Exploiting bioorthogonal chemistry to elucidate protein-lipid binding interactions and other biological roles of phospholipids

Facile preparation of polycyclic halogen-substituted 1,2,3-triazoles by using intramolecular Huisgen cycloaddition

When 1-(ω-azidoalkyl)-2-(2,2-dihalovinyl)arenes were heated in DMF, the intramolecular Huisgen cycloaddition of an azido group with a 1,1-dihalovinyl group afforded 5-halo-1,2,3-triazole-fused tricyclic benzo compounds. Based on the remaining bromo groups, carbon elongation by the Mizoroki-Heck or Suzuki-Miyaura coupling reactions, followed by an intramolecular Friedel-Crafts reaction, afforded polycyclic compounds with fused triazole rings. Thereafter, the bromo groups were converted into 2-nitrophenyl groups via the Suzuki-Miyaura coupling reaction, which was followed by the Cadogan reaction; a fluorescent pentacyclic compound was obtained.

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.

Bifunctional Lipid-Derived Affinity-Based Probes (AfBPs) for Analysis of Lipid-Protein Interactome

Although lipids are not genetically encoded, they are fundamental building blocks of cell membranes and essential components of cell metabolites. Lipids regulate various biological processes, including energy storage, membrane trafficking, signal transduction, and protein secretion; therefore, their metabolic imbalances cause many diseases. Approximately 47 000 lipid species with diverse structures have been identified, but little is known about their crucial roles in cellular systems. Particularly the structural, metabolic, and signaling functions of lipids often arise from interactions with proteins. Lipids attach to proteins not only by covalent bonds but also through noncovalent interactions, which also influence protein functions and localization. Therefore, it is important to explore this lipid-protein "interactome" to understand its roles in health and disease, which may further provide insight for medicinal development. However, lipid structures are generally quite complicated, rendering the systematic characterization of lipid-protein interactions much more challenging.Chemoproteomics is a well-known chemical biology platform in which small-molecule chemical probes are utilized in combination with high-resolution, quantitative mass spectrometry to study protein-ligand interactions in living cells or organisms, and it has recently been applied to the study of protein-lipid interactions as well. The study of these complicated interactions has been advanced by the development of bifunctional lipid probes, which not only enable probes to form covalent cross-links with lipid-interacting proteins under UV irradiation, but are also capable of enriching these proteins through bioorthogonal reactions.In this Account, we will discuss recent developments in bifunctional lipid-derived, affinity-based probes (AfBP)s that have been developed to investigate lipid-protein interactions in live cell systems. First, we will give a brief introduction of fundamental techniques based on AfBPs which are related to lipid research. Then, we will focus on three aspects, including probes developed on the basis of lipidation, lipid-derived probes with different modification positions (e.g., hydrophobic or hydrophilic parts of a lipid), and, finally, in situ biosynthesis of probes through intrinsic metabolic pathways by using chemically modified building blocks. We will present some case studies to describe these probes' design principles and cellular applications. At the end, we will also highlight key limitations of current approaches so as to provide inspirations for future improvement. The lipid probes that have been constructed are only the tip of the iceberg, and there are still plenty of lipid species that have yet to be explored. We anticipate that AfBP-based chemoproteomics and its further advancement will pave the way for a deep understanding of lipid-protein interactions in the future.

Metabolite-Responsive Liposomes Employing Synthetic Lipid Switches Driven by Molecular Recognition Principles

The ability to exert control over lipid properties, including structure, charge, function, and self-assembly characteristics is a powerful tool that can be implemented to achieve a wide range of biomedical applications. Examples in this arena include the development of caged lipids for controlled activation of signaling properties, metabolic labeling strategies for tracking lipid biosynthesis, lipid activity probes for identifying cognate binding partners, approaches for in situ membrane assembly, and liposome triggered release strategies. In this Account, we describe recent advancements in the latter area entailing the development of stimuli-responsive liposomes through programmable changes to lipid self-assembly properties, which can be harnessed to drive the release of encapsulated contents toward applications including drug delivery. We will focus on an emerging paradigm involving liposomal platforms that are sensitized toward chemical agents ranging from metal cations to small organic molecules that exhibit dysregulation in disease states. This has been achieved by developing synthetic lipid switches that are designed to undergo programmed conformational changes upon the recognition of specific target analytes. These structural alterations are leveraged to perturb the packing of lipids within the membrane and thereby drive the release of encapsulated contents.We provide an overview of the inspiration, design, and characterization of liposomes that selectively respond to wide-ranging target analytes. This series of studies began with the development of calcium-responsive liposomes utilizing a lipid switch inspired by sensors including indo-1. Following this successful demonstration, we next showed that the selectivity of the lipid switch could be altered among different metal cations by producing a liposomal platform for which release is induced through zinc binding. Our next goal was to develop metabolite-responsive liposomes in which switching is driven by molecular recognition events involving phosphorylated small molecules. In this work, screening of lipid switches designed to interact with phosphorylated metabolites led to the identification of liposomal formulations that selectivity release contents in the presence of adenosine triphosphate (ATP). Finally, we were able to modulate the metabolite selectivity by rationally designing a modified lipid switch structure that is activated through complexation of inositol-(1,4,5)-trisphosphate (IP₃). These projects show the progression of our approaches for liposome release triggered by molecular recognition principles, building from ion-responsive lipid switches to structures that are activated by small molecules. These "smart" liposomal platforms provide an important addition to the toolbox for controlled cargo release since they respond to ions or small molecules that are commonly overproduced by diseased cells.

Manipulating complex chromatin folding via CRISPR-guided bioorthogonal chemistry

Precise manipulation of chromatin folding is important for understanding the relationship between the three-dimensional genome and nuclear function. Existing tools can reversibly establish individual chromatin loops but fail to manipulate two or more chromatin loops. Here, we engineer a powerful CRISPR system which can manipulate multiple chromatin contacts using bioorthogonal reactions, termed the bioorthogonal reaction-mediated programmable chromatin loop (BPCL) system. The multiinput BPCL system employs engineered single-guide RNAs recognized by discrete bioorthogonal adaptors to independently and dynamically control different chromatin loops formation without cross-talk in the same cell or to establish hubs of multiway chromatin contacts. We use the BPCL system to successfully juxtapose the pluripotency gene promoters to enhancers and activate their endogenous expression. BPCL enables us to independently engineer multiway chromatin contacts without cross-talk, which provides a way to precisely dissect the high complexity and dynamic nature of chromatin folding.

"Flash & Click": Multifunctionalized Lipid Derivatives as Tools To Study Viral Infections

In this perspective article, we describe the current status of lipid tools for studying host lipid-virus interactions at the cellular level. We discuss the potential lipidomic changes that viral infections impose on host cells and then outline the tools available and the resulting options to investigate the host cell lipid interactome. The future outcome will reveal new targets for treating virus infections.

Bioorthogonally activatable cyanine dye with torsion-induced disaggregation for in vivo tumor imaging

Advancement of bioorthogonal chemistry in molecular optical imaging lies in expanding the repertoire of fluorophores that can undergo fluorescence signal changes upon bioorthogonal ligation. However, most available bioorthogonally activatable fluorophores only emit shallow tissue-penetrating visible light via an intramolecular charge transfer mechanism. Herein, we report a serendipitous “torsion-induced disaggregation (TIDA)” phenomenon in the design of near-infrared (NIR) tetrazine (Tz)-based cyanine probe. The TIDA of the cyanine is triggered upon Tz-transcyclooctene ligation, converting its heptamethine chain from S-trans to S-cis conformation. Thus, after bioorthogonal reaction, the tendency of the resulting cyanine towards aggregation is reduced, leading to TIDA-induced fluorescence enhancement response. This Tz-cyanine probe sensitively delineates the tumor in living mice as early as 5 min post intravenous injection. As such, this work discovers a design mechanism for the construction of bioorthogonally activatable NIR fluorophores and opens up opportunities to further exploit bioorthogonal chemistry in in vivo imaging.

Expanding the responsive dyes repertoire is currently a developing field in biorthogonal chemistry. In this article, the authors develop fluorophores that turn on their near-infrared fluorescence upon biorthogonal reaction based on a “torsion-induced disaggregation” approach, allowing for sensitive in vivo imaging of tumors.

1,6-Addition of 1,2,3-NH triazoles to para-quinone methides: Facile access to highly selective N1 and N2 substituted triazoles

The regioselective syntheses of N¹ and N² substituted triazoles through a 1,6-addition reaction of 1,2,3-NH triazoles to p-quinone methide were achieved under mild reaction conditions. The present reactions showed superior results in terms of selectivity, mild reaction conditions, short reaction time and broad substrate scope with good functional-group compatibility. Considering the high synthetic value of N¹- and N²-substituted compounds and p-QM related research, the present strategy will greatly benefit researchers in various fields.

Triazines: Syntheses and Inverse Electron-demand Diels-Alder Reactions

Triazines are an important class of six-membered aromatic heterocycles possessing three nitrogen atoms, resulting in three types of regio-isomers: 1,2,4-triazines (a-triazines), 1,2,3-triazines (v-triazines), and 1,3,5-triazines (s-triazines). Notably, the application of triazines as cyclic aza-dienes in inverse electron-demand Diels-Alder (IEDDA) cycloaddition reactions has been established as a unique and powerful method in N-heterocycle synthesis, natural product preparation, and bioorthogonal chemistry. In this review, we comprehensively summarize the advances in the construction of these triazines via annulation and ring-expansion reactions, especially emphasizing recent developments and challenges. The synthetic transformations of triazines are focused on IEDDA cycloaddition reactions, which have allowed access to a wide scope of heterocycles, including pyridines, carbolines, azepines, pyridazines, pyrazines, and pyrimidines. The utilization of triazine IEDDA reactions as key steps in natural product synthesis is also discussed. More importantly, a particular attention is paid on the bioorthogonal application of triazines in fast click ligation with various strained alkenes and alkynes, which opens a new opportunity for studying biomolecules in chemical biology.

Cellular cholesterol and how to find it

Cholesterol is an essential component of eukaryotic cellular membranes. Information about its subcellular localization and transport pathways inside cells are key for the understanding and treatment of cholesterol-related diseases. In this review we give an overview over the most commonly used methods that contributed to our current understanding of subcellular cholesterol localization and transport routes. First, we discuss methods that provide insights into cholesterol metabolism based on readouts of downstream effects such as esterification. Subsequently, we focus on the use of cholesterol-binding molecules as probes that facilitate visualization and quantification of sterols inside of cells. Finally, we explore different analogues of cholesterol which, when taken up by living cells, are integrated and transported in a similar fashion as endogenous sterols. Taken together, we highlight the challenges and advantages of each method such that researchers studying aspects of cholesterol transport may choose the most pertinent approach for their problem.

Cu(I)-Catalyzed Click Chemistry in Glycoscience and Their Diverse Applications

Copper(I)-catalyzed 1,3-dipolar cycloaddition between organic azides and terminal alkynes, commonly known as CuAAC or click chemistry, has been identified as one of the most successful, versatile, reliable, and modular strategies for the rapid and regioselective construction of 1,4-disubstituted 1,2,3-triazoles as diversely functionalized molecules. Carbohydrates, an integral part of living cells, have several fascinating features, including their structural diversity, biocompatibility, bioavailability, hydrophilicity, and superior ADME properties with minimal toxicity, which support increased demand to explore them as versatile scaffolds for easy access to diverse glycohybrids and well-defined glycoconjugates for complete chemical, biochemical, and pharmacological investigations. This review highlights the successful development of CuAAC or click chemistry in emerging areas of glycoscience, including the synthesis of triazole appended carbohydrate-containing molecular architectures (mainly glycohybrids, glycoconjugates, glycopolymers, glycopeptides, glycoproteins, glycolipids, glycoclusters, and glycodendrimers through regioselective triazole forming modular and bio-orthogonal coupling protocols). It discusses the widespread applications of these glycoproducts as enzyme inhibitors in drug discovery and development, sensing, gelation, chelation, glycosylation, and catalysis. This review also covers the impact of click chemistry and provides future perspectives on its role in various emerging disciplines of science and technology.

Triple, Mutually Orthogonal Bioorthogonal Pairs through the Design of Electronically Activated Sulfamate-Containing Cycloalkynes

Interest in mutually exclusive pairs of bioorthogonal labeling reagents continues to drive the design of new compounds that are capable of fast and predictable reactions. The ability to easily modify S-, N-, and O-containing cyclooctynes (SNO-OCTs) enables electronic tuning of various SNO-OCTs to influence their cycloaddition rates with Type I-III dipoles. As opposed to optimizations based on just one specific dipole class, the electrophilicity of the alkynes in SNO-OCTs can be manipulated to achieve divergent reactivities and furnish mutually orthogonal dual ligation systems. Significant reaction rate enhancements of a difluorinated SNO-OCT derivative, as compared to the parent scaffold, were noted, with the second-order rate constant in cycloadditions with diazoacetamides exceeding 5.13 M-1 s-1. Computational and experimental studies were employed to inform the design of triple ligation systems that encompass three orthogonal reactivities. Finally, polar SNO-OCTs are rapidly internalized by mammalian cells and remain functional in the cytosol for live-cell labeling, highlighting their potential for diverse in vitro and in vivo applications.

Metabolic labeling of glycerophospholipids via clickable analogs derivatized at the lipid headgroup

Metabolic labeling, in which substrate analogs containing diminutive tags can infiltrate biosynthetic pathways and generate labeled products in cells, has led to dramatic advancements in the means by which complex biomolecules can be detected and biological processes can be elucidated. Within this realm, metabolic labeling of lipid products, particularly in a manner that is headgroup-specific, brings about a number of technical challenges including the complexity of lipid metabolic pathways as well as the simplicity of biosynthetic precursors to headgroup functionality. As such, only a handful of strategies for metabolic labeling of lipids have thus far been reported. However, these approaches provide enticing examples of how strategic modifications to substrate structures, particularly by introducing clickable moieties, can enable the hijacking of lipid biosynthesis. Furthermore, early work in this field has led to an explosion in diverse applications by which these techniques have been exploited to answer key biological questions or detect and track various lipid-containing biological entities. In this article, we review these efforts and emphasize recent advancements in the development and application of lipid metabolic labeling strategies.

Engineering of a Red Fluorogenic Protein/Merocyanine Complex for Live-Cell Imaging

A reengineered human cellular retinol binding protein II (hCRBPII), a 15-kDa protein belonging to the intracellular lipid binding protein (iLBP) family, generates a highly fluorescent red pigment through the covalent linkage of a merocyanine aldehyde to an active site lysine residue. The complex exhibits "turn-on" fluorescence, due to a weakly fluorescent aldehyde that "lights up" with subsequent formation of a strongly fluorescent merocyanine dye within the binding pocket of the protein. Cellular penetration of merocyanine is rapid, and fluorophore maturation is nearly instantaneous. The hCRBPII/merocyanine complex displays high quantum yield, low cytotoxicity, specificity in labeling organelles, and compatibility in both cancer cell lines and yeast cells. The hCRBPII/merocyanine tag is brighter than most common red fluorescent proteins.

Cell-Membrane-Based Biomimetic Systems with Bioorthogonal Functionalities

During the past decade, there was a fast development of cell-based biomimetic systems, which are commonly derived from cell membranes, cell vesicles, or living cells. Such systems have unique and inherent bioinspired features originating from their parent biological systems. In particular, they are capable of (i) prolonging blood circulation time, (ii) avoiding immune response, (iii) targeting desired sites, (iv) providing antigens in cancer immunotherapy, and (v) loading and delivering therapeutic or imaging agents. Thus, these biomimetic systems are promising as prevention, detection, diagnosis, and therapeutic modalities. Though promising, these cell-based biomimetic systems are still far from wide application. One of the important reasons is the inevitable difficulty in their further efficient and precise functionalization. Bioorthogonal chemistry results in fast, specific, and high-yielding ligation under mild biological conditions without interactions with surrounding biomolecules or disturbance of the whole biosystem. Moreover, bioorthogonal chemical groups can be introduced into cells, especially into cell membranes, through cellular biosynthesis and metabolic incorporation. Hence, a specific and reliable approach for cell membrane functionalization based on bioorthogonal chemistry has been opportunely put forward and rapidly developed. In this Account, we summarize our recent research on the development of biomimetic systems by integrating bioorthogonal chemistry with biomimetic approaches. First, an exogenously supplied unnatural biosynthetic precursor (e.g., an amino acid or lipid) bearing a bioorthogonal group (e.g., azide or tetrazine) is fed to living cells and metabolically incorporated into targeted biomolecules via cellular biosynthesis regardless of the cell phenotype. After that, different functional molecules can be anchored to the cell membranes through bioorthogonal chemical reactions by using previously inserted "artificial chemical groups". Therefore, this safe, direct, and long-term engineering strategy endows the natural cell-based biomimetic systems with additional chemical or biological performances such as labeling, targeting, imaging, and therapeutic capabilities, providing a powerful tool for the construction of biomimetic systems. Interestingly, we have successfully fabricated various biomimetic systems and applied them in (1) living virus labeling, (2) targeting delivery and enrichment of drugs/imaging agents, and (3) disease theranostics. This Account may contribute to the further development of biomimetic systems and facilitate their biological and biomedical applications in the future. With this Account we also hope to attract more cooperative interests from different fields such as chemistry, materials science, biology, pharmacy, and medicine in promoting lab-to-clinic translation of cell-based biomimetic systems combined with these two cutting-edge techniques.

Design and Synthesis of a BODIPY-Tetrazole Based "Off-On" in-Cell Fluorescence Reporter of Hydrogen Peroxide

BODIPY-linked bithiophene-tetrazoles were designed and synthesized for bioorthogonal photoclick reactions in vitro and in vivo. The reactivity of these tetrazoles toward dimethyl fumarate was found to depend on the BODIPY attachment site, with the meta-linked BODIPY-tetrazole being the most reactive. The resulting pyrazoline cycloadduct showed drastically reduced BODIPY fluorescence. However, BODIPY fluorescence recovered after treatment with hydrogen peroxide. This turn-on effect was attributed to conversion from the pyrazoline to a pyrazole. Finally, we showed that this unique BODIPY-tetrazole off-on fluorescence probe can be used to detect hydrogen peroxide inside HeLa cells.

Click and Fluoresce: A Bioorthogonally Activated Smart Probe for Wash-Free Fluorescent Labeling of Biomolecules

Bioorthogonally activated smart probes greatly facilitate the selective labeling of biomolecules in living system. Herein, we described a novel type of smart probes with tunable reaction rates, high fluorescence turn-on ratio, and easy access. The practicality of such probes was demonstrated by selective labeling of lipid and hCAII in Hela cells.

Cyclopropenes: a new tool for the study of biological systems

Cyclopropenes have become an important mini-tag tool in chemical biology, participating in fast inverse electron demand Diels–Alder and photoclick reactions in biological settings.

The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore

The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.

Synthetic Glycosphingolipids for Live-Cell Labeling

Glycosphingolipids are an important component of cell membranes that are involved in many biological processes. Fluorescently labeled glycosphingolipids are frequently used to gain insight into their localization. However, the attachment of a fluorophore to the glycan part or-more commonly-to the lipid part of glycosphingolipids is known to alter the biophysical properties and can perturb the biological function of the probe. Presented here is the synthesis of novel glycosphingolipid probes with mono- and disaccharide head groups and ceramide moieties containing fatty acids of varying chain length (C4 to C20). These glycosphingolipids bear an azide or an alkyne group as chemical reporter to which a fluorophore can be attached through a bioorthogonal ligation reaction. The fluorescent tag and any linker connected to it can be chosen in a flexible manner. We demonstrate the suitability of the probes by selective visualization of the plasma membrane of living cells by confocal microscopy techniques. Whereas the derivatives with the shorter fatty acids can be directly applied to HEK 293T cells, the hydrophobic glycosphingolipids with longer fatty acids can be delivered to cells using fusogenic liposomes.

Cu-Catalyzed Click Reaction in Carbohydrate Chemistry

Cu(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition (CuAAC), popularly known as the "click reaction", serves as the most potent and highly dependable tool for facile construction of simple to complex architectures at the molecular level. Click-knitted threads of two exclusively different molecular entities have created some really interesting structures for more than 15 years with a broad spectrum of applicability, including in the fascinating fields of synthetic chemistry, medicinal science, biochemistry, pharmacology, material science, and catalysis. The unique properties of the carbohydrate moiety and the advantages of highly chemo- and regioselective click chemistry, such as mild reaction conditions, efficient performance with a wide range of solvents, and compatibility with different functionalities, together produce miraculous neoglycoconjugates and neoglycopolymers with various synthetic, biological, and pharmaceutical applications. In this review we highlight the successful advancement of Cu(I)-catalyzed click chemistry in glycoscience and its applications as well as future scope in different streams of applied sciences.

Using modified aptamers for site specific protein-aptamer conjugations

We have developed a new method for the selective conjugation of target proteins at lysine residues through a protein–aptamer template-directed reaction.

Conjugation of DNA to defined locations on a protein surface will be a powerful tool for positioning functional groups and molecules in biological and biomedical studies. However, tagging protein with DNA is challenging in physiological environments, and requires a bioorthogonal approach. Here, we report a chemical solution to selectively conjugate DNA aptamers with a protein by protein–aptamer template (PAT)-directed reactions. Since protein–aptamer interactions are bioorthogonal, we exploit the PAT as a unique platform for specific DNA–protein cross-linking. We develop a series of modified oligonucleotides for PAT-directed reactions and find an F-carboxyl group as a suitable functionality for selective and site-specific conjugation. The functionality is incorporated into aptamers in our F-carboxyl phosphoramidite with an easy synthesis. We also demonstrate the necessity of a linker between the reactive functionality and the aptamer sequences.

Identification of Critical Paraoxonase 1 Residues Involved in High Density Lipoprotein Interaction

Paraoxonase 1 (PON1) is a high density lipoprotein (HDL)-associated protein with atherosclerosis-protective and systemic anti-oxidant functions. We recently showed that PON1, myeloperoxidase, and HDL bind to one another in vivo forming a functional ternary complex (Huang, Y., Wu, Z., Riwanto, M., Gao, S., Levison, B. S., Gu, X., Fu, X., Wagner, M. A., Besler, C., Gerstenecker, G., Zhang, R., Li, X. M., Didonato, A. J., Gogonea, V., Tang, W. H., et al. (2013) J. Clin. Invest. 123, 3815-3828). However, specific residues on PON1 involved in the HDL-PON1 interaction remain unclear. Unambiguous identification of protein residues involved in docking interactions to lipid surfaces poses considerable methodological challenges. Here we describe a new strategy that uses a novel synthetic photoactivatable and click chemistry-taggable phospholipid probe, which, when incorporated into HDL, was used to identify amino acid residues on PON1 that directly interact with the lipoprotein phospholipid surface. Several specific PON1 residues (Leu-9, Tyr-185, and Tyr-293) were identified through covalent cross-links with the lipid probes using affinity isolation coupled to liquid chromatography with on-line tandem mass spectrometry. Based upon the crystal structure for PON1, the identified residues are all localized in relatively close proximity on the surface of PON1, defining a domain that binds to the HDL lipid surface. Site-specific mutagenesis of the identified PON1 residues (Leu-9, Tyr-185, and Tyr-293), coupled with functional studies, reveals their importance in PON1 binding to HDL and both PON1 catalytic activity and stability. Specifically, the residues identified on PON1 provide important structural insights into the PON1-HDL interaction. More generally, the new photoactivatable and affinity-tagged lipid probe developed herein should prove to be a valuable tool for identifying contact sites supporting protein interactions with lipid interfaces such as found on cell membranes or lipoproteins.

A clickable and photocleavable lipid analogue for cell membrane delivery and release

For drug delivery purposes, the ability to conveniently attach a targeting moiety that will deliver drugs to cells and then enable controlled release of the active molecule after localization is desirable. Toward this end, we designed and synthesized clickable and photocleavable lipid analogue 1 to maximize the efficiency of bioconjugation and triggered release. This compound contains a dibenzocyclooctyne group for bioorthogonal derivatization linked via a photocleavable 2-nitrobenzyl moiety at the headgroup of a synthetic lipid backbone for targeting to cell membranes. To assess delivery and release using this system, we report fluorescence-based assays for liposomal modification and photocleavage in solution as well as through surface immobilization to demonstrate successful liposome functionalization and photoinduced release. In addition, fluorophore delivery to and release from live cells was confirmed and characterized using fluorescence microscopy and flow cytometry analysis in which 1 was delivered to cells, derivatized, and photocleaved. Finally, drug delivery studies were performed using an azide-tagged analogue of camptothecin, a potent anticancer drug that is challenging to deliver due to poor solubility. In this case, the ester attachment of the azide tag acted as a caging group for release by intracellular esterases rather than through photocleavage. This resulted in a dose-dependent response in the presence of liposomes containing delivery agent 1, confirming the ability of this compound to stimulate delivery to the cytoplasm of cells.

Targeting bacteria via iminoboronate chemistry of amine-presenting lipids

Synthetic molecules that target specific lipids serve as powerful tools for understanding membrane biology and may also enable new applications in biotechnology and medicine. For example, selective recognition of bacterial lipids may give rise to novel antibiotics, as well as diagnostic methods for bacterial infection. Currently known lipid-binding molecules primarily rely on noncovalent interactions to achieve lipid selectivity. Here we show that targeted recognition of lipids can be realized by selectively modifying the lipid of interest via covalent bond formation. Specifically, we report an unnatural amino acid that preferentially labels amine-presenting lipids via iminoboronate formation under physiological conditions. By targeting phosphatidylethanolamine and lysylphosphatidylglycerol, the two lipids enriched on bacterial cell surfaces, the iminoboronate chemistry allows potent labelling of Gram-positive bacteria even in the presence of 10% serum, while bypassing mammalian cells and Gram-negative bacteria. The covalent strategy for lipid recognition should be extendable to other important membrane lipids.

Mechanism of samarium-catalyzed 1,5-regioselective azide-alkyne [3 + 2]-cycloaddition: a quantum mechanical investigation

The mechanism of the samarium-catalyzed 1,5-regioselective azide-alkyne [3 + 2]-cycloaddition (SmAAC) reaction has been examined with quantum mechanical calculations at the B3LYP/6-31+G(d,p) level of theory with ECP51MWB on Sm. Four stepwise pathways were located, with two leading to the 5-endocyclic 1,5-disubstituted 1,2,3-triazole product PSmL2 (paths 1 and 2) and the other two to the exocyclic product ExoPSmCl2 (path 3) as well as 1,4-disubstituted 1,2,3-triazole RegPSmL2 (path 4), respectively. Among them, path 2 (R-COM1-TS12-COM2-TS23-COM3-TS3P-PSmL2) is the most favored one both in the gas phase and in toluene solution, which is in good agreement with the experimental data. Moreover, 1,1-insertion forming COM2 in path 2 is the rate-determining step. The computational results also infer that the participation of samarium catalyst changes the distribution of the electrostatic potential on the reactants' surface, which determines the polarization direction of the reactants and formation of different intermediates (COM1 and RegCOM1), and finally affects the regioselectivity. When solvent corrections for toluene are considered, the 1,1-insertion process is discouraged, while the intramolecular [1,3]-shift reaction is facilitated.

Bifunctional fatty acid chemical reporter for analyzing S-palmitoylated membrane protein-protein interactions in mammalian cells

Studying the functions of S-palmitoylated proteins in cells can be challenging due to the membrane targeting property and dynamic nature of protein S-palmitoylation. New strategies are therefore needed to specifically capture S-palmitoylated protein complexes in cellular membranes for dissecting their functions in vivo. Here we present a bifunctional fatty acid chemical reporter, x-alk-16, which contains an alkyne and a diazirine, for metabolic labeling of S-palmitoylated proteins and photo-cross-linking of their involved protein complexes in mammalian cells. We demonstrate that x-alk-16 can be metabolically incorporated into known S-palmitoylated proteins such as H-Ras and IFITM3, a potent antiviral protein, and induce covalent cross-linking of IFITM3 oligomerization as well as its specific interactions with other membrane proteins upon in-cell photoactivation. Moreover, integration of x-alk-16-induced photo-cross-linking with label-free quantitative proteomics allows identification of new IFITM3 interacting proteins.

Retracted Article: Synthesis of diacylglycerol analogs bearing photoaffinity tags for labelling mammalian diacylglycerol kinase

This communication reports the synthesis of diacylglycerol (DAG) probes with different photoaffinity tags for cross-linking and reducing the activity diacylglycerol kinase (DGK).

Anionic deep cavitands enable the adhesion of unmodified proteins at a membrane bilayer

An anionic self-folding deep cavitand is capable of immobilizing unmodified proteins and enzymes at a supported lipid bilayer interface, providing a simple, soft bioreactive surface that allows enzymatic function under mild conditions. The adhesion is based on complementary charge interactions, and the hosts are capable of binding enzymes such as trypsin at the bilayer interface: the catalytic activity is retained upon adhesion, allowing selective reactions to be performed at the membrane surface.

Turning the spotlight on protein-lipid interactions in cells

Protein function is largely dependent on coordinated and dynamic interactions of the protein with biomolecules including other proteins, nucleic acids and lipids. Although powerful methods for global profiling of protein-protein and protein-nucleic acid interactions are available, proteome-wide mapping of protein-lipid interactions is still challenging and rarely performed. The emergence of bifunctional lipid probes with photoactivatable and clickable groups offers new chemical tools for globally profiling protein-lipid interactions under cellular contexts. In this review, we summarize recent advances in the development of bifunctional lipid probes for studying protein-lipid interactions. We also highlight how in vivo photocrosslinking reactions contribute to the characterization of lipid-binding proteins and lipidation-mediated protein-protein interactions.

Ligation strategies for targeting liposomal nanocarriers

Liposomes have been exploited for pharmaceutical purposes, including diagnostic imaging and drug and gene delivery. The versatility of liposomes as drug carriers has been demonstrated by a variety of clinically approved formulations. Since liposomes were first reported, research of liposomal formulations has progressed to produce improved delivery systems. One example of this progress is stealth liposomes, so called because they are equipped with a PEGylated coating of the liposome bilayer, leading to prolonged blood circulation and improved biodistribution of the liposomal carrier. A growing research area focuses on the preparation of liposomes with the ability of targeting specific tissues. Several strategies to prepare liposomes with active targeting ligands have been developed over the last decades. Herein, several strategies for the functionalization of liposomes are concisely summarized, with emphasis on recently developed technologies for the covalent conjugation of targeting ligands to liposomes.

Multiple bonds for the lipid interest

Polyene lipids and alkyne lipids allow study of lipid organization, dynamics and metabolism. Both types of lipids contain multiple bonds as the essential functional group, leading to minimal disturbance of the hydrophobic properties on which the characteristic behavior of lipids is based. Polyene lipids can directly be traced due to their intrinsic fluorescence, while alkyne lipids need the copper-catalyzed click reaction to an azido-reporter for detection. This review describes recent developments in synthesis and application of both types of lipid analogs with emphasis on metabolic tracing and microscopy imaging. This article is part of a Special Issue entitled Tools to study lipid functions.

Raney Ni catalyzed azide-alkyne cycloaddition reaction

Raney Ni efficiently catalyzes acetylene azide cycloaddition reactions to form 1,2,3-triazoles.

A novel alkyne cholesterol to trace cellular cholesterol metabolism and localization

Cholesterol is an important lipid of mammalian cells and plays a fundamental role in many biological processes. Its concentration in the various cellular membranes differs and is tightly regulated. Here, we present a novel alkyne cholesterol analog suitable for tracing both cholesterol metabolism and localization. This probe can be detected by click chemistry employing various reporter azides. Alkyne cholesterol is accepted by cellular enzymes from different biological species (Brevibacterium, yeast, rat, human) and these enzymes include cholesterol oxidases, hydroxylases, and acyl transferases that generate the expected metabolites in in vitro and in vivo assays. Using fluorescence microscopy, we studied the distribution of cholesterol at subcellular resolution, detecting the lipid in the Golgi and at the plasma membrane, but also in the endoplasmic reticulum and mitochondria. In summary, alkyne cholesterol represents a versatile, sensitive, and easy-to-use tool for tracking cellular cholesterol metabolism and localization as it allows for manifold detection methods including mass spectrometry, thin-layer chromatography/fluorography, and fluorescence microscopy.

Global approaches for the elucidation of phosphoinositide-binding proteins

Phosphoinositide lipids (PIPns) control numerous critical biological pathways, typically through the regulation of protein function driven by non-covalent protein-lipid binding interactions. Despite the importance of these systems, the unraveling of the full scope of protein-PIPn interactions has represented a significant challenge due to the massive complexity associated with these events, including the large number of diverse proteins that bind to these lipids, variations in the mechanisms by which proteins bind to lipids, and the presence of multiple distinct PIPn isomers. As a result of this complexity, global methods in which numerous proteins that bind PIPns can be identified and characterized simultaneously from complex samples, which have been enabled by key technological advancements, have become popular as an efficient means for tackling this challenge. This review article provides an overview of advancements in large-scale methods for profiling protein-PIPn binding, including experimental methods, such as affinity enrichment, microarray analysis and activity-based protein profiling, as well as computational methods, and combined computational/experimental efforts.

Enveloped virus labeling via both intrinsic biosynthesis and metabolic incorporation of phospholipids in host cells

An alternative method for labeling fully replicative enveloped viruses was developed, in which both the biosynthesis and metabolic incorporation of phospholipids in host cells were simultaneously utilized to introduce an azide group to the envelope of the vaccinia virus by taking advantage of the host-derived lipid membrane formation mechanism. Such an azide group could be subsequently used to fluorescently label the envelope of the virus via a bioorthogonal reaction. Furthermore, simultaneous dual-labeling of the virus through the virus replication was realized skillfully by coupling this envelope labeling strategy with "replication-intercalation labeling" of viral nucleic acid. For the first time, it is by natural propagation of the virus in its host cells in the presence of fluorophores that simultaneous dual-labeling of living viruses can be mildly realized with high efficiency in facile and mild conditions.

Sum of the parts: mass spectrometry-based metabolomics

Metabolomics is a rapidly growing field of research used in the identification and quantification of the small molecule metabolites within an organism, thereby providing insights into cell metabolism and bioenergetics as well as processes important in clinical medicine, such as disposition of pharmaceutical compounds. It offers comprehensive information about thousands of low-molecular mass compounds (<1500 Da) that represent a wide range of pathways and intermediary metabolism. Because of its vast expansion in the past two decades, mass spectrometry has become an indispensable tool in "omic" analyses. The use of different ionization techniques such as the more traditional electrospray and matrix-assisted laser desorption, as well as recently popular desorption electrospray ionization, has allowed the analysis of a wide range of biomolecules (e.g., peptides, proteins, lipids, and sugars), and their imaging and analysis in the original sample environment in a workup free fashion. An overview of the current state of the methodology is given, as well as examples of application.