Labeled chemical biology tools for investigating sphingolipid metabolism, trafficking and interaction with lipids and proteins

Chemical Tools for Lipid Cell Biology

Lipids are key components of all organisms. We are well educated in their use as fuel and their essential role to form membranes. We also know much about their biosynthesis and metabolism. We are also aware that most lipids have signaling character meaning that a change in their concentration or location constitutes a signal that helps a living cell to respond to changes in the environment or to fulfill its specific function ranging from secretion to cell division. What is much less understood is how lipids change location in cells over time and what other biomolecules they interact with at each stage of their lifetime. Due to the large number of often quite similar lipid species and the sometimes very short lifetime of signaling lipids, we need highly specific tools to manipulate and visualize lipids and lipid-protein interactions. If successfully applied, these tools provide fabulous opportunities for discovery.In this Account, I summarize the development of synthetic tools from our lab that were designed to address crucial properties that allow them to function as tools in live cell experiments. Techniques to change the concentration of lipids by adding a small molecule or by light are described and complemented by examples of biological findings made when applying the tools. This ranges from chemical dimerizer-based systems to synthetic "caged" lipid derivatives. Furthermore, I discuss the problem of locating a lipid in an intact cell. Synthetic molecular probes are described that help to unravel the lipid location and to determine their binding proteins. These location studies require in-cell lipid tagging by click chemistry, photo-cross-linking to prevent further movement and the "caging" groups to avoid premature metabolism. The combination of these many technical features in a single tool allows for the analysis of not only lipid fluxes through metabolism but also lipid transport from one membrane to another as well as revealing the lipid interactome in a cell-dependent manner. This latter point is crucial because with these multifunctional tools in combination with lipidomics we can now address differences in healthy versus diseased cells and ultimately find the changes that are essential for disease development and new therapeutics that prevent these changes.

Synthetic probes and chemical tools in sphingolipid research

Sphingolipids (SLs) are a unique class of nitrogen-linked lipids that are involved in membrane structure, cell signaling, and other important cellular processes. Abnormal sphingolipid metabolism is observed in several diseases including cancer, diabetes, metabolic disorders, and neurodegenerative diseases, such as Alzheimer's. However, the direct study of SLs has been hampered by their ubiquitous presence in cells and their complex metabolism. In the past few decades, efforts have been focused on creating synthetic probes and chemical tools to study SLs and decipher their roles in cellular biology. In this brief perspective, we seek to provide a concise snapshot of recently developed state-of-the-art chemical tools in SL research and the challenges that can be addressed through further development of SL probes.

A photocaged inhibitor of acid sphingomyelinase

Acid sphingomyelinase (ASM) is a potential drug target and involved in rapid lipid signalling events. However, there are no tools available to adequately study such processes. Based on a non cell-permeable PtdIns(3,5)P2 inhibitor of ASM, we developed a compound with o-nitrobenzyl photocages and butyryl esters to transiently mask hydroxyl groups. This resulted in a potent light-inducible photocaged ASM inhibitor (PCAI). The first example of a time-resolved inhibition of ASM was shown in intact living cells.

Synthesis of Fluorescent Membrane-Spanning Lipids for Studies of Lipid Transfer and Membrane Fusion

For uncompromised in vitro assays for intermembrane lipid transfer and membrane fusion fluorescent membrane-spanning lipids have proved to be invaluable tools. These lipids in contrast to phosphoglycerolipids and sphingolipids are resistant to spontaneous as well as protein-mediated intermembrane transfer. Here I describe the synthesis of some homo-substituted fluorescent bipolar membrane-spanning lipids that bear a fluorescent tag either directly or via a phosphoethanolamine spacer to the lipid core. For the synthesis the lipid core of the bipolar membrane-spanning lipids, i.e., the tetraether lipid caldarchaeol, is prepared from cultures of the archaea Thermoplasma acidophilum.

Click reactions with functional sphingolipids

Sphingolipids and glycosphingolipids can regulate cell recognition and signalling. Ceramide and sphingosine-1-phosphate are major players in the sphingolipid pathways and are involved in the initiation and regulation of signalling, apoptosis, stress responses and infection. Specific chemically synthesised sphingolipid derivatives containing small functionalities like azide or alkyne can mimic the biological properties of natural lipid species, which turns them into useful tools for the investigation of the highly complex sphingolipid metabolism by rapid and selective 'click chemistry' using sensitive tags like fluorophores. Subsequent analysis by various fluorescence microscopy techniques or mass spectrometry allows the identification and quantification of the corresponding sphingolipid metabolites as well as the research of associated enzymes. Here we present an overview of recent advances in the synthesis of ceramide and sphingosine analogues for bioorthogonal click reactions to study biosynthetic pathways and localization of sphingolipids for the development of novel therapeutics against lipid-dependent diseases.

Approaches for probing and evaluating mammalian sphingolipid metabolism

Sphingolipid metabolism plays a critical role in regulating processes that control cellular fate. This dynamic pathway can generate and degrade the central players: ceramide, sphingosine and sphingosine-1-phosphate in almost any membrane in the cell, adding an unexpected level of complexity in deciphering signaling events. While in vitro assays have been developed for most enzymes in SL metabolism, these assays are setup for optimal activity conditions and can fail to take into account regulatory components such as compartmentalization, substrate limitations, and binding partners that can affect cellular enzymatic activity. Therefore, many in-cell assays have been developed to derive results that are authentic to the cellular situation which may give context to alteration in SL mass. This review will discuss approaches for utilizing probes for mammalian in-cell assays to interrogate most enzymatic steps central to SL metabolism. The use of inhibitors in conjunction with these probes can verify the specificity of cellular assays as well as provide valuable insight into flux in the SL network. The use of inhibitors specific to each of the central sphingolipid enzymes are also discussed to assist researchers in further interrogation of these pathways.

Synthesis of dansyl labeled sphingosine kinase 1 inhibitor

PF-543 is a non-sphingosine analogue with inhibitory effect against SK1, based on a Ki of 4.3 nM and 130-fold selectivity for SK1 over SK2. Since the development of PF-543, animal studies demonstrated its valuable role in multiple sclerosis, myocardial infarction, and colorectal cancer. We synthesized labeled PF-543 for biochemical studies involving SK1. Overall, the 8-step synthetic route used 3,5-dimethylphenol as the starting material. A docking study of SK1 and SK1 inhibitory activity confirmed the structural similarity between the synthetic dansyl-PF-543 and PF-543. We also provide fluorescence spectra of dansyl-PF-543.

Synthesis of Fluorescent Gangliosides

Labeled gangliosides are invaluable tools to study their transport and metabolism within cells as well as to determine their distribution in membranes, and their interaction with membrane lipids and proteins. Here I describe established procedures to synthesize ganglioside derivatives with a fluorescent tag either attached to its sialooligosaccharide or ceramide portion. These procedures are chosen as to minimize the integrity of the ganglioside molecule and hence, to leave their native skeleton formally intact. The α-position of the stearic acid residue is favorable for the attachment both of hydrophilic and of lipophilic dyes. In some other cases, and starting from lyso-gangliosides, procedures are described by which a fluorescent tag bound to a short acyl chain replaces the native acyl chain of gangliosides.

Lysosphingolipids and sphingolipidoses: Psychosine in Krabbe's disease

Until recently, lipids were considered inert building blocks of cellular membranes. This changed three decades ago when lipids were found to regulate cell polarity and vesicle transport, and the "lipid raft" concept took shape. The lipid-driven membrane anisotropy in form of "rafts" that associate with proteins led to the view that organized complexes of lipids and proteins regulate various cell functions. Disturbance of this organization can lead to cellular, tissue, and organ malfunction. Sphingolipidoses, lysosomal storage diseases that are caused by enzyme deficiencies in the sphingolipid degradation pathway, were found to be particularly detrimental to the brain. These enzyme deficiencies result in accumulation of sphingolipid metabolites in lysosomes, although it is not yet clear how this accumulation affects the organization of lipids in cellular membranes. Krabbe's disease (KD), or globoid cell leukodystrophy, was one of the first sphingolipidosis for which the raft concept offered a potential mechanism. KD is caused by mutations in the enzyme β-galactocerebrosidase; however, elevation of its substrate, galactosylceramide, is not observed or considered detrimental. Instead, it was found that a byproduct of galactosylceramide metabolism, the lysosphingolipid psychosine, is accumulated. The "psychosine hypothesis" has been refined by showing that psychosine disrupts lipid rafts and vesicular transport critical for the function of glia and neurons. The role of psychosine in KD is an example of how the disruption of sphingolipid metabolism can lead to elevation of a toxic lysosphingolipid, resulting in disruption of cellular membrane organization and neurotoxicity. © 2016 Wiley Periodicals, Inc.

Tandem Mass Spectrometry of Sphingolipids: Applications for Diagnosis of Sphingolipidoses

In recent years, mass spectrometry (MS) has become the dominant technology in lipidomic analysis. It is widely used in diagnosis and research of lipid metabolism disorders including those characterized by impairment of lysosomal functions and storage of nondegraded-degraded substrates. These rare diseases, which include sphingolipidoses, have severe and often fatal clinical consequences. Modern MS methods have contributed significantly to achieve a definitive diagnosis, which is essential in clinical practice to begin properly targeted patient care. Here we summarize MS and tandem MS methods used for qualitative and quantitative analysis of sphingolipids (SL) relative to the diagnostic process for sphingolipidoses and studies focusing on alterations in cell functions due to these disorders. This review covers the following topics: Tandem MS is sensitive and robust in determining the composition of sphingolipid classes in various biological materials. Its ability to establish SL metabolomic profiles using MS bench-top analyzers, significantly benefits the first stages of a diagnosis as well as metabolic studies of these disorders. It can thus contribute to a better understanding of the biological significance of SL.

Computer Modeling of Spin Labels: NASNOX, PRONOX, and ALLNOX

Measurement of distances between spin labels using electron paramagnetic resonance with the double electron-electron resonance (DEER) technique is an important method for evaluation of biomolecular structures. Computation of interlabel distances is of value for experimental planning, validation of known structures using DEER-measured distances, and determination of theoretical data for comparison with experiment. This requires steps of building labels at two defined sites on proteins, DNA or RNA; calculation of allowable label conformers based on rotation around torsional angles; computation of pairwise interlabel distances on a per conformer basis; and calculation of an average distance between the two label ensembles. We have described and validated two programs for this purpose: NASNOX, which permits computation of distances between R5 labels on DNA or RNA; and PRONOX, which similarly computes distances between R1 labels on proteins. However, these programs are limited to a specific single label and single target types. Therefore, we have developed a program, which we refer to as ALLNOX (Addition of Labels and Linkers), which permits addition of any label to any site on any target. The main principle in the program is to break the molecular system into a "label," a "linker," and a "target." The user can upload a "label" with any chemistry, define a "linker" based on a SMILES-like string, and then define the "target" site. The flexibility of ALLNOX facilitates theoretical evaluation of labels prior to synthesis and accommodates evaluation of experimental data in biochemical complexes containing multiple molecular types.

Membrane-spanning lipids for an uncompromised monitoring of membrane fusion and intermembrane lipid transfer

A Förster resonance energy transfer-based fusion and transfer assay was developed to study, in model membranes, protein-mediated membrane fusion and intermembrane lipid transfer of fluorescent sphingolipid analogs. For this assay, it became necessary to apply labeled reporter molecules that are resistant to spontaneous as well as protein-mediated intermembrane transfer. The novelty of this assay is the use of nonextractable fluorescent membrane-spanning bipolar lipids. Starting from the tetraether lipid caldarchaeol, we synthesized fluorescent analogs with fluorophores at both polar ends. In addition, we synthesized radioactive glycosylated caldarchaeols. These labeled lipids were shown to stretch through bilayer membranes rather than to loop within a single lipid layer of liposomes. More important, the membrane-spanning lipids (MSLs) in contrast to phosphoglycerides proved to be nonextractable by proteins. We could show that the GM2 activator protein (GM2AP) is promiscuous with respect to glycero- and sphingolipid transfer. Saposin (Sap) B also transferred sphingolipids albeit with kinetics different from GM2AP. In addition, we could unambiguously show that the recombinant activator protein Sap C x His6 induced membrane fusion rather than intermembrane lipid transfer. These findings showed that these novel MSLs, in contrast with fluorescent phosphoglycerolipids, are well suited for an uncompromised monitoring of membrane fusion and intermembrane lipid transfer.

Chemical genetics and its application to moonlighting in glycolytic enzymes

Glycolysis is an ancient biochemical pathway that breaks down glucose into pyruvate to produce ATP. The structural and catalytic properties of glycolytic enzymes are well-characterized. However, there is growing appreciation that these enzymes participate in numerous moonlighting functions that are unrelated to glycolysis. Recently, chemical genetics has been used to discover novel moonlighting functions in glycolytic enzymes. In the present mini-review, we introduce chemical genetics and discuss how it can be applied to the discovery of protein moonlighting. Specifically, we describe the application of chemical genetics to uncover moonlighting in two glycolytic enzymes, enolase and glyceraldehyde dehydrogenase. This led to the discovery of moonlighting roles in glucose homoeostasis, cancer progression and diabetes-related complications. Finally, we also provide a brief overview of the latest progress in unravelling the myriad moonlighting roles for these enzymes.