{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T15:54:05Z","timestamp":1759334045764,"version":"build-2065373602"},"reference-count":88,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T00:00:00Z","timestamp":1758844800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001807","name":"FAPESP","doi-asserted-by":"crossref","award":["2018-13588-0"],"award-info":[{"award-number":["2018-13588-0"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.mdpi.com"],"crossmark-restriction":true},"short-container-title":["Molecules"],"abstract":"<jats:p>A focused library of 1,2,4-thiadiazolidin-3,5-diones (THIA-1\u201310), previously characterized as hydrogen sulfide (H2S) donors, was evaluated for inhibitory activity against cysteine proteases. We included two key cysteine proteases aiming at antiviral drug development\u2014SARS-CoV-2 3CLpro (Mpro) and PLpro\u2014alongside reference enzymes Papain and Cathepsin L. The compounds exhibited distinct selectivity profiles and inhibition mechanisms. The ability to act as covalent inhibitors of 3CLpro in the nanomolar range is of particular interest, with compounds THIA-6, -7, and -10 proving to be the most potent inhibitors of the series, and compounds THIA-1, -2, and -8 proving to be the most selective with respect to the other proteases. We explored the molecular bases of the observed activity profile of THIA-1\u201310 through computational studies, which supported and complemented the experimental findings, paving the way for future structure optimization. The results highlight that inhibitory potency depends not only on electrophilicity but also on the ability to access the catalytic cysteine within the active site. The dual functionality of THIA-1\u201310 as H2S donors and selective cysteine protease inhibitors underscores its potential as a promising lead for therapeutic development.<\/jats:p>","DOI":"10.3390\/molecules30193896","type":"journal-article","created":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T13:30:03Z","timestamp":1758893403000},"page":"3896","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["1,2,4-Thiadiazolidin-3,5-Diones as Inhibitors of Cysteine Proteases"],"prefix":"10.3390","volume":"30","author":[{"given":"Maria Aparecida","family":"Juliano","sequence":"first","affiliation":[{"name":"Department of Biophysics, Escola Paulista Medicina, Universidade Federal S\u00e3o Paulo, Rua Tres de Maio, 100, S\u00e3o Paulo 04044-020, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0010-0338","authenticated-orcid":false,"given":"Marco","family":"Persico","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, School of Medicine, University of Naples \u00abFederico II\u00bb, Via D. Montesano, 49, 80131 Napoli, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3887-8869","authenticated-orcid":false,"given":"Beatrice","family":"Severino","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, School of Medicine, University of Naples \u00abFederico II\u00bb, Via D. Montesano, 49, 80131 Napoli, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-9702-2157","authenticated-orcid":false,"given":"Giuseppe","family":"Tumbarello","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, School of Medicine, University of Naples \u00abFederico II\u00bb, Via D. Montesano, 49, 80131 Napoli, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Debora","family":"Okamoto","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, Universidade Federal de S\u00e3o Paulo, Rua S\u00e3o Nicolau, 210, Diadema 09913-030, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karolina Rosa","family":"Fernandes","sequence":"additional","affiliation":[{"name":"Department of Biophysics, Escola Paulista Medicina, Universidade Federal S\u00e3o Paulo, Rua Tres de Maio, 100, S\u00e3o Paulo 04044-020, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-4572-2960","authenticated-orcid":false,"given":"Gabriel","family":"Trigo","sequence":"additional","affiliation":[{"name":"Department of Biophysics, Escola Paulista Medicina, Universidade Federal S\u00e3o Paulo, Rua Tres de Maio, 100, S\u00e3o Paulo 04044-020, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9407-805X","authenticated-orcid":false,"given":"Aparecida Sadae","family":"Tanaka","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Escola Paulista Medicina, Universidade Federal S\u00e3o Paulo, Rua Tres de Maio, 100, S\u00e3o Paulo 04044-020, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4588-7197","authenticated-orcid":false,"given":"Jos\u00e9 Thalles","family":"Lacerda","sequence":"additional","affiliation":[{"name":"Department of Biophysics, Escola Paulista Medicina, Universidade Federal S\u00e3o Paulo, Rua Tres de Maio, 100, S\u00e3o Paulo 04044-020, SP, Brazil"},{"name":"Department of Pharmaceutical Sciences, Federal University of Pernambuco, Rua Artur de S\u00e1, Recife 50740-521, PE, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5349-1405","authenticated-orcid":false,"given":"Oleh","family":"Tkachuck","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, School of Medicine, University of Naples \u00abFederico II\u00bb, Via D. 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Lett."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1677","DOI":"10.1016\/j.ejmech.2017.10.068","article-title":"1,2,4-Thiadiazolidin-3,5-diones as novel hydrogen sulfide donors","volume":"143","author":"Severino","year":"2018","journal-title":"Eur. J. Med. Chem."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"3181","DOI":"10.1021\/bi1019622","article-title":"A nanomolar-potency small molecule inhibitor of regulator of G-protein signaling proteins","volume":"50","author":"Blazer","year":"2011","journal-title":"Biochemistry"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/j.bbrc.2012.08.015","article-title":"On the size of the active site in proteases. I. Papain","volume":"425","author":"Schechter","year":"2012","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1021\/cc990031u","article-title":"Fluorescence-Quenched Solid Phase Combinatorial Libraries in the Characterization of Cysteine Protease Substrate Specificity","volume":"1","author":"Willert","year":"1999","journal-title":"J. Comb. Chem."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1515\/bchm.1998.379.2.137","article-title":"Revised definition of substrate binding sites of papain-like cysteine proteases","volume":"379","author":"Turk","year":"1998","journal-title":"Biol. Chem."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"12824","DOI":"10.1074\/jbc.M513331200","article-title":"Substrate Profiling of Cysteine Proteases Using a Combinatorial Peptide Library Identifies Functionally Unique Specificities","volume":"281","author":"Choe","year":"2006","journal-title":"J. Biol. Chem."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1074\/mcp.M500004-MCP200","article-title":"High throughput substrate specificity profiling of serine and cysteine proteases using solution-phase fluorogenic peptide microarrays","volume":"4","author":"Gosalia","year":"2005","journal-title":"Mol. Cell. Proteom."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.1046\/j.1432-1327.2001.01973.x","article-title":"S1 subsite specificity of a recombinant cysteine proteinase, CPB, of Leishmania mexicana compared with cruzain, human cathepsin L and Papain using substrates containing non-natural basic amino acids","volume":"268","author":"Alves","year":"2001","journal-title":"Eur. J. Biochem."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/S0014-5793(97)00216-0","article-title":"The crystal structure of human cathepsin L complexed with E-64","volume":"407","author":"Fujishima","year":"1997","journal-title":"FEBS Lett."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1330","DOI":"10.1021\/bi00429a058","article-title":"Crystal Structure of a Papain-E-64 Complex","volume":"28","author":"Varughese","year":"1989","journal-title":"Biochemistry"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1006\/bbrc.1999.1830","article-title":"Inhibition Mechanism of Cathepsin L-Specific Inhibitors Based on the Crystal Structure of Papain\u2013CLIK148 Complex","volume":"266","author":"Tsuge","year":"1999","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1042\/bj2990389","article-title":"E64 [trans-epoxysuccinyl-L-leucylamido-(4-guanidino)butane] analogues as inhibitors of cysteine proteinases: Investigation of S2 subsite interactions","volume":"299","author":"Lachance","year":"1994","journal-title":"Biochem. J."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"5492","DOI":"10.1002\/j.1460-2075.1996.tb00934.x","article-title":"Structure of human procathepsin L reveals the molecular basis of Inhibition by the prosegment","volume":"15","author":"Coulombe","year":"1996","journal-title":"EMBO J."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1515\/bc.2010.145","article-title":"Increase of SARS-CoV 3CL peptidase activity due to macromolecular crowding effects in the milieu composition","volume":"391","author":"Okamoto","year":"2010","journal-title":"Biol. Chem."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1126\/science.abb3405","article-title":"Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors","volume":"368","author":"Zhang","year":"2020","journal-title":"Science"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2926","DOI":"10.1021\/acs.jmedchem.1c00665","article-title":"3CL Protease inhibitors with an electrophilic arylketone moiety as anti-SARS-CoV-2 agents","volume":"65","author":"Konno","year":"2022","journal-title":"J. Med. Chem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2848","DOI":"10.1021\/acs.jmedchem.1c00509","article-title":"Expedited Approach toward the Rational Design of Noncovalent SARS-CoV-2 Main Protease Inhibitors","volume":"65","author":"Kitamura","year":"2022","journal-title":"J. Med. Chem."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1107\/S2052252520012634","article-title":"Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL Mpro: Insights into enzyme mechanism and drug design","volume":"7 Pt 6","author":"Kneller","year":"2020","journal-title":"IUCrJ."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"3202","DOI":"10.1038\/s41467-020-16954-7","article-title":"Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography","volume":"11","author":"Kneller","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_22","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_23","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_24","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1107\/S1399004713031040","article-title":"Structural basis for catalysis and ubiquitin recognition by the severe acute respiratory syndrome coronavirus papain-like protease","volume":"70 Pt 2","author":"Chou","year":"2014","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"eabd4596","DOI":"10.1126\/sciadv.abd4596","article-title":"Activity profiling and crystal structures of inhibitorbound 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_26","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.antiviral.2014.12.015","article-title":"The SARS-coronavirus papain-like protease: Structure, function and Inhibition by designed antiviral compounds","volume":"115","author":"Mesecar","year":"2015","journal-title":"Antivir. Res."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Lv, Z., Cano, K.E., Jia, L., Drag, M., Huang, T.T., and Olsen, S.K. (2022). Targeting SARS-CoV-2 Proteases for COVID-19 Antiviral Development. Front. Chem., 9.","DOI":"10.3389\/fchem.2021.819165"},{"key":"ref_28","first-page":"65","article-title":"Dimethyl Sulfoxide: Yesterday\u2019s Solvent, Today\u2019s Reagent","volume":"361","author":"Tashrifi","year":"2019","journal-title":"Adv. Synth. Catal."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1038\/nprot.2008.63","article-title":"Measuring elastase, proteinase 3 and cathepsin G activities at the surface of human neutrophils with fluorescence resonance energy transfer substrate","volume":"3","author":"Korkmaz","year":"2008","journal-title":"Nat. Protoc."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"16584","DOI":"10.1021\/acsomega.1c01797","article-title":"Inhibition of the 3CL Protease and SARS-CoV-2 Replication by Dalcetrapib","volume":"6","author":"Niesor","year":"2021","journal-title":"ACS Omega"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1002\/cbdv.200800334","article-title":"3-Fluoro-2,4-dioxa-3-phosphadecalins as inhibitors of acetylcholinesterase. A reappraisal of kinetic mechanisms and diagnostic methods","volume":"6","author":"Baici","year":"2009","journal-title":"Chem. Biodivers."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1042\/bj3470123","article-title":"Probing the specificity of cysteine proteinases at subsites remote from the active site analysis of P4, P3, P2\u2032 and P3\u2032 variations in extended substrates","volume":"347","author":"Portaro","year":"2000","journal-title":"Biochem. J."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"16705","DOI":"10.1016\/S0021-9258(17)44813-7","article-title":"Enzyme inhibition by fluoro compounds","volume":"265","author":"Abeles","year":"1990","journal-title":"J. Biol. Chem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1002\/cbic.200301023","article-title":"Fluorine in medicinal chemistry","volume":"5","author":"Banner","year":"2004","journal-title":"Chembiochem"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.1002\/anie.200351268","article-title":"A fluorine scan of thrombin inhibitors to map the fluorophilicity\/fluorophobicity of an enzyme active site: Evidence for C-F\u2026C=O interactions","volume":"42","author":"Olsen","year":"2003","journal-title":"Angew. Chem. Int. Ed. Eng."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Azarkan, M., Maquoi, E., Delbrassine, F., Herman, R., M\u2019Rabet, N., Esposito, R.C., Charlier, P., and Kerff, F. (2020). Structures of the free and inhibitors-bound forms of Bromelain and ananain from Ananas comosus stem and in vitro study of their cytotoxicity. Sci. Rep., 10.","DOI":"10.1038\/s41598-020-76172-5"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1042\/bj2010189","article-title":"L-trans-Epoxysuccinyl-leucylamido(4-guanidino)butane (E-64) and its analogues as inhibitors of cysteine proteinases including cathepsins B, H and L","volume":"201","author":"Barrett","year":"1982","journal-title":"Biochem. J."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"e0004924","DOI":"10.1128\/jvi.00049-24","article-title":"Optimization of quenched fluorescent peptide substrates of SARS-CoV-2 3CLpro main protease (Mpro) from proteomic identification of P6-P6\u2032 active site specificity","volume":"98","author":"Jesus","year":"2024","journal-title":"J. Virol."},{"key":"ref_39","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 noncovalent inhibitors","volume":"12","author":"Osipiuk","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1002\/jcc.540120405","article-title":"Rapid Finite Difference Algorithm, Utilizing Successive Over-Relaxation to Solve Poisson-Boltzmann Equations","volume":"12","author":"Nicholls","year":"1991","journal-title":"J. Comp. Chem."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1002\/jcc.10189","article-title":"Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model","volume":"24","author":"Cossi","year":"2003","journal-title":"J. Comp. Chem."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"12266","DOI":"10.1021\/acs.jmedchem.3c00818","article-title":"Discovery and Mechanism Study of SARS-CoV-2 3C-like Protease Inhibitors with a New Reactive Group","volume":"66","author":"Ren","year":"2023","journal-title":"J. Med. Chem."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/S1093-3263(02)00164-X","article-title":"LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites","volume":"21","author":"Venkatachalam","year":"2003","journal-title":"J. Mol. Graph. Model."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"10626","DOI":"10.1039\/D0SC02823A","article-title":"Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 Mpro by QM\/MM computational methods","volume":"11","author":"Moliner","year":"2020","journal-title":"Chem Sci."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"e151","DOI":"10.1002\/mco2.151","article-title":"The SARS-CoV-2 main protease (Mpro): Structure, function, and emerging therapies for COVID-19","volume":"3","author":"Hu","year":"2020","journal-title":"MedComm"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"3058","DOI":"10.1021\/acs.jcim.1c00449","article-title":"Dynamic Profiling of \u03b2-Coronavirus 3CL Mpro Protease Ligand-Binding Sites","volume":"61","author":"Cho","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Lodola, A., Branduardi, D., De Vivo, M., Capoferri, L., Mor, M., Piomelli, D., and Cavalli, A. (2012). A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0032397"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"12740","DOI":"10.1039\/C7CP01726J","article-title":"Quantum mechanics\/molecular mechanics studies of the mechanism of cysteine protease inhibition by peptidyl-2,3-epoxyketones","volume":"19","author":"Arafet","year":"2017","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"5061","DOI":"10.1021\/jm100112j","article-title":"A medicinal chemist\u2019s guide to molecular interactions","volume":"53","author":"Bissantz","year":"2010","journal-title":"J. Med. Chem."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"3221","DOI":"10.1080\/07391102.2016.1251851","article-title":"Evaluation of Protein-Ligand Affinity Prediction Using Steered Molecular Dynamics Simulations","volume":"35","author":"Okimoto","year":"2017","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"3819","DOI":"10.1080\/07391102.2017.1401002","article-title":"Steered Molecular Dynamics for Studying Ligand Unbinding of Ecdysone Receptor","volume":"36","author":"Hu","year":"2018","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1021\/ci4003574","article-title":"Steered Molecular Dynamics Simulations for Studying Protein-Ligand Interaction in Cyclin-Dependent Kinase 5","volume":"54","author":"Patel","year":"2014","journal-title":"J. Chem. Inf. Model."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1021\/acs.biochem.4c00575","article-title":"The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops Is Determined by Ligand Binding and Interprotomer Allostery","volume":"64","author":"Lee","year":"2025","journal-title":"Biochemistry"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Ullrich, S., and Nitsche, C. (2022). SARS-CoV-2 Papain-Like Protease: Structure, Function and Inhibition. Chembiochem, 23.","DOI":"10.1002\/cbic.202200327"},{"key":"ref_55","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_56","doi-asserted-by":"crossref","first-page":"4681","DOI":"10.1039\/D3SC00166K","article-title":"Unraveling the catalytic mechanism of SARS-CoV-2 papain-like protease with allosteric modulation of C270 mutation using multiscale computational approaches","volume":"14","author":"Shao","year":"2023","journal-title":"Chem. Sci."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"5363","DOI":"10.1021\/pr200621z","article-title":"Proteomic identification of protease cleavage sites characterizes prime and non-prime specificity of cysteine cathepsins B, L, and S","volume":"10","author":"Biniossek","year":"2011","journal-title":"J. Proteome Res."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"J. Comput. Chem."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1042\/bj2870797","article-title":"Crystal structure of papain-E64-c complex. Binding diversity of E64-c to papain S2 and S3 subsites","volume":"287","author":"Kim","year":"1992","journal-title":"Biochem. J."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/s41392-024-01758-8","article-title":"Structure-based design of pan-coronavirus inhibitors targeting host cathepsin L and calpain-1","volume":"9","author":"Xie","year":"2024","journal-title":"Sig. Transduct. Target Ther."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1080\/17460441.2023.2174522","article-title":"An approach combining deep learning and molecule docking for drug discovery of cathepsin L","volume":"18","author":"Li","year":"2023","journal-title":"Expert Opin. Drug Discov."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1002\/cmdc.201300112","article-title":"Optimization of triazine nitriles as rhodesain inhibitors: Structure-activity relationships, bioisosteric imidazopyridine nitriles, and X-ray crystal structure analysis with human cathepsin L","volume":"8","author":"Ehmke","year":"2013","journal-title":"ChemMedChem"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"7048","DOI":"10.1021\/acs.jmedchem.3c02351","article-title":"Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors","volume":"67","author":"Falke","year":"2024","journal-title":"J. Med. Chem."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1002\/pro.5560060421","article-title":"Expression of human cathepsin K in Pichia pastoris and preliminary crystallographic studies of an inhibitor complex","volume":"6","author":"Linnevers","year":"1997","journal-title":"Protein Sci."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1016\/j.bmcl.2004.11.012","article-title":"Tellurium-based cysteine protease inhibitors: Evaluation of novel organotellurium(IV) compounds as inhibitors of human cathepsin B","volume":"15","author":"Cunha","year":"2005","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"3383","DOI":"10.1002\/cbic.202000371","article-title":"Peptidyl Acyloxymethyl Ketones as Activity-Based Probes for the Main Protease of SARS- CoV-2","volume":"21","author":"Verhelst","year":"2020","journal-title":"ChemBioChem"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1021\/acsinfecdis.2c00091","article-title":"Pyronaridine Protects against SARS-CoV-2 Infection in Mouse","volume":"8","author":"Puhl","year":"2022","journal-title":"ACS Inf. Dis."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1002\/ddr.21982","article-title":"Celastrol: A lead compound that inhibits SARS-CoV-2 replication, the activity of viral and human cysteine proteases, and virus-induced IL-6 secretion","volume":"83","author":"Fuzo","year":"2022","journal-title":"Drug Dev. Res."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1782","DOI":"10.1002\/jcc.1131","article-title":"Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds","volume":"22","author":"Ewig","year":"2001","journal-title":"J. Comput. Chem."},{"key":"ref_70","first-page":"1","article-title":"Unconstrained optimization","volume":"Volume 1","author":"Fletcher","year":"1980","journal-title":"Practical Methods of Optimization"},{"key":"ref_71","unstructured":"Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Petersson, G.A., and Nakatsuji, H. (2016). Gaussian 16, Revision C.01, Gaussian, Inc."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1063\/1.449486","article-title":"Natural Population Analysis","volume":"83","author":"Reed","year":"1985","journal-title":"J. Chem. Phys."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1038\/s41467-021-20900-6","article-title":"A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication","volume":"12","author":"Hattori","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1107\/S2052252521001159","article-title":"Crystallographic models of SARS-CoV-2 3CLpro: In-depth assessment of structure quality and validation","volume":"8 Pt 2","author":"Jaskolski","year":"2021","journal-title":"IUCrJ"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: A program to check the stereochemical quality of protein structures","volume":"26","author":"Laskowski","year":"1993","journal-title":"J. Appl. Crystallogr."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of Simple Potential Functions for Simulating Liquid Water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J. Chem. Phys."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/jcc.21367","article-title":"CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields","volume":"31","author":"Vanommeslaeghe","year":"2010","journal-title":"J. Comput. Chem."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1103\/PhysRevA.31.1695","article-title":"Canonical Dynamics: Equilibrium Phase-Space Distributions","volume":"31","author":"Hoover","year":"1985","journal-title":"Phys. Rev. A"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"4613","DOI":"10.1063\/1.470648","article-title":"Constant Pressure Molecular Dynamics Simulation: The Langevin Piston Method","volume":"103","author":"Feller","year":"1995","journal-title":"J. Chem. Phys."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","article-title":"Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes","volume":"23","author":"Ryckaert","year":"1977","journal-title":"J. Comput. Phys."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle Mesh Ewald: An N\u00b7log(N) Method for Ewald Sums in Large Systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1002\/jcc.540150207","article-title":"Derivation of Class II Force Fields. I. Methodology and Quantum Force Field for the Alkyl Functional Group and Alkane Molecules","volume":"15","author":"Maple","year":"1994","journal-title":"J. Comput. Chem."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucl. Acids Res."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"2359","DOI":"10.1002\/jcc.21816","article-title":"SwissParam: A fast force field generation tool for small organic molecules","volume":"32","author":"Zoete","year":"2011","journal-title":"J. Comput. Chem."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"W331","DOI":"10.1093\/nar\/gkx312","article-title":"LigParGen web server: An automatic OPLS-AA parameter generator for organic ligands","volume":"45","author":"Dodda","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1002\/pro.2733","article-title":"Covalent docking using autodock: Two-point attractor and flexible side chain methods","volume":"25","author":"Bianco","year":"2016","journal-title":"Protein Sci."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development of Coot","volume":"66 Pt 4","author":"Emsley","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"10497","DOI":"10.1021\/acs.jmedchem.9b00683","article-title":"Can Cysteine Protease Cross-Class Inhibitors Achieve Selectivity?","volume":"62","author":"Cianni","year":"2019","journal-title":"J. Med. Chem."}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/30\/19\/3896\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T10:55:03Z","timestamp":1759229703000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/30\/19\/3896"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,26]]},"references-count":88,"journal-issue":{"issue":"19","published-online":{"date-parts":[[2025,10]]}},"alternative-id":["molecules30193896"],"URL":"https:\/\/doi.org\/10.3390\/molecules30193896","relation":{},"ISSN":["1420-3049"],"issn-type":[{"type":"electronic","value":"1420-3049"}],"subject":[],"published":{"date-parts":[[2025,9,26]]}}}