Crystal structure of an RNA duplex containing phenyl-ribonucleotides, hydrophobic isosteres of the natural pyrimidines

Chemically modified nucleotide analogs have gained widespread popularity for probing structure-function relationships. Among the modifications that were incorporated into RNAs for assessing the role of individual functional groups, the phenyl nucleotide has displayed surprising effects both in the contexts of the hammerhead ribozyme and pre-mRNA splicing. To examine the conformational properties of this hydrophobic base analog, we determined the crystal structure of an RNA double helix with incorporated phenyl ribonucleotides at 1.97 A resolution. In the structure, phenyl residues are engaged in self-pairing and their arrangements suggest energetically favorable stacking interactions with 3'-adjacent guanines. The presence of the phenyl rings in the center of the duplex results in only moderate changes of the helical geometry. This finding is in line with those of earlier experiments that showed the phenyl analog to be a remarkably good mimetic of natural base function. Because the stacking interactions displayed by phenyl residues appear to be similar to those for natural bases, reduced conformational restriction due to the lack of hydrogen bonds with phenyl as well as alterations in its solvent structure may be the main causes of the activity changes with phenyl-modified RNAs.     

X-ray structures of the Dictyostelium discoideum myosin motor domain with six non-nucleotide analogs

The three-dimensional structures of the truncated myosin head from Dictyostelium discoideum myosin II complexed with dinitrophenylaminoethyl-, dinitrophenylaminopropyl-, o-nitrophenylaminoethyl-, m-nitrophenylaminoethyl-, p-nitrophenylaminoethyl-, and o-nitrophenyl-N-methyl-aminoethyl-diphosphate.beryllium fluoride have been determined to better than 2.3-A resolution. The structure of the protein and nucleotide binding pocket in these complexes is very similar to that of S1dC.ADP.BeF(x) (Fisher, A. J., Smith, C. A., Thoden, J., Smith, R., Sutoh, K., Holden, H. M., and Rayment, I. (1995) Biochemistry 34, 8960-8972). The position of the triphosphate-like moiety is essentially identical in all complexes. Furthermore, the alkyl-amino group plays the same role as the ribose by linking the triphosphate to the adenine binding pocket; however, none of the phenyl groups lie in the same position as adenine in S1dC.MgADP.BeF(x), even though several of these nucleotide analogs are functionally equivalent to ATP. Rather the former location of adenine is occupied by water in the nanolog complexes, and the phenyl groups are organized in a manner that attempts to optimize their hydrogen bonding interactions with this constellation of solvent molecules. A comparison of the kinetic and structural properties of the nanologs relative to ATP suggests that the ability of a substrate to sustain tension and to generate movement correlates with a well defined interaction with the active site water structure observed in S1dC.MgADP.BeF(x).     

Biotin-phenyldiazomethane conjugates as labeling reagents at phosphate in mono and polynucleotides

Molecules 2-5 that include in their structure a biotin moiety as detectable unit and differently substituted phenyl diazo functions as reactive group were prepared as reagents for labeling the phosphate group in mono and polynucleotides. These molecules were shown to react selectively and quantitatively with the model nucleotide 3'-UMP. They were used successfully in the labeling step of DNA and RNA analysis using high-density DNA-chips (or microarrays) technology.     

Enzyme-assisted preparation of D-tert.-leucine.

Optically pure D-tert.-leucine was obtained by the enzymatic hydrolysis of (+/-)-N-acetyl-tert. leucine chloroethyl ester after about 50% conversion, this being catalyzed by a protease from Bacillus licheniformis (Alcalase), and subsequent acidic saponification of the recovered ester. Among the methyl, ethyl, octyl, chloroethyl and trichloroethyl esters, the chloroethyl ester exhibited the highest rate of hydrolysis.     

Solid support synthesis of oligothymidylates using phosphorochloridates and 1-alkylimidazoles.

A study of the synthesis of oligothymidylates via phosphotriester intermediates on a polystyrene support is described. The sequence involves condensation of a phenyl nucleoside-3' -phosphorochloridate with the 5'-hydroxyl group of the carrier bound oligonucleotide derivative in the presence of 1-methylimidazole. Conditions for preparation of the phenyl nucleo-side phosphorochloridate as well as for the condensation on the support are discussed. d-TpTpTpT was obtained in 31% overall yield from carrier bound thymidine in one series of experiments, and d-TpTpTpTpT was obtained in 9% yield in another. The cycle for addition of one nucleotide unit can be completed in about six hours.     

Release of surface enzymes in Enterobacteriaceae by osmotic shock

The process of osmotic shock, which has been used to release degradative enzymes from Escherichia coli, can be applied successfully to other members of the Enterobacteriaceae. Cyclic phosphodiesterase (3'-nucleotidase), 5'-nucleotidase (diphosphate sugar hydrolase), acid hexose phosphatase, and acid phenyl phosphatase are released from Shigella, Enterobacter, Citrobacter, and Serratia strains. Some strains of Salmonella also release these enzymes. Members of Proteus and Providencia groups fail to release enzymes when subjected to osmotic shock and do not show a lag in regrowth, although they do release their acid-soluble nucleotide pools. In contrast to E. coli, release of enzymes from other members of the Enterobacteriaceae studied is affected by growth conditions and strain of organism. None of the organisms was as stable to osmotic shock in exponential phase of growth as was E. coli. Exponential-phase cells of Shigella, Enterobacter, and Citrobacter could be shocked only with 0.5 mm MgCl(2) to prevent irreparable damage to the cells. These observations suggest that this group of degradative enzymes is probably loosely bound to the cytoplasmic membrane through the mediation of divalent cations.     

Synthesis and antiviral activity of acyclovir-5'-(phenyl methoxy alaninyl) phosphate as a possible membrane-soluble nucleotide prodrug

We describe a synthesis of acyclovir-5'-(phenyl methoxy alaninyl) phosphate (2) from acyclovir (1). This compound was designed to act as a lipophilic, membrane-soluble prodrug of the free nucleotide. However, the biological activities of this derivative against a range of viruses indicated poor intracellular phosphate delivery, in marked contrast to the earlier successful delivery of several dideoxy anti-HIV nucleotides.     

Immobilization and chiral recognition of 3,5‐dimethylphenylcarbamates of cellulose and amylose bearing 4‐(trimethoxysilyl)phenylcarbamate groups

A small amount of 4‐(trimethoxysilyl)phenyl groups was randomly introduced onto the 3,5‐dimethylphenylcarbamates of cellulose and amylose by a one‐pot method. The obtained derivatives were then effectively immobilized onto silica gel as chiral packing materials (CPMs) for high‐performance liquid chromatography through intermolecular polycondensation of the trimethoxysilyl groups. The effects of the amount of 4‐(trimethoxysilyl)phenyl groups on immobilization and enantioseparation were investigated. Also, the solvent durability of the immobilized‐type CPMs was examined with the eluents containing chloroform and tetrahydrofuran. When these eluents were used, the chiral recognition abilities of the CPMs for most of the tested racemates were improved to some extent depending on the compounds. Chirality 2010. © 2009 Wiley‐Liss, Inc.     

Specific VDJ gene combinations contribute to the specificity of memory antibodies to the phosphorylcholine hapten.

Based on their fine specificity, two groups of antibodies against the phosphorylcholine (PC) hapten have been described. Group I antibodies react predominantly with the PC moiety of the hapten and group II are directed against the entire hapten including the azophenyl spacer to the protein carrier. We have analyzed the VH gene segment utilization of hybridomas from the memory response to PC by Southern blot analysis and nucleotide sequencing of the functional VDJ rearrangements. Three main specificities of anti-PC antibodies could be distinguished. Anti-PC hybridomas with group I fine specificity utilize the VH1-DFL 16.1-JH1 rearrangement. A major portion of group II antibodies recognized the phenyl-PC part and expressed the same VH1 gene in combination with a member of the SP2 family and JH1 or JH2. The other anti-PC antibodies either used the PJ14-DFL16-JH3 rearrangement in combination with a lambda 1 L chain or a member of the VGam3.8 VH family rearranged to the DFL16.1 and the JH3 gene segments. The PJ14 and VGam3.8 V gene expressing antibodies were directed to the phenyl group and were either not or barely inhibitable by PC chloride. Thus, specific VDJ gene combinations contribute to the fine specificity of antibodies in the memory response to the PC hapten. The use of the S107, Q52, and VGam3.8. VH gene families, together with FL16.1 or SP2 D segments and JH1, JH2, or JH3 results in different fine specificities to the PC, phenyl-PC, or the azophenyl moiety of the PC hapten. These fine specificities of the memory response use V, D, and J segments of the initial T15Id+ response in combination with gene segments usually related to phenyl specificity.     

A Method for the Purification of Phospho(Tyr)calmodulin Free of Nonphosphorylated Calmodulin

Phosphocalmodulin has been shown to have a differential biological activity compared to nonphosphorylated calmodulin when assayed on a variety of calmodulin-dependent systems. However, the phosphocalmodulin preparations used so far in those experiments were not necessarily free of nonphosphorylated calmodulin. Therefore, the results obtained may not unquestionably show the real effect of pure phosphocalmodulin on the systems under study. To solve this problem, we describe here a method for the purification of phospho(Tyr)calmodulin free of nonphosphorylated calmodulin. The procedure consists of the following steps: (i) phosphorylation of calmodulin by a fraction enriched in epidermal growth factor receptor tyrosine kinase from rat liver isolated by calmodulin affinity chromatography, (ii) isolation of a calmodulin/phosphocalmodulin mixture by Ca(2+)-dependent chromatography in phenyl-Sepharose, (iii) purification of phospho(Tyr)calmodulin using an anti-phosphotyrosine antibody immobilized in agarose upon elution with phenyl phosphate, and (iv) removal of phenyl phosphate from the phospho(Tyr)calmodulin preparation by filtration chromatography in a Bio-Gel P-2 column. The obtained phospho(Tyr)calmodulin preparation was highly pure and essentially free of nonphosphorylated calmodulin because of the use of anti-phosphotyrosine affinity chromatography. We demonstrate that this ultrapure phospho(Tyr)calmodulin preparation is totally incapable of activating the calmodulin-dependent cyclic nucleotide phosphodiesterase. In contrast, when a nonpurified phospho(Tyr)calmodulin preparation was used a partial activation of this enzyme was observed.     

Synthesis of benzoyl phenyl benzoates as effective inhibitors for phospholipase A2 and hyaluronidase enzymes

Benzoylation of (hydroxy phenyl) phenyl methanone 2a-g to benzoyl phenyl benzoates 4a-g, a benzophenone analogue, was achieved in good yield. All the newly synthesized compounds were evaluated for their phospholipase A2 [E.C. 3.1.1.4] and hyaluronidase [E.C. 3.2.1.35] enzyme inhibitory activity in snake venom as source and their structure-activity relationship with respect to different groups is reported for the first time. The in vitro PLA2 enzyme inhibitory activity and in vivo anti-inflammatory activity studies of benzoyl phenyl benzoates are illustrated.     

Studies on the Mode of Action of Dipterex

To elucidate the reason of low mammalian toxicity of Dipterex, decomposition of this compound by rabbit tissue was investigated. Though splitting of P-C linkage was not confirmed, two glucuronides, presumably derived from the metabolite (s) of Dipterex, were isolated from the urine. Molar ratio of phosphorus and glucuronic acid in them are both estimated as 1 : 1, and they are observed to differ from trichloroethyl glucuronide. The rapid detoxification might be ascribed to the capacity of glucuronide formation as well as the enzymatic hydrolysis of DDVP, the active ingredient of Dipterex.     

Studies on antiviral glycosides. Synthesis and biological evaluation of various phenyl glycosides.

A variety of analogues and derivatives of phenyl glycosides were synthesized for examination of their biological activities and of the relationship between structure and antiviral activity. For antiviral activity, a 6-deoxy-6-halogeno-D-glucose residue was most suitable for the carbohydrate moiety and p-alkylphenyl groups for the aglycone moiety. Based on these results, p-(sec-butyl)phenyl 6-chloro-6-deoxy-beta-D-glucopyranoside and p-(sec-butyl)phenyl 6-deoxy-6-iodo-beta-D-glucopyranoside were prepared, and the former compound was found to be the most potent antiviral substance, in this series, against influenza and Herpes simplex virus. The anomeric configuration of phenyl glycosides did not contribute to the antiviral activity.     

Novel silicon-containing polyurethanes from vegetable oils as renewable resources. Synthesis and properties

Hydrosilylation of methyl 10-undecenoate (UDM) with phenyl tris(dimethylsiloxy)silane (PTDS) followed by a reduction of carboxylate groups was used to obtain a silicon-containing polyol with terminal primary hydroxyl groups (PSi194). Biobased silicon-containing polyurethanes, with a silicon content between 1.7% and 9.0%, were prepared from epoxidized methyl oleate-based polyether polyol (P184), PSi194, and 4,4'-methylenebis(phenyl isocyanate) (MDI). The thermal, mechanical, and flame-retardant properties of these materials were examined. The most notable change resulting from the incorporation of PSi194 is the appearance of melting endotherms of variable enthalpy and position and a downward shift in the T(g). The incorporation of silicon does not change the thermal stability but enhances the stability of the char under air atmosphere. Polyurethanes with higher silicon content no longer burn in ambient air without complementary oxygen, which suggests that these biobased materials are very interesting for applications that require fire resistance.     

Designed aromatic homo-dipeptides: formation of ordered nanostructures and potential nanotechnological applications

Molecular self-assembly offers new routes for the fabrication of novel materials at the nano-scale. Peptide-based nanostructures represent nano-objects of particular interest, as they are biocompatible, can be easily synthesized in large amounts, can be decorated with functional elements and can be used in various biological and non-biological applications. We had previously revealed the formation of highly ordered tubular structures by the diphenylalanine peptide, the core recognition motif of Alzheimer's beta-amyloid polypeptide, due to specific aromatic interactions. We further confirmed this model and demonstrated that a non-charged peptide analogue, Ac-Phe-Phe-NH2, self-assembled into similar tubular structures. We later explored other amine and carboxyl modified diphenylalanine peptide analogues and revealed that these dipeptides can form ordered tubular structures at the nanometric scale. Moreover, a very similar peptide, the diphenylglycine, self-assembled into ordered nano-spherical assemblies. Here we extend our research and explore the self-assembly of other homo-aromatic dipeptides in which their phenyl side-chains are modified with halogen atoms (di-para-fluoro-Phe, di-pentafluoro-Phe, di-para-iodo-Phe), additional phenyl groups (di-4-phenyl-Phe), or with nitro substitutions (di-para-nitro-Phe). We also probed the effect of the alteration of the phenyl groups with naphtyl groups (di-D-1-Nal and di-D-2-Nal). In all cases, well-ordered nanostructures were obtained and studied by scanning electron microscopy, transmission electron microscopy and vibrational spectroscopy. Taken together, the current work and previous ones define the homo-aromatic dipeptide as a central motif for the formation of ordered self-assembled tubular, spherical and two-dimensional structures at the nano-scale.     

Chiral derivatives of 2-(1-naphthyl)-2-phenylacetic acid

The spectral properties of diastereomeric esters and amides (1b-20b), derived from optically pure 2-(1-naphthyl)-2-phenylacetic acids (1-NPA), were systematically investigated. It was found that all compounds prepared exhibit the NMR spectral nonequivalence (Deltadelta) with regular sign distribution of particular groups according to the predicted model. Further, the analysis of data revealed that the phenyl ring is responsible for a shielding effect (upfield shift) instead of a naphthyl one. This conclusion is supported by the crystallographic analysis showing the almost ap-arrangement of the acid methine hydrogen atom and carbonyl group. In this arrangement, the phenyl ring faces toward the ester part of the molecule while the naphthyl one is orthogonal to the phenyl plane. Therefore, the mutual position of phenyl and alkyl groups with respect to the central molecule co-planarity thus determines the chemical shifts of the alcohol/amine substituents. The relative magnitude of the Deltadelta corresponds to those of Mosher's derivatives.     

Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules

DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix. In this work, we investigated the conformation of the 2′-deoxyadenosine and 2′-deoxycytidine derivatives tethering a phenyl or naphthyl group, introduced in a DNA duplex. The chemical modification experiments using KMnO₄ and 1-cyclohexyl-3 -(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate have shown that the 2′-deoxycytidine lesions form the base pair with guanine while the 2′-deoxyadenosine lesions have less ability of forming the base pair with thymine in solution. Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases. We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. It is also presented that the attached aromatic groups change their orientation by interacting with the minor groove binding netropsin, distamycin and synthetic polyamide. The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides.     

Dental restorative composites fabricated from a novel organic matrix without an additional diluent

Commercial organic matrixes of dental composites generally include diluents such as triethylene glycol dimethacrylate (TEGDMA) to reduce viscosity. However, the diluent exhibits adverse effects such as curing shrinkage and diminished mechanical properties of the dental composites. To overcome these adverse effects, organic monomers that can be used as an organic matrix may be developed. In this study, various novel organic monomers were developed by substituting alkoxy for hydroxyl groups in 2,2-bis[4-(2-hydroxy-3-methacryloyloxy propoxy)phenyl]propane (bis-GMA). Viscosities of the alkoxy-substituted monomers were decreased by increasing substituent size. The viscosity of 2,2-bis[4-(2-ethoxy-3-methacryloyloxy propoxy)phenyl]propane (bis-E-GMA) was higher than the control organic matrix (70 wt % bis-GMA and 30 wt % TEGDMA). However, those of 2,2-bis[4-(2-propoxy-3-methacryloyloxy propoxy)phenyl]propane (bis-Pr-GMA), 2,2-bis[4-(2-butoxy-3-methacryloyloxy propoxy)phenyl]propane (bis-B-GMA), and 2,2-bis[4-(2-pentoxy-3-methacryloyloxy propoxy)phenyl]propane (bis-P-GMA) were lower than the control organic matrix. To this end, these monomers could be used as organic matrixes of dental composites without an additional diluent. Among these monomers, bis-B-GMA exhibited the lowest curing shrinkage. In comparison to the control organic matrix, the curing shrinkage of the bis-B-GMA dental composite was approximately 40%. Additionally, dental composites prepared from bis-B-GMA exhibited excellent mechanical properties.     

Magnetic resonance studies of the binding site interactions between 19F-labeled nitrophenyl haptens and specific mouse myeloma immunoglobulin MOPC-315

The interactions between MOPC-315, a mouse myeloma protein with specificity for nitrophenyl haptens, and 19F-substituted haptens have been investigated using nuclear magnetic resonance (NMR) spectroscopy. The haptens studied are mono- or dinitrophenyl derivatives of gamma-aminobutyric acid, lysine, or glycine which have trifuoromethyl groups attached to the phenyl rings. Upon binding to immunoglobulin, the 19F nucleus experiences a downfield shift whose magnitude depends on the position of the trifluoromethyl group on the phenyl ring but is independent of other structural changes in the hapten such as the number of nitro groups attached to the phenyl ring. Further, the chemical shift of bound hapten is not influenced by the amount of the constant region attached to the binding site; we accordingly conclude that the presence of the distal, constant regions of the immunoglobulin molecule does not influence binding site interactions.