Computer-assisted optimization of reversed-phase HPLC isocratic separation of neutral compounds

An appropriate optimization strategy should be used to find a desired resolution or selectivity with a minimum number of experiments in a limited time, which could assure the baseline separation of all target compounds. It was usually realized by means of a specialized computer program. In this paper, mapping optimization method and overlapping resolution mapping were compared for the optimization of a reversed-phase high-performance liquid chromatography (HPLC) isocratic separation of neutral compounds. The calculated resolutions and separation time of 7 to 10 experiments are fitted by different equations, which were used to build a contour plot with a minimum effective resolution and maximum retention time as a function of a mobile phase composition. The balance between resolution and analysis time could be easily realized by the overlapping of the final overlapping resolution mapping and analysis time mapping. The validity of the two methods was confirmed by some typical experiments. The models are simple, visual, and common without theoretical arithmetic.     

Insoluble eggshell matrix proteins--their peptide mapping and partial characterization by capillary electrophoresis and high-performance liquid chromatography

Avian eggshell matrix proteins were studied by two analytical approaches. Peptide mapping was done by trypsin and pepsin followed by collagenase cleavage; analyses were carried out by capillary electrophoresis and reversed-phase high-performance liquid chromatography (HPLC). Comparison of peptide maps obtained by both methods revealed a complex mixture of peptides in the insoluble layers of the eggshell; it was concluded that there are at least three different insoluble protein/peptide layers in the avian eggshell (cuticle, palisade, and mammillary layer). Partial characterization of peptides in each layer was made by HPLC-mass spectrometry analysis. There is an evidence that the eggshell insoluble proteins contain species susceptible to collagenase cleavage, however, the sequences split by this enzyme probably are not those typical for the main triple-helical core of collagenous proteins. It is proposed that the action of collagenase upon eggshell proteins is caused by the side effect of collagenase described previously with synthetic peptides. Some of the proteins present are probably glycosylated. Fatty acid content in the insoluble eggshell layers (after decalcification) was in the range of 2-4% (which reflected both lipid and lipoproteins bound fatty acids). Porphyrin pigments are dominant in the cuticle layer.     

A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm

Rational drug design involves finding solutions to large combinatorial problems for which an exhaustive search is impractical. Genetic algorithms provide a novel tool for the investigation of such problems. These are a class of algorithms that mimic some of the major characteristics of Darwinian evolution. LEA has been designed in order to conceive novel small organic molecules which satisfy quantitative structure-activity relationship based rules (fitness). The fitness consists of a sum of constraints that are range properties. The algorithm takes an initial set of fragments and iteratively improves them by means of crossover and mutation operators that are related to those involved in Darwinian evolution. The basis of the algorithm, its implementation and parameterization, are described together with an application in de novo molecular design of new retinoids. The results may be promising for chemical synthesis and show that this tool may find extensive applications in de novo drug design projects.     

Analytic study of power spectra of the tent maps near band-splitting transitions

Successive band-splitting transitions occur in the one-dimensional map x_i+1=g(x_i),i=0, 1, 2,... withg(x)=x, (0 x 1/2) –x +, (1/2 <x 1) as the parameter is changed from 2 to 1. The transition point fromN (=2ⁿ) bands to 2Nbands is given by=(2)^1/N (n=0, 1,2,...). The time-correlation function _i=x_ix₀/(x₀)²,x_i x_i–x_i is studied in terms of the eigenvalues and eigenfunctions of the Frobenius-Perron operator of the map. It is shown that, near the transition point=2, _i–[(10–42)/17] _i,0-[(102-8)/51]_i,1 + [(7 + 42)/17](–1)ⁱe^–yi, where2(–2) is the damping constant and vanishes at=2, representing the critical slowing-down. This critical phenomenon is in strong contrast to the topologically invariant quantities, such as the Lyapunov exponent, which do not exhibit any anomaly at=2. The asymptotic expression for _i has been obtained by deriving an analytic form of _i for a sequence of which accumulates to 2 from the above. Near the transition point=(2)^1/N, the damping constant of _i fori N is given by _N=2(^N-2)/N. Numerical calculation is also carried out for arbitrary a and is shown to be consistent with the analytic results.     

Autoignition temperature: comprehensive data analysis and predictive models

ABSTRACT

Here we report a new predictive model for autoignition temperature (AIT), an important physical parameter widely used to assess potential safety hazards of combustible materials. Available structure-AIT data extracted from different sources were critically analysed. Support vector regression (SVR) models on different data subsets were built in order to identify a reliable compound set on which a realistic model could be built. This led to a selection of the dataset containing 875 compounds annotated with AIT values. The thereupon-based SVR model performs reasonably well in cross-validation with the determination coefficient r ² = 0.77 and mean absolute error MAE = 37.8°C. External validation on 20 industrial compounds missing in the training set confirmed its good predictive power (MAE = 28.7°C).     

Conformational analysis of [Met5]-enkephalin: Solvation and ionization considerations

[Met5]-Enkephalin has the sequence Tyr-Gly-Gly-Phe-Met. Only the extended conformation of the peptide has been observed by X-ray crystallography. Nuclear magnetic resonance spectroscopy supports the presence of a turn at Gly 3 and Phe 4 in dimethyl sulfoxide. In this study, the peptide conformational states and thermodynamic properties are understood in terms of ionization state and solvent environment. In the calculation, final conformations obtained from multiple independent Monte Carlo simulated annealing conformational searches are starting points for molecular dynamics simulations. In an aqueous environment given by the use of solvation free energy and the zwitterionic state, dominant structural motifs computed are G-P Type II bend, G-G Type II bend, and G-G Type I bend motifs, in order of increasing free energy. In the calculation of the peptide with neutral N- and C-termini and solvation free energy, the extended conformer dominates (by at least a factor of 2.5), and the conformation of another low free energy conformer superimposes well on the pharmacophoric groups of morphine. Neutralization of charge and solvation induce and stabilize the extended conformation, respectively. A mechanism of inter-conversion between the extended conformer and three bent conformers is supported by /-scatter plots, and by the conformer relative free energies. An estimate of the entropy change of receptor unbinding is 8.3 cal K-1 mol-1, which gives rise to a -2.5 kcal/mol entropy contribution to the free energy of unbinding at 25 °C. The conformational analysis methodology described here should be useful in studies on short peptides and flexible protein surface loops that have important biological implications.     

Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors

We present a computational protocol which uses the known three-dimensional structure of a target enzyme to identify possible ligands from databases of compounds with low molecular weight. This is accomplished by first mapping the essential interactions in the binding site with the program GRID. The resulting regions of favorable interaction between target and ligand are translated into a database query, and with UNITY a flexible 3D database search is performed. The feasibility of this approach is calibrated with thrombin as the target. Our results show that the resulting hit lists are enriched with thrombin inhibitors compared to the total database.     

Characterisation of botulinum toxins type C, D, E, and F by matrix-assisted laser desorption ionisation and electrospray mass spectrometry

In a follow-up of the earlier characterisation of botulinum toxins type A and B (BTxA and BTxB) by mass spectrometry (MS), types C, D, E, and F (BTxC, BTxD, BTxE, BTxF) were now investigated. Botulinum toxins are extremely neurotoxic bacterial toxins, likely to be used as biological warfare agent. Biologically active BTxC, BTxD, BTxE, and BTxF are comprised of a protein complex of the respective neurotoxins with non-toxic non-haemagglutinin (NTNH) and, sometimes, specific haemagglutinins (HA). These protein complexes were observed in mass spectrometric identification. The BTxC complex, from Clostridium botulinum strain 003-9, consisted of a 'type C1 and D mosaic' toxin similar to that of type C strain 6813, a non-toxic non-hemagglutinating and a 33 kDa hemagglutinating (HA-33) component similar to those of strain C-Stockholm, and an exoenzyme C3 of which the sequence was in full agreement with the known genetic sequence of strain 003-9. The BTxD complex, from C. botulinum strain CB-16, consisted of a neurotoxin with the observed sequence identical with that of type D strain BVD/-3 and of an NTNH with the observed sequence identical with that of type C strain C-Yoichi. Remarkably, the observed protein sequence of CB-16 NTNH differed by one amino acid from the known gene sequence: L859 instead of F859. The BTxE complex, from a C. botulinum isolated from herring sprats, consisted of the neurotoxin with an observed sequence identical with that from strain NCTC 11219 and an NTNH similar to that from type E strain Mashike (1 amino acid difference with observed sequence). BTxF, from C. botulinum strain Langeland (NCTC 10281), consisted of the neurotoxin and an NTNH; observed sequences from both proteins were in agreement with the gene sequence known from strain Langeland. As with BTxA and BTxB, matrix-assisted laser desorption/ionisation (MALDI) MS provided provisional identification from trypsin digest peptide maps and liquid chromatography-electrospray (tandem) mass spectrometry (LC-ES MS) afforded unequivocal identification from amino acid sequence information of digest peptides obtained in trypsin digestion.     

Using a process-centered approach to minimize the effort of compliance

 The complexity of different quality standards can, in principle, be covered by different approaches and strategies. In-depth process mapping of quality control (QC) work streams was used by the analytical laboratories of Lonza AG to show up the principle differences in being compliant to different quality systems. The results identified two main drivers for all necessary actions: process-related activities and infrastructure-related activities. In addition, a clear indication of the economic impact of these driving forces was gained, which led the laboratories to decide on a process-oriented approach. This approach has the advantage of being able to reflect the different demands of different quality assurance (QA) regulations within the same QC organizational structure. Following the process helps avoid unnecessary efforts in analytical work and represents a very economical approach, at the same time, providing high flexibility to react to different QA or customer demands. Received: 5 July 2002 Accepted: 12 November 2002 Acknowledgements The process-oriented approach resulted from many, very challenging discussions for which I would like to thank the staff of my organization (Analytics & QC), especially, the QA staff and the LIMS team. Presented at Analytica Conference, 23–26 April 2002, Munich, Germany Correspondence to B. Ciommer     

Controlled enzyme-immobilisation on capillaries for microreactors for peptide mapping

In the present paper, the covalent immobilisation of the digesting enzyme trypsin has been achieved through photo-immobilisation on a portion of a silica capillary, thus leading to the construction of a capillary electrophoretic (CE)-microreactor for peptide mapping. The CE-microreactor is characterised by being a single piece, thus ensuring no fluidic or electrical leakage. The enzyme was immobilised with a surface density of 15.8 g/cm², the stability was high (80% after 38 days) and the rate of conversion was 0.2 ng/s. On-line protein mapping was tested with proteins of different dimensions, showing competitiveness in terms of time (completed map within 15 min) and exhaustive maps of small proteins. The results of the CE-microreactor and the potential to immobilise biocomponents easily on a desired portion of the capillary indicate further developments towards the construction of a variety of miniaturised enzymatic screening devices for high-throughput screening analysis.