Supramolecular chemical biology: designed receptors and dynamic chemical systems

Supramolecular chemistry focuses on the study of species joined by non-covalent interactions, and therefore on dynamic and relatively ill-defined structures. Despite being a well-developed field, it has to face important challenges when dealing with the selective recognition of biomolecules in highly competitive biomimetic media. However, supramolecular interactions reside at the core of chemical biology systems, since many processes in nature are governed by weak, non-covalent, strongly dynamic contacts. Therefore, there is a natural connection between these two research fields, which are not frequently related or share interests. In this feature article, I will highlight our most recent results in the molecular recognition of biologically relevant species, following different conceptual approaches from the most conventional design of elaborated receptors to the less popular dynamic combinatorial chemistry methodology. Selected illustrative examples from other groups will be also included. The discussion has been focused mainly on systems with potential biomedical applications.

Design of C2-symmetric pseudopeptides for in vivo detection of Cu(II) through controlled supramolecular nano-assembly

Pseudopeptides are emerging next-generation soft bioinspired materials for biological applications. Therefore, a new class of C2-symmetric L-valine-derived pseudopeptides has been designed and developed. The newly developed pseudopeptides exhibit intracellular Cu(II) ion detection in live-cell fluorescence studies on RAW264.7 cells. We find that the changes in the amino acid side chain in desired pseudopeptidic moieties lead to a drastic change in their selectivity towards different metal ions. The L-valine-derived pseudopeptides exhibit selectivity towards Cu(II) ions through turn-off fluorescence, and the L-phenylalanine-derived pseudopeptides exhibit selectivity towards Zn(II) ions through turn-on fluorescence. In addition, the L-valine-derived pseudopeptides show an increase in spherical-shaped structures upon incubation with Cu(II) ions during supramolecular nano-assembly formation. In contrast, the L-phenylalanine-derived pseudopeptides show a decrease in spherical-shaped structures upon adding Zn(II) ions. The judiciously designed L-valine-derived and L-phenylalanine-derived bioinspired pseudopeptides are promising for exploring similar effects in various peptidomimetics in advanced biological applications.

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.

Quality Data from Messy Spectra: How Isometric Points Increase Information Content in Highly Overlapping Spectra

Spectroscopic techniques are immensely useful for obtaining information about chemical transformations while they are happening. However, such data are often messy, and it is challenging to extract reliable information from them without careful calibrations or internal standards. This short introductory review discusses how isometric points (points in a spectrum where the signal intensity remains constant throughout the progress of a chemical transformation) can be used to derive high-quality data from messy spectra. Such analyses are helpful in a variety of (bio-)chemical settings, as selected case studies demonstrate.

Controlling enzyme reactions by supramolecular protection and deprotection of oligosaccharide substrates

Protection/deprotection is a powerful strategy in the total synthesis of complex organic molecules but similar tools are nearly absent in enzymatic reactions. We here report supramolecular protective receptors that outcompete an enzyme in the binding of oligosaccharides. The strong binding inhibits the enzymatic reaction and addition of an even stronger ligand for the receptor releases the substrate. These receptors could be used to control products from the same substrate/enzyme mixture and regulate enzymatic reactions reversibly.

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.

A review on recent advances in amino acid and peptide-based fluorescence and its potential applications

Fluorescence is widely used to detect functional groups and ions, and peptides are used in various fields due to their excellent biological activity.

Cationic Pillar[6]arene Induces Cell Apoptosis by Inhibiting Protein Tyrosine Phosphorylation Via Host-Guest Recognition

We reported for the first time that cationic pillar[6]arene (cPA6) could tightly bind to peptide polymer (MW~20–50 kDa), an artificial substrate for tyrosine (Tyr) phosphorylation, and efficiently inhibit Tyr protein phosphorylation through host–guest recognition. We synthesized a nanocomposite of black phosphorus nanosheets loaded with cPA6 (BPNS@cPA6) to explore the effect of cPA6 on cells. BPNS@cPA6 was able to enter HepG2 cells, induced apoptosis, and inhibited cell proliferation by reducing the level of Tyr phosphorylation. Furthermore, BPNS@cPA6 showed a stronger ability of inhibiting cell proliferation in tumor cells than in normal cells. Our results revealed the supramolecular modulation of enzymatic Tyr phosphorylation by the host–guest recognition of cPA6.

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.

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.

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.