Structure-Activity Relationship (SAR) of Novel Antibiotics Targeting LpxH and LpxC in Lipid A Biosynthesis

Abstract

The emergence of multidrug-resistant nosocomial Gram-negative (GN) pathogens has become a major public health threat. Carbapenem-resistant P. aeruginosa, A. baumannii, and extended-spectrum--lactamase (ESBL)-producing Enterobacteriaceae are the top three pathogens that pose the greatest threat to human health in the 2017 WHO report [1]. This alarming list highlights the urgent need to develop new antibiotics, preferably by targeting novel pathways in these bacteria, for which existing resistance mechanisms are lacking. GN bacteria are characterized by enrichment of lipid A-anchored LPS or LOS in the outer monolayer of their outer membrane. Lipid A biosynthesis represents a highly conserved pathway that has never been exploited by commercial antibiotics. Targeted inhibition of the first committed step of lipid A biosynthesis, LpxC, has proven to be a viable route for antibiotic development. However, current efforts have been hindered by unexpected cardiovascular toxicity in vivo. Herein, we report the preclinical characterization of a novel LpxC inhibitor that has slow, tight binding, low pM affinity, oral bioavailability, and an exceptional in vivo safety profile. Additionally, accumulating evidence from our recent studies shows that inhibition of lipid A enzymes downstream of LpxC, such as LpxH, kills bacteria not only by disrupting the essential lipid A biosynthesis, but also by accumulating toxic lipid A intermediates, thus delivering a double punch for bacteria [2, 3]. Our preliminary structural characterization of AZ1 in complex with LpxH has led to the development of more potent inhibitors. By conducting an in-depth structural analysis of LpxH in complex with several generations of AZ1-based inhibitors, we have not only gleaned vital knowledge about the electrostatic forces dictating inhibitor recognition of LpxH, but also developed a suitable candidate for in vivo trials that displays a good safety profile and has a preliminary rate of 80% in recovering mice from lethal infections of Klebsiella pneumoniae.