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-y 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). (c) 2005 Elsevier Ltd. All rights reserved.