The low frequency vibrations of the nucleosides: Uridine,cytidine and inosine. Determination of vibrations associated with the ribose ring

The room temperature far i.r. spectra of the nucleoside cytidine and its deuterated analog cytidine- d₃ have been measured from 200 to 100 cm⁻¹. Several spectral features involving hydroxyl deformations have been identified. Between 200 and 400 cm⁻¹ the spectra of the nucleosides cytidine, uridine and inosine have been compared to those of the respective bases cytosine, uracil and hypoxanthine thereby allowing the identification of several bands associated with deformations of the furanose ribose unit. These frequencies are common among the nucleosides investigated and have been compared to calculated frequencies for “ribose” modes in polynucleotides. Upon cooling to 7 K the cytidine and cytidine-d₃ spectra below 200 cm⁻¹ exhibit a remarkable narrowing resembling a “gas-like” spectra, revealing more spectral features than expected from a group theoretical analysis of the unit cell. The low temperature spectra also exhibit an apparent periodicity. Two equally possible explanations are given; one accounts for the observed periodicity via a vibrational exciton-like theory, while the alternative explanation treats the periodicity as accidental.     

Enhanced stereoselectivity in internucleotidic bond formation by the use of the chiral ribose moiety of thymidine

This paper deals with the synthesis of new cyclic thymidine 3'-phosphoramidite building blocks having a covalent linker between the trityl type 5'-hydroxyl protecting group and the phosphorus atom attached to the 3'-hydroxyl group of thymidine. The ring structures were designed to reduce the conformational freedom around the phosphorus center so that the stereoselectivity in the internucleotide linkage formation would be improved. The linkers were also designed to be removed readily by treatment with aqueous ammonia. These building blocks were synthesized in good yield by one-pot cyclization of the diol precursors with dichloro(N,N-diisopropylamino)phosphine, despite their large-membered ring. Various activators having 1H-tetrazole, imidazole, and triazole structures were investigated to find the best selectivity in the synthesis of thymidylyl(5'-3')thymidine phosphorothioate. It turned out that our cyclic phosphoramidites gave preferentially the R(p) diastereoisomer in high coupling yield applicable to the solid-phase synthesis of oligodeoxynucleotides. It should be noted that high stereoselectivity was achieved without any chiral sources other than the 2'-deoxyribose moiety itself. The mechanistic studies revealed the importance of the steric bulk and the acidity of the activators. It was also found that the steric bulk of the alcoholic nucleophile was an important factor that determined the stereoselectivity in our systems.     

Probing the mechanism of transport and compartmentalisation of polyamines in mammalian cells.

BACKGROUND: Many mammalian cells possess an active polyamine uptake system but little is known about the molecular mechanism of this transporter. The fate of polyamines taken up from the medium and the relationship to polyamine homeostasis remains to be fully established. The aim of this study was to develop a range of modified polyamines, particularly ligands incorporating a fluorophore, to explore the structural tolerances of the polyamine transport system and to probe the intracellular location of polyamines acquired from the medium. RESULTS: We synthesised a wide range of polyamine analogues incorporating cytotoxic agents, fluorescent chromophores and bulky substituents. All of these analogues have been shown to be good competitive inhibitors of spermidine uptake in a range of mammalian cells. Direct evidence for uptake of the fluorescent polyamine analogues and their subcellular distribution was obtained from confocal laser scanning fluorescence microscopy, which showed that they accumulated in granular structures within the cytoplasm and not in the nucleus. We demonstrated that their uptake is through the polyamine transport system by showing that pretreatment with DFMO, a potent inhibitor of polyamine biosynthesis, led to enhanced uptake, and cells deficient in the polyamine transport system did not accumulate these polyamine analogues. CONCLUSIONS: The polyamine transport system has a surprisingly broad structural tolerance. Fluorophore-containing polyamine analogues derived from the extracellular pool are located in granular structures within the cytoplasm and not to any great extent in the nuclei of mammalian cells. These observations might be consistent with a mechanism involving receptor-mediated endocytosis, and the granular 'structures' seen might reflect polyamine compartmentalisation within vesicles.     

Allene oxide. V - oxidation of β-allenic alcohols bearing a trimethylsilyl group on the allenic moiety. Probe of a concerted mechanism in the δ-lactones formation.

β-allenic alcohols substituted by a trimethylsilyl group at the ?1 or ?3 position respectively give rise to γ or δ-lactones. In the last case, a concerted mechanism is involved     

Coupled transport membranes II: : The mechanism of uranium transport with a tertiary amine

This paper describes the parameters controlling the coupled transport of uranium anions through liquid membranes. The membranes consist of a microporous polymeric support with a liquid, tertiary amine complexing agent held within the pores by capillary forces. When this liquid membrane is interposed between two aqueous solutions of unequal ion concentrations, the complexing agent can pick up the anion on one side of the membrane and carry it across the membrane by diffusion in the form of a neutral complex. Ions of opposite charge may be carried in the same direction, or ions of like charge may be carried in the opposite direction. We refer to these two modes of transport as “co-transport” and “counter-transport”, respectively. In the coupled transport of uranium, both co-transport and counter-transport can occur. p]The coupling of the flows of two ions permits one of the ions to be pumped against its concentration gradient. We have demonstrated “uphill diffusion” of uranium against substantial concentration gradients, and at significant rates. A number of factors affect uranium flux, principally the concentrations of uranium and the coupled ion in the aqueous solutions. The base strength of the tertiary amine is also an important parameter.     

Effect of a lateral methyl group on azo-mesogens containing the naphthalene moiety

Two mesogenic homologous series, 2-[4-(4-n-alkoxybenzoyloxy)-2-methylphenylazo]-naphthalenes (I) and 2-[4-(4-n-alkoxybenzoyloxy)-3-methylphenylazo]naphthalenes (II) with a lateral methyl group have been synthesized. Both series are purely nematogenic. The mesomorphic properties of both series are compared with each other and also with the properties of other structurally related series to evaluate the effect of the lateral methyl group on mesomorphism. The chiral nematic (N*) mesophase was induced in the system by doping with a derivative of naturally occurring chiral menthol.     

The Friedel-Crafts allylation of a prenyl group stabilized by a sulfone moiety: expeditious syntheses of ubiquinones and menaquinones

An efficient synthetic method for the protected p-hydroquinone compounds 4 containing the C5 trans allylic sulfone moiety has been developed by the direct Friedel-Crafts allylation of the protected dihydroquinone 2 with 4-chloro-2-methyl-1-phenylsulfonyl-2-butene (7a) or 4-hydroxy-2-methyl-1-phenylsulfonyl-2-butene (7b). Expeditious total syntheses of coenzyme Q-10 and vitamin K2(20) have been demonstrated from these valuable key compounds 4a and 4b.     

Effect of a lateral methyl group on azo-mesogens containing the naphthalene moiety

Two mesogenic homologous series, 2-[4-(4-n-alkoxybenzoyloxy)-2-methylphenylazo]-naphthalenes (I) and 2-[4-(4-n-alkoxybenzoyloxy)-3-methylphenylazo]naphthalenes (II) with a lateral methyl group have been synthesized. Both series are purely nematogenic. The mesomorphic properties of both series are compared with each other and also with the properties of other structurally related series to evaluate the effect of the lateral methyl group on mesomorphism. The chiral nematic (N*) mesophase was induced in the system by doping with a derivative of naturally occurring chiral menthol.     

The effect of the α-cyano moiety on neighboring group participation by the cyclopropyl group

H/α-CN rate ratios have been derived for the solvolysis of sulfonate esters of endo-tricyclo[3.2.1.0^2,4]octan-anti-8-ol and tricyclo[2.2.1.0^2,6]heptan-3-ol. The role of the α-cyano moiety in the stabilization of highly delocalized cations has been evaluated.     

Charge transport in poly-imidazole membranes: a fresh appraisal of the Grotthuss mechanism

A detailed theoretical investigation of the charge transport mechanism in poly(4-vinyl-imidazole) (P4VI), the parent polymer of a series of N-heterocyclic-based membranes used as an electrolyte in proton exchange membrane fuel cells, is presented. In particular, Density Functional Theory (DFT) results obtained for small model systems (protonated imidazole dimers and trimers) suggest that the commonly accepted conduction mechanism, based on a sequential proton transfer between imidazole moieties, could be impeded by the geometrical constraints imposed by the polymeric backbone. Indeed only one kind of proton transfer reaction is energetically allowed between adjacent imidazoles, so that a rotation of the protonated imidazole is required for a second proton transfer. Molecular dynamics simulations on a larger model (15 oligomers with an excess proton) show that the rotation of the imidazole carrying the excess proton is a soft large amplitude motion. These results allow us to propose a new proton conduction mechanism in P4VI, where a frustrated rotation of the protonated imidazole before each proton transfer reaction represents the rate-limiting step. Furthermore, in contrast with the Grotthuss proton transport mechanism in water, our results indicate that here it is the same proton which could be successively transferred. From a chemical point of view, these new insights into the mechanism are relevant for a rational design of modified azole-based systems for Proton Exchange Membrane Fuel Cells.     

The mechanism of addition-reactions to the C 5-atom of the nicotinamide moiety ofNADH

The C 5-atom of the nicotinamide moiety ofNADH undergoes addition-reactions with protons and positive halogen atoms from N-halogen-succinimides; the final products of these reactions were the corresponding 6-hydroxy-(5-halogeno-)-1,4,5,6-tetrahydronicotinamide adenine dinucleotides. A common quantitative mechanism for all these reactions has been worked out, and all kinetic parameters have been reported.Dedicated to Prof.Gerhard Pfleiderer on the occasion of his 65th birthday.     

Nucleosides and nucleotides. 186. Synthesis and biological activities of pyrimidine carbocyclic nucleosides with a hydroxyamino group instead of a hydroxymethyl group at the 4'-position of the sugar moiety.

Pyrimidine carbocyclic nucleosides with a hydroxyamino group instead of a hydroxymethyl group at the 4'-position of the sugar moiety were designed as potential antitumor and/or antiviral agents. Pd (O)-catalyzed reactions of enantiomerically pure (+)-(1R,4S)-4-[(tert-butyldiphenylsilyl)oxy]-1-(ethoxycarbonylo xy)-2- cyclopentene (9) with N3-benzoylthymine and -uracil gave carbocyclic nucleosides 10 and 11. Subsequent Pd (O)-catalyzed reactions of N3-benzoyl-1-[(1R,4S)-4-(ethoxycarbonyloxy)-2-cyclopenten-1- yl]thymine (14) and -uracil (15) with O-benzylhydroxylamine smoothly gave the hydroxyamino-substituted carbocyclic nucleosides 16 and 17. From these nucleosides, the target compounds were prepared after deprotection or further reactions. The 2',3'-didehydro-2',3'-dideoxythymidine (D4T) analogue 20 was the most effective compound, with IC50 values of 27.3 and 34.5 microM against KB and L1210 cells in vitro. Carbocyclic analogues of uridine and cytidine (29 and 32) were less effective than 20 against both cell lines.     

Aminolysis of O-aryl thionobenzoates: amine basicity combines with modulation of the nature of substituents in the leaving group and thionobenzoate moiety to control the reaction mechanism

A kinetic study is reported for aminolysis of O-Y-substituted phenyl thionobenzoates (1a-f) and O-4-nitrophenyl X-substituted thionobenzoates (2a-f) in 80 mol % H2O/20 mol % DMSO at 25.0 +/- 0.1 degrees C. The reaction proceeds through one or two intermediates (i.e., a zwitterionic tetrahedral intermediate T(+/-) and its deprotonated form T(-)) depending on the basicity difference between the nucleophile and nucleofuge, that is, the reaction proceeds through T(+/-) when the leaving aryloxide is less basic than the attacking amine, but through T(+/-) and T(-) when the leaving group is more basic than the amine. However, the reaction mechanism is not influenced by the electronic nature of the substituent X in the nonleaving group. The Hammett plot for the reactions of 2a-f with benzylamine is consisted of two intersecting straight lines, which might be interpreted as a change in the rate-determining step (RDS). However, the Yukawa-Tsuno plot for the same reactions exhibits an excellent linear correlation, indicating that the nonlinear Hammett plot is not due to a change in the RDS but caused by stabilization of the ground-state of the substrate through resonance interaction between the electron-donating substituent X and the thionocarbonyl moiety.     

Organometallic diphenols: The importance of the organometallic moiety on the expression of a cytotoxic effect on breast cancer cells

We have recently reported that the ferrocenyl diphenol compound 1,1-di(4-hydroxyphenyl)-2-ferrocenyl-but-1-ene 1 exhibited strong in vitro anti-proliferative effects on both hormone dependent (MCF7, IC₅₀ = 0.7 μM) and hormone independent (MDA-MB231, IC₅₀ = 0.6 μM) breast cancer cells. In order to assess the importance of the ferrocenyl motif, we have prepared a series of analogs using the organometallic fragments (η⁵-C₅H₄)Cp^∗Fe (7), ((η⁵-C₅H₄)(CH₃)₂phospholyl)Fe (9), (η⁵-C₅H₄)CpRu (10), (η⁵-C₅H₄)Re(CO)₃ (11), and (η⁵-C₅H₄)Mn(CO)₃ (12), and the chlorinated ferrocenyl derivative 1,1-di(4-hydroxyphenyl)-2-ferrocenyl-4-chloro-but-1-ene (4). The nature of the organometallic moiety had a strong influence on estrogen receptor alpha (ERα) recognition, with relative binding affinity (RBA) values ranging from 0.55% to 10.8%. The second isoform of the estrogen receptor, ERβ, was better able to accommodate these compounds, with RBA values ranging from 8.9% to 17.1%. Molecular modeling studies suggest that the orientation of the compounds and their interactions with the residues of ERα and ERβ binding sites are very similar. A study on the MCF7 hormone dependent breast cancer cell line revealed an anti-proliferative effect for the ferrocenyl phenols 1 and 4, while the other compounds displayed either a proliferative effect (9-12), or no effect (7). The anti-proliferative effect of 1 and 4 is also evident in the MDA-MB231 hormone independent breast cancer cell line (IC₅₀(4) = 1 μM), and can be attributed to the cytotoxicity of these compounds, while the other compounds showed no effect on this cell line. The cytotoxicity of 1 and 4 may arise from electron delocalization in the radical cation in alkaline conditions, possibly resulting in a cytotoxic quinone methide formation, while the other complexes do not undergo the formation of this entity, as evidenced by the electrochemical results.     

皂素皂苷脂肪链中甲基绝对构型的确定

利用Sharpless环氧化和Roush反应合成了皂素苷脂肪链中C9脂肪酸单体的两个非对映异构体,即(3S,5S,6S)-3,5-二羟基-6-甲基-δ-辛酸内酯和(3S,5S,6R)-3,5-二羟基-6-甲基-δ-辛酸内酯。通过与天然样品进行理化数据对比,确定了皂素皂苷脂肪链中甲基的绝对构型为S。     

Role of membrane potential and hydrogen bonding in the mechanism of translocation of guanidinium-rich peptides into cells

The results described herein support a mechanistic hypothesis for how guanidine-rich transporters attached to small cargos (MW ca. <3000) can migrate across the lipid membrane of a cell and directly enter the cytosol. Arginine oligomers are found to partition almost completely into the aqueous layer of a water-octanol bilayer. However, when the same partitioning experiment is conducted in the presence of sodium laurate, a representative negatively charged membrane constituent, the arginine oligomer partitions almost completely (>95%) into the octanol layer. In contrast, ornithine oligomers partition almost exclusively into the water layer with and without added sodium laurate. The different partitioning between guanidinium-rich and ammonium-rich oligomers in the presence of sodium laurate is consistent with the ability of the former to form a bidentate hydrogen bonded ion pair. Mono- and dimethylated arginine oligomers, which like ornithine can only efficiently form monodentate hydrogen bonds, were prepared and found to exhibit poor cellular uptake. Ion pair formation converts a once water-soluble agent to a lipid-soluble agent, thereby reducing the energetic penalty for passage of guanidine-rich transporters through the lipid bilayer. Uptake of guanidine-rich transporters is known to be an energy-dependent process, and this requirement for cellular ATP is now rationalized by the inhibition of guanidine-rich transporter uptake in the presence of agents that reduce the membrane potential. Specifically, incubation of cells in buffers with high potassium ion concentrations or pretreatment of cells with gramicidin A reduces the cellular uptake of Fl-aca-arg8-CONH2 by >90%. Furthermore, the reciprocal experiment of hyperpolarizing the cell with valinomycin increased uptake by >1.5 times. In summary, we propose that the water-soluble, positively charged guanidinium headgroups of the transporter form bidentate hydrogen bonds with H-bond acceptor functionality on the cell surface. The resultant ion pair complexes partition into the lipid bilayer and migrate across at a rate related to the membrane potential. The complex dissociates on the inner leaf of the membrane, and the transporter enters the cytosol. This hypothesis does not preclude uptake by other mechanisms, including endocytosis, which is likely to dominate with large cargos.