Synthetic Tripodal Receptors for Carbohydrates. Pyrrole, a Hydrogen Bonding Partner for Saccharidic Hydroxyls

Oligopyrrolic Cages: From Classic Molecular Constructs to Chemically Responsive Polytopic Receptors

Conspectus"Functional molecular systems", discrete and self-assembled constructs where control over molecular recognition, structure, bonding, transport, release, catalytic activity, etc., is readily achieved, are a topic of current interest. Within this broad paradigm, oligopyrrolic cages have garnered attention due to their responsive recognition features. Due to the presence of slightly polar pyrrole subunits which can also behave as hydrogen-bonding donors, these oligopyrrolic cages are potential receptors for various polarized species. In this Account, we summarize recent advances involving the syntheses and study of (1) covalent oligopyrrolic macrobicyclic cages, (2) oligopyrrolic metallacages, and (3) oligopyrrolic noncovalently linked cages. Considered in concert, these molecular constructs have allowed advances in applied supramolecular chemistry; to date, they have been exploited for selective guest encapsulation studies, anion binding and ion-channel formation, and gas absorption, among other applications. While key findings from others will be noted, in this Account will focus on our own contributions to the chemistry of discrete oligopyrrolic macrocycles and their use in supramolecular host-guest chemistry and sensing applications. In terms of specifics, we will detail how oligopyrrole cages with well-defined molecular geometries permit reversible guest binding under ambient conditions and how the incorporation of pyrrole subunits within larger superstructures allows effective control over anion/conjugate acid binding activity under ambient conditions. We will also provide examples that show how derivatization of these rudimentary macrocyclic cores with various sterically congested β-substituted oligopyrroles can provide entry into more complex supramolecular architectures. In addition, we will detail how hybrid systems that include heterocycles other than pyrrole, such as pyridine and naphthyridine, can be used to create self-assembled materials that show promise as gas-absorbing materials and colorimetric reversible sensors. Studies involving oligopyrrolic polymetallic cages and oligopyrrolic supramolecular cages will also be reviewed. First, we will discuss all-carbon-linked oligopyrrolic bicycles and continue on to present systems linked via amines and imines linkages. Finally, we will summarize recent work on pyrrolic cages created through the use of metal centers or various noncovalent interactions. We hope that this Account will provide researchers with an initial foundation for understanding oligopyrrolic cage chemistry, thereby allowing for further advances in the area. It is expected that the fundamental design and recognition principles made in the area of oligopyrrole cages, as exemplified by our contributions, will be of general use to researchers targeting the design of functional molecular systems. As such, we have structured this Account so as to summarize the past while setting the stage for the future.

Regiochemical Effects on the Carbohydrate Binding and Selectivity of Flexible Synthetic Carbohydrate Receptors with Indole and Quinoline Heterocyclic Groups

Synthetic carbohydrate receptors (SCRs) that bind cell-surface carbohydrates could be used for disease detection, drug-delivery, and therapeutics, or for the site-selective modification of complex carbohydrates but their potential has not been realized because of remaining challenges associated with binding affinity and substrate selectivity. We have reported recently a series of flexible SCRs based upon a biaryl core with four pendant heterocyclic groups that bind glycans selectively through noncovalent interactions. Here we continue to explore the role of heterocycles on substrate selectivity by expanding our library to include a series of indole and quinoline heterocycles that vary in their regiochemistry of attachment to the biaryl core. The binding of these SCRs to a series of biologically-relevant carbohydrates was studied by 1H NMR titrations in CD2Cl2 and density-functional theory calculations. We find SCR030, SCR034 and SCR037 are selective, SCR031, SCR032, and SCR039 are strong binders, and SCR033, SCR035, SCR036, and SCR038 are promiscuous and bind weakly. Computational analysis reveals the importance of C-H⋯π and H-bonding interactions in defining the binding properties of these new receptors. By combining these data with those obtained from our previous studies on this class of flexible SCRs, we develop a series of design rules that account for the binding of all SCRs of this class and anticipate the binding of future, not-yet imagined tetrapodal SCRs.

PCage: Fluorescent Molecular Temples for Binding Sugars in Water

The development of synthetic receptors that recognize carbohydrates in water with high selectivity and specificity is challenging on account of their structural complexity and strong hydrophilicity. Here, we report on the design and synthesis of two pyrene-based, temple-shaped receptors for the recognition of a range of common sugars in water. These receptors rely on the use of two parallel pyrene panels, which serve as roofs and floors, capable of forming multiple [C-H···π] interactions with the axially oriented C-H bonds on glycopyranosyl rings in the carbohydrate-based substrates. In addition, eight polarized pyridinium C-H bonds, projecting from the roofs and floors of the temple receptors toward the binding cavities, form [C-H···O] hydrogen bonds, with the equatorially oriented OH groups on the sugars located inside the hydrophobic cavities. Four para-xylylene pillars play a crucial role in controlling the distance between the roof and floor. These temple receptors are highly selective for the binding of glucose and its derivatives. Furthermore, they show enhanced fluorescence upon binding with glucose in water, a property which is useful for glucose-sensing in aqueous solution.

Flexible Synthetic Carbohydrate Receptors as Inhibitors of Viral Attachment

Carbohydrate-receptor interactions are often involved in the docking of viruses to host cells, and this docking is a necessary step in the virus life cycle that precedes infection and, ultimately, replication. Despite the conserved structures of the glycans involved in docking, they are still considered "undruggable", meaning these glycans are beyond the scope of conventional pharmacological strategies. Recent advances in the development of synthetic carbohydrate receptors (SCRs), small molecules that bind carbohydrates, could bring carbohydrate-receptor interactions within the purview of druggable targets. Here we discuss the role of carbohydrate-receptor interactions in viral infection, the evolution of SCRs, and recent results demonstrating their ability to prevent viral infections in vitro. Common SCR design strategies based on boronic ester formation, metal chelation, and noncovalent interactions are discussed. The benefits of incorporating the idiosyncrasies of natural glycan-binding proteins-including flexibility, cooperativity, and multivalency-into SCR design to achieve nonglucosidic specificity are shown. These studies into SCR design and binding could lead to new strategies for mitigating the grave threat to human health posed by enveloped viruses, which are heavily glycosylated viroids that are the cause of some of the most pressing and untreatable diseases, including HIV, Dengue, Zika, influenza, and SARS-CoV-2.

Molecular Interrogation to Crack the Case of O-GlcNAc

The O-linked β-N-acetylglucosamine (O-GlcNAc) modification, termed O-GlcNAcylation, is an essential and dynamic post-translational modification in cells. O-GlcNAc transferase (OGT) installs this modification on serine and threonine residues, whereas O-GlcNAcase (OGA) hydrolyzes it. O-GlcNAc modifications are found on thousands of intracellular proteins involved in diverse biological processes. Dysregulation of O-GlcNAcylation and O-GlcNAc cycling enzymes has been detected in many diseases, including cancer, diabetes, cardiovascular and neurodegenerative diseases. Here, recent advances in the development of molecular tools to investigate OGT and OGA functions and substrate recognition are discussed. New chemical approaches to study O-GlcNAc dynamics and its potential roles in the immune system are also highlighted. It is hoped that this minireview will encourage more research in these areas to advance the understanding of O-GlcNAc in biology and diseases.

A Preorganized Hydrogen-Bonding Motif for the Molecular Recognition of Carbohydrates

The choice between adaptive and preorganized architectures, or of the most effective hydrogen bonding groups to be selected, are dilemmas that supramolecular chemists must address in designing synthetic receptors for such a challenging guest as carbohydrates. In this paper, structurally related architectures featuring two alternative hydrogen bonding motifs were compared to ascertain the structural and functional origin of their binding differences and the advantages that can be expected in monosaccharide recognition. A set of structurally related macrocyclic receptors were prepared, and their binding properties were measured by NMR and ITC techniques in chloroform vs a common saccharidic target, namely, the β-octyl glycoside of D-glucose. Results showed that the diaminocarbazolic motif, recently reported as the constituting unit of highly effective receptors for saccharides in water, is a superior hydrogen bonding motif compared to the previously described diaminopyrrolic motif, which was successfully employed in molecular recognition of carbohydrates in polar organic solvents, due to intrinsic structural and functional factors, rather than to hydrophobic contributions. In addition, the occurrence of a rare example of a thermodynamic template effect exerted by the beta-glucoside has been ascertained, enhancing the synthesis outcome of the otherwise low yielding preparation of the described macrocyclic receptors.

The Discovery and Development of Oxalamide and Pyrrole Small Molecule Inhibitors of gp120 and HIV Entry - A Review

Human immunodeficiency virus type-1 (HIV-1) is the causative agent responsible for the acquired immunodeficiency syndrome (AIDS) pandemic. More than 60 million infections and 25 million deaths have occurred since AIDS was first identified in the early 1980s. Advances in available therapeutics, in particular combination antiretroviral therapy, have significantly improved the treatment of HIV infection and have facilitated the shift from high mortality and morbidity to that of a manageable chronic disease. Unfortunately, none of the currently available drugs are curative of HIV. To deal with the rapid emergence of drug resistance, off-target effects, and the overall difficulty of eradicating the virus, an urgent need exists to develop new drugs, especially against targets critically important for the HIV-1 life cycle. Viral entry, which involves the interaction of the surface envelope glycoprotein, gp120, with the cellular receptor, CD4, is the first step of HIV-1 infection. Gp120 has been validated as an attractive target for anti-HIV-1 drug design or novel HIV detection tools. Several small molecule gp120 antagonists are currently under investigation as potential entry inhibitors. Pyrrole, piperazine, triazole, pyrazolinone, oxalamide, and piperidine derivatives, among others, have been investigated as gp120 antagonist candidates. Herein, we discuss the current state of research with respect to the design, synthesis and biological evaluation of oxalamide derivatives and five-membered heterocycles, namely, the pyrrole-containing small molecule as inhibitors of gp120 and HIV entry.

Shape-persistent pyrrole-based covalent organic cages: synthesis, structure and selective gas adsorption properties

Two cryptand-like, shape persistent [2+3] imine cages (1 and 2) derived from oligopyrrolic precursors (diformyl dipyrrylpyridine 3 and diformyl bipyrrole 4) were prepared. These cages contain open cavities as inferred from solid state structural analyses and act as selective CO2 gas adsorbing materials in the solid state.

Molecular recognition and activation by polyaza macrocyclic compounds based on host-guest interactions

The design and syntheses of supramolecular hosts for the recognition and activation of molecules and anions are one of the most active research fields in supramolecular chemistry, in which polyaza macrocyclic ligands and their complexes have drawn particular attention due to their strong host-guest interactions. This review mainly focuses on the recent progress in the recognition of molecules and anions by polyaza macrocyclic compounds including polyaza macrocycles, polyaza macrobicycles and polyaza macrotricycles, as well as the activation of molecules by polyaza macrocyclic ligands and their metal complexes.

Improved hemicryptophane hosts for the stereoselective recognition of glucopyranosides

Four new enantiomerically and diastereomerically pure hemicryptophane hosts (M-SSS-2/P-SSS-2 and M-RRR-2/P-RRR-2 pairs) were designed for the recognition of sugar derivatives. Their absolute configuration was determined from the circular dichroism spectra and DFT calculations. The host molecules were then used for the stereoselective recognition of glucopyranosides. Binding constants were obtained from (1)H NMR titration experiments showing an increase of affinity for this class of receptors, associated with an improved diastereo- and enantio-differentiation.

Sulfate recognition by a hexaaza cryptand receptor

A hexamine macrobicycle with pyrrolyl spacers was evaluated as an anion receptor in its protonated forms. The protonation constants of the receptor, as well as its association constants with Cl(-), NO3(-), AcO(-), ClO4(-), H2PO4(-), and SO4(2-) were determined by potentiometry at 298.2 ± 0.1 K in H2O-MeOH (50 : 50 v/v) and at an ionic strength of 0.10 ± 0.01 M in KTsO. These studies revealed that the Hnpyrr(n+) receptor has a very high effective association constant value for the SO4(2-) at pH 4.0 (log Keff = 6.42), and it is selective for the uptake of this anion in the presence of the other studied anionic substrates. In particular, the receptor showed very high SO4(2-)/NO3(-) selectivity. Using the indicator-displacement approach the receptor is able to signal the presence of sulfate by a change of color. Single crystal X-ray diffraction determination of [(H6pyrr)(SO4)(H2O)3](SO4)2·9.3H2O revealed the presence of one sulfate anion inside the receptor cavity and showed that the encapsulation of the anion is favored by an array of nine hydrogen bonding interactions, including N-HO, C-HO and water-mediated ones.

Finding a single-molecule receptor for citramalic acid through supramolecular chelation

We have demonstrated that the tritopic hydrogen-bond acceptor 1,3,5-(5,6-dimethylbenzimidazol-1-yl)-2,4,6-trimethylbenzene can act as a perfectly complementary receptor for citramalic acid. The solid-state structure of the cocrystal of the two components show that they form 1:1 pairs where each pair is held together by three near-linear O–H···N hydrogen bonds in a converging manner. The conformational flexibility of both species is apparently no hindrance to the formation of discrete dimeric “cups” wherein each species presents three hydrogen-bond donors/acceptors in a face-to-face orientation.

Sugar recognition: designing artificial receptors for applications in biological diagnostics and imaging

At the cellular level, numerous processes ranging from protein folding to disease development are mediated by a sugar-based molecular information system that is much less well known than its DNA- or protein-based counterparts. The subtle structural diversity of such sugar tags nevertheless offers an excellent, if challenging, opportunity to design receptors for the selective recognition of biorelevant sugars. Over the past 40 years, growing interest in the field of sugar recognition has led to the development of several promising artificial receptors, which could soon find widespread use in medical diagnostics and cell imaging.