Azasugar inhibitors as pharmacological chaperones for Krabbe disease

Krabbe disease is a devastating neurodegenerative disorder characterized by rapid demyelination of nerve fibers. This disease is caused by defects in the lysosomal enzyme β-galactocerebrosidase (GALC), which hydrolyzes the terminal galactose from glycosphingolipids. These lipids are essential components of eukaryotic cell membranes: substrates of GALC include galactocerebroside, the primary lipid component of myelin, and psychosine, a cytotoxic metabolite. Mutations of GALC that cause misfolding of the protein may be responsive to pharmacological chaperone therapy (PCT), whereby small molecules are used to stabilize these mutant proteins, thus correcting trafficking defects and increasing residual catabolic activity in cells. Here we describe a new approach for the synthesis of galacto-configured azasugars and the characterization of their interaction with GALC using biophysical, biochemical and crystallographic methods. We identify that the global stabilization of GALC conferred by azasugar derivatives, measured by fluorescence-based thermal shift assays, is directly related to their binding affinity, measured by enzyme inhibition. X-ray crystal structures of these molecules bound in the GALC active site reveal which residues participate in stabilizing interactions, show how potency is achieved and illustrate the penalties of aza/iminosugar ring distortion. The structure–activity relationships described here identify the key physical properties required of pharmacological chaperones for Krabbe disease and highlight the potential of azasugars as stabilizing agents for future enzyme replacement therapies. This work lays the foundation for new drug-based treatments of Krabbe disease.     

Dried and Fermented Powders of Edible Algae (Neopyropia yezoensis) Attenuate Hepatic Steatosis in Obese Mice

Edible algae Neopyropia yezoensis is used as “Nori”, its dried sheet product, in Japanese cuisine. Its lipid components reportedly improve hepatic steatosis in obese db/db mice. In this study, we prepared “Nori powder (NP)” and “fermented Nori powder (FNP)” to utilize the functional lipids contained in “Nori” and examined their nutraceutical effects in vivo. Male db/db mice were fed a basal AIN-76 diet, a 10% NP-supplemented diet, or a 10% FNP-supplemented diet for 4 weeks. We detected eicosapentaenoic acid (EPA) present in both NP and FNP in the serum and liver of db/db mice in a dose-dependent manner. The NP diet reduced hepatic triglyceride accumulation (by 58%) in db/db mice by modulating gene expression, which resulted in the inhibition of lipogenic enzyme activity. Additionally, NP intake significantly suppressed the expression of inflammatory genes in the liver and hepatic injury marker levels in the sera (by 26%) of db/db mice. The FNP diet also led to a marked reduction in hepatic triglyceride accumulation (by 50%) and hepatic injury (by 28%) in db/db mice, and the mechanism of these alleviative actions was similar to that of the NP diet. Although the EPA content of FNP was one-third that of NP, metabolomic analysis revealed that bioactive betaine analogs, such as stachydrine, betaine, and carnitine, were detected only in FNP. In conclusion, we suggest that (1) mechanical processing of “Nori” makes its lipid components readily absorbable by the body to exert their lipid-lowering effects, and (2) fermentation of “Nori” produces anti-inflammatory molecules and lipid-lowering molecules, which together with the lipid components, can exert hepatic steatosis-alleviating effects.     

Thin-layer chromatography combined with MALDI-TOF-MS and 31P-NMR to study possible selective bindings of phospholipids to silica gel

High-performance thin-layer chromatography (HPTLC) is a highly established separation method in the field of lipid and (particularly) phospholipid (PL) research. HPTLC is not only used to identify certain lipids in a mixture but also to isolate lipids (preparative TLC). To do this, the lipids are separated and subsequently re-eluted from the silica gel. Unfortunately, it is not yet known whether all PLs are eluted to the same extent or whether some lipids bind selectively to the silica gel. It is also not known whether differences in the fatty acyl compositions affect the affinities to the stationary phase. We have tried to clarify these questions by using a readily available extract from hen egg yolk as a selected example of a lipid mixture. After separation, the complete lanes or selected spots were eluted from the silica gel and investigated by a combination of MALDI-TOF MS and ³¹P NMR spectroscopy. The data obtained were compared with the composition of the total extract (without HPTLC). Although there were significant, solvent-dependent losses in the amount of each lipid, the relative composition of the mixture remained constant; there were also only very slight changes in the fatty acyl compositions of the individual PL classes. Therefore, lipid isolation by TLC may be used without any risk of major sample alterations.

Enhanced intravenous transgene expression in mouse lung using cyclic-head cationic lipids

Herein, we report enhanced intravenous mouse lung transfection using novel cyclic-head-group analogs of usually open-head cationic transfection lipids. Design and synthesis of the new cyclic-head lipid N,N-di-n-tetradecyl-3,4-dihydroxy-pyrrolidinium chloride (lipid 1) and its higher alkyl-chain analogs (lipids 2-4) and relative in vitro and in vivo gene transfer efficacies of cyclic-head lipids 1-4 to their corresponding open-head analogs [lipid 5, namely N,N-di-n-tetradecyl-N,N-(2-hydroxyethyl)ammonium chloride and its higher alkyl-chain analogs, lipids 6-8] have been described. In stark contrast to comparable in vitro transfection efficacies of both the cyclic- and open-head lipids, lipids 1-4 with cyclic heads were found to be significantly more efficient (by 5- to 11-fold) in transfecting mouse lung than their corresponding open-head analogs (5-8) upon intravenous administration. The cyclic-head lipid 3 with di-stearyl hydrophobic tail was found to be the most promising for future applications.     

Versatile rare earth hexanuclear clusters for the design and synthesis of highly-connected ftw-MOFs

A series of highly porous MOFs were deliberately targeted to contain a 12-connected rare earth hexanuclear cluster and quadrangular tetracarboxylate ligands. The resultant MOFs have an underlying topology of ftw, and are thus (4,12)-c ftw-MOFs. This targeted rare earth ftw-MOF platform offers the potential to assess the effect of pore functionality and size, via ligand functionalization and/or expansion, on the adsorption properties of relevant gases. Examination of the gas adsorption properties of these compounds showed that the ftw-MOF-2 analogues, constructed from rigid ligands with a phenyl, naphthyl, or anthracene core exhibited a relatively high degree of porosity. The specific surface areas and pore volumes of these analogs are amongst the highest reported for RE-based MOFs. Further studies revealed that the Y-ftw-MOF-2 shows promise as a storage medium for methane (CH₄) at high pressures. Furthermore, Y-ftw-MOF-2 shows potential as a separation agent for the selective removal of normal butane (n-C₄H₁₀) and propane (C₃H₈) from natural gas (NG) as well as interesting properties for the selective separation of n-C₄H₁₀ from C₃H₈ or isobutane (iso-C₄H₁₀).     

Lipid Profiles of the Heads of Four Shrimp Species by UPLC–Q–Exactive Orbitrap/MS and Their Cardiovascular Activities

Lipids are key factors in nutrition, structural function, metabolic features, and other biological functions. In this study, the lipids from the heads of four species of shrimp (Fenneropenaeus chinensis (FC), Penaeus japonicus (PJ), Penaeus vannamei (PV), and Procambarus clarkia (PCC)) were compared and characterized based on UPLC–Q–Exactive Orbitrap/MS. We compared the differences in lipid composition of four kinds of shrimp head using multivariate analysis. In addition, a zebrafish model was used to evaluate pro-angiogenic, anti-inflammatory, anti-thrombotic, and cardioprotective activities of the shrimp head lipids. The lipids from the four kinds of shrimp head had different degrees of pro-angiogenic activities, and the activities of PCC and PJ shrimp lipids were more significant than those of the other two species. Four lipid groups displayed strong anti-inflammatory activities. For antithrombotic activity, only PCC (25 μg/mL) and PV (100 μg/mL) groups showed obvious activity. In terms of cardioprotective activity, the four kinds of lipid groups significantly increased the zebrafish heart rhythms. The heart distances were shortened, except for those of the FC (100 μg/mL) and PJ (25 μg/mL) groups. Our comprehensive lipidomics analysis and bioactivity study of lipids from different sources could provide a basis for the better utilization of shrimp.     

Novel Glycerophospholipid,Lipo- and N-acyl Amino Acids from Bacteroidetes: Isolation,Structure Elucidation and Bioactivity

The ‘core’ metabolome of the Bacteroidetes genus Chitinophaga was recently discovered to consist of only seven metabolites. A structural relationship in terms of shared lipid moieties among four of them was postulated. Here, structure elucidation and characterization via ultra-high resolution mass spectrometry (UHR-MS) and nuclear magnetic resonance (NMR) spectroscopy of those four lipids (two lipoamino acids (LAAs), two lysophosphatidylethanolamines (LPEs)), as well as several other undescribed LAAs and N-acyl amino acids (NAAAs), identified during isolation were carried out. The LAAs represent closely related analogs of the literature-known LAAs, such as the glycine-serine dipeptide lipids 430 (2) and 654. Most of the here characterized LAAs (1, 5–11) are members of a so far undescribed glycine-serine-ornithine tripeptide lipid family. Moreover, this study reports three novel NAAAs (N-(5-methyl)hexanoyl tyrosine (14) and N-(7-methyl)octanoyl tyrosine (15) or phenylalanine (16)) from Olivibacter sp. FHG000416, another Bacteroidetes strain initially selected as best in-house producer for isolation of lipid 430. Antimicrobial profiling revealed most isolated LAAs (1–3) and the two LPE ‘core’ metabolites (12, 13) active against the Gram-negative pathogen M. catarrhalis ATCC 25238 and the Gram-positive bacterium M. luteus DSM 20030. For LAA 1, additional growth inhibition activity against B. subtilis DSM 10 was observed.     

Counterion-mediated pattern formation in membranes containing anionic lipids

Most lipid components of cell membranes are either neutral, like cholesterol, or zwitterionic, like phosphatidylcholine and sphingomyelin. Very few lipids, such as sphingosine, are cationic at physiological pH. These generally interact only transiently with the lipid bilayer, and their synthetic analogs are often designed to destabilize the membrane for drug or DNA delivery. However, anionic lipids are common in both eukaryotic and prokaryotic cell membranes. The net charge per anionic phospholipid ranges from − 1 for the most abundant anionic lipids such as phosphatidylserine, to near − 7 for phosphatidylinositol 3,4,5 trisphosphate, although the effective charge depends on many environmental factors. Anionic phospholipids and other negatively charged lipids such as lipopolysaccharides are not randomly distributed in the lipid bilayer, but are highly restricted to specific leaflets of the bilayer and to regions near transmembrane proteins or other organized structures within the plane of the membrane. This review highlights some recent evidence that counterions, in the form of monovalent or divalent metal ions, polyamines, or cationic protein domains, have a large influence on the lateral distribution of anionic lipids within the membrane, and that lateral demixing of anionic lipids has effects on membrane curvature and protein function that are important for biological control.     

Self‐Assembled Aggregates and Molecular Bilayer Films of a Double‐Chain Fullerene Lipid: Structure and Electrochemistry

The self‐aggregation behavior of C₆₀ fullerenes that bear two octadecyl chains (lipid 1 ) as well as the structures and electrochemical properties of cast films of 1 are described. We also examined the self‐aggregation behavior in organic solvents of three previously reported compounds: C₆₀ with three each of hexadecyl (lipid 2 ), tetradecyl (lipid 3 ), or dodecyl (lipid 4 ) chains. The fullerene lipids in alcohols spontaneously formed spherical aggregates, whose diameters are related to the alkyl‐chain lengths, concentrations of the fullerene lipids, and the solvent polarity. The morphologies of the aggregates showed temperature dependence. Cast films of 1 formed multimolecular bilayer structures that undergo a phase transition typical of lipid bilayer membranes. The electrochemistry of cast films of 1 on an electrode in aqueous medium exhibits temperature dependence.     

Characterisation of membrane phospholipids and glycolipids from a halophilic archaebacterium by high-performance liquid chromatography/electrospray mass spectrometry

Combined high-performance liquid chromatography and electrospray mass spectrometry (LC/ES-MS) has been used for direct characterisation of the polar membrane lipids in total lipid extracts from Halobacterium salinarium, a species of halophilic archaebacterium. The principle phospholipids found were the diphytanyl archaeol phosphatidylglycerol and diphytanyl archaeol phosphatidylglycerolphosphate methyl ester. The application of LC/ES-MS revealed the additional presence of diphytanyl archaeol phosphatidylglycerol sulphate The extracts also contained an archaeol glycolipid, initially detected in preliminary offline ES-MS studies, which was further characterised by LC/ES-MS and by product ion tandem mass spectrometry (MS/MS) as a sulphate ester of diglycosyl-2,3-di-O-phytanyl-sn-glycerol. Whilst archaeol phospho- and glycolipids containing a (C(20)-C(20))-isopranyl glycerol ether core predominated, LC/ES-MS of the extracts from Halobacterium salinarium indicated the presence of an analogue containing one double bond in its isoprenyl ether core as a minor component of the phosphatidylglycerolphosphate methyl ester fraction, providing a further example of the previously recognised existence of isoprenologues of diphytanyl archaeols which occur as minor components of archaebacterial membrane lipids. The value of these techniques in compositional analysis of archaebacterial lipid extracts is discussed.     

Dodecaborate cluster lipids with variable headgroups for boron neutron capture therapy: Synthesis, physical-chemical properties and toxicity

We have prepared two new boron-containing lipids with potential use in boron neutron capture therapy of tumors. These lipids consist of a diethanolamine frame with two myristoyl chains bonded as esters, and a butylene or ethyleneoxyethylene unit linking the doubly negatively charged dodecaborate cluster to the amino function of the frame, obtained by nucleophilic attack of the amino on the tetrahydrofurane and dioxane derivatives, respectively, of closo-dodecaborate. The latter cluster lipid can form liposomes at 25 °C whereas the former lipid at this temperature assembles into bilayer disks. Both lipids form stable liposomes when mixed with suitable helper lipids. The thermotropic behavior was found to be different for the two lipids, with the butylene lipid showing sharp melting transitions at surprisingly high temperatures. Toxicity in vitro and in vivo varies greatly, with the butylene derivative being more toxic than the ethyleneoxyethylene derivative.     

Accurate and reliable quantification of total microalgal fuel potential as fatty acid methyl esters by <Emphasis Type="Italic">in situ</Emphasis> transesterification

In the context of algal biofuels, lipids, or better aliphatic chains of the fatty acids, are perhaps the most important constituents of algal biomass. Accurate quantification of lipids and their respective fuel yield is crucial for comparison of algal strains and growth conditions and for process monitoring. As an alternative to traditional solvent-based lipid extraction procedures, we have developed a robust whole-biomass in situ transesterification procedure for quantification of algal lipids (as fatty acid methyl esters, FAMEs) that (a) can be carried out on a small scale (using 4–7 mg of biomass), (b) is applicable to a range of different species, (c) consists of a single-step reaction, (d) is robust over a range of different temperature and time combinations, and (e) tolerant to at least 50% water in the biomass. Unlike gravimetric lipid quantification, which can over- or underestimate the lipid content, whole biomass transesterification reflects the true potential fuel yield of algal biomass. We report here on the comparison of the yield of FAMEs by using different catalysts and catalyst combinations, with the acid catalyst HCl providing a consistently high level of conversion of fatty acids with a precision of 1.9% relative standard deviation. We investigate the influence of reaction time, temperature, and biomass water content on the measured FAME content and profile for 4 different samples of algae (replete and deplete Chlorella vulgaris, replete Phaeodactylum tricornutum, and replete Nannochloropsis sp.). We conclude by demonstrating a full mass balance closure of all fatty acids around a traditional lipid extraction process.     

Modular synthesis of diphospholipid oligosaccharide fragments of the bacterial cell wall and their use to study the mechanism of moenomycin and other antibiotics

We present a flexible, modular route to GlcNAc-MurNAc-oligosaccharides that can be readily converted into peptidoglycan (PG) fragments to serve as reagents for the study of bacterial enzymes that are targets for antibiotics. Demonstrating the utility of these synthetic PG substrates, we show that the tetrasaccharide substrate lipid IV (3), but not the disaccharide substrate lipid II (2), significantly increases the concentration of moenomycin A required to inhibit a prototypical PG-glycosyltransferase (PGT). These results imply that lipid IV and moenomycin A bind to the same site on the enzyme. We also show the moenomycin A inhibits the formation of elongated polysaccharide product but does not affect length distribution. We conclude that moenomycin A blocks PG-strand initiation rather than elongation or chain termination. Synthetic access to diphospholipid oligosaccharides will enable further studies of bacterial cell wall synthesis with the long-term goal of identifying novel antibiotics.     

Efficient Conversion of Fructose-Based Biomass into Lipids with <Emphasis Type="Italic">Trichosporon fermentans</Emphasis> Under Phosphate-Limited Conditions

Limiting nitrogen supply has been routinely used as the master regulator to direct lipid biosynthesis. However, this strategy does not work with nitrogen-rich substrates, such as Jerusalem artichoke (JA), a fructose-based biomass, while it is difficult to obtain a high carbon-to-nitrogen (C/N) molar ratio. In this study, an alternative strategy to promote lipid accumulation by the oleaginous yeast Trichosporon fermentans CICC 1368 was developed by limiting phosphorous supply, and this strategy was implemented with JA hydrolysate as substrate. We showed that lipid accumulation was directly correlated with the C/P ratio of the culture media for T. fermentans. The time course of cell growth and lipid production was analyzed in a media with an initial C/P ratio of 6342, and the cellular lipid content could reach up to 48.5% of dry biomass. Moreover, JA hydrolysates were used as substrate for microbial lipid accumulation, under high C/P molar ratio condition, lipid yield, lipid content, and lipid coefficient increased by 10, 30, and 34%, respectively. It showed that by limiting phosphorus, the conversion of sugar into lipids can be improved effectively. Limiting phosphorus provides a promising solution to the problem of microbial lipid production with nitrogen-rich natural materials.     

Effect of matrices and additives on phosphorylated and ketodeoxyoctonic acid lipids A analysis by matrix‐assisted laser desorption ionization‐mass spectrometry

Lipid A is a major compound of the outer membrane of gram‐negative bacteria and is a key factor of bacterial virulence. As lipid A's structure differs among bacterial species and varies between strains of the same species, knowing its modifications is essential to understand its implications in the infectious process. To analyze these lipids, matrix‐assisted laser desorption ionization‐mass spectrometry (MALDI‐MS) is a well‐suited method that is fast and efficient. However, there are limitations with the matrix and additives used, such as the suppression of signal or prompt fragmentations that could give a false overview of lipid A composition in biological samples. For a comprehensive analysis of the entire lipid A species present in a sample, we tested 16 matrices and 11 additives on two commercial lipids A. The first commercial one contains single phosphorylation group, and the second contains two phosphorylation and two ketodeoxyoctonic acid (KDO) groups. The lipid A containing KDO groups was essentially detected by the 3‐hydroxypicolinic acid (3‐HPA) matrix, whereas the monophosphorylated lipid A could be detected by 13 matrices out of the 16. We also demonstrated that the signal of diphosphorylated lipid A can be enhanced with the use of additives in the matrix. Our study indicated that the best conditions to obtain a clear signal of both lipids A without prompt fragmentation was the use of 3‐HPA with 10mM trifluoroacetic acid (TFA).     

Lipids ofHeracleum lehmannianum seeds

The lipid complex of the seeds ofHeracleum lehmannianum B. has been studied. The qualitative and quantitative compositions of the neutral lipids and the phospho- and glycolipids, and the fatty acid compositions of the acyl-containing classes of lipids have been determined. It has been shown that the neutral and the polar lipids differ considerably from one another with respect to the level of certain fatty acids. The position-species compositions of the TAGS and of the main components of the phospholipids have been calculated from the results of lipolytic hydrolysis.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Republic of Uzbekistan, Tashkent, fax (3712) 89 14 75. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 10–14, January–February, 1996. Original article submitted June 12, 1995.     

CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations

CHARMM‐GUI Membrane Builder, http://www.charmm‐gui.org/input/membrane , is a web‐based user interface designed to interactively build all‐atom protein/membrane or membrane‐only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance‐based algorithm for faster initial ion displacement, (5) CHARMM inputs for P₂₁ image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM‐GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments. © 2014 Wiley Periodicals, Inc.     

Separation and Classification of Lipids Using Differential Ion Mobility Spectrometry

Correlations between the dimensions of a 2-D separation create trend lines that depend on structural or chemical characteristics of the compound class and thus facilitate classification of unknowns. This broadly applies to conventional ion mobility spectrometry (IMS)/mass spectrometry (MS), where the major biomolecular classes (e.g., lipids, peptides, nucleotides) occupy different trend line domains. However, strong correlation between the IMS and MS separations for ions of same charge has impeded finer distinctions. Differential IMS (or FAIMS) is generally less correlated to MS and thus could separate those domains better. We report the first observation of chemical class separation by trend lines using FAIMS, here for lipids. For lipids, FAIMS is indeed more independent of MS than conventional IMS, and subclasses (such as phospho-, glycero-, or sphingolipids) form distinct, often non-overlapping domains. Even finer categories with different functional groups or degrees of unsaturation are often separated. As expected, resolution improves in He-rich gases: at 70% He, glycerolipid isomers with different fatty acid positions can be resolved. These results open the door for application of FAIMS to lipids, particularly in shotgun lipidomics and targeted analyses of bioactive lipids.     

Labeled vs. Label-Free Raman Imaging of Lipids in Endothelial Cells of Various Origins

Endothelial cells (EC) constitute a single layer of the lining of blood vessels and play an important role in maintaining cardiovascular homeostasis. Endothelial dysfunction has been recognized as a primary or secondary cause of many diseases and it manifests itself, among others, by increased lipid content or a change in the lipid composition in the EC. Therefore, the analysis of cellular lipids is crucial to understand the mechanisms of disease development. Tumor necrosis factor alpha (TNF-α)-induced inflammation of EC alters the lipid content of cells, which can be detected by Raman spectroscopy. By default, lipid detection is carried out in a label-free manner, and these compounds are recognized based on their spectral profile characteristics. We consider (3S,3′S)-astaxanthin (AXT), a natural dye with a characteristic resonance spectrum, as a new Raman probe for the detection of lipids in the EC of various vascular beds, i.e., the aorta, brain and heart. AXT colocalizes with lipids in cells, enabling imaging of lipid-rich cellular components in a time-dependent manner using laser power 10 times lower than that commonly used to measure biological samples. The results show that AXT can be used to study lipids distribution in EC at various locations, suggesting its use as a universal probe for studying cellular lipids using Raman spectroscopy. The use of labeled Raman imaging of lipids in the EC of various organs could contribute to their easier identification and to a better understanding of the development and progression of various vascular diseases, and it could also potentially improve their diagnosis and treatment.     

Electroformation of giant liposomes from spin-coated films of lipids

This paper describes spin-coating of solutions of lipids and using the resulting thin films for electroformation of giant liposomes. Spin-coating made it possible to generate uniform films of lipids with controllable thickness over large surfaces (>25 cm(2)) of indium tin oxide. Establishing a range of thicknesses optimal for electroformation (25-50 nm), we demonstrate formation of giant liposomes from lipids (such as asolectin, phosphatidylserine, and phosphatidylglycerol) that do not readily form giant liposomes from traditional, droplet-derived films. We compared liposomes from a spin-coated film of lipids to liposomes formed from traditional droplet-derived films and found that spin-coated films produced larger (by factor of 2-5) and more abundant liposomes than droplet-derived films of lipids. Electroformation from spin-coated, homogenous lipid films of optimal thickness provided a reproducible way to obtain liposomes with diameters that are predominantly larger than 30 microm over the entire surface of formation.