Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.     

Ceric Ion Initiated Graft Polymerization onto Poly(vinyl Alcohol)

This paper describes the kinetics of the ceric ion-initiated graft co-polymerization of vinyl acetate-acrylonitrile to poly(vinyl alcohol). The graft copolymerization rate R_p was found to be first order with respect to the total concentration of the comonomer mixture [M], the concentration of vinyl alcohol repeating units [PVA], and the mole fraction of vinyl acetate in the comonomer feed mixture. R_p was independent of cerous ion. The grafting rate was independent of ceric ion above a ceric concentration of 0.0020 M but first order in ceric ion below that concentration. Rp initially increased rapidly with [H⁺] to a maximum and then decreased and levelled off at hgher [H⁺]. The rate of ceric ion disappearance was first order in [PVA], independent of [MI, and increased with increasing [H⁺] with a leveling off at high [H⁺]. A reaction mechanism.     

Frequency down-conversion using cascading arrays of coupled nonlinear oscillators

A novel coupling scheme using M≥2 arrays of coupled nonlinear elements arranged in a specific configuration can produce multifrequency patterns or a frequency down-converting effect on an external (input) signal. In such a configuration, each array contains N≥3 nonlinear elements with similar dynamics and each element is coupled unidirectionally within the array. The subsequent arrays in the cascade are coupled in a similar fashion except that the coupling direction is arranged in the opposite direction with respect to that of the preceding array. Previous theoretical work and numerical results have already been reported in [P. Longhini, A. Palacios, V. In, J. Neff, A. Kho, A. Bulsara, Exploiting dynamical symmetry in coupled nonlinear elements for efficient frequency down-conversion, Phys. Rev. E 76 (2007) 026201]. This paper is focused on results of experiments implemented on two distinct systems: the first system is fabricated using discrete component circuits to approximate an overdamped bistable Duffing oscillator described by a quartic potential system, and the second system is built in a microcircuit, where the nonlinearity is described by a hyperbolic tangent function, with the option of applying an external signal to investigate resonant effects. In particular, the circuit implementations for each case use M=2 arrays, but their voltage oscillations already demonstrate that the frequency relations between each of the successive arrays decrease by a rational factor, conforming to earlier theoretical and numerical results for the general case containing M arrays. This behavior is important for efficient frequency down-converting applications which are essential in many communication systems where heterodyning is typically used and it involves multi-step processes with complicated circuitry.     

Enzyme-magnetic nanoparticle conjugates as a rigid biocatalyst for the elimination of toxic aromatic hydrocarbons

An enzyme-magnetic nanoparticle conjugate is prepared via conjugation of Ni(2+) ions onto the surface of magnetic nanoparticles to interact with a six histidine-tagged enzyme. The catalytic properties and enzyme rigidification of the conjugates are more stable at high concentrations of aromatic hydrocarbons.     

Trace analysis of the MIF analogue pareptide in blood plasma by high-performance liquid chromatography and short-wavelength excitation fluorometry

A high-performance liquid chromatographic procedure was developed and applied to analysis of the pharmacologically active MIF analogue pareptide in human plasma. The procedure involves formation of a fluorescent 7-chloro-4-nitrobenzyl-2-oxa-1,3-diazole (NBD-Cl) pareptide derivative followed by separation of the NBD derivative from plasma components on a 30-cm microparticle octadecylsilane bonded column. The separated derivative was quantitated using a short-wavelength excitation fluorometric detector. The detection limit of pareptide in plasma samples was 5 ng or 17 pmoles per ml of plasma. In the absence of plasma, the corresponding on-column detection limit was 0.5 pmoles.     

Confocal fluorescence polarization microscopy for linear unmixing of spectrally similar labels

Studies of biological samples often call for simultaneous identification of multiple molecular or structural components. Multiple labelling fluorescence techniques are a powerful way of achieving this. However, the ability to distinguish a number of fluorescent probes unambiguously can be restricted by the fact that fluorescence spectra are generally broad and overlapping. Recently a technique known as linear unmixing has been combined with spectral imaging to discriminate between multiple fluorophores. In this study a scheme is proposed whereby fluorescence polarization information is used to expand the capability of the linear unmixing technique to accommodate additional fluorescent probes. As a proof-of-concept, it is shown that this polarization-based technique can be used to divide the signals generated by two spectrally similar fluorescent probes into their separate components.     

Phase behavior of CO2-expanded fluorinated microemulsions

The formation of CO2-expanded, fluorinated reverse microemulsions is demonstrated for the system of perfluoropolyether (PFPE) surfactant (ClPFPE-NH4, MW = 632) and PFPE oil (PFPE, MW = 580). The phase behavior of this system is examined as a function of temperature (25-45 degrees C), pressure, CO2 concentration, and water to surfactant molar ratios (W0 = 10 and 20). Visual observations of one-phase behavior consistent with reverse microemulsion formation are further supported by spectroscopic measurements that establish the existence of a bulk water environment within the aqueous core. Microemulsion formation is not observed in the absence of CO2 for this PFPE surfactant/PFPE oil system, and a CO2 content greater than 70 mol % is required to induce microemulsion formation. Over the range of water loadings and temperatures investigated, the lowest cloud point pressure is observed at 46 bar (5 wt % ClPFPE-NH4 in PFPE oil, W0 = 20, xCO2 = 0.7, T = 25 degrees C). In the regions where one-phase behavior is observed, the cloud point pressures increase with temperature, water loadings, and CO2 content. The driving forces of microemulsion formation in the CO2-expanded fluorinated solvent are discussed relative to traditional reverse microemulsions and CO2-continuous microemulsions.     

A Simple Colloidal Synthesis for Gram-Quantity Production of Water-Soluble ZnS Nanocrystal Powders

A simple, inexpensive, and reproducible procedure is described for large-scale synthesis of highly stable nanocrystalline ZnS powders. Cysteine-capped ZnS nanocrystals (NCs) were produced by a colloidal aqueous synthesis, employing a ligand-competition mechanism in which sulfide was introduced into a preformed zinc-cysteine solution. The synthesis procedure resulted in highly concentrated ZnS NC solutions ( approximately 100 mM) which could be ethanol-precipitated, redissolved, and dried to produce fine powders stable for more than 30 months at 4 degrees C. The NC powders were readily dissolved in aqueous solvents to concentrations as high as 300 mM. ZnS NCs could be prepared without cysteine capping, but only at extremely dilute concentrations ( approximately 0.2 mM ZnSO(4)) as per Sooklal et al. J. Phys. Chem. 100, 4551 (1996). The 30-month-old ZnS NC powders retained their original optical and photocatalytic properties and could be handled much like routine shelf chemicals, unaffected by ambient air or moderate moisture and temperature. UV/vis absorption spectroscopy showed band gap energies (E(g)) ranging from 4.82 eV (257 nm lambda(max)) to 4.47 eV (277 nm lambda(max)) for ZnS samples prepared with 0.25-2.0 initial sulfide ratios (as compared to zinc). Samples stored at 4 degrees C for 30 months showed equivalent band gap energies and spectral profiles. The average NC particle size was estimated to be 6.08+/-0.76 nm by high-resolution transmission electron microscopy. Selected-area electron diffraction and X-ray diffraction analyses concurred in suggesting a hexagonal crystal structure, with diffractions near d=3.1, 1.9, and 1.6 ?. The average NC composition of size-fractionated samples was estimated to be Cys(1)Zn(7)S(6). p-Nitrophenol, a model organic, was photocatalytically degraded using 30-month-old ZnS NC powders dissolved in an aqueous buffer. Rates of degradation (first-order rate constant k=0.261 min(-1); t(1/2)=2.66 min) were comparable to those of experiments using freshly prepared ZnS NCs (first-order rate constant k=0.247 min(-1); t(1/2)=2.80 min), further demonstrating the long-term stability of thus-produced NC powders. Copyright 2000 Academic Press.     

Molecular structure parameters in certain semiconducting polymers

The condensation polymers formed by condensing aromatic hydrocarbons or their derivatives with aromatic acids are quite conductive. The room temperature resistivities of 42 polymers studied here range from 10² to 10¹² ohm-cm. It is found that the resistivities are inversely related to the number of fused rings in the hydrocarbon portion of the monomer for either the homopolymers or copolymers. The resistivities are strongly dependent, inversely, upon the acid strength of the acid monomer reactants. For all the polymers studied, the conductivity σ depended upon the pressure P as ln(σ/σ₀) = (b^*/k)P^1/2 where b^* is seen to be an inverse function of the number of fused rings in the monomer in accord with theory. The resistivity ρ varied with absolute temperature T, as ln ρ ∞ (1/T) for all polymers. Thermoelectric powers were determined, and the various relationships established among energy interval, resistivity at “infinite temperature,” carrier concentrations and mobility ratios, number of fused rings, and pressure coefficients are discussed. The polymers are p-type. Doping by Be⁺⁺ or Cu⁺⁺ has a small effect, increasing the conductivity slightly. Electron spin concentrations and carrier concentrations are directly related among the polymers, being found nearly equal for the most conductive but differing by up to nine orders of magnitude in the least conductive polymers.     

Synthetic biohybrid peptidoglycan oligomers enable pan-bacteria-specific labeling and imaging: in vitro and in vivo

Peptidoglycan is the core component of the bacterial cell wall, which makes it an attractive target for the development of bacterial targeting agents. Intercepting its enzymatic assembly with synthetic substrates allows for labeling and engineering of live bacterial cells. Over the past two decades, small-molecule-based labeling agents, such as antibiotics, d-amino acids or monosaccharides have been developed for probing biological processes in bacteria. Herein, peptidoglycan oligomers, substrates for transglycosylation, are prepared for the first time using a top-down approach, which starts from chitosan as a cheap feedstock. A high efficiency of labeling has been observed in all bacterial strains tested using micromolar substrates. In contrast, uptake into mammalian cells was barely observable. Additional mechanistic studies support a hypothesis of bacteria-specific metabolic labeling rather than non-specific binding to the bacterial surface. Eventually, its practicality in bacterial targeting capability is demonstrated in resistant strain detection and in vivo infection models.

Peptidoglycan oligomers have been derived from chitosan, using a top-down bio-hybrid strategy, as highly bacteria-specific substrates.