First artificial receptors and chemosensors toward phosphorylated peptide in aqueous solution

Oligo-Asp tag/Zn(II) complex probe as a new pair for labeling and fluorescence imaging of proteins

To accomplish the selective labeling of a specific protein in complicated biological systems, a peptide tag incorporated into the protein and a complementary small molecular probe are required. Although a variety of peptide tag/probe pairs have been developed as molecular tools for protein analyses, the availability of pairs suitable for real-time imaging of proteins is still limited. We now report a new peptide tag/artificial probe pair composed of a genetically encodable oligo-aspartate sequence (D4 tag, (D4)n, n = 1-3) and the corresponding multinuclear Zn(II) complexes (Zn(II)-DpaTyrs). The strong binding affinity of the Zn(II)-DpaTyr probes with the D4 tag was a result of the multiple coordination bonds and the multivalent effect. It was measured quantitatively by isothermal titration calorimetry. The high affinity between the tag and the probe, indispensable for the selective protein labeling, enabled the pair to be used for the labeling and fluorescence imaging of a membrane-bound receptor protein tethering a triply repeated D4 tag ((D4)3) in an intact cell configuration without significantly affecting the receptor signal transduction.

Metal ion sensing novel calix[4]crown fluoroionophore with a two-photon absorption property

1,3-Alternate calix[4]arene-based fluorescent chemosensors bearing two-photon absorbing chromophores have been synthesized, and their sensing behaviors toward metal ions were investigated via absorption band shifts as well as one- and two-photon fluorescence changes. Free ligands absorb the light at 461 nm and weakly emit their fluorescence at 600 nm when excited by UV-vis radiation at 461 nm, but no two-photon excited fluorescence is emitted by excitation at 780 nm. Addition of an Al(3+) or Pb(2+) ion to a solution of the ligand causes a blue-shifted absorption and enhanced fluorescence due to a declined resonance energy transfer (RET) upon excitation by one- and two-photon processes. Addition of a Pb(2+) ion to a solution of 1.K(+) results in a higher fluorescence intensity than the original 1.Pb(2+) complex regardless of one- or two-photon excitation, due to the allosteric effect induced by the complexation of K(+) with a crown loop.

Triazole-Modified Calix[4]crown as a Novel Fluorescent On−Off Switchable Chemosensor

A novel fluorescent on-off switchable chemosensor 1 with two different types of cationic binding sites is synthesized, which is composed of a triazole-modified calix[4]crown in the 1,3-alternate conformation. Among 15 metal ions examined, the fluorescence of 1 was strongly quenched by Hg2+, Cu2+, Cr3+, and Pb2+; however, the revival of emission from the strongly quenched 1.Pb2+ complex was achievable by the addition of K+, Ba2+, or Zn2+ ions. Thus, metal ion exchange can trigger an on-off switchable fluorescent chemosensor.

Screening systems

Enzyme screening technology has undergone massive developments in recent years, particularly in the area of high-throughput screening and microarray methods. Screening consists of testing each sample of a sample library individually for the targeted reaction. This requires enzyme assays that accurately test relevant parameters of the reaction, such as catalytic turnover with a given substrate and selectivity parameters such as enantio- and regioselectivity. Enzyme assays also play an important role outside of enzyme screening, in particular for drug screening, medical diagnostics, and in the area of cellular and tissue imaging. In the 1990s, methods for high-throughput screening of enzyme activities were perceived as a critical bottleneck. As illustrated partly in this chapter, a large repertoire of efficient screening strategies are available today that allow testing of almost any reaction with high-throughput.

Synthesis of a new artificial host for the binding of dipeptides in water

An artificial peptide receptor was prepared by a simple procedure. Initial binding studies (UV titrations) in buffered water showed preferential complexation of N-acetyl-dipeptide carboxylates containing alanine in the C-terminal position in comparison with simple amino acids, other dipeptides and two tripeptides.

Design of dual-emission chemosensors for ratiometric detection of ATP derivatives

Nucleoside pyrophosphate (nucleoside PP) derivatives are widespread in living cells and play pivotal roles in various biological events. We report novel fluorescence chemosensors for nucleoside PPs that make use of coordination chemistry. The chemosensors, which contain two Zn(II)-dipicolylamine units, bind strongly to nucleoside PPs (K(app)>10(6) M(-1)) in aqueous solution and sense them by a dual-emission change. Detailed fluorescence and UV/Vis spectral studies revealed that the emission changes of the chemosensors upon binding to nucleoside PPs can be ascribed to the loss of coordination between Zn(II) and the acridine fluorophore. This is a unique sensing system based on the anion-induced rearrangement of the coordination. Furthermore, we demonstrated the utility of these chemosensors in real-time monitoring of two important biological processes involving nucleoside PP conversion: the apyrase-catalyzed hydrolysis of nucleoside PPs and the glycosyl transfer catalyzed by beta-1,4-galactosyltransferase.

Design of a Hybrid Biosensor for Enhanced Phosphopeptide Recognition Based on a Phosphoprotein Binding Domain Coupled with a Fluorescent Chemosensor

Protein-based fluorescent biosensors with sufficient sensing specificity are useful analytical tools for detection of biologically important substances in complicated biological systems. Here, we present the design of a hybrid biosensor, specific for a bis-phosphorylated peptide, based on a natural phosphoprotein binding domain coupled with an artificial fluorescent chemosensor. The hybrid biosensor consists of a phosphoprotein binding domain, the WW domain, into which has been introduced a fluorescent stilbazole having Zn(II)-dipicolylamine (Dpa) as a phosphate binding motif. It showed strong binding affinity and high sensing selectivity toward a specific bis-phosphorylated peptide in the presence of various phosphate species such as the monophosphorylated peptide, ATP, and others. Detailed fluorescence titration experiments clearly indicate that the binding-induced fluorescence enhancement and the sensing selectivity were achieved by the cooperative action of both binding sites of the hybrid biosensor, i.e., the WW domain and the Zn(II)-Dpa chemosensor unit. Thus, it is clear that the tethered Zn(II)-Dpa-stilbazole unit operated not only as a fluorescence signal transducer, but also as a sub-binding site in the hybrid biosensor. Taking advantage of its selective sensing property, the hybrid biosensor was successfully applied to real-time and label-free fluorescence monitoring of a protein kinase-catalyzed phosphorylation.

Supramolecular Chemistry in Water

Supramolecular chemistry in water is a constantly growing research area because noncovalent interactions in aqueous media are important for obtaining a better understanding and control of the major processes in nature. This Review offers an overview of recent advances in the area of water-soluble synthetic receptors as well as self-assembly and molecular recognition in water, through consideration of the functionalities that are used to increase the water solubility, as well as the supramolecular interactions and approaches used for effective recognition of a guest and self-assembly in water. The special features and applications of supramolecular entities in aqueous media are also described.

A ratiometric fluorescent sensor for phosphates: Zn2+-enhanced ICT and ligand competition

A pyrene-terpyridine-Zn conjugate has been synthesized and characterized, where Zn2+ acts as an electron acceptor to enhance molecular ICT with a large emission red-shift (>100 nm). It showed a ratiometric fluorescence change upon addition of phosphate anions in buffered aqueous solution. The selective response to phosphates or pyrophosphates involved ICT and ligand competition processes.

Recognition of solvent exposed protein surfaces using anthracene derived receptors

A new class of receptor is described that can selectively bind to the solvent exposed surface of proteins such as cytochrome c and lysozyme with low micromolar affinity over cytochrome c551, alpha-lactalbumin, myoglobin and RNase A, under physiologically relevant conditions (5 mM phosphate, pH 7.4). The use of anthracene as a hydrophobic scaffold allows the receptor to act as a selective chemosensor via fluorescence quenching or FRET. The study reveals that co-operative electrostatic interactions over a large surface area dominate binding. Further investigations reveal that the receptor binds to the solvent exposed heme edge of cytochrome c inhibiting its reaction with small reducing agents and validating the strategy for the disruption of protein function.

Simple but Effective Way to Sense Pyrophosphate and Inorganic Phosphate by Fluorescence Changes

A new fluorescent chemosensor based on the acridine-Zn(II) derivative effectively recognizes pyrophosphate and inorganic phosphate at pH 7.4. Acridine derivative 1 displayed a fluorescent quenching effect with pyrophosphate; on the other hand, a large fluorescent enhancement was observed with inorganic phosphate. [structure: see text].

Dendrimeric Bisphosphonates for Multivalent Protein Surface Binding

A single weak-binding event is multiplied into an efficient receptor site for protein surfaces (<10(-1) to >10(6) M(-1) in buffered aqueous solution) in a biomimetic fashion. This has hitherto been done with natural host/guest pairs, but not with artificial receptors. The organic reaction presented is one of very few that enable chemists to fuse multiple ionic building blocks covalently in highly polar solution; this one-pot reaction proceeds with virtually quantitative yield. According to this concept, other building blocks with aldehyde groups can likewise be multiplied into monodisperse functional dendrimers. Small basic proteins are bound by octameric dendrimers in 1:1 or 1:2 complexes with millimolar to submicromolar affinities. The complexation event is studied independently in buffered aqueous solution by three different spectroscopic methods (PFG-LED, UV/Vis, and fluorescence). Potential new applications include recombinant protein purification through Arg tags on immobilized dendrimers and on/off switching of protein function by reversible active-site capping of enzymes.

Sequence-Specific Recognition and Cooperative Dimerization of N-Terminal Aromatic Peptides in Aqueous Solution by a Synthetic Host

This article describes the selective recognition and noncovalent dimerization of N-terminal aromatic peptides in aqueous solution by the synthetic host compound, cucurbit[8]uril (Q8). Q8 is known to bind two aromatic guests simultaneously and, in the presence of methyl viologen, to recognize N-terminal tryptophan over internal and C-terminal sequence isomers. Here, the binding of Q8 to aromatic peptides in the absence of methyl viologen was studied by isothermal titration calorimetry (ITC), (1)H NMR spectroscopy, and X-ray crystallography. The peptides studied were of sequence X-Gly-Gly, Gly-X-Gly, and Gly-Gly-X (X = Trp, Phe, Tyr, and His). Q8 selectively binds and dimerizes Trp-Gly-Gly (1) and Phe-Gly-Gly (4) with high affinity (ternary K = 10(9)-10(11) M(-)(2)); binding constants for the other 10 peptides were too small to be measured by ITC. Both peptides bound in a stepwise manner, and peptide 4 bound with positive cooperativity. Crystal structures of Q8.1 and Q8.4(2) reveal the basis for selective recognition as simultaneous inclusion of the hydrophobic aromatic side chain into the cavity of Q8 and chelation of the proximal N-terminal ammonium group by carbonyl groups of Q8. The peptide sequence selectivity and positively cooperative dimerization reported here are, to the best of our knowledge, unprecedented for synthetic hosts in aqueous solution. Specific peptide recognition and dimerization by synthetic hosts such as Q8 should be important in the study of dimer-mediated biochemical processes and for the separation of peptides and proteins.

A dithio-coupled kinase and ATPase assay

Kinases and ATPases produce adenosine diphosphate (ADP) as a common product, so an assay that detects ADP would provide a universal means for activity-based screening of enzymes in these families. Because it is known that most kinases accept ATPbetaS (sulfur on the beta-phosphorous) as a substrate in place of adenosine triphosphate (ATP), the authors have developed a continuous assay using this substrate, with detection of the ADPbetaS product using dithio reagents. Such an assay is possible because dithio groups react selectively with ADPbetaS and not with ATPbetaS. Thiol detection was done using both Ellman's reagent (DTNB) and a recently developed fluorescent dithio reagent, DSSA. Therefore, the assay can be run in both absorbance and fluorescence detection modes. The assay was used to perform steady-state kinetic analyses of both hexokinase and myosin ATPase. It was also used to demonstrate the diastereoselectivity of hexokinase (R) and myosin ATPase (S) for the isomers of ATPbetaS, consistent with previous results. When run in fluorescence mode using a plate reader, an average Z' value of 0.54 was obtained, suggesting the assay is appropriate for high-throughput screening.

Identification of a New Class of Low Molecular Weight Antagonists against the Chemokine Receptor CXCR4 Having the Dipicolylamine−Zinc(II) Complex Structure

Several low molecular weight nonpeptide compounds having the dipicolylamine-zinc(II) complex structure were identified as potent and selective antagonists of the chemokine receptor CXCR4. These compounds showed strong inhibitory activity against CXCL12 binding to CXCR4, and the top compound exhibited significant anti-HIV activity. Zinc(II)-dipicolylamine unit-containing compounds proved to be useful and attractive lead compounds for chemotherapy of these diseases as nonpeptide CXCR4 antagonists possessing the novel scaffold structure.

Effective disruption of phosphoprotein-protein surface interaction using Zn(II) dipicolylamine-based artificial receptors via two-point interaction

Protein phosphorylation is ubiquitously involved in living cells, and it is one of the key events controlling protein-protein surface interactions, which are essential in signal transduction cascades. We now report that the small molecular receptors bearing binuclear Zn(II)-Dpa can strongly bind to a bis-phosphorylated peptide in a cross-linking manner under neutral aqueous conditions when the distance between the two Zn(II) centers can appropriately fit in that of the two phosphate groups of the phosphorylated peptide. The binding property was quantitatively determined by ITC (isothermal titration calorimetry), induced CD (circular dichroism), and NMR. On the basis of these findings, we demonstrated that these types of small molecules were able to effectively disrupt the phosphoprotein-protein interaction in a phosphorylated CTD peptide and the Pin1 WW domain, a phosphoprotein binding domain, at a micromolar level. The strategy based on a small molecular disruptor that directly interacts with phosphoprotein is unique and should be promising in developing a designer inhibitor for phosphoprotein-protein interaction.

Arginine- and lysine-specific polymers for protein recognition and immobilization

Free radical polymerization of methacrylamide-based bisphosphonates turns weak arginine binders into powerful polymeric protein receptors. Dansyl-labeled homo- and copolymers with excellent water solubility are accessible through a simple copolymerization protocol. Modeling studies point to a striking structural difference between the stiff rodlike densely packed homopolymer 1 and the flexible copolymer 2 with spatially separated bisphosphonate units. Fluorescence titrations in buffered aqueous solution (pH = 7.0) confirm the superior affinity of the homopolymer toward oligoarginine peptides reaching nanomolar K(D) values for the Tat peptide. Basic proteins are bound almost equally well by 1 and 2 with micromolar affinities, with the latter producing much more soluble complexes. The Arg selectivity of the monomer is transferred to the polymer, which binds Arg-rich proteins 1 order of magnitude tighter than lysine-rich pendants of comparable pI, size, and (Arg/Lys vs Glu/Asp) ratio. Noncovalent deposition of both polymers on glass substrates via polyethyleneimine layers results in new materials suitable for peptide and protein immobilization. RIfS measurements allow calculation of association constants K(a) as well as dissociation kinetics k(D). They generally confirm the trends already found in free solution. Close inspection of electrostatic potential surfaces suggest that basic domains favor protein binding on the flat surface. The high specificity of the bisphosphonate polymers toward basic proteins is demonstrated by comparison with polyvinyl sulfate, which has almost no effect in RIfS experiments. Thus, copolymerization of few different comonomer units without cross-linking enables surface recognition of basic proteins in free solution as well as their effective immobilization on surfaces.

Fluorescent Ratiometry of Tetrahomodioxacalix[4]arene Pyrenylamides upon Cation Complexation

[structure: see text] C-1,2-alternate tetrahomodioxacalix[4]arene pyreneamides were synthesized. Pb(2+) coordination gave a quenched monomer and excimer fluorescence emission, while upon Ca(2+) ion binding, the receptor provides an enhanced excimer and declined monomer emission with ratiometric response. The excimer emission spectra changes are rationalized by frontier molecular orbitals that the effective Py-Py interaction induces emission intensity increases upon Ca(2+) ion complexation, whereas there is no such interaction observed upon Pb(2+) binding.

A fluorescent nanosensor for apoptotic cells

A biocompatible surface-functionalized nanoparticle was designed to sense phosphatidylserine exposed on apoptotic cells. We conjugated synthetic artificial phosphatidylserine binding ligands in a multivalent fashion onto magnetofluorescent nanoparticles. Our results show that (1) the synthetic nanoparticles bind to apoptotic cells, (2) there is excellent correlation with annexin V staining by microscopy, and (3) FACS analysis with nanoparticles allows the measurement of therapeutic apoptosis induction. The described nanomaterials should be useful for a variety of biomedical applications including in vivo imaging of apoptosis.

Photogeneration and Chemistry of Biphenyl Quinone Methides from Hydroxybiphenyl Methanols†

The photosolvolysis of several biphenyl methanols (Ph-PhCH[Ph]OH) substituted with hydroxy or methoxy groups on the benzene ring not containing the -CH(Ph)OH moiety has been studied in aqueous solution. This work is a continuation of our studies of photosolvolysis of hydroxy-substituted arylmethanols that generate quinone methide intermediates, some of which are known to be relevant intermediates in toxicology and in biological and organic chemistry in general. In this study, we further probe the ability of the biphenyl ring system to transmit charge from the ring substituted with a potential electron-donating group (hydroxy and methoxy) to the adjacent benzene ring that contains a labile benzyl alcohol moiety. We show that in systems with a hydroxy substituent, biphenyl quinone methides (BQM) are the first formed intermediates that are detectable by nanosecond laser flash photolysis, and are responsible for the observed overall photosolvolysis reaction of these compounds. The highly conjugated BQM are found to absorb at long wavelengths (lambda(max) 580 and approximately 750 nm for the p,p' and o,p'-isomers, respectively) with relatively long lifetimes in neutral aqueous solution (500 and 30 micros, respectively). The BQM from the o,p'-isomer was found to undergo a competing intramolecular Friedel-Crafts alkylation, to give a fluorene derivative.

Selective recognition of bacterial membranes by zinc(ii)-coordination complexes

Two fluorophore-dipicolylamine-Zn2+ conjugates are shown by epifluorescence microscopy to stain the membranes of bacterial cells in preference to mammalian cells.

Dynamic molecular recognition on the surface of vesicle membranes

The ability of a vesicle-bound receptor to associate with a water-soluble ligand increases with membrane loading level and the presence of membrane additives with cationic N-CH3 groups.

Selective recognition of pyrophosphate in water using a backbone modified cyclic peptide receptor

A cyclic peptide based receptor, bearing two dipicolylamino arms complexed to zinc(II) ions, binds pyrophosphate ions with high affinity and selectivity in aqueous solution as determined using an indicator displacement assay.

Synthetic peptides with selective affinity for apoptotic cells

The appearance of anionic phosphatidylserine (PS) in the outer monolayer of the plasma membrane is a universal indicator of the early/intermediate stages of cell apoptosis. The most common method of detecting PS on a cell surface is to use the protein annexin V; however, in certain applications there is a need for alternative reagents. Recent research indicates that rationally designed zinc 2,2'-dipicolylamine (Zn2+-DPA) coordination complexes can mimic the apoptosis sensing function of annexin V. Here, a series of fluorescently-labelled, tri- and pentapeptides with side chains containing Zn2+-DPA are prepared and shown to selectively bind to anionic vesicle membranes. Fluorescein-labelled versions of the peptides are used to detect apoptotic cells by fluorescence microscopy and flow cytometry.

New reagents for phosphatidylserine recognition and detection of apoptosis

The phospholipid bilayer surrounding animal cells is made up of four principle phospholipid components, phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), and sphingomyelin (SM). These four phospholipids are distributed between the two monolayers of the membrane in an asymmetrical fashion, with PC and SM largely populating the extracellular leaflet and PE and PS restricted primarily to the inner leaflet. Breakdown in this transmembrane phospholipid asymmetry is a hallmark of the early to middle stages of apoptosis. The consequent appearance of PS on the extracellular membrane leaflet is commonly monitored using dye-labeled Annexin V, a 36 kDa, Ca2+-dependent PS binding protein. Substitutes for Annexin V are described, including small molecules, nanoparticles, cationic liposomes, and other proteins that can recognize PS in a membrane surface. Particular attention is given to the use of these reagents for detecting apoptosis.

On-Bead Fluorescence Assay for Serine/Threonine Kinases

[chemical reaction: see text]. A novel fluorescence-based assay for serine/threonine kinases is described. Base-mediated beta-elimination of the phosphate moiety and the Michael addition of a thiol-containing fluorescent molecule allows convenient and efficient detection of the enzyme activity. This approach may be broadly applicable to various serine/threonine kinases.

A luminescence sensor of inositol 1,4,5-triphosphate and its model compound by ruthenium-templated assembly of a bis(Zn2+-cyclen) complex having a 2,2'-bipyridyl linker (cyclen = 1,4,7,10-tetraazacyclododecane)

A new supramolecular complex (Ru(Zn2L4)3) was designed and synthesized as a luminescence sensor for inositol 1,4,5-triphosphate (IP3), which is one of the important second messengers in intracellular signal transduction, and its achiral model compound, cis,cis-1,3,5-cyclohexanetriol triphosphate (CTP3), by a ruthenium(II)-templated assembly of three molecules of a bis(Zn2+-cyclen) complex having a 2,2-bipyridyl linker (Zn2L4). Single-crystal X-ray diffraction analysis of a racemic mixture of Ru(Zn2L4)3 showed that three of the six Zn2+-cyclen units are orientated to face the opposite side of the molecule with three apical ligands (Zn2+-bound HO-) of each of the three Zn2+ located on the same face. 1H NMR and UV titrations of Ru(Zn2L4)3 with CTP3 indicated that Ru(Zn2L4)3 forms a 1:2 complex with CTP3, (Ru(Zn2L4)3)-((CTP3)6-)2, in aqueous solution at neutral pH. In the absence of guest molecules, Ru(Zn2L4)3 (10 microM) has an emission maximum at 610 nm at pH 7.4 (10 mM HEPES with I = 0.1 (NaNO3)) and 25 degrees C (excitation at 300 nm). An addition of 2 equiv of CTP3 induced a 4.2-fold enhancement in the emission of Ru(Zn2L4)3 at 584 nm. In this article, we describe that Ru(Zn2L4)3 is the first chemical sensor that directly responds to CTP3 and IP3 and discriminates these triphosphates from monophosphates and diphosphates. The photodecomposition of Ru(Zn2L4)3, which is inhibited upon complexation with CTP3, and the stereoselective complexation of chiral IP3 by Ru(Zn2L4)3 are also described.

Highly Effective Fluorescent and Colorimetric Sensors for Pyrophosphate over H2PO4- in 100% Aqueous Solution

[Structure: see text]. This study demonstrated that Zinpyr-1*Zn2+ acts as a fluorescent and colorimetric sensor for pyrophosphate at pH 7.4. In addition, Zinpyr-1*Cu2+ and DIARB-1*Cu2+ complexes were found to act as selective fluorescent sensors for pyrophosphate. Furthermore, the chemosensors Zinpyr-1*Zn2+ and Zinpyr-1*Cu2+ show highly selective and ratiometric fluorescence changes for pyrophosphate compared with H2PO4-.

New advances in fluorogenic anion chemosensors

The development of anion chemosensors is an area of recent interest. We make here a comprehensive review of new advances on anion chemosensing, reported in the literature during the year 2004. The review follows a classification of the sensing systems based on design principles. It comprises: the binding site-signalling subunit approach, the displacement approach and the use of fluoro-chemodosimeters. The first two approximations are based on the use of a suitable anion coordination site coupled with a signalling unit which signals the anion coordination process via changes in its fluorescence behaviour. The two basic subunits are covalently linked in the binding site-signalling subunit approach and not in the displacement approach. In both approaches the fluorescence variation is reversible. The third way to the development of fluorogenic chemosensors is the use of chemodosimeters (also called reagents or reactands) that work usually through irreversible chemical reactions coupled with drastic changes in the fluorescence emission behaviour.