Crystal structures of the main peptidase from the SARS coronavirus inhibited by a substrate-like aza-peptide epoxide.
The main peptidase (M(pro)) from the coronavirus (CoV) causing severe acute respiratory syndrome (SARS) is one of the most attractive molecular targets for the development of anti-SARS agents. We report the irreversible inhibition of SARS-CoV M(pro) by an aza-peptide epoxide (APE; k(inact)/K(i) = 1900(+/-400) M(-1) s(-1)). The crystal structures of the M(pro):APE complex in the space groups C2 and P2(1)2(1)2(1) revealed the formation of a covalent bond between the catalytic Cys145 S(gamma) atom of the peptidase and the epoxide C3 atom of the inhibitor, substantiating the mode of action of this class of cysteine-peptidase inhibitors. The aza-peptide component of APE binds in the substrate-binding regions of M(pro) in a substrate-like manner, with excellent structural and chemical complementarity. In addition, the crystal structure of unbound M(pro) in the space group C2 revealed that the "N-fingers" (N-terminal residues 1 to 7) of both protomers of M(pro) are well defined and the substrate-binding regions of both protomers are in the catalytically competent conformation at the crystallization pH of 6.5, contrary to the previously determined crystal structures of unbound M(pro) in the space group P2(1).
Lee
Ting-Wai
TW
Canadian Institute of Health Research Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7.
Cherney
Maia M
MM
Huitema
Carly
C
Liu
Jie
J
James
Karen Ellis
KE
Powers
James C
JC
Eltis
Lindsay D
LD
James
Michael N G
MN
D001665:Binding Sites; D002384:Catalysis; D000086782:Coronavirus 3C Proteases; D018360:Crystallography, X-Ray; D003546:Cysteine Endopeptidases / Q000737:chemistry*; D004852:Epoxy Compounds / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry; D011480:Protease Inhibitors / Q000737:chemistry*; D045473:Severe acute respiratory syndrome-related coronavirus / Q000737:chemistry*
D004852:Epoxy Compounds; D010455:Peptides; D011480:Protease Inhibitors; D003546:Cysteine Endopeptidases; D000086782:Coronavirus 3C Proteases