Rebek imides and their adenine complexes: preferences for Hoogsteen binding in the solid state and in solution

Protein-protein interaction and interference of carcinogenesis by supramolecular modifications

Protein-protein interactions (PPIs) are essential in normal biological processes, but they can become disrupted or imbalanced in cancer. Various technological advancements have led to an increase in the number of PPI inhibitors, which target hubs in cancer cell's protein networks. However, it remains difficult to develop PPI inhibitors with desired potency and specificity. Supramolecular chemistry has only lately become recognized as a promising method to modify protein activities. In this review, we highlight recent advances in the use of supramolecular modification approaches in cancer therapy. We make special note of efforts to apply supramolecular modifications, such as molecular tweezers, to targeting the nuclear export signal (NES), which can be used to attenuate signaling processes in carcinogenesis. Finally, we discuss the strengths and weaknesses of using supramolecular approaches to targeting PPIs.

Enantioselective oxygenation of exocyclic methylene groups by a manganese porphyrin catalyst with a chiral recognition site

The natural enzyme cytochrome P450 is widely recognised for its unique ability to catalyse highly selective oxygen insertion reactions into unactivated C–H bonds under mild conditions. Its exceptional potential for organic synthesis served as an inspiration for the presented biomimetic hydroxylation approach. Via a remote hydrogen bonding motif a high enantioselectivity in the manganese-catalysed oxygenation of quinolone analogues (27 examples, 18–64% yield, 80–99% ee) was achieved. The site-selectivity was completely altered in favour of a less reactive but more accessible position.

A Mn porphyrin complex with a remote hydrogen bonding motif induces a high enantioselectivity in the oxygenation of 3-alkylquinolones. Compared to an achiral Mn complex, the site-selectivity was completely altered in favour of less reactive methylene groups.

Pharmaceutical Applications of Molecular Tweezers, Clefts and Clips

Synthetic acyclic receptors, composed of two arms connected with a spacer enabling molecular recognition, have been intensively explored in host-guest chemistry in the past decades. They fall into the categories of molecular tweezers, clefts and clips, depending on the geometry allowing the recognition of various guests. The advances in synthesis and mechanistic studies have pushed them forward to pharmaceutical applications, such as neurodegenerative disorders, infectious diseases, cancer, cardiovascular disease, diabetes, etc. In this review, we provide a summary of the synthetic molecular tweezers, clefts and clips that have been reported for pharmaceutical applications. Their structures, mechanism of action as well as in vitro and in vivo results are described. Such receptors were found to selectively bind biological guests, namely, nucleic acids, sugars, amino acids and proteins enabling their use as biosensors or therapeutics. Particularly interesting are dynamic molecular tweezers which are capable of controlled motion in response to an external stimulus. They proved their utility as imaging agents or in the design of controlled release systems. Despite some issues, such as stability, cytotoxicity or biocompatibility that still need to be addressed, it is obvious that molecular tweezers, clefts and clips are promising candidates for several incurable diseases as therapeutic agents, diagnostic or delivery tools.

Templated polymerizations on solid supports mediated by complementary nucleoside interactions

The preparation of immobilized poly(methacryloyl nucleosides) and their abilities for template polymerizations is discussed.

Carbon-oxygen hydrogen bonding in biological structure and function

Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago. Although CH···O hydrogen bonding has remained generally underappreciated in the biochemical literature, studies over the last 15 years have begun to yield direct evidence of these interactions in biological systems. In this minireview, we provide a historical context of biological CH···O hydrogen bonding and summarize some major advancements from experimental studies over the past several years that have elucidated the importance, prevalence, and functions of these interactions. In particular, we examine the impact of CH···O bonds on protein and nucleic acid structure, molecular recognition, and enzyme catalysis and conclude by exploring overarching themes and unresolved questions regarding unconventional interactions in biomolecular structure.

Constitutional Self-Organization of Adenine–Uracil-Derived Hybrid Materials

The alkoxysilane nucleobase adenine (A) and uracil (U) precursors described in this paper generate in solution a complex library of hydrogen-bonded aggregates, which can be expressed in the solid state as discrete higher oligomers. The different interconverting outputs that nucleobases may form by oligomerization define a dynamic polyfunctional diversity that may be "extracted selectively" in solid state by sol-gel transcription, under the intrinsic stability of the system. After the sol-gel process, unique constitutional preference for specific geometries in hybrid materials is consistent with a preferential arrangement of nucleobase systems, favoring the self-assembly by the Hoogsteen geometry. FTIR and NMR spectroscopy and X-ray powder diffraction experiments demonstrate the formation of self-organized hybrid supramolecular materials. Electron microscopy reveals the micrometric platelike morphology of the hybrid materials. The M(A-U) hybrid material is nanostructured in ordered circular domains of 5 nm in diameter of alternative light and dark rows with an one-dimensional periodicity of 3.5 A.

Liquid-Crystalline Supramolecular Polymers Formed through Complementary Nucleobase-Pair Interactions

We report how the placement of nucleobase units, thymine, or N6-(4-methoxybenzoyl)adenine, onto the ends of a mesogenic core, bis-4-alkoxy-substituted bis(phenylethynyl)benzene, affects the properties of these materials. We show that addition of these bulky polar groups significantly reduces the range of liquid-crystalline behavior of these compounds. However, mixing two complementary nucleobase-containing AA- and BB-type monomer units together does result in the formation of stable, thermotropic liquid-crystalline (LC) phases. Hydrogen bonding is shown to play an important role in the formation of these LC phases, consistent with the formation of oligomeric or polymeric hydrogen-bonded aggregates. X-ray analyses of these mixed materials are consistent with the formation of smectic C phases.

Geometry and Cooperativity Effects in Adenosine−Carboxylic Acid Complexes

NMR experiments and theoretical investigations were performed on hydrogen bonded complexes of specifically 1- and 7-15N-labeled adenine nucleosides with carboxylic acids. By employing a freonic solvent of CDClF2 and CDF3, NMR spectra were acquired at temperatures as low as 123 K, where the regime of slow hydrogen bond exchange is reached and several higher-order complexes were found to coexist in solution. Unlike acetic acid, chloroacetic acid forms Watson-Crick complexes with the proton largely displaced from oxygen to the nitrogen acceptor in an ion pairing structure. Calculated geometries and chemical shifts of the proton in the hydrogen bridge favorably agree with experimentally determined values if vibrational averaging and solvent effects are taken into account. The results indicate that binding a second acidic ligand at the adenine Hoogsteen site in a ternary complex weakens the hydrogen bond to the Watson-Crick bound carboxylic acid. However, substituting a second adenine nucleobase for a carboxylic acid in the trimolecular complex leads to cooperative binding at Watson-Crick and Hoogsteen faces of adenosine.

Functionalized base-pairs: versatile scaffolds for self-assembly

This article discusses the development of synthetic supramolecular systems derived from hydrogen bond driven base-pairing, with a focus on the self-assembly of individual nucleobase analogues.

Enhancing Hoogsteen interactions: a pyrrole-containing purine nucleoside that competes with guanosine self-assembly

A pyrrole-appended purine nucleoside 1 is described that can form an "extended" three-point Hoogsteen-type interaction due to the stabilization of the donor-acceptor-acceptor (DAA) motif. Nucleoside 1 is shown to bind guanosine 10 (a classic ADD motif) to form ensemble I. This interaction competes effectively with guanosine self-assembly and, as such, is capable of disrupting guanosine quadruplex formation.

Adenine Ribbon with Watson−Crick and Hoogsteen Motifs as the “Double-Sided Adhesive Tape” in the Supramolecular Structure of Adenine and Metal Carboxylate

The cocrystals of adenine and metal (II) quinoline-2-carboxylates (M = Mn2+, Fe2+, Co2+) have been obtained by self-assembly. The complexes are composed of adenine ribbons with the AA22 pairing pattern involving both Watson-Crick and Hoogsteen faces in hydrogen bonding and the neutral molecules of carboxylate positioned in inorganic layers. The very compact supramolecular structure is made by the extensive system of hydrogen bonds and face-to-face pi-pi interactions.

New Rebek imide-type receptors for adenine featuring acetylene-linked pi-stacking platforms

Rebek imide-type molecular clefts with pi-stacking platforms attached to the imide scaffold by an acetylene linker have been prepared by Sonogashira cross-coupling. In the solid state, a novel dimerisation mode for this class of imide receptors was found by crystal structure analysis, whereas efficient 1 : 1 complexation with 9-ethyladenine was observed in CDCl3 solution.

Binding of an Acetic Acid Ligand to Adenosine: A Low-Temperature NMR Study

Binding of an acetic acid (HAc) ligand to adenosine (A) was studied by (1)H NMR spectroscopic techniques. Using a low-melting deuterated Freon mixture as solvent, liquid-state measurements could be performed in the slow exchange regime and allowed a detailed characterization of the formed associates. Thus, at 128 K, trimolecular complexes A.HAc(2) and A(2).HAc with both Watson-Crick and Hoogsteen sites of the central adenine base occupied coexist in various amounts depending on the adenosine:acetic acid molar ratio. Whereas the carboxylic acid OH proton is located closer to the acid for all hydrogen bonds formed, a more deshielded proton at the Watson-Crick site is evidence for a stronger hydrogen bond as compared to the Hoogsteen interaction. For the binding of acetic acid to an adenosine-thymidine base pair in either a Watson-Crick or a Hoogsteen configuration, hydrogen bonds to the available adenine binding site are strengthened as compared to the corresponding hydrogen bonds in the A.HAc(2) complex.

H-Bonded complexes of adenine with Rebek imide receptors are stabilised by cation–π interactions and destabilised by stacking with perfluoroaromatics

A series of Rebek imide receptors with naphthalene or heteroaromatic platforms attached by amide or ester linkers have been prepared from the corresponding acyl chloride or anhydride; the X-ray crystal structure of the receptor-derived anhydride reveals a supramolecular H-bonded helix formation in the crystal; the complexes of adenine bound to the receptors by Hoogsteen H-bonding are found to be stabilised by stacking with a methylquinolinium ion, but destabilised by stacking with a perfluorinated naphthalene.