Peptide aldehyde inhibitors challenge the substrate specificity of the SARS-coronavirus main protease
Identifieur interne : 002364 ( Main/Exploration ); précédent : 002363; suivant : 002365Peptide aldehyde inhibitors challenge the substrate specificity of the SARS-coronavirus main protease
Auteurs : Lili Zhu [Allemagne] ; Shyla George [Allemagne] ; Marco F. Schmidt [Allemagne] ; Samer I. Al-Gharabli [Jordanie] ; Jörg Rademann [Allemagne] ; Rolf Hilgenfeld [Allemagne, République populaire de Chine]Source :
- Antiviral research [ 0166-3542 ] ; 2011.
Descripteurs français
- Pascal (Inist)
- Wicri :
- topic : Médicament.
English descriptors
- KwdEn :
Abstract
SARS coronavirus main protease (SARS-CoV Mpro) is essential for the replication of the virus and regarded as a major antiviral drug target. The enzyme is a cysteine protease, with a catalytic dyad (Cys-145/His-41 ) in the active site. Aldehyde inhibitors can bind reversibly to the active-site sulfhydryl of SARS-CoV Mpro. Previous studies using peptidic substrates and inhibitors showed that the substrate specificity of SARS-CoV Mpro requires glutamine in the P1 position and a large hydrophobic residue in the P2 position. We determined four crystal structures of SARS-CoV Mpro in complex with pentapeptide aldehydes (Ac-EST-LQ-H, Ac-NSFSQ-H, Ac-DSFDQ-H, and Ac-NSTSQ-H). Kinetic data showed that all of these aldehydes exhibit inhibitory activity towards SARS-CoV Mpro, with Ki values in the μM range. Surprisingly, the X-ray structures revealed that the hydrophobic S2 pocket of the enzyme can accommodate serine and even aspartic-acid side-chains in the P2 positions of the inhibitors. Consequently, we reassessed the substrate specificity of the enzyme by testing the cleavage of 20 different tetradecapeptide substrates with varying amino-acid residues in the P2 position. The cleavage efficiency for the substrate with serine in the P2 position was 160-times lower than that for the original substrate (P2 = Leu); furthermore, the substrate with aspartic acid in the P2 position was not cleaved at all. We also determined a crystal structure of SARS-CoV Mpro in complex with aldehyde Cm-FF-H, which has its P1-phenylalanine residue bound to the relatively hydrophilic S1 pocket of the enzyme and yet exhibits a high inhibitory activity against SARS-CoV Mpro, with Ki = 2.24 ± 0.58 μM. These results show that the stringent substrate specificity of the SARS-CoV Mpro with respect to the P1 and P2 positions can be overruled by the highly electrophilic character of the aldehyde warhead, thereby constituting a deviation from the dogma that peptidic inhibitors need to correspond to the observed cleavage specificity of the target protease.
Affiliations:
- Allemagne, Jordanie, République populaire de Chine
- Berlin, District de Leipzig, Hambourg, Saxe (Land)
- Berlin, Hambourg, Leipzig
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<series><title level="j" type="main">Antiviral research</title>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Aldehyde</term>
<term>Antiseptic</term>
<term>Antiviral</term>
<term>Aspartic acid</term>
<term>Crystallography</term>
<term>Cysteine endopeptidases</term>
<term>Design</term>
<term>Drug</term>
<term>Inhibitor</term>
<term>Interaction</term>
<term>Methionine</term>
<term>Peptidases</term>
<term>Peptides</term>
<term>Severe acute respiratory syndrome virus</term>
<term>Substrate specificity</term>
<term>X ray</term>
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<keywords scheme="Pascal" xml:lang="fr"><term>Peptide</term>
<term>Aldéhyde</term>
<term>Inhibiteur</term>
<term>Spécificité substrat</term>
<term>Virus syndrome respiratoire aigu sévère</term>
<term>Peptidases</term>
<term>Antiviral</term>
<term>Médicament</term>
<term>Conception</term>
<term>Cysteine endopeptidases</term>
<term>Méthionine</term>
<term>Acide aspartique</term>
<term>Interaction</term>
<term>Rayon X</term>
<term>Cristallographie</term>
<term>Antiseptique</term>
</keywords>
<keywords scheme="Wicri" type="topic" xml:lang="fr"><term>Médicament</term>
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<front><div type="abstract" xml:lang="en">SARS coronavirus main protease (SARS-CoV Mpro) is essential for the replication of the virus and regarded as a major antiviral drug target. The enzyme is a cysteine protease, with a catalytic dyad (Cys-145/His-41 ) in the active site. Aldehyde inhibitors can bind reversibly to the active-site sulfhydryl of SARS-CoV Mpro. Previous studies using peptidic substrates and inhibitors showed that the substrate specificity of SARS-CoV Mpro requires glutamine in the P1 position and a large hydrophobic residue in the P2 position. We determined four crystal structures of SARS-CoV M<sup>pro</sup>
in complex with pentapeptide aldehydes (Ac-EST-LQ-H, Ac-NSFSQ-H, Ac-DSFDQ-H, and Ac-NSTSQ-H). Kinetic data showed that all of these aldehydes exhibit inhibitory activity towards SARS-CoV M<sup>pro</sup>
, with K<sub>i</sub>
values in the μM range. Surprisingly, the X-ray structures revealed that the hydrophobic S2 pocket of the enzyme can accommodate serine and even aspartic-acid side-chains in the P2 positions of the inhibitors. Consequently, we reassessed the substrate specificity of the enzyme by testing the cleavage of 20 different tetradecapeptide substrates with varying amino-acid residues in the P2 position. The cleavage efficiency for the substrate with serine in the P2 position was 160-times lower than that for the original substrate (P2 = Leu); furthermore, the substrate with aspartic acid in the P2 position was not cleaved at all. We also determined a crystal structure of SARS-CoV M<sup>pro</sup>
in complex with aldehyde Cm-FF-H, which has its P1-phenylalanine residue bound to the relatively hydrophilic S1 pocket of the enzyme and yet exhibits a high inhibitory activity against SARS-CoV M<sup>pro</sup>
, with K<sub>i</sub>
<sub>=</sub>
2.24 ± 0.58 μM. These results show that the stringent substrate specificity of the SARS-CoV M<sup>pro</sup>
with respect to the P1 and P2 positions can be overruled by the highly electrophilic character of the aldehyde warhead, thereby constituting a deviation from the dogma that peptidic inhibitors need to correspond to the observed cleavage specificity of the target protease.</div>
</front>
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<country name="République populaire de Chine"><noRegion><name sortKey="Hilgenfeld, Rolf" sort="Hilgenfeld, Rolf" uniqKey="Hilgenfeld R" first="Rolf" last="Hilgenfeld">Rolf Hilgenfeld</name>
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