Fragments vs metallo-beta-lactamases

With all the attention on COVID-19 over the past few years, it’s easy to forget about bacteria. But they haven’t forgotten about us. Indeed, antibiotic resistance genes are continuing to spread throughout the microbial world. One class of genes encode the metallo-beta-lactamases (MBLs), which hydrolyze beta-lactam antibiotics. In a recent J. Med. Chem. paper, Mihirbaran Mandal, Li Xiao, and colleagues at Merck describe their efforts against these enzymes. (Mihirbaran spoke about this work at the CHI DDC meeting a few weeks ago.)

 

The researchers started by turning to the literature and previous internal efforts. Tetrazole-containing molecules had been identified as MBL inhibitors, and a virtual screen led to the selection of 76 compounds for testing, of which 29 inhibited the enzyme NDM-1, one of several known MBLs. These included fragment-sized compound 13, and a subsequent screen also identified compound 14.

 

Crystal structures of both these molecules revealed that they bind in the active site. The tetrazole makes interactions with one of the catalytic zinc ions, while the proximal sulfonamide moiety in compound 14 makes interactions with both zinc ions by displacing a bridging hydroxide ion. Merging compounds 13 and 14 led to compound 18, with nanomolar activity against NDM-1 as well as two other MBLs.

 

Despite its metal-chelating sulfonamide moiety, compound 18 was inactive against 34 mammalian metalloenzymes tested. It also didn’t inhibit any of 114 potential off-targets in a Eurofins screen. As expected, the molecule alone had no bactericidal activity, but it did enhance the activity of the beta-lactam antibiotic imipenem in MBL-expressing bacteria. Increasing the polarity of the molecule by adding a hydroxyl moiety to a solvent-exposed region and converting a phenyl to a pyridyl ring resulted in compound 23. While less active against isolated MBL enzymes, this molecule was more effective at inhibiting bacterial growth in the presence of imipenem, possibly due to accumulation in the periplasmic space.

 

Compound 23 is clean against off-targets such as hERG, ion channels, and various CYP enzymes. It has reasonable pharmacokinetic properties in mice when dosed intravenously. In a preliminary mouse efficacy study, the compound reduced levels of bacteria in spleen and kidney when dosed with imipenem.

 

This is a nice example of structure-based design starting from fragment-sized molecules. With an abundance of nitrogen atoms and a ClogP < 0, compound 23 looks unusual. Nonetheless, the researchers write that “further evolution of this class of molecules… eventually led to the discovery of several clinical candidates.” I look forward to seeing these described.