Capture efficiency of Escherichia coli in fimbriae-mediated immunoimmobilization

Capturing pathogens on a sensor surface is one of the most important steps in the design of a biosensor. The efficiency of a biosensor at capturing pathogens has direct bearing on its sensitivity. In this work we investigated the capturing of Escherichia coli on substrates modified with antibodies targeting different types of fimbriae: K88ab (F4), K88ac (F4), K99 (F5), 987P (F6), F41, and CFA/I. The results suggest that all these fimbriae can be used for the efficient immobilization of living E. coli cells. The immobilization efficiency was affected by the purity and clone type of the antibody and the fimbriae expression level of the bacteria. For a specific fimbriae type, a higher immobilization efficiency was often observed with the monoclonal antibodies. Immunoimmobilization was utilized in an antibody microarray immersed in a mixed culture of pathogens to demonstrate the rapid and simultaneous label-free detection of multiple pathogens within less than 1 h using a single test. The capture rate of living pathogens exceeds a single bacterium per 100 × 100 μm(2) area per 0.5 h of incubation for a bulk concentration of 10(5) cfu/mL.     

Discovery of aminoglycoside mimetics by NMR-based screening of Escherichia coli A-site RNA

A method is described for the NMR-based screening for the discovery of aminoglycoside mimetics that bind to Escherichia coli A-site RNA. Although aminoglycosides are clinically useful, they exhibit high nephrotoxicity and ototoxicity, and their overuse has led to the development of resistance to important microbial pathogens. To identify a new series of aminoglycoside mimetics that could potentially overcome the problems associated with toxicities and resistance development observed with the aminoglycosides, we have prepared large quantities of E. coli 16 S A-site RNA and conducted an NMR-based screening of our compound library in search for small-molecule RNA binders against this RNA target. From these studies, several classes of compounds were identified as initial hits with binding affinities in the range of 70 microM to 3 mM. Lead optimization through synthetic modifications of these initial hits led to the discovery of several small-molecule aminoglycoside mimetics that are structurally very different from the known aminoglycosides. Structural models of the A-site RNA/ligand complexes were prepared and compared to the three-dimensional structures of the RNA/aminoglycoside complexes.     

Novel multivalent mannose compounds and their inhibition of the adhesion of type 1 fimbriated uropathogenic E. coli

A series of multivalent mannose containing compounds were prepared varying in size from small divalent, to 16-valent glycodenrimers and 21-valent glycopolymers. The molecules were approached via a common mannose building block. As scaffolds dendrimers and dendrons based on the 3,5-di-(2-aminoethoxy)-benzoic acid branching unit were used along with commercially available PAMAM dendrimers. To include larger structures, linear glycopolymers with varying amounts of mannose were prepared via radical polymerization. The compounds were tested for their biological activity using a newly developed ELISA based inhibition assay, for their ability to inhibit the binding of recombinant type I fimbriated E. coli to a monolayer of T24 cell line derived from human urinary bladder epithelium. All compounds showed enhanced affinity as compared to mannose with IC₅₀’s down to the low micromolar range.     

Chirospecific synthesis of spirocyclic beta-lactams and their characterization as potent type II beta-turn inducing peptide mimetics

[reaction: see text] Starting from natural proline, a practical chirospecific synthesis of spirocyclic beta-lactams of type 2 is described when a methylene moiety showing minimal steric demand is employed as a constraint element for adjusting the dihedral angle psi(i + 1). Employing the concept of self-reproduction of chirality, C-formylation of the oxazolidinone 5 afforded the key intermediate 7 taking advantage of an intermediate protection of the bridging element as a vinyl moiety. NMR- and IR-based conformational studies clearly indicated that spiro-beta-lactams of type 2 can serve as efficient beta-turn nucleators.     

Carbon nanodots as peroxidase mimetics and their applications to glucose detection

Carbon nanodots (C-Dots) were found to possess intrinsic peroxidase-like activity, and could catalytically oxidize 3,3',5,5'-tetramethylbenzidine (TMB) by H(2)O(2) to produce a colour reaction. This offers a simple, sensitive and selective colorimetric method for glucose determination in serum.     

Synthesis of tetrahydroisoquinoline-based pseudopeptides and their characterization as suitable reverse turn mimetics

New peptidomimetics containing the Tic moiety were synthesized in enantiomerically pure form and their conformational features were studied by NMR, IR, and molecular modeling techniques. The presence of a reverse turn conformation was observed in all the structures, suggesting the key role of the scaffold as reverse turn inducer. In particular, all the analyses led to the conclusion that a β-turn conformation is mostly stabilized in tetrapeptide mimetic 4b and in hexapeptide mimetics 5a,b. In the case of 5a,b, the C1 stereochemistry plays a central role in determining stable conformations, supporting the formation of a β-hairpin arrangement with a 14-membered intramolecular hydrogen bond ring only in 5b.     

Selective binding of mannose-encapsulated gold nanoparticles to type 1 pili in Escherichia coli

The synthesis, characterization and biological application of mannose encapsulated gold nanoparticles (m-AuNP) are reported. m-AuNP is well dispersed and very stable without aggregation in the media of broad ion strength and pH ranges. The selective binding of m-AuNP to the mannose adhesin FimH of bacterial type 1 pili is demonstrated using transmission electron microscopy. The competition assay with free mannose suggests that m-AuNP binds FimH better than free mannose does. This work demonstrates that carbohydrate attached nanoparticles can be used as an efficient affinity label and a multi-ligand carrier in a biological system.     

Oxazolopiperidin-2-ones as type II' beta-turn mimetics: synthesis and conformational analysis

We describe a straightforward synthesis of 9-substituted 3-aminooxazolidinopiperidin-2-ones 4. Some derivatives were prepared for use in peptide synthesis as rigidified surrogates of the Ala-Pro dipeptide. Analysis of the amide derivatives 14 by NMR experiments and molecular mechanics/dynamics calculations shows that the major isomer 14a has a stronger propensity than the minor isomer 14b to adopt beta-turn conformations, and the calculations indicate that in water 14a adopts a stable betaII' turn conformation.     

Synthesis of novel donor mimetics of UDP-Gal, UDP-GlcNAc, and UDP-GalNAc as potential transferase inhibitors

For the enzymatic transfer of galactose, N-acetylglucosamine, and N-acetylgalactosamine, UDP-Gal (1), UDP-GlcNAc (2), and UDP-GalNAc (3) are employed, and UDP serves as a feedback inhibitor. In this paper the synthesis of the novel UDP-sugar analogues 4, 5, and 6 as potential transferase inhibitors is described. Compounds 4-6 feature C-glycosidic hydroxymethylene linkages between the sugar and nucleoside moieties in contrast to the anomeric oxygens in the natural derivatives 1-3.     

Iterative synthesis of spacered glycodendrons as oligomannoside mimetics and evaluation of their antiadhesive properties

Dendrimer chemistry is an attractive concept for mimicry of the highly branched character of the bioactive carbohydrates found as part of a cell's sugar coat, called the glycocalyx. Glycodendrimers have thus been used to study biological processes occurring on cell surfaces, such as bacterial adhesion. This paper details a new approach in glycodendrimer synthesis, in which a 3,6-diallylated carbohydrate is utilised as core molecule, hydroboration-oxidation is the activating step, and glycosylation with branched and unbranched sugar trichloroacetimidates is used for dendritic growth. To obtain pure dendritic pseudo-tri- and -heptasaccharides in good yields, radical addition of mercaptoethanol to peripheral double bonds was also evaluated with great success. A collection of six new hyperbranched glycodendrons was tested for their potential as inhibitors of type 1 fimbriae-mediated bacterial adhesion in an ELISA and the results were interpreted with regard to sugar valency and spacer characteristics.     

Role of Cell Surface Lipopolysaccharides in Escherichia coli K12 adhesion and transport

The influence of bacterial surface lipopolysaccharides (LPS) on cell transport and adhesion has been examined by use of three mutants of Escherichia coli K12 with well-characterized LPS of different lengths and molecular composition. Two experimental techniques, a packed-bed column and a radial stagnation point flow system, were employed to investigate bacterial adhesion kinetics onto quartz surfaces over a wide range of solution ionic strengths. Although the two systems capture distinct deposition (adhesion) mechanisms because of their different hydrodynamics, similar deposition kinetics trends were observed for each bacterial strain. Bacterial deposition rates were directly related to the electrostatic double layer interaction between the bacteria and quartz surfaces, in qualitative agreement with classic Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. However, DLVO theory does not fully explain the deposition behavior for the bacterial strain with the lengthy, uncharged O-antigen portion of the LPS. Neither the length nor the charge characteristics of the LPS molecule directly correlated to deposition kinetics, suggesting a complex combination of cell surface charge heterogeneity and LPS composition controls the bacterial adhesive characteristics. It is further suggested that bacterial deposition behavior is determined by the combined influence of DLVO interactions, LPS-associated chemical interactions, and the hydrodynamics of the deposition system.     

Computational insights into factor affecting the potency of diaryl sulfone analogs as Escherichia coli dihydropteroate synthase inhibitors

Dihydropteroate synthase (DHPS) is an alluring target for designing novel drug candidates to prevent infections caused by pathogenic Escherichia coli strains. Diaryl Sulfone (SO) compounds are found to inhibit DHPS competitively with respect to the substrate pABA (p-aminobenzoate). The extra aromatic ring of diaryl sulfone compounds found to stabilize them in highly flexible pABA binding loops. In this present study, a statistically significant 3D-QSAR model was developed using a data set of diaryl sulfone compounds. The favourable and unfavourable contributions of substitutions in sulfone compounds were illustrated by contour plot obtained from the developed 3D-QSAR model. Molecular docking calculations were performed to investigate the putative binding mode of diaryl sulfone compounds at the catalytic pocket. DFT calculations were carried out using SCF approach, B3LYP- 6-31 G (d) basis set to compute the HOMO, LUMO energies and their respective location at pABA binding pocket. Further, the developed model was validated by FEP (Free Energy Perturbation) calculations. The calculated relative free energy of binding between the highly potent and less potent sulfone compound was found to be −3.78 kcal/ mol which is comparable to the experimental value of −5.85 kcal/mol. A 10 ns molecular dynamics simulation of inhibitor and DHPS confirmed its stability at pABA catalytic site. Outcomes of the present work provide deeper insight in designing novel drug candidates for pathogenic Escherichia coli strains.     

Mechanistic investigation of UDP-galactopyranose mutase from Escherichia coli using 2- and 3-fluorinated UDP-galactofuranose as probes.

The galactofuranose moiety found in many surface constituents of microorganisms is derived from UDP-D-galactopyranose (UDP-Galp) via a unique ring contraction reaction catalyzed by UDP-Galp mutase. This enzyme, which has been isolated from several bacterial sources, is a flavoprotein. To study this catalysis, the cloned Escherichia coli mutase was purified and two fluorinated analogues, UDP-[2-F]Galf (9) and UDP-[3-F]Galf (10), were chemically synthesized. These two compounds were found to be substrates for the reduced UDP-Galp mutase with the Km values determined to be 65 and 861 microM for 9 and 10, respectively, and the corresponding kcat values estimated to be 0.033 and 5.7 s(-1). Since the fluorine substituent is redox inert, a mechanism initiated by the oxidation of 2-OH or 3-OH on the galactose moiety can thus be firmly ruled out. Furthermore, both 9 and 10 are poorer substrates than UDP-Galf, and the rate reduction for 9 is especially significant. This finding may be ascribed to the inductive effect of the 2-F substituent that is immediately adjacent to the anomeric center, and is consistent with a mechanism involving formation of oxocarbenium intermediates or transition states during turnover. Interestingly, under nonreducing conditions, compounds 9 and 10 are not substrates, but instead are inhibitors for the mutase. The inactivation by 10 is time-dependent, active-site-directed, and irreversible with a K(I) of 270 microM and a k(inact) of 0.19 min(-1). Since the K(I) value is similar to Km, the observed inactivation is unlikely a result of tight binding. To our surprise, the inactivated enzyme could be regenerated in the presence of dithionite, and the reduced enzyme is resistant to inactivation by these fluorinated analogues. It is possible that reduction of the enzyme-bound FAD may induce a conformational change that facilitates the breakdown of the putative covalent enzyme-inhibitor adduct to reactivate the enzyme. It is also conceivable that the reduced flavin bears a higher electron density at N-1, which may play a role in preventing the formation of the covalent adduct or facilitating its breakdown by charge stabilization of the oxocarbenium intermediates/transition states. Clearly, this study has led to the identification of a potent inactivator (10) for this enzyme, and study of its inactivation has also shed light on the possible mechanism of this mutase.     

Theoretical study of disubstituted pyrrolopyrimidines as focal adhesion kinase inhibitors

An in silico molecular modeling study of selected 7H‐pyrrolo[2,3‐d]pyrimidines with FAK inhibitory activities was performed. Rigid docking of each inhibitor at the FAK catalytic site was employed to obtain the most appropriate starting structures, followed by molecular mechanics‐based energy minimizations associated with molecular dynamics at the FAK binding site using the AMBER force field. Theoretical values of interaction energies obtained from the geometry optimization calculations for the protein‐inhibitor complexes were compared with published IC₅₀ values for FAK and showed a reasonable correlation. Based on these results and in view of the geometry of the most potent inhibitors, two new molecular structures were designed as possible FAK inhibitors and submitted to the same theoretical procedures. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Synthesis of new functionalized 5,5-dimethyl-1-pyrroline 1-oxides and their investigation as spin traps

The reactions of 5,5-dimethyl-3-oxo-1-pyrroline 1-oxide (3-oxo-DMPO, 1) with NH₂OH and N₂H₄ afforded oxime (2a) and hydrazone (2b), respectively. The reaction products were studied as spin traps for the short-lived radicals HO^·, Ph^·, PhCO₂ ^·, NC(Me₂)C^·, and NC(Me₂)CO^·. The nitroxides generated in the reactions of the above-mentioned short-lived radicals with nitrones 1 and 2a,b were characterized by ESR spectroscopy. Of these nitrones, oxime 2a is the most effective radical trap.     

Synthesis of novel curcumin analogues and their evaluation as selective cyclooxygenase-1 (COX-1) inhibitors

Curcumin, a major yellow pigment and active component of turmeric, has been shown to possess anti-inflammatory and anti-cancer activities. Recent studies have indicated that cyclooxygenase-1 (COX-1) plays an important role in inflammation and carcinogenesis. In order to find more selective COX-1 inhibitors a series of novel curcumin derivatives was synthesized and evaluated for their ability to inhibit this enzyme using in vitro inhibition assays for COX-1 and COX-2 by measuring PGE(2) production. All curcumin analogues showed a higher rate of COX-1 inhibition. The most potent curcumin compounds were (1E,6E)-1,7-di-(2,3,4-trimethoxyphenyl)-1,6-heptadien-3,5-dione (4) (COX-1: IC(50) = 0.06 microM, COX-2: IC(50) > 100 microM, selectivity index>1666) and (1E,6E)-methyl 4-[7-(4-methoxycarbonyl)phenyl]-3,5-dioxo-1,6-heptadienyl]benzoate (6) (COX-1: IC(50) = 0.05 microM, COX-2: IC(50) > 100 microM, selectivity index > 2000). Curcumin analogues therefore represent a novel class of highly selective COX-1 inhibitors and promising candidates for in vivo studies.     

The effect of solvent polarity on the molecular surface properties and adhesion of Escherichia coli

The elasticity and molecular surface characteristics of Escherichia coli JM109 were investigated via atomic force microscopy (AFM) in solvents expressing different polarities. The nature of bacterial adhesion and surface characteristics was probed in formamide, water, and methanol, with dielectric constants of 111, 80, and 33, respectively. Solvent polarity affected the elasticity of the bacterium, the conformation of the cell surface biopolymers, the height of the surface biopolymers, and measured adhesion forces between the bacterium and silicon nitride. By applying the Hertz model to force-indentation data, we determined that the Young's modulus was greatest in the least polar solvent, with values of 182 +/- 34.6, 12.8 +/- 0.1, and 0.8 +/- 0.3 MPa in methanol, water, and formamide, respectively. The thickness of the biopolymer brush layer on the bacterial surface was quantified using a steric model, and these values increased as polarity increased, with values of 27, 93, and 257 nm in methanol, water, and formamide, respectively. The latter results suggest that highly polar conditions favor extension of the biopolymer brush layer. Cross-sectional analysis performed on tapping mode images of the bacterial cells in methanol, water, and formamide further supported this hypothesis. The image height values are larger, since the image analysis measures the height of the bacterium and the polymer layer, but the trend with respect to solvent polarity was the same as was obtained from the steric model of the brush length. Measured adhesion forces scaled inversely with solvent polarity, with greatest adhesion observed in the least polar solvent, methanol. The combined conformational changes to the bacterial surface and biopolymer layer result in different presentations of macromolecules to a substrate surface, and therefore affect the adhesion forces between the bacterial molecules and the substrate. These results suggest that polarity of the solvent environment can be manipulated as a design parameter to control or modify the bacterial adhesion process.     

An efficient synthesis of triazolo-carbohydrate mimetics and their conformational analysis

A chemical library of 1,2,3-triazole fused carbohydrate mimetics was constructed. To synthesize enantiomerically pure mimetics, we developed a stereo- or diastereodivergent synthetic route from D-glucose, D-mannose and D-galactose as chiral sources. In this synthesis, an In(OTf)(3)-catalyzed tandem azidation-1,3-dipolar cycloaddition reaction of 1,1-dimethoxyhex-5-yne derivatives with TMSN(3) was used as the key step to construct the 4,5,6,7-tetrahydro[1,2,3]triazolo[1,5-a]pyridine framework. Additionally, NMR was used to carry out a conformational analysis of the synthesized mimetics, which are of structural interest since they have an N,O-acetal moiety in place of the anomeric position of normal pyranosides.     

Contact angles and their hysteresis as a measure of liquid-solid adhesion

The wetting behavior of a series of aliphatic polyamides was examined. Polyamides and polyethylene were molded against glass to produce smooth surfaces. After cleaning, chemical composition of the surfaces was verified with X-ray photoelectron spectroscopy. Advancing and receding contact angles were measured from small sessile water drops. Contact angles decreased with amide content while contact angle hysteresis increased. Wetting free energies calculated from contact angles were equal to those from dewetting, suggesting that contact angle hysteresis did not arise from surface anomalies, but from hydrogen bonding between water and the amide groups in the polyamide surfaces.