Cooperative Metal-Coordination and Ion Pairing in Tripeptide Recognition

Mimicking Biological Recognition: Lessons in Binding Hydrophilic Guests in Water

Selective molecular recognition of hydrophilic guests in water plays a fundamental role in a vast number of biological processes, but synthetic mimicry of biomolecular recognition in water still proves challenging both in terms of achieving comparable affinities and selectivities. This Review highlights strategies that have been developed in the field of supramolecular chemistry to selectively and non-covalently bind three classes of biologically relevant molecules: nucleotides, carbohydrates, and amino acids. As several groups have systematically modified receptors for a specific guest, an evolutionary perspective is also provided in some cases. Trends in the most effective binding forces for each class are described, providing insight into selectivity and potential directions for future work.

Conformational selectivity and high-affinity binding in the complexation of N-phenyl amides in water by a phenyl extended calix[4]pyrrole

We report the synthesis of a tetrapyridinium phenyl extended calix[4]pyrrole receptor that shows high binding affinity and selectivity for the complexation of the cis-conformers of N-phenyl amides in water.

We describe the synthesis of a tetrapyridinium phenyl extended calix[4]pyrrole that is soluble in neutral water solution at mM concentrations. We show that, in pure water, the synthesized calix[4]pyrrole receptor selectively binds the cis-(E) conformers of secondary N-phenyl-amides and tertiary N-methyl-N-phenyl-formamide with binding affinities larger than 10³ M^–1. The conformational selectivity is remarkable owing to the energetic preference of amides to adopt the trans-(Z) conformation in solution. In this respect, we used two binding models for the mathematical analyses of the titration data and calculated apparent and intrinsic binding constants. The combined action of hydrogen bonding and the hydrophobic effect that operates in the binding of the amides in water is responsible for the large affinities displayed by the receptor.

Confined Flocculation of Ionic Pollutants by Poly(L-dopa)-Based Polyelectrolyte Complexes in Hydrogel Beads for Three-Dimensional, Quantitative, Efficient Water Decontamination

The development of simple and recyclable adsorbents with high adsorption capacity is a technical imperative for water treatment. In this work, we have successfully developed new adsorbents for the removal of ionic pollutants from water via encapsulation of polyelectrolyte complexes (PECs) made from positively charged poly(allylamine hydrochloride) (PAH) and negatively charged poly(l-3,4-dihydroxyphenylalanine) (PDopa), obtained via the self-polymerization of l-3,4-dihydroxyphenylalanine (l-Dopa). Given the outstanding mass transport through the hydrogel host matrixes, the PDopa-PAH PEC guests loaded inside can effectively and efficiently remove various ionic pollutants, including heavy metal ions and ionic organic dyes, from water. The adsorption efficiency of the PDopa-PAH PECs can be quantitatively correlated to and tailored by the PDopa-to-PAH molar ratio. Because PDopa embodies one catechol group, one carboxyl group, and one amino group in each repeating unit, the resulting PDopa-PAH PECs exhibit the largest capacity of adsorption of heavy metal ions compared to available adsorbents. Because both PDopa and PAH are pH-sensitive, the PDopa-PAH PEC-loaded agarose hydrogel beads can be easily and completely recovered after the adsorption of ionic pollutants by adjusting the pH of the surrounding media. The present strategy is similar to the conventional process of using PECs to flocculate ionic pollutants from water, while in our system flocculation is confined to the agarose hydrogel beads, thus allowing easy separation of the resulting adsorbents from water.

A multiple multicomponent approach to chimeric peptide-peptoid podands

The success of multi-armed, peptide-based receptors in supramolecular chemistry traditionally is not only based on the sequence but equally on an appropriate positioning of various peptidic chains to create a multivalent array of binding elements. As a faster, more versatile and alternative access toward (pseudo)peptidic receptors, a new approach based on multiple Ugi four-component reactions (Ugi-4CR) is proposed as a means of simultaneously incorporating several binding and catalytic elements into organizing scaffolds. By employing α-amino acids either as the amino or acid components of the Ugi-4CRs, this multiple multicomponent process allows for the one-pot assembly of podands bearing chimeric peptide-peptoid chains as appended arms. Tripodal, bowl-shaped, and concave polyfunctional skeletons are employed as topologically varied platforms for positioning the multiple peptidic chains formed by Ugi-4CRs. In a similar approach, steroidal building blocks with several axially-oriented isocyano groups are synthesized and utilized to align the chimeric chains with conformational constrains, thus providing an alternative to the classical peptido-steroidal receptors. The branched and hybrid peptide-peptoid appendages allow new possibilities for both rational design and combinatorial production of synthetic receptors. The concept is also expandable to other multicomponent reactions.

Molecular recognition of organic ammonium ions in solution using synthetic receptors

Ammonium ions are ubiquitous in chemistry and molecular biology. Considerable efforts have been undertaken to develop synthetic receptors for their selective molecular recognition. The type of host compounds for organic ammonium ion binding span a wide range from crown ethers to calixarenes to metal complexes. Typical intermolecular interactions are hydrogen bonds, electrostatic and cation-π interactions, hydrophobic interactions or reversible covalent bond formation. In this review we discuss the different classes of synthetic receptors for organic ammonium ion recognition and illustrate the scope and limitations of each class with selected examples from the recent literature. The molecular recognition of ammonium ions in amino acids is included and the enantioselective binding of chiral ammonium ions by synthetic receptors is also covered. In our conclusion we compare the strengths and weaknesses of the different types of ammonium ion receptors which may help to select the best approach for specific applications.

Remote control of bipyridine-metal coordination within a peptide dendrimer

The metal coordinating ability of a bipyridine ligand at the core of a peptide dendrimer was found to be controlled by the nature of amino acids placed at the dendrimer periphery, with coordination being promoted by anionic residues and inhibited by cationic residues; heterotrimers with mixed charges were preferentially formed.

Recognition of the helix-loop-helix domain of the Id proteins by an artificial luminescent metal complex receptor

Synthetic agents specifically interacting with a protein interface are important not only for the better understanding of protein dimer or complex formation but also for medical applications. Here we describe the recognition of the helix-loop-helix (HLH) dimerization domain of the Id proteins by an artificial luminescent receptor containing two binding sites for a Lewis acid and a Lewis base, respectively. The Id proteins are inhibitors of bHLH transcription factors and play key roles during development of cancer. We show that a receptor/Id-HLH-domain complex was formed cooperatively (K(0.5) approximately 2 microM under physiological conditions) and with moderate specificity, as compared to the related MyoD and Max HLH domains. Accordingly, a preferred receptor binding motif, CYSR(K), was identified within the Id HLH domains. These results are promising and may be exploited to design highly selective synthetic receptors for the Id HLH domain.

Extended Calix[4]arene-Based Receptors for Molecular Recognition and Sensing

Recent advances in the area of recognition and sensing have shown that artificial receptors derived from extended calix[4]arenes bearing multiple π-conjugated fluorophoric or chromophoric systems have found useful to enhance binding affinity, selectivity and sensitivity for recognition and sensing of a targeted ion or molecule. A comprehensive review of various π-conjugation-extended calyx[4]arene-based receptors with the highlight on the design and binding characterization for recognition and sensing is presented.

Sequence recognition and self-sorting of a dipeptide by cucurbit[6]uril and cucurbit[7]uril

Cucurbit[7]uril forms very strong complex with zwitterionic dipeptide Phe-Gly with affinity exceeding 10(7) M(-1) and effectively recognizes peptide sequence of Phe-Gly over Gly-Phe as well as Tyr-Gly over Gly-Tyr and Trp-Gly over Gly-Trp with relative affinities of 23 000, 18 000 and 2000, respectively.

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.

Phenyl-calix[4]arene-Based Fluorescent Sensors: Cooperative Binding for Carboxylates

Tetrakis-(4-carbamoylphenyl)-substituted and tetrakis-(4-amidophenyl)-substituted calix[4]arenes as well as the monomeric biphenylcarbamate have been synthesized as fluorescent receptors for anion sensing. Their binding properties with various anions including F-, CH3COO-, Ph-COO-, and H2PO4- were investigated by fluorescence titrations, Job plot experiments, 1H NMR spectroscopies, and ESI-MS measurements. Importantly, we have found that calix[4]arene-based sensors exhibit greatly enhanced binding affinity and selectivity toward carboxylates. The binding associations of tetrakis-(4-carbamoylphenyl)-substituted calix[4]arene for carboxylates are 1-2 orders of magnitude greater than those of the monomeric biphenylcarbamate sensor. Such an enhancement in the binding affinity and selectivity is attributed to the cooperative binding of the multiple ligating groups as revealed from the ab inito DFT calculations. Although tetrakis-(4-amidophenyl)-substituted calix[4]arene exhibited relatively weaker binding affinity toward anions, its superior binding selectivity for acetate ion over fluoride ion is evident. Our results also suggest that carbamate functionality is a useful H-bond donor for hydrogen-bonding interactions in molecular recognition and supramolecular chemistry.

Supramolecular Analytical Chemistry

A large fraction of the field of supramolecular chemistry has focused in previous decades upon the study and use of synthetic receptors as a means of mimicking natural receptors. Recently, the demand for synthetic receptors is rapidly increasing within the analytical sciences. These classes of receptors are finding uses in simple indicator chemistry, cellular imaging, and enantiomeric excess analysis, while also being involved in various truly practical assays of bodily fluids. Moreover, one of the most promising areas for the use of synthetic receptors is in the arena of differential sensing. Although many synthetic receptors have been shown to yield exquisite selectivities, in general, this class of receptor suffers from cross-reactivities. Yet, cross-reactivity is an attribute that is crucial to the success of differential sensing schemes. Therefore, both selective and nonselective synthetic receptors are finding uses in analytical applications. Hence, a field of chemistry that herein is entitled "Supramolecular Analytical Chemistry" is emerging, and is predicted to undergo increasingly rapid growth in the near future.

Carboxylate binding in polar solvents using pyridylguanidinium salts

A series of thiourea and guanidinium derivatives have been prepared and their ability to bind a carboxylate group has been investigated. Guanidinium 33, featuring two additional amides and a pyridine moiety, proved to be the most potent carboxylate binding site and was able to bind acetate in aqueous solvent systems (K(ass) = 480 M(-1) in 30% H(2)O-DMSO). The pyridine moiety is critical to obtaining strong binding, and comparison with the binding properties of analogous compounds in which the pyridine is replaced by a benzene ring provides a striking example of enthalpy-entropy compensation.

Sequence-Dependent Binding of Dipeptides by an Artificial Receptor in Water

An artificial dipeptide receptor (1) was designed and observed to bind the deprotonated dipeptide Ac-D-Ala-D-Ala-OH in buffered water with K = 33,100 M(-1), whereas other dipeptides such as Ac-Gly-Gly-OH or Ac-D-Val-D-Val-OH were bound less efficiently, by factors of more than 10 (K < 3000 M(-1)). The efficient binding and the pronounced sequence selectivity are the result of a combination of strong electrostatic contacts and size-discriminating hydrophobic interactions. To provide such a combination, a guanidiniocarbonylpyrrole cation was attached to a novel cyclotribenzylene-substituted alanine derivative 5, to provide a hydrophobic bowl-shaped cavity just large enough to bind a methyl group but not any larger alkyl chains, thus causing the receptor to prefer alanine to valine. We describe the synthesis of 1 and the evaluation of its complexation properties in UV and fluorescence titration studies.

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.

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.

A Differential Array of Metalated Synthetic Receptors for the Analysis of Tripeptide Mixtures

A novel library of resin-bound receptors within a cross-reactive differential array for the identification and discrimination of tripeptides and tripeptide mixtures is reported. Pattern recognition using principal component analysis showed complete discrimination of four similar tripeptides and three tripeptide mixtures. The library is comprised of a Cu(II)-centered core with two proximally appended tripeptide arms emanating outward. One tripeptide arm was prepared using combinatorial chemistry to generate the differential nature of the library. Thirty resin-bound receptors were randomly selected from the library and placed within a silicon microchip array that included integrated microfluidics elements, and an indicator-uptake assay was used for colorimetric signaling. The indicator Orange G yielded an accurate measure of the degree of association between receptors and analytes as determined by kinetic analysis of the indicator-uptake assays. Within this paper we detail the method used for differential sensing using a novel receptor library. This work further demonstrates the power and utility of a differential array of synthetic receptors for identification and discrimination of complex bioanalytes.