Bisthiazolidines: A Substrate-Mimicking Scaffold as an Inhibitor of the NDM-1 Carbapenemase

Pathogenic Gram-negative bacteria resistant to almost all beta-lactam antibiotics are a major public health threat. Zn(II)-dependent or metallo-beta-lactamases (MBLs) produced by these bacteria inactivate most beta-lactam antibiotics, including the carbapenems, which are last line therapies for life-threatening Gram-negative infections. NDM-1 is a carbapenemase belonging to the MBL family that is rapidly spreading worldwide. Regrettably, inhibitors of MBLs are not yet developed. Here we present the bisthiazolidine (BTZ) scaffold as a structure with some features of beta-lactam substrates, which can be modified with metal-binding groups to target the MBL active site. Inspired by known interactions of MBLs with beta-lactams, we designed four BTZs that behave as in vitro NDM-1 inhibitors with K-i values in the low micromolar range (from 7 +/- 1 to 19 +/- 3 mu M). NMR spectroscopy demonstrated that they inhibit hydrolysis of imipenem in NDM-1-producing Escherichia coli. In vitro time kill cell-based assays against a variety of bacterial strains harboring bla(NDM-1) including Acinetobacter baumannii show that the compounds restore the antibacterial activity of imipenem. A crystal structure of the most potent heterocycle (L-CS319) in complex with NDM-1 at 1.9 angstrom resolution identified both structural determinants for inhibitor binding and opportunities for further improvements in potency.