Variation in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ Across Genotypes, Nucleotide States, and Species

Abstract

The recent increase in antibiotic resistance in disease-causing bacteria calls for new approaches to drug target selection and drug development. Targeting proteins involved in the bacterial cell division process provides a novel mechanism of action that bypasses problems associated with the increasingly ineffective variants of older antibiotics. One potentially powerful target for inhibition is the bacterial cytoskeletal protein FtsZ, a GTPase homolog of eukaryotic tubulin. This highly conserved and essential protein acts as a scaffold to recruit other cell division machinery and can exert mechanical forces that may be responsible for constriction of the division site. Recent work on an allosteric inhibitor (PC190723) has shown promising in vitro and in vivo antimicrobial activities on Staphylococcus aureus, however the mechanism of drug action and its effect on FtsZ of other bacterial species is unclear. Here, we examine the structural environment of the FtsZ-PC190723 binding pocket using Molecular Dynamics simulations and PocketFEATURE, a statistical method that performs pairwise comparisons of small molecule binding sites based on 3D structure information. By comparing all currently existing FtsZ crystal structures to the crystalized FtsZ-PC190723 complex, we observe that species and nucleotide binding state have significant impact on the structural properties of the binding site, with a GDP-bound Staph-FtsZ displaying the highest similarity to the inhibitor complex. However, during extended Molecular Dynamics simulations, this similarity is negated upon introduction of point mutations known to nullify the inhibitor's antimicrobial affect. Together, these results give insight into the mechanism and specificity of PC190723 interaction with various bacterial FtsZ.