Synthesis and Recognition Properties of Cucurbit[8]uril Derivatives

Challenges and Opportunities of Functionalized Cucurbiturils for Biomedical Applications

Cucurbit[n]uril (CB[n]) macrocycles (especially CB[5] to CB[8]) have shown exceptional attributes since their discovery in 2000. Their stability, water solubility, responsiveness to several stimuli, and remarkable binding properties have enabled a growing number of biological applications. Yet, soon after their discovery, the challenge of their functionalization was set. Nevertheless, after more than two decades, a myriad of CB[n] derivatives has been described, many of them used in cells or in vivo for advanced applications. This perspective summarizes key advances of this burgeoning field and points to the next opportunities and remaining challenges to fully express the potential of these fascinating macrocycles in biology and biomedical sciences.

Gold and Silver Chains from Tetrahydrothiophenocucurbit[6]uril as Au or Ag-Nanoparticles

Tetrahydrothiophenocucurbit[5 and 6]uril has been synthesized from tetrathiophenoglycoluril diether, providing thioether functionality at the exterior equatorial position of the cucurbituril cage. This functionality has been investigated for chemical modification through sulfoxide formation and subsequent Pummerer rearrangement to the acetoxy derivative of the tetrahydrothiophenocucurbit[5]uril. Nanoparticles of Au and Ag were prepared in the presence of tetrahydrothiophenocucurbit[6]uril, which curiously led to the formation of nanoparticle chains, growing in length over days to weeks.

Rational Design of Self-Assembling Supramolecular Protein Nanostructures Utilizing the Cucurbit[8]Uril Macrocyclic Host

Self-assembly is a phenomenon that governs molecular structural organization in nature, therefore raising research interest for the fabrication of novel nanomaterials with diverse applications in biocatalysis, biomedicine, material templating, and biosensor development. In this chapter we provide protocols for the development of supramolecular protein complexes based on host-guest interactions in the presence of the macrocyclic host, cucurbit[8]uril (CB[8]). CB[8] is reported to exhibit high binding affinity towards the tripeptide Phe-Gly-Gly (FGG), therefore it can be utilized as a selective adhesive of protein molecules, after fusion of FGG to an accessible protein surface.

The Cyclobutanocucurbit[5-8]uril Family: Electronegative Cavities in Contrast to Classical Cucurbituril while the Electropositive Outer Surface Acts as a Crystal Packing Driver

The structural parameters for the cyclobutanoQ[5-8] family were determined through single crystal X-ray diffraction. It was found that the electropositive cyclobutano methylene protons (CH2) are important in forming interlinking crystal packing arrangements driven by the dipole-dipole interactions between these protons and the portal carbonyl O of a near neighbor. This type of interaction was observed across the whole family. Electrostatic potential maps also confirmed the electropositive nature of the cyclobutano CH2 but, more importantly, it was established that the cavities are electronegative in contrast to classical Q[5-8], which are near neutral.

Azobenzene-Based Macrocyclic Arenes: Synthesis, Crystal Structures, and Light-Controlled Molecular Encapsulation and Release

Azobenzene (azo)-based macrocycles are highly fascinating in supramolecular chemistry because of their light-responsiveness. In this work, a series of azo-based macrocyclic arenes 1, 2, 3, and 4, distinguished by the substituted positions of azo groups, is rationally designed and synthesized via a fragment-cyclization method. From the crystal and computed structures of 1, 2, and 3, we observe that the cavity size of these azo-macrocycles decreases gradually upon E→Z photoisomerization. Moreover, light-controlled host-guest complexations between azo-macrocycle 1 and guest molecules (7,7,8,8-tetracyanoquinodimethane, terephthalonitrile) are successfully achieved. This work provides a simple and effective method to prepare azo-macrocycles, and the light-responsive molecular-encapsulation systems in this work may further advance the design and applications of novel photo-responsive host-guest systems.

In Vitro and In Vivo Sequestration of Phencyclidine by Me4 Cucurbit[8]uril*

We report investigations of the use of cucurbit[8]uril (CB[8]) macrocycles as an antidote to counteract the in vivo biological effects of phencyclidine. We investigate the binding of CB[8] and its derivative Me4 CB[8] toward ten drugs of abuse (3-9, 12-14) by a combination of 1 H NMR spectroscopy and isothermal titration calorimetry in phosphate buffered water. We find that the cavity of CB[8] and Me4 CB[8] are able to encapsulate the 1-amino-1-aryl-cyclohexane ring system of phencyclidine (PCP) and ketamine as well as the morphinan skeleton of morphine and hydromorphone with Kd values ≤50 nm. In vitro cytotoxicity (MTS metabolic and adenylate kinase cell death assays in HEK293 and HEPG2 cells) and in vivo maximum tolerated dose studies (Swiss Webster mice) which were performed for Me4 CB[8] indicated good tolerability. The tightest host⋅guest pair (Me4 CB[8]⋅PCP; Kd =2 nm) was advanced to in vivo efficacy studies. The results of open field tests demonstrate that pretreatment of mice with Me4 CB[8] prevents subsequent hyperlocomotion induction by PCP and also that treatment of animals previously dosed with PCP with Me4 CB[8] significantly reduces the locomotion levels.

Site-selective modification of proteins using cucurbit[7]uril as supramolecular protection for N-terminal aromatic amino acids

Cucurbit[7,8]urils are known to form inclusion complexes with aromatic amino acids, hosting the hydrohobic side chains within the cavity and adjacent cations within the portal of the macrocyclic host. Here we show that cucurbit[7]uril binding with N-terminal phenylalanine significantly reduces the nucleophilicity of the amine, likely due to an increase in stability of the ammonium ion, rendering it unreactive at neutral pH. Using insulin as a model protein, we show that this supramolecular protection strategy can drive selectivity of N-terminal amine conjugation away from the preferred B chain N-terminal phenylalanine towards the A chain N-terminal glycine. Cucurbit[7]uril can therefore be used as a supramolecular protecting group for site-selective protein modification.

Cocrystallization with a clip-type molecule catcher: a new method to determine structures of liquid molecules

In order to measure the precise structure of liquid molecules by X-ray single-crystal diffraction, we report a new and easy method using a glycoluril-derived molecular clip as a molecule catcher to form cocrystals with liquid molecules.

Supramolecular chemistry of substituted cucurbit[n]urils

This review covers important advances in the field of substituted cucurbit[n]urils.

Acyclic Cucurbit[n]uril-type Receptors: Preparation, Molecular Recognition Properties and Biological Applications

This article traces the development of acyclic cucurbit[n]uril-type receptors with a focus on work from the Isaacs group. First, we describe the synthesis of methylene bridged glycoluril dimers capped with aromatic sidewalls which allowed us to probe the interconversion of the S- and C-shaped dimers which is a fundamental step in CB[n] formation. The C-shaped compounds were found to undergo discrete self-assembly (dimerization) in both water and organic solvents which lead us to investigate multicomponent self-sorting systems. We supressed the self-association of 8 by electrostatic repulsion in the putative dimer which allowed expression of its innate molecular recognition properties toward methylene blue and related planar cationic dyes. Longer glycoluril oligomers (trimer - hexamer, acyclic decamer) were prepared by starving the CB[n]-forming reaction of formaldehyde. The longer oligomers (e.g. 15 and 16) bind to alkylammonium ions in water ≈ 100-fold weaker than macrocyclic CB[n] highlighting the high preorganization of the acyclic but polycyclic framework. We prepared a wide variety of acyclic CB[n] compounds (wall variants, solubilizing group variants, linker variants) based on glycoluril trimer and tetramer. In particular, 26 and 27 have been shown to possess a wide variety of chemically and biologically interesting functions. For example, 26 was used to formulate the insoluble drug Albendazole and treat mice bearing SK-OV-3 xenograft tumors. Compound 27 binds tightly to the neuromuscular blocking agents rocuronium, vecuronium, and cisatracurium and acts as an in vivo reversal agent for these compounds in anesthetized rats. Container 27 was also found to modulate the hyperlocomotive effect of rats that had been treated with methamphetamine. Finally, 38 has been used as a cross reactive component of sensor arrays that are capable of classifying and quantifying cancer related nitroamines and a range of over the counter drugs. Overall, the work demonstrates that acyclic CB[n]-type compounds are nicely pre-organized and therefore retain the essential aspects of the recognition properties of macrocyclic CB[n] but allow for more straightforward tailoring of structure and solubility that enables a variety of chemically and biologically important applications.

An easy gene assembling strategy for light-promoted transfection by combining host-guest interaction of cucurbit[7]uril and gold nanoparticles

Cucurbit[7]uril (CB[7]), a representative member of the host family cucurbit[n]uril, can host-guest interact with many guest molecules such as adamantane, viologen and naphthalene derivatives. This host-guest interaction provides an easy strategy in gene vector assembling. Furthermore, CB[7] can self-assemble on gold nanospheres (AuNSs). Herein, the combination of CB[7] and AuNSs provides both advantages of host-guest interaction and photo-thermal effect of AuNSs. In this study, polyethyleneimine (PEI) and polyethylene glycol (PEG) were separately interacted with CB[7] via host-guest interaction. Then by assembling on AuNSs, PEI and PEG were combined together to condense DNA into polyplexes as well as enhance circulation stability of the polyplexes. These gene vectors were found to have high cellular uptake efficiency and low cytotoxicity. Furthermore, the well distributed AuNSs in the polyplexes could transform light into heat under light exposure because of the photo-thermal effect. This was found to effectively promote the entry of gene into cytoplasm and highly enhanced gene transfection efficiency.

Predicting Binding Free Energies: Frontiers and Benchmarks

Binding free energy calculations based on molecular simulations provide predicted affinities for biomolecular complexes. These calculations begin with a detailed description of a system, including its chemical composition and the interactions among its components. Simulations of the system are then used to compute thermodynamic information, such as binding affinities. Because of their promise for guiding molecular design, these calculations have recently begun to see widespread applications in early-stage drug discovery. However, many hurdles remain in making them a robust and reliable tool. In this review, we highlight key challenges of these calculations, discuss some examples of these challenges, and call for the designation of standard community benchmark test systems that will help the research community generate and evaluate progress. In our view, progress will require careful assessment and evaluation of new methods, force fields, and modeling innovations on well-characterized benchmark systems, and we lay out our vision for how this can be achieved.

Dimeric molecular clips based on glycoluril

Phenylene-bridged glycoluril dimers are used for the construction of supramolecular host molecules with high affinity towards methylviologen in water.

Twisted Cucurbit[n]urils

Two new twisted cucurbiturils, cucurbit[13]uril (tQ[13]) and cucurbit[15]uril (tQ[15]), have been synthesized and separated, and their structures have been confirmed by NMR spectroscopy and MALDI-TOF mass spectrometry together with the X-ray structures of two new complexes, {Dy(H2O)4Cd(H2O)4tQ[13]}·2.5[CdCl4]·65H2O and {Cd0.5(H2O)2tQ[15]}·[CdCl4]·47H2O. tQ[15] is the largest cucurbit[n]uril (Q[n]) in the Q[n] family reported to date. The X-ray diffraction studies of both complexes indicated that these large tQ[n]s effectively exhibit two different cavities-a central cavity and two side cavities. Preliminary host-guest behavior by each of the new systems was investigated by NMR studies.

Redox-Responsive Viologen-Mediated Self-Assembly of CB[7]-Modified Patchy Particles

Sulfonated surface patches of poly(styrene)-based colloidal particles (CPs) were functionalized with cucurbit[7]uril (CB[7]). The macrocycles served as recognition units for diphenyl viologen (DPV(2+)), a rigid bridging ligand. The addition of DPV(2+) to aqueous suspensions of the particles triggered the self-assembly of short linear and branched chainlike structures. The self-assembly mechanism is based on hydrophobic/ion-charge interactions that are established between DPV(2+) and surface-adsorbed CB[7]. DPV(2+) guides the self-assembly of the CPs by forming a ternary DPV(2+)⊂(CB[7])2 complex in which the two CB[7] macrocycles are attached to two different particles. Viologen-driven particle assembly was found to be both directional and reversible. Whereas sodium chloride triggers irreversible particle disassembly, the one-electron reduction of DPV(2+) with sodium dithionite causes disassembly that can be reversed via air oxidation. Thus, this bottom-up synthetic supramolecular approach allowed for the reversible formation and directional alignment of a 2D colloidal material.