Stefan Kubik

Conformation and anion binding properties of cyclic hexapeptides containing L-4-hydroxyproline and 6-aminopicolinic acid subunits

Two cyclic hexapeptides containing alternating all R and all S configured l-(4R/S)-hydroxyproline and 6-aminopicolinic acid subunits are presented, and the influence of the hydroxyl groups on the solubility, conformation, and receptor properties is investigated. Cyclopeptide 2, containing the natural 4R configured hydroxyproline, adopts a conformation similar to that of the unsubstituted peptide 1, which is able to bind anions such as halides and sulfate in aqueous solution. 2 also interacts with these anions, but whereas 1 forms sandwich type 2:1 complexes, in which the anion is bound by two cyclopeptide moieties, 2 forms 1:1 complexes. The stabilities of the halide and sulfate complexes of 2 range between 100 and 102 M−1 in 80% D2O/CD3OD. Complex formation is detectable even in water, but with slightly smaller stability constants. Using this information a quantitative evaluation of the stability of the 2:1 complexes of 1, for which overall stability constants in the order 104 to 105 M−2 in 80% D2O/CD3OD were observed, was made. In contrast to 2, the conformation of 3, containing the non-natural 4S configured hydroxyproline, is strongly affected by the presence of the hydroxyl groups. In d6-DMSO and methanol/water mixtures a slow conformational equilibrium between two C3-symmetrical conformers is observed, and 3 is thus much less preorganized for anion binding than either 1 or 2.

Dynamic combinatorial development of a neutral synthetic receptor that binds sulfate with nanomolar affinity in aqueous solution

Using dynamic combinatorial disulfide chemistry we have developed a new generation of neutral synthetic receptors for anions, based on a macrobicyclic peptide structure. These receptors show an exceptional affinity and selectivity for sulfate ions in aqueous solution [log K(a) = 8.67 in 41 mol% (67 volume%) acetonitrile in water]. The high affinity depends on a delicate balance between rigidity and flexibility in the structure of the receptor.

Anion-binding properties of a cyclic pseudohexapeptide containing 1,5-disubstituted 1,2,3-triazole subunits.

A C(3) symmetric cyclic pseudohexapeptide containing 2-aminopicoline-derived subunits and 1,5-disubstituted 1,2,3-triazole rings is introduced as a potent anion receptor. This macrocycle was designed to mimic both the conformation and the receptor properties of a previously described cyclic hexapeptide containing alternating L-proline and 6-aminopicolinic acid subunits. Conformational analyses demonstrate that the cyclic peptide and the cyclic pseudopeptide are structurally closely related. Most importantly, both exhibit a converging arrangement of the NH groups, hence a good preorganization for anion binding. As a consequence, the pseudopeptide also very efficiently interacts with halide and sulfate ions, and this is the case even in competitive aqueous solvent mixtures. However, there are clear differences in the structures of both compounds, which translate into characteristic differences in receptor properties. Specifically, (i) the pseudopeptide possesses an anion affinity intrinsically higher than that of the cyclopeptide, (ii) the pseudopeptide is well preorganized for anion binding in a wider range of solvents from aprotic to protic, (iii) anion affinity in aprotic solvents is very high and associated with complexation equilibria that are slow on the NMR time-scale, (iv) the propensity of the pseudopeptide to form sandwich-type 2:1 complexes with two receptor molecules surrounding one anion is significantly lower than that of the cyclopeptide. A solvent-dependent calorimetric characterization of the binding equilibria of both compounds provided clear evidence for the stabilizing effect of hydrophobic interactions between the receptor subunits in such 2:1 complexes. The pseudopeptide thus represents the first member of a new family of anion receptors whose properties may be fine-tuned by varying the side chains in the periphery of the cavity.

Synthesis of α,α-dialkylated amino acids with adenine or thymine residues a new mild and facile hydrolysis of hydantoins

Abstract The synthesis of α,α-dialkylated amino acids which contain two adenine or thymine residues in their side chains is presented. In this context, a mild method for the cleavage of hydantoins is introduced.

Circular dichroism and ultraviolet spectroscopyof complexes of amylose

Abstract The circular dichroism of the complexes formed between slightly hydroxypropylated amylose and cyclomalto-hexaose, -heptaose, and -octaose ( α -, β-, and γ -cyclodextrin) with nine different achiral ketones and phenolphthalein has been investigated. In the complexes with the ketones, the amylose helix has a conformation with six glucose units per turn, whereas, in the complex with phenolphthalein, it has seven.

Influence of linker structure on the anion binding affinity of biscyclopeptides

A systematic analysis is presented on the influence of the linking unit between two cyclopeptide rings on the affinity of such biscyclopeptide-based anion receptors in aqueous solvent mixtures. Although the differences in the affinity and selectivity of these receptors towards a given anion are not very pronounced, there are profound differences in the thermodynamics of anion complexation. Enthalpic and entropic contributions both (1) play a role in determining the binding affinity and (2) show significant variation as the linking structure is changed. A decrease in conformational rigidity of the linker improves the entropic advantage for complex formation, but not necessarily the overall complex stability. This effect may be due, in part, to the fact that structural constraints within more rigid linkers might prevent efficient interactions between the host and guest. The optimal linker, which exhibits both favourable enthalpic and entropic contributions, was identified using de novo structure-based design methods as implemented in the HostDesigner software.

A Cyclopeptide‐Derived Molecular Cage for Sulfate Ions That Closes with a Click

The 2:1 sandwich-type complexes formed between a cyclopeptide with alternating L-proline and 6-aminopicolinic acid subunits and inorganic anions can be stabilized by covalently linking a tris-alkyne and a tris-azide derivative of this peptide through copper-catalyzed azide-alkyne cycloaddition. The resulting triply linked bis-cyclopeptide can interact with anions such as sulfate ions in aqueous solution by including them into the cavity between the two cyclopeptide rings, where they can form hydrogen bonds to amide NH groups, distributed along the inner surface. The binding kinetics of this system differ significantly from those of a bis-cyclopeptide that contains only one linker because the rate of guest exchange is considerably slower. Thermodynamically, the stability of the sulfate complex of the triply linked bis-cyclopeptide approaches a log K(a) value of 6 in H(2)O/CH(3)OH 1:1 (v/v) which is, however, only approximately one order of magnitude larger than affinity of the more flexible monolinked analogue. Titration calorimetry revealed that this behavior is mainly due to the change in the binding enthalpy from exothermic to endothermic upon increasing the number of linkers. Results from NMR spectroscopy and X-ray crystallography indicate that the mono- and triply linked bis-cyclopeptides adopt similar conformations in their complexes with sulfate ions, but the complex formation is enthalpically unfavorable for the cage. The substantial entropic contribution to sulfate complexation of this receptor more than compensates for this disadvantage, so that the overall sulfate affinity of both bis-cyclopeptides ends up in the same range. These investigations provide important insight into the structure-property relationships of such receptors, thus leading the way to further structural improvement.

Fine Tuning of the Cation Affinity of Artificial Receptors Based on Cyclic Peptides by Intramolecular Conformational Control

A series of cyclic hexapeptides consisting of alternating 4-substituted 3-aminobenzoic acid units (R = CH3, Cl, CH2OCH3, OCH3, COOCH3) and residues of the natural amino acid proline has been prepared and their ion affinities have been investigated. Whereas the unsubstituted parent compound (R = H) is able to bind cations through cation−π interactions with the aromatic subunits, as well as anions through hydrogen bonding with the peptide NH groups, the introduction of substituents at the 4-positions of the aromatic rings results in complete loss of the anion affinity. The cation complex stabilities depend on the substituents and cover a wide range from Ka = 140 M−1 for R = CH3 to Ka = 10800 M−1 for R = COOCH3 (Ka = 1260 M−1 for R = H) with n-butyltrimethylammonium picrate. The conformations of the peptides in solution have been determined by one- and two-dimensional NMR techniques and FT-IR spectroscopy. It was found that all the substituents prevent the peptides from adopting the necessary conformation for anion binding. For one receptor (R = OCH3), the results have been corroborated by a crystal structure determination. AM1 calculations have been used to estimate the electrostatic potential surfaces of the substituted aromatic subunits. The variation in the cation complex stabilities can be mainly attributed to the effects of the substituents on the solution conformations of the peptides. The influence of the substituents on the electrostatic potentials of the aromatic peptide subunits appears to be less important.

Structural Analysis of an Isolated Cyclic Tetrapeptide and its Monohydrate by Combined IR/UV Spectroscopy

Cyclopeptides are an important class of substances in nature, and their physiological effects are frequently based on the tendency to form bioactive conformations. Therefore the investigation of their structure yields an understanding of their functionalities. Mass-selective combined IR/UV spectroscopy in molecular beam experiments represents an ideal tool for structural analyses on isolated molecules in the gas phase, such as the investigated cyclo[L-Tyr(Me)-D-Pro](2) peptide and its complexes with water. Using the chosen spectroscopic method in combination with DFT calculations, an assignment of a structure with two intramolecular hydrogen bonds for the naked cyclopeptide is possible. For the monohydrated cluster two isomers have to be discussed: in one of them the water molecule is simply attached to the assigned monomer structure as hydrogen donor, whereas the second isomer can be characterized by a water molecule that is inserted into one of the intramolecular hydrogen bonds.

Highly efficient cyclosarin degradation mediated by a β-cyclodextrin derivative containing an oxime-derived substituent

Summary The potential of appropriately substituted cyclodextrins to act as scavengers for neurotoxic organophosphonates under physiological conditions was evaluated. To this end, a series of derivatives containing substituents with an aldoxime or a ketoxime moiety along the narrow opening of the β-cyclodextrin cavity was synthesized, and the ability of these compounds to reduce the inhibitory effect of the neurotoxic organophosphonate cyclosarin on its key target, acetylcholinesterase, was assessed in vitro. All compounds exhibited a larger effect than native β-cyclodextrin, and characteristic differences were noted. These differences in activity were correlated with the structural and electronic parameters of the substituents. In addition, the relatively strong effect of the cyclodextrin derivatives on cyclosarin degradation and, in particular, the observed enantioselectivity are good indications that noncovalent interactions between the cyclodextrin ring and the substrate, presumably involving the inclusion of the cyclohexyl moiety of cyclosarin into the cyclodextrin cavity, contribute to the mode of action. Among the nine compounds investigated, one exhibited remarkable activity, completely preventing acetylcholinesterase inhibition by the (−)-enantiomer of cyclosarin within seconds under the conditions of the assay. Thus, these investigations demonstrate that decoration of cyclodextrins with appropriate substituents represents a promising approach for the development of scavengers able to detoxify highly toxic nerve agents.