Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis from <i>Mycobacterium tuberculosis</i>

Abstract

The enhanced intracellular survival (Eis) protein of <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) is a versatile acetyltransferase that multiacetylates aminoglycoside antibiotics abolishing their binding to the bacterial ribosome. When overexpressed as a result of promoter mutations, Eis causes drug resistance. In an attempt to overcome the Eis-mediated kanamycin resistance of <i>Mtb</i>, we designed and optimized structurally unique thieno[2,3-<i>d</i>]pyrimidine Eis inhibitors toward effective kanamycin adjuvant combination therapy. We obtained 12 crystal structures of enzyme-inhibitor complexes, which guided our rational structure-based design of 72 thieno[2,3-<i>d</i>]pyrimidine analogues divided into three families. We evaluated the potency of these inhibitors <i>in vitro</i> as well as their ability to restore the activity of kanamycin in a resistant strain of <i>Mtb</i>, in which Eis was upregulated. Furthermore, we evaluated the metabolic stability of 11 compounds <i>in vitro</i>. This study showcases how structural information can guide Eis inhibitor design.