Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors

To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.     

Binary and ternary phenylboronic acid complexes with saccharides and Lewis bases

Cumulative formation constants for the association of three boronic acids (phenylboronic acid and its ortho-anilinomethyl and ortho-benzylaminomethyl derivatives) with four saccharides (fructose, glucose, mannitol, and sorbitol) were determined by potentiometric titration. Similarly, the constants for the formation binary complexes of the three boronic acids with (hydrogen) phosphate, (hydrogen) citrate, or imidazole were determined. Finally, the formation of ternary complexes of the boronic acids, phosphate, citrate or imidazole, and the saccharides were determined based on the determined values of the binary complexes. The previously unrecognized ternary complexes are significant in all systems investigated, and under some solution compositions, they can be the dominant species in solution over a wide pH range. A value of 15-25 kJ mol⁻¹ was determined for the energy of the B-N interaction in the benzylmethyl derivative based on the relative stabilities of the ternary phosphate complexes of the three boronic acids. The data are used to rationalize the medium dependence of stepwise formation constants and the apparent acidity constants of previous literature reports.     

Probing Hydrogen Bonding to Bound Dioxygen in Synthetic Models for Heme Proteins: The Importance of Precise Geometry

Distal hydrogen bonding in natural dioxygen binding proteins is crucial for the discrimination between different potential ligands such as O₂ or CO. In the present study, we probe the chemical requirements for proper distal hydrogen bonding in a series of synthetic model compounds for dioxygen‐binding heme proteins. The model compounds 1‐Co to 7‐Co bear different distal residues. The hydrogen bonding in their corresponding dioxygen adducts is directly measured by pulse EPR spectroscopy. The geometrical requirements for this interaction to take place were found to be narrow and very specific. Only two model complexes, 1‐Co and 7‐Co , form a hydrogen bond to bound dioxygen, which was characterized in terms of geometry and nature of the bond. The geometry and dipolar nature of this interaction in 1‐Co ‐O₂ is more similar to the one in natural cobalt myoglobin (Co‐Mb), making 1‐Co the best model compound in the entire series.     

Polymers for Anion Recognition and Sensing

In biological systems, the selective and high‐affinity recognition of anionic species is accomplished by macromolecular hosts (anion‐binding proteins) that have been “optimized” through evolution. Surprisingly, it is only recently that chemists have systematically attempted to develop anion‐responsive synthetic macromolecules for potential applications in medicine, national security, or environmental monitoring. Recent results indicating that unique features of polymeric systems such as signal amplification, multivalency, and cooperative behavior may be exploited productively in the context of anion recognition and sensing are documented. The wide variety of interactions—including Lewis acid/base, ion‐pairing, and hydrogen bonding—that have been employed for this purpose is reflected in the structural diversity of anion‐responsive macromolecules identified to date.     

Synthetic Receptors Based on Abiotic Cyclo(pseudo)peptides

Work on the use of cyclic peptides or pseudopeptides as synthetic receptors started even before the field of supramolecular chemistry was firmly established. Research initially focused on the development of synthetic ionophores and involved the use of macrocycles with a repeating sequence of subunits along the ring to facilitate the correlation between structure, conformation, and binding properties. Later, nonnatural amino acids as building blocks were also considered. With growing research in this area, cyclopeptides and related macrocycles developed into an important and structurally diverse receptor family. This review provides an overview of these developments, starting from the early years. The presented systems are classified according to characteristic structural elements present along the ring. Wherever possible, structural aspects are correlated with binding properties to illustrate how natural or nonnatural amino acids affect binding properties.     

Mercury binding by ferrocenoyl peptides with sulfur-containing side chains: Electrochemical, spectroscopic and structural studies

Ferrocenoyl peptides incorporating amino acids derived from either l-methionine, l-cysteine or dl-homocysteine have been synthesised and investigated as agents for heavy metal binding and detection. Heavy metal-peptide interactions have been characterised using cyclic voltammetry to follow changes in the potential of the Fe(II)/Fe(III) redox couple, revealing that these systems interact with mercury(II) ions more strongly than with other thiophilic heavy metals such as cadmium(II), silver(I) and lead(II). Proton NMR experiments have demonstrated 1:1 peptide:mercury binding and enabled quantitative characterisation of this binding interaction. Crystal structures for two of these ferrocenoyl peptide derivatives have been elucidated, revealing that these compounds adopt a P-1,3′ open solid state conformation in the absence of mercury; this arrangement precludes intramolecular hydrogen bonding between chains, while extensive intermolecular hydrogen bonding is evident. The particular affinity of these systems for mercury(II) opens the possibility of incorporating them in new, biologically inspired sensors for detecting this toxic pollutant.     

氢键识别超分子聚合物的新进展

近年来,由于氢键作用对聚合物的热力学性质、微观自组装、结晶及液晶行为的重要影响,氢键识别在超分子聚合物的分子设计与结构控制方面的应用受到广泛关注。本文系统介绍了氢键识别体系的类型与性质,以及分子结构、分子内氢键对氢键识别强度的影响,讨论了羧酸与吡啶间氢键识别体系、与核苷相关的氢键识别体系以及四重氢键识别体系在超分子聚合物中的最新应用,主要介绍了氢键识别超分子聚合物的合成、结构、性质及功能。     

Hydrogen‐Bond‐Mediated Asymmetric Catalysis

The utilization of hydrogen bonding as an activation force has become a powerful tool in asymmetric organocatalysis. Significant advances have been made in the recent past in this emerging field. Due to space constraints, this Focus Review summarizes only the key aspects with an emphasis on catalysis based on chiral ureas and thioureas, diols, and phosphoric acids. The examples provided neatly demonstrate that chiral ureas and thioureas, diols, and phosphoric acids display effective and unique activation modes of catalysis for a broad spectrum of asymmetric organic transformations, including single‐step and multiple‐step cascade reactions. These functionalities, which have the ability to afford efficient H‐bond activation of electrophiles including C?O, C?N, aziridines, and epoxides, have established their status as “privileged” functional groups in the design of organocatalysts.     

Crystal structure of 1:1 Complexes between urea and two crown ether derivatives of phthalic acid, 2,3,5,6,8,9,11,12,14,15-decahydrobenzo[1,4,7,10,13,16]hexaoxacyclo-octadecin-18,19-dicarboxylic acid (i) and 2,3,5,6,8,9,11,12-octahydro-benzo[1,4,7,10,13]pentaoxacyclopentadecin-15,16-dicarboxylic acid (II)

The crystal structures of the titlke compounds have been determined by X-ray diffraction. Urea, I crystallizes in the triclinic PI space group with cell dimensions a = 8.336(2), b = 11.009(2), c = 13.313(2) Å, α = 105.55(3), β = 103.62(3), γ = 104.63(3)° and Z = 2 final R value 0.072 for 2105 observations. Urea, II crystallizes in the orthorhombic P2₁2₁2₁ space group with cell dimensions a = 8.750(2), b = 10.844(3) and c = 21.215(3) Å and Z = 4, final R value 0.083 for 599 observations. All the hydrogen atoms were located in the complex urea, I ; urea molecules form hydrogen bonded dimers about centers of symmetry, these dimers are sandwiched between macrocyclic rings forming one simple and one bifurcated hydrogen bond from the “endo” hydrogen atoms to the ether oxygen atoms. These units are held by hydrogen bonding between the urea molecules and carboxylic acids in two other units; these hydrogen bonds are cyclic involving eight atoms -(N-H(exo)…O(keto)-C-O-H…O(urea)-C)-. Only one carboxylic acid group per molecule takes part in these hydrogen bonds, the other forms a short, 2.490(7) Å, internal bond to the acceptor keto oxygen atom. N(H)…O bonds range from 2.930(7) to 3.206(7) Å, O(H)…O is 2.475(6) Å. In the complex urea, II each urea is hydrogen bonded to three different host molecules and vice versa; the urea “endo” hydrogen atoms bond to the ether oxygen atoms, while both “exo” hydrogen atoms take part in cyclic hydrogen bonds to carboxylic acids. There is not internal hydrogen bond. N(H)…O bonds range from 2.83 to 3.26(2) A and the O-…O bonds are 2.55 and 2.56(2) Å.     

A comparison of the structure and bonding in the aliphatic boronic R–B(OH)<Subscript>2</Subscript> and borinic R–BH(OH) acids (R=H; NH<Subscript>2</Subscript>, OH,and F): a computational investigation

Boronic acids, R–B(OH)₂, play an important role in synthetic, biological, medicinal, and materials chemistry. This investigation compares the structure and bonding surrounding the boron atoms in the simple aliphatic boronic acids, R–B(OH)₂ (R=H; NH₂, OH, and F), and the analogous borinic acids, R–BH(OH). Geometry optimizations were performed using second-order Møller–Plesset perturbation theory (MP2) with the Dunning–Woon aug-cc-pVTZ, aug-cc-pVQZ, and aug-cc-pV5Z basis sets; single-point CCSD(FC)/aug-cc-pVTZ//MP2(FC)/aug-cc-pVTZ level calculations were used to generate a QCI density for natural bond orbital analyses of the bonding. The optimized boron–oxygen bond lengths for the X–B–O_t–H trans-branch of the endo-exo form of the boronic acids and for the X–B–O–H cis-branch of the boronic and borinic acids (X=N, O, and F, respectively) decrease as the electronegativity of X increases. The boron–oxygen bond lengths are generally longer in the endo-exo or anti forms of the boronic acids than in the corresponding borinic acids. NBO analyses suggest the boron–oxygen bond in H₂BOH is a double bond; the boron–oxygen bonding in the remaining boronic and borinic acids in this study has a significant contribution from dative pπ–pπ bonding. Values for Δ\({\text{H}}_{298}^{0}\) for the highly balanced reaction, R–B(OH)₂ + R–BH₂ → 2 R–BH(OH), suggest that the bonding surrounding the boron atom is stronger in the borinic acid than in the corresponding boronic acid.     

Isolable Chiral Aggregates of Achiral π‐Conjugated Carboxylic Acids

The induced aggregation of achiral building blocks by a chiral species to form chiral aggregates with memorized chirality has been observed for a number of systems. However, chiral memory in isolated aggregates of achiral building blocks remains rare. One possible reason for this discrepancy could be that not much is understood in terms of designing these chiral aggregates. Herein, we report a strategy for creating such isolable chiral aggregates from achiral building blocks that retain chiral memory after the facile physical removal of the chiral templates. This strategy was used for the isolation of chiral homoaggregates of neutral achiral π‐conjugated carboxylic acids in pure aqueous solution. Under what we have termed an “interaction–substitution” mechanism, we generated chiral homoaggregates of a variety of π‐conjugated carboxylic acids by using carboxymethyl cellulose (CMC) as a mediator in acidic aqueous solutions. These aggregates were subsequently isolated from the CMC templates whilst retaining their memorized supramolecular chirality. Circular dichroism (CD) spectra of the aggregates formed in the acidic CMC solution exhibited bisignated exciton‐coupled signals of various signs and intensities that were maintained in the isolated pure homoaggregates of the achiral π‐conjugated carboxylic acids. The memory of the supramolecular chirality in the isolated aggregates was ascribed to the substitution of COOH/COOH hydrogen‐bonding interaction between the carboxylic acid groups within the aggregates for the hydrogen‐bonding interactions between the COOH groups of the building blocks and the chiral templates. We expect that this “interaction–substitution” procedure will open up a new route to isolable pure chiral aggregates from achiral species.     

Thermodynamic analysis of receptors based on guanidinium/boronic acid groups for the complexation of carboxylates, alpha-hydroxycarboxylates, and diols: driving force for binding and cooperativity

The thermodynamics of guanidinium and boronic acid interactions with carboxylates, alpha-hydroxycarboxylates, and diols were studied by determination of the binding constants of a variety of different guests to four different hosts (7-10). Each host contains a different combination of guanidinium groups and boronic acids. The guests included molecules with carboxylate and/or diol moieties, such as citrate, tartrate, and fructose, among others. The Gibbs free energies of binding were determined by UV/Vis absorption spectroscopy, by use of indicator displacement assays. The receptor based on three guanidinium groups (7) was selective for the tricarboxylate guest. The receptors that incorporated boronic acids (8-10) had higher affinities for guests that included alpha-hydroxycarboxylate and catechol moieties over guests containing only carboxylates or alkanediols. Isothermal titration calorimetry revealed the enthalpic and entropic contributions to the Gibbs free energies of binding. The binding of citrate and tartrate was investigated with hosts 7-10, for which all the binding events were exothermic, with positive entropy. Because of the selectivity of hosts 8-10, a simple boronic acid (14) was also investigated and determined to be selective for alpha-hydroxycarboxylates and catechols over amino acids and alkanediols. Further, the cooperativity of 8 and 9 in binding tartrate was also investigated, revealing little or no cooperativity with 8, but negative cooperativity with 9. A linear entropy/enthalpy compensation relationship for all the hosts 7-10, 14, and the carboxylate-/diol-containing guests was also obtained. This relationship indicates that increasing enthalpy of binding is offset by similar losses in entropy for molecular recognition involving guanidinium and boronic acid groups.     

The relationship among pKa, pH, and binding constants in the interactions between boronic acids and diols—it is not as simple as it appears

In our continuing efforts into designing boronic acid-based sensors that recognize cell-surface carbohydrates, it has been necessary to examine various factors that affect the binding affinity between a boronic acid moiety and a diol. The current prevailing view is that the strongest boronic acid/diol complexes are generated by a combination of high solution pH and a low boronic acid pK_a. However, there has never been a systematic examination of the relationship among the binding constants, boronic acid pK_a, and the pH of the solution. Herein we report our findings with a series of 25 arylboronic acids with various substituents and their binding affinities with diols. We have found that (1) the relationship between the pK_a of monosubstituted phenylboronic acid and its substituents can be described using a Hammet plot; (2) the optimal pH for binding is not always above the pK_a of the boronic acid, and is affected by the pK_a values of the boronic acid and the diol, and other unknown factors; and (3) the general belief that boronic acids with lower pK_a values show greater binding affinities for diols is not always true.     

Dopamine selective molecularly imprinted polymers via post-imprinting modification

A novel synthetic dopamine receptor bearing bidentate binding sites were prepared by covalent imprinting using a disulfide linkage which is cleaved and oxidized to a non-covalent sulfoxide recognition group. The used templates have dopamine-like structures connected to an allyl moiety via a disulfide and to a 4-vinylphenyl group via a cyclic boronic diester. After the polymerization, the ester bonds were hydrolyzed and the disulfide bond was reduced to remove the template moiety from the polymer matrix, followed by the oxidation to transform the thiol residues into sulfonic acid (post imprinted process). The imprinted polymer adsorbed dopamine selectively in aqueous solution with the two-point interaction, i.e. the formation of cyclic boronic diester and electrostatic interaction with the sulfonic acid residue.     

Synergistic effect between metal coordination and hydrogen bonding in phosphate and halide recognition

The equilibrium constant for binding of dimethyl phosphate to a Co(III) complex in water increases from 6.2 to 210 M-1 upon addition of a single hydrogen bond between the bound phosphate and the metal complex. Crystal structure reveals that the hydrogen bond distance is 1.96 A. The synergistic effect between metal coordination and hydrogen bonding can also be observed for fluoride binding but not for bromide binding.     

Synthesis, evaluation, and computational studies of naphthalimide-based long-wavelength fluorescent boronic Acid reporters

Boronic acids that change fluorescence properties upon sugar binding are very useful for the synthesis of carbohydrate sensors. Along this line, boronic acids that fluoresce beyond 500 nm are especially useful. A series of boronic acid fluorescent reporter compounds based on the 4-amino-1,8-naphthalimide structure have been synthesized (1a-d) and evaluated under near physiological conditions. These compounds showed good water solubility and significant changes in fluorescence properties after binding with sugars, with the emission wavelength being at around 570 nm. Analogues in this series with different substitutions showed similar properties. We have also examined the mechanism of the observed fluorescence changes for these compounds.     

Asymmetric catalysis by chiral hydrogen-bond donors

Hydrogen bonding is responsible for the structure of much of the world around us. The unusual and complex properties of bulk water, the ability of proteins to fold into stable three-dimensional structures, the fidelity of DNA base pairing, and the binding of ligands to receptors are among the manifestations of this ubiquitous noncovalent interaction. In addition to its primacy as a structural determinant, hydrogen bonding plays a crucial functional role in catalysis. Hydrogen bonding to an electrophile serves to decrease the electron density of this species, activating it toward nucleophilic attack. This principle is employed frequently by Nature's catalysts, enzymes, for the acceleration of a wide range of chemical processes. Recently, organic chemists have begun to appreciate the tremendous potential offered by hydrogen bonding as a mechanism for electrophile activation in small-molecule, synthetic catalyst systems. In particular, chiral hydrogen-bond donors have emerged as a broadly applicable class of catalysts for enantioselective synthesis. This review documents these advances, emphasizing the structural and mechanistic features that contribute to high enantioselectivity in hydrogen-bond-mediated catalytic processes.     

Two closely related {4‐[(N‐substituted amino)(diethoxyphosphoryl)methyl]phenyl}boronic acids

Organic phosphonic acids and organic phosphonic acid esters have been of much interest due to their applications in the fields of medicine, agriculture and industrial chemistry. Boronic acids can act as synthetic intermediates and building blocks and are used in sensing, protein manipulation, therapeutics, biological labelling and separation. The additional introduction of an aminophosphonic acid group into a boronic acid may give new opportunities for application. To study the structure of such multifunctional compounds, we prepared two new derivatives which can be easily converted to the corresponding phosphonic acids. In the title compounds, {4‐[(butylamino)(diethoxyphosphoryl)methyl]phenyl}boronic acid monohydrate, C₁₅H₂₇BNO₅P·H₂O, (I), and {4‐[(diethoxyphosphoryl)(4‐nitroanilino)methyl]phenyl}boronic acid, C₁₇H₂₂BN₂O₇P, (II), three different substituents are attached to a central C—H group, namely 4‐boronophenyl, diethoxyphosphoryl and amine. Compound (I) crystallizes as a monohydrate and O_B—H…N hydrogen bonds link neighbouring molecules into chains along the [001] direction. The solvent water molecule connects two such chains running in opposite directions. Compound (II) crystallizes as an ansolvate and classical hydrogen bonds result in a layer structure in the (001) plane.     

Chemistry and Biology of the Zaragozic Acids (Squalestatins)

New natural products seldom arouse much excitement. However, with their unprecedented and heavily oxygenated molecular structure, and potentially lucrative biological activity, the zaragozic acids (squalestatins) provoked a flurry of activity among academic and industrial chemists and biologists in the early 1990s. Since they are powerful inhibitors of squalene synthase, the enzyme catalyzing the first committed step on the biosynthetic pathway to cholesterol, hopes were high that the zaragozic acids would follow the huge commercial success of the mevinic acids by becoming second-generation cholesterol-lowering drugs. The unusual and characteristic 2,8-dioxabicyclo[3.2.1]octane-3,4,5-tricarboxylic acid “core” structure of the zaragozic acids stimulated a large number of diverse synthetic studies, ranging from the traditional to the avant garde. In this review we attempt to bring together for the first time the chemistry and biology of this fascinating class of molecules.