Discovery and structural characterization of an allosteric inhibitor of bacterial cis‐prenyltransferase

Abstract

Undecaprenyl pyrophosphate synthase (UPPs) is an essential enzyme in a key bacterial cell wall synthesis pathway. It catalyzes the consecutive condensations of isopentenyl pyrophosphate (IPP) groups on to a trans-farnesyl pyrophosphate (FPP) to produce a C55 isoprenoid, undecaprenyl pyrophosphate (UPP). Here we report the discovery and co-crystal structures of a druglike UPPs inhibitor in complex with Streptococcus pneumoniae UPPs, with and without substrate FPP, at resolutions of 2.2 and 2.1 Å , respectively. The UPPs inhibitor has a low molecular weight (355 Da), but displays potent inhibition of UPP synthesis in vitro (IC 50 50 nM) that translates into excellent whole cell antimicrobial activity against pathogenic strains of Streptococcal species (MIC 90 0.4 mg mL 21). Interestingly, the inhibitor does not compete with the substrates but rather binds at a site adjacent to the FPP binding site and interacts with the tail of the substrate. Based on the structures, an allosteric inhibition mechanism of UPPs is proposed for this inhibitor. This inhibition mechanism is supported by biochemical and biophysical experiments, and provides a basis for the development of novel antibiotics targeting Streptococcus pneumoniae.

Prenyltransferases as key enzymes in primary and secondary metabolism

“…2). Undecaprenyl monophosphate acts as a lipid carrier in the peptidoglycan biosynthesis of bacterial cell wall and therefore serves as a target for antibacterial drugs (Danley et al 2015).…”

Structure of undecaprenyl pyrophosphate synthase from Acinetobacter baumannii

“…Some UPPS inhibitors such as bisphosphonates not only bind to the primary S1/S2 sites for the substrates but also to the nearby secondary sites (Guo et al, 2007). Other 'allosteric' inhibitors can directly occupy the secondary sites in the hydrophobic tunnel to block chain elongation (Danley et al, 2015). However, owing to the common mechanism of substrate binding and catalysis that is presumably shared by bacterial UPPS and human hCIT/NgBR, these inhibitors might fall short of the desired specificity for a good antibiotic drug.…”

The search for novel treatment strategies forStreptococcus pneumoniaeinfections

“…reported in vitro UPPs inhibition by UK-106 051, a carboxamide analogue, leading to inhibition of pneumococcal growth, yet no in vivo confirmation has been attempted (Danley et al . 2015 ). Since then, few papers on the use of UPPS inhibitors against a variety of bacteria were published, all reporting early stage preclinical data (Concha et al .…”