Insights into the Target Interaction of Naturally Occurring Muraymycin Nucleoside Antibiotics

Abstract

Muraymycins are a subclass of antimicrobially active uridine-derived natural products. Biological data on several muraymycin analogues have been reported, including some inhibitory in vitro activities toward their target protein, the bacterial membrane enzyme MraY. However, a structure-activity relationship (SAR) study on naturally occurring muraymycins based on such in vitro data has been missing so far. In this work, we report a detailed SAR investigation on representatives of the four muraymycin subgroups A-D using a fluorescence-based in vitro MraY assay. For some muraymycins, inhibition of MraY with IC₅₀ values in the low-picomolar range was observed. These inhibitory potencies were compared with antibacterial activities and were correlated to modelling data derived from a previously reported X-ray crystal structure of MraY in complex with a muraymycin inhibitor. Overall, these results will pave the way for the development of muraymycin analogues with optimized properties as antibacterial drug candidates.

Keywords: activity assays; antibiotics; natural products; nucleosides; structure-activity relationships.

Figure 1

A: Overlay of muraymycins A1 3 (hydrocarbon scaffold in orange) and D2 8 (hydrocarbon scaffold in light blue) in complex with MraY from Aquifex aeolicus (grey), with the position of 8 derived from the previously reported X-ray co-crystal structure^[11] and the position of 3 derived from in silico modelling. The orange arrow indicates the position of the fatty acyl side chain of 3, which points into a hydrophobic cleft of the protein. B: Overlay of muraymycins A1 3 (orange) and D2 8 (light blue) from the aforementioned complexes with MraY, showing parts of MraY (thin stick representations) which mediate key interactions (light grey for 3, dark grey for 8). The orange arrow indicates the position of the fatty acyl side chain of 3, which does not show specific key interactions with the protein.

Scheme 1

MraY-catalyzed reaction of Park’s nucleotide 1 towards lipid I 2 (undecaprenyl phosphate represented schematically; UDP = uridine diphosphate; UMP = uridine monophosphate). The exact composition of the pentapeptide moiety can vary in different bacteria.^[4]