Integrated project views: decision support platform for drug discovery project teams

Drug discovery teams continuously have to decide which compounds to progress and which experiments to perform next, but the data required to make informed decisions is often scattered, inaccessible, or inconsistent. In particular, data tend to be stored and represented in a compound-centric or assay-centric manner rather than project-centric as often needed for effective use in drug discovery teams. The Integrated Project Views (IPV) system has been created to fill this gap; it integrates and consolidates data from various sources in a project-oriented manner. Its automatic gathering and updating of project data not only ensures that the information is comprehensive and available on a timely basis, but also improves the data consistency. Due to the lack of suitable off-the-shelf solutions, we were prompted to develop custom functionality and algorithms geared specifically to our drug discovery decision making process. In 10 years of usage, the resulting IPV application has become very well-accepted and appreciated, which is perhaps best evidenced by the observation that standalone Excel spreadsheets are largely eliminated from project team meetings.     

ArQiologist: an integrated decision support tool for lead optimization

This paper describes ArQiologist, a Web-based tool that integrates chemical, analytical, biological, and computational data to facilitate decision support for lead optimization at ArQule. It features an easy-to-use graphical query builder that allows queries to be saved, reused, and shared by researchers. Query results can be viewed with built-in data browsers or exported with structures to external applications such as Microsoft Excel or Spotfire for further analysis.     

Neutron activation analysis for assessing chemical composition of dry dog foods

Brazil holds the second largest population of domestic dogs in the world, with 33 million dogs, only behind the United States. The annual consumption of dog food in the country is 1.75 million tons, corresponding to the World’s sixth in trade turnover. Dog food is supposed to be a complete and balanced diet, formulated with high quality ingredients. All nutrients and minerals required for an adequate nutrition of dogs are added to the formulation to ensure longevity and welfare. In this context, the present study aimed at assessing the chemical composition of dry dog foods commercialized in Brazil. Thirty-four samples were acquired in the local market of Piracicaba and analyzed by instrumental neutron activation analysis (INAA) to determine the elements As, Br, Ca, Co, Cr, Cs, Fe, K, La, Na, Rb, Sb, Sc, Se, U, and Zn. In general, the concentrations of Ca, Fe, K, Na, and Zn complied with the values required by the Association of American Feed Control Officials (AAFCO). To evaluate the safety of dog food commercialized in Brazil, further investigation is necessary to better understand the presence of toxic elements found in this study, i.e. Sb and U. INAA was useful for the screening analysis of different types and brands of dry dog foods for the determination of both essential and toxic elements.     

Evaluation of relative MS response factors of drug metabolites for semi‐quantitative assessment of chemical liabilities in drug discovery

Drug metabolism studies are performed in drug discovery to identify metabolic soft spots, detect potentially toxic or reactive metabolites and provide an early insight into potential species differences. The relative peak area approach is often used to semi‐quantitatively estimate the abundance of metabolites. Differences in the liquid chromatography‐mass spectrometry responses result in an underestimation or overestimation of the metabolite and misinterpretation of results. The relative MS response factors (RF) of 132 structurally diverse drug candidates and their 233 corresponding metabolites were evaluated using a capillary‐liquid chromatography/high‐resolution mass spectrometry system. All of the synthesized metabolites discussed here were previously identified as key biotransformation products in discovery investigations or predicted to be formed. The most commonly occurring biotransformation mechanisms such as oxygenation, dealkylation and amide cleavage are represented within this dataset. However, relatively few phase II metabolites were evaluated because of the limited availability of authentic standards. Approximately 85% of these metabolites had a relative RF in the range between 0.2 (fivefold under‐prediction) and 2.0 (twofold over‐prediction), and the median MS RF was 0.6. Exceptions to this included very small metabolites that were hardly detectable. Additional experiments performed to understand the impact of the MS platform, flow rate and concentration suggested that these parameters do not have a significant impact on the RF of the compounds tested. This indicates that the use of relative peak areas to semi‐quantitatively estimate the abundance of metabolites is justified in the drug discovery setting in order to guide medicinal chemistry efforts. Copyright © 2017 John Wiley & Sons, Ltd.     

A predictive tool for assessing (13)C NMR chemical shifts of flavonoids

Herein are presented the (1)H and (13)C NMR data for seven monohydroxyflavones (3-, 5-, 6-, 7-, 2'-, 3'-, and 4'-hydroxyflavone), five dihydroxyflavones (3,2'-, 3,3'-, 3,4'-, 3,6-, 2',3'-dihydroxyflavone), a trihydroxyflavone (apigenin; 5,7,4'-trihydroxyflavone), a tetrahydroxyflavone (luteolin; 5,7,3',4'-tetrahydroxyflavone), and three glycosylated hydroxyflavones (orientin; luteolin-6C-beta-D-glucoside, homoorientin; luteolin-8C-beta-D-glucoside, vitexin; apigenin-8C-beta-D-glucoside). When these NMR spectra are compared, it is possible to assess the impact of flavone modification and to elucidate detailed structural and electronic information for these flavonoids. A simple predictive tool for assigning flavonoid (13)C chemical shifts, which is based on the cumulative differences between the monohydroxyflavones and flavone (13)C chemical shifts, is demonstrated. The tool can be used to accurately predict (13)C flavonoid chemical shifts and it is expected to be useful for rapid assessment of flavonoid (13)C NMR spectra and for assigning substitution patterns in newly isolated flavonoids.     

Relevance of leaf surface contamination for assessing chemical composition of bromeliads in a restinga forest

Resuspended soil and other airborne particles adhered to the leaf surface affect the chemical composition of the plant. A well-defined cleaning procedure is necessary to avoid this problem, providing a correct assessment of the inherent chemical composition of bromeliads. To evaluate the influence of a washing procedure, INAA was applied for determining chemical elements in the leaves of bromeliads from Vriesea carinata species, both non-washed and washed with Alconox, EDTA and bi-distilled water. Br, Ce, Hg, La, Sc, Se, Sm and Th showed higher mass fractions in non-washed leaves. The washing procedure removed the exogenous material without leaching chemical elements from inside the tissues.     

A passive chemical dosimeter for assessing long-term exposure in air containing aniline and aniline derivatives

A passive chemical dosimeter for assessing long-term exposure to toxic substances (aniline and its derivatives) in the atmosphere of inhabitable premises was described. The compounds to be determined were accumulated on an absorption filter due to a chemical reaction with a selective agent upon the many-hour exposure of the device. Analytical performance of chemical dosimeters (diffusion coefficients, chemisorption pre-concentration rate, and detection limits) was evaluated. The concentrations of aniline, p-chloroaniline, 3,4-dichloroaniline, and o-toluidine in the air of chemical laboratories and smoking rooms were determined.     

Integrated optical NIR-evanescent wave absorbance sensorfor chemical analysis

A new, long-path integrated optical (IO) sensor for the detection of non-polar organic substances is described. The sensing layer deposited on a planar multimode IO structure is built by a suitable silicone polymer with lower refractive index (RI). It acts as a hydrophobic matrix for the reversible enrichment of non-polar organic contaminants from water or air. Light from the near-infrared (NIR) range is coupled into the planar structure and the evanescent wave part of the light field penetrating into the silicone layer interacts with the enriched organic species. As a result, light is absorbed at the characteristic frequencies of the corresponding C-H, N-H or O-H overtone and combination band vibrations of the analytes. To perform evanescent field absorbance (EFA) measurements, the arc-shaped strip waveguide structure of 172 mm interaction length was adapted to a tungsten-halogen lamp and an InGaAs diode array spectrograph over gradient index fibers. Dimethyl-co-methly(phenyl)polysiloxanes with varying degrees of phenylation were prepared and used as sensitive coating materials for the IO structure. Light attenuation in the arc-shaped waveguides is high and typical insertion losses in the range of 14-18 dB were obtained. When the coated sensors were brought in contact with aqueous samples, the light transmission decreases, which is due to the formation of H(2)O micro-emulsions in the silicone superstrates. Nevertheless, after reaching constant light transmissions, absorbance spectra of aqueous trichloroethene samples were successfully collected. For gas measurements, where water cross sensitivity problems are absent, the sensitivity of the IO device for trichloroethene was tested as a function of the RI of the silicone superstrate. The slope of the TCE calibration function increases by a factor of 10 by using a poly(methylphenylsiloxane) layer with a RI of 1.449 instead of poly(dimethylsiloxane) (RI: 1.41). A comparison of the IO-EFA and an earlier developed fiber-optic EFA sensor for trichloroethene measurements in the gas phase showed an increase in sensitivity per unit length of the waveguide by a factor of up to 120.     

Integrated optical NIR-evanescent wave absorbance sensorfor chemical analysis

A new, long-path integrated optical (IO) sensor for the detection of non-polar organic substances is described. The sensing layer deposited on a planar multimode IO structure is built by a suitable silicone polymer with lower refractive index (RI). It acts as a hydrophobic matrix for the reversible enrichment of non-polar organic contaminants from water or air. Light from the near-infrared (NIR) range is coupled into the planar structure and the evanescent wave part of the light field penetrating into the silicone layer interacts with the enriched organic species. As a result, light is absorbed at the characteristic frequencies of the corresponding C-H, N-H or O-H overtone and combination band vibrations of the analytes. To perform evanescent field absorbance (EFA) measurements, the arc-shaped strip waveguide structure of 172 mm interaction length was adapted to a tungsten-halogen lamp and an InGaAs diode array spectrograph over gradient index fibers. Dimethyl-co-methly(phenyl)polysiloxanes with varying degrees of phenylation were prepared and used as sensitive coating materials for the IO structure. Light attenuation in the arc-shaped waveguides is high and typical insertion losses in the range of 14–18 dB were obtained. When the coated sensors were brought in contact with aqueous samples, the light transmission decreases, which is due to the formation of H₂O micro-emulsions in the silicone superstrates. Nevertheless, after reaching constant light transmissions, absorbance spectra of aqueous trichloroethene samples were successfully collected. For gas measurements, where water cross sensitivity problems are absent, the sensitivity of the IO device for trichloroethene was tested as a function of the RI of the silicone superstrate. The slope of the TCE calibration function increases by a factor of 10 by using a poly(methylphenylsiloxane) layer with a RI of 1.449 instead of poly(dimethylsiloxane) (RI: 1.41). A comparison of the IO-EFA and an earlier developed fiber-optic EFA sensor for trichloroethene measurements in the gas phase showed an increase in sensitivity per unit length of the waveguide by a factor of up to 120.     

The nih-epa chemical information system in support of structure elucidation2

Progress in the development of the NIH—EPA chemical information system is reviewed.     

CRMs for quality control of determinations of chemical forms of elements in support to EU legislation

The concern for the control of toxic chemical forms of elements in the environment is reflected by an increasing number of analyses performed by research and routine laboratories. The European Commission has recognised the need to include some of these species in the list of dangerous substances to be monitored, e.g. in the marine environment or in groundwater. However, in most cases, the specifications are far from being sufficient in respect to the chemical forms of the element to be determined. Furthermore, these determinations are in most cases based on multi-step analytical techniques which are often prone to errors (e.g. at the extraction, derivatization or separation steps). Certified reference materials (CRMs) certified for their content in chemical forms of elements are, therefore, necessary to ensure the accuracy of these measurements and hence the respect of the regulations. However, the lack of CRMs for speciation analysis hampers the quality control of determinations which in turn leads to an incomparability of data produced; so far the number of CRMs produced by international organisations, e.g. NIST (USA), NIES (Japan), NRCC (Canada) and BCR (Belgium), is very limited and concerns mainly compounds such as e.g. methyl-mercury and butyltin compounds in biological matrices or sediments. The Standards, Measurements and Testing Programme (formerly BCR) of the European Commission has started a series of projects for the improvement of speciation analysis in environmental matrices, the final aim of which being the production of a variety of environmental CRMs. The existing EU legislation involving chemical forms of elements is presented, the requirements for the preparation of CRMs for speciation analysis are discussed and an update of the most recent CRMs produced within the Standards, Measurements and Testing Programme (SM&T) is given.     

CRMs for quality control of determinations of chemical forms of elements in support to EU legislation

The concern for the control of toxic chemical forms of elements in the environment is reflected by an increasing number of analyses performed by research and routine laboratories. The European Commission has recognised the need to include some of these species in the list of dangerous substances to be monitored, e.g. in the marine environment or in groundwater. However, in most cases, the specifications are far from being sufficient in respect to the chemical forms of the element to be determined. Furthermore, these determinations are in most cases based on multi-step analytical techniques which are often prone to errors (e.g. at the extraction, derivatization or separation steps). Certified reference materials (CRMs) certified for their content in chemical forms of elements are, therefore, necessary to ensure the accuracy of these measurements and hence the respect of the regulations. However, the lack of CRMs for speciation analysis hampers the quality control of determinations which in turn leads to an incomparability of data produced; so far the number of CRMs produced by international organisations, e.g. NIST (USA), NIES (Japan), NRCC (Canada) and BCR (Belgium), is very limited and concerns mainly compounds such as e.g. methyl-mercury and butyltin compounds in biological matrices or sediments. The Standards, Measurements and Testing Programme (formerly BCR) of the European Commission has started a series of projects for the improvement of speciation analysis in environmental matrices, the final aim of which being the production of a variety of environmental CRMs. The existing EU legislation involving chemical forms of elements is presented, the requirements for the preparation of CRMs for speciation analysis are discussed and an update of the most recent CRMs produced within the Standards, Measurements and Testing Programme (SM&T) is given.     

Liquid chromatographic methods for the therapeutic drug monitoring of methotrexate as clinical decision support for personalized medicine: A brief review

Methotrexate (MTX) is an antifolate drug used for several diseases. Depending on the disease, MTX can be administered at low dose (LDMTX) in some autoimmune diseases, like rheumatoid arthritis, or at high dose (HDMTX) in some cancers, such as acute lymphoblastic leukemia. After absorption, MTX is metabolized in the liver to 7‐hydroxymethotrexate and in the intestine to 2,4‐diamino‐N10‐methylpteroic acid (DAMPA). Moreover, inside red blood cells, MTX is converted to active metabolites, MTX polyglutamates (MTXPGs), contributing to its pharmacodynamics. Owing to its narrow therapeutic range, and inter‐ and intra‐patient variability, either noneffectiveness and/or toxicity may occur. Because of the existence of a relationship between drug therapeutic outcome and its systemic concentration, therapeutic drug monitoring (TDM) may ensure the effectiveness and safety of MTX use. In order to monitor the optimization of patient clinical response profile, several analytical methods have been described for TDM in biological samples. These include liquid chromatography (LC) coupled with ultraviolet detection, fluorescence detection or mass spectrometry, each one presenting advantages and drawbacks. This paper reviews the most commonly used techniques for sample preparation and critically discusses the current LC methods applied for the TDM of MTX in biological samples, at LDMTX and HDMTX.     

An alkylsilyl-tethered, high-capacity solid support amenable to diversity-oriented synthesis for one-bead, one-stock solution chemical genetics

The synthesis and use of an alkylsilyl-tethered large (500-600 microm) polystyrene resin (1) are disclosed. An optimized Suzuki coupling of bromine-functionalized polystyrene and a silicon-functionalized alkylborane generates the silicon-substituted polystyrene 1 in large scale (>100 g). Resin loading is accomplished by activation as the silyl triflate, which can accommodate even sterically encumbered secondary alcohols and phenols. Treatment with HF/pyridine for linker cleavage is mild, efficient, and amenable to an automated, large-scale distribution system. This platform delivers, minimally, 50 nmol of each small molecule derived from a diversity-oriented, split-pool synthesis on a per bead basis for use in both forward and reverse chemical genetic assays. This technology satisfies many requirements of a one bead-one stock solution approach to chemical genetics.     

Influence of the chemical nature of the oxide support on selectivity of iron catalysts for carbon monoxide hydrogenation

The influence of the nature of the oxide support on selectivity of Fe catalysts in Fischer-Tropsch synthesis at atmospheric pressure has been studied. It was found that selectivity towards lower olefins increases with increasing basicity of the oxide support. It is suggested that this effect is due to participation of basic oxide sites in hydrogen-atom abstraction from the surface metal-alkyl complex.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 30, No. 3, pp. 152–157, May–June, 1994.The authors are grateful to V. V. Pryanikova, M. G. Petrosyan, and A. M. Puzii for assistance with individual experiments.     

Evaluation of SARs for the prediction of eye irritation/corrosion potential: structural inclusion rules in the BfR decision support system

The proposed REACH regulation within the European Union (EU) aims to minimise the number of laboratory animals used for human hazard and risk assessment while ensuring adequate protection of human health and the environment. One way to achieve this goal is to develop non-testing methods, such as (quantitative) structure-activity relationships ([Q]SARs), suitable for identifying toxicological hazard from chemical structure and physicochemical properties alone. A database containing data submitted within the EU New Chemicals Notification procedure was compiled by the German Bundesinstitut für Risikobewertung (BfR). On the basis of these data, the BfR built a decision support system (DSS) for the prediction of several toxicological endpoints. For the prediction of eye irritation and corrosion potential, the DSS contains 31 physicochemical exclusion rules evaluated previously by the European Chemicals Bureau (ECB), and 27 inclusion rules that define structural alerts potentially responsible for eye irritation and/or corrosion. This work summarises the results of a study carried out by the ECB to assess the performance of the BfR structural rulebase. The assessment included: (a) evaluation of the structural alerts by using the training set of 1341 substances with experimental data for eye irritation and corrosion; and (b) external validation by using an independent test set of 199 chemicals. Recommendations are made for the further development of the structural rules in order to increase the overall predictivity of the DSS.