Biosynthesis of uridine diphosphate N-Acetylglucosamine: An underexploited pathway in the search for novel antibiotics?

Abstract

Although the prevalence of antibiotic resistance is increasing at an alarming rate, there are a dwindling number of effective antibiotics available. Thus, the development of novel antibacterial agents should be of utmost importance. Peptidoglycan biosynthesis has been and is still an attractive source for antibiotic targets; however, there are several components that remain underexploited. In this review, we examine the enzymes involved in the biosynthesis of one such component, UDP-N-acetylglucosamine, an essential building block and precursor of bacterial peptidoglycan. Furthermore, given the presence of a similar biosynthesis pathway in eukaryotes, we discuss the current knowledge on the differences and similarities between the bacterial and eukaryotic enzymes. Finally, this review also summarises the recent advances made in the development of inhibitors targeting the bacterial enzymes.

Keywords: UDP-N-acetylglucosamine biosynthesis; antibiotic resistance; bifunctional GlmU; glucosamine-6-phosphate synthase; peptidoglycan biosynthesis; phosphoglucosamine mutase.

FIGURE 1

Biosynthesis pathway of UDP‐N‐acetylglucosamine in prokaryotes (left) and eukaryotes (right)

FIGURE 2

Reaction mechanisms of the (a) glutamine hydrolysis and (b) conversion of fructose‐6‐phosphate to glucosamine‐6‐phosphate catalysed by GlmS

FIGURE 3

Structure of Escherichia coli (Ec) GlmS enzyme. (a) Cartoon structure of EcGlmS (PDB: 4AMV) monomeric unit bound to fructose‐6‐phosphate (Fru‐6‐P) (green). (b) Cartoon structure of bound EcGlmS demonstrating the dimer conformation. (c) Cartoon structure of EcGlmS isomerase active site bound with Fru‐6‐P, with key residues shown as sticks. (d) Cartoon structure of EcGlmS glutaminase active site, with key residues shown as sticks. (e) Cartoon structure of EcGlmS (PDB: 3OOJ) in the unliganded form demonstrating the inactive hexamer conformation. Residues are coloured by nitrogen (blue), oxygen (red), and sulfur (yellow). Images were generated using PyMOL v 2.2 (Schrödinger)

FIGURE 4

Inhibitors of the bacterial GlmS enzyme

FIGURE 5

Reaction mechanism of the interconversion of glucosamine‐6‐phosphate and glucosamine‐1‐phosphate catalysed by GlmM

FIGURE 6

Structure of Bacillus anthracis (Ba) GlmM enzyme. (a) Cartoon structure of BaGlmM (PDB: 3PDK) monomeric unit. (b) Cartoon structure of BaGlmM in the unliganded form demonstrating the dimer conformation. (c) Cartoon structure of BaGlmM dimerisation interface, with key residues shown as sticks. (d) Cartoon structure of BaGlmM, with residues within the active site shown as sticks. Residues are coloured by nitrogen (blue) and oxygen (red). Images were generated using PyMOL v 2.2 (Schrödinger)

FIGURE 7

Comparison of prokaryotic GlmM and eukaryotic GNPNAT/AGM1 enzymes. (a) Cartoon structure of Candida albicans AGM1 (PDB: 2DKA) in the unliganded form illustrating monomeric conformation. Image was generated using PyMOL v 2.2 (Schrödinger). (b) Sequence alignment of B. anthracis GlmM, Homo sapiens GNPNAT and C. albicans AGM1 demonstrating conservation of a common motif (bold) among phosphoglucomutases, phosphoglucosamine mutases, and phosphoacetylglucosamine mutases. (c) Sequence alignment of the active site residues of B. anthracis GlmM, H. sapiens GNPNAT and C. albicans AGM1 demonstrating conservation of the metal‐binding and phosphate‐binding sites (bold) and difference in sugar‐binding loop (bold) between the prokaryotic and eukaryotic enzymes

FIGURE 8

Glucosamine‐6‐phosphate analogues as inhibitors of GlmM

FIGURE 9

Reaction mechanism of the (a) acetylation and (b) uridylation of GlcN‐1‐P catalysed by the bifunctional GlmU enzyme

FIGURE 10

Structure of E. coli (Ec) GlmU enzyme. (a) Cartoon structure of EcGlmU (PDB: 2OI6) monomeric unit. (b) Cartoon structure of EcGlmU in complex with UDP‐GlcNAc, CoA and GlcN‐1‐P illustrating the trimeric conformation. (c) Cartoon structure of EcGlmU acetyltransferase site bound with the substrate glucosamine‐1‐phospahet (GlcN‐1‐P), with key active site residues shown as sticks. (d) Cartoon structure of EcGlmU uridyltransferase site bound with the reaction product UDP‐N‐acetylglucosamine (UDP‐GlcNAc) (PDB: 2OI7), with key active site residues shown as sticks. (e) Cartoon structure of EcGlmU allosteric site (PDB: 2OI6), with key residues involved shown as sticks. Residues are coloured by nitrogen (blue), oxygen (red), and sulfur (yellow). Images were generated using PyMOL v 2.2 (Schrödinger)

FIGURE 11

Comparison of the prokaryotic GlmU enzyme and the eukaryotic UDP‐GlcNAc pyrophosphorylase enzymes. (a) Cartoon structure of the uridyltransferase domain of E. coli GlmU (pink) (PDB: 2OI6) superimposed on the cartoon structure of H. sapiens AGX2 (cyan) (PDB: 1JVD). (b) Sequence alignment of pyrophosphorylase fingerprint from E. coli GlmU, H. sapiens AGX1 and C. albicans UAP1, demonstrating conservation of the motif (bold) across UDP‐GlcNAc pyrophosphorylase enzymes from different domains. (c) Cartoon structure of H. sapiens AGX2 (PDB: 1JVD) in complex with UDP‐GlcNAc illustrating dimeric conformation. Cartoon structure images were generated using PyMOL v 2.2 (Schrödinger)

FIGURE 12

Inhibitors of the acetyltransferase activity of the bifunctional GlmU enzyme

FIGURE 13

Inhibitors of the uridyltransferase activity of the bifunctional GlmU enzyme