Fragment-wise design of inhibitors to 3C proteinase from enterovirus 71

•Contribution of sub-components to inhibitor potency to EV71 3Cpro were investigated•P2 groups need to be oriented to bind at the S2 subsite•S3 and S4 interacting moieties were required to generate sufficient potency•Hydrophobicity in S4 interacting moiety is helpful for cellular uptake•The data provide the basis for designing a new generation of inhibitors to 3Cpro