804444993500_cit24","doi-asserted-by":"publisher","first-page":"1381","DOI":"10.2174\/1385272822666180803123137","article-title":"Organodiselenides:\nOrganic Catalysis and Drug Design Learning from Glutathione Peroxidase","volume":"23","author":"Dalla\nTiezza","year":"2019","journal-title":"Curr. Org. Chem."},{"key":"2026081804444993500_cit25","doi-asserted-by":"publisher","first-page":"1020","DOI":"10.2174\/138955708785740625","article-title":"Selenium Compounds and Apoptotic\nModulation: A New Perspective in Cancer Therapy","volume":"8","author":"Sanmartin","year":"2008","journal-title":"Mini Rev. Med. Chem."},{"key":"2026081804444993500_cit26","doi-asserted-by":"publisher","first-page":"628","DOI":"10.3390\/molecules23030628","article-title":"Selenides\nand Diselenides:\nA Review of Their Anticancer and Chemopreventive Activity","volume":"23","author":"Alvarez-Perez","year":"2018","journal-title":"Mol. A J. Synth. Chem. Nat. Prod. Chem."},{"key":"2026081804444993500_cit27","doi-asserted-by":"publisher","first-page":"1703","DOI":"10.1039\/c7mt00083a","article-title":"Organoselenium\nCompounds as Mimics of Selenoproteins\nand Thiol Modifier Agents","volume":"9","author":"Barbosa","year":"2017","journal-title":"Metallomics"},{"key":"2026081804444993500_cit28","doi-asserted-by":"publisher","first-page":"1287","DOI":"10.1590\/S0100-879X2006005000171","article-title":"Pharmacology and Toxicology\nof Diphenyl Diselenide in Several Biological Models","volume":"40","author":"Rosa","year":"2007","journal-title":"Braz. J. Med. Biol."},{"key":"2026081804444993500_cit29","doi-asserted-by":"publisher","first-page":"1196","DOI":"10.1021\/TX0601105","article-title":"Ebselen, a\nSeleno-Organic Antioxidant,\nas an Electrophile","volume":"19","author":"Sakurai","year":"2006","journal-title":"Chem. Res. Toxicol."},{"key":"2026081804444993500_cit30","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.freeradbiomed.2013.03.006","article-title":"Organochalcogen Peroxidase\nMimetics as Potential Drugs: A Long Story of a Promise Still Unfulfilled","volume":"66","author":"Orian","year":"2014","journal-title":"Free Rad. Biol. Med."},{"key":"2026081804444993500_cit31","doi-asserted-by":"publisher","first-page":"2055","DOI":"10.1590\/S0103-50532010001100006","article-title":"Diphenyl Diselenide a Janus-Faced\nMolecule","volume":"21","author":"Nogueira","year":"2010","journal-title":"J. Braz. Chem. 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Chem."},{"key":"2026081804444993500_cit35","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1016\/J.RVSC.2020.11.023","article-title":"Diphenyl Diselenide\nand Cidofovir Present Anti-Viral Activity against Bovine Alphaherpesvirus\n2 in vitro and in a Sheep Model","volume":"134","author":"Amaral","year":"2021","journal-title":"Res. Vet. Sci."},{"key":"2026081804444993500_cit36","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1093\/MMY\/MYAA115","article-title":"Ebselen\nand Diphenyl Diselenide against\nFungal Pathogens: A Systematic Review","volume":"59","author":"Benelli","year":"2021","journal-title":"Med.\nMycol."},{"key":"2026081804444993500_cit37","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/J.TOXLET.2009.04.026","article-title":"Convulsant Effect of\nDiphenyl Diselenide in Rats and Mice and Its Relationship to Plasma\nLevels","volume":"189","author":"Prigol","year":"2009","journal-title":"Toxicol. Lett."},{"key":"2026081804444993500_cit38","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1177\/1087057103252618","article-title":"The Effect\nof Freeze\/Thaw\nCycles on the Stability of Compounds in DMSO","volume":"8","author":"Kozikowski","year":"2003","journal-title":"J. Biomol. Screen."},{"key":"2026081804444993500_cit39","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.1016\/J.TOXREP.2018.10.002","article-title":"A Dose-Dependent\nEffect of Dimethyl\nSulfoxide on Lipid Content, Cell Viability and Oxidative Stress in\n3T3-L1 Adipocytes","volume":"5","author":"Dludla","year":"2018","journal-title":"Toxicol. Reports"},{"key":"2026081804444993500_cit40","doi-asserted-by":"publisher","first-page":"3855","DOI":"10.15419\/bmrat.v7i7.614","article-title":"Comparative Cytotoxic\nEffects of Methanol, Ethanol and DMSO on Human Cancer Cell Lines","volume":"7","author":"Nguyen","year":"2020","journal-title":"Biomed. Res. 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