Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases

Abstract

Antimicrobial resistance (AMR) is a global health problem. Despite the enormous efforts made in the last decade, threats from some species, including drug-resistant Neisseria gonorrhoeae, continue to rise and would become untreatable. The development of antibiotics with a different mechanism of action is seriously required. Here, we identified an allosteric inhibitory site buried inside eukaryotic mitochondrial heme-copper oxidases (HCOs), the essential respiratory enzymes for life. The steric conformation around the binding pocket of HCOs is highly conserved among bacteria and eukaryotes, yet the latter has an extra helix. This structural difference in the conserved allostery enabled us to rationally identify bacterial HCO-specific inhibitors: an antibiotic compound against ceftriaxone-resistant Neisseria gonorrhoeae. Molecular dynamics combined with resonance Raman spectroscopy and stopped-flow spectroscopy revealed an allosteric obstruction in the substrate accessing channel as a mechanism of inhibition. Our approach opens fresh avenues in modulating protein functions and broadens our options to overcome AMR.

Monomer-dimer structural comparison in quinol-dependent nitric oxide reductase reveals a functional basis for superior enzymatic activity in the dimer

“…Recent work by Nishida and colleagues explored finding a conserved, allosteric inhibitory site in HCO enzymes, (eukaryotic and prokaryotic) including mammalian CcO and bacterial qNOR, to improve the selectivity of inhibitors to reduce unwanted toxicity against host cells. A promising inhibitor, specific to bacterial HCO’s, had a proposed inhibitory mechanism whereby the substrate access channel is partially obstructed 8 . Our current work can also offer an alternate strategy for targeting the dimerization site, such as TM2 and 10, to suppress the enzymatic activity of qNOR upon the dissociation of the functional dimer in vivo by chemicals, which would help combat antimicrobial-resistant pathogens.…”

“…Given that cellular respiration is an essential biological process for all kingdoms of life and that NORs of pathogens are essential for survival in their hosts, HCO enzymes are a key target for the development of antimicrobial drugs. Indeed, recent work on screening for an allosteric inhibitor for the HCO enzymes demonstrated the great potential for obtaining new antimicrobial reagents 8 . Thus, gathering detailed structural and functional information on the HCO enzymes is imperative for future drug design efforts.…”