Structure-Based Design of Bisubstrate Tetracycline Destructase Inhibitors That Block Flavin Redox Cycling

Tetracyclines (TCs) are an important class of antibiotics
threatened
by an emerging new resistance mechanismenzymatic inactivation.
These TC-inactivating enzymes, also known as tetracycline destructases
(TDases), inactivate all known TC antibiotics, including drugs of
last resort. Combination therapies consisting of a TDase inhibitor
and a TC antibiotic represent an attractive strategy for overcoming
this type of antibiotic resistance. Here, we report the structure-based
design, synthesis, and evaluation of bifunctional TDase inhibitors
derived from anhydrotetracycline (aTC). By appending a nicotinamide
isostere to the C9 position of the aTC D-ring, we generated bisubstrate
TDase inhibitors. The bisubstrate inhibitors have extended interactions
with TDases by spanning both the TC and presumed NADPH binding pockets.
This simultaneously blocks TC binding and the reduction of FAD by
NADPH while “locking” TDases in an unproductive FAD
“out” conformation.