Synthesis of homoceramides, novel ceramide analogues, and their lack of effect on the growth of hippocampal neurons

The synthesis of a new series of D-erythro-homoceramide analogues is described. Several synthetic approaches were investigated. Homoceramides can be successfully synthesized from L-homoserine as chiral building block and a protected Weinreb-amide as a key intermediate. The synthesis of short-chain analogues with a heptyl side chain, as well as with a phenyl residue in the sphingoid part (instead of the naturally occurring tridecyl side chain), was effected. The homoceramides 15-17 and 24 were investigated for their potential to reverse the inhibitory effect of fumonisin B(1) on axonal growth. Unfortunately, none of the tested compounds showed any biological activity due to their lack of metabolism to glucosylhomoceramide.     

Development of a formulation of Pirodavir using 2-hydroxypropyl-β-cyclodextrin

Pirodavir, 4-[2-[1-(6-Methyl-3-pyridazinyl)-4-piperidinyl]ethoxy]benzoic acid ethyl ester, is an antiviral compound which has low aqueous solubility (<0.01 mg/ml). The compound is a weak base (pKa 5.8) with high lipophicity (logP 4.44). Ionization of the compound increases the solubility in acidic medium to 2.3 mg/ml at pH 2.4. However, a low pH is not acceptable for nasal application as this would induce irritation. Extensive solubility studies were performed using different types of substituted cyclodextrins in order to select an appropriate derivate capable of increasing solubility to an acceptable level for formulations for nasal application. Aqueous solubility of pirodavir increased in a linear fashion with increasing concentration of most of the substituted cyclodextrins. However, using 2-hydropropyl-β-cyclodextrin (HPBCD) the solubility increased in a non-linear fashion. Based on these studies HPBCD was selected as the most appropriate excipient. To support a clinical study on the treatment of rhinovirus cold by intranasal Pirodavir formulations were developed containing up to 5 mg/ml of pirodavir and up to 10% of HPBCD. Stability of the formulations was studied and found to be acceptable.     

A Synthetic Substrate of DNA Polymerase Deviating from the Bases,Sugar, and Leaving Group of Canonical Deoxynucleoside Triphosphates

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Highlights? A highly modified nucleotide as substrate for polymerases ? The reversibility of the polymerase reaction at the template level ? Synthesis of a nucleoside with two anomeric centers     

False Results Caused by Solvent Impurity in Tetrahydrofuran for MALDI TOF MS Analysis of Amines

Tetrahydrofuran (THF) is one of the most frequently used solvents in the MALDI TOF MS analysis of synthetic compounds. However, it should be used with caution because a trace amount of 4-hydroxybutanal (HBA) might be generated and accumulated in THF during storage. Since only a tiny amount of analytes is required in MALDI MS measurements, a trace amount of HBA might have a significant effect on the MS results. It was found that HBA will quickly react with primary and secondary amino compounds, leading to false results about the sample composition with an extra series of ions with additional mass of 70 Da in between. The formation of HBA can be inhibited by butylated hydroxytoluene (BHT) antioxidant. Therefore, when THF is required as the solvent for sample preparation, it is strongly recommended to use a BHT-stabilized one, at least for the analysis of compounds with amino groups.

SOS: A simple interactive program for ab initio oligonucleotide sequencing by mass spectrometry

Mass spectra of oligonucleotides derived from collision-induced dissociation following electrospray ionization provide an effective means of sequence determination, at the 20-mer level and below. An interactive, stand-alone computer program, Simple Oligonucleotide Sequencer (SOS) has been developed for rapid oligonucleotide sequencing from mass spectra, under user control on a residue by residue basis. Modifications can be defined in any combination for the base, sugar or backbone. Sequence ladders can be independently constructed in both the 5' --> 3' directions and 3' --> 5' directions, and graphically compared for homology and overlap. A particular advantage of this method is the ability to easily erase and rebuild alternate subsequences. The program can be used for ab initio sequencing of modified or unmodified oligonucleotides, for rapid verification of sequence, and in studies of fragmentation processes of model oligonucleotide derivatives.     

Facile synthesis of a chiral polymeric helix; folding by intramolecular hydrogen bonding

In a single condensation step, a poly-ureidophthalimide is synthesized, which folds into a chiral, helical architecture according to circular dichroism spectroscopy.     

A short path synthesis of [13C/15N] multilabeled pyrimidine nucleosides starting from glucopyranose nucleosides

The synthesis of fully [13C/15N] labeled pyrimidine nucleosides has been achieved from 13C-glucose and labeled nucleobases. The reaction scheme leads directly to the protected nucleosides without the need for the inversion of configuration of C-3 of 13C-glucose. This was achieved by an oxitative ring-opening reaction removing the carbon with the wrong configuration.     

Electrophoretic deposition of bacterial cells

The possibility to use alternating current electrophoretic deposition (AC-EPD) to deposit living cells in the form of Staphylococcus aureus and Escherichia coli on stainless steel was assessed. The experimental results revealed that these bacteria can be successfully deposited on metallic surfaces from demineralized water and sucrose based solutions using asymmetric unbalanced electric fields. Cell viability of the deposited bacteria was influenced by the strain and deposition medium.     

Matrix suppression and analyte suppression effects of quaternary ammonium salts in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry: an investigation of suppression mechanism

In the matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI TOF MS) analysis of some quaternary ammonium salts (QASs), very clean spectra of the quaternary ammonium ions were recorded with a strong matrix suppression effect (MSE). The QASs also showed a considerable analyte suppression effect (ASE). It was demonstrated that the MSE and ASE of the QASs can be explained well by the cluster ionization model. According to this model, MALDI ions are formed from charged matrix/analyte clusters. Various analyte ions and matrix ions might coexist in the cluster, and they will compete for the limited number of net charges available. If enough quaternary ammonium ions are present in the cluster, they will take away the net charges, thus resulting in the MSE and ASE. Our results also suggest that ‘the cluster ionization model’ is not in conflict with ‘the theory of ionization via secondary gas‐phase reactions’. The initial MALDI ions produced from charged matrix/analyte clusters will collide with other molecules or ions in the MALDI plume. Depending on the properties of the initial ions and the composition of the MALDI plume, secondary gas‐phase reactions might result from these collisions. The final ions observed are the combined results of ‘cluster ionization’ and ‘ionization via secondary gas‐phase reactions’. Copyright © 2009 John Wiley & Sons, Ltd.