Aryl phosphate complexation by cationic cyclodextrins. An enthalpic advantage for guanidinium over ammonium and unusual enthalpy-entropy compensation

A Quinoline-Appended Cyclodextrin Derivative as a Highly Selective Receptor and Colorimetric Probe for Nucleotides

The design and development of specific recognition and sensing systems for biologically important anionic species has received growing attention in recent years, as they play significant roles in biology, pharmacy, and environmental sciences. Herein, a new supramolecular sensing probe L1 was developed for highly selective differentiation of nucleotides. L1 displayed extremely marked absorption and emission differentiation upon binding with nucleotide homologs of AMP, ADP, and ATP, due to the divergent spatial orientations of guests upon binding, which allowed for a naked-eye colorimetric differentiation for nucleotides. A differentiating mechanism was unambiguously rationalized by using various spectroscopic studies and theoretical calculations. Furthermore, we successfully demonstrated that L1 can be applied to the real-time monitoring of the enzyme-catalyzed phosphorylation/dephosphorylation processes and thus demonstrated an unprecedented visualizable strategy for selectively differentiating the structurally similar nucleotides and real-time monitoring of biological processes via fluorescent and colorimetric changes.

A biomimetic strategy for the selective recognition of organophosphates in 100% water: synergies of electrostatic interactions, cavity embedment and metal coordination

A biomimetic receptor allows selective recognition of organophosphates in water thanks to multipoint recognition associating coordination, electrostatics and cavity hosting.

Development of Dipicolylamine-Modified Cyclodextrins for the Design of Selective Guest-Responsive Receptors for ATP

The construction of supramolecular recognition systems based on specific host–guest interactions has been studied in order to design selective chemical sensors. In this study, guest-responsive receptors for ATP have been designed with cyclodextrins (CyDs) as a basic prototype of the turn-on type fluorescent indicator. We synthesized dipicolylamine (DPA)-modified CyD–Cu²⁺ complexes (Cu·1α, Cu·1β, and Cu·1γ), and evaluated their recognition capabilities toward phosphoric acid derivatives in water. The UV-Vis absorption and fluorescence spectra revealed that Cu·1β selectively recognized ATP over other organic and inorganic phosphates, and that β-CyD had the most suitable cavity size for complexation with ATP. The 1D and 2D NMR analyses suggested that the ATP recognition was based on the host–guest interaction between the adenine moiety of ATP and the CyD cavity, as well as the recognition of phosphoric moieties by the Cu²⁺–DPA complex site. The specific interactions between the CyD cavity and the nucleobases enabled us to distinguish ATP from other nucleoside triphosphates, such as guanosine triphosphate (GTP), uridine triphosphate (UTP), and cytidine triphosphate (CTP). This study clarified the basic mechanisms of molecular recognition by modified CyDs, and suggested the potential for further application of CyDs in the design of highly selective supramolecular recognition systems for certain molecular targets in water.

Design and Function of Supramolecular Recognition Systems Based on Guest-Targeting Probe-Modified Cyclodextrin Receptors for ATP

In this study, we have developed a rational design strategy to obtain highly selective supramolecular recognition systems of cyclodextrins (CyDs) on the basis of the lock and key principle. We designed and synthesized dipicolylamine (dpa)-modified γ-CyD-Cu²⁺ complexes possessing an azobenzene unit (Cu·1-γ-CyD) and examined how they recognized phosphoric acid derivatives in water. The results revealed that Cu·1-γ-CyD recognized ATP with high selectivity over other phosphoric acid derivatives. The significant blue shift in the UV-vis spectra and ¹H NMR analysis suggested that the selective ATP recognition was based on the multipoint interactions between the adenine moiety of ATP and both the CyD cavity and the azobenzene unit in addition to the recognition of phosphoric moieties by the Cu-dpa complex site. Our unique receptor made it capable of distinguishing ATP from AMP and ADP, revealing the discrimination of even a length of one phosphoric group. This study demonstrates that, compared to conventional recognition systems of CyDs, this multipoint recognition system confers a higher degree of selectivity for certain organic molecules, such as ATP, over their similar derivatives.

Surface charge tunability as a powerful strategy to control electrostatic interaction for high efficiency silencing, using tailored oligopeptide-modified poly(beta-amino ester)s (PBAEs)

Here we present an extended family of pBAEs that incorporate terminal oligopeptide moieties synthesized from both positive and negative amino acids. Polymer formulations of mixtures of negative and positive oligopeptide-modified pBAEs are capable of condensing siRNA into discrete nanoparticles. We have demonstrated that efficient delivery of nucleic acids in a cell-type dependent manner can be achieved by careful control of the pBAE formulation. In addition, our approach of adding differently charged oligopeptides to the termini of poly(β-amino ester)s is of great interest for the design of tailored complexes having specific features, such as tuneable zeta potential. We anticipate that this surface charge tunability may be a powerful strategy to control unwanted electrostatic interactions, while preserving high silencing efficiency and reduced toxicity.

Development and mechanistic studies of an optimized receptor for trimethyllysine using iterative redesign by dynamic combinatorial chemistry

Iterative monomer redesign leads to a Kme₃-peptide receptor with 10-fold tighter affinity and 5-fold improved selectivity over Kme₂ than the original receptor. Thermodynamic analysis provides insight into this improvement.

Association mechanism of S-dinitrophenyl glutathione with two glutathione peroxidase mimics: 2, 2 cent-ditelluro- and 2, 2 cent-diseleno-bridged b-cyclodextrins

Complex formation of the glutathione peroxidase mimics 2,2′-ditelluro-bridged β-cyclodextrin (1) and 2,2′-diseleno-bridged β-cyclodextrin (2), with S-substituted dinitrophenyl glutathione (3) were determined by ultraviolet-visible (UV-Vis) absorption spectroscopy in phosphate buffer (pH 7.4) and ¹H-NMR spectroscopy. Molecular mechanics (MM2) modeling calculations were used to deduce a three-dimensional model for each complex. The dinitrophenyl (DNP) group of 3 appears to penetrate the cavity of β-cyclodextrin (β-CD) or 1, but it is located between the two secondary rims of 2. The complexes’ stability constants (K_s) from 19 to 37 °C, Gibbs free energy changes (ΔG°), ΔH° and TΔS° for 1:1 complexes of β-CD, 1 and 2 with ligand 3 as obtained from UV-Vis spectra were compared. The binding of 3 by the three cyclodextrin hosts generally decreased in the order of 1>2>β-CD. The binding ability of 3 by β-CD, 1 and 2 was discussed with regard to the size/shape-fit concept, the induced-fit interaction, and the cooperative interaction of the dual hydrophobic cavities. The binding ability of 1>2 indicated that the length of linkage between two cyclodextrin units plays a crucial role in the interaction with 3.

Arginine coordination in enzymatic phosphoryl transfer: evaluation of the effect of Arg166 mutations in Escherichia coli alkaline phosphatase

Arginine residues are commonly found in the active sites of enzymes catalyzing phosphoryl transfer reactions. Numerous site-directed mutagenesis experiments establish the importance of these residues for efficient catalysis, but their role in catalysis is not clear. To examine the role of arginine residues in the phosphoryl transfer reaction, we have measured the consequences of mutations to arginine 166 in Escherichia coli alkaline phosphatase on hydrolysis of ethyl phosphate, on individual reaction steps in the hydrolysis of the covalent enzyme-phosphoryl intermediate, and on thio substitution effects. The results show that the role of the arginine side chain extends beyond its positive charge, as the Arg166Lys mutant is as compromised in activity as Arg166Ser. Through measurement of individual reaction steps, we construct a free energy profile for the hydrolysis of the enzyme-phosphate intermediate. This analysis indicates that the arginine side chain strengthens binding by approximately 3 kcal/mol and provides an additional 1-2 kcal/mol stabilization of the chemical transition state. A 2.1 A X-ray diffraction structure of Arg166Ser AP is presented, which shows little difference in enzyme structure compared to the wild-type enzyme but shows a significant reorientation of the bound phosphate. Altogether, these results support a model in which the arginine contributes to catalysis through binding interactions and through additional transition state stabilization that may arise from complementarity of the guanidinum group to the geometry of the trigonal bipyramidal transition state.

Transverse tunneling through DNA hydrogen bonded to an electrode

Guanidinium ions tethered to an electrode form electrical contacts to DNA via hydrogen bonding with the backbone phosphates, thus providing a sequence-independent electrical connector for native DNA submerged in an aqueous electrolyte. DNA adlayers on a guanidinium modified electrode can be imaged by scanning tunneling microscopy with tens of pS gap conductance. The image resolution suggests that multiatom contacts contribute to the tunnel conductance, so we estimate that the single-nucleotide pair conductance may be on the order of 1 pS.

Thermodynamics of Hydrophobic Interactions: Entropic Recognition of a Hydrophobic Moiety by Poly(Ethylene Oxide)–Zinc Porphyrin Conjugates

The recognition of 4-alkylpyridines by water-soluble poly(ethylene oxide)-zinc porphyrin conjugates was studied with a focus on the thermodynamic parameters of binding. Microcalorimetric studies indicated that binding of the alkyl group of the guest in water is driven by the entropic term (delta DeltaH0 = DeltaH0(4-pentylpyridine) - DeltaH0(4-methylpyridine) = +1.7 kJ mol(-1), deltaT DeltaS0 = TDeltaS0(4-pentylpyridine) - TDeltaS0(4-methylpyridine) = +11.8 kJ mol(-1) at 298 K), thus showing the significance of water reorganization during host-guest interaction. The enthalpy-entropy compensation temperature of binding of 4-alkylpyridines was as low as 38 K; only below this temperature could the enthalpic term be a driving force. The binding affinity was modulated by the addition of cations and by varying the degree of polymerization of poly(ethylene oxide), which suggests that guest binding is coupled with polymer conformation.

Polyethylene Imine Derivatives (‘Synzymes') Accelerate Phosphate Transfer in the Absence of Metal

The efficient integration of binding, catalysis, and multiple turnovers remains a challenge in building enzyme models. We report that systematic derivatization of polyethylene imine (PEI) with alkyl (C(2)-C(12)), benzyl, and guanidinium groups gives rise to catalysts ('synzymes') with rate accelerations (k(cat)/k(uncat)) of up to 10(4) for the intramolecular transesterification of 2-hydroxypropyl-p-nitrophenyl phosphate, HPNP, in the absence of metal. The synzymes exhibit saturation kinetics (K(M) approximately 250 microM, k(cat) approximately 0.5 min(-1)) and up to 2340 turnovers per polymer molecule. Catalysis can be specifically and competitively inhibited by anionic and hydrophobic small molecules. The efficacy of catalysis is determined by the PEI derivatization pattern. The derivatization reagents exert a synergistic effect, i.e., their combinations increase catalysis by more than the sum of each single modification. The pH-rate profile for k(cat)/K(M) is bell shaped with a maximum at pH 7.85 and can be explained as a combination of two effects that both have to be operative for optimal activity: K(M) increases at high pH due to deprotonation of PEI amines that bind the anionic substrate and kcat decreases as the availability of hydroxide decreases at low pH. Thus, catalysis is based on substrate binding by positively charged amine groups and the presence of hydroxide ion in active sites in an environment that is tuned for efficient catalysis. Inhibition studies suggest that the basis of catalysis and multiple turnovers is differential molecular recognition of the doubly negatively charged transition state (over singly charged ground state and product): this contributes a factor of at least 5-10-fold to catalysis and product release.

Per(6-guanidino-6-deoxy)cyclodextrins: synthesis, characterisation and binding behaviour toward selected small molecules and DNA

Per(6-guanidino-6-deoxy)-cyclodextrins , and are novel derivatives, resulting from homogeneous introduction of the guanidino group at the primary side of alpha-, beta- and gamma-cyclodextrins. The products were obtained from the corresponding amino derivatives, as direct guanidinylation of the known bromo-cyclodextrins provided mixtures. The new compounds were fully characterized by NMR spectroscopy and other analytical methods, and their interaction with guest molecules was studied. Strong complexation with 4-nitrophenyl phosphate () disodium salt was observed (K(binding) approximately 5 x 10(4) M(-1)), whereas the non-phosphorylated substrate nitrobenzene () formed a very weak complex. 2D ROESY spectra revealed cavity inclusion in both cases, however the orientation of was opposite to that of , such that the phosphate group is oriented toward the primary side facing the guanidine groups. The strong affinity of towards the phosphorylated guest suggested that interaction with DNA was possible. The new compounds were found to completely inhibit the migration of ultra pure calf thymus DNA during agarose gel electrophoresis, whereas no effects were observed with guanidine alone or with the plain cyclodextrins. Further, the condensation of DNA into nanoparticles in the presence of was demonstrated by atomic force microscopy, confirming strong electrostatic interaction between the biopolymer and the multicationic products . The strong guanidine-phosphate interactions between and DNA were therefore attributed to the clustering of the guanidine groups in the primary area of the cyclodextrin. Cavity effects could not be assessed.

How cyclodextrins can mask their toxic effect on the blood–brain barrier

The toxicity of monosubstituted n-alkyldimethylammonium-beta-cyclodextrins (DMA-C(n)-CD with n=2, 4 and 12) towards endothelial cells of an in vitro model of the blood-brain barrier (BBB) was evaluated and compared to that of the native beta-CD. DMA-C(12)-CD was found to be non-toxic below 10mM due to the self-inclusion of the alkyl chain in the CD cavity. A high percentage of passage (30%) of DMA-C(12)-CD through the endothelial cells has been measured.

Kanamycin A-derived cationic lipids as vectors for gene transfection

Cationic lipids nowadays constitute a promising alternative to recombinant viruses for gene transfer. We have recently explored the transfection potential of a new class of lipids based upon the use of aminoglycosides as cationic polar headgroups. The encouraging results obtained with a first cholesterol derivative of kanamycin A prompted us to investigate this family of vectors further, by modulating the constituent structural units of the cationic lipid. For this study, we have investigated the transfection properties of a series of new derivatives based on a kanamycin A scaffold. The results primarily confirm that aminoglycoside-based lipids are efficient vectors for gene transfection both in vitro and in vivo (mouse airways). Furthermore, a combination of transfection and physicochemical data revealed that some modifications of the constitutive subunits of kanamycin A-based vectors were associated with substantial changes in their transfection properties.

Probing Binding-Mode Diversity in Guanidinium-Oxoanion Host-Guest Systems

An attempt to experimentally estimate the role of binding-mode diversity (structural fuzziness) on the molecular recognition seen in the prominent guanidinium-oxoanion host-guest pair is described. The global heat response as measured by isothermal titration calorimetry in acetonitrile, which was obtained from the interaction of five different but structurally closely related guanidinium hosts with three rigid phosphinate guests of decreasing accessibility of their binding sites, is correlated to provide a trend analysis. All host-guest associations of 1:1 stoichiometry in this series are strongly enthalpy-driven. The change in complexation entropy can be related to the tightness of the mutual fit of the host-guest partners, which approaches a minimum limit and is interpreted as the unique lock-and-key binding mode. The ordinary host-guest complexation in this ensemble features substantial positive entropy changes that correlate inversely with the binding interface area. This finding excludes desolvation effects as the major cause of entropy production, and provides evidence for the existence of a broad variety of complex configurations rather than a single binding mode to represent the associated host-guest pair. This result bears on the molecular design of systems that vitally depend on structural fidelity, such as nanoassemblies or homogeneous catalysis.