Surface recognition and fluorescence sensing of histone by dansyl-appended cyclophane-based resorcinarene trimer

A cyclophane-based resorcinarene trimer (3) bearing a dansyl moiety as an environmentally sensitive fluorophore was prepared by stepwise condensation of a tetraaza[6.1.6.1]paracyclophane skeleton with a dansyl moiety and three resorcinarene derivatives having heptacarboxylic acid residues in this sequence. The dansyl-appended cyclophane exhibited the following fluorescence properties regarding solvent polarity dependency and histone surface recognition: With increasing dioxane contents in dioxane/water solvents, the fluorescence intensity originating from the dansyl moiety of 3 increased along with a concomitant blue shift of the fluorescence maximum (lambdaem). The microenvironmentally sensitive fluorescence properties of dansyl fluorophore were maintained, even when the dansyl moiety was covalently attached to a cyclophane. Most interestingly, the cyclophane-based resorcinarene trimer exhibited recognition and fluorescence sensing capabilities toward histone, a small basic protein of eukaryotic chromatins. The fluorescence intensity originating from 3 increased along with a concomitant blue shift of lambdaem upon the addition of histone, reflecting the formation of 3-histone complexes. A relatively large fluorescence polarization (P) value was obtained for the 3-histone complexes (0.15), reflecting highly restricted conformations of 3, and the obtained P value was much larger than that of 3 alone in aqueous medium (0.07). The binding constant (K) of 3 with histone (unit basis) was estimated to be 2.1 x 106 M-1. On the other hand, upon the addition of acetylated histone (Ac-histone) to an aqueous solution containing 3, the extent of change in fluorescence intensity originating from the dansyl group of 3 was almost negligible, indicating that the electrostatic interactions between 3 and Ac-histone were weak. In addition, the fluorescence spectral changes were also small or negligible upon the addition of other proteins such as albumin, ovalbumin, peanut agglutinin, myoglobin, concanavalin A, cytochrome c, and lysozyme, having isoelectric points of 4.7, 4.8, 5.7-6.7, 6.8, 7.1, 9, and 11.0, respectively, to an aqueous solution containing 3.     

Multivalent binding of small guest molecules and proteins to molecular printboards inside microchannels

Beta-Cyclodextrin (beta-CD) monolayers have been immobilized in microchannels. The host-guest interactions on the beta-CD monolayers inside the channels were comparable to the interactions on beta-CD monolayers on planar surfaces, and a divalent fluorescent guest attached with a comparable binding strength. Proteins were attached to these monolayers inside microchannels in a selective manner by employing a strategy that uses streptavidin and orthogonal linker molecules. The design of the chip, which involved a large channel that splits into four smaller channels, allowed the channels to be addressed separately and led to the selective immobilization of antibodies. Experiments with labeled antibodies showed the selective immobilization of these antibodies in the separate channels.     

Strong guest binding by cyclodextrin hosts in competing nonpolar solvents and the unique crystalline structure

6-O-Modified β-cyclodextrins, such as heptakis(6-O-triisopropylsilyl)-β-cyclodextrin (TIPS-β-CD) and heptakis(6-O-tert-butyldimethylsilyl)-β-cyclodextrin (TBDMS-β-CD), formed 2:1 inclusion complexes with pyrene in benzene and cyclohexane with high association constants. The X-ray crystalline structure of the TIPS-β-CD-pyrene complex obtained from the benzene solution showed that one pyrene molecule was incorporated in the form of a sandwich-type complex with two benzene molecules within the cavity of the dimer formed by two TIPS-β-CD molecules.     

Janus-like squaramide-based hosts: dual mode of binding and conformational transitions driven by ion-pair recognition

New tripodal squaramide-based hosts have been synthesised and structurally characterised by spectroscopic methods. In 2.5?% (v/v) [D(6)]DMSO in CDCl(3), compound 4 formed dimeric assemblies [log?K(dim)=3.68(8)] as demonstrated by (1)H?NMR spectroscopy and UV dilution experiments. AFM and SEM analyses revealed the formation of a network of bundled fibres, which indicates a preferential mechanism for aggregation. These C(3)-symmetric tripodal hosts exhibited two different and mutually exclusive modes of binding, each one easily accessible by simultaneous reorientation of the squaramide groups. In the first, a convergent disposition of the NH squaramide protons allowed the formation of an array of N-H???X(-) hydrogen bonds with anions. In the second mode, reorientation of carbonyl squaramide groups allowed multiple C=O???H interactions with ammonium cations. The titration of 4 with different tetraalkylammonium iodides persistently showed the formation of 1:1 complexes, as well as 1:2 and 1:3 complexes. The corresponding stoichiometries and binding affinities of the complexes were evaluated by multi-regression analysis. The formation of high-order complexes, supported by ROESY, NOESY and mass spectrometry experiments, has been attributed to the insertion of NR(4)I ion pairs between the carbonyl and NH protons of the squaramide groups located in adjacent arms of 4. The observed effects reflect the induction of significant conformational changes in the hosts, mainly in relation to the relative orientation of the squaramide groups adapting their geometries to incoming ion-pair complementary substrates. The results presented herein identify and fully describe two different modes of ion-pair recognition aimed at directing conformational transitions in the host, therefore establishing a base for controlling more elaborate movements of molecular devices through ion-pair recognition.     

Synthesis of redox active large macrocyclic hosts and the recognition of secondary ammonium salts

Interconvertible macrocyclic hosts containing thiol groups or a disulfide linkage in the binding cavity have been synthesized. The binding affinities of the reduced and oxidized forms toward benzylammoium derivatives are completely reverse. Formation of pseudorotaxane is suggested upon the host-guest complexation.     

Dual-mode recognition of oxalate by protonated azacryptate hosts; conformational response of the guest maximizes pi-stacking interactions

Exceptionally large complexation constants for oxalate encapsulated within azacryptand hosts are partly explained by pi-stacking interactions between C=O and aromatic rings.     

Synthesis, structures and inclusion properties of tetranaphthalides: new macrocyclic clathrate hosts

Novel tetranaphthalide host compounds 3 and 4 bearing isomeric naphthalene moieties have been synthesized and their inclusion properties were investigated. These host compounds enclathrated several kinds of ketones, cyclic ethers, amides, sulfoxides and aromatic compounds. The structures of two representative inclusion compounds containing different host molecules and a common guest (dimethyl sulfoxide) were investigated by X-ray diffraction to determine the nature of guest inclusion and to rationalize their distinctly different thermal decomposition profiles.     

Protonated N-confused porphyrin dimer: formation, structure, and guest binding

The protonation of 3,3'-bis(meso-tetratolyl-2-aza-21-carbaporphyrin) with various acids was studied. The stepwise formation of mono-, di-, and tetracationic species was shown on the basis of UV-vis-near-IR and low-temperature (1)H NMR. Upon going from di- to tetraprotonated form, the bis(porphyrinoid) skeleton changes its conformation from cisoid to bent-transoid, which was found by single-crystal X-ray analyses, 2D NMR, and density functional theory (DFT) calculations. The formation of cation-anion complexes was established in both the solid state and solution. The substitution of anions was studied by spectrophotometric and (1)H NMR titrations. A pronounced decrease of the HOMO-LUMO gap in the tetraprotonated species was shown by cyclovoltametry and time-dependent DFT calculations.     

Multivalent gold glycoclusters: high affinity molecular recognition by bacterial lectin PA-IL

Multivalent protein-carbohydrate interactions are involved in the initial stages of many fundamental biological and pathological processes through lectin-carbohydrate binding. The design of high affinity ligands is therefore necessary to study, inhibit and control the processes governed through carbohydrate recognition by their lectin receptors. Carbohydrate-functionalised gold nanoclusters (glyconanoparticles, GNPs) show promising potential as multivalent tools for studies in fundamental glycobiology research as well as biomedical applications. Here we present the synthesis and characterisation of galactose functionalised GNPs and their effectiveness as binding partners for PA-IL lectin from Pseudomonas aeruginosa. Interactions were evaluated by hemagglutination inhibition (HIA), surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) assays. Results show that the gold nanoparticle platform displays a significant cluster glycoside effect for presenting carbohydrate ligands with almost a 3000-fold increase in binding compared with a monovalent reference probe in free solution. The most effective GNP exhibited a dissociation constant (K(d)) of 50 nM per monosaccharide, the most effective ligand of PA-IL measured to date; another demonstration of the potential of glyco-nanotechnology towards multivalent tools and potent anti-adhesives for the prevention of pathogen invasion. The influence of ligand presentation density on their recognition by protein receptors is also demonstrated.     

Chiral biscavitand propellers: synthesis, conformations and multiple guest binding

[structure: see text]. The synthesis and properties of molecules containing two cavitand bowls, with interbowl linkages comprising one carbon atom at various oxidation levels, are reported. A carbonyl-bridged biscavitand binds three CH2Cl2 molecules in the solid state through a helical conformation. Evidence for the same chiral conformation in the solution phase is presented.     

Multivalent recognition of bis- and tris-Zn-porphyrins by N-methylimidazole functionalized gold nanoparticles

N-Methylimidazole-functionalized gold nanoparticles behave as multivalent ligands for porphyrin arrays with an increase in binding strength of up to three order of magnitude with respect to a monovalent system.     

Self-assembly and selective guest binding of three-dimensional open-framework solids from a macrocyclic complex as a trifunctional metal building block

The nickel(II) hexaazamacrocyclic complex (1) containing pendant pyridine groups has been synthesized by the one-pot template condensation reaction of amine and formaldehyde. From the self-assembly of 1 with deprotonated cis,cis-1,3,5-cyclohexanetricarboxylic acid, H2CTC- and CTC3-, three-dimensional supramolecular open-frameworks of [Ni(C20H32N8)][C6H9(COOH)2(COO)]2 x 4H2O (2) and [Ni(C20H32N8)]3[C6H9(COO)3]2 x 16H2O (3), respectively, have been constructed. The solids 2 and 3 are insoluble in all solvents. X-ray crystal structure of 2 indicates that each nickel(II) macrocyclic complex binds two H2CTC- ions in trans position and two pendant pyridine groups of the macrocyclic complex are involved in hydrogen-bonding interactions with the hydroxy groups of H2CTC- belonging to the neighboring macrocyclic complexes, which provides the beltlike one-dimensional chain composed of rectangular synthons. The one-dimensional chains are linked together through lattice water molecules by the hydrogen-bonding interactions to generate two-dimensional networks, which are again connected to each other by the offset pi-pi stacking interactions between the pendant pyridine rings to give rise to a three-dimensional structure in which channels are present. The X-ray crystal structure of 3 indicates that each nickel(II) macrocyclic unit binds two CTC3- ions in trans position and each CTC3- ion coordinates three nickel(II) macrocyclic complexes to form a two-dimensional layer, in which pendant pyridine rings are involved in the hydrogen bonding and the herringbone pi-pi interaction. Between the layers, the pendant pyridine rings belonging to the neighboring layers participate in the offset pi-pi stacking interactions, which gives rise to a three-dimensional network structure. The network creates channels running parallel to the a, b, and c axes, which are filled with guest water molecules. The X-ray powder diffraction patterns indicate that the frameworks of 2 and 3 are deformed upon removal of water guests but restored upon rebinding of water. The host solids 2 and 3 bind [Cu(NH3)4](ClO4)2 in MeCN with a binding constant (Kf) of 210 M(-1) and 710 M(-1), respectively, while they do not bind [Cu(en)2](ClO4)2 (en = ethylenediamine). The dried solids of 2 and 3 do not interact with benzene and toluene, but they differentiate methanol, ethanol, and phenol in toluene solvent with the Kf values of 42, 14, and 12 M(-1), respectively, for 2, and 13, 8.2, and 8.9 M(-1), respectively, for 3. In terms of binding sites for guest molecules, the solid 3 has greater capacity than the solid 2.     

Five-fold-symmetric macrocyclic aromatic pentamers: high-affinity cation recognition, ion-pair-induced columnar stacking, and nanofibrillation

Described in this study is a conceptually new class of five-fold-symmetric cavity-containing planar pentameric macrocycles with their interior decorated by five convergently aligned, properly spaced carbonyl oxygen atoms. These cation-binding oxygens enclose a hydrophilic lumen of 2.85 ? in radius and thus display high-affinity binding toward alkali metal cations, and possibly many other cations, too. Arising from their high-affinity recognition of metal ions, these planar macrocycles form cation- or ion-pair-induced one-dimensional columnar aggregates, and subsequently fascinating fibrillation results.     

Hg2+ recognition by triptycene-derived heteracalixarenes: selectivity tuned by bridging heteroatoms and macrocyclic cavity

The binding properties of triptycene-derived oxacalixarenes containing 1,8-naphthyridine subunits 1a and 1b toward metal ions were investigated in detail by spectroscopic methods. A couple of new N,O-bridged diazadioxacalixarenes 2a, 2b were synthesized and their binding properties to metal ions were also evaluated. The results showed that the oxacalixarene 1a, a cis-isomer with a boat-like 1,3-alternate conformation and a symmetrical cavity structure, exhibited a highly selective fluorescence response toward Hg(2+) ions, while 1b, 2a and 2b did not show selective response towards any specific metal ions. Such selectivity can thus be controlled by the bridging heteroatoms and cavity structures of the macrocycles. Moreover, it was found that the fluorescence of 1a was considerably quenched upon the addition of Hg(2+), and a 1?:?2 stoichiometry host-guest complex was proposed on the basis of the Job plot and (1)H NMR titrations.     

Exploring the binding ability of polyammonium hosts for anionic substrates: selective size-dependent recognition of different phosphate anions by bis-macrocyclic receptors

Binding of mono-, di-, and triphosphate, adenosine diphosphate (ADP), and adenosine triphosphatase (ATP) with receptors L1-L3, composed of two [9]aneN(3) units separated by a 2,9-dimethylene-1,10-phenanthroline (L1), a 2,6-dimethylenepyridine (L2), or a 2,3-dimethylenequinoxaline (L3) spacer, has been studied by means of potentiometric titrations, (1)H and (31)P NMR measurements in aqueous solutions, and molecular modeling calculations. In the case of inorganic phosphates, the binding properties of the receptors appear to be determined by their geometrical features, in particular the distance between the two [9]aneN(3) units imposed by the spacer separating the two macrocyclic units. While L1 is able to selectively bind triphosphate over di- and monophosphate, L3 selectively coordinates the smaller monophosphate anion. Finally, L2 shows preferential binding of diphosphate. (1)H and (31)P NMR measurements show that the complexes are essentially stabilized by charge-charge and hydrogen-bonding interactions between the anion and the protonated amine groups of the macrocyclic subunits of the receptors. Molecular dynamics simulations suggest that the larger distance between the two macrocyclic units of L1 allows this receptor to form a larger number of hydrogen-bonding contacts with triphosphate, justifying its selectivity toward this anion. Conversely, in the case of L3, the two facing [9]aneN3 units give rise to a cleft of appropriate dimensions where the small monophosphate anion can be conveniently hosted. Considering nucleotide coordination, L1 is a better receptor for ATP and ADP than L2, thanks to the higher ability of phenanthroline to establish stabilizing π stacking and hydrophobic interactions with the adenine units of the guests.     

Self-assembly of a ternary architecture driven by cooperative Hg2+ ion binding between cucurbit[7]uril and crown ether macrocyclic hosts

A novel supramolecular assembly comprising CB[7], styrylpyridinium dye (1) and Hg(2+) forms in aqueous solution based on the hydrophobic effect and metal-ligand and ion-dipole interactions. The binding of Hg(2+) to 1·CB[7] displays positive cooperativity relative to 1 itself.     

Determination of binding energies between cyclodextrins and aromatic guest molecules by microcalorimetry

The inclusion of substituted benzoic acids in -CD or selectively methylated -CDs was investigated by titration microcalorimetry. All thermodynamic functions of the inclusion process G°, H° and S° could be obtained very accurately within one experiment. A very strong influence of the substitution pattern at both the host and the guest on the stability of the inclusion compounds was found.     

Sanglifehrin-cyclophilin interaction: degradation work,synthetic macrocyclic analogues,X-ray crystal structure,and binding data

Sanglifehrin A (SFA) is a novel immunosuppressive natural product isolated from Streptomyces sp. A92-308110. SFA has a very strong affinity for cyclophilin A (IC(50) = 6.9 +/- 0.9 nM) but is structurally different from cyclosporin A (CsA) and exerts its immunosuppressive activity via a novel mechanism. SFA has a complex molecular structure consisting of a 22-membered macrocycle, bearing in position 23 a nine-carbon tether terminated by a highly substituted spirobicyclic moiety. Selective oxidative cleavage of the C(26)=C(27) exocyclic double bond affords the spirolactam containing fragment 1 and macrolide 2. The affinity of 2 for cyclophilin (IC(50) = 29 +/- 2.1 nM) is essentially identical to SFA, which indicates that the interaction between SFA and cyclophilin A is mediated exclusively by the macrocyclic portion of the molecule. This observation was confirmed by the X-ray crystal structure resolved at 2.1 A of cyclophilin A complexed to macrolide 16, a close analogue of 2. The X-ray crystal structure showed that macrolide 16 binds to the same deep hydrophobic pocket of cyclophilin A as CsA. Additional valuable details of the structure-activity relationship were obtained by two different chemical approaches: (1) degradation work on macrolide 2 or (2) synthesis of a library of macrolide analogues using the ring-closing metathesis reaction as the key step. Altogether, it appears that the complex macrocyclic fragment of SFA is a highly optimized combination of multiple functionalities including an (E,E)-diene, a short polypropionate fragment, and an unusual tripeptide unit, which together provide an extremely strong affinity for cyclophilin A.