Design, Synthesis, and Biological Evaluation of Mono- and Diamino-Substituted Squaramide Derivatives as Potent Inhibitors of Mycobacterial Adenosine Triphosphate (ATP) Synthase

Amides of squaric acid are new drug candidates with activity against mycobacteria. Like the approved drug bedaquiline, these compounds achieve efficacy by inhibiting mycobacterial ATP synthase. However, squaramides have a different binding site than bedaquiline and possess the potential to inhibit bedaquiline-resistant strains. We developed an optimized synthesis for monoamino-substituted squaric acid analogues. Guided by an atomic model of a squaramide compound bound to its target, we synthesized 31 new monoamino/diamino-substituted squaric acid derivates. The efficacy of these compounds was determined in whole-cell assays against Mycobacterium tuberculosis and Mycobacterium avium. The molecular target was confirmed with measurement of inhibition of Mycobacterium smegmatis ATP synthase and by using M. tuberculosis strains that modulate the expression of ATP synthase. Compared to earlier squaramides, several analogues demonstrated micromolar activity against M. tuberculosis, improved microsomal stability in vitro, and reduced cytotoxicity. These properties contribute to the preclinical development of this class of compound.