Thermodynamic properties in the molecular dynamics ensemble applied to the gaussian core model fluid

The thermodynamic properties of pressure, energy, isothermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound are considered in a classical molecular dynamics ensemble. These properties were obtained using the treatment of Lustig [J. Chem. Phys. 100, 3048 (1994)] and Meier and Kabelac [J. Chem. Phys. 124, 064104 (2006)], whereby thermodynamic state variables are expressible in terms of phase-space functions determined directly from molecular dynamics simulations. The complete thermodynamic information about an equilibrium system can be obtained from this general formalism. We apply this method to the gaussian core model fluid because the complex phase behavior of this simple model provides a severe test for this treatment. Waterlike and other anomalies are observed for some of the thermodynamic properties of the gaussian core model fluid.     

An overview of drug screening using primary and embryonic stem cells

Cellular technologies are widely used in drug discovery to treat human diseases. Most studies involve the expression of recombinant targets in immortalized cells and measure drug interactions using simple, quantifiable responses. Such cells are also amenable to high throughput screening (HTS) methods. However, the cell phenotype employed in HTS is often determined by the assay technology available, rather than the physiological relevance of the cell background. They are, therefore, suboptimal surrogates for cells that accurately reflect human diseases. Consequently, there is growing interest in adopting primary and embryonic stem cells in drug discovery. Primary cells are already used in secondary screening assays in conjunction with confocal imaging techniques, as well as in target validation studies employing, for example, gene silencing approaches. Stem cells can be grown in unlimited quantities and can be derived from transgenic animals engineered to express disease causing proteins better coupling the molecular target with function in vivo. Human stem cells also offer unique opportunities for drug discovery in that they can be directed to specific phenotypes thus providing a framework to identify tissue-selective agents. Organizing stem cells into networks resembling those in native tissues, potentially returns drug discovery back to the highly successful pharmacological methods of the past, in which organ and tissue based systems were used, but with the advantage that they can be utilized using modern HTS technologies. This emerging area will lead to discovery of compounds whose effect in vivo is more predictable thereby increasing the efficiency of drugs that ameliorate human disease.     

Metrological approaches to drug development. Fast screening using universal biosensors at the stage of drug development

We expect that in the near future drug development will become the most interesting and demanded application of the suggested approach. Taking a known drug as the reference point and performing its chemical modification, one can sharply reduce the time and financial expenses for bioactivity testing of new substances and experimentally predict its general toxicity on a biological model the most adequate to human body.     

Calculations using a set of evenly spaced S-type gaussian functions

A basis set of evenly spaced S-type Gaussian functions with common exponents is examined. Formulas for common one- and two-electron integrals are derived. Because of thesymmetry of this basis set, a very compact two-electron integral list is produced. The number of two-electron integrals that must be stored is approximately eight times the number of basis functions. Use of this basis set in an SCF calculation is examined. Numerical results show that this approach works well for molecules containing only small atoms such as hydrogen, helium, or lithium, but that the method has problems with the core orbitals of heavier atoms. Procedures for augementing this basis set in calculations involving heavier atoms are examined.     

High throughput screening or drug impurity profiles using gradients in normal phase chromatography

Summary Developmental drug substances and a variety of precursors and process-related impurities were separated using mobile phase gradients under normal phase conditions. These separation conditions produced efficient separations in a fraction of the time necessary for comparable reversed-phase separations. The use of elevated temperatures, polar modifiers and moderate levels of acidic and basic additives allowed highly polar analytes to be eluted with high efficiency and selectivity using fast flow rates. Reproducibility for retention time and peak areas was demonstrated to be very good despite very short equilibration times.     

High-speed solubility screening assay using ultra-performance liquid chromatography/mass spectrometry in drug discovery

Ultra-performance liquid chromatography (UPLC) was investigated as an alternative to high-performance liquid chromatography (HPLC) for analyzing pharmaceutical drug candidates. We previously developed a 96-well-based high-speed solubility assay system (HSSOL) using HPLC/UV and a LogD assay system (HSLogD) using HPLC/MS [Y. Dohta, T. Yamashita, S. Horiike, T. Nakamura, T. Fukami, Anal. Chem. 79 (2007) 8312]. We have introduced the UPLC/MS system into this previously developed HSSOL system to increase throughput. Results obtained by the UPLC/MS and HPLC/UV systems showed good agreement, validating the usefulness of the UPLC/MS system. A high-speed solubility assay system was developed employing the UPLC/MS system, thereby tripling the throughput.     

Computation of surface tensions using expanded ensemble simulations

A method for the direct simulation of the surface tension is examined. The technique is based on the thermodynamic route to the interfacial tension and makes use of the expanded ensemble simulation method for the calculation of the free energy difference between two inhomogeneous systems with the same number of particles, temperature, and volume, but different interfacial area. The method is completely general and suitable for systems with either continuous or discontinuous interactions. The adequacy of the expanded ensemble method is assessed by computing the interfacial tension of the planar vapor-liquid interface of Lennard-Jones, Lennard-Jones dimers, Gay-Berne, and square-well model fluids; in the latter, the interactions are discontinuous and the present method does not exhibit the asymmetry of other related methods, such as the test area. The expanded ensemble simulation results are compared with simulation data obtained from other techniques (mechanical and test area) with overall good agreement.     

Shape-selective fluorescent sensing ensemble using a tweezer-type metalloreceptor

[reaction: see text] A fluorescent sensing ensemble for pyridine-derived compounds is described. The receptor portion of the ensemble is prepared from a bisimidazole pyridine which coordinates copper to form a well-defined cavity. Small heteroaromatic guests such as adenine bind strongly in the cavity. The fluorescent response is provided by a dye which is coordinated to the receptor and quenched by the metal ion. The dye is released upon guest binding providing up to 25-fold fluorescence increases.     

Rational approximations of the Arrhenius integral using Jacobi fractions and gaussian quadrature

The aim of this work is to find approaches for the Arrhenius integral by using the n-th convergent of the Jacobi fractions. The n-th convergent is a rational function whose numerator and denominator are polynomials which can be easily computed from three-term recurrence relations. It is noticed that such approaches are equivalent to the one established by the Gauss quadrature formula and it can be seen that the coefficients in the quadrature formula can be given as a function of the coefficients in the recurrence relations. An analysis of the relative error percentages in the approximations is also presented.     

Bioluminescence and chemiluminescence in drug screening

Drug screening, that is, the evaluation of the biological activity of candidate drug molecules, is a key step in the drug discovery and development process. In recent years, high-throughput screening assays have become indispensable for early stage drug discovery because of the developments in synthesis technologies, such as combinatorial chemistry and automated synthesis, and the discovery of an increasing number of new pharmacological targets.Bioluminescence and chemiluminescence represent suitable detection techniques for high-throughput screening because they allow rapid and sensitive detection of the analytes and can be applied to small-volume samples. In this paper we report on recent applications of bioluminescence and chemiluminescence in drug screening, both for in vitro and in vivo assays. Particular attention is devoted to the latest and most innovative bioluminescence and chemiluminescence-based technologies for drug screening, such as assays based on genetically modified cells, bioluminescence resonance energy transfer (BRET)-based assays, and in vivo imaging assays using transgenic animals or bioluminescent markers. The possible relevance of bioluminescence and chemiluminescence techniques in the future developments of high-throughput screening technologies is also discussed.     

Selection of in silico drug screening results for G-protein-coupled receptors by using universal active probes

We developed a new protocol for in silico drug screening for G-protein-coupled receptors (GPCRs) using a set of "universal active probes" (UAPs) with an ensemble docking procedure. UAPs are drug-like compounds, which are actual active compounds of a variety of known proteins. The current targets were nine human GPCRs whose three-dimensional (3D) structures are unknown, plus three GPCRs, namely β(2)-adrenergic receptor (ADRB2), A(2A) adenosine receptor (A(2A)), and dopamine D3 receptor (D(3)), whose 3D structures are known. Homology-based models of the GPCRs were constructed based on the crystal structures with careful sequence inspection. After subsequent molecular dynamics (MD) simulation taking into account the explicit lipid membrane molecules with periodic boundary conditions, we obtained multiple model structures of the GPCRs. For each target structure, docking-screening calculations were carried out via the ensemble docking procedure, using both true active compounds of the target proteins and the UAPs with the multiple target screening (MTS) method. Consequently, the multiple model structures showed various screening results with both poor and high hit ratios, the latter of which could be identified as promising for use in in silico screening to find candidate compounds to interact with the proteins. We found that the hit ratio of true active compounds showed a positive correlation to that of the UAPs. Thus, we could retrieve appropriate target structures from the GPCR models by applying the UAPs, even if no active compound is known for the GPCRs. Namely, the screening result that showed a high hit ratio for the UAPs could be used to identify actual hit compounds for the target GPCRs.     

Rapid screening and characterization of drug metabolites using a new quadrupole-linear ion trap mass spectrometer

The application of a new hybrid RF/DC quadrupole-linear ion trap mass spectrometer to support drug metabolism and pharmacokinetic studies is described. The instrument is based on a quadrupole ion path and is capable of conventional tandem mass spectrometry (MS/MS) as well as several high-sensitivity ion trap MS scans using the final quadrupole as a linear ion trap. Several pharmaceutical compounds, including trocade, remikiren and tolcapone, were used to evaluate the capabilities of the system with positive and negative turbo ionspray, using either information-dependent data acquisition (IDA) or targeted analysis for the screening, identification and quantification of metabolites. Owing to the MS/MS in-space configuration, quadrupole-like CID spectra with ion trap sensitivity can be obtained without the classical low mass cutoff of 3D ion traps. The system also has MS(3) capability which allows fragmentation cascades to be followed. The combination of constant neutral loss or precursor ion scan with the enhanced product ion scan was found to be very selective for identifying metabolites at the picogram level in very complex matrices. Owing to the very high cycle time and, depending on the mass range, up to eight different MS experiments could be performed simultaneously without compromising chromatographic performance. Targeted product ion analysis was found to be complementary to IDA, in particular for very low concentrations. Comparable sensitivity was found in enhanced product ion scan and selected reaction monitoring modes. The instrument is particularly suitable for both qualitative and quantitative analysis.     

Detection of anions using a fluorescent alizarin-phenylboronic acid ensemble

Selective anion-induced organization of phenylboronic acids and alizarin results in a new TURN-ON fluorescent sensor for anions in MeOH.     

Development of octanol membranes for drug screening

Most drugs permeate biological membranes via passive diffusion and it is generally assumed that the main barrier is the lipophilic structure of the membranes. However, it has been observed that an unstirred water layer adjacent to the membrane surface can in some cases be just as effective barrier as the lipophilic membrane itself. Hydrophilic cyclodextrins can enhance drug delivery through biological membranes by increasing the availability of dissolved drug molecules immediate to the membrane surface, i.e., by increasing drug delivery through the unstirred water layer. We have developed an artificial octanol membrane that is cheap and simple to prepare. The novel membrane consists of a hydrated semi-permeable cellophane membrane with a molecular weight cut off (MWCO) of 12,000–14,000 that mimics the unstirred water layer and a lipophilic membrane of pure n-octanol in a nitrocellulose matrix. The membrane was used to investigate the effects of 2-hydroxypropyl-β-cyclodextrin (HPβCD) on the flux of hydrocortisone through the membrane. In aqueous HPβCD saturated with hydrocortisone the drug concentration gradient, over the unstirred water layer, increased with increasing HPβCD concentration which resulted in enhanced drug delivery through the membrane. When excess HPβCD was present in the donor phase the octanol/water partition coefficient decreased with increasing HPβCD concentration that lead to decreased drug delivery through the membrane.     

Time-dependent self-consistent field approximation for semiclassical dynamics using gaussian wavepackets in phase space

Gaussian wavepackets in phase space, which are constructed to have the exact first and second moments with respect to the coordinates and momenta, are used to develop self-consistent equations of motion for the semiclassical time evolution of interacting anharmonic systems. The equations apply to pure as well as to mixed states and may, therefore, be particularly useful for molecular dynamics in condensed phases.     

Applications of SHAPES screening in drug discovery

The SHAPES strategy combines nuclear magnetic resonance (NMR) screening of a library of small drug-like molecules with a variety of complementary methods, such as virtual screening, high throughput enzymatic assays, combinatorial chemistry, X-ray crystallography, and molecular modeling, in a directed search for new medicinal chemistry leads. In the past few years, the SHAPES strategy has found widespread utility in pharmaceutical research. To illustrate a variety of different implementations of the method, we will focus in this review on recent applications of the SHAPES strategy in several drug discovery programs at Vertex Pharmaceuticals.     

A microfluidic device for whole-animal drug screening using electrophysiological measures in the nematode C. elegans

This paper describes the fabrication and use of a microfluidic device for performing whole-animal chemical screens using non-invasive electrophysiological readouts of neuromuscular function in the nematode worm, C. elegans. The device consists of an array of microchannels to which electrodes are attached to form recording modules capable of detecting the electrical activity of the pharynx, a heart-like neuromuscular organ involved in feeding. The array is coupled to a tree-like arrangement of distribution channels that automatically delivers one nematode to each recording module. The same channels are then used to perfuse the recording modules with test solutions while recording the electropharyngeogram (EPG) from each worm with sufficient sensitivity to detect each pharyngeal contraction. The device accurately reported the acute effects of known anthelmintics (anti-nematode drugs) and also correctly distinguished a specific drug-resistant mutant strain of C. elegans from wild type. The approach described here is readily adaptable to parasitic species for the identification of novel anthelmintics. It is also applicable in toxicology and drug discovery programs for human metabolic and degenerative diseases for which C. elegans is used as a model.     

Virtual screening and rational drug design method using structure generation system based on 3D-QSAR and docking

An efficient virtual and rational drug design method is presented. It combines virtual bioactive compound generation with 3D-QSAR model and docking. Using this method, it is possible to generate a lot of highly diverse molecules and find virtual active lead compounds. The method was validated by the study of a set of anti-tumor drugs. With the constraints of pharmacophore obtained by DISCO implemented in SYBYL 6.8, 97 virtual bioactive compounds were generated, and their anti-tumor activities were predicted by CoMFA. Eight structures with high activity were selected and screened by the 3D-QSAR model. The most active generated structure was further investigated by modifying its structure in order to increase the activity. A comparative docking study with telomeric receptor was carried out, and the results showed that the generated structures could form more stable complexes with receptor than the reference compound selected from experimental data. This investigation showed that the proposed method was a feasible way for rational drug design with high screening efficiency.