Evidence for Substrate Binding-Induced Zwitterion Formation in the Catalytic Cys-His Dyad of the SARS-CoV Main Protease
- Publication type:
- Journal article
- Metadata:
-
- Autoren
- Alexander Paasche
- Andreas Zipper
- Simon Schaefer
- John Ziebuhr
- Tanja Schirmeister
- Bernd Engels
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000342184800011&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1021/bi400604t
- Externe Identifier
- Clarivate Analytics Document Solution ID: AP6JT
- PubMed Identifier: 25196915
- ISSN
- 0006-2960
- Ausgabe der Veröffentlichung
- 37
- Zeitschrift
- BIOCHEMISTRY
- Paginierung
- 5930 - 5946
- Datum der Veröffentlichung
- 2014
- Status
- Published
- Titel
- Evidence for Substrate Binding-Induced Zwitterion Formation in the Catalytic Cys-His Dyad of the SARS-CoV Main Protease
- Sub types
- Article
- Ausgabe der Zeitschrift
- 53
Data source: Web of Science (Lite)
- Other metadata sources:
-
- Autoren
- Alexander Paasche
- Andreas Zipper
- Simon Schäfer
- John Ziebuhr
- Tanja Schirmeister
- Bernd Engels
- DOI
- 10.1021/bi400604t
- eISSN
- 1520-4995
- ISSN
- 0006-2960
- Ausgabe der Veröffentlichung
- 37
- Zeitschrift
- Biochemistry
- Sprache
- en
- Online publication date
- 2014
- Paginierung
- 5930 - 5946
- Datum der Veröffentlichung
- 2014
- Status
- Published
- Herausgeber
- American Chemical Society (ACS)
- Herausgeber URL
- http://dx.doi.org/10.1021/bi400604t
- Datum der Datenerfassung
- 2023
- Titel
- Evidence for Substrate Binding-Induced Zwitterion Formation in the Catalytic Cys-His Dyad of the SARS-CoV Main Protease
- Ausgabe der Zeitschrift
- 53
Data source: Crossref
- Abstract
- The coronavirus main protease (M(pro)) represents an attractive drug target for antiviral therapy of coronavirus (CoV) infections, including severe acute respiratory syndrome (SARS). The SARS-CoV M(pro) and related CoV proteases have several distinct features, such as an uncharged Cys-His catalytic dyad embedded in a chymotrypsin-like protease fold, that clearly separate these enzymes from archetypical cysteine proteases. To further characterize the catalytic system of CoV main proteases and to obtain information about improved inhibitors, we performed comprehensive simulations of the proton-transfer reactions in the SARS-CoV M(pro) active site that lead to the Cys(-)/His(+) zwitterionic state required for efficient proteolytic activity. Our simulations, comprising the free enzyme as well as substrate-enzyme and inhibitor-enzyme complexes, lead us to predict that zwitterion formation is fostered by substrate binding but not inhibitor binding. This indicates that M(pro) employs a substrate-induced catalytic mechanism that further enhances its substrate specificity. Our computational data are in line with available experimental results, such as X-ray geometries, measured pKa values, mutagenesis experiments, and the measured differences between the kinetic parameters of substrates and inhibitors. The data also provide an atomistic picture of the formerly postulated electrostatic trigger involved in SARS-CoV M(pro) activity. Finally, they provide information on how a specific microenvironment may finely tune the activity of M(pro) toward specific viral protein substrates, which is known to be required for efficient viral replication. Our simulations also indicate that the low inhibition potencies of known covalently interacting inhibitors may, at least in part, be attributed to insufficient fostering of the proton-transfer reaction. These findings suggest ways to achieve improved inhibitors.
- Addresses
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg , Emil-Fischer-Straße 42, 97074 Würzburg, Germany.
- Autoren
- Alexander Paasche
- Andreas Zipper
- Simon Schäfer
- John Ziebuhr
- Tanja Schirmeister
- Bernd Engels
- DOI
- 10.1021/bi400604t
- eISSN
- 1520-4995
- Externe Identifier
- PubMed Identifier: 25196915
- Funding acknowledgements
- Deutsche Forschungsgemeinschaft: SFB 630
- Volkswagen Foundation:
- Open access
- false
- ISSN
- 0006-2960
- Ausgabe der Veröffentlichung
- 37
- Zeitschrift
- Biochemistry
- Schlüsselwörter
- Cysteine
- Cysteine Endopeptidases
- Histidine
- Viral Proteins
- Catalytic Domain
- Substrate Specificity
- Entropy
- Models, Molecular
- Static Electricity
- Molecular Dynamics Simulation
- Coronavirus 3C Proteases
- Sprache
- eng
- Medium
- Print-Electronic
- Online publication date
- 2014
- Paginierung
- 5930 - 5946
- Datum der Veröffentlichung
- 2014
- Status
- Published
- Datum der Datenerfassung
- 2014
- Titel
- Evidence for substrate binding-induced zwitterion formation in the catalytic Cys-His dyad of the SARS-CoV main protease.
- Sub types
- Research Support, Non-U.S. Gov't
- Journal Article
- Ausgabe der Zeitschrift
- 53
Data source: Europe PubMed Central
- Abstract
- The coronavirus main protease (M(pro)) represents an attractive drug target for antiviral therapy of coronavirus (CoV) infections, including severe acute respiratory syndrome (SARS). The SARS-CoV M(pro) and related CoV proteases have several distinct features, such as an uncharged Cys-His catalytic dyad embedded in a chymotrypsin-like protease fold, that clearly separate these enzymes from archetypical cysteine proteases. To further characterize the catalytic system of CoV main proteases and to obtain information about improved inhibitors, we performed comprehensive simulations of the proton-transfer reactions in the SARS-CoV M(pro) active site that lead to the Cys(-)/His(+) zwitterionic state required for efficient proteolytic activity. Our simulations, comprising the free enzyme as well as substrate-enzyme and inhibitor-enzyme complexes, lead us to predict that zwitterion formation is fostered by substrate binding but not inhibitor binding. This indicates that M(pro) employs a substrate-induced catalytic mechanism that further enhances its substrate specificity. Our computational data are in line with available experimental results, such as X-ray geometries, measured pKa values, mutagenesis experiments, and the measured differences between the kinetic parameters of substrates and inhibitors. The data also provide an atomistic picture of the formerly postulated electrostatic trigger involved in SARS-CoV M(pro) activity. Finally, they provide information on how a specific microenvironment may finely tune the activity of M(pro) toward specific viral protein substrates, which is known to be required for efficient viral replication. Our simulations also indicate that the low inhibition potencies of known covalently interacting inhibitors may, at least in part, be attributed to insufficient fostering of the proton-transfer reaction. These findings suggest ways to achieve improved inhibitors.
- Autoren
- Alexander Paasche
- Andreas Zipper
- Simon Schäfer
- John Ziebuhr
- Tanja Schirmeister
- Bernd Engels
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/25196915
- DOI
- 10.1021/bi400604t
- eISSN
- 1520-4995
- Ausgabe der Veröffentlichung
- 37
- Zeitschrift
- Biochemistry
- Schlüsselwörter
- Catalytic Domain
- Coronavirus 3C Proteases
- Cysteine
- Cysteine Endopeptidases
- Entropy
- Histidine
- Models, Molecular
- Molecular Dynamics Simulation
- Static Electricity
- Substrate Specificity
- Viral Proteins
- Sprache
- eng
- Country
- United States
- Paginierung
- 5930 - 5946
- Datum der Veröffentlichung
- 2014
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2015
- Titel
- Evidence for substrate binding-induced zwitterion formation in the catalytic Cys-His dyad of the SARS-CoV main protease.
- Sub types
- Journal Article
- Research Support, Non-U.S. Gov't
- Ausgabe der Zeitschrift
- 53
Data source: PubMed
- Beziehungen:
- Property of