SARS-CoV-2 Mpro inhibitors and activity-based probes for patient-sample imaging

Wioletta Rut; Katarzyna Groborz; Linlin Zhang; Xinyuanyuan Sun; Mikolaj Zmudzinski; Bartlomiej Pawlik; Xinyu Wang; Dirk Jochmans; Johan Neyts; Wojciech Młynarski; Rolf Hilgenfeld; Marcin Drag

doi:10.1038/s41589-020-00689-z

SARS-CoV-2 M^pro inhibitors and activity-based probes for patient-sample imaging

Wioletta Rut^*, Katarzyna Groborz, Linlin Zhang, Xinyuanyuan Sun, Mikolaj Zmudzinski, Bartlomiej Pawlik, Xinyu Wang, Dirk Jochmans, Johan Neyts, Wojciech Młynarski, Rolf Hilgenfeld, Marcin Drag

^*Corresponding author for this work

Institute of Biochemistry

Abstract

In December 2019, the first cases of infection with a novel coronavirus, SARS-CoV-2, were diagnosed. Currently, there is no effective antiviral treatment for COVID-19. To address this emerging problem, we focused on the SARS-CoV-2 main protease that constitutes one of the most attractive antiviral drug targets. We have synthesized a combinatorial library of fluorogenic substrates with glutamine in the P1 position. We used it to determine the substrate preferences of the SARS-CoV and SARS-CoV-2 main proteases. On the basis of these findings, we designed and synthesized a potent SARS-CoV-2 inhibitor (Ac-Abu-dTyr-Leu-Gln-VS, half-maximal effective concentration of 3.7 µM) and two activity-based probes, for one of which we determined the crystal structure of its complex with the SARS-CoV-2 M^pro. We visualized active SARS-CoV-2 M^pro in nasopharyngeal epithelial cells of patients suffering from COVID-19 infection. The results of our work provide a structural framework for the design of inhibitors as antiviral agents and/or diagnostic tests. [Figure not available: see fulltext.].

Original language	English
Journal	Nature Chemical Biology
ISSN	1552-4450
DOIs	https://doi.org/10.1038/s41589-020-00689-z
Publication status	Published - 22.10.2020

Funding

The Drag laboratory is supported by the National Science Center in Poland and the ‘TEAM/2017-4/32’ project, which is conducted within the TEAM program of the Foundation for Polish Science cofinanced by the European Union under the European Regional Development Fund. Work in the Hilgenfeld laboratory was supported by the SCORE project of the European Union (grant agreement no. 101003627), by DZIF and by the Government of Schleswig-Holstein through its Structure and Excellence Fund, as well as by a close partnership between the Possehl Foundation (Lübeck) and the University of Lübeck. Work in the Neyts laboratory was similarly supported by the SCORE project of the European Union (grant agreement no. 101003627). X.W. received funding of the China Scholarship Council (grant no. 201806170087). L.Z. is supported by a stipend from DZIF. W.R. is a beneficiary of a START scholarship from the Foundation for Polish Science. The Mlynarski laboratory (B.P. and W.M.) is supported by the FIXNET project, which is conducted within the TEAM-NET program of the Foundation for Polish Science cofinanced by the European Union under the European Regional Development Fund (no POIR.04.04.00-00-1603/18). We thank A. Piekarska (Medical University of Lodz, Poland) for an expert consultation in clinical assessments of patients with COVID-19.

Research Areas and Centers

Academic Focus: Center for Infection and Inflammation Research (ZIEL)

DFG Research Classification Scheme

2.11-01 Biochemistry

Coronavirus related work

Research on SARS-CoV-2 / COVID-19

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1038/s41589-020-00689-z

Cite this

@article{bd81096eb24e40c6a1fd27a4097c6cf3,

title = "SARS-CoV-2 Mpro inhibitors and activity-based probes for patient-sample imaging",

abstract = "In December 2019, the first cases of infection with a novel coronavirus, SARS-CoV-2, were diagnosed. Currently, there is no effective antiviral treatment for COVID-19. To address this emerging problem, we focused on the SARS-CoV-2 main protease that constitutes one of the most attractive antiviral drug targets. We have synthesized a combinatorial library of fluorogenic substrates with glutamine in the P1 position. We used it to determine the substrate preferences of the SARS-CoV and SARS-CoV-2 main proteases. On the basis of these findings, we designed and synthesized a potent SARS-CoV-2 inhibitor (Ac-Abu-dTyr-Leu-Gln-VS, half-maximal effective concentration of 3.7 µM) and two activity-based probes, for one of which we determined the crystal structure of its complex with the SARS-CoV-2 Mpro. We visualized active SARS-CoV-2 Mpro in nasopharyngeal epithelial cells of patients suffering from COVID-19 infection. The results of our work provide a structural framework for the design of inhibitors as antiviral agents and/or diagnostic tests. [Figure not available: see fulltext.].",

author = "Wioletta Rut and Katarzyna Groborz and Linlin Zhang and Xinyuanyuan Sun and Mikolaj Zmudzinski and Bartlomiej Pawlik and Xinyu Wang and Dirk Jochmans and Johan Neyts and Wojciech M{\l}ynarski and Rolf Hilgenfeld and Marcin Drag",

note = "Funding Information: The Drag laboratory is supported by the National Science Center in Poland and the {\textquoteleft}TEAM/2017-4/32{\textquoteright} project, which is conducted within the TEAM program of the Foundation for Polish Science cofinanced by the European Union under the European Regional Development Fund. Work in the Hilgenfeld laboratory was supported by the SCORE project of the European Union (grant agreement no. 101003627), by DZIF and by the Government of Schleswig-Holstein through its Structure and Excellence Fund, as well as by a close partnership between the Possehl Foundation (L{\"u}beck) and the University of L{\"u}beck. Work in the Neyts laboratory was similarly supported by the SCORE project of the European Union (grant agreement no. 101003627). X.W. received funding of the China Scholarship Council (grant no. 201806170087). L.Z. is supported by a stipend from DZIF. W.R. is a beneficiary of a START scholarship from the Foundation for Polish Science. The Mlynarski laboratory (B.P. and W.M.) is supported by the FIXNET project, which is conducted within the TEAM-NET program of the Foundation for Polish Science cofinanced by the European Union under the European Regional Development Fund (no POIR.04.04.00-00-1603/18). We thank A. Piekarska (Medical University of Lodz, Poland) for an expert consultation in clinical assessments of patients with COVID-19. Publisher Copyright: {\textcopyright} 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",

year = "2020",

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day = "22",

doi = "10.1038/s41589-020-00689-z",

language = "English",

journal = "Nature Chemical Biology",

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T1 - SARS-CoV-2 Mpro inhibitors and activity-based probes for patient-sample imaging

AU - Rut, Wioletta

AU - Groborz, Katarzyna

AU - Zhang, Linlin

AU - Sun, Xinyuanyuan

AU - Zmudzinski, Mikolaj

AU - Pawlik, Bartlomiej

AU - Wang, Xinyu

AU - Jochmans, Dirk

AU - Neyts, Johan

AU - Młynarski, Wojciech

AU - Hilgenfeld, Rolf

AU - Drag, Marcin

N1 - Funding Information: The Drag laboratory is supported by the National Science Center in Poland and the ‘TEAM/2017-4/32’ project, which is conducted within the TEAM program of the Foundation for Polish Science cofinanced by the European Union under the European Regional Development Fund. Work in the Hilgenfeld laboratory was supported by the SCORE project of the European Union (grant agreement no. 101003627), by DZIF and by the Government of Schleswig-Holstein through its Structure and Excellence Fund, as well as by a close partnership between the Possehl Foundation (Lübeck) and the University of Lübeck. Work in the Neyts laboratory was similarly supported by the SCORE project of the European Union (grant agreement no. 101003627). X.W. received funding of the China Scholarship Council (grant no. 201806170087). L.Z. is supported by a stipend from DZIF. W.R. is a beneficiary of a START scholarship from the Foundation for Polish Science. The Mlynarski laboratory (B.P. and W.M.) is supported by the FIXNET project, which is conducted within the TEAM-NET program of the Foundation for Polish Science cofinanced by the European Union under the European Regional Development Fund (no POIR.04.04.00-00-1603/18). We thank A. Piekarska (Medical University of Lodz, Poland) for an expert consultation in clinical assessments of patients with COVID-19. Publisher Copyright: © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

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Y1 - 2020/10/22

N2 - In December 2019, the first cases of infection with a novel coronavirus, SARS-CoV-2, were diagnosed. Currently, there is no effective antiviral treatment for COVID-19. To address this emerging problem, we focused on the SARS-CoV-2 main protease that constitutes one of the most attractive antiviral drug targets. We have synthesized a combinatorial library of fluorogenic substrates with glutamine in the P1 position. We used it to determine the substrate preferences of the SARS-CoV and SARS-CoV-2 main proteases. On the basis of these findings, we designed and synthesized a potent SARS-CoV-2 inhibitor (Ac-Abu-dTyr-Leu-Gln-VS, half-maximal effective concentration of 3.7 µM) and two activity-based probes, for one of which we determined the crystal structure of its complex with the SARS-CoV-2 Mpro. We visualized active SARS-CoV-2 Mpro in nasopharyngeal epithelial cells of patients suffering from COVID-19 infection. The results of our work provide a structural framework for the design of inhibitors as antiviral agents and/or diagnostic tests. [Figure not available: see fulltext.].

AB - In December 2019, the first cases of infection with a novel coronavirus, SARS-CoV-2, were diagnosed. Currently, there is no effective antiviral treatment for COVID-19. To address this emerging problem, we focused on the SARS-CoV-2 main protease that constitutes one of the most attractive antiviral drug targets. We have synthesized a combinatorial library of fluorogenic substrates with glutamine in the P1 position. We used it to determine the substrate preferences of the SARS-CoV and SARS-CoV-2 main proteases. On the basis of these findings, we designed and synthesized a potent SARS-CoV-2 inhibitor (Ac-Abu-dTyr-Leu-Gln-VS, half-maximal effective concentration of 3.7 µM) and two activity-based probes, for one of which we determined the crystal structure of its complex with the SARS-CoV-2 Mpro. We visualized active SARS-CoV-2 Mpro in nasopharyngeal epithelial cells of patients suffering from COVID-19 infection. The results of our work provide a structural framework for the design of inhibitors as antiviral agents and/or diagnostic tests. [Figure not available: see fulltext.].

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DO - 10.1038/s41589-020-00689-z

M3 - Journal articles

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JF - Nature Chemical Biology

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