Fluorophore targeting to cellular proteins via enzyme-mediated azide ligation and strain-promoted cycloaddition

Methods for targeting of small molecules to cellular proteins can allow imaging with fluorophores that are smaller, brighter, and more photostable than fluorescent proteins. Previously, we reported targeting of the blue fluorophore coumarin to cellular proteins fused to a 13-amino acid recognition sequence (LAP), catalyzed by a mutant of the Escherichia coli enzyme lipoic acid ligase (LplA). Here, we extend LplA-based labeling to green- and red-emitting fluorophores by employing a two-step targeting scheme. First, we found that the W37I mutant of LplA catalyzes site-specific ligation of 10-azidodecanoic acid to LAP in cells, in nearly quantitative yield after 30 min. Second, we evaluated a panel of five different cyclooctyne structures and found that fluorophore conjugates to aza-dibenzocyclooctyne (ADIBO) gave the highest and most specific derivatization of azide-conjugated LAP in cells. However, for targeting of hydrophobic fluorophores such as ATTO 647N, the hydrophobicity of ADIBO was detrimental, and superior targeting was achieved by conjugation to the less hydrophobic monofluorinated cyclooctyne (MOFO). Our optimized two-step enzymatic/chemical labeling scheme was used to tag and image a variety of LAP fusion proteins in multiple mammalian cell lines with diverse fluorophores including fluorescein, rhodamine, Alexa Fluor 568, ATTO 647N, and ATTO 655.     

Phage display evolution of a peptide substrate for yeast biotin ligase and application to two-color quantum dot labeling of cell surface proteins

Site-specific protein labeling with Escherichia coli biotin ligase (BirA) has been used to introduce fluorophores, quantum dots (QDs), and photocross-linkers onto recombinant proteins fused to a 15-amino acid acceptor peptide (AP) substrate for BirA and expressed on the surface of living mammalian cells. Here, we used phage display to engineer a new and orthogonal biotin ligase-AP pair for site-specific protein labeling. Yeast biotin ligase (yBL) does not recognize the AP, but we discovered a new 15-amino acid substrate for yBL called the yeast acceptor peptide (yAP), using two generations of phage display selection from 15-mer peptide libraries. The yAP is not recognized by BirA, and thus, we were able to specifically label AP and yAP fusion proteins coexpressed in the same cell with differently colored QDs. We fused the yAP to a variety of recombinant proteins and demonstrated biotinylation by yBL at the N-terminus, C-terminus, and within a flexible internal region. yBL is extremely sequence-specific, as endogenous proteins on the surface of yeast and HeLa cells are not biotinylated. This new methodology expands the scope of biotin ligase labeling to two-color imaging and yeast-based applications.     

Specific labeling of cell surface proteins with chemically diverse compounds

The specific and covalent labeling of fusion proteins with synthetic molecules opens up new ways to study protein function in the living cell. Here we present a novel method that allows for the specific and exclusive extracellular labeling of proteins on the surfaces of live cells with a large variety of synthetic molecules including fluorophores, protein ligands, or quantum dots. The approach is based on the specific labeling of fusion proteins of acyl carrier protein with synthetic molecules through post-translational modification catalyzed by phosphopantetheine transferase. The specificity and versatility of the labeling should allow it to become an important tool for studying and manipulating cell surface proteins and for complementing existing approaches in cell surface engineering.     

Solid Phase Supported “Click”-Chemistry Approach for the Preparation of Water Soluble Gold Nanoparticle Dimers

We investigated the potential of the Cu(I) catalyzed azide-alkyne cycloaddition between water soluble azide and alkyne functionalized gold nanoparticles in terms of dimer formation via a solid phase support. Alkyne and azide lipoic acid derivatives are prepared and utilized as stabilizing ligands for 15?nm gold colloids. For the solid phase supported click reaction first citrate stabilized gold nanoparticles are immobilized on amine terminated silicon wafers. In the following step the citrate ligands of the upper free accessible nanoparticle surface are exchanged against a mixture of the alkyne derivative of lipoic acid and lipoic acid. Upon addition of lipoic acid/lipoic acid azide derivative stabilized 15?nm gold nanoparticles and the Cu(I) catalyst solution covalent interparticle coupling between immobilized and gold nanoparticles added is achieved. The formed structures are analyzed by scanning electron microscopy directly on the solid support. It is demonstrated that the yield of dimeric structures on the solid phase support increases with increased molar ratio of the catalyst, thus indicating that dimers are indeed formed by covalent bond formation. Upon treatment with ultrasound the formed structures could be released and detected with transmission electron microscopy measurements.     

Improved Stabilities of Labeling Probes for the Selective Modification of Endogenous Proteins in Living Cells and In Vivo

To date, various affinity-based protein labeling probes have been developed and applied in biological research to modify endogenous proteins in cell lysates and on the cell surface. However, the reactive groups on the labeling probes are also the cause of probe instability and nonselective labeling in a more complex environment, e. g., intracellular and in vivo. Here, we show that labeling probes composed of a sterically stabilized difluorophenyl pivalate can achieve efficient and selective labeling of endogenous proteins on the cell surface, inside living cells and in vivo. As compared with the existing protein labeling probes, probes with the difluorophenyl pivalate exhibit several advantages, including long-term stability in stock solutions, resistance to enzymatic hydrolysis and can be customized easily with diverse fluorophores and protein ligands. With this probe design, endogenous hypoxia biomarker in living cells and nude mice were successfully labeled and validated by in vivo, ex vivo, and immunohistochemistry imaging.     

Multicolor imaging of cell surface proteins

We report on a method for the multicolor imaging of cell surface proteins which is based on the labeling of carrier protein (CP) fusion proteins with different fluorophores. In one application, different generations of a cell surface protein can be sequentially labeled to discriminate between old and newly made copies. In another application, fusions to different CPs can be selectively labeled with different fluorophores in one sample. Both applications open up new ways for studying the properties of cell surface proteins of living cells.     

Specific and stable fluorescence labeling of histidine-tagged proteins for dissecting multi-protein complex formation

Labeling of proteins with fluorescent dyes offers powerful means for monitoring protein interactions in vitro and in live cells. Only a few techniques for noncovalent fluorescence labeling with well-defined localization of the attached dye are currently available. Here, we present an efficient method for site-specific and stable noncovalent fluorescence labeling of histidine-tagged proteins. Different fluorophores were conjugated to a chemical recognition unit bearing three NTA moieties (tris-NTA). In contrast to the transient binding of conventional mono-NTA, the multivalent interaction of tris-NTA conjugated fluorophores with oligohistidine-tagged proteins resulted in complex lifetimes of more than an hour. The high selectivity of tris-NTA toward cumulated histidines enabled selective labeling of proteins in cell lysates and on the surface of live cells. Fluorescence labeling by tris-NTA conjugates was applied for the analysis of a ternary protein complex in solution and on surfaces. Formation of the complex and its stoichiometry was studied by analytical size exclusion chromatography and fluorescence quenching. The individual interactions were dissected on solid supports by using simultaneous mass-sensitive and multicolor fluorescence detection. Using these techniques, formation of a 1:1:1 stoichiometry by independent interactions of the receptor subunits with the ligand was shown. The incorporation of transition metal ions into the labeled proteins upon labeling with tris-NTA fluorophore conjugates provided an additional sensitive spectroscopic reporter for detecting and monitoring protein-protein interactions in real time. A broad application of these fluorescence conjugates for protein interaction analysis can be envisaged.     

Tandem hetero diels-alder reaction: synthesis of oxygenated macrocycles

[structure: see text]. C2-symmetric, oxygenated macrocycles have been synthesized from simple acyclic precursors in a single step by a tandem hetero Diels-Alder reaction. Thermolysis and Lewis acid catalysis can effect this novel transformation. The tandem reaction product is formed in preference to the intramolecular cycloaddition product, and an explanation for this result is proposed.     

碳纳米管上分子印迹微反应器的构建及催化Diels-Alder反应研究

分子印迹聚合物（MIP）在合成与催化方面的应用受到越来越多的关注.传统的本体聚合生成的聚合物往往具有活性中心的利用率低、活性中心不均一、底物难以到达等问题.由于纳米材料具有很高的比表面积,将MIP制备成纳米级别的材料将有可能解决这些问题.本研究的目的是在纳米材料上构建分子印迹微反应器(MIM).通过多壁碳纳米管(MWNTs)上羟基的酯化反应在碳纳米管表面枝接双键,以蒽和马来酸的加成反应产物为模板分子,甲基丙烯酸(MAA)为功能单体,乙二醇二甲基丙烯酸酯(EDMA)为交联剂,通过微波辐射聚合在碳纳米管表面枝接一层厚度约为30 nm 的分子印迹催化剂. 该催化剂对蒽和马来酸的加成反应具有明显的催化作用,反应开始后的180min内,催化反应速率是不加催化剂反应速率的1.77倍. 催化动力学遵守Michaelis-Menten方程,催化反应最大速率（vmax）为0.713 umolL-1S-1,米氏常数（KM）为17735.24 umolL-1.     

A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites

The development of novel anti-infectives requires unprecedented strategies targeting pathways which are solely present in pathogens but absent in humans. Following this principle, we developed inhibitors of lipoic acid ( LA ) salvage, a crucial pathway for the survival of LA auxotrophic bacteria and parasites but non-essential in human cells. An LA -based probe was selectively transferred onto substrate proteins via lipoate protein ligase (LPL) in intact cells, and their binding sites were determined by mass spectrometry. Probe labeling served as a proxy of LPL activity, enabling in situ screenings for cell-permeable LPL inhibitors. Profiling a focused compound library revealed two substrate analogs ( LAMe and C3 ) as inhibitors, which were further validated by binding studies and co-crystallography. Importantly, LAMe exhibited low toxicity in human cells and achieved killing of Plasmodium falciparum in erythrocytes with an EC₅₀ value of 15 μM, making it the most effective LPL inhibitor reported to date.     

Single-cell FRET imaging of transferrin receptor trafficking dynamics by Sfp-catalyzed, site-specific protein labeling

Fluorescence imaging of living cells depends on an efficient and specific method for labeling the target cellular protein with fluorophores. Here we show that Sfp phosphopantetheinyl transferase-catalyzed protein labeling is suitable for fluorescence imaging of membrane proteins that spend at least part of their membrane trafficking cycle at the cell surface. In this study, transferrin receptor 1 (TfR1) was fused to peptide carrier protein (PCP), and the TfR1-PCP fusion protein was specifically labeled with fluorophore Alexa 488 by Sfp. The trafficking of transferrin-TfR1-PCP complex during the process of transferrin-mediated iron uptake was imaged by fluorescence resonance energy transfer between the fluorescently labeled transferrin ligand and TfR1 receptor. We thus demonstrated that Sfp-catalyzed small molecule labeling of the PCP tag represents a practical and efficient tool for molecular imaging studies in living cells.     

Entropic intermediates and hidden rate-limiting steps in seemingly concerted cycloadditions. Observation, prediction, and origin of an isotope effect on recrossing

An unusual intramolecular kinetic isotope effect (KIE) in the reaction of dichloroketene with cis-2-butene does not fit with a simple asynchronous cycloaddition transition state, but it can be predicted from trajectory studies on a bifurcating energy surface. The origin of the KIE is related to a high propensity for transition state recrossing in this system, with heavier masses recrossing less. The KIE can also be predicted by a statistical model that treats the cycloaddition as a stepwise mechanism, the rate-limiting second step being associated with an entropic barrier for formation of the second carbon-carbon bond. The relevance of this stepwise mechanism to other asynchronous but seemingly concerted cycloadditions is suggested by examination of organocatalytic Diels-Alder reactions.     

Repetitive reversible labeling of proteins at polyhistidine sequences for single-molecule imaging in live cells.

Sensitive live-cell fluorescence microscopy and single-molecule imaging are severely limited by rapid photobleaching of fluorescent probes. Herein, we show how to circumvent this problem using a novel, generic labeling strategy. Small nickel-nitrilotriacetate fluorescent probes are reversibly bound to oligohistidine sequences of exposed proteins on cell surfaces, permitting selective observation of the proteins by fluorescence microscopy. Photobleached probes are removed by washing and replaced by new fluorophores, thus enabling repetitive acquisition of single-molecule trajectories on the same cell and allowing variation of experimental conditions between acquisitions. This method offers free choice of fluorophores while being minimally perturbing. The strength of the method is demonstrated by labeling engineered polyhistidine sequences of the serotonin-gated 5-HT(3) receptor on the surface of live mammalian cells. Single-molecule microscopy reveals pronounced heterogeneous mobility patterns of the 5-HT(3) receptor. After activating the receptor with serotonin, the number of immobile receptors increases substantially, which might be important for receptor regulation at synapses.     

Effect of Lewis acid catalysts on Diels-Alder and hetero-Diels-Alder cycloadditions sharing a common transition state

The thermal and Lewis acid catalyzed cycloadditions of beta,gamma-unsaturated alpha-ketophosphonates and nitroalkenes with cyclopentadiene have been explored by using density functional theory (DFT) methods. In both cases, only a single highly asynchronous bis-pericyclic transition state yielding both Diels-Alder and hetero-Diels-Alder cycloadducts could be located. Stepwise pathways were found to be higher in energy. On the potential energy surface, the bis-pericyclic cycloaddition transition state is followed by the Claisen rearrangement transition state. No intermediates were located between these transition states. Claisen rearrangement transition states are also highly asynchronous, but bond lengths are skewed in the opposite direction compared to the bis-pericyclic transition states. The relative positions of the bis-pericyclic and Claisen rearrangement transition states may control periselectivity due to the shape of the potential energy surface and corresponding dynamical influences. Inspection of the thermal potential energy surface (PES) indicates that a majority of downhill paths after the bis-pericyclic transition state lead to the Diels-Alder cycloadducts, whereas a smaller number of downhill paths reach the hetero-Diels-Alder products with no intervening energy barrier. Lewis acid catalysts alter the shape of the surface by shifting the cycloaddition and the Claisen rearrangement transition states in opposite directions. This topographical change qualitatively affects the branching ratio after the bis-pericyclic transition state and ultimately reverses the periselectivity of the cycloaddition giving a preference for hetero-Diels-Alder cycloadducts.     

Phosphine-mediated [4 + 2] annulation of bis(enones): a Lewis base catalyzed "mock Diels-Alder" reaction

Lewis-base-catalyzed cycloisomerization of bis(enones) to decalins has been demonstrated as an alternative to the traditional Lewis acid catalyzed Diels-Alder cycloaddition. In this process, a trialkylphosphine mediates both bond formation steps in two distinct catalytic cycles. The single-pot operation generates two carbon-carbon bonds and up to five contiguous stereocenters in one step, starting from achiral, aliphatic substrates; eight examples are provided. [reaction: see text]     

经由o-Quinonemethide的trans-Hexahydrocannabinol的简便合成

建立了一个在质子性溶剂中经由o-quinonemethide中间体的trans-hexahydrocannabinol的简便合成方法. 用对甲苯磺酸为催化剂, 加热回流resorcinol衍生物和citronellal之间偶联产物的甲醇溶液, 酚的脱保护、o-quinonemethides的生成以及分子内狄尔斯-阿尔德环加成反应一步完成, 产率为93%～95%.     

A total synthesis of xestodecalactone a and proof of its absolute stereochemistry: interesting observations on dienophilic control with 1,3-disubstituted nonequivalent allenes

A concise total synthesis of xestodecalactone A, utilizing a Diels-Alder strategy is described. The focal Diels-Alder reaction relied on an "ynoate" dienophile to rapidly assemble the required resorcylinic acid scaffold. During this study, Diels-Alder cycloaddition reactions involving 1,3-disubstituted nonequivalent allene dienophiles were studied, and some surprising results were encountered.     

Theoretical insights into the metal-free and formal [2 + 2 + 2] cycloaddition strategy via intramolecular cascade propargylic ene/Diels-Alder reactions with tautomerization

A metal-free and formal [2 + 2 + 2] cycloaddition of triynes has emerged recently as a novel methodology for the synthesis of fused tricyclic compounds via an intramolecular cascade propargylic ene reaction, Diels-Alder cycloaddition and tautomerization. DFT calculations on three model systems reveal that the ene reaction with low distortion energy makes the metal-free strategy feasible and, as the rate-determining step, affects the regioselectivity of unsymmetric triynes. Furthermore, the types of final products depend on H-transfer during tautomerization after the Diels-Alder reaction. Generally, the different tethered atoms between the yne moieties are responsible for the different regioselectivities and the final products in the [2 + 2 + 2] cycloadditions. On the basis of a comprehensive theoretical investigation into the mechanism, triynes involving cyclic ynes have been designed and are predicted to react to afford fused tetracyclic products under milder conditions due to dramatically lower energy barriers and by altering the rate-determining step to the Diels-Alder reaction.     

Synthesis of lupinacidins A and B via sequential cycloaddition-double elimination

The first synthesis of lupinacidins A and B, tumor cell invasion inhibitors of microbial origin, has been achieved in four operational steps from 3-methoxy-2-methyl-2-cyclohexenone via the Diels-Alder cycloaddition of a conjugated cyclohexadiene derivative with a juglone-derived sulfinyl quinone followed by sequential elimination of a sulfenic acid and ethylene to afford protected forms of the target molecules.