Gapmer Antisense Oligonucleotides Containing 2′,3′-Dideoxy-2′-fluoro-3′-C-hydroxymethyl-β-d-lyxofuranosyl Nucleotides Display Site-Specific RNase H Cleavage and Induce Gene Silencing

Off-target effects remain a significant challenge in the therapeutic use of gapmer antisense oligonucleotides (AONs). Over the years various modifications have been synthesized and incorporated into AONs, however, precise control of RNase H-induced cleavage and target sequence selectivity has yet to be realized. Herein, the synthesis of the uracil and cytosine derivatives of a novel class of 2′-deoxy-2′-fluoro-3′-C-hydroxymethyl-β-d -lyxo-configured nucleotides has been accomplished and the target molecules have been incorporated into AONs. Experiments on exonuclease degradation showed improved nucleolytic stability relative to the unmodified control. Upon the introduction of one or two of the novel 2′-fluoro-3′-C-hydroxymethyl nucleotides as modifications in the gap region of a gapmer AON was associated with efficient RNase H-mediated cleavage of the RNA strand of the corresponding AON:RNA duplex. Notably, a tailored single cleavage event could be engineered depending on the positioning of a single modification. The effect of single mismatched base pairs was scanned along the full gap region demonstrating that the modification enables a remarkable specificity of RNase H cleavage. A cell-based model system was used to demonstrate the potential of gapmer AONs containing the novel modification to mediate gene silencing.     

Large-Scale Synthesis of a Niche Olefin Metathesis Catalyst Bearing an Unsymmetrical N-Heterocyclic Carbene (NHC) Ligand and its Application in a Green Pharmaceutical Context

A large-scale synthesis of known Ru olefin metathesis catalyst VII featuring an unsymmetrical N-heterocyclic carbene (NHC) ligand with one 2,5-diisopropylphenyl (DIPP) and one thiophenylmethylene N-substituent is reported. The optimised procedure does not require column chromatography in any step and allows for preparation of up to 0.5 kg batches of the catalyst from simple precursors. The application profile of the obtained catalyst was studied in environmentally friendly dimethyl carbonate (DMC). Although VII exhibited low efficiency in cross-metathesis (CM) with electron-deficient partners, good to excellent results were noted for substrates featuring easy to isomerise C−C double bonds. This includes polyfunctional substrates of medicinal chemistry interest, such as analogues of psychoactive 5F-PB-22 and NM-2201 and two PDE5 inhibitors—Sildenafil and Vardenafil. Finally, a larger scale ring-closing metathesis (RCM) of a Vardenafil derivative was conducted in DMC, allowing for straightforward isolation of the expected product (23 g) in high yield and with low Ru contamination level (7.7 ppm).     

The influence of Lewis acid catalyst on the kinetic and molecular mechanism of nitrous acid elimination from 5-nitro-3-phenyl-4,5-dihydroisoxazole: DFT computational study

Chemistry of Heterocyclic Compounds - The molecular mechanism of nitrous acid elimination from 5-nitro-3-phenyl-4,5-dihydroisoxazole systems has been explored using DFT computational study. It was...     

Analysis of Cibacron blue F3G-A interaction with therapeutic proteins by MALDI-TOF mass spectrometry

The formation of the complexes between Cibacron blue F3G-A and two therapeutic proteins, recombinant human interferon-alpha2b and recombinant human growth hormone, was investigated. The method of time-resolved limited proteolysis coupled with MALDI-TOF mass spectrometry was used. The analysis of peptide maps revealed that A(17)HR(19) and L(20)HQLAFDTYQEFEEAYIPK(38) of hGH, and R(14)TLMLLAQMR(23) and D(33)RHDFGFPQEEFGNQFQK(50) of hIFN-alpha2b, exhibit affinity to Cibacron blue F3G-A. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Nanolayers of selected porphyrin and phthalocyanine dyes on solid substrates studied by electronic absorption and IR reflection–absorption spectroscopy

Electronic absorption and IR reflection–absorption spectra in non-polarized and in polarized light for lead porphyrin as well as magnesium and lead phthalocyanine dyes when deposited in the form of Langmuir–Blodgett (LB) nanolayers on solid inorganic surfaces (quartz, semiconductor and metal) were measured. Some IR bands of the Langmuir–Blodgett dye layers’ spectra show frequency shifts and changes in the relative intensities as well as in half widths when compared with the vibrational features of powdered dyes dispersed in KBr pellets, which were used as references. The FT-IR spectroscopic examination of the Langmuir–Blodgett layers allowed to estimate electron redistribution at the interface between dye layer and solid substrates. The Langmuir–Blodgett films of different thicknesses (3, 5, 10 layers) were studied at various angles of IR beam incidence and different light polarizations. The most spectacular results were obtained for the grazing incidence (80°) and films of 5 layers for dyes on the Au substrate. The IR spectroscopy was supported with electronic absorption studies (UV–vis) to follow interaction at interface between the dye layers and the substrates as well as to evaluate linear dichroism and to determine arrangement of molecules in the Langmuir–Blodgett films. Molecular arrangement in the Langmuir–Blodgett layers was discussed. It was shown that the dye molecular planes are rather randomly oriented in the Langmuir–Blodgett films with a tendency that the Q_y and Q_x transition moments in the phthalocyanine macroring are slightly directed along the y-axis (Langmuir–Blodgett dipping direction) and the x-axis direction, respectively.     

Man-tailored cellulose-based carriers for invertase immobilization

Cellulose-based carriers Granocel were specially prepared and optimised for covalent immobilization of enzymes. The effects of carrier characteristics such as pore size, chemistry of anchor groups and their density on invertase immobilization efficiency were evaluated. It was found that the preferential adsorption/binding of the enzyme to a carrier during coupling and its activity after immobilization depended on microenvironmental effects created by hydrophilic surface of the carrier, functional groups and their activators. The best preparations (activity approx. 300 U/mL, high storage stability) were obtained for NH₂-Granocel activated with glutaraldehyde. It is probably due to Granocel modification with pentaethylenehexamine that gave a 19-atom spacer arm. The enzyme concentration in coupling mixture was optimised as well. The kinetic parameters of sucrose hydrolysis for native and immobilized invertase were evaluated. Compared to the native invertase, K _m value of immobilized enzyme was only twice higher with about three times lower substrate inhibition. Reaction runs in a well mixed batch reactors with native and immobilized invertase showed slightly slower reaction rate in the case of the enzyme covalently bound to Granocel. Very good stability of cellulose-based carrier was proved experimentally by 20 successive reaction runs in a batch reactor.     

Size‐Controlled Formation of Noble‐Metal Nanoparticles in Aqueous Solution with a Thiol‐Free Tripeptide

A combinatorial screening revealed the peptide H‐His‐d ‐Leu‐d ‐Asp‐NH₂ ( 1 ) as an additive for the generation of monodisperse, water‐soluble palladium nanoparticles with average diameters of 3 nm and stabilities of over 9 months. The tripeptide proved to be also applicable for the size‐controlled formation of other noble‐metal nanoparticles (Pt and Au). Studies with close analogues of peptide 1 revealed a specific role of each of the three amino acids for the formation and stabilization of the nanoparticles. These data combined with microscopic and spectroscopic analyses provided insight into the structure of the self‐assembled peptidic monolayer around the metal core. The results open interesting prospects for the development of functionalized metal nanoparticles.     

Separating sets by lower and upper semicontinuous functions with a closed graph

In this paper we characterize the pairs (A^?, A⁺) of disjoint subsets of perfectly normal topological space which can be separated by a lower and an upper semicontinuous function with a closed graph.