Crystal structure of a complex between β-glucopyranose and a macrocyclic receptor with dendritic multicharged water solubilizing chains

Probing the Importance of Host Symmetry on Carbohydrate Recognition

The design of molecular cages with low symmetry could allow for more specific tuning of their properties and better mimic the unsymmetrical and complex environment of protein pockets. However, the added value of lowering symmetry of molecular receptors has been rarely demonstrated. Herein, C₃ - and C₁ -symmetrical cages, presenting the same recognition sites, have been synthesized and investigated as hosts for carbohydrate recognition. Structurally related derivatives of glucose, galactose and mannose were found to have greater affinity to the receptor with the lowest symmetry than to their C₃ -symmetrical analogue. According to the host cavity modelling, the C₁ symmetry receptor exhibits a wider opening than its C₃ -symmetrical counterpart, providing easier access and thus promoting guest proximity to binding sites. Moreover, our results show the high stereo- and substrate selectivity of the C₁ symmetry cage with respect to its C₃ counterpart in the recognition of sugars.

Recognition Site Modifiable Macrocycle: Synthesis, Functional Group Variation and Structural Inspection

Traditional macrocyclic molecules encode recognition sites in their structural backbones, which limits the variation of the recognition sites and thus, would restrict the adjustment of recognition properties. Here, we report a new oligoamide-based macrocycle capable of varying the recognition functional groups by post-synthesis modification on its structural backbone. Through six steps of common reactions, the parent macrocycle (9) can be produced in gram scale with an overall yield of 31%. The post-synthesis modification of 9 to vary the recognition sites are demonstrated by producing four different macrocycles (10-13) with distinct functional groups, 2-methoxyethoxyl (10), hydroxyl (11), carboxyl (12) and amide (13), respectively. The ¹H NMR study suggests that the structure of these macrocycles is consistent with our design, i.e., forming hydrogen bonding network at both rims of the macrocyclic backbone. The ¹H-¹H NOESY NMR study indicates the recognition functional groups are located inside the cavity of macrocycles. At last, a preliminary molecular recognition study shows 10 can recognize n-octyl-β-D-glucopyranoside (14) in chloroform.

Binding modes of methyl α-d-glucopyranoside to an artificial receptor in crystalline complexes

Compared to the numerous X-ray crystal structures of protein-carbohydrate complexes, the successful elucidation of the crystal structures of complexes between artificial receptors and carbohydrates has been very rarely reported in the literature. In this work, we describe the binding modes of two complexes formed between methyl α-d-glucopyranoside and an artificial receptor belonging to the class of compounds consisting of a 1,3,5-trisubstituted 2,4,6-trialkylbenzene scaffold. It is particularly noteworthy that these two complexes are present in one crystal structure, as was observed by us for the first time in the case of the recently reported three crystal structures of the complexes with methyl β-d-glucopyranoside, each containing two different receptor-carbohydrate complexes. The noncovalent interactions stabilizing the new complexes are compared with those observed in the aforementioned crystalline complexes with methyl β-d-glucopyranoside.

Aromatic Helical Foldamers as Nucleophilic Catalysts for the Regioselective Acetylation of Octyl β-d-Glucopyranoside

Two indolocarbazole-naphthyridine foldamers 2 and 3 that fold into helical conformations were prepared. The 4-(N,N-dimethylamino)pyridine (DMAP) moiety was introduced at one end of the foldamer strands to develop foldamer-based catalysts for the site-selective acylation of polyols. These foldamers adopt helical conformations containing internal cavities capable of binding octyl β-d-glucopyranoside. The association constants were determined to be 1.9 (±0.1)×10⁵  M^-1 for 2 and 2.1 (±0.1)×10⁵  M^-1 for 3 in CH₂ Cl₂ at 25 °C. In the presence of DMAP, 2 or 3 as the catalysts, octyl β-d-glucopyranoside was subjected to acetylation under identical reaction conditions. The DMAP-catalysed reaction afforded the random distribution of the monoacetylates (6-OAc : 4-OAc : 3-OAc : 2-OAc=33 : 24 : 41 : 2). In contrast, foldamers 2 and 3 led to the predominant formation of 6-OAc. The relative distributions were estimated to be 6-OAc : 4-OAc : 3-OAc=88 : 4 : 6 : ∼0 with 2 and 6-OAc : 4-OAc : 3-OAc : 2-OAc=90 : 3 : 6 : 1 with 3.

Aqueous recognition of purine and pyrimidine bases by an anthracene-based macrocyclic receptor

A water-soluble bis-anthracenyl tetralactam binds biogenic heterocycles with high affinities in aqueous solution, rising to 107 M-1 for the purine hypoxanthine. Recognition occurs through a combination of hydrogen bonding and hydrophobic interactions, and results in fluorescence changes which suggest applications in sensing.

Metalloglycosidase Mimics: Oxidative Cleavage of Saccharides Promoted by Multinuclear Copper Complexes under Physiological Conditions

Degradation of saccharides is relevant to the design of catalytic therapeutics, the production of biofuels, inhibition of biofilms, as well as other applications in chemical biology. Herein, we report the design of multinuclear Cu complexes that enable cleavage of saccharides under physiological conditions. Reactivity studies with para-nitrophenyl (pNP)-conjugated carbohydrates show that dinuclear Cu complexes exhibit a synergistic effect and promote faster and more robust cleavage of saccharide substrates, relative to the mononuclear Cu complex, while no further enhancement is observed for the tetranuclear Cu complex. The use of scavengers for reactive oxygen species confirms that saccharide cleavage is promoted by the formation of superoxide and hydroxyl radicals through Cu^II/I redox chemistry, similar to that observed for native copper-containing lytic polysaccharide monooxygenases (LMPOs). Differences in selectivity for di- and tetranuclear Cu complexes are modest. However, these are the first reported small multinuclear Cu complexes that show selectivity and reactivity against mono- and disaccharide substrates and form a basis for further development of metalloglycosidases for applications in chemical biology.

Artificial Metalloenzymes: Recent Developments and Innovations in Bioinorganic Catalysis

Cellular life is orchestrated by the biochemical components of cells that include nucleic acids, lipids, carbohydrates, proteins, and cofactors such as metabolites and metals, all of which coalesce and function synchronously within the cell. Metalloenzymes allow for such complex chemical processes, as they catalyze a myriad of biochemical reactions both efficiently and selectively, where the metal cofactor provides additional functionality to promote reactivity not readily achieved in their absence. While the past 60 years have yielded considerable insight on how enzymes catalyze these reactions, a need to engineer and develop artificial metalloenzymes has been driven not only by industrial and therapeutic needs, but also by innate human curiosity. The design of miniature enzymes, both rationally and through serendipity, using both organic and inorganic building blocks has been explored by many scientists over the years and significant progress has been made. Herein, recent developments over the past 5 years in areas that have not been recently reviewed are summarized, and prospects for future research in these areas are addressed.

Allosteric Recognition of Homomeric and Heteromeric Pairs of Monosaccharides by a Foldamer Capsule

The recognition of either homomeric or heteromeric pairs of pentoses in an aromatic oligoamide double helical foldamer capsule was evidenced by circular dichroism (CD), NMR spectroscopy, and X-ray crystallography. The cavity of the host was predicted to be large enough to accommodate simultaneously two xylose molecules and to form a 1:2 complex (one container, two saccharides). Solution and solid-state data revealed the selective recognition of the α-4 C1 -d-xylopyranose tautomer, which is bound at two identical sites in the foldamer cavity. A step further was achieved by sequestering a heteromeric pair of pentoses, that is, one molecule of α-4 C1 -d-xylopyranose and one molecule of β-1 C4 -d-arabinopyranose despite the symmetrical nature of the host and despite the similarity of the guests. Subtle induced-fit and allosteric effects are responsible for the outstanding selectivities observed.

Biomimetic carbohydrate recognition

Binding saccharides with non-covalent interactions is challenging, especially in the natural medium of water, but synthetic carbohydrate receptors can be surprisingly effective.

2,3-Dibutoxynaphthalene-based tetralactam macrocycles for recognizing precious metal chloride complexes

Two new tetralactam macrocycles with 2,3-dibutoxynaphthalene groups as sidewalls have been synthesized and characterized. The macrocycle containing isophthalamide bridges can bind square-planar chloride coordination complexes of gold(III), platinum(II), and palladium(II) in CDCl3, while the macrocycle with 2,6-pyridine dicarboxamide bridging units cannot. This may be due to the shrunken cavity caused by intramolecular hydrogen bonds in the latter tetralactam macrocycle. The binding of the isophthalamide-based macrocycle is mainly driven by hydrogen bonds and electrostatic interactions. This naphthalene-based macrocycle has similar binding affinities to all the three abovementioned precious metal chloride complexes. This is in contrast to the fact that the tetralactam macrocycle with anthracene as the sidewalls only show good binding affinities to AuCl4 -. The superior binding to all three complexes may be due to the conformational diversity of the naphthalene-based macrocycle, which make it conformationally adaptive to maximize the binding affinities. In addition, the macrocycle shows fluorescent quenching when adding the chloride metal complexes in its solution and may be used as a fluorescent sensor for the detection of these coordination complexes.

Selective recognition of acetylcholine over choline by a fluorescent cage

A fluorescent hemicryptophane has been synthesized and can be used as a turn on receptor of acetylcholine. A binding constant of 2.4 × 104 M-1 was measured for this neurotransmitter, and its selective and sensitive detection over choline and choline phosphate was achieved. NMR and DFT calculations provide insight into the interactions involved in this selective recognition process.

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

This review summarizes the supramolecular properties of tetralactam macrocycles that have parallel aromatic sidewalls and four NH residues directed into the macrocyclic cavity. These macrocycles are versatile hosts for a large number of different guest structures in water and organic solvents, and they are well-suited for a range of supramolecular applications. The macrocyclic cavity contains a mixture of polar functional groups and non-polar surfaces which is reminiscent of the amphiphilic binding pockets within many proteins. In water, the aromatic surfaces in the tetralactam cavity drive high affinity due the hydrophobic effect and the NH groups provide secondary interactions that induce binding selectivity. In organic solvents, the supramolecular factors are reversed; the polar NH groups drive high affinity and the aromatic surfaces provide the secondary interactions. In addition to an amphiphilic cavity, macrocyclic tetralactams exhibit conformational flexibility, and the combination of properties enables them to be effective hosts for a wide range of guest molecules including organic biscarbonyl derivatives, near-infrared dyes, acenes, precious metal halide complexes, trimethylammonium ion-pairs, and saccharides.

Synthesis, Racemic X-ray Crystallographic, and Permeability Studies of Bioactive Orbitides from Jatropha Species

Orbitides are small cyclic peptides with a diverse range of therapeutic bioactivities. They are produced by many plant species, including those of the Jatropha genus. Here, the objective was to provide new structural information on orbitides to complement the growing knowledge base on orbitide sequences and activities by focusing on three Jatropha orbitides: ribifolin (1), pohlianin C (7), and jatrophidin (12). To determine three-dimensional structures, racemic crystallography, an emerging structural technique that enables rapid crystallization of biomolecules by combining equal amounts of the two enantiomers, was used. The high-resolution structure of ribifolin (0.99 Å) was elucidated from its racemate and showed it was identical to the structure crystallized from its l-enantiomer only (1.35 Å). Racemic crystallography was also used to elucidate high-resolution structures of pohlianin C (1.20 Å) and jatrophidin (1.03 Å), for which there was difficulty forming crystals without using racemic mixtures. The structures were used to interpret membrane permeability data in PAMPA and a Caco-2 cell assay, showing they had poor permeability. Overall, the results show racemic crystallography can be used to obtain high-resolution structures of orbitides and is useful when enantiopure samples are difficult to crystallize or solution structures from NMR are of low resolution.

Carbohydrate binding through first- and second-sphere coordination within aromatic oligoamide metallofoldamers

Aromatic oligoamide capsules that fold upon metal binding recognize carbohydrate guests in solution as evidenced by CD and NMR titrations. Crystallographic data reveal that, besides their structural role, metal ions also contribute to guest recognition through either first- or second-sphere coordination.

Hexaphenolic Rigid Cages Prepared by Self-Organization of C3 v Tridentates

Coordination cages were composed by self-organization of rigid C_{3 v}-symmetric heptaarene tridentates and Pd(II) precursors. The heptaarene framework involves one mesitylene, three phenol, and three pyridine moieties, which were connected by Suzuki coupling reactions. The treatment of the tridentates with Pd(dppp)(OTf)₂ or Pd(en)(NO₃)₂ in a 2:3 molar ratio furnished coordination cages, which was ascertained by crystallography, ¹H NMR and DOSY measurements, and ESI-TOFMS and UV-vis spectra. The cages have six phenolic hydroxy groups inside and were expected to incorporate hydrogen-bonding guest molecules such as saccharides. CD and DOSY measurements showed that octyl hexoside guests could be incorporated into the cage.

A high throughput screening method for the nano-crystallization of salts of organic cations

The generation of solid salts of organic molecules is important to the chemical and pharmaceutical industry. Commonly used salt screening methods consume a lot of resources. We employed a combination of ion exchange screening and vapour diffusion for crystallization. This technique is semi-automatic and requires just nanoliters of the solution of the analyte to be crystallized. This high throughput screening yielded single crystals of sufficient size and quality for single-crystal X-ray structure determination using an in-house X-ray diffractometer. The broad scope of our method has been shown by challenging it with 7 very different organic cations, whose aqueous solubilities vary by a factor of almost 1000. At least one crystal structure for 6 out of 7 tested cations was determined; 4 out of the successful 6 ones had never been crystallized before. Our method is extremely attractive for high throughput salt screening, especially for active pharmaceutical ingredients (APIs), as about 40% of all APIs are cationic salts. Additionally, our screening is a new and very promising procedure for the crystallization of salts of organic cations.

Determination of the Molecular Structures of Ferric Enterobactin and Ferric Enantioenterobactin Using Racemic Crystallography

Enterobactin is a secondary metabolite produced by Enterobacteriaceae for acquiring iron, an essential metal nutrient. The biosynthesis and utilization of enterobactin permits many Gram-negative bacteria to thrive in environments where low soluble iron concentrations would otherwise preclude survival. Despite extensive work carried out on this celebrated molecule since its discovery over 40 years ago, the ferric enterobactin complex has eluded crystallographic structural characterization. We report the successful growth of single crystals containing ferric enterobactin using racemic crystallization, a method that involves cocrystallization of a chiral molecule with its mirror image. The structures of ferric enterobactin and ferric enantioenterobactin obtained in this work provide a definitive assignment of the stereochemistry at the metal center and reveal secondary coordination sphere interactions. The structures were employed in computational investigations of the interactions of these complexes with two enterobactin-binding proteins, which illuminate the influence of metal-centered chirality on these interactions. This work highlights the utility of small-molecule racemic crystallography for obtaining elusive structures of coordination complexes.

Optimizing side chains for crystal growth from water: a case study of aromatic amide foldamers

The growth of crystals of aromatic compounds from water much depends on the nature of the water solubilizing functions that they carry. Rationalizing crystallization from water, and structure elucidation, of aromatic molecular and supramolecular systems is of general value across various fields of chemistry. Taking helical aromatic foldamers as a test case, we have validated several short polar side chains as efficient substituents to provide both solubility in, and crystal growth ability from, water. New 8-amino-2-quinolinecarboxylic acids bearing charged or neutral aminomethyl, carboxymethyl, sulfonic acid, or bis(hydroxymethyl)-methoxy side chains in position 4 or 5, were prepared on a multi gram scale. Fmoc protection of the main chain amine and suitable protections of the side chains ensured compatibility with solid phase synthesis. One tetrameric and five octameric oligoamides displaying these side chains were synthesized and shown to be soluble in water. In all cases but one, crystals were obtained using the hanging drop method, thus validating the initial design principle to combine polarity and rigidity. The only case that resisted crystallization appeared to be due to exceedingly high water solubility endowed by eight sulfonic acid functions. The neutral side chain did provide crystal growth ability from water but contributed poorly to solubility.