Selective binding of two-armed diketopiperazine receptors to side-chain-protected peptides

The binding properties of two-armed receptors based on a diketopiperazine template toward side-chain-protected peptides have been elucidated. Selective binding of these diketopiperazine receptors is not limited to side-chain-free peptides, but combinatorial on-bead assays show that also side-chain-protected peptides are recognized with high specificity. Furthermore, the screening of several dye-marked diketopiperazine receptors against an encoded side-chain-protected tripeptide library demonstrated not only their high binding specificities but also revealed that small structural changes suffice to alter the binding preferences significantly.     

Macrocyclic diketopiperazine receptors: effect of macrocyclization on the binding properties of two-armed receptors

The synthesis of macrocyclic two-armed diketopiperazine receptors and their binding properties toward peptides is described. Macrocyclization with short linkers led to receptors with significantly modified binding properties compared to their flexible open chain parent receptors, whereas with long linkers the original binding selectivities were largely retained.     

Diketopiperazine receptors: a novel class of highly selective receptors for binding small peptides

A novel class of receptors consisting of a rigid diketopiperazine backbone and peptidic side chains has been developed with the use of combinatorial chemistry. These diketopiperazine receptors interact with peptidic substrates with high specificity as shown in combinatorial on-bead assays. The central diketopiperazine moiety can be easily obtained from natural 4-hydroxyproline and serves as a rigidifying template for the peptidic modules which allow for structural as well as functional variations. Screenings of several dye-marked receptor prototypes against an encoded tripeptide library demonstrated not only the high binding specificities of the diketopiperazine receptors towards peptides but also revealed that small structural changes induce significant changes in their binding properties.     

Protein-Loop Mimetics: A Diketopiperazine-Based Template to Stabilize Loop Conformations in Cyclic Peptides Containing the NPNA and RGD Motifs

We explore here an approach to mimic the structures and biological functions of protein loops in small synthetic molecules, by grafting the loop of interest onto an organic template comprising a bicyclic diketopiperazine, prepared by the formal coupling of (2S,4S)-4-aminoproline (Pro(NH₂)) and aspartic acid (Asp). The Fmoc-protected template 4 is used to prepare cyclo(-Ala¹-Asn²-Pro³-Asn⁴-Ala⁵- Ala⁶-Temp-) ( 5 ) and cyclo(-Ala¹-Arg²-Gly³-Asp⁴-Temp-) ( 6 ) (where Temp = template derived from 4 ), containing the Asn-Pro-Asn-Ala (NPNA) and Arg-Gly-Asp (RGD) motifs. The conformational properties of these molecules are studied in aqueous solution by NMR and simulated-annealing methods. The NPNA motif, an immunodominant epitope on the circumsporozoite surface protein of the malaria parasite Plasmodium falciparum, is shown to adopt a stable type-I β-turn in 5 . The template in 5 adopts a preferred conformation with Pro(NH₂)χ₁ ≈? ?35° and the Asp moiety χ₁ ≈? 70°. A different template conformation is inferred for 6 , with Pro(NH₂)χ₁ ≈? 0°, but the ARGD loop appears by NMR to undergo rapid conformational averaging. Solid-phase binding assays reveal that 6 displays modest antagonist activity towards both the integrin α_IIbβ₃ and α_vβ₃ receptors.     

Two new fluorescent Zn2+ sensors exhibiting different sensing mode with subtle structural changes

Two novel receptors HL-1 and HL-2 without and with hydroxyl groups were designed and synthesised. Both receptors showed highly selective coordination towards Zn²⁺ and exhibited diverse sensing behaviour due to the structural variations. HL-1 showed monotonous ‘turn-on’ response towards Zn²⁺ while HL-2 displayed highly Zn²⁺ sensitive ‘turn on’ and ‘ratiometric’ properties. Detailed Job plot experiment, single crystal data, ¹H NMR, ESI-MS, UV–vis and density functional theory calculation studies were conducted to understand the binding modes of HL-1 and HL-2 with Zn²⁺. These results revealed the binding stoichiometric ratio between receptors and Zn²⁺ were 1:1 with low detection limits and high binding constants.     

Highly effective acyclic carbohydrate receptors consisting of aminopyridine, imidazole, and indole recognition units

Neutral imidazole/aminopyridine- and indole/aminopyridine-based receptors, 1 and 2, have been established as highly effective and selective carbohydrate receptors. These receptors effectively recognise neutral carbohydrates through multiple interactions, including neutral hydrogen bonds and CH...pi interactions between the sugar CH groups and the aromatic rings of the receptors. The design of these receptors was inspired by the binding motifs observed in the crystal structures of protein-carbohydrate complexes. The formation of very strong complexes with beta-glucopyranoside 5, beta-maltoside 8, and alpha-maltoside 9 in organic media has been characterised by 1H NMR spectroscopy and confirmed by a second, independent technique, namely fluorescence spectroscopy. The syntheses, molecular-modelling studies, binding properties of the receptors 1 and 2 toward selected mono- and disaccharides as well as comparative binding studies with receptors 3 and 4 are described.     

Synthesis of a Novel Tricyclic Dipeptide Template and Its Incorporation into a Cyclic Peptide Mimetic Containing an NPNA Motif

A novel tricyclic dipeptide template, formally derived by coupling (2S,4S)-4-aminoproline (Pro(NH₂)) and (S)-2-(carboxymethyl)proline (Pro(CH₂COOH)) as a diketopiperazine, has been synthesized in a form suitable for solid-phase peptide synthesis using Fmoc chemistry. This template was incorporated into the cyclic molecule cyclo(-Ala¹-Asn²-Pro³-Asn⁴-Ala⁵-Ala⁶-Temp-) (Temp = template), whose conformation in H₂O was studied by NMR methods. Average solution structures derived by restrained simulated annealing point to a highly populated βI-turn within the Asn-Pro-Asn-Ala motif and also indicate which conformations are likely to be preferred by the template.     

Hydrogen bonding receptors of tetraamide derivatives derived from thiacalix[4]arene in cone- and 1,3-alternate conformation

Novel ditopic receptors of tetraamide derivatives possessing four 2-pyridyl groups derived from thiacalix[4]arene in cone- and 1,3-alternate conformation were prepared. The structure of one of the tetraamide derivatives was confirmed by a single crystal X-ray analysis. The tetrathiacalix[4]arene tetraamides show strong intramolecular hydrogen bonding. The binding behaviour towards Ag⁺ and halides has been investigated by ¹H NMR titration experiments.     

Unprecedented chiral molecular recognition in a C3-symmetric environment.

The enantiomeric recognition of alpha-chiral primary ammonium ions has been studied with benzene-based tripodal tris(oxazoline) receptors. Contrary to the literature and our expectation, a good level of chiral discrimination is observed with one of the tripodal receptors, which provides a C3-symmetric chiral environment on guest binding. The chiral discrimination has been found to be general in the case of alpha-aryl substituted guests, suggesting pi-pi interactions as an important factor. This result raises a question with respect to the origin of the chiral discrimination since little steric or electronic difference is expected between the diastereomeric inclusion complexes. Binding studies by NMR titration and isothermal titration calorimetry show that the chiral discrimination results from the different thermodynamic stabilities between the diastereomeric complexes and that the host-guest complex formation is driven by favorable enthalpy changes with a minor negative contribution by entropy changes. The X-ray crystal structures for both of the diastereomeric inclusion complexes are resolved, which unambiguously show the binding mode and provide clues on the origin of the chiral discrimination. Bond angle analyses indicate that the minor complex experiences a larger steric strain, which is discernible when it is viewed from "three-body" interactions between the host and the guest. The guest and oxazoline phenyl rings are well stacked, indicating interplay of the pi-pi interactions. The pi-pi interactions are believed to stabilize host-guest complexes, thereby endowing the highly flexible receptors with a substantial enantio-discrimination.     

1,10-邻菲啰啉并咪唑衍生物阴离子受体的合成及识别性能

设计合成了2个1,10-邻菲啰啉并咪唑衍生物阴离子受体2-(2-羟基苯基)-1H-咪唑[4,5-f][1,10]邻菲啰啉(1)和2-(2-羟基-5-溴苯基)-1H-咪唑[4,5-f][1,10]邻菲啰啉(2), 受体2的结构由X射线单晶衍射分析确证. 通过紫外-可见光谱滴定及 ¹H NMR滴定研究了这2个受体对F^-, Cl^-, Br^-, I^-, H₂PO₄^-和AcO^- 6种阴离子的识别传感作用及作用机理. 结果表明, 受体对AcO^-, F^-和H₂PO₄^-有较强的传感作用, 溶液颜色由淡黄色变为黄色; 对Cl^-的作用较弱; 而对Br^-和I^-则无明显作用. 通过机理研究发现, 受体与F^-, H₂PO₄^-和AcO^-形成1: 1的氢键超分子, 当阴离子的量超过受体的1倍以后, 咪唑氮上的氢转移到阴离子; 受体与Cl^-以氢键形成超分子复合物, 而与Br^-和I^-作用很弱.     

Binding cooperativity of two different Lewis acid groups at the edge of ferrocene

The binding properties of heteronuclear bidentate Lewis acids, in which an organoboron and an organotin moiety are attached adjacent to each other at one of the Cp rings of ferrocene, have been studied. Treatment of [1,2-fc(SnMe2Cl)(BClMe)] (1-Cl) (fc = ferrocenediyl) with one equivalent of pyridine or 4-dimethylaminopyridine (DMAP) resulted in diastereoselective complexation of boron. Adducts 2 and 3 have been studied by multinuclear NMR, and the stereoselectivity of complexation was further confirmed by single crystal X-ray diffraction of 2. The importance of cooperative effects that involve an intramolecular B-ClSn interaction on the diastereoselectivity is evident from comparison with binding studies on the phenyl-substituted analogue [1,2-fc(SnMe2Cl)(BPhMe)] (1-Ph). Complexation of 1-Ph led to diastereomeric mixtures of adducts 4 and 5, respectively, which were identified by multinuclear NMR including NOESY experiments. The solid-state structure of one of the diastereomers of 5 was confirmed by X-ray crystallography. Facile isomerization was found in solution and the barrier of activation was determined by VT NMR studies (4: Delta(#)(298) = 54.9+/-0.4 kJ mol(-1); 5: Delta(#)(298) = 70.3+/-0.1 kJ mol(-1)). Competitive binding of pyridine to 1-Cl and [FcB(Cl)Me] (Fc = ferrocenyl) showed that cooperative effects between tin and boron lead to significant Lewis acidity enhancement. Binding of a second nucleophile in the presence of excess of base occurred also at boron. The novel zwitterionic complexes [1,2-fc(BMe(py)2)(SnMe2Cl2)] (6) and [1,2-fc(BMe(dmap)(2))(SnMe(2)Cl2)] (7) formed, which consist of boronium cation and stannate anion moieties. The structure of 7 in the solid-state was confirmed by X-ray crystallography. Multinuclear NMR data and competition experiments indicate weak binding of chloride to tin in 7 and partial dissociation in solution.     

新型Schiff碱分子钳对中性分子的识别性能研究

采用差紫外光谱法考察了3种新型Schiff碱分子钳对一系列二苯甲酮、芳香二胺的识别性能.测定了主客体间的结合常数(Ka)和自由能变化(ΔG0).结果表明,分子钳对所考察的客体显示良好的识别作用,主客体间形成1:1型超分子配合物.讨论了识别作用的推动力与形状、大小匹配和几何互补等因素对形成主客体配合物的影响,并利用核磁氢谱与计算机模拟作为辅助手段对主要的实验结果与现象进行了解释.     

Electrophoretic affinity measurements on microchip. Determination of binding affinities between diketopiperazine receptors and peptide ligands

ACE on a microchip (MC-ACE) is introduced as a fast and reliable method to determine binding affinities. It is based on monitoring the change in the ionic mobility of a receptor upon binding to a ligand, or vice versa. The method is complementary to other standard methods for binding affinity determinations, like isothermal titration calorimetry (ITC), NMR, UV-Vis spectroscopy, etc. and allows for affinity studies of weak to strong binding interactions. The method is attractive since it principally allows for the analysis of the binding affinity of multiple receptors to a given ligand and requires comparatively small quantities of the binding partners (particularly in comparison to affinity measurements on capillary). We demonstrate the applicability of MC-ACE for the determination of the binding affinities between acid-rich diketopiperazine receptors and basic tripeptides in aqueous solution.     

Synthesis of fused hydroxy dihydropyrroles and unexpected dihydropyrazine and dihydroquinoxaline derivatives based on heterocyclic ketene aminals

The one-pot four-component synthesis of highly functionalized fused hydroxyl dihydropyrroles and dihydropyrazines from readily available diamines, 1,1-bis (methylsulfanyl)-2-nitroethene, phenylglyoxal monohydrates, and C-H acids have been developed. This strategy provides an efficient, catalyst-free approach for easy access to various new hydroxyl-dihydropyrrole and dihydropyrazine rings in good to high yields. The products were confirmed by ¹H and ¹³C NMR, IR, mass, and X-ray crystal structure analyses.     

Kinetics and thermodynamics of amine and diamine signaling by a trifluoroacetyl azobenzene reporter group

[reaction: see text] (Trifluoroacetyl)azobenzene dyes were previously employed as amine reporter groups (chemosensors) in a dendrimer-based monomolecular imprinting system. Kinetic and binding studies with a range of amines and diamines show that the highly selective signaling observed for alkane diamines by these imprinted dendrimers arises from a kinetic effect due to intramolecular general base-catalyzed carbinolamine formation with the dye itself. The relationship between diamine structure and carbinolamine stability and rate of formation is described.     

4-氨基吡啶分子模板聚合物选择性识别及结合性质的研究

以4-氨基吡啶为模板分子制备了对4-氨基吡啶具有特异选择性的模板聚合物.制得的棒状聚合物经研磨、过筛后,采用平衡结合方法评价了该模板聚合物的结合特性.Scatchard分析表明,在所研究的浓度范围内,聚合物中形成了两类不同的结合位点,这两类结合位点的离解常数采用多点结合模型计算得到的值分别为6.0μmol/L和1.2mmol/L.底物选择性表明,与其它结构相似的分子相比,该聚合物对模板分子4-氨基吡啶显示了很强的结合能力.₁HNMR研究及4-氨基吡啶共振结构分析表明,模板分子与聚合物中的结合位点之间的作用为离子作用.     

Highly sensitive chiral shift reagent bearing two zinc porphyrins

A new type of chiral receptor (R,R)- or (S,S)-1b with C(2) symmetry was synthesized. An induced-fit type of binding behavior of 1b for diamines was revealed by CD spectroscopy. NMR studies demonstrated that 1b can function as a highly sensitive chiral shift reagent for the determination of the enantiomeric purity of chiral diamines, aziridine, and isoxazoline at the microgram level. [structure: see text]     

Calix[4]arene‐Based Rotaxane Host Systems for Anion Recognition

The synthesis, structure and anion binding properties of the first calix[4]arene‐based [2]rotaxane anion host systems are described. Rotaxanes 9? Cl and 12? Cl, consisting of a calix[4]arene functionalised macrocycle wheel and different pyridinium axle components, are prepared via adaption of an anion templated synthetic strategy to investigate the effect of preorganisation of the interlocked host’s binding cavity on anion binding. Rotaxane 12? Cl contains a conformationally flexible pyridinium axle, whereas rotaxane 9? Cl incorporates a more preorganised pyridinium axle component. The X‐ray crystal structure of 9? Cl and solution phase ¹H NMR spectroscopy demonstrate the successful interlocking of the calix[4]arene macrocycle and pyridinium axle components in the rotaxane structures. Following removal of the chloride anion template, anion binding studies on the resulting rotaxanes 9? PF₆ and 12? PF₆ reveal the importance of preorganisation of the host binding cavity on anion binding. The more preorganised rotaxane 9? PF₆ is the superior anion host system. The interlocked host cavity is selective for chloride in 1:1 CDCl₃/CD₃OD and remains selective for chloride and bromide in 10 % aqueous media over the more basic oxoanions. Rotaxane 12? PF₆ with a relatively conformationally flexible binding cavity is a less effective and discriminating anion host system although the rotaxane still binds halide anions in preference to oxoanions.     

(Thio)ureido anion receptors based on a 1,3-alternate oxacalix[2]arene[2]pyrimidine scaffold

In pursuit of highly preorganized macrocyclic host molecules for the complexation of anions, a series of oxacalix[2]arene[2]pyrimidine-based bis(thio)ureido receptors were synthesized and fully characterized. The pincer-like 1,3-alternate conformation of the oxacalix[4]arene scaffold, essential for an efficient host-guest interaction, was visualized by single-crystal X-ray analysis and supported by variable-temperature NMR studies. The anion binding properties of the receptors were evaluated via (1)H NMR titration experiments, showing intermolecular interactions with H(2)PO(4)(-), AcO(-), BzO(-), and Cl(-) ions. The host molecule bearing 4-nitrophenyl substituents on the bisurea binding pocket showed association constants in the range of 200-400 M(-1) in the strongly competitive solvent mixture of DMSO/0.5% H(2)O.     

Synthesis and peptide binding properties of methoxypyrrole amino acids (MOPAS)

[structure: see text] Methoxypyrrole amino acids (MOPAS) have been prepared and were introduced into small peptides with hairpin structures. The intra- and intermolecular binding properties of this heterocyclic amino acid mimicking a dipeptido beta-strand was investigated by NMR titration and X-ray crystal structure analysis. The data reveal a hydrogen bonding pattern that is complementary to a peptide beta-sheet.