Novel inhibitors of bacterial cell wall synthesis

Over the past forty years, efforts to discover antibacterials have yielded a wide variety of chemical structures, almost exclusively natural products, which inhibit many steps in cell wall synthesis. Although screening for new cell wall inhibitors has been continuous during that period, there have been few reports of new drugs. With the advent of genomics, high resolution X-ray crystallography and the recognition of the need for new antibiotics to combat resistant organisms, there has been a resurgence in interest in this validated target area.     

Pulvinones as bacterial cell wall biosynthesis inhibitors

Pulvinones were synthesized (>180) in arrays and evaluated as inhibitors of early stage cell wall biosynthesis enzymes MurA-MurD. Several pulvinones inhibited Mur enzymes with IC(50)'s in the 1-10 microg/mL range and demonstrated antibacterial activity against Gram-positive bacteria including methicillin-resistant Staphyloccus aureus, vancomycin-resistant Enterococcus faecalis, and penicillin-resistant Streptococcus pneumoniae.     

Structure based discovery of small molecule suppressors targeting bacterial lysozyme inhibitors

The production of lysozyme inhibitors, competitively binding to the lysozyme active site, is a bacterial strategy to prevent the lytic activity of host lysozymes. Therefore, suppression of the lysozyme–inhibitor interaction is an interesting new approach for drug development since restoration of the bacterial lysozyme sensitivity will support bacterial clearance from the infected sites. Using molecular modelling techniques the interaction of the Salmonella PliC inhibitor with c-type lysozyme was studied and a protein–protein interaction based pharmacophore model was created. This model was used as a query to identify molecules, with potential affinity for the target, and subsequently, these molecules were filtered using molecular docking. The retained molecules were validated as suppressors of lysozyme inhibitory proteins using in vitro experiments revealing four active molecules.     

Macrocyclic inhibitors of the bacterial cell wall biosynthesis enzyme MurD

Computer-based molecular design has been used to produce a series of new macrocyclic systems targeted against the bacterial cell wall biosynthetic enzyme MurD. Following their preparation, which involved a novel metathesis-based cyclisation as the key step, these systems were found to show good inhibition when assayed against the MurD enzyme.     

A transition state analog of lysozyme catalysis prepared from the bacterial cell wall tetrasaccharide.

Treatment of the cell wall tetrasaccharide GlcNAcbeta(1 leads to 4)-MurNAc-beta(1 leads to 4)-GlcNAc-beta(1 leads to 4)-MurNAc with alkali resulted in the formation of the unsaturated tetrasaccharide GlcNAc-beta(1 leads to 4)-MurNAc-beta(1 leads to 4)-GlcNAc-beta(1 leads to 4)-delta2,3-2-acetamido-2-deoxy-D-glucoseen. The same compound was also formed by transglycosylation upon incubation of the unmodified tetrasaccharide with the unsaturated disaccharide GlcNAc-beta(1 leads to 4)-delta2,3-2-acetamido-2-deoxy-D-glucoseen (Tipper, D. J. (1968) Biochemistry 7, 1441-1449) and hen egg white lysozyme. The unsaturated tetrasaccharide was further characterized by paper electrophoresis, amino sugar analysis, and NMR. From NMR analysis it is concluded that the delta2,3-2-acetamido-2-deoxy-D-glucoseen at the reducing end of the unsaturated tetrasaccharide has a half-chair conformation. This conformation is similar to the one proposed for the sugar at subsite D in the lysozyme-substrate complex in the transition state. Addition of the unsaturated tetrasaccharide to a solution of hen egg white lysozyme quenched the fluorescence of the enzyme and shifted the fluorescence maximum to the blue, similar to the effect produced by the parent compound. The association constant of the unsaturated tetrasaccharide and lysozyme was measured at pH 6.0 and 24 degrees by spectrofluorimetry and microcalorimetry and found to be 1.45 X 10(5) M-1 and 2.5 X 10(5) M-1, respectively. The average value is 100 times higher than that found for the binding of unmodified tetrasaccharide to the enzyme under the same conditions. The unsaturated tetrasaccharide proved to be a better inhibitor of the lysis of Micrococcus luteus cells than the parent compound by a factor of 35. These results support the hypothesis that the active site of the enzyme is constructed so as to bind the transition state for the reaction it catalyzes more firmly than the substrate itself.     

Microbial inhibitors of lysozyme

Lysozyme is one of the most important factors of innate immunity, possessing anti-microbial action against a wide range of microorganisms due to cationic nature of protein and, in a lesser degree, due to muramidase activity. In the process of evolution, different mechanisms of lysozyme inhibition, defined as anti-lysozyme activity (ALA), were formed in microorganisms. The usage of the delayed antagonism principle allowed to reveal anti-lysozyme sign in microorganisms of different phylogenetic groups. In the review, data on the occurrence and level of anti-lysozyme activity in pathogens and representatives of normal microflora were presented; findings on nature and genetic determinants of lysozyme inhibitors are given. questions on drug regulation of ALA of the causative agents in infectious diseases and dysbiotic conditions are discussed.     

Studies on bacterial cell wall inhibitors III. 3-amino-3-deoxy-D-glucose,an inhibitor of bacterial cell wall synthesis

It was shown that 3-amino-3-deoxy-D-glucose, one of the constituents of the kanamycin molecule and a metabolite of Bacillus sp., inhibits the bacterial synthesis of cell wall. The antibiotic (100 μg/ml) significantly inhibits the growth of Straphylococcis aureus FDA 209P as well as the incorporation of DL-[¹⁴C]alanine into the acid-insoluble macromolecular fraction of its growing cells in the presence of chloramphenicol (100 μg/ml). In contrast, the antibiotic doed not affect the incorporation of [³H]thymidine, [³H]uridine and L-[¹⁴C]leucine. The other constituents of kanamycin, 6-amino-6-deoxy-D-glucose and deoxystreptamine do not inhibit the synthesis of bacterial cell wall peptidoglycan.     

Cell wall substrate specificity of six different lysozymes and lysozyme inhibitory activity of bacterial extracts

We have investigated the specificity of six different lysozymes for peptidoglycan substrates obtained by extraction of a number of gram-negative bacteria and Micrococcus lysodeikticus with chloroform/Tris-HCl buffer (chloroform/buffer). The lysozymes included two that are commercially available (hen egg white lysozyme or HEWL, and mutanolysin from Streptomyces globisporus or M1L), and four that were chromatographically purified (bacteriophage lambda lysozyme or LaL, bacteriophage T4 lysozyme or T4L, goose egg white lysozyme or GEWL, and cauliflower lysozyme or CFL). HEWL was much more effective on M. lysodeikticus than on any of the gram-negative cell walls, while the opposite was found for LaL. Also the gram-negative cell walls showed remarkable differences in susceptibility to the different lysozymes, even for closely related species like Escherichia coli and Salmonella Typhimurium. These differences could not be due to the presence of lysozyme inhibitors such as Ivy from E. coli in the cell wall substrates because we showed that chloroform extraction effectively removed this inhibitor. Interestingly, we found strong inhibitory activity to HEWL in the chloroform/buffer extracts of Salmonella Typhimurium, and to LaL in the extracts of Pseudomonas aeruginosa, suggesting that other lysozyme inhibitors than Ivy exist and are probably widespread in gram-negative bacteria.     

Molecular basis of bacterial defense against host lysozymes: X-ray structures of periplasmic lysozyme inhibitors PliI and PliC

Lysozymes play a key role in the innate immune system of vertebrates and invertebrates by hydrolyzing peptidoglycan, a vital component of the bacterial cell wall. Gram-negative bacteria produce various types of lysozyme inhibitors that allow them to survive the bactericidal action of lysozyme when their outer membrane is permeabilized. So far, three lysozyme inhibitor families have been described: the Ivy (inhibitor of vertebrate lysozyme) family, the MliC/PliC (membrane-associated/periplasmic lysozyme inhibitor of C-type lysozyme) family, and the PliI (periplasmic lysozyme inhibitor of I-type lysozyme) family. Here, we report high-resolution crystal structures of Salmonella typhimurium PliC (PliC-St) and Aeromonas hydrophila PliI (PliI-Ah). The structure of PliI-Ah is the first in the recently discovered PliI family of lysozyme inhibitors, while the structure of PliC-St is the first structure of a periplasmic lysozyme inhibitor from the PliC/MliC family. Using small-angle X-ray scattering, we demonstrate that both PliC-St and PliI-Ah form stable dimers in solution. The functional dimer architecture of PliC-St is very different from that of the recently described MliC from Pseudomonas aeruginosa (MliC-Pa), despite the close resemblance of their monomers. Furthermore, PliI-Ah has distinctly different monomer and dimer folds compared to PliC, MliC, and Ivy proteins. Site-directed mutagenesis suggests that the inhibitory action of PliI-Ah proceeds via an insertion of a loop containing the conserved SGxY motif into the active center of I-type lysozymes. This motif is related to the functional SGxxY motif found in the MliC/PliC family.     

Breaching the great wall: peptidoglycan and microbial interactions

Once thought to be a process that occurred only in a few human pathogens, release of biologically active peptidoglycan fragments during growth by Gram-negative bacteria controls many types of bacterial interaction, including symbioses and interactions between microorganisms. This Perspective explores the role of peptidoglycan fragments in mediating a range of microbial-host interactions, and discusses the many systems in which peptidoglycan fragments released during bacterial growth might be active.     

Combinatorial enzymatic assay for the screening of a new class of bacterial cell wall inhibitors

We have developed a screening assay by thin-layer chromatography (TLC) to identify inhibitors for the bacterial essential enzymes MurA, -B, and -C. Libraries of compounds were synthesized using the mix-and-split combinatorial chemistry approach. Screening of the pooled compounds using the developed assay revealed the presence of many pools active in vitro. Pools of interest were tested for antibacterial activity. Individual molecules in the active pools were synthesized and retested with the TLC assay and with bacteria. We focused on the best five compounds for further analysis. They were tested for inhibition on each of the three enzymes separately, and showed no inhibition of MurA or MurB activity but were all inhibitors of MurC enzyme. This approach yielded interesting lead compounds for the development of novel antibacterial agents.     

Phosphorylated hydroxyethylamines as novel inhibitors of the bacterial cell wall biosynthesis enzymes MurC to MurF

Enzymes involved in the biosynthesis of bacterial peptidoglycan represent important targets for development of new antibacterial drugs. Among them, Mur ligases (MurC to MurF) catalyze the formation of the final cytoplasmic precursor UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid. We present the design, synthesis and biological evaluation of a series of phosphorylated hydroxyethylamines as new type of small-molecule inhibitors of Mur ligases. We show that the phosphate group attached to the hydroxyl moiety of the hydroxyethylamine core is essential for good inhibitory activity. The IC₅₀ values of these inhibitors were in the micromolar range, which makes them a promising starting point for the development of multiple inhibitors of Mur ligases as potential antibacterial agents. In addition, 1-(4-methoxyphenylsulfonamido)-3-morpholinopropan-2-yl dihydrogen phosphate 7a was discovered as one of the best inhibitors of MurE described so far.     

Identification of the folding inhibitors of hen-egg lysozyme: gathering the right tools

The unfolded state of proteins displays a surprisingly rich amount of local native structure, which appears to be critical for driving the protein to its native state. Peptides with the same sequence of the corresponding structured segments can be used to interfere with the correct folding of the protein. Using model simulations, we investigate the folding of hen-egg lysozyme, identifying its key segments. Activity assays, NMR and circular dichroism experiments are used to screen the peptides which are able to inhibit the folding of lysozyme. Few peptides, corresponding to the segments of the protein which are structured in the unfolded state, are identified to have significant inhibitory effects.     

Small molecule inhibitors of lysozyme amyloid aggregation

Protein amyloid aggregation is associated with a number of important human pathologies, but the precise mechanisms underlying the toxicity of amyloid aggregates are still incompletely understood. In this context, drugs capable of blocking or interfering with the aggregation of amyloidogenic proteins should be considered in strategies aimed at the development of novel therapeutic agents. Human lysozyme variants have been shown to form massive amyloid deposits in the livers and kidneys of individuals affected by hereditary systemic amyloidosis. Currently, there are no clinical treatments available to prevent or reverse formation of such amyloid deposits. We have recently described a number of di- and trisubstituted aromatic compounds that block the formation of soluble oligomers and amyloid fibrils of the β-amyloid peptide (Aβ) and protect hippocampal neurons in culture from Aβ-induced toxicity. Here, we show that some of those compounds inhibit the formation and disrupt preformed amyloid fibrils from both human and hen egg white lysozyme. These results suggest that these small molecule compounds may serve as prototypes for the development of drugs for the prevention or treatment of different types of amyloidoses.     

Cell wall degradation ofStaphylococcus aureus by lysozyme

In contrast to former findings lysozyme was able to attack the cell walls ofStaphylococcus aureus under acid conditions. However, experiments with¹⁴C-labelled cell walls and ribonuclease indicated that, under these conditions, lysozyme acted less as an muralytic enzyme but more as an activator of pre-existing autolytic wall enzymes. Electron microscopic studies showed that under these acid conditions the cell walls were degraded by a new mechanism (i.e. attack from the inside). This attack on the cell wall started asymmetrically within the region of the cross wall and induced the formation of periodically arranged lytic sites between the cytoplasmic membrane and the cell wall proper. Subsequently, a gap between the cell wall and the cytoplasmic membrane resulted and large cell wall segments became detached and suspended in the medium. The sequence of lytic events corresponded to processes known to take place during wall regeneration and wall formation. In the final stage of lysozyme action at pH 5 no cell debris but stabilized protoplasts were to be seen without detectable alterations of the primary shape of the cells. At the same time long extended ribbon-like structures appeared outside the bacteria. The origin as well as the chemical nature of this material is discussed. Furthermore, immunological implications are considered.