The substrate specificity of SARS coronavirus 3C-like proteinase

Abstract

The 3C-like proteinase of severe acute respiratory syndrome coronavirus (SARS) has been proposed to be a key target for structural based drug design against SARS. We have designed and synthesized 34 peptide substrates and determined their hydrolysis activities. The conserved core sequence of the native cleavage site is optimized for high hydrolysis activity. Residues at position P4, P3, and P3' are critical for substrate recognition and binding, and increment of beta-sheet conformation tendency is also helpful. A comparative molecular field analysis (CoMFA) model was constructed. Based on the mutation data and CoMFA model, a multiply mutated octapeptide S24 was designed for higher activity. The experimentally determined hydrolysis activity of S24 is the highest in all designed substrates and is close to that predicted by CoMFA. These results offer helpful information for the research on the mechanism of substrate recognition of coronavirus 3C-like proteinase.

Fig. 1

The superimposed 22 substrate structures and the contour plot of the CoMFA model. This result indicates that increasing positive charge at position P3 is favored (blue), and large hydrophobic residue at position P2 is favored (green), which is compatible with the crystal structure. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this paper.)