Protein dynamics revealed by hydrogen/deuterium exchange mass spectrometry: Correlation between experiments and simulation

Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful technique for studying protein dynamics, which is an important factor governing protein functions. However, the process of hydrogen/deuterium exchange (HDX) of proteins is highly complex and the underlying mechanism has not yet been fully elucidated. Meanwhile, molecular dynamics (MD) simulation is a computational technique that can be used to elucidate HDX behaviour on proteins and facilitate interpretation of HDX-MS data. This article aims to summarize the current understandings on the mechanism of HDX and its correlation with MD simulation, to discuss the recent developments in the techniques of HDX-MS and MD simulation and to extend the perspectives of these two techniques in protein dynamics study.

Rapid detection and quantitation of drugs-of-abuse by wooden-tip electrospray ionization mass spectrometry

Determination of drugs-of-abuse in body fluids of drug abusers is important for the law enforcement as well as the treatment and rehabilitation. In this study, wooden-tip electrospray ionization mass spectrometry (WT-ESI-MS), a simple and cost-effective technique, was developed for rapid detection and quantitation of common drugs-of-abuse, including methamphetamine, methylenedioxymethamphetamine (MDMA), cocaine, heroin and tetrahydrocannabinol (THC), in urine and oral fluid, following our previous successful demonstration for rapid and sensitive detection of ketamine and nor-ketamine in urine and oral fluid by this technique. It was found that the limit-of-detection for methamphetamine could fully fulfill the cut-off value requirements of the international standards, and those of MDMA and cocaine could fulfill some of the requirements. The linear range, accuracy and precision for quantitation of the drugs were generally satisfactory, except for THC for which the analytical performance still needs to be improved. Analysis of one sample could typically be completed within minutes. These results indicated that WT-ESI-MS could be used for rapid screening of drugs-of-abuse in urine, oral fluid as well as other body fluids.

Lavender essential oil ameliorates depression-like behavior and increases neurogenesis and dendritic complexity in rats

Depression is a major health issue that causes severe societal economic and health burden. Aromatherapy, a practice that uses essential oils for preventive and therapeutic purposes, represents a promising therapeutic alternative for the alleviation of depressive symptoms. Lavender essential oil (LEO) has been the focus of clinical studies due to its positive effect on mood. An animal model of chronic administration of high dose corticosterone to induce depression- and anxiety-like behavior and reduced neurogenesis was used to explore the biological changes brought by aromatherapy. Twenty-four adult male Sprague Dawley rats were randomly assigned into four groups: Control, corticosterone (Cort) group with high dose of corticosterone, LEO group with daily exposure to LEO by inhalation, and LEO + Cort. At the end of the 14-day treatment period, behavioral tests were carried out. Serum samples were collected 2-3 days after the 14-day period treatment and before perfusion to carry out biochemical analyses to measure BDNF, corticosterone and oxytocin. After perfusion, brains were collected for immunohistochemical analysis to detect BrdU and DCX positive cells in the hippocampus and subventricular zone. Results showed that treatment with LEO ameliorated the depression-like behavior induced by the chronic administration of corticosterone as observed in the LEO + Cort group. Cort treatment reduced the number of BrdU positive cells in the hippocampus and the subventricular zone. Treatment with LEO prevented the corticosterone-induced reduction in the number of BrdU positive cells (LEO + Cort group) demonstrating the neurogenic effect of LEO under high corticosterone conditions. Chronic administration of high dose of corticosterone significantly reduced the dendritic complexity of immature neurons. On the contrary, treatment with LEO increased dendritic complexity of immature neurons under high corticosterone conditions (LEO + Cort group). The improved neurogenesis and dendritic complexity observed in the LEO + Cort group demonstrated a clear restorative effect of LEO under high corticosterone conditions. However, 2-3 days after the treatment, the levels of BDNF were upregulated in the LEO and LEO + Cort groups. Furthermore, the concentration of oxytocin in serum, 2-3 days after the treatment, showed to be upregulated in the LEO group alone. The present study has provided evidence of the biological effect of LEO on neuroplasticity and neurogenesis. Also, this study contributes to the understanding of the mechanism of action of LEO in an animal model where depression- and anxiety-like behavior and reduced neurogenesis were induced by high corticosterone administration.

Establishment of a spectral database for classification of edible oils using matrix-assisted laser desorption/ionization mass spectrometry

In this study, we aim to establish a comprehensive spectral database for analysis of edible oils using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). More than 900 edible oil samples, including 30 types of edible oils, were analyzed and compared, and the characteristic peaks and spectral features of each edible oil were obtained. Edible oils were divided into eight groups based on their characteristic spectral patterns and principal component analysis results. An overall correct rate of 97.2% (98.1% for testing set) was obtained for classification of 435 edible oil products using partial least square-discriminant analysis, with nearly 100% correct rate for commonly used edible oils. Differentiation of counterfeit edible oils, repeatedly cooked edible oils and gutter oils from normal edible oils could also be achieved based on the MALDI-MS spectra. The establishment of this spectral database provides reference spectra for spectral comparison and allows rapid classification of edible oils by MALDI-MS.

Targeting the Thioredoxin Reductase-Thioredoxin System from Staphylococcus aureus by Silver Ions

The thioredoxin system, which is composed of NADPH, thioredoxin reductase (TrxR), and thioredoxin (Trx), is one of the major disulfide reductase systems used by bacteria against oxidative stress. In particular, this reductase system is crucial for the survival of the pathogenic bacterium Staphylococcus aureus, which lacks a natural glutathione/glutaredoxin (Grx) system. Although silver ions and silver-containing materials have been used as antibacterial agents for centuries, the antibacterial mechanism of silver is not well-understood. Herein, we demonstrate that silver ions bind to the active sites of S. aureus TrxR and Trx with dissociation constants of 1.4 ± 0.1 μM and 15.0 ± 5.0 μM and stoichiometries of 1 and 2 Ag⁺ ions per protein, respectively. Importantly, silver ion binding leads to oligomerization and functional disruption of TrxR as well as Trx. Silver also depleted intracellular thiol levels in S. aureus, disrupting bacterial thiol-redox homeostasis. Our study provides new insights into the antibacterial mechanism of silver ions. Moreover, the Trx and TrxR system might serve as a feasible target for the design of antibacterial drugs.

Ethylenediamine-modified amyloid fibrils of hen lysozyme with stronger adsorption capacity as rapid nano-biosorbents for removal of chromium(vi) ions

The development of amine-fortified amyloid fibrils of hen lysozyme as biosorbents for Cr(vi) removal is reported. Through –COO⁻/ethylenediamine conjugation, the nanofibers have higher net positive charge, offering rapid and stronger charge-based absorption of Cr(vi).

Rapid screening of mixed edible oils and gutter oils by matrix-assisted laser desorption/ionization mass spectrometry

Authentication of edible oils is a long-term issue in food safety, and becomes particularly important with the emergence and wide spread of gutter oils in recent years. Due to the very high analytical demand and diversity of gutter oils, a high throughput analytical method and a versatile strategy for authentication of mixed edible oils and gutter oils are highly desirable. In this study, an improved matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) method has been developed for direct analysis of edible oils. This method involved on-target sample loading, automatic data acquisition and simple data processing. MALDI-MS spectra with high quality and high reproducibility have been obtained using this method, and a preliminary spectral database of edible oils has been set up. The authenticity of an edible oil sample can be determined by comparing its MALDI-MS spectrum and principal component analysis (PCA) results with those of its labeled oil in the database. This method is simple and the whole process only takes several minutes for analysis of one oil sample. We demonstrated that the method was sensitive to change in oil compositions and can be used for measuring compositions of mixed oils. The capability of the method for determining mislabeling enables it for rapid screening of gutter oils since fraudulent mislabeling is a common feature of gutter oils.

Ebselen as a potent covalent inhibitor of New Delhi metallo-β-lactamase (NDM-1)

We identified a potent NDM-1 inhibitor that formed a S–Se bond with the Cys²²¹ residue at the active site, thereby exhibiting a new inhibition mechanism with broad spectrum inhibitory potential.

Structure-based design, synthesis, and biological evaluation of isatin derivatives as potential glycosyltransferase inhibitors

Peptidoglycan glycosyltransferase (PGT) has been shown to be an important pharmacological target for the inhibition of bacterial cell wall biosynthesis. Structure-based virtual screening of about 3,000,000 commercially available compounds against the crystal structure of the glycosyltransferase (GT) domain of the Staphylococcus aureus penicillin-binding protein 2 (S. aureus PBP2) resulted in identification of an isatin derivative, 2-(3-(2-carbamimidoylhydrazono)-2-oxoindolin-1-yl)-N-(m-tolyl)acetamide (4) as a novel potential GT inhibitor. A series of 4 derivatives were synthesized. Several compounds showed more active antimicrobial activity than the initial hit compound 4, in particular 2-(3-(2-carbamimidoylhydrazono)-2-oxoindolin-1-yl)-N-(3-nitrophenyl)acetamide (4l), against Gram-positive Bacillus subtilis and S. aureus with MIC values of 24 and 48 μg/mL, respectively. Saturation transfer difference (STD) NMR study revealed that there is a binding contact between 4l and the GT domain of S. aureus PBP2. Competitive STD-NMR further proved that 4l and moenomycin A bind to GT domain in a competitive manner. Molecular docking study suggests a potential binding pocket of 4l in the GT domain of S. aureus PBP2. Taken together, compound 4l would provide a new scaffold for further development of potent GT inhibitors.

Electrospray Ionization on Solid Substrates

Development of electrospray ionization on solid substrates (solid-substrate ESI) avoids the clogging problem encountered in conventional capillary-based ESI, allows more convenient sampling and permits new applications. So far, solid-substrate ESI with various materials, e.g., metals, paper, wood, fibers and biological tissue, has been developed, and applications ranging from analysis of pure compounds to complex mixtures as well as in vivo study were demonstrated. Particularly, the capability of solid-substrate ESI in direct analysis of complex samples, e.g., biological fluids and foods, has significantly facilitated mass spectrometric analysis in real-life applications and led to increasingly important roles of these techniques nowadays. In this review, various solid-substrate ESI techniques and their applications are summarized and the prospects in this field are discussed.

Mass spectrometry: towards in vivo analysis of biological systems

In vivo analysis is of paramount importance in monitoring physiological processes that take place in living organisms. Mass spectrometry, an analytical technique with high speed, sensitivity and specificity, is indispensable in biochemical studies nowadays. However, traditional mass spectrometric techniques are of limited applicability in direct analysis of living organisms due to various constraints, e.g., the necessity of ionization of analytes under vacuum and perturbation of physiological functions of living organisms during analysis. Recent development of mass spectrometry, particularly the development of ambient ionization techniques, has opened the door for direct analysis of living organisms. These new mass spectrometric techniques have the features that the ionization processes take place under atmospheric pressure and no or only little sample preparation is required, thus are well suited for analysis of living specimens without significantly perturbing their physiological states. The role of these mass spectrometric techniques in in vivo analysis has been increasingly important in recent years and is expected to be further expanded in the future. In this review, the use of various mass spectrometric techniques in in vivo analysis of biological systems is summarized and the prospects are discussed.

Analytical properties of solid-substrate electrospray ionization mass spectrometry

Conventional electrospray ionization mass spectrometry (ESI-MS) uses a capillary for sample loading and ionization. Along with the development of ambient ionization techniques, ESI-MS using noncapillary emitters has attracted more interest in recent years. Following our recent report on ESI-MS using wooden tips (Anal. Chem. 83, 8201-8207 (2011)), the technique was further investigated and extended in this study. Our results revealed that the wooden tips could serve as a chromatographic column for separation of sample components. Sequential and exhaustive ionization was observed for proteins and salts on wooden tips with salts ionized sooner and proteins later. Nonconductive materials that contain microchannels/pores could be used as tips for ESI-MS analysis with sample solutions loaded to the sharp-ends only, since rapid diffusion of sample solutions by capillary action would enable the tips to become conductive. Tips of inert materials such as bamboo, fabrics, and sponge could be used for sample loading and ionization, while samples such as tissue, mushroom, and bone could form tips to induce ionization for direct analysis with application of a high voltage.