Heidi E. Bostic

Exploiting Bioorthogonal Chemistry to Elucidate Protein–Lipid Binding Interactions and Other Biological Roles of Phospholipids

Lipids play critical roles in a litany of physiological and pathophysiological events, often through the regulation of protein function. These activities are generally difficult to characterize, however, because the membrane environment in which lipids operate is very complex. Moreover, lipids have a diverse range of biological functions, including the recruitment of proteins to membrane surfaces, actions as small-molecule ligands, and covalent protein modification through lipidation. Advancements in the development of bioorthogonal reactions have facilitated the study of lipid activities by providing the ability to selectively label probes bearing bioorthogonal tags within complex biological samples. In this Account, we discuss recent efforts to harness the beneficial properties of bioorthogonal labeling strategies in elucidating lipid function. Initially, we summarize strategies for the design and synthesis of lipid probes bearing bioorthogonal tags. This discussion includes issues to be considered when deciding where to incorporate the tag, particularly the presentation within a membrane environment. We then present examples of the application of these probes to the study of lipid activities, with a particular emphasis on the elucidation of protein-lipid binding interactions. One such application involves the development of lipid and membrane microarray analysis as a high-throughput platform for characterizing protein-binding interactions. Here we discuss separate strategies for binding analysis involving the immobilization of either whole liposomes or simplified isolated lipid structures. In addition, we present the different strategies that have been used to derivatize membrane surfaces via bioorthogonal reactions, either by using this chemistry to produce functionalized lipid scaffolds that can be incorporated into membranes or through direct modification of intact membrane surfaces. We then provide an overview of the development of lipid activity probes to label and identify proteins that bind to a particular lipid from complex biological samples. This process involves the strategy of activity-based proteomics, in which proteins are collectively labeled on the basis of function (in this case, ligand binding) rather than abundance. We summarize strategies for designing and applying lipid activity probes that allow for the selective labeling and characterization of protein targets. Additionally, we briefly comment on applications other than studying protein-lipid binding. These include the generation of new lipid structures with beneficial properties, labeling of tagged lipids in live cells for studies involving fluorescence imaging, elucidation of covalent protein lipidation, and identification of biosynthetic lipid intermediates. These applications illustrate the early phase of the promising field of applying bioorthogonal chemistry to the study of lipid function.

Optimization of a pipemidic acid autotaxin inhibitor.

Autotaxin (ATX, NPP2) has recently been shown to be the lysophospholipase D responsible for synthesis of the bioactive lipid lysophosphatidic acid (LPA). LPA has a well-established role in cancer, and the production of LPA is consistent with the cancer-promoting actions of ATX. Increased ATX and LPA receptor expression have been found in numerous cancer cell types. The current study has combined ligand-based computational approaches (binary quantitative structure-activity relationship), medicinal chemistry, and experimental enzymatic assays to optimize a previously identified small molecule ATX inhibitor, H2L 7905958 (1). Seventy prospective analogs were analyzed via computational screening, from which 30 promising compounds were synthesized and screened to assess efficacy, potency, and mechanism of inhibition. This approach has identified four analogs as potent as or more potent than the lead. The most potent analog displayed an IC(50) of 900 nM with respect to ATX-mediated FS-3 hydrolysis with a K(i) of 700 nM, making this compound approximately 3-fold more potent than the previously described lead.

Phosphatidylinositol 3,4,5-Trisphosphate Activity Probes for the Labeling and Proteomic Characterization of Protein Binding Partners

Phosphatidylinositol polyphosphate lipids, such as phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P₃], regulate critical biological processes, many of which are aberrant in disease. These lipids often act as site-specific ligands in interactions that enforce membrane association of protein binding partners. Herein, we describe the development of bifunctional activity probes corresponding to the headgroup of PI(3,4,5)P₃ that are effective for identifying and characterizing protein binding partners from complex samples, namely cancer cell extracts. These probes contain both a photoaffinity tag for covalent labeling of target proteins and a secondary handle for subsequent detection or manipulation of labeled proteins. Probes bearing different secondary tags were exploited, either by direct attachment of a fluorescent dye for optical detection or by using an alkyne that can be derivatized after protein labeling via click chemistry. First, we describe the design and modular synthetic strategy used to generate multiple probes with different reporter tags of use for characterizing probe-labeled proteins. Next, we report initial labeling studies using purified protein, the PH domain of Akt, in which probes were found to label this target, as judged by in-gel detection. Furthermore, protein labeling was abrogated by controls including competition with an unlabeled PI(3,4,5)P₃ headgroup analogue as well as through protein denaturation, indicating specific labeling. In addition, probes featuring linkers of different lengths between the PI(3,4,5)P₃ headgroup and photoaffinity tag led to variations in protein labeling, indicating that a shorter linker was more effective in this case. Finally, proteomic labeling studies were performed using cell extracts; labeled proteins were observed by in-gel detection and characterized using postlabeling with biotin, affinity chromatography, and identification via tandem mass spectrometry. These studies yielded a total of 265 proteins, including both known and novel candidate PI(3,4,5)P₃-binding proteins.

Microplate-Based Characterization of Protein-Phosphoinositide Binding Interactions Using a Synthetic Biotinylated Headgroup Analogue

Membrane lipids act as important regulators of a litany of important physiological and pathophysiological events. Many of them act as site-specific ligands for cytosolic proteins in binding events that recruit receptors to the cell surface and control both protein function and subcellular localization. Phosphatidylinositol phosphates (PIP(n)s) are a family of signaling lipids that regulate numerous cellular processes by interacting with a myriad of protein binding modules. Characterization of PIP(n)-binding proteins has been hampered by the lack of a rapid and convenient quantitative assay. Herein, microplate-based detection is presented as an effective approach to characterizing protein-PIP(n) binding interactions at the molecular level. With this assay, the binding of proteins to isolated PIP(n) headgroups is detected with high sensitivity using a platform that is amenable to high-throughput screening. In the studies described herein, biotinylated PI-(4,5)-P(2) headgroup analogue 1 was designed, synthesized, and immobilized onto 96-well streptavidin-coated microplates to study receptor binding. This assay was used to characterize the binding of the PH domain of beta-spectrin to this headgroup. The high affinity interaction that was detected for surface association (K(d, surf) = 6 nM +/- 3), demonstrates that receptor binding modules can form high affinity interactions with lipid headgroups outside of a membrane environment. The results also indicate the feasibility of the assay for rapid characterization of PIP(n)-binding proteins as well as the promise for high-throughput analysis of protein-PIP(n) binding interactions. Finally, this assay was also employed to characterize the inhibition of the binding of receptors to the PIP(n)-derivatized microplates using solution phase competitors. This showcases the viability of this assay for rapid screening of inhibitors of PIP(n)-binding proteins.

Photocurrent Generation from Porphyrin/Fullerene Complexes Assembled in a Tethered Lipid Bilayer

A modular photocurrent generation system, based on amphiphilic porphyrin and fullerene species assembled in a tethered lipid bilayer matrix, is reported here. The key findings are (1) the amount of photoactive species can be quantitatively controlled in each leaflet of the bilayer and (2) the sequential formation of the bilayer allows a directional organization of these agents on electrodes. Photocurrent generation from seven differently configured photoactive bilayers is studied, which reveals several critical factors in achieving efficient photoinduced electron transfer across lipid membranes. Detailed fluorescence characterization is performed on porphyrin samples either in liposomes or surface-tethered bilayers; and the observed fluorescence quenching is correlated with photocurrents generated from the electrode-immobilized lipid films. The potential usefulness of this lipid-based approach is discussed in connection to several existing molecular photovoltaic systems.

Microarray analysis of Akt PH domain binding employing synthetic biotinylated analogs of all seven phosphoinositide headgroup isomers.

Signaling lipids control many of the most important biological pathways, typically by recruiting cognate protein binding targets to cell surfaces, thereby regulating both their function and subcellular localization. A critical family of signaling lipids is that of the phosphatidylinositol polyphosphates (PIP(n)s), which is composed of seven isomers that vary based on phosphorylation pattern. A key protein that is activated upon PIP(n) binding is Akt, which then plays important roles in regulating the cell cycle, and is thus aberrant in disease. Characterization of protein-PIP(n) binding interactions is hindered by the complexity of the membrane environment and of the PIP(n) structures. Herein, we describe two rapid assays of use for characterizing protein-PIP(n) binding interactions. First, a microplate-based binding assay was devised to characterize the binding of effectors to immobilized synthetic PIP(n) headgroup-biotin conjugates corresponding to all seven isomers. The assay was implemented for simultaneous analysis of Akt-PH domain, indicating PI(3,4,5)P(3) and PI(3,4)P(2) as the primary ligands. In addition, density-dependant studies indicated that the amount of ligand immobilized on the surface affected the amplitude of protein binding, but not the affinity, for Akt-PH. Since the PIP(n) ligand motifs used in this analysis lack the membrane environment and glycerolipid backbone, yet still exhibit high-affinity protein binding, these results narrow down the structural requirements for Akt recognition. Additionally, binding detection was also achieved through microarray analysis via the robotic pin printing of ligands onto glass slides in a miniaturized format. Here, fluorescence-based detection provided sensitive detection of binding using minimal amounts of materials. Due to their high-throughput and versatile attributes, these assays provide invaluable tools for probing and perturbing protein-membrane binding interactions.

Synthesis and evaluation of heterocyclic analogues of bromoxynil.

One attractive strategy to discover more active and/or crop-selective herbicides is to make structural changes to currently registered compounds. This strategy is especially appealing for those compounds with limited herbicide resistance and whose chemistry is accompanied with transgenic tools to enable herbicide tolerance in crop plants. Bromoxynil is a photosystem II (PSII) inhibitor registered for control of broadleaf weeds in several agronomic and specialty crops. Recently at the University of Tennessee-Knoxville several analogues of bromoxynil were synthesized including a previously synthesized pyridine (2,6-dibromo-5-hydroxypyridine-2-carbonitrile sodium salt), a novel pyrimidine (4,6-dibromo-5-hydroxypyrimidine-2-carbonitrile sodium salt), and a novel pyridine N-oxide (2,6-dibromo-1-oxidopyridin-1-ium-4-carbonitrile). These new analogues of bromoxynil were also evaluated for their herbicidal activity on soybean (Glycine max), cotton (Gossypium hirsutum), redroot pigweed (Amaranthus retroflexus), velvetleaf (Abutilon theophrasti), large crabgrass (Digitaria sanguinalis), and pitted morningglory ( Ipomoea lacunose ) when applied at 0.28 kg ha(-1). A second study was conducted on a glyphosate-resistant weed (Amaranthus palmeri) with the compounds being applied at 0.56 kg ha(-1). Although all compounds were believed to inhibit PSII by binding in the quinone binding pocket of D1, the pyridine and pyridine-N-oxide analogues were clearly more potent than bromoxynil on Amaranthus retroflexus. However, application of the pyrimidine herbicide resulted in the least injury to all species tested. These variations in efficacy were investigated using molecular docking simulations, which indicate that the pyridine analogue may form a stronger hydrogen bond in the pocket of the D1 protein than the original bromoxynil. A pyridine analogue was able to control the glyphosate-resistant Amaranthus palmeri with >80% efficacy. The pyridine analogues of bromoxynil showed potential to have a different weed control spectrum compared to bromoxynil. A pyridine analogue of bromoxynil synthesized in this research controlled several weed species greater than bromoxynil itself, potentially due to enhanced binding within the PSII binding pocket. Future research should compare this analogue to bromoxynil using optimized formulations at higher application rates.

Effects of Oriented Surface Dipole on Photoconversion Efficiency in an Alkane/Lipid‐Hybrid‐Bilayer‐Based Photovoltaic Model System

When a phospholipid monolayer containing a zinc-coordinated porphyrin species formed atop a self-assembled monolayer of heptadecafluoro-1-decanethiol (CF3(CF2)7(CH2)2SH) is subjected to photoelectrochemical current generation, a significant modulation effect is observed. Compared with devices that contain similar photoactive lipid monolayers but formed on 1-dodecanethiol SAMs, these fluorinated hybrid bilayers produce a >60% increase in cathodic currents and a similar decrease in anodic currents. Photovoltages recorded from these hybrid bilayers are found to vary in the same fashion. The modulation of photovoltaic responses in these hybrid-bilayer-based devices is explained by the opposite surface dipoles associated with the thiols employed in this study, which in one case (fluorothiol) increase and in another (alkanethiol) decrease the work function of the underlying gold substrates. A similar trend of photovoltage/photocurrent modulation is also observed if fullerene is used as the photoagent in these devices. Our results reveal the intricacy of orientated surface dipole in influencing the photovoltaic processes, and its subtle interplay with other factors related to the photoagents, such as their location and orientation within the organic matrix.