Efficient generation,storage, and manipulation of fully flexible pharmacophore multiplets and their use in 3-D similarity searching

Pharmacophore triplets and quartets have been used by many groups in recent years, primarily as a tool for molecular diversity analysis. In most cases, slow processing speeds and the very large size of the bitsets generated have forced researchers to compromise in terms of how such multiplets were stored, manipulated, and compared, e.g., by using simple unions to represent multiplets for sets of molecules. Here we report using bitmaps in place of bitsets to reduce storage demands and to improve processing speed. Here, a bitset is taken to mean a fully enumerated string of zeros and ones, from which a compressed bitmap is obtained by replacing uniform blocks ("runs") of digits in the bitset with a pair of values identifying the content and length of the block (run-length encoding compression). High-resolution multiplets involving four features are enabled by using 64 bit executables to create and manipulate bitmaps, which "connect" to the 32 bit executables used for database access and feature identification via an extensible mark-up language (XML) data stream. The encoding system used supports simple pairs, triplets, and quartets; multiplets in which a privileged substructure is used as an anchor point; and augmented multiplets in which an additional vertex is added to represent a contingent feature such as a hydrogen bond extension point linked to a complementary feature (e.g., a donor or an acceptor atom) in a base pair or triplet. It can readily be extended to larger, more complex multiplets as well. Database searching is one particular potential application for this technology. Consensus bitmaps built up from active ligands identified in preliminary screening can be used to generate hypothesis bitmaps, a process which includes allowance for differential weighting to allow greater emphasis to be placed on bits arising from multiplets expected to be particularly discriminating. Such hypothesis bitmaps are shown to be useful queries for database searching, successfully retrieving active compounds across a range of structural classes from a corporate database. The current implementation allows multiconformer bitmaps to be obtained from pregenerated conformations or by random perturbation on-the-fly. The latter application involves random sampling of the full range of conformations not precluded by steric clashes, which limits the usefulness of classical fingerprint similarity measures. A new measure of similarity, The Stochastic Cosine, is introduced here to address this need. This new similarity measure uses the average number of bits common to independently drawn conformer sets to normalize the cosine coefficient. Its use frees the user from having to ensure strict comparability of starting conformations and having to use fixed torsional increments, thereby allowing fully flexible characterization of pharmacophoric patterns.     

Numerical investigation of the effects of classical phase space structure on a quantum system with decoherence

We present a detailed numerical study of a chaotic classical system and its quantum counterpart. The system is a special case of a kicked rotor and for certain parameter values possesses cantori dividing chaotic regions of the classical phase space. We investigate the diffusion of particles through a cantorus. A quantum analysis confirms that the cantori act as barriers. We numerically estimate the classical phase space flux through the cantorus per kick and relate this quantity to the behavior of the quantum system. We introduce decoherence via environmental interactions with the quantum system and observe the subsequent increase in the transport of quantum particles through the boundary.     

New algorithm for optimal parameter estimation with linear constraints

This paper presents a new algorithm for optimal parameter estimation problems with linear constraints. The algorithm developed is based on least absolute-value approximations. The problem is solved first using a least-error-square technique, where we add to the cost function the equality constraints via Lagrange multipliers, to obtain a good estimate for the residuals of the measurements, having gained this information, we choose a number of measurements with the smallest residuals. This number equals the number of parameters to be estimated minus the number of constraints. Using these measurements together with the constraints, we obtain a number of observations equal to the number of parameters to be estimated. By using this technique, we show that there is no need to either iterate or use linear programming to obtain the estimation.This work was supported by the Natural Sciences and Engineering Research Council of Canada, Grant A4146.     

The synthesis of some substituted macrocyclic ether-ester compounds

A series of macrocyclic ether-esters has been prepared by treating various glycols with adipoyl chloride and various substituted malonyl, succinyl and glutaryl chlorides. The prepared compounds include: 15-ethyl- and 15-phenyl-1,4,7,10,13-pentaoxacyclohexadecane-14,16-dione (5 and 6); 15-methyl-, 15-phenyl-, cis-cyclohexo-[o]-and benzo-[o]-1,4,7,10,13-pentaoxacycloheptadecane-14,17-dione (7–10); trans,trans-1,4,7,10,13,18,21,24,27,30-de-caoxacyclotetratriacontane-15, 32-diene-14,17,31,34-tetraone (11); 1,4,7,10,13-pentaoxacyclooctadecane-14,18-dione (12); 15,15,16,16,17,17-hexafluoro- and 16-methyl-1,4,7,10,13-pentaoxacyclooctadecane-14,18-dione (13 and 14); 1,4,7,10-tetraoxacyclohexadecane-11,16-dione (15); and 1,4,7,10,13-pentaoxacyclononadecane-14,19-dione (16).     

Molecular recognition: comparative study of a tunable host-guest system by using a fluorescent model system and collision-induced dissociation mass spectrometry on dendrimers

Host-guest interactions between the periphery of adamantylurea-functionalized dendrimers (host) and ureido acetic acid derivatives (guest) were shown to be specific, strong and spatially well-defined. The binding becomes stronger when using phosphonic or sulfonic acid derivatives. In the present work we have quantified the binding constants for the host-guest interactions between two different host motifs and six different guest molecules. The host molecules, which resemble the periphery of a poly(propylene imine) dendrimer, have been fitted with an anthracene-based fluorescent probe. The two host motifs differ in terms of the length of the spacer between a tertiary amine and two ureido functionalities. The guest molecules all contain an acidic moiety (either a carboxylic acid, a phosphonic acid, or a sulfonic acid) and three of them also contain an ureido moiety capable of forming multiple hydrogen bonds to the hosts. The binding constants for all 12 host-guest complexes have been determined by using fluorescence titrations by monitoring the increase in fluorescence of the host upon protonation by the addition of the guest. The binding constants could be tuned by changing the design of the acidic part of the guest. The formation of hydrogen bonds gives, in all cases, higher association constants, demonstrating that the host is more than a proton sensor. The host with the longer spacer (propyl) shows higher association constants than the host with the shorter spacer (ethyl). The gain in association constants are higher when the urea function is added to the guests for the host with the longer spacer, indicating a better fit. Collision-induced dissociation mass spectrometry (CID-MS) is used to study the stability of the six motifs using the corresponding third generation dendrimer. A similar trend is found when the six different guests are compared.     

Stem cell survival is severely compromised by the thymidineanalog EdU (5-ethynyl-2′-deoxyuridine), an alternative to BrdU for proliferation assays and stem cell tracing

Stem cell therapy has opened up the possibility of treating numerous degenerating diseases. However, we are still merely at the stage of identifying appropriate sources of stem cells and exploring their full differentiation potential. Thus, tracking the stem cells upon in vivo engraftment and during in vitro co-culture is very important and is an area of research embracing many pitfalls. 5-Ethynyl-2′-deoxyuridine (EdU), a rather new thymidine analog incorporated into DNA, has recently been suggested to be a novel highly valid alternative to other dyes for labeling of stem cells and subsequent tracing of their proliferation and differentiation ability. However, our results herein do not at any stage support this recommendation, since EdU severely reduces the viability of stem cells. Accordingly, we found that transplanted EdU-labeled stem cells hardly survive upon in vivo transplantation into regenerating muscle, whereas stem cells labeled in parallel with another dye survived very well and also participated in myofiber formation. Similar data were obtained upon in vitro myogenic culture, and further analysis showed that EdU reduced cell numbers by up to 88 % and increased the cell volume of remaining cells by as much as 91 %. Even at low EdU concentrations, cell survival and phenotype were substantially compromised, and the myogenic differentiation potential was inhibited. Since we examined both primary derived cells and cell lines from several species with the same result, this appears to be a common trait of EdU. We therefore suggest that EdU labeling should be avoided (or used with precaution) for stem cell tracing purposes.

Experimental and Kinetic Modeling Study of Methanol Ignition and Oxidation at High Pressure

A detailed chemical kinetic model for oxidation of CH₃OH at high pressure and intermediate temperatures has been developed and validated experimentally. Ab initio calculations and Rice–Ramsperger–Kassel–Marcus/transition state theory (RRKM/TST) analysis were used to obtain rate coefficients for , , , and . The experiments, involving CH₃OH/O₂ mixtures diluted in N₂, were carried out in a high‐pressure flow reactor at 600–900 K and 20–100 bar, varying the reaction stoichiometry from very lean to fuel‐rich conditions. Under the conditions studied, the onset temperature for methanol oxidation was not dependent on the stoichiometry, whereas increasing pressure shifted the ignition temperature toward lower values. Model predictions of the present experimental results, as well as rapid compression machine data from the literature, were generally satisfactory. The governing reaction pathways have been outlined based on calculations with the kinetic model. Unlike what has been observed for unsaturated hydrocarbons, the oxidation pathways for CH₃OH under the investigated conditions were very similar to those prevailing at higher temperatures and lower pressures. At the high pressures, the modeling predictions for onset of reaction were particularly sensitive to the reaction.     

Rapid prototyping of polymer microsystems via excimer laser ablation of polymeric moulds

This study presents a novel method for rapid prototyping of polymer microsystems. The method is based on excimer laser ablation of a thermally and mechanically stable polymer, such as PEEK (poly-ether-ether-ketone). A negative of the desired microsystem is laser machined in PEEK, which can then be used directly for hot embossing or injection moulding of a series of prototypes. This approach is very rapid and considerably cheaper than more traditional approaches to toolmaking, while still performing well in terms of reproduction of tool dimensions. The reduction in time and cost for a master tool using this method opens up new possibilities for testing small series in the R&D phase of a microsystem. Finally, two particular applications of the technique are presented.     

Thiol- and disulfide-modified oligonucleotide monolayer structures on polycrystalline and single-crystal Au(111) surfaces

We provide a comprehensive study of single- (ss) and double-strand (ds) oligonucleotides with either 25 or 10 bases or base pairs (bp) immobilized on polycrystalline and single-crystal Au(111) surfaces. The study is based on X-ray photoelectron spectroscopy, cyclic and differential pulse voltammetry, interfacial capacitance data, and electrochemical scanning tunnelling microscopy (in situ STM). The sequences used were the 25-bp sequence from the BRCA1 gene (25-mer), while the 10-bp oligonucleotides contained solely linear adenine and thymine sequences. The oligonucleotides were modified by the dimethoxytrityl group (DMT) via a disulfide group [DMT-S-S-ss25-mer and DMT-S-S-ds(AT)₁₀], a pure disulfide group (A₁₀-S-S-T₁₀), or a thiol group [HS-ss25-mer and HS-ds-(AT)₁₀], all via a hexamethylene linker. The overall pattern suggests strategies for controlled adsorption of DNA-based molecules and recognition of complementary strands or other molecules.     

Determination of average degree of polymerisation and distribution of oligosaccharides in a partially acid-hydrolysed homopolysaccharide: a comparison of four experimental methods applied to mannuronan

The average degree of polymerisation (DP) and distribution of oligosaccharides in partially acid hydrolysed mannuronans were quantitatively evaluated by 1H NMR, electrospray ionisation mass spectrometry (ESI-MS), micellar electrokinetic capillary chromatography with UV detection (MEKC-UV), and high-pressure anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). Our investigation shows that 1H NMR, MEKC-UV and, in particular, HPAEC-PAD can be used as quantitative tools to aid the investigation of polysaccharide structure, function and synthesis. For the latter two techniques, especially, this represents a significant new development as it enables calculation of the quantity of individual oligomers of nominal DP by direct analysis of a defined oligomer mixture. Appropriate statistical averages of number and weight distributions were also calculated and found to fit very well to predicted Kuhn distributions that assume random depolymerisation.