Bigger data,collaborative tools and the future of predictive drug discovery

Over the past decade we have seen a growth in the provision of chemistry data and cheminformatics tools as either free websites or software as a service commercial offerings. These have transformed how we find molecule-related data and use such tools in our research. There have also been efforts to improve collaboration between researchers either openly or through secure transactions using commercial tools. A major challenge in the future will be how such databases and software approaches handle larger amounts of data as it accumulates from high throughput screening and enables the user to draw insights, enable predictions and move projects forward. We now discuss how information from some drug discovery datasets can be made more accessible and how privacy of data should not overwhelm the desire to share it at an appropriate time with collaborators. We also discuss additional software tools that could be made available and provide our thoughts on the future of predictive drug discovery in this age of big data. We use some examples from our own research on neglected diseases, collaborations, mobile apps and algorithm development to illustrate these ideas.     

The Future of Biological Mass Spectrometry

Biological applications of mass spectrometry have grown exponentially since the discovery of MALDI and electrospray ionization techniques. This growth has been further fueled by the massive volume of DNA sequence information that is now available. An ambitious goal of some of this research is to monitor the level and modification of all proteins and metabolites in a biological sample such as plasma. A major research effort in mass spectrometry and related disciplines has been expended over the past several years toward reaching this and other less ambitious goals, and considerable progress has been made; but the presently available tools are clearly not sufficient for these very difficult tasks. In this “critical insight” discussion we suggest that recent advances in time-of-flight (TOF) technology with MALDI ionization may provide some important new tools for achieving the goals of biological research.     

Metrology and protometrology: the ordinal question

Laboratory medicine provides results for quantities as well as for properties having no magnitude. The terminology of the latter is less well established and sources are contradictory. Two recent papers on “protometrology” published in this journal offer an opportunity to discuss the necessary concept systems. The delineations of “metrology” versus “protometrology”, “observation” versus “measurement”, and the generic division of “property” are examined with emphasis on avoiding conflict with the International Vocabulary of Metrology. It is suggested that having “examination” as a top generic concept coupled with systematic modifiers for division, especially ‘nominal’ and ‘ordinal’, is a preferable terminological solution.

Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

Computational methods for docking ligands have been shown to be remarkably dependent on precise protein conformation, where acceptable results in pose prediction have been generally possible only in the artificial case of re-docking a ligand into a protein binding site whose conformation was determined in the presence of the same ligand (the “cognate” docking problem). In such cases, on well curated protein/ligand complexes, accurate dockings can be returned as top-scoring over 75% of the time using tools such as Surflex-Dock. A critical application of docking in modeling for lead optimization requires accurate pose prediction for novel ligands, ranging from simple synthetic analogs to very different molecular scaffolds. Typical results for widely used programs in the “cross-docking case” (making use of a single fixed protein conformation) have rates closer to 20% success. By making use of protein conformations from multiple complexes, Surflex-Dock yields an average success rate of 61% across eight pharmaceutically relevant targets. Following docking, protein pocket adaptation and rescoring identifies single pose families that are correct an average of 67% of the time. Consideration of the best of two pose families (from alternate scoring regimes) yields a 75% mean success rate.     

Evaluation of high-performance liquid chromatography for determination of phenolic compounds in pear horticultural cultivars

Summary An analytical evaluation of an HPLC method with diode array detection to separate and quantify polyphenolic compounds from pears has been made. The method was applied to the quantitative analysis of phenolics from five pear horticultural cultivars (“Agua”, “Blanquilla”, “Conference”, “Pasagrana” and “Decana”) in both peel and pulp matrices and evaluated for precision and accuracy. Precision was taken as the reproducibility in peak area of the polyphenols of interest as well as in the slope of calibration graphs. Values ranged 2–5%. Accuracy was evaluated by recovery of all polyphenolic compounds from both peel and pulp in all pears investigated. Accuracy values ranged 92–102%, and were independent of the polyphenolic structure, horticultural cultivar and matrix. Identification was by comparing retention times and UV spectra with those of standards when commercially available. When not available commercially, provisional identification was according to spectral characteristics as well as from isolation and hydrolysis data. Application of the method revealed differences between peel and pulp in all cases studied; the higher levels of phenolics were found in the peels. “Decana” and “Pasagrana” cultivars showed the highest phenolic content compounds whereas “Conference” showed the lowest.     

Chemically Modified Carbon Nanotubes for Use in Electroanalysis

The discovery of carbon nanotubes has had a profound impact on many areas of science and technology, not least that of electroanalysis. The properties and applications of carbon nanotubes themselves have been well reviewed in the literature and a number of reviews with an electrochemical emphasis have been published. However, the modification of carbon nanotubes has recently been the focus of much research, primarily to improve their solubility in various solvents. Yet modified carbon nanotube electrodes also allow the electrochemist to tailor the properties of the carbon nanotubes, or the electrode surface to impart desired properties such as enhanced sensing capabilities. In this review we attempt to comprehensively cover the different chemical and electrochemical modification strategies and research carried out using modified carbon nanotubes for electroanalytical and bioanalytical applications. Furthermore we also discuss the use of modified carbon nanotubes in electrocatalysis and biocatalysis from an analytical aspect, as well as seeking to dispel some of the myths surrounding the “electrocatalytic” properties of carbon nanotubes.     

Radiocarbon dating of an ancient Japanese document “Minamoto no Yoritomo Sodehan Migyosho” by accelerator mass spectrometry

We measured radiocarbon age of an ancient document “Minamoto no Yoritomo Sodehan Migyosho”. The content tells that it was issued in 1189 by “Minamoto no Yoritomo” known as the virtually first shogun in Japan to grant “Matsugi” family the privilege of controlling craftsmen of foundry industry. Paleographical views, however, suggested that it can be a counterfeit. The radiocarbon dating clarified that the document was written not in the 12th but after the 16th century.     

A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A,a selective kappa opioid receptor agonist

Combined ligand-based and target-based drug design approaches provide a synergistic advantage over either method individually. Therefore, we set out to develop a powerful virtual screening model to identify novel molecular scaffolds as potential leads for the human KOP (hKOP) receptor employing a combined approach. Utilizing a set of recently reported derivatives of salvinorin A, a structurally unique KOP receptor agonist, a pharmacophore model was developed that consisted of two hydrogen bond acceptor and three hydrophobic features. The model was cross-validated by randomizing the data using the CatScramble technique. Further validation was carried out using a test set that performed well in classifying active and inactive molecules correctly. Simultaneously, a bovine rhodopsin based “agonist-bound” hKOP receptor model was also generated. The model provided more accurate information about the putative binding site of salvinorin A based ligands. Several protein structure-checking programs were used to validate the model. In addition, this model was in agreement with the mutation experiments carried out on KOP receptor. The predictive ability of the model was evaluated by docking a set of known KOP receptor agonists into the active site of this model. The docked scores correlated reasonably well with experimental pK _i values. It is hypothesized that the integration of these two independently generated models would enable a swift and reliable identification of new lead compounds that could reduce time and cost of hit finding within the drug discovery and development process, particularly in the case of GPCRs.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Danube River Water Data Modelling by Multivariate Data Analysis

 A data set (48×19) consisting of Danube river water analytical data collected at Galati site, Romania, during a four-year period has been treated by principal components analysis (PCA). The PCA indicated that seven latent factors (“hardness”, “biochemical”, “waste inlets”, “turbidity”, “acidity”, “soil extracts” and “organic wastes”) are responsible for the data structure and explain over 80 % of the total variance of the system. Its complexity is further proved by the application of multiple linear regression analysis on the absolute principal components scores (APCS) where the contribution of each natural or anthropogenic sources in the factor formation is shown. The apportioning makes clear that each variable participates to a different extent to each source and, in this way, no pure natural or pure anthropogenic influence could be determined. No specific seasonality for the variables in consideration is found. Received January 24, 2001. Revision July 6, 2001.     

Chromatography: The separation technique of the 20th century

Summary M. S. Tswett contemplated the possibility of “chromatography” in 1899–1901 while carrying out his first research work on the physico-chemical structure of plant chlorophylls, and he reported “on a new category of adsorption analysis” in 1903. The evolution of chromatography followed the advances of this century: each decade brought new innovations based logically from the previous one. By the end of the 20th Century chromatography has became the most widely used separation technique in chemistry and biochemistry: thus, it is no exaggeration to call it the separation technique of the 20th Century. This paper investigates the evolution of the various branches of chromatography. An essential condition for all fruitful research is to have at one’s disposal a satisfactory technique. “Tout progrès scientific est un progrès de méthode” as somebody once remarked. Unfortunately the methodology is frequently the weakest aspect of scientific investigations.     

Distribution of selected trace elements in samples of sediment,suspension and water taken along the Isar River,Bavaria

The three phases “dissolved solids”, “suspended solids” and “sediment” of four sampling sites along the river Isar were analysed by INAA. In these as well as in the different grain-size fractions between<2 and 63 μm 17 trace elements were determined. Compared with the values of other rivers in Middle Europe the river Isar is still below the levels of significant pollution.     

MALDI-TOF MS stability study of model poly(p-phenylene terephthalamide)s

In the present study, we address the possibility of matrix-assisted laser desorption/ionization (MALDI)–time-of-flight MS analysis-induced chain fragmentation in poly(p-phenylene terephthalamide) (PPD-T) by considering two possible sources: (1) grinding-induced fragmentation resulting from the evaporation–grinding MALDI sample preparation method (E-G method) and (2) in-source/metastable fragmentation induced by the MALDI laser. An analysis of variance (ANOVA) statistical study found, with a high probability, that obtaining MALDI spectra with the effective laser area as large as possible (the “fanned-out” setting) did not cause any chain fragmentation due to the E-G MALDI sample preparation method, even when three additional grinding steps were used. However, the effect of laser fluence was less clear. A significant effect of laser fluence was observed for lower mass oligomers (<1,400 Da), but there was essentially no effect for higher mass species up to our limit of ANOVA measurement (∼2,300 Da). Plausible explanations are presented to explain these observations. The most likely scenario is that “unexpected” end-group modifications occur during PPD-T synthesis, producing small quantities of low mass species, which are amplified by the MALDI-EG extraction procedure.     

Sub-micron wear measurement using activities under the free handling limit

In the present work we demonstrate the development of a thin layer activation (TLA) method to be able to measure micrometer wear or less by using radioactive tracing. In order to activate very swallow depths we decreased the bombarding energy to the “linear” region of the cross-section curve. The disadvantage of the method is that the wear curve will be “linear” near to the surface instead of “constant” as is the case with the usual (high energy) TLA. The advantage is that the activity of the sample will be much lower and it is concentrated in the swallower studied depth. The other possible method is irradiation under small angle (15 to 30° or even grazing incidence), which also causes a near-surface concentration of the activity produced. Both methods are demonstrated with the most suitable nuclear reactions and some commonly used industrial materials.     

Step wise and dissociative mechanisms of the electron transfer in electrochemical reactions involving organosilicon compounds: Molecular-thermodynamic approach1

Electrochemical reduction of organochlorosilanes and oxidation of hexaorganodisilanes may occur via dissociative and stepwise mechanisms, the choice between which is determined by the balance between fundamental structural parameters of elementoorganic molecules. The formation of radical anions of silyl-substituted chloromethane in the conditions of an electrochemical experiment is shown. The formation is due to α-silicon stabilization of the intermediate during the electron transfer. The role of conjugation and hyperconjugation in the organosilicon compounds’ reactivity is analyzed. When employing terms “ stepwise ” and “ dissociative ” mechanisms of the electron transfer, we follow tradition introduced and developed by J.-M. Saveant’s group [1] and recommended by the IUPAC Commission on Electrochemical Nomenclature [2]. The terms refer to an electrochemically reversible transfer of electron whose kinetics does not limit the process rate as a whole and to an electrochemically irreversible transfer which involves a bond cleavage in an elementary act of electron transfer. The term “ activation ” mechanism, which is sometimes applied to electrochemically irreversible processes, is more universal; however, it is somewhat not unique as compared with the term “ dissociative.” Coupled with “ associative,” the latter may be used for indicating processes that involve the formation of a bond in an elementary act of electron transfer.     

Lactam acetals and acid amides. 31. Synthesis,protonation, and basicities of some heterocyclic enamino ketones

The protonation of cyclic enamino ketones of the pyrrolidine, piperidine, and hexahydroazepine series, as well as their noncyclic analogs, was studied by PMR spectroscopy. It is shown that the presence of a CH₂ or CH₃ group in the “enamine” position leads to C protonation (in CF₃COOH). In the case of enamino ketones that do not contain substituents in the “enamine” α position N-and O-protonated forms are observed in CF₃COOH. The measured pK_a values (in 10% alcohol) and the ΔpK_a values (in nitromethane) of the enamino ketones show that the compounds for which C protonation is characteristic are two to three orders of magnitude more basic than in the case of compounds that do not contain substituents in the “enamine” α position; this is explained by the different character of protonation. See [1] for communication 30. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 344–348, March, 1980     

Linearly polarized white fluorescence from shish-kebab type liquid crystalline poly(P-phenylenevinvlene)s with (P-phenylene)s as kebab

Liquid crystalline(LC) polymers with a shish-kebab-type moiety on their cross-conjugated(p-phenylene)s-poly(p-phenylenevinylene) s main chains were synthesized through Gilch polymerization in order to develop a kind of polymers available for linearly polarized white-light-emitting from single chain.In this system,the 2,5-bis(4’-alkoxyphenyl)benzene as the "kebabs" connects with poly(p-phenylenevinylene)(PPV) main chain backbone using its molecular gravity center and the PPV as the "shish" or "skewer"(the "shish-kebab").The polymers possess desirable properties such as excellent solubility and liquid crystalline properties.To drop the "kebabs" of the 2,5-bis(4’-alkoxyphenyl)benzene into the orientation microgroove of aligned polyimide film,not only the "shish" of polymer main chain can be aligned by the virtue of orientation of "kebabs" but also the uniform cross-conjugated structure between the "kebabs" and "shish" can be broken. Then,the alignment of the polymer main chain showed yellow light emission and was also accompanied by orientation of the LC side chains showing blue light emission,this gave rise to a notable linearly polarized white fluorescence.     

Multivariate analysis of HT/GC-(IT)MS chromatographic profiles of triacylglycerol for classification of olive oil varieties

The ability of multivariate analysis methods such as hierarchical cluster analysis, principal component analysis and partial least squares-discriminant analysis (PLS-DA) to achieve olive oil classification based on the olive fruit varieties from their triacylglycerols profile, have been investigated. The variations in the raw chromatographic data sets of 56 olive oil samples were studied by high-temperature gas chromatography with (ion trap) mass spectrometry detection. The olive oil samples were of four different categories (“extra-virgin olive oil”, “virgin olive oil”, “olive oil” and “olive-pomace” oil), and for the “extra-virgin” category, six different well-identified olive oil varieties (“hojiblanca”, “manzanilla”, “picual”, “cornicabra”, “arbequina” and “frantoio”) and some blends of unidentified varieties. Moreover, by pre-processing methods of chemometric (to linearise the response of the variables) such as peak-shifting, baseline (weighted least squares) and mean centering, it was possible to improve the model and grouping between different varieties of olive oils. By using the first three principal components, it was possible to account for 79.50% of the information on the original data. The fitted PLS-DA model succeeded in classifying the samples. Correct classification rates were assessed by cross-validation.     

An advanced multivariate statistical approach to study coastal sediment data

The present paper deals with the application of classical and fuzzy principal components analysis to a large data set from coastal sediment analysis. Altogether 126 sampling sites from the Atlantic Coast of the USA are considered and at each site 16 chemical parameters are measured. It is found that four latent factors are responsible for the data structure (“natural”, “anthropogenic”, “bioorganic”, and “organic anthropogenic”). Additionally, estimating the scatter plots for factor scores revealed the similarity between the sampling sites. Geographical and urban factors are found to contribute to the sediment chemical composition. It is shown that the use of fuzzy PCA helps for better data interpretation especially in case of outliers.     

Instrumental detection limits in total reflection X-ray fluorescence: Comparison of cut-off and monochromatic excitation devices

“Cut-off” reflectors, which allow obtaining a reflected beam with almost no high energy radiation, as well as different monochromator devices that reflect a beam of monoenergetic and polarized radiation are the most widely employed artifacts to perform the excitation radiation improvement in analytical “non-expensive” TR spectrometers. The aim of this work consisted in testing several monochromator devices: a multilayer structured mirror for soft X-rays (0.7–12.5 nm), as well as different bent and flat crystals of wavelength dispersive spectrometers. The achieved instrumental detection limits for the selected monochromator device are compared with the values obtained using a Suprasil Cut-off reflector and a C-W multilayer (d∼5 nm). Several human corporal fluid samples were analyzed to compare the spectral characteristics when using the Cut-Off Reflector and the RAP flat crystal, respectively.