Hydrolytic reactions of thymidine 5'-o-phenyl-N-alkylphosphoramidates, models of nucleoside 5'-monophosphate prodrugs

To obtain detailed data on the kinetics of hydrolytic reactions of triester-like nucleoside 5'-O-aryl-N-alkylphosphoramidates, potential prodrugs of antiviral nucleoside monophosphates, the hydrolysis of diastereomeric (Rp/Sp) thymidine 5'-{O-phenyl-N-[(1S)-2-oxo-2-methoxy-1-methylethyl]phosphoramidate} (3), a phosphoramidate derived from the methyl ester of L-alanine, has been followed by reversed-phase HPLC over the range from Ho=0 to pH 8 at 90 degrees C. According to the time-dependent product distributions, the hydrolysis of 3 proceeds at pH<4 by two parallel routes, namely by nucleophilic displacement of the alaninyl ester moiety by a water molecule and by hydrolysis of the carboxylic ester linkage that allows intramolecular attack of the carboxy group on the phosphorus atom, thereby resulting in the departure of either thymidine or phenol without marked accumulation of any intermediates. Both routes represent about half of the overall disappearance of 3. The departure of phenol eventually leads to the formation of thymidine 5'-phosphate. At pH>5, the predominant reaction is hydrolysis of the carboxylic ester linkage followed by intramolecular displacement of a phenoxide ion by the carboxylate ion and hydrolysis of the resulting cyclic mixed anhydride into an acyclic diester-like thymidine 5'-phosphoramidate. The latter product accumulated quantitatively without any indication of further decomposition. Hydroxide-ion-catalyzed P--OPh bond cleavage of the starting material 3 occurred as a side reaction. Comparative measurements with thymidine 5'-{N-[(1S)-2-oxo-2-methoxy-1-methylethyl]phosphoramidate} (4) revealed that, under acidic conditions, this diester-like compound is hydrolyzed by P--N bond cleavage three orders of magnitude more rapidly than the triester-like 3. At pH>5, the stability order is reversed, with 3 being hydrolyzed six times as rapidly as 4. Mechanisms of the partial reactions are discussed.     

Hydrolysis of Phosphodiester Bonds within RNA Hairpin Loops in Buffer Solutions: the Effect of Secondary Structure on the Inherent Reactivity of RNA Phosphodiester Bonds

The hydrolysis of phosphodiester bonds of chimeric 2′-O-methyloligoribonucleotides was studied in buffer solutions. Pseudo-first-order rate constants for cleavage of phosphodiester bonds within hairpin loops were calculated and compared with those for cleavage of phosphodiester bonds within double-stranded stems and linear single-stranded oligonucleotides. No large differences in reactivity were observed: some of the hairpin structures studied were slightly less and others slightly more reactive than the linear reference. These results suggest that phosphodiester bonds within small hairpin loops are conformationally free to cleave by an in-line mechanism, but also that the secondary structure may influence the reactivity of phosphodiester bonds.     

Solid-phase synthesis of oligonucleotide glycoconjugates bearing three different glycosyl groups: orthogonally protected bis(hydroxymethyl)-N,N'-bis(3-hydroxypropyl)malondiamide phosphoramidite as key building block

Diethyl O,O'-(methoxymethylene)bis(hydroxymethyl)malonate (3) was observed to undergo a stepwise aminolysis when treated with 3-aminopropanol. This allowed convenient preparation of bis(hydroxymethyl)-N,N'-bis(3-hydroxypropyl)malondiamide bearing orthogonal levulinyl (Lev) and tert-butyldiphenylsilyl (TBDPS) protections at the two N-hydroxypropyl groups (8). One of the hydroxylmethyl functions was then protected with a 4,4'-dimethoxytrityl (DMTr) group, and the other one was phosphitylated to obtain a methyl N,N-diisopropylphosphoramidite (1). This building block was used for the synthesis of oligonucleotide glycoconjugates (25 and 26) carrying three different sugar units. After conventional phosphoramidite chain assembly of the sequence containing 1, the 5'-terminal DMTr group was removed and an appropriate glycosyl 6-O-phosphoramidite was coupled. The remaining protections of the branching unit were removed in the order of Lev and TBDPS, and the exposed hydroxyl functions were reacted one after another with the desired glycosyl 6-O-phosphoramidites. Global deprotection and cleavage of the conjugate from the support were achieved by conventional ammonolysis.     

Sensitive miniature single-particle immunoassay of prostate-specific antigen using time-resolved fluorescence

The present study describes the development of a quantitative miniaturized single microparticle immunoassay. The main objective of the study was to evaluate the performance of a miniature heterogeneous immunoassay on a single microparticle in respect to assay kinetics, volume, and sensitivity, binding capacity of microparticles and sensitivity using europium(III) nanoparticle labels. The performance of the single microparticle assay of prostate-specific antigen (PSA) was investigated using different-sized microparticles (60-920 μm in diameter) and microtiter well as a solid-phase. Equilibration time of the assay was shown to be dependent in a linear manner on surface-to-volume ratio, i.e. larger surface-to-volume translated to a faster reaction. However, no correlation between PSA binding capacity and equilibration time was observed in these kinetic studies. Only moderate improvement in assay kinetics was found when PSA binding capacity was increased on a microparticle. Using europium(III) nanoparticle labels, 107 nm in diameter, coated with streptavidin a detection sensitivity of 30 ng l⁻¹ (0.1 amol) was achieved in 1 μl total assay volume per microparticle. This was 50-fold higher compared to the same assay performed with intrinsically fluorescent europium(III) labels.     

The Acid-Catalyzed Hydrolysis of Anomeric Alkyl Fructofuranosides

Abstract

The rate constants for the hydrolysis of some al-kyl α- and β-d-fructofuranosides in aqueous perchloric acid have been determined at various temperatures. The effects of varying the aglycon structure on the hydrolysis rate suggest, together with the markedly positive entropies of activation, that the substrate, protonated on the glycosidic oxygen atom, undergoes a rate-limiting unimolecular heterolysis to form a glycosyl oxocar-benium ion. The rate variations in mixtures of aqueous perchloric acid and dimethyl sulfoxide are interpreted as lending further support for the proposed mechanism.     

Continuous learning methods in two-buyer pricing problem

This paper presents continuous learning methods in a monopoly pricing problem where the firm has uncertainty about the buyers’ preferences. The firm designs a menu of quality-price bundles and adjusts them using only local information about the buyers’ preferences. The learning methods define different paths, and we compare how much profit the firm makes on these paths, how long it takes to learn the optimal tariff, and how the buyers’ utilities change during the learning period. We also present a way to compute the optimal path in terms of discounted profit with dynamic programming and complete information. Numerical examples show that the optimal path may involve jumps where the buyer types switch from one bundle to another, and this is a property which is difficult to include in the learning methods. The learning methods have, however, the benefit that they can be generalized to pricing problems with many buyers types and qualities.     

Orthogonally protected cyclo-beta-tetrapeptides as solid-supported scaffolds for the synthesis of glycoclusters

Two novel peptide scaffolds, viz. cyclo[(N(alpha)-Alloc)Dpr-beta-Ala-(N(alpha)-Fmoc)Dpr-beta-Ala] (1) and cyclo[(N(alpha)-Alloc)Dpr-alpha-azido-beta-aminopropanoyl-(N(alpha)-Fmoc)Dpr-beta-Ala] (2), composed of orthogonally protected 2,3-diaminopropanoyl (Dpr) and beta-alanyl residues, have been described. Fmoc chemistry on a backbone amide linker derivatized resin has been used for the chain assembly. Selective removal of the 4-methyltrityl (Mtt) and 1-methyl-1-phenylethyl protections (PhiPr) exposes the beta-amino and carboxyl terminus, respectively, and on-resin cyclization then gives the desired orthogonally protected cyclo-beta-tetrapeptides (1 and 2). The alpha-amino groups, bearing the Fmoc and Alloc protections and the azide mask, allow stepwise orthogonal derivatization of these solid-supported cyclo-beta-tetrapeptide cores (1 and 2). This has been demonstrated by attachments of various sugar units [viz., acetyl- or toluoyl-protected carboxymethyl alpha-d-glycopyranosides (13-15) and methyl 6-O-(4-nitrophenoxycarbonyl)-alpha-d-glycopyranosides (22-24)] to obtain diverse di- and trivalent glycoclusters (33-42). Acidolytic release (TFA) from the support, followed by conventional NaOMe-catalyzed transesterification (33-40) or hydrazine-induced acyl substitution in DMF (41 and 42), gives the fully deprotected clusters (43-52) as final products.     

Search for B+/--->[K(-/+)pi(+/-)](D)K+/- and upper limit on the b-->u amplitude in B+/--->DK+/-

We search for B+/--->[K(-/+)pi(+/-)](D)K+/- decays, where [K(-/+)pi(+/-)](D) indicates that the K-/+pi(+/-) pair originates from the decay of a D0 or D (0). Results are based on 120x10(6) Upsilon(4S)-->BB decays collected with the BABAR detector at SLAC. We set an upper limit on the ratio R(Kpi) identical with[Gamma(B+-->[K(-)pi(+)](D)K+)+Gamma(B--->[K(+)pi(-)](D)K-)][Gamma(B+-->[K(+)pi(-)](D) / K+)+Gamma(B--->[K(-)pi(+)](D)K-)]<0.026 (90% C.L.). This constrains the amplitude ratio r(B) identical with|A(B--->D 0K-)/A(B--->D0K-)|<0.22 (90% C.L.), consistent with expectations. The small value of r(B) favored by our analysis suggests that the determination of the Cabibbo-Kobayashi-Maskawa phase gamma from B-->DK will be difficult.     

Growth and properties of self‐catalyzed (In,Mn)As nanowires

Mn‐assisted molecular beam epitaxy is used for the growth of (In,Mn)As nanowires (NWs) on GaAs(111)B. The transmission electron microscopy measurements revealed that despite the relatively high growth temperature regime this technique can be used to obtain (In,Mn)As NWs with high crystalline quality without any crystal defects, such as dislocations, stacking faults or precipitates inside the investigated NWs or on their side‐walls, although the growth processes of NWs were accompanied by the formation of MnAs precipitates between the NWs at the interface of the wetting layer. The results obtained are of importance for the realization of new spintronic nanostructured materials. (© 2016 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

3-Acetyloxy-2-cyano-2-(alkylaminocarbamoyl)propyl groups as biodegradable protecting groups of nucleoside 5´-mono-phosphates

Thymidine 5′-bis[3-acetyloxy-2-cyano-2-(2-phenylethylcarbamoyl)propyl]phosphate (1) has been prepared and the removal of phosphate protecting groups by hog liver carboxyesterase (HLE) at pH 7.5 and 37 °C has been followed by HPLC. The first detectable intermediates are the (R(P))- and (S(P))-diastereomers of the monodeacetylated triester 14, which subsequently undergo concurrent retro-aldol condensation to diester 4 and enzyme-catalyzed hydrolysis to the fully deacetylated triester 15. The former pathway predominates, representing 90% of the overall breakdown of 14. The diester 4 undergoes the enzymatic deacetylation 700 times less readily than the triester, but gives finally thymidine 5′-monophosphate as the desired main product. To elucidate the potential toxicity of the electrophilic 2-cyano-N-(2-phenylethyl)acrylamideby-product 17 released upon the deprotection, the hydrolysis of 1 has also been studied in the presence of glutathione (GSH).