Lantibiotics are ribosomally synthesized peptides that undergo posttranslational modifications to their mature, antimicrobial form. They are characterized by the unique amino acids lanthionine and methyllanthionine, introduced by means of dehydration of Ser͞Thr residues followed by reaction of the resulting dehydro amino acids with cysteines to form thioether linkages. Two-component lantibiotics use two peptides that are each posttranslationally modified to yield two functionally distinct products that act in synergy to provide bactericidal activity. By using genetic data instead of isolation, a two-component lantibiotic, haloduracin, was identified in the genome of the Gram-positive alkaliphilic bacterium Bacillus halodurans C-125. We show that heterologously expressed and purified precursor peptides HalA1 and HalA2 are processed by the purified modification enzymes HalM1 and HalM2 in an in vitro reconstitution of the biosynthesis of a two-component lantibiotic. The activity of each HalM enzyme is substratespecific, and the assay products exhibit antimicrobial activity after removal of their leader sequences at an engineered Factor Xa cleavage site, indicating that correct thioether formation has occurred. Haloduracin's biological activity depends on the presence of both modified peptides. The structures of the two mature haloduracin peptides Hal␣ and Hal␤ were investigated, indicating that they have similarities as well as some distinct differences compared with other two-component lantibiotics.lanthionine ͉ dehydroalanine ͉ antibiotic

Modification of the phosphate groups of lipid A with 4-amino-4-deoxy-L-arabinose (L-Ara4N Lipopolysaccharide (LPS)1 is an immunogenic glycolipid that constitutes most of the outer leaflet of the outer membrane of Gram-negative bacteria (1-4). LPS consists of three domains, which are the O-antigen, the core oligosaccharide, and the lipid A moiety (1-4). The O-antigen functions as a protective barrier, whereas the core sugars maintain outer membrane integrity and provide an attachment site for the O-antigen (1-4). Lipid A is the hydrophobic membrane anchor of LPS, and it is the active (endotoxin) component of LPS, accounting for many of the pathophysiological effects associated with Gram-negative sepsis (5-7).The Kdo 2 -lipid A portion of LPS is sufficient to support growth in Escherichia coli and Salmonella typhimurium (2). Covalent modifications to Kdo 2 -lipid A can be induced by environmental stimuli, such as low Mg 2ϩ concentrations or low pH (8 -10). As shown in Fig. 1 for S. typhimurium, these modifications include the incorporation of palmitate (11, 12), the addition of phosphoethanolamine (pEtN) (13-15), and/or the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) moieties (13,16,17). The modification of at least one phosphate residue with L-Ara4N is required for maintaining resistance to certain cationic antimicrobial peptides of the innate immune system and to the antibiotic polymyxin (18,19). Resistance is due, in part, to the neutralization of the negative charges of lipid A by L-Ara4N, reducing the affinity of lipid A for cationic substances (20) and preventing these anti-microbial compounds from penetrating the outer membrane.The addition of pEtN and L-Ara4N groups to lipid A is controlled by the PmrA/PmrB two-component regulatory system, which is activated by low pH, high Fe 3ϩ levels, or indirectly, by low concentrations of Mg 2ϩ via the PhoP/PhoQ system through the action of PmrD (9). Activated PmrA stimulates transcription at the pmrCAB, pmrE(ugd) , and pmrHFIJKLM loci (19,21). Constitutive pmrA (pmrA c ) mutants of E. coli and S. typhimurium are polymyxin-resistant, and they modify their lipid A with L-Ara4N and pEtN groups under all growth conditions (17,18,22). Inactivation of either pmrE or the genes in the pmrHFIJKLM operon results in complete loss of polymyxin resistance and of L-Ara4N-modified lipid A in pmrA c bacterial cells (19,21,23). Similarly, pmrA c mutants harboring a nonpolar disruption of the pmrC(eptA) gene are unable * This research was supported by National Institutes of Health Grant GM-51310 (to C. R. H. R.). The Duke University NMR Center is partially supported by P30-CA-14236. NMR instrumentation in the Center was funded by the National Science Foundation, the National Institutes of Health, the North Carolina Biotechnology Center, and Duke University. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fac...

The zinc-dependent enzyme LpxC catalyzes the deacetylation of UDP-3-O-acyl-GlcNAc, the first committed step of lipid A biosynthesis. Lipid A is an essential component of the outer membranes of most Gram-negative bacteria, including Escherichia coli, Salmonella enterica and Pseudomonas aeruginosa, making LpxC an attractive target for antibiotic design. The inhibition of LpxC by a novel N-aroyl-L-threonine hydroxamic acid (CHIR-090) from a recent patent application (International Patent WO 2004/062601 A2 to Chiron and the University of Washington) is reported here. CHIR-090 possesses remarkable antibiotic activity against both E. coli and P. aeruginosa, comparable to that of ciprofloxacin. The biological activity of CHIR-090 is explained by its inhibition of diverse LpxC orthologs at low nM concentrations, including that of Aquifex aeolicus, for which structural information is available. The inhibition of A. aeolicus LpxC by CHIR-090 occurs in two steps. The first step is rapid and reversible, with a K i of 1.0 -1.7 nM, depending on the method of assay. The second step involves the conversion of the EI complex with a half-life of about a minute to a tightly bound form. The second step is functionally irreversible but does not result in the covalent modification of the enzyme, as judged by electrospray-ionization mass spectrometry. CHIR-090 is the first example of a slow, tight-binding inhibitor for LpxC, and may be the prototype for a new generation of LpxC inhibitors with therapeutic applicability.The emergence of multi-drug resistant bacterial pathogens is a growing public health concern (1). Human and animal pathogens are developing resistance to every major class of commercial antibiotic, both natural and synthetic. New antibiotics directed against previously unexploited bacterial targets are urgently needed (2-4).Zinc-dependent hydrolases are a well-studied class of proteins, many of which have set successful precedents for mechanism-based inhibitor design (5-7). Several bacterial metalloamidases have been identified as potential antibiotic targets (7). Among them is LpxC, a zincdependent, cytoplasmic deacetylase involved in the biosynthesis of the lipid A component of lipopolysaccharide (Scheme 1) (8-11).LpxC removes the acetate group from the nitrogen atom at the glucosamine 2 position of UDP-3-O-acyl-N-acetylglucosamine (Scheme 1) (12,13). This reaction is the first committed step of lipid A biosynthesis (14) and is essential for bacterial growth (12,13 Despite its unique substrate specificity and sequence, LpxC does share some mechanistic features with other important metallo-amidases. As in thermolysin (18), angiotensinconverting enzyme (5,19), the matrix metallo-proteinases (6), and peptide N-deformylase (20), a single transition metal ion is required for LpxC catalytic activity (9) and a glutamate side chain in the LpxC active site is thought to activate the Zn 2+ -bound water (21). Selective chelation of the LpxC active site Zn 2+ ion by certain small molecules containing hydroxamic acid group...

The zinc-dependent UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) catalyzes the first committed step in the biosynthesis of lipid A, the hydrophobic anchor of lipopolysaccharide (LPS) that constitutes the outermost monolayer of Gram-negative bacteria. As LpxC is crucial for the survival of Gram-negative organisms and has no sequence homology to known mammalian deacetylases or amidases, it is an excellent target for the design of new antibiotics. The solution structure of LpxC from Aquifex aeolicus in complex with a substrate-analog inhibitor, TU-514, reveals a novel alpha/beta fold, a unique zinc-binding motif and a hydrophobic passage that captures the acyl chain of the inhibitor. On the basis of biochemical and structural studies, we propose a catalytic mechanism for LpxC, suggest a model for substrate binding and provide evidence that mobility and dynamics in structural motifs close to the active site have key roles in the capture of the substrate.

Summary The lantibiotic haloduracin consists of two post-translationally processed peptides, Halα and Halβ, that act in synergy to provide bactericidal activity. An in vitro haloduracin production system was utilized to examine the biological impact of disrupting individual thioether rings in each peptide. Surprisingly, the Halα B-ring, which contains a highly conserved CTLTXEC motif, was expendable. This motif has been proposed to interact with haloduracin’s predicted target, lipid II. Exchange of the glutamate residue in this motif for alanine or glutamine did completely abolish antibacterial activity. This study also established that Halα-Ser26 and Halβ-Ser22 escape dehydration, requiring revision of the Halβ structure previously proposed. Extracellular proteases secreted by the producer strain can remove the leader peptide, and the Halα cystine that is dispensable for bioactivity protects Halα from further proteolytic degradation.

Lipopolysaccharide, the major constituent of the outer monolayer of the outer membrane of Gram-negative bacteria, is anchored into the membrane through the hydrophobic moiety lipid A, a hexaacylated disaccharide. The zinc-dependent metalloamidase UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) catalyzes the second and committed step in the biosynthesis of lipid A. LpxC shows no homology to mammalian metalloamidases and is essential for cell viability, making it an important target for the development of novel antibacterial compounds. Recent NMR and X-ray studies of the LpxC from Aquifex aeolicus have provided the first structural information about this family of proteins. Insight into the catalytic mechanism and the design of effective inhibitors could be facilitated by more detailed structural and biochemical studies that define substrate-protein interactions and the roles of specific residues in the active site. Here, we report the synthesis of the (13)C-labeled substrate-analogue inhibitor TU-514, and the subsequent refinement of the solution structure of the A. aeolicus LpxC-TU-514 complex using residual dipolar couplings. We also reevaluate the catalytic role of an active site histidine, H253, on the basis of both its pK(a) as determined by NMR titration and pH-dependent kinetic analyses. These results provide a structural basis for the design of more potent LpxC inhibitors than those that are currently available.

The lantibiotic synthetases LctM and HalM2 are bifunctional enzymes that catalyze both the dehydration of serine and threonine residues and the Michael-type additions of cysteine residues to the resulting dehydroamino acids in their substrate peptides. Using Fourier transform mass spectrometry to analyze these activities in vitro, the dehydration is shown to take place by a distributive mechanism, with build-up of intermediates observed in electrospray mass spectra. The cyclization activity of HalM2 was monitored through alkylation of free cysteines in intermediates, providing access to the regioselectivity of lanthionine ring formation using high-resolution tandem mass spectrometry. HalM2 is shown to catalyze the cyclization process in a largely N- to C-terminal directional fashion, forming a total of four lanthionine rings in its HalA2 substrate. These studies advance a model for lantibiotic production where substrate binding via an N-terminal leader results in dehydration and cyclization on similar time scales and with a high, though not strict, propensity for N-to-C directionality.

The deacetylation of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine (UDP-3-O-acylGlcNAc) by LpxC is the committed reaction of lipid A biosynthesis. CHIR-090, a novel N-aroyl-Lthreonine hydroxamic acid, is a potent, slow, tight-binding inhibitor of the LpxC deacetylase from the hyperthermophile Aquifex aeolicus, and it has excellent antibiotic activity against P. aeruginosa and E. coli, as judged by disk diffusion assays. We now report that CHIR-090 is also a two-step slow, tight-binding inhibitor of Escherichia coli LpxC with K i = 4.0 nM, K i * = 0.5 nM, k 5 = 1.9 min -1 and k 6 = 0.18 min -1 . CHIR-090 at low nM levels inhibits LpxC orthologues from diverse Gram-negative pathogens, including Pseudomonas aeruginosa, Neisseria meningitidis, and Helicobacter pylori. In contrast, CHIR-090 is a relatively weak competitive and conventional inhibitor (lacking slow, tight-binding kinetics) of LpxC from Rhizobium leguminosarum (K i = 340 nM), a Gram-negative plant endosymbiont that is resistant to this compound. The K M (4.8 μM) and the k cat (1.7 s -1 ) of R. leguminosarum LpxC with UDP-3-O-(R-3-hydroxymyristoyl)-Nacetylglucosamine as the substrate are similar to values reported for E. coli LpxC. R. leguminosarum LpxC therefore provides a useful control for validating LpxC as the primary target of CHIR-090 in vivo. An E. coli construct in which the chromosomal lpxC gene is replaced by R. leguminosarum lpxC is resistant to CHIR-090 up to 100 μg/mL, or 400 times above the minimal inhibitory concentration for wild-type E. coli. Given its relatively broad spectrum and potency against diverse Gram-negative pathogens, CHIR-090 is an excellent lead for the further development of new antibiotics targeting the lipid A pathway.The emergence of multi-drug resistant bacteria in hospital and community clinics has created an urgent need for new antibiotics (1,2). About half of the multi-drug resistant bacteria are Gram-negative pathogens (2), including strains of Escherichia coli, Pseudomonas aeruginosa (1), and Acinetobacter baumannii (3). Inhibitors that exploit traditional antibiotic targets, such as peptidoglycan, DNA replication or protein biosynthesis (4), are becoming less effective (2). These obstacles could be overcome by developing inhibitors of novel targets required for bacterial growth (5,6).The biosynthesis of the lipid A component of lipopolysaccharide (LPS), a unique, outermembrane lipid that shields Gram-negative bacteria from environmental stresses (7,8), is a promising target for new antibiotic development (9-12). The lipid A moiety of LPS is a hexaacylated disaccharide of glucosamine (7,8) (Figure 1). Although inhibition of any one of the first six enzymes of lipid A biosynthesis is lethal to E. coli (8), the most promising target identified to date is LpxC (9-12), a unique deacetylase that is selective for UDP-3-O-(R-3-*Author to whom correspondence should be addressed: C. R. H. Raetz at (919) Fax (919) LpxC is a zinc-dependent amidase with a catalytic mechanism related to that of carboxypeptida...