Supramolecular multivalency effects enhance imine formation in aqueous medium allowing for dynamic modification of enzymatic activity

Imine formation under physiological conditions represents a challenging reaction due to the strong propensity of aldimines to be hydrolyzed. Herein we disclose the remarkable effect of supramolecular multivalency on increasing imine stability. A family of reactive aldehydes was synthesized bearing supramolecularly-active sites within their structure. The imine formation activity for such aldehydes was evaluated and compared with model aldehydes. The reaction of the best-performing species - containing two carboxylate groups-with a set of amines showed a significant decrease in imine yields as the degree of supramolecular multivalency between sidechains decreased. The reversible conjugation of amino acid derivatives and small peptides was also assayed, with excellent selectivities for the imine formation at the Nα position even in substrates containing competing sites. Preliminary results on protein bioconjugation revealed that a model enzyme could be dynamically inhibited upon reaction with the aldehyde, with its native activity being recovered by displacing the imine bonds with a suitable chemical effector (i.e., acylhydrazide).

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.

Regio- and stereoselective synthesis of spiropyrrolidine-oxindole and bis-spiropyrrolizidine-oxindole grafted macrocycles through [3 + 2] cycloaddition of azomethine ylides

A convenient and efficient method for the regioselective macrocyclization of triazole bridged spiropyrrolidine-oxindole, and bis-spiropyrrolizidine-oxindole derivatives was accomplished through intra and self-intermolecular [3 + 2] cycloaddition of azomethine ylides. The chalcone isatin precursors 9a-i required for the click reaction were obtained from the reaction of N-alkylazidoisatin 4 and propargyloxy chalcone 8a-i which in turn were obtained by the aldol condensation of propargyloxy salicylaldehyde 6 and substituted methyl ketones 7a-i. The regio- and stereochemical outcome of the cycloadducts were assigned based on 2D NMR and confirmed by single crystal XRD analysis. High efficiency, mild reaction conditions, high regio- and stereoselectivity, atom economy and operational simplicity are the exemplary advantages of the employed macrocyclization procedure.

Mixed Macrocycles Derived from 2,6-Diformylpyridine and Opposite Enantiomers of trans-1,2-Diaminocyclopentane and trans-1,2-Diaminocyclohexane

The condensation reaction of 2,6-diformylpyridine with an equimolar mixture of opposite enantiomers of trans-1,2-diaminocyclopentane and trans-1,2-diaminocyclohexane using a dynamic combinatorial chemistry approach has been examined. In nonmetal-templated reactions, depending on reaction conditions, mixed 2 + 1 + 1 macrocyclic imine or bigger mixed 4 + 2 + 2 imine macrocycle are formed selectively. The 2 + 1 + 1 imine used as a precursor in the templated by Cd^II ions produces a library of enlarged chiral mixed imines coordinated with metal cations among which the hexanuclear Cd^II complex of 6 + 3 + 3 imine was isolated and characterized. All macrocyclic imine compounds have been reduced to the corresponding macrocyclic amines, which have been further transformed into their hydrochlorides. Each macrocyclic compound has been obtained as two enantiomers. For imine macrocycles and for the hydrochloride derivatives of macrocyclic amines, their X-ray crystal structures have been determined. In particular, the crystals of protonated 4 + 2 + 2 macrocyclic amine, which contains two types of diastereomeric cations differing in terms of inverted twists of pyridine moieties, and hexanuclear Cd^II complex of 6 + 3 + 3 imine, which gives a deeper insight into the expansion reaction, have been investigated. A heterochiral self-sorting of 2 + 2 and 2 + 1 + 1 macrocyclic imines has been confirmed by a competition reaction of 2,6-diformylpyridine, racemic trans-1,2-diaminocyclopentane, and racemic trans-1,2-diaminocyclohexane and theoretical calculations.

The role of the side chain in the conformational and self-assembly patterns of C2-symmetric Val and Phe pseudopeptidic derivatives

Side chain as the main conformational and self-assembly structural factor for C₂-pseudopeptides.

Supramolecularly assisted synthesis of chiral tripodal imidazolium compounds

Supramolecular interactions based on amide groups direct the preferential formation of tritopic instead of monotopic or ditopic imidazolium compounds.

Oligocarboxylates as useful templates in dynamic combinatorial chemistry

Dynamic combinatorial chemistry deals with systems (libraries) of multiple compounds formed by reversible reactions. Interactions of all library components with introduced template molecule are reflected in modification of library composition and are analysed simultaneously. In our studies we investigated a single-substrate dynamic combinatorial library of macrocycles, based on dipicolinic acid diamide, with disulphide bond exchange as the reversible reaction. The library components equipped with hydrogen bond donors interact with anionic guests – carboxylates which act as templates inducing amplification of selected library members. We proved that quantitative analysis of interactions with templates is possible, which led us to a novel method of analysis of association constants of static receptors introduced to the system. With a large set of carboxylates differing in number of anionic groups, size, shape, and flexibility of the linker, we proved that the library is very sensitive to structural parameters of the template. We also showed that with mediation of a photoswitchable azobenzene-based template it is possible to change the library composition by light stimulus. Similarly, with mediation of EDTA the library is sensitive to introduction of metal cations.

Cu2+ recognition by N,N'-benzylated bis(amino amides)

Two new C₂-symmetric N,N'-benzylated bis(amino amides) have been synthesised and their interaction with different transition metals studied using a variety of techniques including UV-Vis and CD spectroscopy or ESI-MS. The determination of the corresponding stability constants with Cu²⁺ has been possible, in H₂O/CH₃CN 7/3 v/v, for one of these ligands (4) using potentiometric titrations. The results obtained reveal that N-benzylation affords significant changes to their properties and is accompanied by an appreciable decrease in the corresponding complexation stability constants. However, this, along with the low kinetics associated to Ni²⁺, facilitates the recognition of Cu²⁺ by 4 that can be followed by the naked-eye up to the submillimolar range. Very interestingly, the chiral nature of this ligand provides an intense and well defined CD curve for the corresponding Cu²⁺ complex, very sensitive to the coordination geometry, facilitating the analysis of this interaction even at the μM range. The formation by both ligands (3 and 4) of square planar complexes with Cu²⁺ and Ni²⁺ displaying a 1 : 1 stoichiometry was confirmed by their X-ray crystal structures.

Entropy-driven homochiral self-sorting of a dynamic library

The efficient homochiral self-sorting of pseudopeptidic macrocycles, observed from a simple dynamic library, is driven by entropy.

From simplicity to complex systems with bioinspired pseudopeptides

This feature article highlights some of the recent advances in creating complexity from simple pseudopeptidic molecules. The bioinspired approaches discussed here allowed an increase in the structural, chemical and interactional complexity (see figure).

Bisferrocenyl-functionalized pseudopeptides: access to separated ionic and electronic contributions for electrochemical anion sensing

Pseudopeptidic receptors containing ferrocene fragments have been prepared and their response to a series of anions was measured by a voltammetry of microparticles methodology.

A General Method for Synthesis of Unclosed Cryptands via H-Bond Templated Macrocyclization and Subsequent Mild Postfunctionalization

A practical four-step synthesis of a model 26-membered N-Boc-protected macrocycle, starting from commercially available and inexpensive materials, is reported. The crucial macrocyclization step does not require high-dilution conditions and is completed in a short time (8 h). The high yield of macrocyclization (61%) is achieved owing to templation by intramolecular H-bonds and a chloride anion, which both help to adopt a favorable folded conformation of the open-chain intermediate. Finally, mild, selective, and efficient incorporation of intraannular amide function leading to five diversely functionalized unclosed cryptands (UCs) is described.

Synthesis of Spiroligomer-Containing Macrocycles

We demonstrate the synthesis and characterization of the solution conformations of a collection of functionalized spiroligomer-based macrocycles. These macrocycles contain 14 independently controllable stereocenters and four independently controllable functional groups on a highly preorganized scaffold. These molecules are being developed to display complex, preorganized surfaces for binding proteins and to create enzyme-like active sites. In this work, we demonstrate the convergent synthetic approach to this new class of macrocycles and demonstrate that the conformational properties of these molecules can be changed by altering the configuration stereocenters within the backbone.

Introducing a static receptor to compete with a dynamic combinatorial library in template binding

Association constants can be obtained from HPLC analysis of a system comprising a dynamic combinatorial library and a static host.

"Choose-a-size" approach in dynamic combinatorial chemistry: a single substrate dynamic combinatorial library of oligomacrocycles that adapts to the size and shape of carboxylates

A neutral anion binding receptor based on dipicolinic acid diamide was equipped with thiol groups in the amidic side arms. After the thiol was oxidized to disulfide groups with I2, a mixture of cyclic oligomers (a library) was obtained. The distribution of macrocycles can be controlled kinetically during the oxidation process or thermodynamically at basic conditions via disulfide bond exchange. The library proved to be very sensitive to templation with various carboxylates in DMSO. The amplification pattern reflects the structural features of the anionic template and is sensitive to changes in the template's geometry. The application of carboxylates with multiple functional groups resulted in very strong amplification of the large penta- and hexameric macrocycles. The thermodynamic parameters of some templation effects were rationalized using a simple model and confirmed using competitive NMR titration.

Advances in anion supramolecular chemistry: from recognition to chemical applications

Since the start of this millennium, remarkable progress in the binding and sensing of anions has been taking place, driven in part by discoveries in the use of hydrogen bonding, as well as the previously under-exploited anion-π interactions and halogen bonding. However, anion supramolecular chemistry has developed substantially beyond anion recognition, and now encompasses a diverse range of disciplines. Dramatic advance has been made in the anion-templated synthesis of macrocycles and interlocked molecular architectures, while the study of transmembrane anion transporters has flourished from almost nothing into a rapidly maturing field of research. The supramolecular chemistry of anions has also found real practical use in a variety of applications such as catalysis, ion extraction, and the use of anions as stimuli for responsive chemical systems.

Transient substrate-induced catalyst formation in a dynamic molecular network

In biology enzyme concentrations are continuously regulated, yet for synthetic catalytic systems such regulatory mechanisms are underdeveloped. We now report how a substrate of a chemical reaction induces the formation of its own catalyst from a dynamic molecular network. After complete conversion of the substrate, the network disassembles the catalyst. These results open up new opportunities for controlling catalysis in synthetic chemical systems.

Bioinspired chemistry based on minimalistic pseudopeptides

For years researchers have tried to understand the molecular behavior of complex biomolecules through the development of small molecules that can partially mimic their function. Now researchers are implementing the reverse approach: using the structural and mechanistic knowledge obtained from those complex systems to design small molecules with defined properties and for specific applications. One successful strategy for constructing bioinspired, minimalistic molecules is to combine natural building blocks that provide functional elements with abiotic fragments that serve as structural scaffolds. Therefore pseudopeptidic compounds, most of them based on C2 symmetric structures, represent a unique opportunity to explore and evaluate this approach. Some of these molecules are as simple as two amino acids connected by a diamino spacer. The results in this Account show how bioinspired minimalistic pseudopeptides can form ordered structures, participate in the recognition and transcription of information events in molecular devices, and catalyze reactions. This strategy allows researchers to design and prepare a variety of open-chain and macrocyclic compounds leading to systems that can self-aggregate to form hierarchically ordered micro- and nanostructures. In addition, small changes in the molecule or external stimuli can regulate the self-aggregation pattern. In the same way, researchers can also tune the molecular movements of simple pseudopeptides through environmental factors, providing a means to control new molecular devices. In addition, some of the prepared model compounds have shown interesting properties in molecular recognition and even as sensors for several targets of interest. Finally we have observed remarkable catalytic activities from these types of molecules, although those results are still far from the efficiency shown by natural peptides. This family of pseudopeptidic compounds offers the opportunity for the more elaborate design of relatively simple abiotic but bioinspired systems that display specific properties. In addition, the results can provide additional information that will increase the molecular understanding of the basic principles that underlie the extraordinary behavior of natural systems.

Fluorescent acridine-based receptors for H2PO4(-)

Two new pseudopeptidic molecules (one macrocyclic and one open chain) containing an acridine unit have been prepared. The fluorescence response of these receptors to a series of acids was measured in CHCl(3). Receptors are selective to H(2)PO(4)(-) versus HSO(4)(-), and an even higher selectivity is found over other anions such as Cl(-), Br(-), CH(3)COO(-), and CF(3)COO(-). We show that the macrocyclic receptor is more selective for H(2)PO(4)(-) than the related open chain receptor. The supramolecular interactions of triprotonated receptors with different anions have been modeled in silico and have been studied by different experimental techniques. Optimized geometries obtained by computational calculations agree well with experimental data, in particular fluorescence experiments, suggesting that the selective supramolecular interaction takes places through coordination of the anions to the triprotonated form of the receptor.