Selective Degradation and Inhibition of SARS-CoV-2 3CLpro by MMP14 Reveals a Novel Strategy for COVID-19 Therapeutics

DOI record: { "DOI": "10.3390/ijms26199401", "ISSN": [ "1422-0067" ], "URL": "http://dx.doi.org/10.3390/ijms26199401", "abstract": "<jats:p>Novel therapies to treat infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of respiratory coronavirus disease 2019 (COVID-19), would be of great clinical value to combat the current and future pandemics. Two viral proteases, papain-like protease (PLpro) and the main protease 3-chymotrypsin-like protease (3CLpro), are vital in processing the SARS-CoV-2 polyproteins (pp1a and pp1ab) and in releasing 16 nonstructural proteins, making them attractive antiviral drug targets. In this study, we investigated the degradation of the SARS-CoV-2 main protease 3CLpro by matrix metalloproteinase-14 (MMP14). MMP14 is known to recognize over 10 distinct substrate cleavage sequences. Through sequence analysis, we identified 17 and 10 putative MMP14 cleavage motifs within the SARS-CoV-2 3CLpro and PLpro proteases, respectively. Despite the presence of potential sites in both proteins, our in vitro proteolysis assays demonstrated that MMP14 selectively binds to and degrades 3CLpro, but not PLpro. This selective proteolysis by MMP14 results in the complete loss of 3CLpro enzymatic activity. In addition, SARS-CoV-2 pseudovirus replication was inhibited in 293 T cells when either full-length MMP14 or its catalytic domain (cat-MMP14) were overexpressed, presumably due to 3CLpro degradation by MMP14. Finally, to prevent MMP14 from degrading off-target proteins, we propose a new recombinant pro-PL-MMP14 construct that can be activated only by another SARS-CoV-2 protease, PLpro. These findings could open the potential of an alternative therapeutic strategy against SARS-CoV-2 infection.</jats:p>", "alternative-id": [ "ijms26199401" ], "author": [ { "ORCID": "https://orcid.org/0000-0003-2570-8120", "affiliation": [ { "name": "Department of Pharmaceutical Science, College of Pharmacy & Biophysics Core, the Research Resource Center, University of Illinois Chicago, Chicago, IL 60607, USA" }, { "name": "Biophysics Core, the Research Resource Center, University of Illinois Chicago, Chicago, IL 60607, USA" } ], "authenticated-orcid": false, "family": "Lee", "given": "Hyun", "sequence": "first" }, { "affiliation": [ { "name": "Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA" } ], "family": "Hwang", "given": "Yunjeong", "sequence": "additional" }, { "ORCID": "https://orcid.org/0000-0002-8613-2340", "affiliation": [ { "name": "Biophysics Core, the Research Resource Center, University of Illinois Chicago, Chicago, IL 60607, USA" } ], "authenticated-orcid": false, "family": "Mulder", "given": "Elizabeth J.", "sequence": "additional" }, { "affiliation": [ { "name": "Biophysics Core, the Research Resource Center, University of Illinois Chicago, Chicago, IL 60607, USA" } ], "family": "Song", "given": "Yuri", "sequence": "additional" }, { "affiliation": [ { "name": "Biophysics Core, the Research Resource Center, University of Illinois Chicago, Chicago, IL 60607, USA" } ], "family": "Choi", "given": "Calista", "sequence": "additional" }, { "affiliation": [ { "name": "Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA" } ], "family": "Rong", "given": "Lijun", "sequence": "additional" }, { "affiliation": [ { "name": "Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA" } ], "family": "Azar", "given": "Dimitri T.", "sequence": "additional" }, { "affiliation": [ { "name": "Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA" } ], "family": "Han", "given": "Kyu-Yeon", "sequence": "additional" } ], "container-title": "International Journal of Molecular Sciences", "container-title-short": "IJMS", "content-domain": { "crossmark-restriction": true, "domain": [ "www.mdpi.com" ] }, "created": { "date-parts": [ [ 2025, 9, 26 ] ], "date-time": "2025-09-26T08:31:28Z", "timestamp": 1758875488000 }, "deposited": { "date-parts": [ [ 2025, 9, 26 ] ], "date-time": "2025-09-26T08:37:28Z", "timestamp": 1758875848000 }, "funder": [ { "DOI": "10.13039/100000002", "award": [ "R01 R01EY033758 (NEI)", "R21AI168744 (NIAID)", "P30 EY001792 (NEI)" ], "doi-asserted-by": "crossref", "id": [ { "asserted-by": "crossref", "id": "10.13039/100000002", "id-type": "DOI" } ], "name": "National Institutes of Health" }, { "award": [ "G1781" ], "name": "Eversight" } ], "indexed": { "date-parts": [ [ 2025, 9, 26 ] ], "date-time": "2025-09-26T09:10:08Z", "timestamp": 1758877808115, "version": "3.44.0" }, "is-referenced-by-count": 0, "issue": "19", "issued": { "date-parts": [ [ 2025, 9, 26 ] ] }, "journal-issue": { "issue": "19", "published-online": { "date-parts": [ [ 2025, 10 ] ] } }, "language": "en", "license": [ { "URL": "https://creativecommons.org/licenses/by/4.0/", "content-version": "vor", "delay-in-days": 0, "start": { "date-parts": [ [ 2025, 9, 26 ] ], "date-time": "2025-09-26T00:00:00Z", "timestamp": 1758844800000 } } ], "link": [ { "URL": "https://www.mdpi.com/1422-0067/26/19/9401/pdf", "content-type": "unspecified", "content-version": "vor", "intended-application": "similarity-checking" } ], "member": "1968", "original-title": [], "page": "9401", "prefix": "10.3390", "published": { "date-parts": [ [ 2025, 9, 26 ] ] }, "published-online": { "date-parts": [ [ 2025, 9, 26 ] ] }, "publisher": "MDPI AG", "reference": [ { "DOI": "10.1056/NEJMoa030781", "article-title": "A novel coronavirus associated with severe acute respiratory syndrome", "author": "Ksiazek", "doi-asserted-by": "crossref", "first-page": "1953", "journal-title": "N. 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