3SNB

Crystal structure of SARS coronavirus main protease complexed with Ac-DSFDQ-H (soaking)

Summary for 3SNB

• Entry DOI: 10.2210/pdb3snb/pdb
• Related: 2h2z 3SN8 3SNA 3SNC 3SND 3SNE
• Related PRD ID: PRD_001118
• Descriptor: 3C-like proteinase, Peptide aldehyde inhibitor Ac-DSFDQ-H (3 entities in total)
• Functional Keywords: 3c-like proteinase, protease, ac-dsfdq-h, covalent bound, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: SARS coronavirus (SARS-CoV)
• Cellular location: Non-structural protein 3: Host membrane; Multi-pass membrane protein (Potential). Non-structural protein 4: Host membrane; Multi-pass membrane protein (Potential). Non-structural protein 6: Host membrane; Multi-pass membrane protein (Potential). Non-structural protein 7: Host cytoplasm, host perinuclear region (By similarity). Non-structural protein 8: Host cytoplasm, host perinuclear region (By similarity). Non-structural protein 9: Host cytoplasm, host perinuclear region (By similarity). Non-structural protein 10: Host cytoplasm, host perinuclear region (By similarity): P0C6U8
• Total number of polymer chains: 2
• Total formula weight: 34499.26

Authors

Zhu, L.,Hilgenfeld, R. (deposition date: 2011-06-29, release date: 2011-09-07, Last modification date: 2012-12-12)

Primary citation

Zhu, L.,George, S.,Schmidt, M.F.,Al-Gharabli, S.I.,Rademann, J.,Hilgenfeld, R.
Peptide aldehyde inhibitors challenge the substrate specificity of the SARS-coronavirus main protease.
Antiviral Res., 92:204-212, 2011

PubMed Abstract: SARS coronavirus main protease (SARS-CoV M(pro)) 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 M(pro). Previous studies using peptidic substrates and inhibitors showed that the substrate specificity of SARS-CoV M(pro) requires glutamine in the P1 position and a large hydrophobic residue in the P2 position. We determined four crystal structures of SARS-CoV M(pro) in complex with pentapeptide aldehydes (Ac-ESTLQ-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(pro), with K(i) 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(pro) 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(pro), with K(i)=2.24±0.58 μM. These results show that the stringent substrate specificity of the SARS-CoV M(pro) 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.

PubMed: 21854807
DOI: 10.1016/j.antiviral.2011.08.001

Experimental method

X-RAY DIFFRACTION (2.4 Å)