Rapid and quantitative measurement of metabolic stability without chromatography or mass spectrometry

Metabolic stability measurements are a critical component of preclinical drug development. Available measurement strategies rely on chromatography and mass spectrometry, which are expensive and labor intensive. We have developed a general method to determine the metabolic stability of virtually any compound by quantifying cofactors in the mechanism of cytochrome P450 enzymes using fluorescence intensity measurements. While many previous studies have shown that simple measurements of cofactor depletion do not correlate with substrate conversion (i.e., metabolic stability) in P450 systems, the present work employs a reaction engineering approach to simplify the overall rate equation, thus allowing the accurate and quantitative determination of substrate depletion from simultaneous measurements of NADPH and oxygen depletion. This method combines the accuracy and generality of chromatography with the ease, throughput, and real-time capabilities of fluorescence.

Effect of gold nanoparticle morphology on adsorbed protein structure and function

Many biomedical applications of gold nanoparticles (NPs) rely on proteins that are covalently attached or adsorbed on the NP surface. The biological functionality of the protein-NP conjugate depends on the protein's ability to interact with target molecules, which is affected by NP characteristics such as size, curvature, aspect ratio, morphology, crystal structure, and surface chemistry. In the present study, the effect of gold nanoparticle morphology on the structure and function of adsorbed enzymes, lysozyme (Lyz) and α-chymotrypsin (ChT), has been investigated. Gold nanospheres (AuNS) were synthesized with diameters 10.6 ± 1 nm, and gold nanorods (AuNR) were synthesized with dimensions of (10.3 ± 2) × (36.4 ± 9) nm. Under saturating conditions, proteins adsorb with a higher surface density on AuNR when compared to AuNS. In the case of Lyz, adsorption on AuNS and AuNR resulted in a 10% and 15% loss of secondary structure, respectively, leading to conjugate aggregation and greatly reduced enzymatic activity. ChT retained most of its secondary structure and activity on AuNS and AuNR at low surface coverages; however, as protein loading approached monolayer conditions on AuNR, a 40% loss in secondary structure and 86% loss of activity was observed. Subsequent adsorption of ChT in multilayers on the AuNR surface allowed the conjugates to recover activity and remain stable. It is clear that AuNP morphology does affect adsorbed protein structure; a better understanding of these differences will be essential to engineer fully functional nanobioconjugates.

Polyphenolic glycosides and aglycones utilize opposing pathways to selectively remodel and inactivate toxic oligomers of amyloid β

Substantial evidence suggests that soluble prefibrillar oligomers of the Aβ42 peptide associated with Alzheimer's disease are the most cytotoxic aggregated Aβ isoform. Limited previous work has revealed that aromatic compounds capable of remodeling Aβ oligomers into nontoxic conformers typically do so by converting them into off-pathway aggregates instead of dissociating them into monomers. Towards identifying small-molecule antagonists capable of selectively dissociating toxic Aβ oligomers into soluble peptide at substoichiometric concentrations, we have investigated the pathways used by polyphenol aglycones and their glycosides to remodel Aβ soluble oligomers. We find that eleven polyphenol aglycones of variable size and structure utilize the same remodeling pathway whereby Aβ oligomers are rapidly converted into large, off-pathway aggregates. Strikingly, we find that glycosides of these polyphenols all utilize a distinct remodeling pathway in which Aβ oligomers are rapidly dissociated into soluble, disaggregated peptide. This disaggregation activity is a synergistic combination of the aglycone and glycone moieties because combinations of polyphenols and sugars fail to disaggregate Aβ oligomers. We also find that polyphenolic glycosides and aglycones use the same opposing pathways to remodel Aβ fibrils. Importantly, both classes of polyphenols fail to remodel nontoxic Aβ oligomers (which are indistinguishable in size and morphology to Aβ soluble oligomers) or promote aggregation of freshly disaggregated Aβ peptide; thus revealing that they are specific for remodeling toxic Aβ conformers. We expect that these and related small molecules will be powerful chemical probes for investigating the conformational and cellular underpinnings of Aβ-mediated toxicity.

Electrospun polyvinylpyrrolidone fibers with high concentrations of ferromagnetic and superparamagnetic nanoparticles

Electrospun polymer fibers were prepared containing mixtures of different proportions of ferromagnetic and superparamagnetic nanoparticles. The magnetic properties of these fibers were then explored using a superconducting quantum interference device. Mixed superparamagnetic/ferromagnetic fibers were examined for mesoscale magnetic exchange coupling, which was not observed as theoretically predicted. This study includes some of the highest magnetic nanoparticle loadings (up to 50 wt%) and the highest magnetization values (≈ 25 emu/g) in an electrospun fiber to date and also demonstrates a novel mixed superparamagnetic/ferromagnetic system.

Ultra-performance ion-pairing liquid chromatography with on-line electrospray ion trap mass spectrometry for heparin disaccharide analysis

A high-resolution method for the separation and analysis of disaccharides prepared from heparin and heparan sulfate (HS) using heparin lyases is described. Ultra-performance liquid chromatography in a reverse-phase ion-pairing mode efficiently separates eight heparin/HS disaccharides. The disaccharides can then be detected and quantified using electrospray ionization mass spectrometry. This method is particularly useful in the analysis of small amounts of biological samples, including cells, tissues, and biological fluids, because it provides high sensitivity without being subject to interference from proteins, peptides, and other sample impurities.

Control of the heparosan N-deacetylation leads to an improved bioengineered heparin

The production of the anticoagulant drug heparin from non-animal sources has a number of advantages over the current commercial production of heparin. These advantages include better source material availability, improved quality control, and reduced concerns about animal virus or prion impurities. A bioengineered heparin would have to be chemically and biologically equivalent to be substituted for animal-sourced heparin as a pharmaceutical. In an effort to produce bioengineered heparin that more closely resembles pharmaceutical heparin, we have investigated a key step in the process involving the N-deacetylation of heparosan. The extent of N-deacetylation directly affects the N-acetyl/N-sulfo ratio in bioengineered heparin and also impacts its molecular weight. Previous studies have demonstrated that the presence and quantity of N-acetylglucosamine in the nascent glycosaminoglycan chain, serving as the substrate for the subsequent enzymatic modifications (C5 epimerization and O-sulfonation), can impact the action of these enzymes and, thus, the content and distribution of iduronic acid and O-sulfo groups. In this study, we control the N-deacetylation of heparosan to produce a bioengineered heparin with an N-acetyl/N-sulfo ratio and molecular weight that is similar to animal-sourced pharmaceutical heparin. The structural composition and anticoagulant activity of the resultant bioengineered heparin was extensively characterized and compared to pharmaceutical heparin obtained from porcine intestinal mucosa.

E. coli K5 fermentation and the preparation of heparosan, a bioengineered heparin precursor

Heparosan is an acidic polysaccharide natural product, which serves as the critical precursor in heparin biosynthesis and in the chemoenzymatic synthesis of bioengineered heparin. Heparosan is also the capsular polysaccharide of Escherichia coli K5 strain. The current study was focused on the examination of the fermentation of E. coli K5 with the goal of producing heparosan in high yield and volumetric productivity. The structure and molecular weight properties of this bacterial heparosan were determined using polyacrylamide gel electrophoresis (PAGE) and Fourier transform mass spectrometry. Fermentation of E. coli K5 in a defined medium using exponential fed-batch glucose addition with oxygen enrichment afforded heparosan at 15 g/L having a number average molecular weight of 58,000 Da and a weight average molecular weight of 84,000 Da.

Kinesin I ATPase manipulates biohybrids formed from tubulin and carbon nanotubes

This chapter describes a method for the formation of novel protein-nanotube hybrid conjugates. Specifically, we took advantage of the self-assembly and self-recognition properties of tubulin cytoskeletal protein immobilized onto carbon nanotubes to form nanotube-based biohybrids. Further biohybrid hierarchical integration in assemblies enabled molecular-level manipulation on engineered surfaces, as demonstrated with biocatalyst kinesin 1 ATPase molecular motor. The method presented herein can be extended for the preparation of biocatalyst-based or protein-based assemblies to be used as sensors or biological templates for nanofabrication.

A rewired green fluorescent protein: folding and function in a nonsequential, noncircular GFP permutant

The sequential order of secondary structural elements in proteins affects the folding and activity to an unknown extent. To test the dependence on sequential connectivity, we reconnected secondary structural elements by their solvent-exposed ends, permuting their sequential order, called "rewiring". This new protein design strategy changes the topology of the backbone without changing the core side chain packing arrangement. While circular and noncircular permutations have been observed in protein structures that are not related by sequence homology, to date no one has attempted to rationally design and construct a protein with a sequence that is noncircularly permuted while conserving three-dimensional structure. Herein, we show that green fluorescent protein can be rewired, still functionally fold, and exhibit wild-type fluorescence excitation and emission spectra.

Aromatic small molecules remodel toxic soluble oligomers of amyloid beta through three independent pathways

In protein conformational disorders ranging from Alzheimer to Parkinson disease, proteins of unrelated sequence misfold into a similar array of aggregated conformers ranging from small oligomers to large amyloid fibrils. Substantial evidence suggests that small, prefibrillar oligomers are the most toxic species, yet to what extent they can be selectively targeted and remodeled into non-toxic conformers using small molecules is poorly understood. We have evaluated the conformational specificity and remodeling pathways of a diverse panel of aromatic small molecules against mature soluble oligomers of the Aβ42 peptide associated with Alzheimer disease. We find that small molecule antagonists can be grouped into three classes, which we herein define as Class I, II, and III molecules, based on the distinct pathways they utilize to remodel soluble oligomers into multiple conformers with reduced toxicity. Class I molecules remodel soluble oligomers into large, off-pathway aggregates that are non-toxic. Moreover, Class IA molecules also remodel amyloid fibrils into the same off-pathway structures, whereas Class IB molecules fail to remodel fibrils but accelerate aggregation of freshly disaggregated Aβ. In contrast, a Class II molecule converts soluble Aβ oligomers into fibrils, but is inactive against disaggregated and fibrillar Aβ. Class III molecules disassemble soluble oligomers (as well as fibrils) into low molecular weight species that are non-toxic. Strikingly, Aβ non-toxic oligomers (which are morphologically indistinguishable from toxic soluble oligomers) are significantly more resistant to being remodeled than Aβ soluble oligomers or amyloid fibrils. Our findings reveal that relatively subtle differences in small molecule structure encipher surprisingly large differences in the pathways they employ to remodel Aβ soluble oligomers and related aggregated conformers.

Conductive cable fibers with insulating surface prepared by coaxial electrospinning of multiwalled nanotubes and cellulose

Core-sheath multiwalled carbon nanotube (MWNT)-cellulose fibers of diameters from several hundreds of nanometers to several micrometers were prepared by coaxial electrospinning from a nonvolatile, nonflammable ionic liquid (IL) solvent, 1-methyl-3-methylimidazolium acetate ([EMIM][Ac]). MWNTs were dispersed in IL to form a gel solution. This gel core solution was electrospun surrounded by a sheath solution of cellulose dissolved in the same IL. Electrospun fibers were collected in a coagulation bath containing ethanol-water to remove the IL completely and dried to form core-sheath MWNT-cellulose fibers having a cable structure with a conductive core and insulating sheath. Enzymatic treatment of a portion of a mat of these fibers with cellulase selectively removed the cellulose sheath exposing the MWNT core for connection to an electrode. These MWNT-cellulose fiber mats demonstrated excellent conductivity because of a conductive pathway of bundled MWNTs. Fiber mat conductivity increased with increasing ratio of MWNT in the fibers with a maximum conductivity of 10.7 S/m obtained at 45 wt % MWNT loading.

Electrospinning of nanomaterials and applications in electronic components and devices

Electrospinning of nanomaterial composites are gaining increased interest in the fabrication of electronic components and devices. Performance improvement of electrospun components results from the unique properties associated with nanometer-scaled features, high specific surface areas, and light-weight designs. Electrospun nanofiber membrane-containing polymer electrolytes show improved ionic conductivity, electrochemical stability, low interfacial resistance, and improved charge-discharge performance than those prepared from conventional membranes. Batteries with non-woven electrospun separators have increased cycle life and higher rate capabilities than ones with conventional separators. Electrospun nanofibers may also be used as working electrodes in lithium-ion batteries, where they exhibit excellent rate capability, high reversible capacity, and good cycling performance. Moreover, the high surface area of electrospun activated carbon nanofibers improves supercapacitor energy density. Similarly, nanowires having quasi-one-dimensional structures prepared by electrospinning show high conductivity and have been used in ultra-sensitive chemical sensors, optoelectronics, and catalysts. Electrospun conductive polymers can also perform as flexible electrodes. Finally, the thin, porous structure of electrospun nanofibers provides for the high strain and fast response required for improved actuator performance. The current review examines recent advances in the application of electrospinning in fabricating electronic components and devices.

Gene delivery in three-dimensional cell cultures by superparamagnetic nanoparticles

Three-dimensional (3D) cellular assays closely mimic the in vivo milieu, providing a rapid, inexpensive system for screening drug candidates for toxicity or efficacy in the early stages of drug discovery. However, 3D culture systems may suffer from mass transfer limitations, particularly in delivery of large polypeptide or nucleic acid compounds. Nucleic acids (e.g., genes, silencing RNA) are of particular interest both as potential therapeutics and due to a desire to modulate the gene-expression patterns of cells exposed to small-molecule pharmacological agents. In the present study, polyethylenimine (PEI)-coated superparamagnetic nanoparticles (SPMNs) were designed to deliver interfering RNA and green fluorescent protein (GFP) plasmids through a collagen-gel matrix into 3D cell cultures driven by an external magnetic field. The highest transfection efficiency achieved was 64% for siRNA and 77% for GFP plasmids. Delivery of an shRNA plasmid against GFP by PEI-coated SPMNs silenced the GFP expression with 82% efficiency. We further demonstrated that this delivery approach could be used for screening interfering RNA constructs for therapeutic or toxic effects for cells grown in 3D cultures. Four known toxic shRNA plasmids were delivered by PEI-coated SPMNs into 3D cell cultures, and significant toxicities (41-51% cell death) were obtained.

Antistaphylococcal nanocomposite films based on enzyme-nanotube conjugates

Infection with antibiotic-resistant pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) is one of the primary causes of hospitalizations and deaths. To address this issue, we have designed antimicrobial coatings incorporating carbon nanotube-enzyme conjugates that are highly effective against antibiotic-resistant pathogens. Specifically, we incorporated conjugates of carbon nanotubes with lysostaphin, a cell wall degrading enzyme, into films to impart bactericidal properties against Staphylococcus aureus and Staphylococcus epidermidis. We fabricated and characterized nanocomposites containing different conjugate formulations and enzyme loadings. These enzyme-based composites were highly efficient in killing MRSA (>99% within 2 h) without release of the enzyme into solution. Additionally, these films were reusable and stable under dry storage conditions for a month. Such enzyme-based film formulations may be used to prevent growth of pathogenic and antibiotic-resistant microorganisms on various common surfaces in hospital settings. Polymer and paint films containing such antimicrobial conjugates, in particular, could be advantageous to prevent risk of staphylococcal-specific infection and biofouling.

Numerical and Monte Carlo simulations of phenolic polymerizations catalyzed by peroxidase

Numerical and Monte Carlo simulations of horseradish peroxidase-catalyzed phenolic polymerizations have been performed. Kinetic constants for the simulations were fit to data from the oxidation and polymerization of bisphenol A. Simulations of peroxidase-catalyzed phenolic polymerization were run as a function of enzyme concentration and radical transfer and radical coupling rate constants. Predictions were performed with respect to conversion vs. time and number average molecular weight and polydispersity vs. conversion. It is shown that the enzymatic polymerization of phenols can be optimized with respect to high molecular weights by employing low enzyme concentrations and phenols with low radical coupling rate constants coupled with relatively high radical transfer rate constants. Such phenols may be identified by using linear free energy relationships that relate radical reactivity to electron donating/withdrawing potential of the phenolic substituent.

Peroxidases depolymerize lignin in organic media but not in water

Horseradish peroxidase and milk lactoperoxidase, while unable to degrade either synthetic or natural lignins in aqueous solutions, vigorously depolymerize polyconiferyl alcohol, milled wood lignin, and kraft pine lignin in dioxane, dimethylformamide, or methyl formate containing 5% aqueous buffer (10 mM acetate, pH 5). Horseradish peroxidase, solubilized in organic media by chemical modification, can also degrade lignin in native lignocellulose (wheat straw).

Apocynin derivatives interrupt intracellular signaling resulting in decreased migration in breast cancer cells

Cancer cells are defined by their ability to divide uncontrollably and metastasize to secondary sites in the body. Consequently, tumor cell migration represents a promising target for anticancer drug development. Using our high-throughput cell migration assay, we have screened several classes of compounds for noncytotoxic tumor cell migration inhibiting activity. One such compound, apocynin (4-acetovanillone), is oxidized by peroxidases to yield a variety of oligophenolic and quinone-type compounds that are recognized inhibitors of NADPH oxidase and may be inhibitors of the small G protein Rac1 that controls cell migration. We report here that while apocynin itself is not effective, apocynin derivatives inhibit migration of the breast cancer cell line MDA-MB-435 at subtoxic concentrations; the migration of nonmalignant MCF10A breast cells is unaffected. These compounds also cause a significant rearrangement of the actin cytoskeleton, cell rounding, and decreased levels of active Rac1 and its related G protein Cdc42. These results may suggest a promising new route to the development of novel anticancer therapeutics.

Unnatural polyketide analogues selectively target the HER signaling pathway in human breast cancer cells

Receptor tyrosine kinases are critical targets for the regulation of cell survival. Cancer patients with abnormal receptor tyrosine kinases (RTK) tend to have more aggressive disease with poor clinical outcomes. As a result, human epidermal growth factor receptor kinases, such as EGFR (HER1), HER2, and HER3, represent important therapeutic targets. Several plant polyphenols including the type III polyketide synthase products (genistein, curcumin, resveratrol, and epigallocatechin-3-galate) possess chemopreventive activity, primarily as a result of RTK inhibition. However, only a small fraction of the polyphenolic structural universe has been evaluated. Along these lines, we have developed an in vitro route to the synthesis and subsequent screening of unnatural polyketide analogues with N-acetylcysteamine (SNAc) starter substrates and malonyl-coenzyme A (CoA) and methylmalonyl-CoA as extender substrates. The resulting polyketide analogues possessed a similar structural polyketide backbone (aromatic-2-pyrone) with variable side chains. Screening chalcone synthase (CHS) reaction products against BT-474 cells resulted in identification of several trifluoromethylcinnamoyl-based polyketides that showed strong suppression of the HER2-associated PI3K/AKT signaling pathway, yet did not inhibit the growth of nontransformed MCF-10A breast cells (IC(50)>100 microM). Specifically, 4-trifluoromethylcinnamoyl pyrone (compound 2 e) was highly potent (IC(50)<200 nM) among the test compounds toward proliferation of several breast cancer cell lines. This breadth of activity likely stems from the ability of compound 2 e to inhibit the phosphorylation of HER1, HER2, and HER3. Therefore, these polyketide analogues might prove to be useful drug candidates for potential breast cancer therapy.

Three-dimensional cell culture microarray for high-throughput studies of stem cell fate

We have developed a novel three-dimensional (3D) cellular microarray platform to enable the rapid and efficient tracking of stem cell fate and quantification of specific stem cell markers. This platform consists of a miniaturized 3D cell culture array on a functionalized glass slide for spatially addressable high-throughput screening. A microarray spotter was used to deposit cells onto a modified glass surface to yield an array consisting of cells encapsulated in alginate gel spots with volumes as low as 60 nL. A method based on an immunofluorescence technique scaled down to function on a cellular microarray was also used to quantify specific cell marker protein levels in situ. Our results revealed that this platform is suitable for studying the expansion of mouse embryonic stem (ES) cells as they retain their pluripotent and undifferentiated state. We also examined neural commitment of mouse ES cells on the microarray and observed the generation of neuroectodermal precursor cells characterized by expression of the neural marker Sox-1, whose levels were also measured in situ using a GFP reporter system. In addition, the high-throughput capacity of the platform was tested using a dual-slide system that allowed rapid screening of the effects of tretinoin and fibroblast growth factor-4 (FGF-4) on the pluripotency of mouse ES cells. This high-throughput platform is a powerful new tool for investigating cellular mechanisms involved in stem cell expansion and differentiation and provides the basis for rapid identification of signals and conditions that can be used to direct cellular responses.

Artificial organelles: digital microfluidic platform for proteoglycan and glycoprotein biosynthesis

The development of artificial organelles is a new, fast-growing field in which a variety of techniques have been employed. This article gives a brief overview of the history of artificial organelles, and describes the development of an artificial endoplasmic reticulum and Golgi organelle on a digital microfluidic platform. This device should be useful in high-throughput combinatorial proteoglycan/glycoprotein synthesis, providing critical information about the control of biosynthetic pathways for these important signaling molecules.

Resveratrol selectively remodels soluble oligomers and fibrils of amyloid Abeta into off-pathway conformers

Misfolded proteins associated with diverse aggregation disorders assemble not only into a single toxic conformer but rather into a suite of aggregated conformers with unique biochemical properties and toxicities. To what extent small molecules can target and neutralize specific aggregated conformers is poorly understood. Therefore, we have investigated the capacity of resveratrol to recognize and remodel five conformers (monomers, soluble oligomers, non-toxic oligomers, fibrillar intermediates, and amyloid fibrils) of the Abeta1-42 peptide associated with Alzheimer disease. We find that resveratrol selectively remodels three of these conformers (soluble oligomers, fibrillar intermediates, and amyloid fibrils) into an alternative aggregated species that is non-toxic, high molecular weight, and unstructured. Surprisingly, resveratrol does not remodel non-toxic oligomers or accelerate Abeta monomer aggregation despite that both conformers possess random coil secondary structures indistinguishable from soluble oligomers and significantly different from their beta-sheet rich, fibrillar counterparts. We expect that resveratrol and other small molecules with similar conformational specificity will aid in illuminating the conformational epitopes responsible for Abeta-mediated toxicity.

Analysis of E. coli K5 capsular polysaccharide heparosan

Heparosan is the key precursor for the preparation of bioengineered heparin, a potential replacement for porcine intestinal heparin, an important anticoagulant drug. The molecular weight (MW) distribution of heparosan produced by the fermentation of E. coli K5 was investigated. Large-slab isocratic and mini-slab gradient polyacrylamide gel electrophoresis (PAGE) were used to analyze the MW and polydispersity of heparosan. A preparative method that allowed fractionation by continuous-elution PAGE was used to obtain heparosan MW standards. The MWs of the heparosan standards were determined by electrospray ionization Fourier-transform mass spectrometry (ESI-FT-MS). A ladder of the standards was then used to determine the MW properties of polydisperse heparosan samples. Unbleached and bleached heparosan produced by fermentation of E. coli K5 had similar number-averaged MWs (M(N)), weight-averaged MWs (M(W)), and MW ranges of 3,000 to 150,000 Da.