Controlling the biological effects of spermine using a synthetic receptor

Polyamines play an important role in biology, yet their exact function in many processes is poorly understood. Artificial host molecules capable of sequestering polyamines could be useful tools for studying their cellular function. However, designing synthetic receptors with affinities sufficient to compete with biological polyamine receptors remains a huge challenge. Binding affinities of synthetic hosts are typically separated by a gap of several orders of magnitude from those of biomolecules. We now report that a dynamic combinatorial selection approach can deliver a synthetic receptor that bridges this gap. The selected receptor binds spermine with a dissociation constant of 22 nM, sufficient to remove it from its natural host DNA and reverse some of the biological effects of spermine on the nucleic acid. In low concentrations, spermine induces the formation of left-handed DNA, but upon addition of our receptor, the DNA reverts back to its right-handed form. NMR studies and computer simulations suggest that the spermine complex has the form of a pseudo-rotaxane. The spermine receptor is a promising lead for the development of therapeutics or molecular probes for elucidating spermine's role in cell biology.     

Differential receptor arrays and assays for solution-based molecular recognition

Nature has inspired an emergent supramolecular field of synthetic receptor arrays and assays for the pattern-based recognition of various bioanalytes and metal species. The synthetic receptors are not necessarily selective for a particular analyte, but the combined signal response from the array is diagnostic for the analyte. This tutorial review describes recent work in the literature for this emerging supramolecular field and details basic array and assay design principles. We review the analytes targeted, signaling types used, and pattern recognition.Developing specific receptors for the solution-based analysis of complex analytes and mixtures is a daunting task. A solution to this difficult task has been inspired by nature's use of arrays of receptors in the senses of taste and smell. An emerging field within supramolecular chemistry is the use of synthetic and readily available receptors in array formats for the detection of analytes in solution. Each receptor in a differential array does not necessarily have selectivity for a particular analyte, but the combined fingerprint response can be extracted as a diagnostic pattern visually, or using chemometric tools. This new genre of molecular recognition is advancing rapidly with several groups developing novel array platforms and receptors.     

Triphenylene: A versatile molecular receptor

Since the late seventies, the search for new molecular receptors has been constant in perfecting the affinity and selectivity of recognition in different media. At present, a renewed interest in (host:guest) chemistry focuses on the molecular detection of specific targets such as biological, pollutant, toxic or explosive species. This review of triphenylene-based receptors outlines their recent contribution to molecular recognition. Two main structural approaches were investigated to transform a simple triphenylene moiety into a host for neutral aromatic compounds or cations, by tailoring multivalent molecules provided with or without a flatten cavity. The properties of different receptors are presented along with the latest synthetic methods to prepare high-value triphenylenes and the perspectives in the field of sensing. In addition, the role of functionalized triphenylenes in extended (host:guest) systems is illustrated by the main examples of discotic liquid crystals and porous coordination polymers involving this polyaromatic compound.     

Assembling OX40 aptamers on a molecular scaffold to create a receptor-activating aptamer

We show that a molecular scaffold can be utilized to convert a receptor binding aptamer into a receptor agonist. Many receptors (including tumor necrosis receptor family members) are activated when they are multimerized on the cell surface. Molecular scaffolds have been utilized to assemble multiple receptor binding peptide ligands to generate activators of such receptors. We demonstrate that an RNA aptamer that recognizes OX40, a member of the tumor necrosis factor receptor superfamily, can be converted into a receptor-activating aptamer by assembling two copies on an olignucleotide-based scaffold. The OX40 receptor-activating aptamer is able to induce nuclear localization of nuclear factor-kappaB, cytokine production, and cell proliferation, as well as enhance the potency of dendritic cell-based tumor vaccines when systemically delivered to mice.     

The role of adenosine receptor agonists in regulation of hematopoiesis

The review summarizes data evaluating the role of adenosine receptor signaling in murine hematopoietic functions. The studies carried out utilized either non-selective activation of adenosine receptors induced by elevation of extracellular adenosine or by administration of synthetic adenosine analogs having various proportions of selectivity for a particular receptor. Numerous studies have described stimulatory effects of non-selective activation of adenosine receptors, manifested as enhancement of proliferation of cells at various levels of the hematopoietic hierarchy. Subsequent experimental approaches, considering the hematopoiesis-modulating action of adenosine receptor agonists with a high level of selectivity to individual adenosine receptor subtypes, have revealed differential effects of various adenosine analogs. Whereas selective activation of A? receptors has resulted in suppression of proliferation of hematopoietic progenitor and precursor cells, that of A? receptors has led to stimulated cell proliferation in these cell compartments. Thus, A? and A? receptors have been found to play a homeostatic role in suppressed and regenerating hematopoiesis. Selective activation of adenosine A? receptors has been found to act curatively under conditions of drug- and radiation-induced myelosuppression. The findings in these and further research areas will be summarized and mechanisms of hematopoiesis-modulating action of adenosine receptor agonists will be discussed.     

Molecular recognition of ADP over ATP in aqueous solution by a polyammonium receptor containing a pyrimidine residue

The synergistic action of the different binding groups of the polyfunctional HL receptor leads to the recognition of ADP over ATP in water, with a selectivity coefficient of up to 116, a phenomenon which is unprecedented in the context of synthetic receptors in water. The recognition is mostly due to the good matching between H(3)L(2+) and the protonated forms of ADP.     

Dynamic combinatorial development of a neutral synthetic receptor that binds sulfate with nanomolar affinity in aqueous solution

Using dynamic combinatorial disulfide chemistry we have developed a new generation of neutral synthetic receptors for anions, based on a macrobicyclic peptide structure. These receptors show an exceptional affinity and selectivity for sulfate ions in aqueous solution [log K(a) = 8.67 in 41 mol% (67 volume%) acetonitrile in water]. The high affinity depends on a delicate balance between rigidity and flexibility in the structure of the receptor.     

ATP detection using a label-free DNA aptamer and a cationic tetrahedralfluorene

A simple and sensitive method for ATP detection using a label-free DNA aptamer as the recognition element and ethidium bromide (EB) as the signal reporter is reported. The ATP-binding aptamer undergoes a conformational switch from the aptamer duplex to the aptamer/target complex upon target binding, which induces the fluorescence change of intercalated EB emission. Good selectivity between ATP and CTP, GTP or UTP has been demonstrated, which is due to the specific recognition between the ATP aptamer and ATP. Using EB alone as a signal reporter, the ATP detection limit was estimated to be approximately 0.2 mM. When a light harvesting cationic tetrahedralfluorene was used as an energy donor to sensitize the intercalated EB emission, a 10-fold increase in detection limit and a 2-fold increase in detection selectivity was demonstrated. The sensitivity and selectivity of the tetrahedralfluorene sensitized assay is comparable to or better than most fluorescent ATP assays with multiple labels.     

Transport of alkali halides through a liquid organic membrane containing a ditopic salt-binding receptor

A ditopic receptor is shown to have an impressive ability to recognize and extract the ion pairs of various alkali halides into organic solution. X-ray diffraction analysis indicates that the salts are bound in the solid state as contact ion pairs. Transport experiments, using a supported liquid membrane and high salt concentration in the source phase, show that the ditopic receptor can transport alkali halide salts up to 10-fold faster than a monotopic cation or anion receptor and 2-fold faster than a binary mixture of cation and anion receptors. All transport systems exhibit the same qualitative order of ion selectivity; that is, for a constant anion, the cation selectivity order is K+ > Na+ > Li+, and for a constant cation, the anion transport selectivity order is I- > Br- > Cl-. The data suggest that with a ditopic receptor, the polarity of the receptor-salt complex can be lowered if the salt is bound as an associated ion pair, which leads to a faster diffusion through the membrane and a higher maximal flux.     

One-armed artificial receptors for the binding of polar tetrapeptides in water: probing the substrate selectivity of a combinatorial receptor library

We have recently developed a new class of one-armed artificial receptors 1 for the binding of the polar tetrapeptide N-Ac-D-Glu-L-Lys-D-Ala-D-Ala-OH (EKAA) 2 in water using a combined combinatorial and statistical approach. We have now further probed the substrate selectivity of this receptor library 1 by screening a second tetrapeptide substrate (3) with the inverse sequence N-Ac-D-Ala-D-Ala-L-Lys-D-Glu-OH (AAKE). This "inverse" substrate is also efficiently bound by our receptors, with K(ass) approximately 6000 M(-1) for the best receptors, as determined both by a quantitative on-bead binding assay and by UV and fluorescence titration studies in free solution. Hence, the inverse tetrapeptide 3 is in general bound two to three times less efficiently than the "normal" peptide 2 (K(ass) approximately 17,000 M(-1)), even though the complexation mainly involves long-range electrostatic interactions and both the receptor and substrate are rather flexible. Molecular modeling and ab initio calculations have been used to rationalize the observed substrate selectivity and to analyze the various binding interactions within the complex.     

Achieving High Affinity and Selectivity for Asymmetric Dimethylarginine by Putting a Lid on a Box

The methylation states of Lys and Arg represent a particularly challenging set of targets to distinguish selectively in water using synthetic receptors. To date, trimethyllysine (Kme3) is the only post translational modification (PTM) of the eight possible methylation states of Lys and Arg that can be recognized selectively. Here, we report the first synthetic receptor capable of selectively recognizing asymmetric dimethylarginine (Rme2a). This was achieved by using a biased dynamic combinatorial chemistry (DCC) library to generate a receptor mimicking the 5‐sided box‐like shape of Rme2 reader proteins, a feature that has been hypothesized to impart selectivity. Additionally, we synthesized a thioether‐linked analogue of the resulting receptor to provide a novel scaffold with maintained selectivity but greater stability. This work introduces strategies that can be applied towards achieving selectivity based on subtle differences in hydrophilic guests in aqueous solutions.     

The first synthetic receptor for the RGD sequence

[structure: see text] The combination of an optimized arginine receptor unit with a semirigid linker carrying a strategically placed primary ammonium group leads to the first synthetic RGD receptor. It binds to the free RGD peptide as well as to cyclo(RGDfV) in water with association constants around 1000 M(-1). RGD mimetics such as benzamidine 6 are not recognized, rendering the new host a prototype of a new class of receptors selective for the true RGD sequence in peptides.     

Competitive Assay for Theophylline Based on an Abasic Site‐Containing DNA Duplex Aptamer and a Fluorescent Ligand

A fluorescence assay for theophylline, one of the common drugs for acute and chronic asthmatic conditions, has been developed based on an abasic site‐containing DNA duplex aptamer (AP aptamer) in combination with an abasic site‐binding fluorescent ligand, riboflavin. The assay is based on the competitive binding of theophylline and riboflavin at the abasic (AP) site of the AP aptamer. In the absence of theophylline, riboflavin binds to the receptor nucleotide opposite the AP site, which leads to fluorescence quenching of the riboflavin. Upon addition of theophylline, competitive binding occurs between theophylline and riboflavin, which results in an effective fluorescence restoration due to release of riboflavin from the AP site. From an examination of the optimization of the AP aptamers, the complex of riboflavin with a 23‐mer AP aptamer (5′‐TCT GCG TCC AGX GCA ACG CAC AC‐3′/5′‐GTG TGC GTT GCC CTG GAC GCA GA‐3′; X : the AP site (Spacer C3, a propylene residue)) possessing cytosine as a receptor nucleotide was found to show a selective and effective fluorescence response to theophylline; the limit of detection for theophylline was 1.1 μM . Furthermore, fluorescence detection of theophylline was successfully demonstrated with high selectivity in serum samples by using the optimized AP aptamer and riboflavin.     

Combined study of anion recognition by a carbazole-based neutral tripodal receptor in a competitive environment

Anion recognition studies have been carried out on a series of neutral synthetic receptors in which carbazole-2-carboxamide has been used as building block. Different ligands which include one to three carbazole units in their structure have been prepared. Binding experiments have been performed under competitive conditions in DMSO and DMSO-water solutions. The tripodal receptor offered a better host-guest association due to the synergistic effect of a well arranged set of hydrogen bonds. A selective response towards the biologically important pyrophosphate anion has been achieved. This selectivity is enhanced when studies are carried out with an increasing water content, which gets as high as 20% (v/v) in NMR experiments. The significance of this result lies in the use of a neutral receptor which exclusively interacts with the anionic guest through hydrogen bonding. The influence of multiple equilibria in the studied system has been analysed. Several techniques ((1)H NMR, (31)P NMR, mass spectrometry, diffusion-NMR, ITC, absorption and emission spectroscopy) have been employed to get a better understanding of the different processes taking place in solution for the evaluated receptors.     

Screening of 5-HT1A receptor antagonists using molecularly imprinted polymers

Molecular imprinting produces network polymers with recognition sites for imprint molecules. The high binding affinity and selectivity in conjunction with the polymers' physical robustness positions molecular imprinted polymers (MIPs) as candidates for use as preliminary screens in drug discovery. As such, MIPs can serve as crude mimics of native receptors. In an effort to evaluate the relationship between MIPs and native receptors, imprinted polymers for WAY-100635, an antagonist of the serotonin (5-HT) receptor subtype 5-HT1A were prepared. The resulting MIP P(WAY) was evaluated as an affinity matrix in the screening of serotonin receptor antagonists with known affinities for the native receptor. Rough correlations in affinity between the synthetic P(WAY) and native receptor 5-HT1A were found. These findings provide some support for the analogy between MIPs and native receptors and their possible use as surrogates.     

Stepwise molding of a highly selective ribonucleopeptide receptor

The structural characteristics of RNA-peptide (RNP) complexes are suitable for molding of a ligand-binding pocket of the RNP complex in a stepwise manner. The first step involves molding of the RNA subunit by in vitro selection of an RNP pool originating from an RNA library and the peptide, as previously reported for the construction of an ATP-binding RNP complex from an RRE RNA-Rev peptide complex. The second step involves selection from an RNP library consisting of Rev peptides with randomized amino acid residues and the RNA subunit selected in the first molding. The ATP-binding pocket produced by sequential molding of RNA and peptide subunits shows higher affinity to ATP and a distinct specificity for ATP versus dATP as compared to the ATP-binding RNP receptor in which only the RNA subunit has been molded. The second step selection from the peptide-based RNP library allows expansion of the ATP recognition surface, consisting of both RNA and peptide subunits, to enhance the affinity and selectivity to discriminate ATP against dATP. Our approach of stepwise molding offers the advantage of increasing the diversity of the RNP library by utilizing characteristics of different biopolymers. The ribonucleopeptide-based, multi-subunit approach is also extendable to other biomacromolecular assemblies, which may yield artificial receptors and enzymes with increased specificity and more diverse chemical activities.     

Mimicking receptor for methylmercury preconcentration based on ion-imprinting

Solid-phase extraction (SPE) based on molecularly imprinted polymers (MIPs) were used to develop selective separation and preconcentration for methylmercury ion from complex matrixes. In this study, an ion-imprinting polymer was prepared to make artificial organomercury lyase preorganizing three methacryloyl-(l)-cysteine methylester (MAC) monomers and one methylmercury ion in a three-coordinate form by template polymerization, with the goal preparing a solid-phase which has the high selectivity for methylmercury ions.Methylmercury-imprinted beads were produced by a dispersion polymerization technique with use methylmercury-methacryloyl-(l)-cysteine (MM-MAC) complex monomer and ethylene glycoldimethacrylate (EDMA). After removal of methylmercury ions, methylmercury-imprinted beads were used for solid-phase extraction and determination of mercury compounds. Methylmercury adsorption and selectivity studies of methylmercury versus other metal ions which Hg(II), Zn(II), Pb(II) and Cd(II) were reported and distribution and selectivity coefficients of these ions with respect to methylmercury were calculated here.ICP-OES and HPLC-DAD determinations of methylmercury and mercury ions in the certified reference, LUTS-1 from the National Research Council of Canada and synthetic sea water showed that the interfering matrix had been almost removed during preconcentration. The methylmercury-imprinted solid-phase as mimic receptor was good enough for methylmercury determination in complex matrixes.     

Molecular recognition of insulin by a synthetic receptor

The discovery of molecules that bind tightly and selectively to desired proteins continues to drive innovation at the interface of chemistry and biology. This paper describes the binding of human insulin by the synthetic receptor cucurbit[7]uril (Q7) in vitro. Isothermal titration calorimetry and fluorescence spectroscopy experiments show that Q7 binds to insulin with an equilibrium association constant of 1.5 × 10(6) M(-1) and with 50-100-fold selectivity versus proteins that are much larger but lack an N-terminal aromatic residue, and with >1000-fold selectivity versus an insulin variant lacking the N-terminal phenylalanine (Phe) residue. The crystal structure of the Q7·insulin complex shows that binding occurs at the N-terminal Phe residue and that the N-terminus unfolds to enable binding. These findings suggest that site-selective recognition is based on the properties inherent to a protein terminus, including the unique chemical epitope presented by the terminal residue and the greater freedom of the terminus to unfold, like the end of a ball of string, to accommodate binding. Insulin recognition was predicted accurately from studies on short peptides and exemplifies an approach to protein recognition by targeting the terminus.