Pseudopeptidic Cages as Receptors for N-Protected Dipeptides

Molecular Recognition of Tyrosine-Containing Polypeptides with Pseudopeptidic Cages Unraveled by Fluorescence and NMR Spectroscopies

The molecular recognition of Tyr-containing peptide copolymers with pseudopeptidic cages has been studied using a combination of fluorescence and NMR spectroscopies. Fluorescence titrations rendered a reasonable estimation of the affinities, despite the presence of dynamic quenching masking the unambiguous detection of the supramolecular complexes. Regarding NMR, the effect of polypeptide (PP) binding on relaxation and diffusion parameters of the cages is much more reliable than the corresponding chemical shift perturbations. To that, purification of the commercial PPs is mandatory to obtain biopolymers with lower polydispersity. Thus, the relaxation/diffusion-filtered 1H spectra of the cages in the absence vs presence of the PPs represent a suitable setup for the fast detection of the noncovalent interactions. Additional key intermolecular NOE cross-peaks supported by molecular models allow the proposal of a structure of the supramolecular species, stabilized by the Tyr encapsulation within the cage cavity and additional attractive polar interactions between the side chains of cage and PP, thus defining a binding epitope with a potential for implementing sequence selectivity. Accordingly, the cages bearing positive/negative residues prefer to bind the peptides having complementary negative/positive side chains close to the target Tyr, suggesting an electrostatic contribution to the interaction. Overall, our results show that both techniques represent a powerful and complementary combination for studying cage-to-PP molecular recognition processes.

Molecular cages for biological applications

Artificial receptors able to recognise biologically relevant molecules or ions have gained interest in the chemical community because they offer a plethora of posibilities. Molecular cage compounds are polycyclic compounds with a cavity designed for the encapsulation of guest species. Once inside the host cavity, the substrate can be transported through membranes and protected from the action of enzymes or other reactive species, thus offering the possibility of interfering with biological systems. Commonly, enzymes have been an inspiration for chemists in the search and design of defined cavities for different purposes. However, the chemical preparation of molecular cages has struggled with many synthetic challenges but this effort is worthwhile as they are a very promising tool for many applications ranging from sensing, delivery, purification or even promotion of/prevention from chemical modifications. Since the early reports at the end of the 60s, this field has experienced a growing interest; this review summarises the progress in the preparation and study of cage-like compounds highlighting their importance in biological applications.

Substrate Protection in Controlled Enzymatic Transformation of Peptides and Proteins

Proteins are involved in practically every single biological process. The many enzymes involved in their synthesis, cleavage, and posttranslational modification (PTM) carry out highly specific tasks with no usage of protecting groups. Yet, the chemists' strategy of protection/deprotection potentially can be highly useful, for example, when a specific biochemical reaction catalyzed by a broad-specificity enzyme needs to be inhibited, during infection of cells by enveloped viruses, in the invasion and spread of cancer cells, and upon mechanistic investigation of signal-transduction pathways. Doing so requires highly specific binding of peptide substrates in aqueous solution with biologically competitive affinities. Recent development of peptide-imprinted cross-linked micelles allows such protection and affords previously impossible ways of manipulating peptides and proteins in enzymatic transformations.

Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages

The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.

General Method for Peptide Recognition in Water through Bioinspired Complementarity

A general method for peptide recognition has been elusive despite decades of research. Strong binding and selectivity among closely related peptides are necessary for biological applications but have been difficult to achieve with synthetic receptors. With inspiration from highly specific protein-protein and protein-ligand interactions, protein-sized, water-soluble imprinted nanoparticles were prepared via templated polymerization of peptides within cross-linked micelles. Combination of hydrophobic and polar interactions afforded micromolar to submicromolar binding affinities for selected tripeptides. A "golden pair" of functional monomers was identified to enhance both the affinity and selectivity of binding, and enabled differentiation of subtly different sequences including single-point variation of lysine by arginine and insertion of a single glycine at the N- or C-terminus. Biological peptides (β-amyloid peptides) afforded even stronger binding (tens of nanomolar) due to a larger number of complementary interactions between the host and the guest, opening doors to a wide range of biological applications.

Supramolecular cages as differential sensors for dicarboxylate anions: guest length sensing using principal component analysis of ESI-MS and 1H-NMR raw data

Dynamic covalent libraries (DCLs) have been widely used in the development of differential sensors. Inspired by recent studies which use supramolecular recognition systems for sensing, we report the use of a tris(-pyridylmethyl)amine (TPMA)-based supramolecular cage as a differential sensor for dicarboxylate anions. In particular, a library of molecular cages constituted by linkers differing in size and flexibility was allowed to equilibrate toward a series of guests differing in molecular size. The differential system was able to discriminate a series of dicarboxylates depending on their chain length. This differentiation was evaluated through the application of the Principal Component Analysis (PCA) method using interpolated and raw data obtained from ESI-MS. Interestingly, while the 1H NMR spectra of the differential system did not allow for the discrimination of the analytes by the naked eye, PCA of the raw data from the spectra revealed information on the chain length of the guest and also on the odd-even character of the carbon chain.

Sequence-Selective Recognition of Peptides in Aqueous Solution: A Supramolecular Approach through Micellar Imprinting

Sequence-selective recognition of peptides in water has been one of the most important and yet unsolved problems in bioorganic and supramolecular chemistry. The motivation comes from not only the importance of these molecules in biology but also the fundamental challenges involved in the research. Molecular imprinting in doubly cross-linked surfactant micelles offers a unique solution to this problem by creating a "supramolecular code" on the micelle surface that matches the structural features of the peptide chain. Hydrophobic "dimples" are constructed on imprinted micelles that match the hydrophobic side chains of the peptide precisely in size and shape. Polar binding functionalities are installed at correct positions to interact with specific acidic and basic groups on the peptide. Secondary hydrogen-bonding and electrostatic interactions are introduced through imprinting to enhance the binding affinity and specificity further. Binding affinities of tens of nanomolar are readily achieved in water for biological peptides with over a dozen residues. Excellent binding selectivity is observed even for subtly different peptides. The synthesis of these protein-sized nanoparticles involves a one-pot reaction complete within 2 days; purification requires nothing but precipitation and solvent washing. These features make the molecularly imprinted nanoparticles (MINPs) highly promising peptide-binding "artificial antibodies" for chemical and biological applications.

Enediyne-Comprising Amino Aldehydes in the Passerini Reaction

Multicomponent reactions represent a highly efficient approach to a broad spectrum of structurally diverse compounds starting from simple and affordable compounds. A focused library of tweezers-like compounds is prepared by employing the multicomponent Passerini reaction comprising enediyne-derived amino aldehydes. The reaction proceeds under mild conditions yielding Passerini products in good to excellent yields. Postcondensation modifications of Passerini products are demonstrated through a simple deprotection/coupling approach comprising amino functionality, furnishing enediyne cores with highly decorated arms.

Sensing, Transport and Other Potential Biomedical Applications of Pseudopeptides

Pseudopeptides are privileged synthetic molecules built from the designed combination of peptide-like and abiotic artificial moieties. Consequently, they are benefited from the advantages of both families of chemical structures: modular synthesis, chemical and functional diversity, tailored three-dimensional structure, usually high stability in biological media and low non-specific toxicity. Accordingly, in the last years, these compounds have been used for different biomedical applications, ranging from bio-sensing, ion transport, the molecular recognition of biologically relevant species, drug delivery or gene transfection. This review highlights a selection of the most remarkable and recent advances in this field.

Diasteroselective multi-component assemblies from dynamic covalent imine condensation and metal-coordination chemistry: mechanism and narcissistic stereochemistry self-sorting

Self-assembly of a modified tris(2-pyridylmethyl)amine TPMA ligand, zinc(ii) or cobalt(ii) ions, and amino acids have been used effectively as stereo dynamic optical probes for the determination of the enantiomeric excess of free amino acids either using Electronic or Vibrational Circular Dichroism (CD and VCD). Herein, we report the mechanistic and stereochemical study of the self-assembly process which reveals a complex equilibrium in solution where even small variations in the experimental conditions can profoundly affect the final products of the reaction. In particular, variation on the metal stoichiometry switch give rises to an entirely enantio narcissistic self-assembly of the structure.

Enantio narcissistic self-assembly is observed in a multi-metallic structure used as stereodynamic probe for CD measurements.

Pseudopeptidic compounds for the generation of dynamic combinatorial libraries of chemically diverse macrocycles in aqueous media

The combination of pseudopeptidic dithiol building blocks leads to the generation of highly diverse dynamic libraries of macrocycles in aqueous media.

The interaction of amino acids with macrocyclic pH probes of pseudopeptidic nature

The fluorescence quenching, by a series of amino acids, of pseudopeptidic compounds acting as probes for cellular acidity has been investigated.

Cu(2+), Zn(2+), and Ni(2+) Complexes of C2-Symmetric Pseudopeptides with an Aromatic Central Spacer

Two new tetradentate C2-symmetric pseudopeptidic ligands derived from Val and Phe containing two amino and two amido groups and a central o-substituted aromatic spacer have been prepared. Their complexes with Cu(2+), Zn(2+), and Ni(2+) have been studied by potentiometry, UV-vis spectrophotometry, FT-IR, and ESI-MS. The presence of the aromatic spacer provides Cu(2+) complexes with stability constants several orders of magnitude higher than those observed for related ligands containing aliphatic central spacers. Besides, the formation of [MH-2L] complex species is favored. Crystal structures for the corresponding Cu(2+) and Ni(2+) have been obtained, revealing the metal atom in an essentially square-planar geometry, although, in several instances, the oxygen atom of an amide carbonyl of a second complex species can act as a fifth coordination site. In the case of Zn(2+), the only crystal structure obtained displays a square-pyramidal arrangement of the metal center. Finally, preliminary experiments show the catalytic activity of some of these complexes, in particular, Zn(2+) complexes, for epoxide ring-opening with using aniline as the nucleophile in a ligand accelerated process.

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).

Supramolecular protection from the enzymatic tyrosine phosphorylation in a polypeptide

Two pseudopeptidic cages bind the EYE peptide motif of poly(EY) in buffered water, as shown by NMR and fluorescence spectroscopy. This supramolecular interaction protects the Tyr residues from the enzymatic phosphorylation by PTK.

Stereoselective recognition of the Ac-Glu-Tyr-OH dipeptide by pseudopeptidic cages

Pseudopeptidic molecular cages are appealing receptors since they can display different polar and non-polar interaction sites in a modular framework and a controlled disposition. Inspired by previous host-guest knowledge, two pseudopeptidic molecular cages based on serine and threonine (CySer and CyThr, respectively) were designed and synthesized as hosts for the binding of the four possible stereoisomers of the Ac-Glu-Tyr-OH dipeptide, a target sequence of tyrosine kinases. The careful NMR titration experiments in aqueous acetonitrile allowed the determination of the binding constants and reflected a difference in the stability of the corresponding diastereomeric host-guest complexes. The CySer cage proved to be slightly more efficient than the CyThr counterpart, although both showed similar stereoselectivity trends: LL > DD ≥ LD > DL. This stereoselective binding was retained in the gas phase, as shown by ESI-MS competition experiments using the enantiomer-labelled method (EL), as well as CID experiments. Thus, the MS-determined discriminations follow the same trends observed by NMR, suggesting that the stereoselectivity observed for these systems must be mainly dictated by the polar host-guest interactions. Despite the stereoselective binding of short peptide sequences in competitive media being a challenging issue in supramolecular chemistry, our results demonstrate the power of pseudopeptidic cages in molecular recognition with foreseen implications in chemical biology.

Copper(ii) complexes of macrocyclic and open-chain pseudopeptidic ligands: synthesis, characterization and interaction with dicarboxylates

Cu(ii) complexes of pseudopeptides interact with very similar dicarboxylates of biological interest (malate and aspartate) affording strikingly different outcomes.

Coordination behaviour of new open chain and macrocyclic peptidomimetic compounds with copper(ii)

Two valine-derived bis(amino amides) ligands have been prepared and fully characterized.