Mechanism of Inhibition of SARS-CoV-2 Mpro by N3 Peptidyl Michael Acceptor Explained by QM/MM Simulations and Design of New Derivatives with Tunable Chemical Reactivity
The SARS-CoV-2 main protease (Mpro) is essential for replication of the virus responsible for the COVID-19 pandemic, and one of the main targets for drug design. Here, we simulate the inhibition process of SARS-CoV-2 Mpro with a known Michael acceptor (peptidyl) inhibitor, N3. The free energy landscape for the mechanism of the formation of the covalent enzyme-inhibitor product is computed with QM/MM molecular dynamics methods. The simulations show a two-step mechanism, and give structures and calculated barriers in good agreement with experiment. Using these results and information from our previous investigation on the proteolysis reaction of SARS-CoV-2 Mpro, we design two new, synthetically accessible N3-analogues as potential inhibitors, in which the recognition and warhead motifs are modified. QM/MM modelling of the mechanism of inhibition of Mpro by these novel compounds indicates that both may be promising candidates as drug leads against COVID-19, one as an irreversible inhibitor and one as a potential reversible inhibitor..
Medienart: |
Preprint |
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Erscheinungsjahr: |
2021 |
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Erschienen: |
2021 |
Enthalten in: |
chemRxiv.org - (2021) vom: 18. Nov. Zur Gesamtaufnahme - year:2021 |
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Sprache: |
Englisch |
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Beteiligte Personen: |
Arafet, Kemel [VerfasserIn] |
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Links: |
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doi: |
10.26434/chemrxiv.12941819 |
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funding: |
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PPN (Katalog-ID): |
XCH018737463 |
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520 | |a The SARS-CoV-2 main protease (Mpro) is essential for replication of the virus responsible for the COVID-19 pandemic, and one of the main targets for drug design. Here, we simulate the inhibition process of SARS-CoV-2 Mpro with a known Michael acceptor (peptidyl) inhibitor, N3. The free energy landscape for the mechanism of the formation of the covalent enzyme-inhibitor product is computed with QM/MM molecular dynamics methods. The simulations show a two-step mechanism, and give structures and calculated barriers in good agreement with experiment. Using these results and information from our previous investigation on the proteolysis reaction of SARS-CoV-2 Mpro, we design two new, synthetically accessible N3-analogues as potential inhibitors, in which the recognition and warhead motifs are modified. QM/MM modelling of the mechanism of inhibition of Mpro by these novel compounds indicates that both may be promising candidates as drug leads against COVID-19, one as an irreversible inhibitor and one as a potential reversible inhibitor. | ||
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700 | 1 | |a Serrano-Aparicio, Natalia |e verfasserin |4 aut | |
700 | 1 | |a Lodola, Alessio |e verfasserin |4 aut | |
700 | 1 | |a Mulholland, Adrian |e verfasserin |4 aut | |
700 | 1 | |a González, Florenci V. |e verfasserin |4 aut | |
700 | 1 | |a Swiderek, Katarzyna |e verfasserin |4 aut | |
700 | 1 | |a Moliner, Vicent |e verfasserin |4 aut | |
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