PurA is the main target of aurodox, a type III secretion system inhibitor.

Anti-microbial resistance (AMR) is one of the greatest threats to global health. The continual battle between the emergence of AMR and the development of drugs will be extremely difficult to stop as long as traditional anti-biotic approaches are taken. In order to overcome this impasse, we here focused on the type III secretion system (T3SS), which is highly conserved in many Gram-negative pathogenic bacteria. The T3SS is known to be indispensable in establishing disease processes but not essential for pathogen survival. Therefore, T3SS inhibitors may be innovative anti-infective agents that could dramatically reduce the evolutionary selective pressure on strains resistant to treatment. Based on this concept, we previously identified a polyketide natural product, aurodox (AD), as a specific T3SS inhibitor using our original screening system. However, despite its promise as a unique anti-infective drug of AD, the molecular target of AD has remained unclear. In this paper, using an innovative chemistry and genetic biology-based approach, we show that AD binds to adenylosuccinate synthase (PurA), which suppresses the production of the secreted proteins from T3SS, resulting in the expression of bacterial virulence both in vitro and in vivo experiments. Our findings illuminate the potential of PurA as a target of anti-infective drugs and vaccination and could open a avenue for application of PurA in the regulation of T3SS.

Biosynthesis of Aurodox, a Type III Secretion System Inhibitor from Streptomyces goldiniensis.

The global increase in antimicrobial-resistant infections means that there is a need to develop new antimicrobial molecules and strategies to combat the issue. Aurodox is a linear polyketide natural product that is produced by Streptomyces goldiniensis, yet little is known about aurodox biosynthesis or the nature of the biosynthetic gene cluster (BGC) that encodes its production. To gain a deeper understanding of aurodox biosynthesis by S. goldiniensis, the whole genome of the organism was sequenced, revealing the presence of an 87 kb hybrid polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) BGC. The aurodox BGC shares significant homology with the kirromycin BGC from S. collinus Tϋ 365. However, the genetic organization of the BGC differs significantly. The candidate aurodox gene cluster was cloned and expressed in a heterologous host to demonstrate that it was responsible for aurodox biosynthesis and disruption of the primary PKS gene (aurAI) abolished aurodox production. These data supported a model whereby the initial core biosynthetic reactions involved in aurodox biosynthesis followed that of kirromycin. Cloning aurM* from S. goldiniensis and expressing this in the kirromycin producer S. collinus Tϋ 365 enabled methylation of the pyridone group, suggesting this is the last step in biosynthesis. This methylation step is also sufficient to confer the unique type III secretion system inhibitory properties to aurodox. IMPORTANCE Enterohemorrhagic Escherichia coli (EHEC) is a significant global pathogen for which traditional antibiotic treatment is not recommended. Aurodox inhibits the ability of EHEC to establish infection in the host gut through the specific targeting of the type III secretion system while circumventing the induction of toxin production associated with traditional antibiotics. These properties suggest aurodox could be a promising anti-virulence compound for EHEC, which merits further investigation. Here, we characterized the aurodox biosynthetic gene cluster from Streptomyces goldiniensis and established the key enzymatic steps of aurodox biosynthesis that give rise to the unique anti-virulence activity. These data provide the basis for future chemical and genetic approaches to produce aurodox derivatives with increased efficacy and the potential to engineer novel elfamycins.

Insights into the structure-activity relationship of a type III secretion system inhibitor, aurodox.

Aurodox was originally isolated in 1972 as a linear polyketide compound exhibiting antibacterial activity against Gram-positive bacteria. We have since identified aurodox as a specific inhibitor of the bacterial type III secretion system (T3SS) using our original screening system for inhibition of T3SS-mediated hemolysis in enteropathogenic Escherichia coli (EPEC). In this research, we synthesized 15 derivatives of aurodox and evaluated EPEC T3SS inhibitory activity as well as antibacterial activity against EPEC. One of the derivatives was highly selective for T3SS inhibition, equivalent to that of aurodox, but without exhibiting antibacterial activity (69-fold selectivity). This work revealed the structure-activity relationship for the inhibition of T3SS by aurodox and suggests that the target of T3SS is distinct from the target for antibacterial activity.

Characterization of the Mode of Action of Aurodox, a Type III Secretion System Inhibitor from Streptomyces goldiniensis.

Recent work has demonstrated that the polyketide natural product Aurodox from Streptomyces goldiniensis is able to block the pathogenesis of the murine pathogen Citrobacter rodentium In this work, we aimed to gain a better understanding of the mechanism of action of the compound. We show that Aurodox downregulates the expression of the type III secretion systems of enteropathogenic and enterohemorrhagic Escherichia coli Furthermore, we have used transcriptomic analysis to show that Aurodox inhibits the expression at the transcriptional level by repressing the master regulator, ler Our data support a model in which Aurodox acts upstream of ler and not directly on the secretion system itself. Finally, we have shown that Aurodox, unlike some traditional antibiotics, does not induce expression of RecA, which is essential for the production of Shiga toxin. We propose that these properties nominate Aurodox as a promising antivirulence therapy for the treatment of these infections.

An NF-κB-based high-throughput screen identifies piericidins as inhibitors of the Yersinia pseudotuberculosis type III secretion system.

The type III secretion system (T3SS) is a bacterial appendage used by dozens of Gram-negative pathogens to subvert host defenses and cause disease, making it an ideal target for pathogen-specific antimicrobials. Here, we report the discovery and initial characterization of two related natural products with T3SS-inhibitory activity that were derived from a marine actinobacterium. Bacterial extracts containing piericidin A1 and the piericidin derivative Mer-A 2026B inhibited Yersinia pseudotuberculosis from triggering T3SS-dependent activation of the host transcription factor NF-κB in HEK293T cells but were not toxic to mammalian cells. As the Yersinia T3SS must be functional in order to trigger NF-κB activation, these data indicate that piericidin A1 and Mer-A 2026B block T3SS function. Consistent with this, purified piericidin A1 and Mer-A 2026B dose-dependently inhibited translocation of the Y. pseudotuberculosis T3SS effector protein YopM inside CHO cells. In contrast, neither compound perturbed bacterial growth in vitro, indicating that piericidin A1 and Mer-A 2026B do not function as general antibiotics in Yersinia. In addition, when Yersinia was incubated under T3SS-inducing culture conditions in the absence of host cells, Mer-A 2026B and piericidin A1 inhibited secretion of T3SS cargo as effectively as or better than several previously described T3SS inhibitors, such as MBX-1641 and aurodox. This suggests that Mer-A 2026B and piericidin A1 do not block type III secretion by blocking the bacterium-host cell interaction, but rather inhibit an earlier stage, such as T3SS needle assembly. In summary, the marine-derived natural products Mer-A 2026B and piericidin A1 possess previously uncharacterized activity against the bacterial T3SS.

A small-molecule inhibitor of the bacterial type III secretion system protects against in vivo infection with Citrobacter rodentium.

The type III secretion system (T3SS) is highly conserved in many Gram-negative pathogenic bacteria and functions as an injector of bacterial proteins (effectors) into host cells. T3SSs are involved in establishing disease processes, but this machinery is not essential for bacterial growth or homeostasis. Thus, T3SS is expected to be a candidate therapeutic target, and inhibitors of T3SSs could potentially reduce virulence without causing bacterial death, thereby avoiding any subsequent development of resistance. We identified a linear polyketide compound, aurodox, as a specific T3SS inhibitor from the culture broth of Streptomyces sp. using a screening system for the T3SS-mediated hemolysis of enteropathogenic Escherichia coli (EPEC) established by our group. Aurodox strongly inhibited T3SS-mediated hemolysis with an IC(50) value of 1.5 µg ml(-1) without affecting bacterial growth in liquid media. We also demonstrated that aurodox specifically inhibits the secretion of type III-secreted proteins such as EspB, EspF and Map, without affecting the expression of the housekeeping protein GroEL. Furthermore, an in vivo infection study using mice clearly indicated that the administration of aurodox allowed the mice to survive a lethal dose of Citrobactor rodentium, a model bacterium for human pathogens such as EPEC. Thus, our in vivo study directly demonstrated for the first time that this putative T3SS inhibitor can be applied as a novel class of anti-infective agents.

Differential susceptibilities of enterococcal species to elfamycin antibiotics.

The elfamycins are a class of naturally occurring antibiotics not currently used in the therapy of human disease. Enterococcus faecium and closely related species (Enterococcus durans and Enterococcus hirae) are susceptible to these antibiotics, while isolates of Enterococcus faecalis and other enterococcal species are highly resistant. Among enterococci, susceptibility or resistance to elfamycins appears to be determined by the bacterial protein synthesis elongation factor EF-Tu. Elfamycin susceptibility may be a useful adjunct for rapidly distinguishing E. faecalis and E. faecium in the clinical microbiology laboratory and/or as a supplementary test for use in determining the species of enterococci.

A83016F, a new member of the aurodox family.

A new member of the aurodox family of antibiotics, A83016F, has been isolated from an unidentified actionmycete designated A83016. The structure and relative stereochemistry of A83016F were elucidated by NMR examination of the parent compound and its diacetate derivative. A83016F exhibits only weak antimicrobial activity.

Comparison of the Tu elongation factors from Staphylococcus aureus and Escherichia coli: possible basis for elfamycin insensitivity.

In a previous study (C. C. Hall, J. D. Watkins, and N. H. Georgopapadakou, Antimicrob. Agents Chemother. 33:322-325, 1989), the elongation factor Tu (EF-Tu) from Staphylococcus aureus was found to be insensitive to a series of kirromycin analogs which were inhibitory to the EF-Tu from Escherichia coli. In the present study, the EF-Tu from S. aureus was partially purified and characterized. Its apparent molecular mass was approximately 41,000 Da, and the enzyme copurified with EF-Ts (molecular mass, 34,000 Da). S. aureus EF-Tu differed from its E. coli counterpart in that it bound negligible amounts of [3H]GDP, in addition to being insensitive to pulvomycin and aurodox (50% inhibitory concentrations, approximately 100 and 1,000 microM, respectively, versus 2 and 0.2 microM, respectively, for E. coli). The results are consistent with the formation of a stable EF-Tu.EF-Ts complex that affects the interaction of EF-Tu with guanine nucleotides and inhibitors.

The structure of heneicomycin.

The antibiotic heneicomycin (1), C44H62N2O11, was isolated from cultures of Streptomyces filipinensis as an amorphous yellow powder. Mass spectral and NMR analysis showed the compound to be a deoxy modification of aurodox (2), a member of the elfamycin antibiotic family. A marked change in mass spectral fragmentation compared to aurodox and 1H NMR couplings indicated the absence of the hydroxyl at position 30 of aurodox (position 3 of the tetrahydropyran).

Antibiotic SB22484: a novel complex of the aurodox group. I. Taxonomy of the producing organism, isolation of the antibiotics and chemical and biological characterization.

Antibiotic SB22484 is a novel member of the aurodox type antibiotic group produced in submerged-fermentation cultures of Streptomyces sp. NRRL 15496. The antibiotic complex is composed of two pairs of isomers with MW's of 752 and 766. The individual isomers, which were separated by preparative HPLC, equilibrate to a mixture of the isomer pair when left in aqueous solution. In vitro, SB22484 antibiotics strongly inhibited neisseriae and were also active against Streptococci, Ureaplasma urealyticum and Haemophilus influenzae.

Effects of nucleotide- and aurodox-induced changes in elongation factor Tu conformation upon its interactions with aminoacyl transfer RNA. A fluorescence study.

The effects of GDP and of aurodox (N-methylkirromycin) on the affinity of elongation factor Tu (EF-Tu) for aminoacyl-tRNA (aa-tRNA) have been quantified spectroscopically by using Phe-tRNA(Phe)-Fl8, a functionally active analogue of Phe-tRNA(Phe) with a fluorescein dye convalently attached to the s4U-8 base. The association of EF-Tu.GDP with Phe-tRNA(Phe)-Fl8 resulted in an average increase of 33% in fluorescein emission intensity. This spectral change was used to monitor the extent of ternary complex formation as a function of EF-Tu.GDP concentration, and hence to obtain a dissociation constant, directly and at equilibrium, for the EF-Tu.GDP-containing ternary complex. The Kd for the Phe-tRNA(Phe)-Fl8.EF-Tu.GDP complex was found to average 28.5 microM, more than 33,000-fold greater than the Kd of the Phe-tRNA(Phe)-Fl8.EF-Tu.GTP complex under the same conditions. In terms of free energy, the delta G degree for ternary complex formation at 6 degrees C was -11.5 kcal/mol with GTP and -5.8 kcal/mol with GDP. Thus, the hydrolysis of the ternary complex GTP results in a dramatic decrease in the affinity of EF-Tu for aa-tRNA, thereby facilitating the release of EF-Tu.GDP from the aa-tRNA on the ribosome. Aurodox (200 microM) decreased the Kd of the GDP complex by nearly 20-fold, to 1.46 microM, and increased the Kd of the GTP complex by at least 6-fold. The binding of aurodox to EF-Tu therefore both considerably strengthens EF-Tu.GDP affinity for aa-tRNA and also weakens EF-Tu.GTP affinity for aa-tRNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Conformation and reactivity changes induced by N-methylkirromycin (aurodox) in elongation factor Tu.

Kirromycin and related antibiotics inhibit protein synthesis in bacteria by acting on elongation factor Tu (EF-Tu). We have studied the effects of N-methylkirromycin (aurodox) on some molecular properties of this protein. The binding of the antibiotic causes a dramatic variation in the protein fluorescence emission spectrum with the appearance of a new maximum at around 340 nm. Addition of aurodox to trypsinized EF-Tu resulted in an emission spectrum similar to that of the denatured intact factor. Fluorescence lifetime analysis performed by a multifrequency phase fluorometer indicated that the fluorescence emission of the factor is heterogeneous with the major component having a lifetime near 4.8 ns in the absence and 6.6 ns in the presence of the antibiotic. These results were interpreted in terms of an antibiotic-induced environmental modification of the unique tryptophan residue of the protein leading to an increase in its quantum yield. However, aurodox did not modify the solvent exposure of this residue, as judged by fluorescence quenching experiments. Moreover, 1-anilino-8-naphthalenesulfonate (ANS) binding studies, as well as analysis of the protein reactivity toward the sulfhydryl group reagent 5,5'-dithiobis(2-nitrobenzoate) (DTNB), showed that, in the presence of aurodox, the behavior of the EF-Tu-GDP complex nears that of EF-Tu.GTP. These results strongly support the hypothesis that aurodox not only confers a "GTP-like" conformation to the EF-Tu.GDP complex but also produces a less stable folding of the protein around the tryptophan residue that may contribute to the multiple functional effects of this antibiotic.

Effects of elfamycins on elongation factor Tu from Escherichia coli and Staphylococcus aureus.

Six kirromycin analogs (elfamycins) were compared on the basis of their inhibition of Escherichia coli poly(U)-directed poly(Phe) synthesis and stimulation of elongation factor Tu (EF-Tu)-associated GTPase activity. The elfamycins tested were kirromycin, aurodox, efrotomycin, phenelfamycin A, unphenelfamycin, and L-681,217. The last three lack the pyridone ring present in the other elfamycins. All the elfamycins inhibited poly(U)-dependent poly(Phe) synthesis and stimulated EF-Tu-associated GTPase activity, suggesting that the pyridone ring is not essential for activity. The six elfamycins were also examined in a poly(U)-directed, poly(Phe)-synthesizing system derived from Staphylococcus aureus and had 50% inhibitory concentrations of greater than or equal to 1 mM. When S. aureus ribosomes and E. coli elongation factors were combined in a hybrid poly(Phe)-synthesizing system, aurodox produced essentially complete inhibition of poly(Phe) synthesis with a 50% inhibitory concentration of 0.13 microM. This suggests that the observed high MICs of kirromycin and its congeners in S. aureus reflect a kirromycin-resistant EF-Tu rather than permeability constraints.

Characterization of the GTPase reaction of elongation factor Tu. Determination of the stereochemical course in the presence of antibiotic X5108.

The stereochemical course of the GTPase of elongation factor Tu from Escherichia coli has been determined by making use of the reaction dependent on antibiotic X5108 (an N-methylated derivative of kirromycin). Guanosine 5'-(gamma-thio)triphosphate stereospecifically labeled with 17O and 18O in the gamma-position was hydrolyzed in the presence of elongation factor Tu and X5108. The configuration of the product, inorganic [16O, 17O, 18O]thiophosphate was analyzed by 31P NMR after its stereospecific incorporation into adenosine 5'-(beta-thio)triphosphate. The analysis showed that the hydrolysis proceeds with inversion of configuration at the transferred phosphorus, implying that there is not a phosphoenzyme intermediate. Incubation of [beta gamma-18O, gamma-18O3]GTP with elongation factor Tu leaves the 18O-labeling unaltered, as shown by 31P NMR. No exchange of oxygens with water nor beta gamma-beta positional isotope exchange occurs, implying that not even transient cleavage can occur with the elongation factor alone. Only on interaction with X5108, kirromycin, or ribosomes does the cleavage occur, most likely by a single step, in-line transfer of the terminal phosphorus from GDP to a water oxygen. These properties of the GTP hydrolysis mechanism of elongation factor Tu are similar to those of elongation factor G.

Synthetic analogs of aurodox and kirromycin active on elongation factor Tu from Escherichia coli.

The activities of kirromycin oxime, aurodox 2,4-dinitrophenylhydrazone and four O-derivatives of aurodox have been compared to those of kirromycin (mocimycin) and its natural N-methyl analog aurodox in the in vitro system of E. coli. All synthetic derivatives were able to inhibit protein biosynthesis like the original antibiotics. Moreover, the analogs did promote all the effects of kirromycin on the reactions dependent on elongation factor Tu. From these results it can be concluded that the acidic hydroxyl and keto functions of kirromycin and aurodox are not directly involved in the action of the antibiotics on elongation factor Tu and can, thus, be chemically modified without loss of activity. In most cases, however, derivatization lowered the affinity of the antibiotic for elongation factor Tu. This suggests that the pyridone moiety of kirromycin and aurodox and the first part of its side chain should play a role in the association of these antibiotics with elongation factor Tu.

Spectrophotometric and kinetic studies on the interaction of antibiotic X5108, the N-methylated derivative of kirromycin, with elongation factor Tu from Escherichia coli.

The absorption spectrum of antibiotic X5108, the N-methylated derivative of kirromycin, has been found to be decreased in intensity on binding to elongation factor (EF)-Tu . GDP, EF-Tu . GTP, and nucleotide-free EF-Tu. This has allowed the binding of X5108 to be studied directly. In agreement with previous studies, a 1:1 stoichiometry is observed, with a dissociation constant of less than 1 microM. Identical results were obtained with all three EF-Tu species. The absorption spectrum of X5108 in increasing concentrations of isopropyl alcohol first intensifies and then decreases, 80% isopropyl alcohol giving the same spectrum as that of X5108 bound to EF-Tu. This result is interpreted as showing that the chromophoric moiety of X5108 is bound in a highly hydrophobic environment on EF-Tu. The rate of binding of X5108 to EF-Tu . GDP was measured using a stopped flow spectrophotometer. This rate was proportional to the concentration of X5108, giving a second order binding rate constant of 4.8 X 10(3) M-1 s-1. Since this is several orders of magnitude too slow for a diffusion-controlled reaction, the results are interpreted based on a two-step binding process. A half-time of about 10 min is calculated for the dissociation of X5108 from EF-Tu . GDP. The fact that X5108 bound to EF-Tu is not in rapid equilibrium with X5108 free in solution needs to be considered in studies on the effect of X5108 and kirromycin on partial reactions of protein biosynthesis.

Induction of resistance to aurodox by aurodox in the antibiotic-producing culture, Streptomyces goldiniensis.

The sensitivity of protein and aurodox synthesis to aurodox was examined in relationship to the development of resistance to aurodix on Streptomyces goldiniensis during fermentation. It was found that the culture remains sensitive to the antibiotic as long as no aurodox is present in the medium. Resistance only develops when aurodox is present, either exogenously added or endogenously synthesized by the culture. These observations suggest that the development of resistance is an inducible process, and evidence is presented indicating that aurodox induces a specific resistance system in S. goldiniensis.