Structures of Enterovirus 71 3C proteinase (strain E2004104-TW-CDC) and its complex with rupintrivir

The crystal structure of 3C proteinase (3C(pro)) from Enterovirus 71 (EV71) was determined in space group C222(1) to 2.2 angstrom resolution. The fold was similar to that of 3C(pro) from other picornaviruses, but the difference in the beta-ribbon reported in a previous structure was not observed. This beta-ribbon was folded over the substrate-binding cleft and constituted part of the essential binding sites for interaction with the substrate. The structure of its complex with rupintrivir (AG7088), a peptido-mimetic inhibitor, was also characterized in space group P2(1)2(1)2(1) to 1.96 angstrom resolution. The inhibitor was accommodated without any spatial hindrance despite the more constricted binding site; this was confirmed by functional assays, in which the inhibitor showed comparable potency towards EV71 3C(pro) and human rhinovirus 3C(pro), which is the target that rupintrivir was designed against.