The Cytotoxic Effect of α-Synuclein Aggregates

Parkinson's disease is a neurodegenerative disorder involving a functional protein, α-synuclein, whose primary function is related to vesicle trafficking. However, α-synuclein is prone to form aggregates, and these inclusions, known as Lewy bodies, are the hallmark of Parkinson's disease. α-synuclein can alter its conformation and acquire aggregating capacity, forming aggregates containing β-sheets. This protein's pathogenic importance is based on its ability to form oligomers that impair synaptic transmission and neuronal function by increasing membrane permeability and altering homeostasis, generating a deleterious effect over cells. First, we establish that oligomers interfere with the mechanical properties of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane, as demonstrated by nanoindentation curves. In contrast, nanoindentation revealed that the α-synuclein monomer's presence leads to a much more resistant lipid bilayer. Moreover, the oligomers’ interaction with cell membranes can promote lactate dehydrogenase (LDH) release, suggesting the activation of cytotoxic events.     

Disorder arising from the location of enantiomers in a twist-boat structure: 2,6-trans-2,4,6-tris(trichloromethyl)-1-oxa-3,5-dithian

Crystals of the title compound are orthorhombic, Pca2₁;a=27.586(4),b=10.509(3),c=11.080(2) Å,V=3212(1) ų,Z=8. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by full-matrix least squares to a finalR value of 0.055 using 2043 reflections. One of the two independent molecules in the asymmetric unit is disordered. The disorder is manifested mainly between the oxygen atom and one sulfur atom and is caused by opposite enantiomers occupying corresponding positions in different unit cells. The endocyclic torsion angles in both independent molecules are very similar but the disposition of the heteroatoms on the twist-boat framework is different in the two molecules. Site occupancy of the two models on this framework in the disordered molecule is in the ratio 2179 with the smaller proportion being very similar to the ordered molecule and the remainder similar to that found in the normal molecule oftrans-4-chloro-2,4,6-tris(trichloromethyl)-1-oxa-3,5-dithian (Irving and Irving, 1988).     

High-throughput purification of combinatorial libraries I: a high-throughput purification system using an accelerated retention window approach

We have developed a high-throughput purification system to purify combinatorial libraries at a 50-100-mg scale with a throughput of 250 samples/instrument/day. We applied an accelerated retention window method to shorten the purification time and targeted one fraction per injection to simplify data tracking, lower QC workload, and simplify the postpurification processing. First, we determined the accurate retention time and peak height for all compounds using an eight-channel parallel LC/UV/MS system, and calculated the specific preparative HPLC conditions for individual compounds. The preparative HPLC conditions include the compound-specific gradient segment for individual compounds with a fixed gradient slope and the compound-specific UV or ELSD threshold for triggering a fraction collection device. A unique solvent composition or solvent strength was programmed for each compound in the preparative HPLC in order to elute all compounds at the same target time. Considering the possible deviation of the predicted retention time, a 1-min window around the target time was set to collect peaks above a threshold based on UV or ELSD detection. Dual column preparative instruments were used to maximize throughput. We have purified more than 500 000 druglike compounds using this system in the past 3 years. We report various components of this high-throughput purification system and some of our purification results.     

Studies with dithizone: Part XXI. The Relationship between pH12 and Molar Solubility

The effect of changes of ionic strength on the partition of an analytically important weak acid between a variety of aqueous and immiscible organic phases has been studied with respect to new measurements on dithizone (3-mercapto-1,5-diphenylformazan) and di(p-tolyl)thiocarbazone. A linear relationship has been deduced between the pH at which 50% extraction takes place and S_r,o (the solubility of the reactant in the organic phase), and confirmed by measurements of pH_{$\text{1}\text{2}$}, and S_r,o for a large number of organic solvents. The solubilities of the reagents in water, S_r, are also reported. The form of the relationship between pH and log D, and between pH_{$\text{1}\text{2}$} and log S_r,o is the same whether a solution of dithizone consists of a single species or a mixture of thiol and thione forms in tautomeric equilibrium.     

The determination of small amounts of long-chain tertiary alkylamines and quarternary ammonium salts

Bromocresol green has been investigated as an alternative to ammonium erdmannate for the absorptiometric determination of small amounts of long-chain alkylamines and quaternary ammonium salts in aqueous solution in a solvent extraction procedure. The molecular absorption coefficient of the reagent at 615 nm is about 3 times that of the erdmannate ion at 353 nm; visual methods of comparison are simplified by the blue colour of the bromocresol green anion The sensitivity of both the bromocresol green and the erdmannate method may be increased by stripping the coloured reagents into a small volume of aqueous solution. Both methods are free of interference from iron, but the present procedure has the disadvantage of a blank which depends both on the pH and on the concentration of excess reagent.     

A genetic algorithm for structure-based de novo design

Genetic algorithms have properties which make them attractive in de novo drug design. Like other de novo design programs, genetic algorithms require a method to reduce the enormous search space of possible compounds. Most often this is done using information from known ligands. We have developed the ADAPT program, a genetic algorithm which uses molecular interactions evaluated with docking calculations as a fitness function to reduce the search space. ADAPT does not require information about known ligands. The program takes an initial set of compounds and iteratively builds new compounds based on the fitness scores of the previous set of compounds. We describe the particulars of the ADAPT algorithm and its application to three well-studied target systems. We also show that the strategies of enhanced local sampling and re-introducing diversity to the compound population during the design cycle provide better results than conventional genetic algorithm protocols.     

Formation and structure of a novel enediyne-RNA base covalent adduct

The structure of an unusual covalent adduct formed by thiol-activated neocarzinostatin chromophore (NCS-chrom) and a RNA-DNA hybrid having an overhang of four unpaired residues at the 3'-end of the RNA strand has been elucidated by MS and NMR spectroscopic analyses. Unlike previously characterized adducts formed by NCS-chrom on the sugar residue of the DNA target, this adduct has been found to be on one of the uracil bases in the RNA overhang. Covalent linkage is between C-6 of the post-activated NCS-chrom and C-5 of the uracil. A novel mechanism involving adduction of the NCS-chrom C-6 radical, generated by 2-mercaptoethanol activation, to C-5 of the uracil at the U9 position of the RNA 11-mer, oxidation by dioxygen, reduction by the thiol, and subsequent dehydration is proposed for adduct formation.     

Coloured liquid anion-exchangers

Of the several stable and coloured uninegative ions examined, trans-bis(dimethylglyoximato) dinitritocobaltate(III) ([Co(C₄H₇O₂)₂(NO₂)₂]^-, termed goldenate ion, G^-) can advantageously replace the erdmannate ion in the formation of a more photochemically stable coloured anion-exchanger derived from Aliquat-336 chloride. Quantitative spectrophotometric measurements of its displacement by chloride, bromide and perchlorate ions were made and are discussed together with literature data to examine the effect of parameters such as the nature of the cation and of the anion and change in the organic solvent on the relative and absolute values of extraction constants.