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GC-376, a peptidomimetic 3CL protease inhibitor, has shown significant efficacy against coronaviruses. Recently, a GC-376-based PROTAC was developed to target and induce the proteasome-mediated degradation of the dimeric SARS-CoV-2 3CLPro protein. Extending this approach, the current study investigates the application of the GC-376 PROTAC to the 3CPro protease of enteroviruses, specifically characterizing its interaction with CVB3 3CPro through X-ray crystallography, NMR (Nuclear Magnetic Resonance) and biochemical techniques. The crystal structure of CVB3 3CPro bound to the GC-376 PROTAC precursor was obtained at 1.9 \u00c5 resolution. The crystallographic data show that there are some changes between the binding of CVB3 3CPro and SARS-CoV-2 3CLPro, but the overall similarity is strong (RMSD on C-alpha 0.3 \u00c5). The most notable variation is the orientation of the benzyloxycarbonyl group of GC-376 with the S4 subsite of the proteases. NMR backbone assignment of CVB3 3CPro bound and unbound to the GC-376 PROTAC precursor (80% and 97%, respectively) was obtained. This information complemented the investigation, by NMR, of the interaction of CVB3 3CPro with the GC-376 PROTAC, and its precursor allows us to define that the GC-376 PROTAC binds to CVB3 3CPro in a mode very similar to that of the precursor. The NMR relaxation data indicate that a quench of dynamics of a large part of the protein backbone involving the substrate-binding site and surrounding regions occurs upon GC-376 PROTAC precursor binding. This suggests that the substrate cavity, by sampling different backbone conformations in the absence of the substrate, is able to select the suitable one necessary to covalently bind the substrate, this being the latter reaction, which is the fundamental step required to functionally activate the enzymatic reaction. The inhibition activity assay showed inhibition potency in the micromolar range for GC-376 PROTAC and its precursor. Overall, we can conclude that the GC-376 PROTAC fits well within the binding sites of both proteases, demonstrating its potential as a broad-spectrum antiviral agent.<\/jats:p>","DOI":"10.3390\/biom14101260","type":"journal-article","created":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T06:23:18Z","timestamp":1728282198000},"page":"1260","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["A Structural Investigation of the Interaction between a GC-376-Based Peptidomimetic PROTAC and Its Precursor with the Viral Main Protease of Coxsackievirus B3"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-8685-7648","authenticated-orcid":false,"given":"Alessia","family":"De Santis","sequence":"first","affiliation":[{"name":"Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy"},{"name":"Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deborah","family":"Grifagni","sequence":"additional","affiliation":[{"name":"Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy"},{"name":"Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Orsetti","sequence":"additional","affiliation":[{"name":"Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy"},{"name":"Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7408-2828","authenticated-orcid":false,"given":"Elena","family":"Lenci","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6172-0368","authenticated-orcid":false,"given":"Antonio","family":"Rosato","sequence":"additional","affiliation":[{"name":"Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy"},{"name":"Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8699-0847","authenticated-orcid":false,"given":"Mariapina","family":"D\u2019Onofrio","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1774-9301","authenticated-orcid":false,"given":"Andrea","family":"Trabocchi","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2376-3321","authenticated-orcid":false,"given":"Simone","family":"Ciofi-Baffoni","sequence":"additional","affiliation":[{"name":"Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy"},{"name":"Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0526-6732","authenticated-orcid":false,"given":"Francesca","family":"Cantini","sequence":"additional","affiliation":[{"name":"Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy"},{"name":"Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7963-6241","authenticated-orcid":false,"given":"Vito","family":"Calderone","sequence":"additional","affiliation":[{"name":"Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy"},{"name":"Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,10,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1146\/annurev-biochem-060310-170328","article-title":"The ubiquitin code","volume":"81","author":"Komander","year":"2012","journal-title":"Annu. Rev. Biochem."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1146\/annurev-biochem-060815-014922","article-title":"Ubiquitin Ligases: Structure, Function, and Regulation","volume":"86","author":"Zheng","year":"2017","journal-title":"Annu. Rev. Biochem."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.cell.2016.03.003","article-title":"Types of Ubiquitin Ligases","volume":"165","author":"Morreale","year":"2016","journal-title":"Cell"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1146\/annurev.biochem.78.101807.093809","article-title":"RING domain E3 ubiquitin ligases","volume":"78","author":"Deshaies","year":"2009","journal-title":"Annu. Rev. Biochem."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/nrm2673","article-title":"Ubiquitin-like protein activation by E1 enzymes: The apex for downstream signalling pathways","volume":"10","author":"Schulman","year":"2009","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1038\/nrm2780","article-title":"Building ubiquitin chains: E2 enzymes at work","volume":"10","author":"Ye","year":"2009","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1146\/annurev.biochem.78.081507.101607","article-title":"Recognition and processing of ubiquitin-protein conjugates by the proteasome","volume":"78","author":"Finley","year":"2009","journal-title":"Annu. Rev. Biochem."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"5214","DOI":"10.1039\/D2CS00193D","article-title":"PROTACs: Past, present and future","volume":"51","author":"Li","year":"2022","journal-title":"Chem. Soc. Rev."},{"key":"ref_9","unstructured":"Jones, M.K.L.H. (2022). PROTAC Degraders Mechanism, Recent Advances, and Future Challenges. Protein Homeostasis in Drug Discovery: A Chemical Biology Perspective, John Wiley & Sons, Inc."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1002\/anie.201507978","article-title":"Small-Molecule PROTACS: New Approaches to Protein Degradation","volume":"55","author":"Toure","year":"2016","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"6495","DOI":"10.1021\/acs.jmedchem.3c02416","article-title":"Discovery of First-in-Class PROTAC Degraders of SARS-CoV-2 Main Protease","volume":"67","author":"Alugubelli","year":"2024","journal-title":"J. Med. Chem."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1021\/acsmedchemlett.3c00498","article-title":"Development of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3-Chymotrypsin-like Protease of SARS-CoV-2","volume":"15","author":"Grifagni","year":"2024","journal-title":"ACS Med. Chem. Lett."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"116202","DOI":"10.1016\/j.ejmech.2024.116202","article-title":"Design, synthesis, and biological evaluation of first-in-class indomethacin-based PROTACs degrading SARS-CoV-2 main protease and with broad-spectrum antiviral activity","volume":"268","author":"Desantis","year":"2024","journal-title":"Eur. J. Med. Chem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"27248","DOI":"10.1021\/jacs.3c12678","article-title":"A Chemical Strategy for the Degradation of the Main Protease of SARS-CoV-2 in Cells","volume":"145","author":"Sang","year":"2023","journal-title":"J. Am. Chem. Soc."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1038\/s41422-020-0356-z","article-title":"Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease","volume":"30","author":"Ma","year":"2020","journal-title":"Cell Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"11754","DOI":"10.1128\/JVI.01348-12","article-title":"Broad-spectrum antivirals against 3C or 3C-like proteases of picornaviruses, noroviruses, and coronaviruses","volume":"86","author":"Kim","year":"2012","journal-title":"J. Virol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1093\/jb\/mvad113","article-title":"Protein degraders\u2014From thalidomide to new PROTACs","volume":"175","author":"Ito","year":"2024","journal-title":"J. Biochem."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"4771","DOI":"10.1182\/blood-2011-05-356063","article-title":"Cereblon expression is required for the antimyeloma activity of lenalidomide and pomalidomide","volume":"118","author":"Zhu","year":"2011","journal-title":"Blood"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1111\/bjh.12708","article-title":"Immunomodulatory agents lenalidomide and pomalidomide co-stimulate T cells by inducing degradation of T cell repressors Ikaros and Aiolos via modulation of the E3 ubiquitin ligase complex CRL4(CRBN.)","volume":"164","author":"Gandhi","year":"2014","journal-title":"Br. J. Haematol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2466","DOI":"10.1016\/j.bmc.2019.02.048","article-title":"Cereblon versus VHL: Hijacking E3 ligases against each other using PROTACs","volume":"27","author":"Girardini","year":"2019","journal-title":"Bioorg. Med. Chem."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"8216","DOI":"10.1039\/D2CS00387B","article-title":"Discovery of small molecule ligands for the von Hippel-Lindau (VHL) E3 ligase and their use as inhibitors and PROTAC degraders","volume":"51","author":"Diehl","year":"2022","journal-title":"Chem. Soc. Rev."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1763","DOI":"10.1126\/science.1085658","article-title":"Coronavirus main proteinase (3CLpro) structure: Basis for design of anti-SARS drugs","volume":"300","author":"Anand","year":"2003","journal-title":"Science"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1080\/14728222.2021.1952985","article-title":"Enteroviruses and coronaviruses: Similarities and therapeutic targets","volume":"25","author":"Kalander","year":"2021","journal-title":"Expert Opin. Ther. Targets"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1968","DOI":"10.1007\/s00284-020-02082-4","article-title":"The Function and Mechanism of Enterovirus 71 (EV71) 3C Protease","volume":"77","author":"Wen","year":"2020","journal-title":"Curr. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1002\/rmv.1883","article-title":"Enteroviral proteases: Structure, host interactions and pathogenicity","volume":"26","author":"Laitinen","year":"2016","journal-title":"Rev. Med. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"4339","DOI":"10.1128\/JVI.01123-12","article-title":"3C protease of enterovirus 68: Structure-based design of Michael acceptor inhibitors and their broad-spectrum antiviral effects against picornaviruses","volume":"87","author":"Tan","year":"2013","journal-title":"J. Virol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1615","DOI":"10.1134\/S0006297917130041","article-title":"Enteroviruses: Classification, Diseases They Cause, and Approaches to Development of Antiviral Drugs","volume":"82","author":"Nikonov","year":"2017","journal-title":"Biochem. Biokhimiia"},{"key":"ref_28","first-page":"1","article-title":"Immunopathological basis of virus-induced myocarditis","volume":"11","author":"Maier","year":"2004","journal-title":"Clin. Dev. Immunol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e23","DOI":"10.2741\/928","article-title":"Coxsackievirus experimental heart diseases","volume":"8","author":"Gauntt","year":"2003","journal-title":"Front. Biosci."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1097\/MOP.0000000000000303","article-title":"Enteroviruses in the early 21st century: New manifestations and challenges","volume":"28","author":"Lugo","year":"2016","journal-title":"Curr. Opin. Pediatr."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e0133222","DOI":"10.1128\/jvi.01332-22","article-title":"Enterovirus 3C Protease Cleaves TRIM7 To Dampen Its Antiviral Activity","volume":"96","author":"Fan","year":"2022","journal-title":"J. Virol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/0014-5793(89)80109-7","article-title":"Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. A distinct protein superfamily with a common structural fold","volume":"243","author":"Gorbalenya","year":"1989","journal-title":"FEBS Lett."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1074\/jbc.M310875200","article-title":"Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase","volume":"279","author":"Fan","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"4562","DOI":"10.1021\/acs.jmedchem.9b01828","article-title":"\u03b1-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment","volume":"63","author":"Zhang","year":"2020","journal-title":"J. Med. Chem."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"3213","DOI":"10.1093\/emboj\/cdf327","article-title":"Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain","volume":"21","author":"Anand","year":"2002","journal-title":"Embo J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/S0006-291X(67)80055-X","article-title":"On the size of the active site in proteases. I. Papain","volume":"27","author":"Schechter","year":"1967","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Singh, E., Khan, R.J., Jha, R.K., Amera, G.M., Jain, M., Singh, R.P., Muthukumaran, J., and Singh, A.K. (2020). A comprehensive review on promising anti-viral therapeutic candidates identified against main protease from SARS-CoV-2 through various computational methods. J. Genet. Eng. Biotechnol., 18.","DOI":"10.1186\/s43141-020-00085-z"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Azevedo, P., Camargo, P.G., Constant, L.E.C., Costa, S.D.S., Silva, C.S., Rosa, A.S., Souza, D.D.C., Tucci, A.R., Ferreira, V.N.S., and Oliveira, T.K.F. (2024). Statine-based peptidomimetic compounds as inhibitors for SARS-CoV-2 main protease (SARS-CoV-2 Mpro). Sci. Rep., 14.","DOI":"10.1038\/s41598-024-59442-4"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Hayek-Orduz, Y., V\u00e1squez, A.F., Villegas-Torres, M.F., Caicedo, P.A., Achenie, L.E.K., and Gonz\u00e1lez Barrios, A.F. (2022). Novel covalent and non-covalent complex-based pharmacophore models of SARS-CoV-2 main protease (M(pro)) elucidated by microsecond MD simulations. Sci. Rep., 12.","DOI":"10.1038\/s41598-022-17204-0"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"105458","DOI":"10.1016\/j.antiviral.2022.105458","article-title":"Structure and inhibition of SARS-CoV-1 and SARS-CoV-2 main proteases by oral antiviral compound AG7404","volume":"208","author":"Bueno","year":"2022","journal-title":"Antivir. Res."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"G\u00f6hl, M., Zhang, L., El Kilani, H., Sun, X., Zhang, K., Br\u00f6nstrup, M., and Hilgenfeld, R. (2022). From Repurposing to Redesign: Optimization of Boceprevir to Highly Potent Inhibitors of the SARS-CoV-2 Main Protease. Molecules, 27.","DOI":"10.3390\/molecules27134292"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2925","DOI":"10.1021\/acs.biochem.1c00414","article-title":"Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode","volume":"60","author":"Lockbaum","year":"2021","journal-title":"Biochemistry"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2794","DOI":"10.1021\/acs.jmedchem.0c02258","article-title":"Design, Synthesis, and Biological Evaluation of Peptidomimetic Aldehydes as Broad-Spectrum Inhibitors against Enterovirus and SARS-CoV-2","volume":"65","author":"Dai","year":"2022","journal-title":"J. Med. Chem."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"7849","DOI":"10.1016\/j.bmc.2010.09.050","article-title":"Synthesis and evaluation of pyrazolone compounds as SARS-coronavirus 3C-like protease inhibitors","volume":"18","author":"Ramajayam","year":"2010","journal-title":"Bioorg. Med. Chem."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1371","DOI":"10.1042\/BST0391371","article-title":"Recent development of 3C and 3CL protease inhibitors for anti-coronavirus and anti-picornavirus drug discovery","volume":"39","author":"Ramajayam","year":"2011","journal-title":"Biochem. Soc. Trans."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"3709","DOI":"10.1016\/j.bmcl.2013.05.021","article-title":"Macrocyclic inhibitors of 3C and 3C-like proteases of picornavirus, norovirus, and coronavirus","volume":"23","author":"Mandadapu","year":"2013","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.antiviral.2017.02.007","article-title":"Identification and evaluation of potent Middle East respiratory syndrome coronavirus (MERS-CoV) 3CL(Pro) inhibitors","volume":"141","author":"Kumar","year":"2017","journal-title":"Antivir. Res."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"7646","DOI":"10.1074\/jbc.M807947200","article-title":"Structural basis of inhibition specificities of 3C and 3C-like proteases by zinc-coordinating and peptidomimetic compounds","volume":"284","author":"Lee","year":"2009","journal-title":"J. Biol. Chem."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1016\/j.febslet.2008.12.059","article-title":"Individual and common inhibitors of coronavirus and picornavirus main proteases","volume":"583","author":"Kuo","year":"2009","journal-title":"FEBS Lett."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1107\/S2053230X16018513","article-title":"Coxsackievirus B3 protease 3C: Expression, purification, crystallization and preliminary structural insights","volume":"72","author":"Fili","year":"2016","journal-title":"Acta Crystallogr. Sect. F Struct. Biol. Commun."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1107\/S0907444909047337","article-title":"XDS","volume":"66","author":"Kabsch","year":"2010","journal-title":"Acta Crystallogr. D. Biol. Crystallogr."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1107\/S0907444900013780","article-title":"An approach to multi-copy search in molecular replacement","volume":"56","author":"Vagin","year":"2000","journal-title":"Acta Cryst. D"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1107\/S0907444909052925","article-title":"PHENIX: A comprehensive Python-based system for macromolecular structure solution","volume":"66","author":"Adams","year":"2010","journal-title":"Acta Crystallogr. D. Biol. Crystallogr."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development of Coot","volume":"66","author":"Emsley","year":"2010","journal-title":"Acta Cryst. D"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1107\/S0907444909042073","article-title":"MolProbity: All-atom structure validation for macromolecular crystallography","volume":"66","author":"Chen","year":"2010","journal-title":"Acta Cryst. D"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1007\/BF00178261","article-title":"Amino acid type determination in the sequential assignment procedure of uniformly 13C\/15N-enriched proteins","volume":"3","author":"Grzesiek","year":"1993","journal-title":"J. Biomol. NMR"},{"key":"ref_57","unstructured":"Keller, R. (2004). The Computer Aided Resonance Assignment Tutorial, Cantina."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.pnmrs.2013.02.001","article-title":"Using chemical shift perturbation to characterise ligand binding","volume":"73","author":"Williamson","year":"2013","journal-title":"Prog. Nucl. Magn. Reson. Spectrosc."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"5984","DOI":"10.1021\/bi00185a040","article-title":"Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation","volume":"33","author":"Farrow","year":"1994","journal-title":"Biochemistry"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"12593","DOI":"10.1021\/ja00079a052","article-title":"The Importance of Not Saturating H2o in Protein Nmr\u2014Application to Sensitivity Enhancement and Noe Measurements","volume":"115","author":"Grzesiek","year":"1993","journal-title":"J. Am. Chem. Soc."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1006\/jmbi.1994.0073","article-title":"Backbone dynamics of Escherichia coli ribonuclease HI: Correlations with structure and function in an active enzyme","volume":"246","author":"Mandel","year":"1995","journal-title":"J. Mol. Biol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1006\/jmre.2000.2170","article-title":"HYDRONMR: Prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations","volume":"147","author":"Huertas","year":"2000","journal-title":"J. Magn. Reson."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"11000","DOI":"10.1073\/pnas.96.20.11000","article-title":"Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes","volume":"96","author":"Matthews","year":"1999","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"2016","DOI":"10.1021\/jm010435c","article-title":"Structure-based design of a parallel synthetic array directed toward the discovery of irreversible inhibitors of human rhinovirus 3C protease","volume":"45","author":"Johnson","year":"2002","journal-title":"J. Med. Chem."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"8933","DOI":"10.1021\/ja049297h","article-title":"A simple method for improving protein solubility and long-term stability","volume":"126","author":"Golovanov","year":"2004","journal-title":"J. Am. Chem. Soc."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"7388","DOI":"10.1016\/j.bmc.2008.06.015","article-title":"Design, synthesis, and evaluation of 3C protease inhibitors as anti-enterovirus 71 agents","volume":"16","author":"Kuo","year":"2008","journal-title":"Bioorg. Med. Chem."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"4417","DOI":"10.1038\/s41467-020-18233-x","article-title":"Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease","volume":"11","author":"Fu","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Lin, C., Zhu, Z., Jiang, H., Zou, X., Zeng, X., Wang, J., Zeng, P., Li, W., Zhou, X., and Zhang, J. (2024). Structural Basis for Coronaviral Main Proteases Inhibition by the 3CLpro Inhibitor GC376. J. Mol. Biol., 436.","DOI":"10.1016\/j.jmb.2024.168474"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"116629","DOI":"10.1016\/j.ejmech.2024.116629","article-title":"Development of novel antivrial agents that induce the degradation of the main protease of human-infecting coronaviruses","volume":"275","author":"Cheng","year":"2024","journal-title":"Eur. J. Med. Chem."}],"container-title":["Biomolecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-273X\/14\/10\/1260\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:11:25Z","timestamp":1760112685000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-273X\/14\/10\/1260"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,6]]},"references-count":69,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2024,10]]}},"alternative-id":["biom14101260"],"URL":"https:\/\/doi.org\/10.3390\/biom14101260","relation":{},"ISSN":["2218-273X"],"issn-type":[{"value":"2218-273X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,6]]}}}