NMR studies of interactions between periplasmic chaperones from uropathogenic E. coli and pilicides that interfere with chaperone function and pilus assembly

Adherence of uropathogenic Escherichia coli to host tissue is mediated by pili, which are hair-like protein structures extending from the outer cell membrane of the bacterium. The chaperones FimC and PapD are key components in pilus assembly since they catalyse folding of subunits that are incorporated in type 1 and P pili, respectively, and also transport the subunits across the periplasmic space. Recently, compounds that inhibit pilus biogenesis and interfere with chaperone-subunit interactions have been discovered and termed pilicides. In this paper NMR spectroscopy was used to study the interaction of different pilicides with PapD and FimC in order to gain structural knowledge that would explain the effect that some pilicides have on pilus assembly. First relaxation-edited NMR experiments revealed that the pilicides bound to the PapD chaperone with mM affinity. Then the pilicide-chaperone interaction surface was investigated through chemical shift mapping using 15N-labelled FimC. Principal component analysis performed on the chemical shift perturbation data revealed the presence of three binding sites on the surface of FimC, which interacted with three different classes of pilicides. Analysis of structure-activity relationships suggested that pilicides reduce pilus assembly in E. coli either by binding in the cleft of the chaperone, or by influencing the orientation of the flexible F1-G1 loop, both of which are part of the surface by which the chaperone forms complexes with pilus subunits. It is suggested that binding to either of these sites interferes with folding of the pilus subunits, which occurs during formation of the chaperone-subunit complexes. In addition, pilicides that influence the F1-G1 loop also appear to reduce pilus formation by their ability to dissociate chaperone-subunit complexes.     

Synthesis and evaluation of dihydroimidazolo and dihydrooxazolo ring-fused 2-pyridones—targeting pilus biogenesis in uropathogenic bacteria

Dihydrothiazolo ring-fused 2-pyridones have previously been shown to inhibit pilus assembly in uropathogenic Escherichia coli. Methods have now been developed to synthesize both dihydroimidazolo and dihydrooxazolo ring-fused 2-pyridones. To obtain the nitrogen analogs, Cbz-protected imidazolines were reacted with an acyl-Meldrum's acid derivative under acidic conditions. To prepare the oxygen analogs, a one-pot procedure was developed that allowed synthesis of dihydrooxazolo ring-fused 2-pyridones starting from acylated serine derivatives. After hydrolysis to their corresponding carboxylic acids and lithium carboxylates, biological evaluation revealed that the sulfur could be replaced by an oxygen atom and still maintains the ability to inhibit pilus assembly in uropathogenic E. coli. However, introducing a secondary amine instead of oxygen resulted in a substantial decrease in biological activity.     

Stereoselective synthesis of optically active beta-lactams, potential inhibitors of pilus assembly in pathogenic bacteria

[reaction: see text] Optically active beta-lactams 3 are obtained in excellent yields (up to 93%) and with complete stereoselectivity from Meldrum's acid derivatives 1 and Delta(2)-thiazolines 2. A selective reduction to aldehydes 5 (R = Ar or CH(2)Ar) was then accomplished by using DIBAL-H. This rigid framework, with stereochemistry different than that of penicillin, is designed to be a suitable scaffold for the development of compounds inhibiting pilus formation in uropathogenic Escherichia coli.     

Functionalization of bicyclic 2-pyridones targeting pilus biogenesis in uropathogenic Escherichia coli

Substituted bicyclic 2-pyridones, termed pilicides, prevent pilus assembly in uropathogenic Escherichia coli. Based on the bioactive methyl ester protected 2-pyridone 4, further functionalization at C-6 has yielded a set of new compounds, which have been evaluated for their ability to inhibit pilus formation in uropathogenic E. coli. The key intermediate in the synthesis was formylated 2-pyridone 5, which could be obtained via a Vilsmeier reaction. This versatile intermediate was converted into secondary and tertiary amines via reductive amination and could also be converted to other interesting functionalities using simple chemical transformations.     

Synthetic polymer nanoparticles conjugated with FimH(A) from E. coli pili to emulate the bacterial mode of epithelial internalization

Amphiphilic block copolymer nanoparticles are conjugated with uropathogenic Escherichia coli type 1 pilus adhesin FimH(A) through amidation chemistry to enable bladder epithelial cell binding and internalization of the nanoparticles in vitro.     

Antimicrobial photodynamic efficacy of side-chain functionalized benzo[a]phenothiazinium dyes

5-(Ethylamino)-9-diethylaminobenzo[a]phenothiazinium chloride (EtNBS) is a photosensitizer (PS) with broad antimicrobial photodynamic activity. The objective of this study was to determine the antimicrobial photodynamic effect of side chain/end group modifications of EtNBS on two representative bacterial Gram-type-specific strains. Two EtNBS derivatives were synthesized, each functionalized with a different side-chain end-group, alcohol or carboxylic acid. In solution, both exhibited photochemical properties consistent with those of the EtNBS parent molecule. In vitro photodynamic therapy experiments revealed an initial Gram-type-specificity with two representative strains; both derivatives were phototoxic to Staphylococcus aureus 29,213 but the carboxylic acid derivative was nontoxic to Escherichia coli 25,922. This difference in photodynamic efficacy was not due to a difference in the binding of the two molecules to the bacteria as the amount of both derivatives bound by bacteria was identical. Interestingly, the carboxylic acid derivative produced no fluorescence emission when observed in cultures of E. coli via fluorescence microscopy. These early findings suggest that the addition of small functional groups could achieve Gram-type-specific phototoxicity through altering the photodynamic activity of PSs and deserve further exploration in a larger number of representative strains of each Gram type.     

Alkyl-CoA disulfides as inhibitors and mechanistic probes for FabH enzymes

The first step of the reaction catalyzed by the homodimeric FabH from a dissociated fatty acid synthase is acyl transfer from acyl-CoA to an active site cysteine. We report that C1 to C10 alkyl-CoA disulfides irreversibly inhibit Escherichia coli FabH (ecFabH) and Mycobacterium tuberculosis FabH with relative efficiencies that reflect these enzymes' differential acyl-group specificity. Crystallographic and kinetic studies with MeSSCoA show rapid inhibition of one monomer of ecFabH through formation of a methyl disulfide conjugate with this cysteine. Reaction of the second subunit with either MeSSCoA or acetyl-CoA is much slower. In the presence of malonyl-ACP, the acylation rate of the second subunit is restored to that of the native ecFabH. These observations suggest a catalytic model in which a structurally disordered apo-ecFabH dimer orders on binding either the first substrate, acetyl-CoA, or the inhibitor MeSSCoA, and is restored to a disordered state on binding of malonyl-ACP.     

Cranberry derived proanthocyanidins reduce bacterial adhesion to selected biomaterials

Catheter associated urinary tract infections (CAUTI) linked with the uropathogens Escherichia coli (E. coli) and Enterococcus faecalis (E. faecalis) account for the majority of nosocomial infections acquired in the clinical environment. Because these infections develop following initial adhesion of the bacterial pathogens to the catheter surface, there is increased interest in developing effective methods to inhibit attachment of cells to biomaterials used in the manufacture of indwelling devices. High molecular weight proanthocyanidins (PAC) extracted from the North American cranberry (Vaccinium macrocarpon) were examined for their potential to reduce the initial adhesion of uropathogenic bacteria (E. coli CFT073 and E. faecalis 29212) to two model biomaterials, poly(vinyl chloride) (PVC) and polytetrafluoroethylene (PTFE). Well-controlled experiments conducted in a parallel-plate flow chamber (PPFC) demonstrated decreased attachment of both bacteria to PVC and PTFE when either the bacteria, biomaterial or both surfaces were treated with PAC. Most significant inhibition of bacterial adhesion was observed for the condition where both the bacteria and biomaterial surfaces were coated with PAC. Additional experiments conducted with nonbiological model particles demonstrate comparable extents of adhesion inhibition, supporting a nonbiospecific mechanism of PAC action. The results of this study are promising for the implementation of PAC in the clinical milieu for prevention of device associated infection as the proposed functional modification is independent of antibacterial mechanisms that may give rise to resistant strains.     

Interpolymer complex between poly(ethylene oxide) and poly(carboxylic acid)

An interpolymer complex was prepared by mixing aqueous solutions of poly(ethylene oxide) (PEO) and of a poly(carboxylic acid), i.e., poly(acrylic acid)(PAA), poly(methacrylic acid)(PMAA), or styrene-maleic acid copolymer(PSMA). The complexation mechanism was discussed on the basis of results of such experimental methods as viscosity, potentiometric titration, and turbidimetry. The hydrogen bond is primarily involved in these complexations, but the influence of hydrophobic interaction on complexation can not be ignored. If the degree of dissociation α of carboxylic acid or the degree of polymerization P_n of PEO was perceptibly changed, a stable complex was obtained at about α 0.1 or P_n (PEO) = 40 for PMAA, 200 for PAA. This fact indicates that more than a definite number of binding sites are necessary for a stable interpolymer complex to be formed and that cooperative interaction among active sites plays an important role in complex formation.     

Physical Properties of Biopolymers Assessed by Optical Tweezers: Analysis of Folding and Refolding of Bacterial Pili

Bacterial adhesion to surfaces mediated by specific adhesion organelles that promote infections, as exemplified by the pili of uropathogenic E. coli, is studied mostly at the level of cell–cell interactions and thereby reflects the averaged behavior of multiple pili. The role of pilus rod structure has therefore only been estimated from the outcome of experiments involving large numbers of organelles at the same time. It has, however, lately become clear that the biomechanical behavior of the pilus shafts play an important, albeit hitherto rather unrecognized, role in the adhesion process. For example, it has been observed that shafts from two different strains, even though they are similar in structure, result in large differences in the ability of the bacteria to adhere to their host tissue. However, in order to identify all properties of pilus structures that are of importance in the adhesion process, the biomechanical properties of pili must be assessed at the single‐molecule level. Due to the low range of forces of these structures, until recently it was not possible to obtain such information. However, with the development of force‐measuring optical tweezers (FMOT) with force resolution in the low piconewton range, it has lately become possible to assess forces mediated by individual pili on single living bacteria in real time. FMOT allows for a more or less detailed mapping of the biomechanical properties of individual pilus shafts, in particular those that are associated with their elongation and contraction under stress. This Mi‐ nireview presents the FMOT technique, the biological model system, and results from assessment of the biomechanical properties of bacterial pili. The information retrieved is also compared with that obtained by atomic force microscopy.     

Patterning of biomolecules on a poly(-caprolactone) film surface functionalized by ion implantation

Biomolecule patterning is important due to its potential applications in biodevices, tissue engineering, and drug delivery. In this study, we developed a new method for a biomolecular patterning on poly(-caprolactone) (PCL) films based on ion implantation. Ion implantation on a PCL film surface resulted in the formation of carboxylic acid groups. The generated carboxylic acid groups were used for the covalent immobilization of amine-functionalized p-DNA, followed by hybridization with fluorescently tagged c-DNA. Biotin-amine was also covalently immobilized on the carboxylic acid generated PCL surfaces. Successful biotin-specific binding of streptavidin further confirmed the potential of this strategy for patterning of various biomolecules.     

Carbapenem biosynthesis: confirmation of stereochemical assignments and the role of CarC in the ring stereoinversion process from L-proline

(5R)-Carbapen-2-em-3-carboxylic acid is the simplest structurally among the naturally occurring carbapenem beta-lactam antibiotics. It co-occurs with two saturated (3S,5S)- and (3S,5R)-carbapenam carboxylic acids. Confusion persists in the literature about the signs of rotation and absolute configurations of these compounds that is resolved in this paper. (3S,5S)-Carbapenam carboxylic acid was prepared from L-pyroglutamic acid to unambiguously establish its absolute configuration as identical to the natural product isolated from Serratia marcescens and from overexpression of the biosynthetic genes carAB in Escherichia coli. L-Proline labeled with deuterium or tritium at the diastereotopic C-5 methylene loci was shown to incorporate one label at the bridgehead of (3S,5S)-carbapenam carboxylic acid, but not into the "inverted" (3S,5R)-carbapenam carboxylic acid or the final carbapenem product. CarC, the third enzyme of the biosynthetic pathway required to synthesize the carbapenem, was demonstrated in cell-free studies to be dependent on alpha-ketoglutarate and ascorbate in keeping with weak sequence identities with other non-heme iron, alpha-ketoglutarate-dependent oxygenases. CarC mediated the stereoinversion of synthetic (3S,5S)-carbapenam carboxylic acid to the (5R)-carbapenem as judged by bioassay. These findings suggest that L-proline is desaturated to pyrroline-5-carboxylic acid prior to uptake into the biosynthetic pathway. The loss of the bridgehead hydrogen from the (3S,5S)-carbapenam during the ring inversion process to form the epimeric (3S,5R)-carbapenam and desaturation to the (5R)-carbapenem are proposed to be coupled by CarC to the reduction of dioxygen to drive the formation of these higher energy products, an unprecedented reaction for this enzyme class.     

Pilicides-small molecules targeting bacterial virulence

In a time of emerging bacterial resistance there is a vital need for new targets and strategies in antibacterial therapy. Using uropathogenic Escherichia coli as a model pathogen we have developed a class of compounds, pilicides, which inhibit the formation of virulence-associated organelles termed pili. The pilicides interfere with a highly conserved bacterial assembly and secretion system called the chaperone-usher pathway, which is abundant in a vast number of Gram-negative pathogens and serves to assemble multi-protein surface fibers (pili/fimbriae). This class of compounds provides a platform to gain insight into important biological processes such as the molecular mechanisms of the chaperone-usher pathway and the sophisticated function of pili. Pili are primarily involved in bacterial adhesion, invasion and persistence to host defenses. On this basis, pilicides can aid the development of new antibacterial agents.     

Design, synthesis, and biochemical evaluation of 1,5,6,7-tetrahydro-6,7-dioxo-9-D-ribitylaminolumazines bearing alkyl phosphate substituents as inhibitors of lumazine synthase and riboflavin synthase

The last two steps in the biosynthesis of riboflavin, an essential metabolite that is involved in electron transport, are catalyzed by lumazine synthase and riboflavin synthase. To obtain structural probes and inhibitors of these two enzymes, two ribityllumazinediones bearing alkyl phosphate substituents were synthesized. The synthesis involved the generation of the ribityl side chain, the phosphate side chain, and the lumazine system in protected form, followed by the simultaneous removal of three different types of protecting groups. The products were designed as intermediate analogue inhibitors of lumazine synthase that would bind to its phosphate-binding site as well as its lumazine binding site. Both compounds were found to be effective inhibitors of Bacillus subtilislumazine synthase as well as Escherichia coli riboflavin synthase. Molecular modeling of the binding of one of the two compounds provided a structural explanation for how these compounds are able to effectively inhibit both enzymes. In phosphate-free buffer, the phosphate moieties of the inhibitors were found to contribute positively to their binding to Mycobacterium tuberculosis lumazine synthase, resulting in very potent inhibitors with Ki values in the low nanomolar range. The additional carbonyl in the dioxolumazine system versus the purinetrione system was found to make a positive contribution to its binding to E. coli riboflavin synthase.     

Conformational studies on phenyl thioglycosides: a remote effect on disaccharide linkage by phenyl aglycons attenuates recognition of galabiosides by a bacterial adhesin

Phenyl S-galabiosides display altered conformational properties, as compared to phenyl O-galabiosides, characterised by a remote effect on the galabiose intersaccharidic glycoside bond by the phenyl aglycon, resulting in significantly lowered affinity for the PapG class II adhesin of uropathogenic E. coli.     

Escherichia coli quinolinate synthetase does indeed harbor a [4Fe-4S] cluster

Quinolinic acid is an intermediate in the biosynthesis of nicotinamide-containing redox cofactors. The ultimate step in the formation of quinolinic acid in prokaryotes is the condensation of iminosuccinate and dihydroxyacetone phosphate, which is catalyzed by the product of the nadA gene in Escherichia coli. A combination of UV-vis, M?ssbauer, and EPR spectroscopies, along with analytical methods for the determination of iron and sulfide, demonstrates for the first time that anaerobically purified quinolinate synthetase (NadA) from E. coli contains one [4Fe-4S] cluster per polypeptide. The protein is active, catalyzing the formation of quinolinic acid with a Vmax [ET]-1 of 0.01 s-1.     

INACTIVATION OF GRAM-NEGATIVE BACTERIA BY PHOTOSENSITIZED PORPHYRINS

Photosensitization of Escherichia coli and Pseudomonas aeruginosa cells by deuteroporphyrin (DP) is shown to be possible in the presence of the polycationic agent polymyxin nonapeptide (PMNP). Previous studies established complete resistance of Gram-negative bacteria to the photodynamic effects of porphyrins. The present results show that combined treatment of E. coli or P. aeruginosa cultures with DP and PMNP inhibit cell growth and viability. No antibacterial activity of PMNP alone could be demonstrated and cell viability remained unchanged. Spectroscopically, PMNP was found to bind DP, a mechanism which probably assists its penetration into the cell's membranes. Insertion of DP into the cells was monitored by the characteristic fluorescence band of bound DP at 622 nm. Binding times were 5-40 min and the extent of binding increased with decreasing the pH from 8.5 to 6.5. DP binding constants, as well as the concentrations of PMNP which were required for maximal effect on the various Gram-negative bacteria, were determined fluorometrically. By the treatment of DP, PMNP and light the growth of E. coli and P. aeruginosa cultures was stopped and the viability of the culture was dramatically reduced. Within 60 min of treatment the survival fraction of E. coli culture was 9 x 10(-6) and that of P. aeruginosa was 5.2 x 10(-4). Electron microscopy depicted ultrastructural alterations in the Gram-negative cells treated by DP and PMNP. The completion of cell division was inhibited and the chromosomal domain was altered markedly.     

FT-IR and FT-raman spectroscopy study of the cyclic anhydride intermediates for the esterification of cellulose: III. Cyclic anhydrides formed by the isomers of cyclohexanedicarboxylic acid

Multifunctional carboxylic acids have been used as crosslinking agents for cotton and wood pulp cellulose. In our previous research, we found that a polycarboxylic acid esterifies cellulose through the formation of a 5-membered cyclic anhydride intermediate by the dehydration of two carboxyl groups. In this research, we studied the formation of cyclic anhydride intermediates by different isomers of cyclohexanedicarboxylic acid (CHA) so that we can elucidate the effects of molecular structure on the formation of the anhydride intermediates. We found that both cis-and trans-1,2-CHA form 5-membered anhydride intermediates when temperature reaches their melting points and that cis-1,2-CHA forms the cyclic anhydride at temperatures lower than does trans-1,2-CHA. 1,3-CHA forms 6-membered cyclic anhydride at temperatures much higher than its melting point. The formation of a 5-membered cyclic anhydride intermediates takes place at temperatures lower than that of a 6-membered anhydride. This is probably the main reason why those polycarboxylic acids with their carboxylic acid groups bonded to the adjacent carbons of the molecular backbones are more effective crosslinking agents for cellulose than those with their carboxylic groups bonded to the alternative carbons. No formation of cyclic anhydride was found for 1,4-CHA. The formation of a five-membered cyclic anhydride was accelerated by monosodium phosphate, which is used as a catalyst for the esterification of cotton cellulose by polycarboxylic acids.     

Investigation of the formation of poly(ethylene terephthalate) with model molecules. IV. Catalysis of the esterification of ethylene glycol with benzoic acid and of the condensation of ethylene glycol monobenzoate

The esterfication of ethylene glycol (EG) with benzoic acid (BA) is an acid-catalyzed reaction which leads, as a first intermediate, to ethylene glycol monobenzoate (EGMB). This compound has an ? OH group which is more active towards carboxylic groups than the first ? OH group of EG. Moreover, it is a key intermediate in the formation of sideproducts containing diethylene glycol (DEG) moieties. The condensation reaction of EGMB was particularly studied in the presence of carboxylic acids or metal derivatives as catalysts. Titanium is the most active. Sb, which is widely used in the industrial synthesis of PET, needs to be present at a high level of concentration to show an activity. The presence of carboxylic groups in the reaction medium does not affect its activity, but it is necessary to remove the ethylene glycol as soon as it is formed in order to keep it active during the condensation reaction.     

Interaction of different metal ions with carboxylic acid group: a quantitative study

The binding strength of the carboxylic acid group (-COOH) with different divalent metal ions displays considerable variation in arachidic acid (AA) thin films. It is considered that in AA thin films the metal ions straddle the hydrophilic regions of the stacked bilayers of AA molecules via formation of carboxylates. In this study first the uptake of different divalent cations in films of AA is estimated by atomic absorption spectroscopy (AAS). Through the amount of cation uptake, it is found that the strength of binding of different cations varies as Ca2+>Co2+>Pb2+>Cd2+. Variation in the binding strength of different ions is also manifested in experiments where AA thin films are exposed to metal ion mixtures. The higher binding strength of AA with certain metal ions when exposed individually, as well as the preference over the other metal ions when exposed to mixtures, reveal some interesting deviation from the expected behavior based on considerations of ionic radii. For example, Pb2+ is always found to bind to AA much more strongly than Cd2+ even though the latter has smaller ionic radius, indicating that other factors also play an important role in governing the binding strength trends apart from the effects of ionic radii. Then, to get a more meaningful knowledge regarding the binding capability, first-principles calculations based on density functional theory have been applied to study the interaction of different cations with the simplest carboxylic acid, acetic acid, that can result in formation of metal diacetates. Their electronic and molecular structures, cohesive energies, and stiffness of the local potential energy well at the cation (M) site are determined and attempts are made to understand the diversity in geometry and the properties of binding of different metal ions with -COOH group. We find that the calculated M-O bond energies depend sensitively on the chemistry of M atom and follow the experimentally observed trends quite accurately. The trends in M-O bond energies and hence the total M-acetate binding energy trends can actually be related to their molecular structures that fall into different categories: Ca and Cd have tetrahedral coordination; Fe, Ni, and Co exhibit planar 4-fold coordination; and Pb is off-centered from the planar structure (forming pyramidal structure) due to its stereochemically active lone pair of electrons.