Irinotecan inhibits cell proliferation and thus is used for the primary treatment of colorectal cancer. Metabolism of irinotecan involves incorporation of β-glucuronic acid to facilitate excretion. During transit of the glucuronidated product through the gastrointestinal tract, an induced upregulation of gut microbial β-glucuronidase (GUS) activity may cause severe diarrhea and thus force many patients to stop treatment. We herein report the development of uronic isofagomine (UIFG) derivatives that act as general, potent inhibitors of bacterial GUSs, especially those of Escherichia coli and Clostridium perfringens. The best inhibitor, C6-nonyl UIFG, is 23,300-fold more selective for E. coli GUS than for human GUS (Ki = 0.0045 and 105 μM, respectively). Structural evidence indicated that the loss of coordinated water molecules, with the consequent increase in entropy, contributes to the high affinity and selectivity for bacterial GUSs. The inhibitors also effectively reduced irinotecan-induced diarrhea in mice without damaging intestinal epithelial cells. Hsien-Ya Lin, Chia-Yu Chen, Ting-Chien Lin and colleagues perform structure-guided modifications of the compound uronic isofagomaine in order to engineer a highly specific and potent inhibitor of gut bacterial β-glucuronidases (GUSs). The authors present eight crystal structures and demonstrate in vivo efficacy of the optimised C6-alkyl derivative inhibitor in mice models. This study may enhance the development of inhibitors of microbial GUS for use in colorectal cancer therapy to minimize the undesired side effects of irinotecan treatment. [ABSTRACT FROM AUTHOR]