NMR tools for biotechnology

Elucidation of the chemical and morphological structure of double-network (DN) hydrogels by high-resolution magic angle spinning (HRMAS) NMR spectroscopy

(1)H HRMAS NMR spectroscopy is applied to gain insight into the chemical and morphological structure of double-network (DN) hydrogels, prepared from poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) and poly(acrylamide) (PAAm). The method enables one to obtain detailed information at the molecular level about the formation of covalent bonds between the two polymer networks through non-reacted double bonds of the cross-linker N,N'-methylene bis(acrylamide) (MBAA). Evidence to the existence of strong hydrogen-bond interactions based on the N-H group of the PAMPS as a hydrogen-bond donor and the C=O group of the PAAm as a hydrogen-bond acceptor is also provided. These findings clarify the origin of the toughening mechanism and the exceptionally strong mechanical properties of DN gels, further supported by microhardness data.

Concentration profiling in rat tissue by high-resolution magic-angle spinning NMR spectroscopy: investigation of a model drug

The utility of high-resolution magic-angle spinning (HR-MAS) NMR for studying drug delivery in whole tissues was explored by dosing female Sprague-Dawley rats with topical or injectable benzoic acid (BA). In principle, HR-MAS NMR permits the detection of both intra- and extracellular compounds. This is an advantage over the previous detection of topically applied BA using microdialysis coupled to HPLC/UV as microdialysis samples only the extracellular space. Skin and muscle samples were analyzed by (1)H HR-MAS NMR, and BA levels were determined using an external standard solution added to the sample rotor. One to two percent of the BA topical dose was detected in the muscle, showing that BA penetrated through the dermal and subcutaneous layers. Since BA was not detected in the muscle in the microdialysis studies, the NMR spectra revealed the intracellular localization of BA. The amount of BA detected in muscle after subcutaneous injection correlated with the distance from the dosing site. Overall, the results suggest that HR-MAS NMR can distinguish differences in the local concentration of BA varying with tissue type, dosage method, and tissue proximity to the dosing site. The results illustrate the potential of this technique for quantitative analysis of drug delivery and distribution and the challenges to be addressed as the method is refined.

Development of a Functionalized Xenon Biosensor

NMR-based biosensors that utilize laser-polarized xenon offer potential advantages beyond current sensing technologies. These advantages include the capacity to simultaneously detect multiple analytes, the applicability to in vivo spectroscopy and imaging, and the possibility of "remote" amplified detection. Here, we present a detailed NMR characterization of the binding of a biotin-derivatized caged-xenon sensor to avidin. Binding of "functionalized" xenon to avidin leads to a change in the chemical shift of the encapsulated xenon in addition to a broadening of the resonance, both of which serve as NMR markers of ligand-target interaction. A control experiment in which the biotin-binding site of avidin was blocked with native biotin showed no such spectral changes, confirming that only specific binding, rather than nonspecific contact, between avidin and functionalized xenon leads to the effects on the xenon NMR spectrum. The exchange rate of xenon (between solution and cage) and the xenon spin-lattice relaxation rate were not changed significantly upon binding. We describe two methods for enhancing the signal from functionalized xenon by exploiting the laser-polarized xenon magnetization reservoir. We also show that the xenon chemical shifts are distinct for xenon encapsulated in different diastereomeric cage molecules. This demonstrates the potential for tuning the encapsulated xenon chemical shift, which is a key requirement for being able to multiplex the biosensor.

Quantitative high-resolution on-line NMR spectroscopy in reaction and process monitoring

On-line nuclear magnetic resonance spectroscopy (on-line NMR) is a powerful technique for reaction and process monitoring. Different set-ups for direct coupling of reaction and separation equipment with on-line NMR spectroscopy are described. NMR spectroscopy can be used to obtain both qualitative and quantitative information from complex reacting multicomponent mixtures for equilibrium or reaction kinetic studies. Commercial NMR probes can be used at pressures up to 35 MPa and temperatures up to 400 K. Applications are presented for studies of equilibria and kinetics of complex formaldehyde-containing mixtures as well as homogeneously and heterogeneously catalyzed esterification kinetics. Direct coupling of a thin-film evaporator is described as an example for the benefits of on-line NMR spectroscopy in process monitoring.

Preparation, physical properties, on-bead binding assay and spectroscopic reliability of 25 barcoded polystyrene-poly(ethylene glycol) graft copolymers

Here we describe the preparation of 25 beaded polystyrene-poly(ethylene glycol) graft copolymers from six spectroscopically active styrene monomers: styrene, 2,5-dimethylstyrene, 4-methylstyrene, 2,4-dimethylstyrene, 4-tert-butylstyrene, and 3-methylstyrene. These polymers were thoroughly characterized by Raman, infrared, and (1)H/(13)C NMR spectroscopies, and differential scanning calorimetry. Determination of the swelling properties, peptide synthesis, and on-bead streptavidin-alkaline phosphatase (SAP) binding assay further established that their physical and chemical properties where not significantly altered by the diversity of their encoded polystyrene core. Each of the 25 resins displayed a unique Raman and infrared vibrational fingerprint, which was converted into a "spectroscopic barcode". The position of each bar matches the peak wavenumber in the corresponding spectrum but is independent of its intensity. From this simplified representation similarity maps comparing 35 000 resin pairs were generated to establish the spectroscopic barcoding as a reliable encoding methodology. In effect, in 99% of the cases, the highest similarity coefficients were obtained for resin pairs prepared from the same styrene derivatives even after SAP binding assay. We have also shown that a small but unique combination of a resin's vibrations (30-40%) is sufficient for its identification. However, in rare cases where a resin's vibrational signature has been severely compromised, both the Raman and infrared barcodes were synergistically and reliably utilized to unequivocally identify its chemical make up.

NMR-based screening technologies

NMR-based ligand screening is now an established field in its own right. In recent years, advances in both methodology and hardware have broadened its range of applications and pushed back practical limitations, leading to the growing importance of NMR screening as a tool in industrial drug research. An overview of new screening methods and applications is presented here, and ways in which NMR-screening is being used in cooperation with other screening techniques are discussed.

Viral-induced self-assembly of magnetic nanoparticles allows the detection of viral particles in biological media

Monodisperse magnetic nanoparticles conjugated with virus-surface-specific antibodies self-assemble in the presence of specific viral particles to create supramolecular structures with enhanced magnetic properties, as detected by magnetic resonance methods (NMR/MRI). The observed magnetic relaxation changes that occur upon viral-induced assembly allowed for highly sensitive and selective detection of a virus in complex biological media. The developed method was shown to specifically detect adenovirus-5 and herpes simplex virus-1 at concentrations of 5 viral particles/10 muL without the need of extensive sample preparation. The applications of this new method span from high-throughput NMR detection of viruses in biological samples to potential MR imaging of viral distribution in vivo.

Mass spectrometric analysis of combinatorial peptide libraries derived from the tandem repeat unit of MUC2 mucin

Four 19-member synthetic peptide libraries, based on the TX1TX2T epitope motif of the mucin-2 gastrointestinal glycoprotein (MUC2) and ranging in peptide length from dipeptides to 15-mers (XT, TXT, TQTXT and KVTPTPTPTGTQTXT), were synthesized by combinatorial solid phase peptide synthesis using the portioning-mixing combinatorial approach, and analysed by electrospray ionization mass spectrometry at different (1000-10000) resolutions. Most of the components of the individual libraries could be easily identified in a single-stage molecular mass screening experiment. The resolving power of the instrument becomes an important factor above 800-1000 Da molecular mass, when predominantly multiply charged molecular ions are formed. Approaches to the identification of isobars (glutamine/lysine), isomers leucine/isoleucine) and sequence variations by tandem mass spectrometry, and/or by high-performance liquid chromatography-mass spectrometry are outlined.

Quantitative on-line high-resolution NMR spectroscopy in process engineering applications

In many technical processes, complex multicomponent mixtures have to be handled, for example, in reaction or separation equipment. High-resolution NMR spectroscopy is an excellent tool to study these mixtures and gain insight in their behavior in the processes. For on-line studies under process conditions, flow NMR probes can be used in a wide range of temperature and pressure. A major challenge in engineering applications of NMR spectroscopy is the need for quantitative evaluation. Flow rates, recovery times, and other parameters of the on-line NMR experiments have to be optimized for this purpose. Since it is generally prohibitive to use deuterated solvents in engineering applications, suitable techniques for field homogenization and solvent signal suppression are needed. Two examples for the application of on-line NMR spectroscopic experiments in process engineering are presented, studies on chemical equilibria and reaction kinetics of the technically important system formaldehyde-water-methanol and investigations on reactive gas absorption of CO(2) in aqueous solutions of monoethanolamine.

Production of lovastatin examined by an integrated approach based on chemometrics and DOSY-NMR

Microbial secondary metabolites are one of the sources of therapeutic molecules in the pharmaceutical industry. Product quality and high yields of secondary metabolites are the main goals for the commercial success of a fermentation process. Our novel approach was based on the decision-tree algorithm to determine the key variables correlated with the process outcome and on DOSY-NMR to identify both co-metabolites and impurities, and it improves fermentation systems and speeds up bioprocess development. The approach has been validated in the case of lovastatin production from Aspergillus terreus.

Magnetic relaxation switches capable of sensing molecular interactions

Highly sensitive, efficient, and high-throughput biosensors are required for genomic and proteomic data acquisition in complex biological samples and potentially for in vivo applications. To facilitate these studies, we have developed biocompatible magnetic nanosensors that act as magnetic relaxation switches (MRS) to detect molecular interactions in the reversible self-assembly of disperse magnetic particles into stable nanoassemblies. Using four different types of molecular interactions (DNA-DNA, protein-protein, protein-small molecule, and enzyme reactions) as model systems, we show that the MRS technology can be used to detect these interactions with high efficiency and sensitivity using magnetic relaxation measurements including magnetic resonance imaging (MRI). Furthermore, the magnetic changes are detectable in turbid media and in whole-cell lysates without protein purification. The developed magnetic nanosensors can be used in a variety of biological applications such as in homogeneous assays, as reagents in miniaturized microfluidic systems, as affinity ligands for rapid and high-throughput magnetic readouts of arrays, as probes for magnetic force microscopy, and potentially for in vivo imaging.

DNA-based magnetic nanoparticle assembly acts as a magnetic relaxation nanoswitch allowing screening of DNA-cleaving agents

Monodisperse magnetic nanoparticles conjugated with complementary oligonucleotide sequences self-assemble into stable magnetic nanoassemblies resulting in a decrease of the spin-spin relaxation times (T2) of neighboring water protons. When these nanoassemblies are treated with a DNA cleaving agent, the nanoparticles become dispersed, switching the T2 of the solution back to original values. These qualities render the developed nanoparticles and their nanoassemblies as magnetic relaxation switches capable of screening for DNA-cleaving compounds by magnetic resonance methods such as MRI and NMR.

Nuclear magnetic resonance and plant metabolic engineering

Nuclear magnetic resonance (NMR) can be used to measure metabolite levels and metabolic fluxes, to probe the intracellular environment, and to follow transport and energetics nondestructively. NMR methods are therefore powerful aids to understanding plant metabolism and physiology. Both spectroscopy and imaging can help overcome the unique challenges that plants present to the metabolic engineer by detecting, identifying, quantifying, and localizing novel metabolites in vivo and in extracts; revealing the composition and physical state of cell wall and other polymers; allowing the identification of active pathways; providing quantitative measures of metabolic flux; and testing hypotheses about the effects of engineered traits on plant physiological function. The aim of this review is to highlight recent studies in which NMR has contributed to metabolic engineering of plants and to illustrate the unique characteristics of NMR measurements that give it the potential to make greater contributions in the future.

Applications of NMR in drug discovery

NMR, already some 50 years old, has long been an invaluable analytical method in industry for verification of chemical synthesis and compound characterisation. The range of molecular information accessible through NMR, however, offers a far larger horizon of applications. Of these, ligand screening by NMR has emerged as a very promising new method in drug discovery. Its unmatched screening sensitivity, combined with the abundance of available information on the structure and nature of molecular binding, justifies the growing interest in this dynamically expanding NMR application.

Analysis of multiple samples using multiplex sample NMR: selective excitation and chemical shift imaging approaches

Two improved approaches for the rapid analysis of multiple samples using multiplex sample NMR are described. In the first approach, frequency-selective 90 degrees radio frequency pulses and large pulsed field gradients are applied to excite and detect multiple samples in rapid succession. This method is advantageous for samples with relatively long longitudinal (T1) relaxation times. In the second approach, chemical shift imaging is applied to acquire both the spectral and spatial information of multiple samples simultaneously. Chemical shift imaging is more time-consuming than selective excitation; however, it is advantageous for detecting samples with short T1's and for signal averaging. Both approaches demonstrate the potential of multiplex sample NMR for carrying out high-throughput NMR detection.

NMR spectroscopy in drug discovery: tools for combinatorial chemistry, natural products, and metabolism research

NMR spectroscopy has enjoyed many advances recently, and the pace of development shows no signs of slowing. This article focuses on advances that have affected solution-state NMR. These advances fall into three general categories: new experimental techniques (new pulse sequence tools), improved hardware and more powerful software. These advances are allowing NMR to help solve important problems in the field of drug discovery. Their impact is widespread. NMR spectroscopy is now being used to determine protein structures, to monitor ligand-receptor binding, to study diffusion, to analyze mixtures using LC-NMR, to analyze solid-phase synthesis resins and to determine the structures of organic small molecules. NMR spectroscopy can provide both qualitative and quantitative information, and can be used in both routine analytical applications and demanding research applications. The applications described here can benefit numerous disciplines in drug discovery, including natural products research, synthetic medicinal chemistry, metabolism studies, drug production, quality control, rational drug design and combinatorial chemistry.

Online NMR for monitoring biocatalysed reactions

Monitoring biocatalysed reactions and metabolic pathways using NMR spectroscopy is of growing interest. As a non-invasive analytical method providing simultaneous information about intracellular and extracellular constituents, it is superior to other analytical techniques and has a wide range of applications: kinetics and stoichiometrics of metabolic events, metabolic fluxes and enzyme activities can be detected in situ or after taking a sample from the biotransformation mixture. New NMR pulse sequences provide even more valuable experiments in these fields. Research topics range from the monitoring of polymer formation to fermentations producing beverages or antibiotics. Routine monitoring of industrial fermentations by NMR seems to be imminent.

Polarization transfer in lipid membranes

Polarization transfer is a key experiment for the detection of insensitive nuclei by NMR. Transfer in liquids is often achieved through J-coupling using the INEPT experiment, while in solids the dipolar coupling is used with cross polarization. Liquid crystals, including lipid membranes, are intermediate cases between solids and liquids. In the present article, we compare several transfer methods for lipid membranes spinning at the magic angle. It is shown that the most commonly used cross polarization technique is, in most cases, advantageously replaced by refocused INEPT or even by the NOE enhancement experiment, a method that is not normally used in that context. In principle, these enhancement techniques could be applied to other systems, including biological tissues and, more generally, soft matter systems that are neither solid nor liquid by NMR standards.

Applications of NMR in drug discovery

In the half-century since its discovery, nuclear magnetic resonance (NMR) has become the single most powerful form of spectroscopy in both chemistry and structural biology. The dramatic technical advances over the past 10-15 years, which continue apace, have markedly increased the range of applications for NMR in the study of protein-ligand interactions. These form the basis for its most exciting uses in the drug discovery process, which range from the simple identification of whether a compound (or a component of a mixture) binds to a given protein, through to the determination of the full three-dimensional structure of the complex, with all the information this yields for structure-based drug design.

Direct-injection NMR (DI-NMR): a flow NMR technique for the analysis of combinatorial chemistry libraries

A new tool for analyzing compound libraries by NMR has been developed. Aliquots of solution-state samples (between 120 and 350 microL) are directly injected, using a standard liquids handler, into an NMR (LC-NMR) flow probe. Automated NMR software tracks--and suppresses--intense signals arising from the nondeuterated solvents used (if any) and acquires high-sensitivity one-dimensional 1H NMR spectra. An 88-member combinatorial library, dissolved in DMSO and stored in a 96-well microtiter plate, has been analyzed a number of ways using this technique. This nondestructive technique, which we call direct-injection NMR (DI-NMR) and which is embodied in our versatile automated sample changer (VAST) hardware, has proven to be both routine and robust. Our success in automatically acquiring the NMR data for entire plates of library compounds (within 4-8 h) has caused us to develop new ways to display and analyze the resulting NMR data, as will be shown here.

Binding of ethidium to DNA measured using a 2D diffusion-modulated gradient COSY NMR experiment

The binding of ethidium bromide to a DNA hairpin (dU(5)-hairpin) was investigated using a novel 2D diffusion-modulated gradient correlation spectroscopy (DMG-COSY) experiment to evaluate the applicability of this technique for studying the binding of drugs to DNA. The DMG-COSY experiment includes a preparation period during which coherent magnetization is attenuated due to molecular self-diffusion. Magnetization then evolves due to scalar coupling during an evolution delay, and is detected using gradient pulses for coherence selection. The time-domain data are processed in an analogous manner as for gradient-selected COSY experiments. The diffusion coefficient for uridine in DMSO solution was determined from the H5-H6 crosspeak intensities for a series of 2D DMG-COSY experiments that differed in the magnitude of the gradient pulses applied during the preparation period of the DMG-COSY experiment. The diffusion coefficient for uridine calculated from the DMG-COSY experiments was identical (within experimental error) to that determined from 1D diffusion experiments (5.24x10(-6) cm(2)/s at 26 degrees C). The diffusion coefficients for ethidium bromide and for the dU(5)-hairpin were first measured separately using the DMG-COSY experiment, and then measured in the putative complex. The diffusion coefficient for free ethidium bromide (4.15x10(-6) cm(2)/s at 26 degrees C) was considerably larger than for the dU(5)-hairpin (1. 60x10(-6) cm(2)/s at 26 degrees C), as expected for the smaller molecule. The diffusion coefficient for ethidium was markedly decreased upon addition of the dU(5)-hairpin, consistent with complex formation (1.22x10(-6) cm(2)/s at 26 degrees C). Complex formation of 1:1 stoichiometry between ethidium and the stem of the dU(5)-hairpin was verified independently by fluorescence spectroscopy. These results demonstrate the utility of the DMG-COSY experiment for investigating the binding of drugs to DNA in aqueous solution.

Biomolecular NMR: recent advances in liquids, solids and screening

The past year has witnessed significant advances in NMR analysis of bio-macromolecules from a broad array of disciplines. First, great progress in the development of methods for measuring residual dipolar couplings in nematic media promises to increase both the size of systems to be studied and the accuracy with which structures can be determined. Second, the ability of solid-state NMR to provide structural information on biological systems is undergoing rapid expansion as a result of recent developments. The structural details that can be derived for biomolecules in the liquid and solid states can be used for the rational design of high-affinity ligands. Such studies are now complemented by NMR screening of synthetic and natural molecular libraries. Several NMR screening protocols have been designed that employ both rational and random elements.