The 3C-like protease (3CL pro) of severe acute respiratory syndrome associated coronavirus (SARS-CoV) is vital for SARS-CoV replication and is a promising drug target. Recombinant 3CL pro was expressed in Pichia pastoris GS115 as a 42 kDa protein that displayed a K m of 15 ยฑ 2 ฮผM with Dabcyl-KTSAVLQSGFRKME-Edans as substrate. Purified 3CL pro was used for inhibition and kinetic assays with seven flavonoid compounds. The IC 50 of six flavonoid compounds were 47-381 ฮผM. Quercetin, epigallocatechin gallate and gallocatechin gallate (GCG) displayed good inhibition toward 3CL pro with IC 50 values of 73, 73 and 47 ฮผM, respectively. GCG showed a competitive inhibition pattern with K i value of 25 ยฑ 1. 7 ฮผM. In molecular docking experiments, GCG displayed a binding energy of -14 kcal mol -1 to the active site of 3CL pro and the galloyl moiety at 3-OH position was required for 3CL pro inhibition activity. ยฉ 2012 Springer Science+Business Media B. V.