Substrate specificity and rational design of peptidomimetic inhibitors for SARS coronavirus main protease.

The main protease (Mpro) of severe acute respiratory syndrome coronavirus (SARS CoV) is a key enzyme for viral replication, and is thus an attractive target for anti-SARS CoV drug development. Mpro belongs to the family of 3C-like cysteine proteases. The basic design of peptidomimetic inhibitors involved a warhead that can form covalent modifications to the –SH group of the active site residue Cys145 and a substrate peptide sequence that forms favourable interactions with the protease. We systematically profiled the substrate specificity of Mpro, which forms the basis of a rational design of peptidomimetic inhibitors.1 First, we created a library of protein-based substrates, and profiled the preference of amino acid residues at each of the P5 to P3’ positions. Based on the substrate-specificity profile, we created ‘superreactive’ substrate sequences. In addition, a novel peptidomimetic inhibitor was synthesised using nitrile as the warhead.2 A number of inhibitors were synthesised to test the role of N-terminal protective groups and the substrate peptide sequences. Finally, the crystal structure of Mpro in complex with the best inhibitor was determined to provide a better understanding of protease-inhibitor interactions. The results on substrate specificity profile of Mpro have been reported.1 To profile the substratespecificity of the SARS-CoV Mpro, saturated mutagenesis was performed at each of the P5 to P3’ positions of the WT auto-cleavage sequences Hong Kong Med J 2014;20(Suppl 4):S18-21 RFCID project number: 06060432 KB Wong *, DCC Wan, HF Chow