Design of antibacterial peptide-like conjugated molecule with broad spectrum antimicrobial ability

Increasing multidrug-resistant(MDR) superbugs emerge worldwide causing a public health crisis. Consequently, it is urgent to find new antibiotics with efficient broad-spectrum antimicrobial activity. By virtue of versatility in molecular design, a new peptide-like cell membrane-broken molecule, oligo-(7,7′-bifluoren-benzo[c][1,2,5]thiadiazole)(OFBT) possessing a conjugated backbone and eight pendant guanidyl moieties was designed and synthesized. OFBT exhibits favorable broad-spectrum of antimicrobial activity to pathogens including Gram-negative and Gram-positive bacteria, and fungi with the minimum inhibitory concentration(MIC)below 3.0 μM. Moreover, OFBT exhibits high selectivity for pathogens over human cells to make it a promising broad spectrum antimicrobial agent.     

A nanoporous chiral metal-organic framework material that exhibits reversible guest adsorption

Assembly of the novel homochiral ligand L(S) (where L(S) is 1,4-benzylidene-bis(S,S)-4-yl-3,5-bis(1-hydroxyethyl)-1,2,4-triazole) and AgNO3 generates a robust, porous, chiral and cationic framework that exhibits reversible guest adsorption.     

(Hetero)arene-fused boroles: a broad spectrum of applications

(Hetero)arene-fused boroles are a class of compounds containing a 5-membered boron diene-ring. Based on their molecular framework, the (hetero)arene-fused boroles can be considered as boron-doped polycyclic antiaromatic hydrocarbons and are thus of great interest. Due to the vacant p_z orbital on the 3-coordinate boron atom, the antiaromaticity and strain of the 5-membered borole ring, (hetero)arene-fused boroles possess strong electron accepting abilities and Lewis acidity. By functionalization, they can be tuned to optimize different properties for specific applications. Herein, we summarize synthetic methodologies, different strategies for their functionalization, and applications of (hetero)arene-fused boroles.

(Hetero)arene-fused boroles, ‘antiaromatic’ 2n-electron π-systems, more stable and more functionalizable than boroles, offer greater potential for a variety of applications.     

Conducting polythiophenes with a broad spectrum of reactive groups

The development of reliable and reproducible chemistries for the immobilization of biomolecules to a conducting polymer is a key challenge in the design and preparation of a CP‐based biosensor. In this article, the syntheses and electropolymerization of a series of new 3‐alkylthiophene derivatives functionalized with the most used reactive groups in immobilization chemistry, including maleimide, azide, and anhydride, are described. Despite the nucleophilic or electrophilic nature of the reactive groups, the synthesized thiophene monomers exhibit rather good polymerizability, and the reactive groups withstand the polymerization conditions and are correctly incorporated into the resulting electroactive polymers. The reactivity of the pendant reactive groups of the resulting polymers to attach biomolecules has been examined with different redox‐active, photoactive compounds as well as recognition elements as model compounds. It has been confirmed that with well‐established procedures developed for the immobilization of enzymes, the model compounds can be easily and selectively bound onto these new conducting polymers without the loss of their optical and electrochemical activity. Therefore, these conductive materials with a broad spectrum of reactive groups will provide a useful platform for developing CP‐based biosensors for a wide range of applications. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4547–4558, 2005     

SCMTR: a chloride-selective, membrane-anchored peptide channel that exhibits voltage gating

The design, synthesis, and characterization of a synthetic chloride membrane transporter, SCMTR (synthetic chloride membrane transporter, "scimitar"), are presented. The compound [CH3(CH2)17]2NCOCH2OCH2CO-GGGPGGG-OBzl inserts rapidly into liposomes and planar lipid bilayers. SCMTR has a 1.3 +/- 0.01 nS chloride diffusion pathway (>10:1 Cl/K selectivity). Evidence was also obtained for voltage gating behavior.     

Coordination-driven self-assembly directs a single-crystal-to-single-crystal transformation that exhibits photocontrolled fluorescence

Coordination-driven self-assembly is employed to direct a single-crystal-to-single-crystal [2 + 2] photodimerization that exhibits tunable fluorescence.     

A rationally designed pyrrolysyl-tRNA synthetase mutant with a broad substrate spectrum

Together with tRNA(CUA)(Pyl), a rationally designed pyrrolysyl-tRNA synthetase mutant N346A/C348A has been successfully used for the genetic incorporation of a variety of phenylalanine derivatives with large para substituents into superfolder green fluorescent protein at an amber mutation site in Escherichia coli. This discovery greatly expands the genetically encoded noncanonical amino acid inventory and opens the gate for the genetic incorporation of other phenylalanine derivatives using engineered pyrrolysyl-tRNA synthetase-tRNA(CUA)(Pyl) pairs.     

A redesigned vancomycin engineered for dual D-Ala-D-ala And D-Ala-D-Lac binding exhibits potent antimicrobial activity against vancomycin-resistant bacteria

The emergence of bacteria resistant to vancomycin, often the antibiotic of last resort, poses a major health problem. Vancomycin-resistant bacteria sense a glycopeptide antibiotic challenge and remodel their cell wall precursor peptidoglycan terminus from d-Ala-d-Ala to d-Ala-d-Lac, reducing the binding of vancomycin to its target 1000-fold and accounting for the loss in antimicrobial activity. Here, we report [Ψ[C(═NH)NH]Tpg(4)]vancomycin aglycon designed to exhibit the dual binding to d-Ala-d-Ala and d-Ala-d-Lac needed to reinstate activity against vancomycin-resistant bacteria. Its binding to a model d-Ala-d-Ala ligand was found to be only 2-fold less than vancomycin aglycon and this affinity was maintained with a model d-Ala-d-Lac ligand, representing a 600-fold increase relative to vancomycin aglycon. Accurately reflecting these binding characteristics, it exhibits potent antimicrobial activity against vancomycin-resistant bacteria (MIC = 0.31 μg/mL, VanA VRE). Thus, a complementary single atom exchange in the vancomycin core structure (O → NH) to counter the single atom exchange in the cell wall precursors of resistant bacteria (NH → O) reinstates potent antimicrobial activity and charts a rational path forward for the development of antibiotics for the treatment of vancomycin-resistant bacterial infections.     

White LEDs as broad spectrum light sources for spectrophotometry: demonstration in the visible spectrum range in a diode-array spectrophotometric detector

Although traditional lamps, such as deuterium lamps, are suitable for bench-top instrumentation, their compatibility with the requirements of modern miniaturized instrumentation is limited. This study investigates the option of utilizing solid-state light source technology, namely white LEDs, as a broad band spectrum source for spectrophotometry. Several white light LEDs of both RGB and white phosphorus have been characterized in terms of their emission spectra and energy output and a white phosphorus Luxeon LED was then chosen for demonstration as a light source for visible-spectrum spectrophotometry conducted in CE. The Luxeon LED was fixed onto the base of a dismounted deuterium (D(2) ) lamp so that the light-emitting spot was geometrically positioned exactly where the light-emitting spot of the original D(2) lamp is placed. In this manner, the detector of a commercial CE instrument equipped with a DAD was not modified in any way. As the detector hardware and electronics remained the same, the change of the deuterium lamp for the Luxeon white LED allowed a direct comparison of their performances. Several anionic dyes as model analytes with absorption maxima between 450 and 600 nm were separated by CE in an electrolyte of 0.01 mol/L sodium tetraborate. The absorbance baseline noise as the key parameter was 5 × lower for the white LED lamp, showing clearly superior performance to the deuterium lamp in the available, i.e. visible part of the spectrum.     

Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge

Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Recently, we disclosed the eNTRy rules, a key lesson of which is that the introduction of a primary amine enhances OM permeation in certain contexts. To understand the molecular basis for this finding, we perform an extensive set of molecular dynamics (MD) simulations and free energy calculations comparing the permeation of aminated and amine-free antibiotic derivatives through the most abundant OM porin of E. coli, OmpF. To improve sampling of conformationally flexible drugs in MD simulations, we developed a novel, Monte Carlo and graph theory based algorithm to probe more efficiently the rotational and translational degrees of freedom visited during the permeation of the antibiotic molecule through OmpF. The resulting pathways were then used for free-energy calculations, revealing a lower barrier against the permeation of the aminated compound, substantiating its greater OM permeability. Further analysis revealed that the amine facilitates permeation by enabling the antibiotic to align its dipole to the luminal electric field of the porin and form favorable electrostatic interactions with specific, highly-conserved charged residues. The importance of these interactions in permeation was further validated with experimental mutagenesis and whole cell accumulation assays. Overall, this study provides insights on the importance of the primary amine for antibiotic permeation into Gram-negative pathogens that could help the design of future antibiotics. We also offer a new computational approach for calculating free-energy of processes where relevant molecular conformations cannot be efficiently captured.

A rapid pathway sampling method combining Monte Carlo and graph theory, developed to describe permeation pathways through outer membrane porins, can distinguish between structurally similar analogs with different permeabilities.     

Simultaneous determination of a broad spectrum of nonconjugated xenobiotics by high-performance liquid chromatography-tandem mass spectrometry

A procedure was developed for screening 23 corticosteroids, 12 anabolic steroids, 23 diuretics, and 49 central nervous system stimulants and narcotics. The sample preparation includes extraction, the evaporation of the organic extract in a nitrogen flow, and the dissolution of the dry residue. The extract was analyzed by high-performance liquid chromatography-tandem mass spectrometry with atmospheric pressure electrospray ionization under different recording conditions. Negatively charged ions were recorded to determine corticosteroids and diuretics, while positively charged ions, to determine anabolic steroids, diuretics, stimulants, and narcotics. Mass spectra were obtained for all test compounds; the characteristic ions, retention times, detection limits, degree of ionization suppression by the matrix, and recovery were determined for all analytes.     

V-doped SnS2: a new intermediate band material for a better use of the solar spectrum

Intermediate band materials can boost photovoltaic efficiency through an increase in photocurrent without photovoltage degradation thanks to the use of two sub-bandgap photons to achieve a full electronic transition from the valence band to the conduction band of a semiconductor structure. After having reported in previous works several transition metal-substituted semiconductors as able to achieve the electronic structure needed for this scheme, we propose at present carrying out this substitution in sulfides that have bandgaps of around 2.0 eV and containing octahedrally coordinated cations such as In or Sn. Specifically, the electronic structure of layered SnS(2) with Sn partially substituted by vanadium is examined here with first principles quantum methods and seen to give favourable characteristics in this respect. The synthesis of this material in nanocrystalline powder form is then undertaken and achieved using solvothermal chemical methods. The insertion of vanadium in SnS(2) is found to produce an absorption spectrum in the UV-Vis-NIR range that displays a new sub-bandgap feature in agreement with the quantum calculations. A photocatalytic reaction-based test verifies that this sub-bandgap absorption produces highly mobile electrons and holes in the material that may be used for the solar energy conversion, giving experimental support to the quantum calculations predictions.     

On the nature of antimicrobial activity: a model for protegrin-1 pores

We conducted over 150 ns of simulation of a protegrin-1 octamer pore in a lipid bilayer composed of palmitoyloleoyl-phosphatidylethanolamine (POPE) and palmitoyloleoyl-phosphatidylglycerol (POPG) lipids mimicking the inner membrane of a bacterial cell. The simulations improve on a model of a pore proposed from recent NMR experiments and provide a coherent understanding of the molecular mechanism of antimicrobial activity. Although lipids tilt somewhat toward the peptides, the simulated protegrin-1 pore more closely follows the barrel-stave model than the toroidal-pore model. The movement of ions is investigated through the pore. The pore selectively allows negatively charged chloride ions to pass through at an average rate of one ion every two nanoseconds. Only two events are observed of sodium ions crossing through the pore. The potential of mean force is calculated for the water and both ion types. It is determined that the chloride ions move through the pore with ease, similarly to the water molecules with the exception of a zone of restricted movement midway through the pore. In bacteria, ions moving through the pore will compromise the integrity of the transmembrane potential. Without the transmembrane potential as a countermeasure, water will readily flow inside the higher osmolality cytoplasm. We determine that the diffusivity of water through a single PG-1 pore is sufficient to cause fast cell death by osmotic lysis.     

Surface-grafted hybrid material consisting of gold nanoparticles and dextran exhibits mobility and reversible aggregation on a surface

Gold nanoparticles linked to linear carboxylated dextran chains were attached to 3-aminopropyltriethoxysilane-functionalized glass surfaces. This method provides novel hybrid nanostructures on a surface with the unique optical properties of gold nanoparticles. The particles attached to the surface retain the capability to aggregate and disaggregate in response to their environment. This procedure presents an alternative method to the immobilization of gold nanoparticles onto planar substrates. Compared to gold nanoparticle monolayers, larger particle surface densities were obtained. Exposure to hydrophobic environments changes the conformation of the hydrophilic dextran chains, causing the gold nanoparticles to aggregate and inducing changes in the absorption spectrum such as red-shifting and broadening of the plasmon absorption peaks. These changes, characteristic of particle aggregation, are reversible. When the substrates are dried and then immersed in an aqueous environment, these changes can be visually observed in a reversible fashion and the sample changes color from the red color of colloidal gold to a bluish-purple color of aggregated nanoparticles. Surface-bound nanoparticles that retain their mobility when attached to a surface by means of a flexible polymer chain could expand the use of aggregation-based assays to solid substrates.     

Synthesis and antimicrobial activity of a perfluoroalkyl-containing quaternary ammonium salt

A novel perfluoroalkyl-containing quaternary ammonium salt 5 was designed and synthesized. Consequently, the antimicrobial activities of compound 5 were measured with Escherichia coli 8099 as a Gram-negative strain and Staphylococcus aureus ATCC 6538 as a Gram-positive strain. Both the minimum inhibitory concentration (MIC, the lowest concentration of compound 5 that inhibits microbial growth) values of quaternary ammonium salt 5 against Escherichia coli 8099 and Staphylococcus aureus ATCC 6538 were 7.8 μg/ml.