4JHZ

Structure of E. coli beta-Glucuronidase bound with a novel, potent inhibitor 2-[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]-N-[(1S,2S,5S)-2,5-dimethoxycyclohexyl]acetamide

Summary for 4JHZ

• Entry DOI: 10.2210/pdb4jhz/pdb
• Related: 3K46 3K4A 3K4D 3LPF 3LPG
• Descriptor: Beta-glucuronidase, 2-[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]-N-[(1S,2S,5S)-2,5-dimethoxycyclohexyl]acetamide (3 entities in total)
• Functional Keywords: alpha/beta barrel, sugar-binding domain, beta-sandwich domain, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 139037.62

Authors

Roberts, A.B.,Wallace, B.D.,Redinbo, M.R. (deposition date: 2013-03-05, release date: 2013-08-28, Last modification date: 2024-11-20)

Primary citation

Roberts, A.B.,Wallace, B.D.,Venkatesh, M.K.,Mani, S.,Redinbo, M.R.
Molecular Insights into Microbial beta-Glucuronidase Inhibition to Abrogate CPT-11 Toxicity.
Mol.Pharmacol., 84:208-217, 2013

PubMed Abstract: Bacterial β-glucuronidases expressed by the symbiotic intestinal microbiota appear to play important roles in drug-induced epithelial cell toxicity in the gastrointestinal (GI) tract. For the anticancer drug CPT-11 (irinotecan) and the nonsteroidal anti-inflammatory drug diclofenac, it has been shown that removal of the glucuronide moieties from drug metabolites by bacterial β-glucuronidases in the GI lumen can significantly damage the intestinal epithelium. Furthermore, selective disruption of bacterial β-glucuronidases by small molecule inhibitors alleviates these side effects, which, for CPT-11 {7-ethyl-10-[4-(1-piperidino)-1-piperidino]}, can be dose limiting. Here we characterize novel microbial β-glucuronidase inhibitors that inhibit Escherichia coli β-glucuronidase in vitro with Ki values between 180 nM and 2 μM, and disrupt the enzyme in E. coli cells, with EC50 values as low as 300 nM. All compounds are selective for E. coli β-glucuronidase without inhibiting purified mammalian β-glucuronidase, and they do not impact the survival of either bacterial or mammalian cells. The 2.8 Å resolution crystal structure of one inhibitor bound to E. coli β-glucuronidase demonstrates that it contacts and orders only a portion of the "bacterial loop" present in microbial, but not mammalian, β-glucuronidases. The most potent compound examined in this group was found to protect mice against CPT-11-induced diarrhea. Taken together, these data advance our understanding of the chemical and structural basis of selective microbial β-glucuronidase inhibition, which may improve human drug efficacy and toxicity.

PubMed: 23690068
DOI: 10.1124/mol.113.085852

Experimental method

X-RAY DIFFRACTION (2.831 Å)