Inhibiting the Iron-regulated Heme Oxygenase (HemO) of Pseudomonas aeruginosa via Competitive and Non-competitive Mechanisms

Abstract

The discovery and development of new antimicrobials has become a top priority as resistance to known therapeutics continues to grow. While most antimicrobials target essential functions, some in the field question this historical approach and instead propose targeting virulence factors, rendering pathogens non-pathogenic. In most Gram-negative bacteria, virulence is globally regulated by iron via the ferric uptake regulator (Fur). Recent studies show that in the host, iron is preferentially acquired via heme uptake and utilization. Pseudomonas aeruginosa encodes two heme uptake systems, both of which terminate in the oxidative cleavage of heme by the iron-regulated heme oxygenase (HemO). HemO is required for the efficient utilization of heme as an iron source in P. aeruginosa. Thus, inhibiting HemO will globally reduce virulence via disrupting the utilization of heme as an iron source. Previous work identified small-molecule inhibitors of HemO via computer-aided drug design techniques, which were validated in vitro and in vivo. Several of those compounds were further explored for optimization using medicinal chemistry, biochemistry, and microbiology techniques. Compounds were synthesized, characterized, and assessed for binding, inhibitory activity in cellulo, and antimicrobial activity. Binding was analyzed by fluorescence quenching, saturation transfer difference (STD)-NMR, heteronuclear single quantum coherence (HSQC) NMR, molecular dynamics simulations, and hydrogen-deuterium exchange mass spectrometry (HXMS). Two lead compounds were shown to bind in the heme-binding site of HemO with low micromolar affinity. Another lead compound was shown to bind to a previously unidentified back site of HemO, which was identified in silico and verified with HXMS. To analyze the mechanism of back side inhibition of HemO, site-directed mutagenesis eliminated a salt bridge (D99-R188) adjacent to the back site. These mutations disrupted the essential hydrogen-bonding network in the distal pocket, as evidenced by poor stability of intermediates and altered structural dynamics. Together, these data show that inhibiting HemO with small-molecules can be achieved on two sites of the enzyme, both the heme-binding site and the newly discovered back site. Future work includes improvement of heme-binding site inhibitors, development of novel inhibitors, and confirming the antivirulent activity of HemO inhibitors in an infection model.