Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis

We
report that alkyl-substituted bisphosphonates have activity
against Bacillus anthracis Sterne (0.40
μg/mL), Mycobacterium smegmatis (1.4 μg/mL), Bacillus subtilis (1.0 μg/mL), and Staphylococcus aureus (13 μg/mL). In many cases, there is no effect of serum binding,
as well as low activity against a human embryonic kidney cell line.
Targeting of isoprenoid biosynthesis is involved with 74 having IC50 values of ∼100 nM against heptaprenyl
diphosphate synthase and 200 nM against farnesyl diphosphate synthase. B. subtilis growth inhibition was rescued by addition
of farnesyl diphosphate, menaquinone-4 (MK-4), or undecaprenyl phosphate
(UP), and the combination of MK-4 and UP resulted in a 25× increase
in ED50, indicating targeting of both quinone and cell
wall biosynthesis. Clostridioides difficile was inhibited by 74, and since this organism does not
synthesize quinones, cell wall biosynthesis is the likely target.
We also solved three X-ray structures of inhibitors bound to octaprenyl
diphosphate and/or undecaprenyl diphosphate synthases.