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

TL;DR

This paper shows that the enzyme MMP14 can selectively destroy a key SARS-CoV-2 protein, 3CLpro, offering a new approach for treating COVID-19.

Contribution

The study reveals that MMP14 can selectively degrade SARS-CoV-2 3CLpro and proposes a novel pro-PL-MMP14 construct for targeted antiviral therapy.

Findings

MMP14 selectively binds to and degrades SARS-CoV-2 3CLpro but not PLpro.

MMP14-mediated degradation of 3CLpro inhibits SARS-CoV-2 pseudovirus replication in 293 T cells.

A recombinant pro-PL-MMP14 construct is proposed to prevent off-target degradation.

Abstract

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.

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