Strapped and other topographically nonplanar calixpyrrole analogues. Improved anion receptors

Calixpyrroles and related macrocycles are non-aromatic synthetic anion receptors that have attracted considerable attention in recent years. The unfunctionalized, parent calix[4]pyrrole system, also known as octamethylporphyrinogen, may be prepared in one step and in high yield from pyrrole and acetone, and is an effective anion receptor, showing a preference for fluoride, phosphate, carboxylate and chloride anions in organic media. Efforts to improve the anion binding affinity of calix[4]pyrrole and to modify its inherent selectivity have led to the synthesis of a variety of new, modified calixpyrroles. Among the most effective of these are derivatives that contain bridging "straps". In this Feature Article, the preparation and properties of these and other topographically nonplanar calixpyrrole analogues are reviewed from the perspective of the anion recognition chemist.     

Bismethylene triphosphate nucleotides of uridine 4-phosphate analogues: a new class of anionic pyrimidine nucleotide analogues

Cytidine-5'-triphosphate synthase (CTPS) catalyzes the formation of cytidine triphosphate (CTP) from glutamine, uridine 5'-triphosphate (UTP), and adenosine 5'-triphosphate (ATP). This reaction proceeds via formation of the high-energy intermediate UTP-4-phosphate (UTP-4-P). Stable analogues of UTP-4-P may be potent inhibitors of CTPS and useful as lead structures for the development of anticancer and antiviral agents. Several bismethylene triphosphate (BMT) nucleotides of uridine 4-phosphate (U-4-P) analogues have been prepared. A key step was the selective methanolysis, with the aid of a tin catalyst, of the 5' ester moiety of 2',3',5'-tri-O-acetyl or tri-O-benzoyl U-4-P analogues. We believe this represents the first general approach to the selective cleavage of 5' benzoyl esters in benzoylated nucleosides. Mitsunobu coupling of these 5'-deprotected U-4-P analogues to an unsymmetrical, protected BMT bearing a free phosphonic acid moiety at one of the terminal positions gave fully protected BMT-U-4-P analogues. Global deprotection of these species was achieved using TMSBr followed by treatment with NH4OH-MeOH or NH4OH-pyridine. The resulting BMT nucleotides represent a new class of anionic pyrimidine nucleotide analogues.     

硫脲类阴离子受体的设计合成与阴离子识别

硫脲类化合物具有生物活性,是优良的氢键供体,与阴离子特别是含氧阴离子形成氢键配合物。本文设计合成了系列二苯基硫脲衍生物,通过取代基效应调控硫脲衍生物分子内电转移过程,阴离子与硫脲基团结合后,增强了分子内供体的给电子能力,进一步促进电荷转移过程,据此识别不同的阴离子。由于主体分子与阴离子间形成氢键的能力及阴离子碱性的差异,可达到选择性结合的目的。     

The recognition of nucleotides with model beta-hairpin receptors: investigation of critical contacts and nucleotide selectivity

[reaction: see text] We have investigated the factors that contribute to binding of ATP by a designed 12-residue beta-hairpin peptide, WKWK, and have determined its selectivity for binding to the naturally occurring nucleotide triphosphates. We have previously shown that WKWK creates an ATP binding pocket on one face of the beta-hairpin consisting of two Trp and two Lys residues. Mutation of the two Lys residues on the binding face of the beta-hairpin resulted in a lower affinity, indicating that each is involved in ATP binding and that each residue contributes approximately -1.5 kcal/mol to the energy of complexation. Replacement of either Trp residue of the ATP binding pocket with Phe or Leu destabilizes the complex formed with ATP by approximately 1 kcal/mol, indicating that both Trp residues participate in interactions with ATP. For binding to the nucleotide triphosphates, the order of binding affinity was shown to follow dTTP > GTP > ATP > CTP, with differences in binding energies spanning as much as 1.6 kcal/mol. NMR analysis demonstrates that both aromatic interactions with the Trp side chains and CH-pi interactions between the ribose protons and the Trp residues may contribute significantly to binding. The results from our model system provide useful thermodynamic information regarding protein-nucleic acid interactions that occur at the surface of a beta-sheet.     

Quantitative analysis of receptors for adenosine nucleotides obtained via in vitro selection from a library incorporating a cationic nucleotide analog.

5-(3"-Aminopropynyl)-2'-deoxyuridine (dJ), a modified nucleoside with a side chain carrying a cationic functional group, was incorporated into an oligonucleotide library, which was amplified using the Vent DNA polymerase in a polymerase chain reaction (PCR). When coupled to an in vitro selection procedure, PCR amplification generated receptors that bind ATP. This is the first example of an in vitro selection generating oligonucleotide receptors where the oligonucleotide library has incorporated a cationic nucleotide functionality. The selection yielded functionalized receptors having sequences differing from a motif known to arise in a standard selection experiment using only natural nucleotides. Surprisingly, both the natural and the functionalized motifs convergently evolved to bind not one, but two ATP molecules cooperatively. Likewise, the affinity of the receptors for ATP had converged; in both cases, the receptors are half saturated at the 3 mM concentrations of ATP presented during the selection. The convergence of phenotype suggests that the outcome of this selection experiment was determined by features of the environment during which selection occurs, in particular, a highly loaded affinity resin used in the selection step. Further, the convergence of phenotype suggests that the optimal molecular phenotype has been achieved by both selections for the selection conditions. This interplay between environmental conditions demanding a function of a biopolymer and the ability of the biopolymer to deliver that function is strictly analogous to that observed during natural selection, illustrating the nature of life as a self-sustaining chemical system capable of Darwinian evolution.     

两种阴离子识别受体的合成及识别研究

两种同时包含酚羟基和二酰胺基团的的阴离子识别受体被设计和合成,通过紫外-可见光谱研究了受体分子和不同阴离子客体间的识别作用。研究结果发现,受体分子1在干燥的DMSO溶液中能选择性识别AcO-,其识别顺序为:AcO->F->H2PO4->Cl-,Br-,I-;受体分子2显示出对F-较强的识别作用,其识别顺序为:F->AcO->H2PO4-,Cl-,Br-,I-。同时通过紫外-可见光谱和核磁滴定实验,研究了只包含二酰胺基团的受体分子3对阴离子的识别作用,发现起识别作用的是二酰胺基团,但这种作用力非常小,不能有效地进行阴离子识别。进一步通过核磁共振滴定实验和理论研究,证实受体分子1和2在有效的阴离子识别过程中,酚羟基比酰胺基团起着更为重要的作用。     

Design and synthesis of novel tweezer anion receptors based on deoxycholic acid

A novel type of molecular tweezer receptors based on deoxycholic acid has been designed and synthesized and their binding properties were examined by UV-vis spectral titration. These molecular tweezers showed a high selectivity toward F- over Cl-,Br-, I-, AcO-, H2PO4-.     

Green approaches for the synthesis of nucleotides,their conjugates and analogues

Abstract

We have developed original one-pot and protecting group-free approaches, which are also user-friendly and reliable, to synthesize nucleotides and derivatives starting from nucleoside 5’-monophosphates. Both methods present convenient set-up, i.e., non-dry solvents and reagents, substrates in their sodium or acid form, and commercially available and cheap phosphorus reagents as sodium and potassium salts.     

新型脱氧胆酸钳形阴离子受体的设计合成及其对阴离子的识别性能研究

具有对阴离子选择性识别的人工受体的设计合成是生物有机化学和超分子化学前沿富于挑战性的领域之一[1].在许多识别阴离子的人工受体化合物中,脲和硫脲衍生物是重要的中性受体化合物之一.     

Syntheses and base-pairing properties of locked nucleic acid nucleotides containing hypoxanthine, 2,6-diaminopurine, and 2-aminopurine nucleobases

Second generation 2'-O,4'-C-methylene-linked nucleotides 1-3 containing hypoxanthine, 2,6-diaminopurine, and 2-aminopurine nucleobases were synthesized and incorporated into locked nucleic acid (LNA) oligonucleotides by means of the automated phosphoramidite method. The required phosphoramidite monomeric units were efficiently prepared via convergent synthesis. The glycosyl donor 4 was stereoselectively coupled with hypoxanthine and 6-chloro-2-aminopurine to give the 4'-C-branched nucleosides 5 and 17. The methods for conversion of 5 and 17 into phosphoramidites 11, 25, and 29 were developed and described in full details for the first time. Hybridization properties of LNA octamers containing the new LNA nucleotides were assessed against perfect and singly mismatched DNA. The binding studies revealed that all LNA octamers hybridize very efficiently to DNA following Watson-Crick base-pairing rules with increased binding affinity compared to the DNA analogues. The unique properties of the nucleotides 1-3 make them very useful for further strengthening of the LNA technology.     

Novel anion receptors for selective recognition of dimethyl phosphinate and carboxylate

We have designed and synthesized new anion receptors 1 and 2, which have amide NH, pyrrole NH and vinyl CH as hydrogen bond donors. These receptors are selective for dimethyl phosphinate and carboxylates. Due to electron withdrawing effect of the cyano group which is trans to the vinyl hydrogen with respect to carbon-carbon double bond, receptor 1 has higher binding constants for phosphinate and carboxylate than those of receptor 2. Modeling studies shows that cyano group polarized all three hydrogens through planar π-electron network. In addition, receptor 1 gave orange colored 1,4-addition product for cyanide.     

New strategy and methods for constructing artificial macrocyclic anion receptors. Selective binding of tetrahedral oxoanions

A new rational strategy for assembling highly selective neutral macrocyclic anionic receptors proposed by the authors is considered. The strategy includes preliminary theoretical modeling of supramolecular complexes, analysis of synthetic paths for receptor preparation, selection and synthesis of building blocks followed by their cyclocondensation under thermo-dynamic control in the presence of acid corresponding to the target template anion, which provides anion-induced combinatorial selection of the macrocyclic ligand in the emerging dynamic combinatorial library. Analysis of the properties of the obtained anion receptors showed that the number of hydrogen bonds formed between the receptor and the guest anion mainly determines the binding energy. The receptor selectivity for a particular anion is determined by the nature of coordination sites, their geometry in the macrocyclic cavity, and the overall conformation rigidity of the macrocycle. Using the developed strategy and novel synthetic approaches, a large series of highly selective anion receptors with record binding constants (up to 10^p7 L mol^p-1 in both highly and weakly solvating media) was constructed and the structures of the host—guest complexes were studied in detail by both experimental and theoretical methods     

Aryl h-phosphonates. 14. Synthesis of new nucleotide analogues with phosphonate-phosphate internucleosidic linkage

[reaction: see text] Aryl nucleoside H-phosphonates 3 and aryl nucleoside P-acylphosphonates 4, generated in situ from the appropriate H-phosphonate 1 and acylphosphonate monoesters 2, respectively, reacted rapidly in the presence of tertiary amines to produce in high yields the extended, pyrophosphate analogues, diaryl dinucleoside phosphonate-phosphate derivatives 6. These, depending on a substituent on the alpha-carbon of the phosphonate moiety, either underwent transformation into the dinucleoside phosphonate-phosphate 7 or afforded nucleoside H-phosphonates 8 and aryl nucleoside phosphate 9.     

Bile acid-based cyclic bisbenzimidazolium receptors for anion recognition: highly improved receptors for fluoride and chloride ions

The anion binding properties of bile acid-based cyclic bisbenzimidazolium receptors 6-8 bridged with m-xylene, p-xylene, and 2,6-dimethylpyridine have been studied. Receptors 6 and 7 exhibit much higher binding affinity for fluoride and chloride ions, respectively, as compared to the imidazolium receptors 1 and 2. Receptor 8, however, shows high selectivity but very low binding affinity for anions due to the presence of pyridyl nitrogen. The single-crystal X-ray structure of imidazolium receptor 10-(Br)2 containing pyridyl spacer reveals the binding pattern.     

Cytosine-substituted metalloporphyrins: receptors for recognition of nucleotides in ion-selective electrodes

A new series of cytosine-substituted metalloporphyrin conjugates (containing Co(II) and Zn(II) as the coordinated metals) were designed and investigated as nucleotide receptors in PVC-membrane-based ion-selective electrodes under neutral conditions. The potentiometric results indicate that these systems, in particular the Co(II)-containing complex, may be potentially useful sensors for complementary nucleotide substrates in the presence of 10 mol% tridodecylmethylammonium chloride (K(Pot.)(5'-GMP/5'-AMP)= 0.045).     

New polydentate macrocyclic ligands of hybrid amine-imine and amide-imine types as artificial anion receptors. Synthesis and study of anion binding

Three new macrocyclic Schiff bases containing an amine or amide structural fragment along with imine groups were synthesized by condensation of 2,6-bis(2-aminophenyliminomethyl)pyridine (1) and N, N’-bis(2-aminophenyl)pyridine-2,6-dicarboxamide (2) with 2,5-diformylpyrrole (₃) and 2,2-bis(5-formylpyrrol-2-yl)propane (4). The reaction of compound 1 with 3 proceeds abnormally and is accompanied by redox disproportionation of compound 1 in the first step. The structure of the macrocyclic product of this reaction was established by X-ray diffraction analysis. Spectrophotometric titration showed that hybrid macrocycle 10, which was prepared by condensation of compound 2 with 4, possesses the properties of an anion receptor and selectively binds hydrosulfate and dihydrophosphate anions in the presence of bromide and nitrate anions. The structures of 10 and its adduct with the hydrosulfate anion were calculated by density functional theory.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 161–168, January, 2005.     

缩氨基硫脲受体的合成及阴离子识别规律研究

设计合成了新型缩氨基硫脲受体分子,利用紫外-可见吸收光谱考察了其对F-,Cl-,Br-,I-,CH3COO-,HSO4-,H2PO4-和NO3-8种阴离子的识别作用。当加入F-,CH3COO-,H2PO4-时,溶液颜色立刻由无色转变为黄色,而加入其它阴离子则无变化,从而实现对这3种阴离子的裸眼检测。通过计算可知,两种受体分子对CH3COO-和H2PO4-的识别作用呈现出有规律的变化,即对同种阴离子:受体B1受体B2,且主客体间形成1∶1的配合物。质子溶剂效应实验证明了受体分子与阴离子之间以氢键作用方式相结合。     

Synthesis and anion recognition studies of new ureylbenzamide-based receptors

A new group of ureylbenzamide-based receptors (1–4) has been synthesized; its binding affinity and capacity to form supramolecular complexes in solution with different anions have been investigated. For designing these receptors, it was considered a combination of the positions of the urea and amide groups (ortho and meta), and the chromophore groups naphthyl and nitrophenyl, yielding four receptors. The position and chromophore structure affected the acidity of the urea and amide hydrogens in the order 4>3>2>1. All the spectroscopic studies showed a significant change of 1 and 2 compared with 3 and 4 in the presence of different TBAX salts in acetonitrile. The ¹H-NMR spectra show a preferential interaction of the anions with the urea group in receptors 1 and 2 due to the less steric hindrance, while there is a cooperative interaction of amide group in receptors 3 and 4 due to the closeness of both groups.     

Synthesis and anion recognition properties of pyrrole-bearing acyclic receptors

A new series of acyclic anion receptors (1-4) based on methyl 5-(aminomethyl)-1H-pyrrole-2-carboxylate were designed and synthesized. The anion recognition properties of these receptors were examined by ¹H NMR spectroscopy and rationalized by density functional theoretical calculation. Receptor 1 displays the highest affinity and selectivity for anionic guests mainly due to the intramolecular hydrogen bonds and rigid molecular geometry.