Eukaryotic Ribosomal Expansion Segments as Antimicrobial Targets.

Diversity in eukaryotic rRNA structure and function offers possibilities of therapeutic targets. Unlike ribosomes of prokaryotes, eukaryotic ribosomes contain species-specific rRNA expansion segments (ESs) with idiosyncratic structures and functions that are essential and specific to some organisms. Here we investigate expansion segment 7 (ES7), one of the largest and most variable expansions of the eukaryotic ribosome. We hypothesize that ES7 of the pathogenic fungi Candida albicans (ES7CA) could be a prototypic drug target. We show that isolated ES7CA folds reversibly to a native-like state. We developed a fluorescence displacement assay using an RNA binding fluorescent probe, F-neo. F-neo binds tightly to ES7CA with a Kd of 2.5 × 10-9 M but binds weakly to ES7 of humans (ES7HS) with a Kd estimated to be greater than 7 µM. The fluorescence displacement assay was used to investigate the affinities of a library of peptidic aminosugar conjugates (PAs) for ES7CA. For conjugates with highest affinities for ES7CA (NeoRH, NeoFH, and NeoYH), the lowest dose needed to induce mortality in C. albicans (minimum inhibitory concentration, MIC) was determined. PAs with the lowest MIC values were tested for cytotoxicity in HEK293T cells. Molecules with high affinity for ES7CA in vitro induce mortality in C. albicans but not in HEK293T cells. The results are consistent with the hypothesis that ESs represent useful targets for chemotherapeutics directed against eukaryotic pathogens.

Parallel, open-channel lateral flow (immuno) assay substrate based on capillary-channeled polymer films.

Presented here is a novel implementation of polypropylene capillary-channeled polymer (C-CP) films, functionalized for bioaffinity separations and implemented as a platform for lateral flow (immuno) assays. The parallel ∼80 µm × 80 µm channels pass test solutions down the 30 mm film length via spontaneous wicking action, setting up the possibility for immobilizing different capture agents in the respective channels. The base-film modification process is divided into two steps: ultraviolet light treatment to improve hydrophillicity of the polypropylene substrate and the physical adsorption of a functionalized lipid tethered ligand (LTL) as a selective capture agent. The entire modification procedure is performed under ambient conditions in an aqueous solution without extreme pH conditions. In this demonstration, physical adsorption of a biotinylated-LTL onto the UV-treated PP surface selectively captures Texas Red-labeled streptavidin (SAv-TR) in the presence of enhanced green fluorescence protein (EGFP), which passes without retention in less than 5 s. In addition to the fluorescence imaging of the protein solutes, matrix assisted laser desorption/ionization-mass spectrometry (MALDI-MS) was used to confirm the formation of the LTL-SAv conjugates on the channel surface as well as to demonstrate an alternative means of probing the capture step. The present effort sets the groundwork for further development of C-CP films as a parallel, multi-analyte LFA platform; a format that to-date has not been described.

Comparison of analytical protein separation characteristics for three amine-based capillary-channeled polymer (C-CP) stationary phases.

Capillary-channeled polymer (C-CP) fiber stationary phases are finding utility in the realms of protein analytics as well as downstream processing. We have recently described the modification of poly(ethylene terephthalate) (PET) C-CP fibers to affect amine-rich phases for the weak anion-exchange (WAX) separation of proteins. Polyethylenimine (PEI) is covalently coupled to the PET surface, with subsequent cross-linking imparted by treatment with 1,4-butanediol diglycidyl ether (BUDGE). These modifications yield vastly improved dynamic binding capacities over the unmodified fibers. We have also previously employed native (unmodified) nylon 6 C-CP fibers as weak anion/cation-exchange (mixed-mode) and hydrophobic interaction chromatography (HIC) phases for protein separations. Polyamide, nylon 6, consists of amide groups along the polymer backbone, with primary amines and carboxylic acid end groups. The analytical separation characteristics of these three amine-based C-CP fiber phases are compared here. Each of the C-CP fiber columns in this study was shown to be able to separate a bovine serum albumin/hemoglobin/lysozyme mixture at high mobile phase linear velocity (∼70 mm s(-1)) but with different elution characteristics. These differences reflect the types of protein-surface interactions that are occurring, based on the active group composition of the fiber surfaces. This study provides important fundamental understanding for the development of surface-modified C-CP fiber columns for protein separation.

Preliminary assessment of the modification of polystyrene-divinylbenzene resin with lipid-tethered ligands for selective separations.

Functionalized lipid tethered ligands use physical adsorption to anchor reactive head groups to hydrophobic supports. We previously demonstrated the use of these species adsorbed onto polypropylene capillary-channeled polymer fibers. The general use of lipid tethered ligands on other hydrophobic chromatographic supports is demonstrated here for polystyrene-divinylbenzene. Evaluation of ligand adsorption conditions was performed using a fluorescein isocyanate head group to quantify the extent of loading by UV-Vis absorbance and by fluorescence microscopy. Selective protein capture was demonstrated by the detection of Texas Red labeled streptavidin (using fluorescence microscopy imaging, with quantification assessed through the depletion of solution-phase protein using UV-Vis absorbance. A second demonstration of the coupling involved an iminodiacetic acid head group lipid tethered ligand to capture the cationic dye, methylene blue. Two common means of alleviating nonspecific binding, adsorption in detergent media and use of a bovine serum albumin block, were evaluated. The first was found to cause release of the ligands, while the second was nominally effective. Indeed, the lipid tethered ligands itself may be most effective at impeding nonspecific binding. While further optimization and chromatographic evaluation is required, the general viability of this ligand immobilization method onto this common polymer support is demonstrated.

Evaluation of synthesized lipid tethered ligands for surface functionalization of polypropylene capillary-channeled polymer fiber stationary phases.

Polypropylene (PP) capillary-channeled polymer (C-CP) fibers have been used in this laboratory as stationary phases for high performance liquid chromatography and solid phase extraction of proteins. Greater selectivity has been realized through the functionalization of the PP fibers through the physical adsorption of commercially available head group-modified poly(ethylene glycol) lipids (PEG-lipids), where the head group is chosen to affect affinity separations. We refer to this general surface modification methodology as lipid tethered ligands (LTLs). In this study, LTLs were synthesized by solid phase synthesis. In comparison to the commercial PEG-lipids, the synthesized LTLs contain no chemically labile phosphate groups. Instead of an ester linkage in the commercial lipids, amide functionality was used in the synthesized LTLs to attach the lipids and ligands. By use of fluorescence imaging of FITC-labeled LTLs, the synthesized LTL was shown to be superior to the commercial LTL in terms of the adsorption efficiency to PP C-CP fibers, the resistance to solvent wash from the PP C-CP fibers, and their chemical stability under acidic, neutral and basic conditions. The PP C-CP fibers functionalized with a synthesized LTL that was biotinylated at the head group are shown to be capable of capturing streptavidin from E. coli cell lysate more efficiently than the PP C-CP fibers functionalized with the commercial biotinylated PEG-lipid. The functionalization of PP C-CP fibers with the synthesized LTLs is a simple, but highly efficient, method to generate novel stationary phases with a variety of functionalities for solid phase extraction and liquid chromatography.

Biotin-functionalized poly(ethylene terephthalate) capillary-channeled polymer fibers as HPLC stationary phase for affinity chromatography.

Native poly(ethylene terephthalate) (PET) capillary-channeled polymer (C-CP) fibers have been used as the stationary phase for high-performance liquid chromatography (HPLC) of proteins via reversed-phase and ion-exchange processes. Functionalization can be used to bring about greater selectivity through surface modification. PET fibers were treated with ethylenediamine to generate primary amine groups on the fiber surface, enabling subsequent covalent attachment of ligands. The ninhydrin test for primary amines revealed surface densities of 13.9-60.0 µmol m(-2) for PET fibers exposed for periods of 3-12 min. Here, 8-amino-3,6-dioxaoctanoic acid was linked to the EDA-treated PET fiber surface as a hydrophilic spacer, and then D-biotin was attached on the end of the spacer as an affinity ligand. The streptavidin binding capacity and binding homogeneity were studied on the biotin-functionalized PET C-CP fiber microbore column. The selectivity of the biotin surface functionalization was assessed by spiking lysate with Texas Red-labeled streptavidin and enhanced green fluorescent protein. Greater than 99% selectivity was realized. This ligand-coupling strategy from standard solid-phase peptide synthesis used in stationary phase functionalization creates great potential for PET C-CP fiber-packed HPLC columns to perform a variety of chromatographic separations.

Fine-tuning miR-21 expression and inhibition of EMT in breast cancer cells using aromatic-neomycin derivatives.

MicroRNAs (miRs) are a class of endogenously expressed non-coding RNAs that negatively regulate gene expression within cells and participate in maintaining cellular homeostasis. By targeting 3' UTRs of target genes, individual miRs can control a wide array of gene expressions. Previous research has shed light upon the fact that aberrantly expressed miRs within cells can pertain to diseased conditions, such as cancer. Malignancies caused due to miRs are because of the high expression of onco-miRs or feeble expression of tumor-suppressing miRs. Studies have also shown miRs to engage in epithelial to mesenchymal transition (EMT), which allows cancer cells to become more invasive and metastasize. miR-21 is an onco-miR highly expressed in breast cancer cells and targets protein PTEN, which abrogates EMT. Therefore, we discuss an approach where in-house-developed peptidic amino sugar molecules have been used to target pre-miR-21 to inhibit miR-21 biogenesis, and hence antagonize its tumor-causing effect and inhibit EMT. Our study shows that small-molecule-based fine-tuning of miR expression can cause genotypic as well as phenotypic changes and also reinstates the potential and importance of nucleic acid therapeutics.

Grafting polymerization of glycidyl methacrylate onto capillary-channeled polymer (C-CP) fibers as a ligand binding platform: Applications in immobilized metal-ion affinity chromatography (IMAC) protein separations.

Immobilized metal-ion affinity chromatography (IMAC) is a valuable method for preparative and analytical-scale protein separations. Nylon 6 capillary-channeled polymer (C-CP) fibers were grafted with glycidyl methacrylate (GMA) as a monomer with ceric ammonium nitrate (in dilute nitric acid) used as the initiator. The polymerization reaction occurs rapidly (15 min) in a residential microwave. Iminodiacetic acid (IDA) is then attached to the grafted GMA polymers by reacting with the reactive terminal epoxide groups. Different parameters regarding the grafting time, initiator concentration and conversion time were investigated to find the optimal conditions for the entire modification process. The resulting nylon-IDA fibers were characterized by attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) and scanning electron microscopy (SEM). The resulting carboxyl density and copper binding capacity were determined to be 612 ±â€¯21 µmol g-1 and 375 ±â€¯12 µmol g-1, respectively. When charged with Cu2+ ions and packed in a column format, the nylon-IDA fibers can be applied as an IMAC stationary phase for the separation of histidine rich proteins. The performance of this novel phase was evaluated through the separation of a mixture of model proteins (cytochrome C, α-chymotrypsinogen A and lysozyme) and a recombinant histidine-tagged protein (his-tagged ubiquitin). Despite multi-step modifications, columns of the modified fibers still maintain the anticipated high levels of throughput and efficiency, with binding capacities of 6.89 ±â€¯0.56 mg lysozyme g-1 fiber and 6.32 ±â€¯0.12 mg His-tagged ubiquitin g-1 fiber.

Qualitative assessment of extractables from single-use components and the impact of reference standard selection.

The advent of single-use bioprocess systems used for the delivery, storage or manufacture of biopharmaceuticals has introduced a new potential source for extractables and leachables (E&L) as these systems are comprised of polymeric materials. Several industry working groups, the FDA and USP have issued guidance and draft guidance on E&L analyses for a variety of applications. These documents typically indicate that mass spectrometry should be applied for discovery of E&L's but provide little guidance as to the exact analytical methodology which should be used. We investigated the extractable profiles of a model single-use bioprocessing system consisting of a single-use bioprocess bag, connector tubing, and a hydrophilic disk filter including filter housing. Extractions were performed in water, ethanol, ethanol/water (50:50) and saline solutions. Extracts were analyzed using a stepwise analytical methodology including a variety of screening and mass spectrometry methods We then used this model system to demonstrate the use of recursive feature finding to automatically detect unique extractables followed by statistical filtering to focus on differentially present extractables which were above the analytical evaluation threshold (AET). We further show the significant affects of standard selection on the number of compounds determined to be above AET when reducing liquid chromatography-mass spectrometry (LC/MS) data. A relative response factor database consisting of 14 structurally diverse commercially available polymer additives was used to arrive at an LC/MS identification threshold. The results of this study demonstrate that significant care should be taken when selecting standards for LC/MS analysis to avoid under reporting of extractables and leachables.

Microwave-assisted, grafting polymerization preparation of strong cation exchange nylon 6 capillary-channeled polymer fibers and their chromatographic properties.

Native nylon 6 C-CP fibers were modified with 2-acrylamido-2-methylpropanesulfonic acid (AMPS) via the microwave-assisted grafting polymerization to affect a strong cation exchange stationary phase. Various concentrations of AMPS and the initiator potassium persulfate (KPS) were used in the modifications. The resultant nylon-SO3H fibers were characterized by Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR), scanning electron microscopy (SEM) and acid-base titrations. The chromatographic properties, including column permeability, protein separation quality, and protein binding capacity, of the nylon-SO3H fiber columns were also studied. The cation exchange ligand densities on the modified fibers (SO3H) were determined to be 50-317 µmol g-1, in comparison to the cation (COOH) density of 28 µmol g-1 of native nylon 6 fibers. The modified fiber phase showed increased lysozyme dynamic loading capacities (up to ∼13 mg mL-1 bed volume) at a linear velocity of ∼90 cm min-1, while native nylon 6 showed only ∼1 mg mL-1 lysozyme loading capacity. Fast (30 s-3 min) gradient separations of myoglobin, α-chymotrypsinogen A, and lysozyme were achieved on nylon-SO3H columns, with the separation resolution and peak capacity characterized. The efficiency of surface re-equilibration was probed with an eye toward using the phase as the second dimension in comprehensive two-dimensional liquid chromatography (2D-LC). The results indicate that this nylon-SO3H fiber phase has a good deal of potential for use in high-throughput analytical and preparative protein separations.

Microwave-assisted grafting polymerization modification of nylon 6 capillary-channeled polymer fibers for enhanced weak cation exchange protein separations.

A weak cation exchange liquid chromatography stationary phase (nylon-COOH) was prepared by grafting polyacrylic acid on to native nylon 6 capillary-channeled polymer (C-CP) fibers via a microwave-assisted radical polymerization. To the best of our knowledge, this is the first study of applying microwave-assisted grafting polymerization to affect nylon material for protein separation. The C-CP fiber surfaces were characterized by attenuated total reflection (ATR) infrared spectroscopy and scanning electron microscope (SEM). The anticipated carbonyl peak at 1722.9 cm-1 was found on the nylon-COOH fibers, but was not found on the native fiber, indicating the presence of the polyacrylic acid on nylon fibers after grafting. The nylon-COOH phase showed a ∼12× increase in lysozyme dynamic binding capacity (∼12 mg mL-1) when compared to the native fiber phase (∼1 mg mL-1). The loading capacity of the nylon-COOH phase is nearly independent of the lysozyme loading concentration (0.05-1 mg mL-1) and the mobile phase linear velocity (7.3-73 mm s-1). The reproducibility of the lysozyme recovery from the nylon-COOH (RSD = 0.3%, n = 10) and the batch-to-batch variability in the functionalization (RSD = 3%, n = 5) were also investigated, revealing very high levels of consistency. Fast baseline separations of myoglobin, α-chymotrypsinogen A, cytochrome c and lysozyme were achieved using the nylon-COOH column. It was found that a 5× increase in the mobile phase linear velocity (7.3-to-36.5 mm s-1) had little effect on the separation resolution. The microwave-assisted grafting polymerization has great potential as a generalized surface modification methodology across the applications of C-CP fibers.

Evaluation of loading characteristics and IgG binding performance of Staphylococcal protein A on polypropylene capillary-channeled polymer fibers.

The loading characteristics of recombinant Staphyloccocus aureus protein A (rSPA) on polypropylene (PP) capillary-channeled polymer (C-CP) fibers were investigated through breakthrough curves and frontal analysis. The dynamic adsorption data was fit to various isotherm models to assess the possible mode of rSPA-PP fiber adsorption. Among them, the Langmuir-linear model fit the experimental data best, suggesting a two-stage mechanism of adsorption. The first stage involves the formation of a monolayer coverage, which follows the Langmuir isotherm. When the adsorbate concentration increases, solute starts to adsorb onto the already adsorbed layer, following a linear adsorption response. The relationship between the rSPA loading and flow rate and column length was also investigated. These two parameters are related through the residence time of rSPA in the column. It was determined that loading at the flow rate of 0.5 mL min(-1) (∼28 mm s(-1)) with a 1×10(-5) M (0.5 mg mL(-1)) rSPA feed concentration on a 30-cm (0.762 mm i.d.) column could conveniently produce a reasonable binding capacity of rSPA on PP surface within only 6 min. Under those conditions, the rSPA binding at 50% breakthrough was found to be ∼2.1 mg g(-1) fiber. Operation of the rSPA-modified columns across ten complete processing cycles using clean-in-place conditions (including urea, guanidine HCl, and NaOH) commonly used in the bioprocessing industry allows assessment of the robustness of the rSPA capture layers. In all cases, the robustness was quite good, with the relative responses providing insights to the rSPA/PP surface structure.

Polyethylenimine modified poly(ethylene terephthalate) capillary channeled-polymer fibers for anion exchange chromatography of proteins.

Native poly(ethylene terephthalate) (PET) capillary-channeled polymer (C-CP) fibers have been previously studied as stationary phases for reversed phase and affinity protein separations. In this study, surface modified PET C-CP fibers were evaluated for the anion exchange separation of proteins. The native PET C-CP fibers were aminated using polyethylenimine (PEI) followed by a 1,4-butanediol diglycidyl ether (BUDGE) cross-linking step. Subsequent PEI/BUDGE treatments can be employed to further develop the polyamine layer on the fiber surfaces. The PEI densities of the modified fibers were quantified through the ninhydrin reaction, yielding values of 0.43-0.89µmolg(-1). The surface modification impact on column permeability was found to be 0.66×10(-11) to 1.33×10(-11)m(2), depending on the modification time and conditions. The dynamic binding capacities of the modified fiber media were determined to be 1.99-8.54mgmL(-1) bed volume, at linear velocities of 88-438cmmin(-1) using bovine serum albumin as the model protein. It was found that increasing the mobile phase linear velocity (up to 438cmmin(-1)) had no effect on the separation quality for a synthetic protein mixture, reflecting the lack of van Deemter C-term effects for the C-CP fiber phase. The low-cost, easy modification method and the capability of fast protein separation illustrate great potential in the use of PEI/BUDGE-modified PET C-CP fibers for high-throughput protein separation and downstream processing.

A pH Sensitive High-Throughput Assay for miRNA Binding of a Peptide-Aminoglycoside (PA) Library.

MicroRNAs (miRNA) are small RNAs that have a regulatory role in gene expression. Because of this regulatory role, miRNAs have become a new target for therapeutic compounds. Here, we outline an approach to target specific miRNAs using a high throughput capable assay and a 215 compound peptidic-aminosugar (PA) library. Aminosugars have been shown in a number of recent reports as important lead compounds that bind miRNA. In order to screen for compounds that bind miRNA, we have developed a high throughput displacement assay using a fluorescein-neomycin conjugated molecule (F-neo) as a probe for competitive miRNA binding compounds. We have applied the F-neo assay to four different miRNA constructs and the assay is applicable to most miRNAs, at various stages of processing. The results of the screen were validated by the determination of the IC50 for a select group of compounds from the library. For example, we identified eight compounds that bind to hsa-miR 504 with higher affinity than the parent neomycin. From the F-neo displacement assay we found that the number of binding sites differs for each miRNA, and the binding sites appear to differ both physically and chemically, with different affinity of the compounds resulting from the size of the molecule as well as the chemical structure. Additionally, the affinity of the compounds was dependent on the identity and position of the amino acid position of conjugation and the affinity of the compounds relative to other compounds in the library was miRNA dependent with the introduction of a second amino acid.

Rapid synthesis, RNA binding, and antibacterial screening of a peptidic-aminosugar (PA) library.

A 215-member mono- and diamino acid peptidic-aminosugar (PA) library, with neomycin as the model aminosugar, was systematically and rapidly synthesized via solid phase synthesis. Antibacterial activities of the PA library, on 13 bacterial strains (seven Gram-positive and six Gram-negative bacterial strains), and binding affinities of the PA library for a 27-base model of the bacterial 16S ribosomal A-site RNA were evaluated using high-throughput screening. The results of the two assays were correlated using Ribosomal Binding-Bacterial Inhibition Plot (RB-BIP) analysis to provide structure-activity relationship (SAR) information. From this work, we have identified PAs that can discriminate the E. coli A-site from the human A-site by up to a 28-fold difference in binding affinity. Aminoglycoside-modifying enzyme activity studies indicate that APH(2″)-Ia showed nearly complete removal of activity with a number of PAs. The synthesis of the compound library and screening can both be performed rapidly, allowing for an iterative process of aminoglycoside synthesis and screening of PA libraries for optimal binding and antibacterial activity for lead identification.