Probing autoinducer-2 based quorum sensing: the biological consequences of molecules unable to traverse equilibrium states

Bacteria have developed a cell-to-cell communication system, termed quorum sensing (QS), which allows for the population-dependent coordination of their behavior via the exchange of chemical signals. Autoinducer-2 (AI-2), a class of QS signals derived from 4,5-dihydroxy-2,3-pentandione (DPD), has been revealed as a universal signaling molecule in a variety of bacterial species. In spite of considerable interest, the study of putative AI-2 based QS systems remains a challenging topic in part due to the rapid interconversion between the linear and cyclic forms of DPD. Herein, we report the design and development of efficient syntheses of carbocyclic analogues of DPD, which are locked in the cyclic form. The synthetic analogues were evaluated for the modulation of AI-2-based QS in Vibrio harveyi and Salmonella typhimurium. No agonists were uncovered in either V. harveyi or S. typhimurium assay, whereas weak to moderate antagonists were found against V. harveyi. On the basis of NMR analyses and DFT calculations, the heterocyclic oxygen atom within DPD appears necessary to promote hydration at the C3 position of cyclic DPD to afford the active tetrahydroxy species. These results also shed light on the interaction between the heterocyclic oxygen atom and receptor proteins as well as the importance of the linear form and dynamic equilibrium of DPD as crucial requirements for activation of AI-2 based QS circuits.     

C4-Alkoxy-HPD: A Potent Class of Synthetic Modulators Surpassing Nature in AI-2 Quorum Sensing

Bacteria have developed cell-to-cell communication mechanisms, termed quorum sensing (QS), that regulate bacterial gene expression in a cell population-dependent manner. Autoinducer-2 (AI-2), a class of QS signaling molecules derived from (4S)-4,5-dihydroxy-2,3-pentanedione (DPD), has been identified in both Gram-negative and Gram-positive bacteria. Despite considerable interest in the AI-2 QS system, the biomolecular communication used by distinct bacterial species still remains shrouded. Herein, we report the synthesis and evaluation of a new class of DPD analogues, C4-alkoxy-5-hydroxy-2,3-pentanediones, termed C4-alkoxy-HPDs. Remarkably, two of the analogues were more potent QS agonists than the natural ligand, DPD, in Vibrio harveyi. The findings presented extend insights into ligand-receptor recognition/signaling in the AI-2 mediated QS system.     

An expeditious synthesis of DPD and boron binding studies

A practical synthesis has been developed for DPD (4,5-dihydroxypentane-2,3-dione), an unstable small molecule that is proposed to be the source of universal signaling agents for quorum sensing in bacteria. The synthesis allows preparation of isotopically labeled DPD and ent-DPD as well as detailed studies of spontaneous binding to borate to give the unusual borate complex 6, the signal for marine bacteria such as Vibrio harveyi. [reaction: see text]     

Deconvoluting interspecies bacterial communication

The universal bacterial signal molecule autoinducer-2 (AI-2) is derived from 4,5-dihydroxy-2,3-pentanedione (DPD). DPD exists in a complex equilibrium between multiple forms, and NMR spectroscopy has now been used to establish that the extent of the structural diversity displayed by DPD over a broad pH range is even greater than previously posited.     

An Efficient Synthesis of Optically Active [4-13C] Labelled Quorum Sensing Signal Autoinducer-2

A new synthetic route for the quorum sensing signal Autoinducer-2 (AI-2) is described and used for the preparation of [4-¹³C]-AI-2 starting from [1-¹³C]-bromoacetic acid. The key step in this process was the enantioselective reduction of an intermediate ketone. This synthesis provides, selectively, both enantiomers of the labelled or unlabelled parent compound, (R) or (S)-4,5-dihydroxypentane-2,3-dione (DPD) and was used for an improved synthesis of [1-¹³C]-AI-2.     

Analysing traces of autoinducer-2 requires standardization of the <Emphasis Type="Italic">Vibrio harveyi</Emphasis> bioassay

Autoinducer-2 (furanosyl borate diester) is a biologically active compound whose role as a universal bacterial signalling molecule is currently under intense investigation. Because of its instability and the low concentrations of it found in biological samples, its detection relies at present on a bioassay that measures the difference in the timing of the luminescence of the Vibrio harveyi BB170 sensor strain with and without externally added AI-2. Here we systematically investigated which parameters affected the fold induction values of luminescence obtained in the bioassay and developed a modified protocol. Our experiments showed that growth and luminescence of V. harveyi BB170 are strongly influenced by trace elements. In particular, addition of Fe³⁺ within a certain concentration range to the growth medium of the preinoculum culture improved the reproducibility and reduced the variance of the bioassay. In contrast, trace elements and vitamins introduced directly into the bioassay caused inhibitory effects. The initial density and luminescence of the sensor strain are very important and the values required for these parameters were defined. Borate interferes with the detection of AI-2 by giving false positive results. The response of V. harveyi BB170 to chemically synthesized AI-2 in the bioassay is nonlinear except over a very small concentration range; it is maximum over three orders of magnitude and shows inhibition above 35 μM. Based on the modified protocol, we were able to detect AI-2 in the absence of inhibitors with maximum fold induction values for the positive control (chemically synthesized AI-2) of >120 with a standard deviation of ~30% in a reliable and reproducible way.     

Stereoselective synthesis of pseudopeptide microbial agent AI-77-B

[structure: see text]. An efficient and highly stereoselective synthesis of the gastroprotective natural product AI-77-B is described. The stereocenters of the hydroxy amino acid moiety were generated by an ester-derived titanium-enolate-mediated syn-aldol reaction, a Curtius rearrangement, and application of Dondoni's aldehyde homologation. Condensation with the dihydroisocoumarin fragment and subsequent deprotecting transformations furnished optically active AI-77-B.     

Improvements in the N,N-diethyl-p-phenylenediamine method for the determination of free and combined residual chlorine through the use of FIA

In the determination of free and combined chlorine, the reaction of permanganate standards with N,N-diethyl-p-phenylenediamine (DPD) exhibits nonlinearity presumably because both the colored semiquinoid product and the colorless quinoid product are both formed. The titrimetric DPD method titrates both of the products while the colorimetric method monitors only the colored semiquinoid products. This results in a nonlinear response for the colorimetric method above 1.0 mg/l. as Cl(2). Under FIA conditions, the nonlinearity of the DPD colorimetric method is eliminated in the 0.1-5.0 mg/l. (as Cl(2)) range and the linear range is expanded to 0.1-8.0 mg/l. as Cl(2). Also, relative standard deviations are improved by 0.5-11% relative to the colorimetric method and 1.5-4.0% relative to the titrimetric method. The FIA method was developed further to sequentially determine both free and combined chlorine, since chloramine was found to have a negligible interference in the free chlorine determination.     

“On–off–on” pyrene-based fluorescent chemosensor for the selective recognition of Cu2+ and S2− ions and its utilization in live cell imaging

A new “on–off–on” fluorescence chemosensor (DPD) was designed, synthesized, and characterized based on pyrene and benzothiozole hydrazide. The probe DPD shows high affinity towards Cu²⁺ ions and the DPD-Cu²⁺ ensemble shows high sensitivity towards S²⁻ ions through the displacement method in the presence of other interfering ions. The detection limits of DPD for Cu²⁺ and S²⁻ ions were found to be 0.73 and 0.87 nM, respectively. Furthermore, the receptor was effectively applied to recognize Cu²⁺ and S²⁻ ions in real samples and live A549 cells through imaging studies.     

An unexpected switch in the modulation of AI-2-based quorum sensing discovered through synthetic 4,5-dihydroxy-2,3-pentanedione analogues

Quorum sensing (QS) has traditionally referred to a mechanism of communication within a species of bacteria. However, emerging research implicates QS in interspecies communication and competition, and such systems have been proposed in a wide variety of bacteria. The AI-2-based QS system represents the most studied of these proposed interspecies systems, and has been proposed to regulate diverse functions such as bioluminescence, expression of virulence factors, and biofilm formation. As such, the development of modulatory compounds, both agonists and antagonists, is of great interest for the treatment of bacterial infections and the study of unknown AI-2-based QS systems. Toward this end, we have designed and synthesized a panel of 4,5-dihydroxy-2,3-pentanedione/AI-2 analogues and evaluated their effects on the AI-2 QS of various bacteria. The panel of compounds exhibited differential effects in the bacterial cell lines examined, providing a platform for the development of broad-spectrum modulators of AI-2-based QS.     

L-asparaginase fromErwinia carotovora

A large-scale process was developed to purify L-asparaginase from submerged cultures of Erwinia carotovora. Cells from 880 L of fermentation broth were harvested and washed using a plate and frame type filter press. A cellular acetone powder was prepared from the washed cells by suspending the cells twice in acetone and the residual acetone was removed by washing the acetone powder in the filter press with 10 mM phosphate buffer (pH 7.0). The cellular acetone powder was extracted with 10 mM borate buffer at pH 9.5. The enzyme-rich borate extract was recovered by filtration and clarified by an in-line bag filter. The filtrate was adjusted to pH 7.5 and filtered through a 1-micron bag filter precoated with Celite and then through a 0.22-micron cartridge filter. The cell-free extract, containing 21 x 10(6) IU of enzyme and 448 g of total protein, was applied to an L-asparagine Sepharose 6 Fast Flow affinity column (9 L) using a bag filter loaded with Cell Debris Remover as an in-line prefilter. The affinity gel was prepared by coupling L-Asn at pH 9.0 to epoxy-activated Sepharose 6 Fast Flow beads. A total of 14 x 10(6) IU of enzyme (35 g protein) was eluted at pH 9.0 in 10.5 L. The eluted enzyme was determined to be greater than 90% pure using sodium dodecyl sulfate polyacrylamide gel electrophoresis. The total process time from whole broth to affinity column elution was 68 h and the enzyme yield was 38%. This improved process for the 880 L fermentation broth produced a cell-free extract of high specific activity, shortened the process time, increased the column capacity, and yielded a product with high purity.     

A multivalent probe for AI-2 quorum-sensing receptors

Multivalency is a common principle in the recognition of cellular receptors, and multivalent agonists and antagonists have played a major role in understanding mammalian cell receptor biology. The study of bacterial cell receptors using similar approaches, however, has lagged behind. Herein we describe our efforts toward the development of a dendrimer-based multivalent probe for studying AI-2 quorum-sensing receptors. From these studies, we have discovered a chemical probe specific for Lsr-type AI-2 quorum-sensing receptors with the potential for enabling the identification of new bacterial species that utilize AI-2 as a quorum-sensing signaling molecule.     

The Pacman effect: a supramolecular strategy for controlling the excited-state dynamics of pillared cofacial bisporphyrins

The molecular recognition properties of dizinc(II) bisporphyrin anchored by dibenzofuran (DPD), Zn2(DPD) (1), were evaluated as a strategy for utilizing the Pacman effect to control the excited-state properties of cofacial bisporphyrin motifs. Crystallographic studies establish that DPD furnishes a cofacial system with vertical flexibility and horizontal preorganization. The structure determination of a substrate-bound DPD species, Zn2(DPD)(2-aminopyrimidine) (2), completes a set of structurally homologous zinc(II) porphyrin host and host-guest complexes, which offer a direct structural comparison for the Pacman effect upon substrate complexation. Binding studies reveal that pyrimidine encapsulation by the DPD framework is accompanied by a markedly reduced entropic penalty (approximately 60 J mol(-1)K(-1)) with respect to traditional face-to-face bisporphyrin systems, giving rise to a smaller conformational energy cost upon substrate binding. Transient absorption spectroscopy reveals that substrate encapsulation within the DPD cleft dramatically affects excited-state dynamics of cofacial bisporphyrins. The emission lifetime of host-guest complex 2 increases by more than an order of magnitude compared to free host 1. In the absence of the guest, the excited-state dynamics are governed by torsional motion of the porphyrin rings about the aryl ring of the DPD pillar. Host-guest binding attenuates this conformational flexibility, thereby removing efficient nonradiative decay pathways. Taken together, these findings support the exceptional ability of the DPD system to structurally accommodate reaction intermediates during catalytic turnover and provide a novel supramolecular approach toward developing a reaction chemistry derived directly from the excited states of Pacman constructs.     

Structure and derivatization of the product from carbonylation of lithium triethylborohydride

Treatment of the reactive product from carbonylation of lithium triethylborohydride with the electrophilic reagent chlorotrimethylsilane does not produce the expected α-hydroxyborane derivative. Instead, a borinate arising through migration of a second ethyl group from boron to carbon is obtained. This result is rationalized in terms of the initial product being a borate having two possible constitutions. The borate nature of this initial product is confirmed by ¹¹B NMR.     

Dynamics on the HOCO potential energy surface studied by dissociative photodetachment of HOCO- and DOCO-

An experimental study of the dissociative photodetachment (DPD) dynamics of HOCO(-) and DOCO(-) at a photon energy of 3.21 eV has been carried out to probe the potential energy surface of the HOCO free radical and the dynamics of the OH+CO-->H+CO(2) reaction. These photoelectron-photofragment coincidence experiments allow the identification of photodetachment processes leading to the production of stable HOCO free radicals and both the H+CO(2) and OH+CO dissociation channels on the neutral surface. Isotopic substitution by deuterium in the parent ion is observed to reduce the product branching ratio for the D+CO(2) channel, consistent with tunneling playing a role in this dissociation pathway. Other isotope effects on the detailed partitioning of kinetic energy between photoelectrons and photofragments are also discussed. The results are compared to recent theoretical predictions of this DPD process, and evidence for the involvement of vibrationally excited HOCO(-) anions is discussed.     

Ab initio QM/MM molecular dynamics study on the excited-state hydrogen transfer of 7-azaindole in water solution

Ab initio molecular dynamics (AIMD) simulations for the excited-state hydrogen transfer (ESHT) reaction of 7-azaindole (7AI-(H2O)n; n = 1, 2) clusters in the gas phase and in water are presented. The effective fragment potential (EFP) is employed to model the surrounding water molecules. The AIMD simulations for 7AI-H2O and 7AI-(H2O)2 clusters show an asynchronous hydrogen transfer at t approximately 50 fs after the photoexcitation. While the ESHT mechanism for 7AI-H2O in water does not change appreciably compared with that in the gas phase, the AIMD simulations on 7AI-(H2O)2 in water solution exhibit two different mechanisms. Since the tautomer form is lower in energy compared to the normal form in the S1 state, 7AI and (H2O) n fragments separate from each other after the ESHT. With the use of the results of the AIMD trajectories, the minimum energy conical intersection point in the tautomer region has also been located.     

Use of capillary electrophoresis as a versatile tool to measure interaction constants between a KDR‐binding PEGylated lipopeptide and pegylated phospholipid micelles

In the frame of our molecular imaging activities, a PEGylated lipopeptide has been developed as a specific ligand for the human vascular endothelial growth factor receptor 2, which is considered as one of the important molecular marker of angiogenesis. In this study, the potential of affinity capillary electrophoresis (ACE) is evaluated to measure the interactions of an active PEGylated lipopeptide, its hydrolysis product and its precursor consisting of a peptide structure with different micelles including Brij‐35, Tween‐20, and pegylated phospholipids. Given the amphiphilic structure of the PEGylated lipopeptide, a MEKC method allowing the simultaneous separation of the compounds of interest was set up, using low percentages of acetonitrile. Analytes were resolved using a BGE consisting of 100 mM borate buffer pH 9.0, 1 mM Brij, and 25% acetonitrile. Optimized conditions were then used to perform ACE experiments. The affinity constants of the analytes with the micelles were calculated on the basis of their mobility decrease when surfactant concentration increased in the electrolyte. The use of different linearization models to estimate affinity constants was discussed and comparison of different surfactants was reported. PEGylated lipopeptide interacted more strongly with pegylated phospholipid micelles than with Brij‐35 or Tween‐20. Moreover, it is likely that the chemical structure of the compounds, and particularly the lipidic part of the molecules, significantly affects the interaction with micelles. In conclusion, the ACE method can be readily applied to investigate interactions of our targeting lipopeptides with various micelles currently used for the preparation of pharmaceutical vehicles.     

Electron transfer versus nucleophilic pathways in the ion-pair annihilation of organoborate anions by carbonylmanganese(I) cations

Substituted carbonylmanganese cations [Mn(CO)₅L]⁺, where L=py, PPh₃ and PPh₂Me, readily react with various organoborate anions (tetramethylborate, methyltriphenylborate and tetraphenylborate) in THF solution to afford a mixture of dimanganese carbonyls, hydridomanganese carbonyls and alkylmanganese carbonyls. The formation of the dimanganese carbonyl dimers as well as the hydridomanganese carbonyls suggests the involvement of 19-electron carbonylmanganese radicals that stem from an initial electron transfer. On the other hand, the acetonitrile-substituted analogue [Mn(CO)₅(CH₃CN)]⁺ reacts with the same borate anions to afford the alkylated RMn(CO)₅, where R=CH₃ and C₆H₅, as the sole carbonylmanganese product. As such, this alkylative annihilation is best formulated as a direct attack on the carbonyl carbon by the borate nucleophile. The two different pathways can be understood in terms of the balance between the electrophilicity of the carbonyl ligand and the electron affinity of the carbonylmanganese cation.     

Separation of Ribose-5-phosphate,Ribose-1-phosphate,Deoxyribose-1-phosphate by High Performance Liquid Chromatography and Spectrophotometric Determination Using 2-Cyanoacetamide

Abstract

A simple procedure for separation of ribose-5-phosphate, deoxyribose-1-phosphate and ribose-1-phosphate is based on high performance liquid chromatography using reversed phase 4 × 300 mm “μ Bondapak/NH₂” column. The column is equilibrated with 0.13 M borate buffer (pH 7.5) followed by gradient elution of ribose-5-phosphate, deoxyribose-1-phosphate and ribose-1-phosphate using water, 0.05 M borate buffer containing 0.1 M MgCl₂ (pH 9.6) and 0.05 M sodium acetate-acetic acid buffer containing 0.1 M MgCl₂ (pH 5.0) as eluants respectively. Eluates of borate complex “μ Bondapak/NH₂” column are brought to pH 9.6 by the addition of 1 N KOH and enzymatically hydrolysed with alkaline phosphatase (EC 3.1.3.1) to release the free pentoses. The free pentoses are mixed with a reagent solution prepared from aqueous solution of 2% cyanoacetamide and 0.6 M borate buffer (pH 9.6), and the mixture is boiled for 10 minutes and the absorbance of the product is measured at 276 nm using a spectrophotometer.     

Bottom-up coarse-graining of a simple graphene model: the blob picture

The coarse-graining of a simple all-atom 2D microscopic model of graphene, in terms of "blobs" described by center of mass variables, is presented. The equations of motion of the coarse-grained variables take the form of dissipative particle dynamics (DPD). The coarse-grained conservative forces and the friction of the DPD model are obtained via a bottom-up procedure from molecular dynamics (MD) simulations. The separation of timescales for blobs of 24 and 96 carbon atoms is sufficiently pronounced for the Markovian assumption, inherent to the DPD model, to provide satisfactory results. In particular, the MD velocity autocorrelation function of the blobs is well reproduced by the DPD model, provided that the effect of friction and noise is taken into account. However, DPD cross-correlations between neighbor blobs show appreciable discrepancies with respect to the MD results. Possible extensions to mend these discrepancies are briefly outlined.