Data visualization during the early stages of drug discovery

Multidimensional compound optimization is a new paradigm in the drug discovery process, yielding efficiencies during early stages and reducing attrition in the later stages of drug development. The success of this strategy relies heavily on understanding this multidimensional data and extracting useful information from it. This paper demonstrates how principled visualization algorithms can be used to understand and explore a large data set created in the early stages of drug discovery. The experiments presented are performed on a real-world data set comprising biological activity data and some whole-molecular physicochemical properties. Data visualization is a popular way of presenting complex data in a simpler form. We have applied powerful principled visualization methods, such as generative topographic mapping (GTM) and hierarchical GTM (HGTM), to help the domain experts (screening scientists, chemists, biologists, etc.) understand and draw meaningful decisions. We also benchmark these principled methods against relatively better known visualization approaches, principal component analysis (PCA), Sammon's mapping, and self-organizing maps (SOMs), to demonstrate their enhanced power to help the user visualize the large multidimensional data sets one has to deal with during the early stages of the drug discovery process. The results reported clearly show that the GTM and HGTM algorithms allow the user to cluster active compounds for different targets and understand them better than the benchmarks. An interactive software tool supporting these visualization algorithms was provided to the domain experts. The tool facilitates the domain experts by exploration of the projection obtained from the visualization algorithms providing facilities such as parallel coordinate plots, magnification factors, directional curvatures, and integration with industry standard software. © 2006 American Chemical Society.

Guiding local regression using visualisation

Solving many scientific problems requires effective regression and/or classification models for large high-dimensional datasets. Experts from these problem domains (e.g. biologists, chemists, financial analysts) have insights into the domain which can be helpful in developing powerful models but they need a modelling framework that helps them to use these insights. Data visualisation is an effective technique for presenting data and requiring feedback from the experts. A single global regression model can rarely capture the full behavioural variability of a huge multi-dimensional dataset. Instead, local regression models, each focused on a separate area of input space, often work better since the behaviour of different areas may vary. Classical local models such as Mixture of Experts segment the input space automatically, which is not always effective and it also lacks involvement of the domain experts to guide a meaningful segmentation of the input space. In this paper we addresses this issue by allowing domain experts to interactively segment the input space using data visualisation. The segmentation output obtained is then further used to develop effective local regression models.

Transglutaminases as tanning agents for the leather industry

This study was aimed at determining whether the protein crosslinking enzymes, transglutaminases, had the potential to be used as tanning agents, using native bovine hide and purified soluble rat tail collagen as real and model substrates, respectively. We demonstrate that transglutaminases (TGs) were capable of covalently crosslinking collagen molecules together such that on average every collagen molecule contained at least one epsilon(gamma-glutamyl)lysine crosslink. However, transglutaminase-mediated crosslinking did not affect the denaturation temperature of either native bovine hide or soluble rat tail collagens when used in isolation or together with other proteins and bifunctional diamines as crosslinking facilitators. In an initial study into the effect of TG-mediated crosslinking on the tensile strength of chrome-tanned bovine hide, such crosslinking led to a 30 per cent decrease in tensile strength. Despite a change in the gel melting point mediated by epsilon(gamma-glutamyl)lysine crosslinking, the use of transglutaminases as alternative tanning agents seems unlikely given the present data.

Some aspects of the analytical chemistry of malathion

A thorough investigation of the recommended colorimetric method for the determination of malathion (an organophosphorus pesticide) has led to the identification of the major cause of all the problems with which the method suffers. The method, which involves the extraction of the copper (II) complex or the hydrolysis product of malathion from aqueous solution into immiscible organic solvents, has many drawbacks. For example, the colour of the organic extract fades very quickly and a slight increase in the contact time of the hydrolysis product and the copper reagent within the aqueous solution, results in a decrease in the ab-solute absorbance. Also, the presence of any reducing agents can be a significant source of error. In the present work, it has been shown that the basic cause of all these problems is the ability of copper (II) ion to be reduced to copper (I) ion. It has further been shown that these problems can be resolved by re-placing copper (II) by bismuth (III). This has led to the development of a modified colorimetric method for the determination. of malathion, which has distinct advantages over all other existing methods in terms of reagents required, ease in application, avoidance of interferences and stability of colour for extended periods of time. The modified colorimetric method described above has been further improved by making use of a ligand exchange reaction involving dithizone. The resulting final organic extract in this case is bright orange in colour, the absorbance of which can be measured even with simple photometers. The usefulness of the modified colorimetric method has been demonstrated by determining malathion in technical products, and in aqueous solution containing the compound down to sub ppm levels. The scope and applicability of atomic absorption spectrophotometry has been extended by demonstrating for the first time that the technique can be used for the indirect determination of malathion. Almost all of the work described above has been accepted for publication by international journals and considerable interest in the work has been shown by chemists working in the field of pesticide analysis and research.

Evaluation of disinfecting procedures for aseptic transfer in hospital pharmacy departments

Current practice in National Health Service (NHS) hospitals employs 70% Industrial Methylated Spirit spray for surface disinfection of components required in Grade A pharmaceutical environments. This study seeks to investigate other agents and procedures that may provide more effective sanitisation. Several methods are available to test the efficacy of disinfectants against vegetative organisms. However, no methods currently available test the efficacy of disinfectants against spores on the hard surfaces encountered in the pharmacy aseptic processing environment. Therefore, a method has been developed to test the efficacy of disinfectants against spores, modified from British Standard 13697 and Association of Analytical Chemists standards. The testing procedure was used to evaluate alternative biocides and disinfection methods for transferring components into hospital pharmacy cleanrooms, and to determine which combinations of biocide and application method have the greatest efficacy against spores of Bacillus subtilis subspecies subtilis 168, Bacillus subtilis American Type Culture Collection (ATCC) 6633, and Bacillus pumilis ATCC 27142. Stainless steel carrier test plates were used to represent the hard surfaces in hospital pharmacy cleanrooms. Plates were inoculated with 10(7)-10(8) colony-forming units per milliliter (CFU/mL) and treated with the various biocide formulations, using different disinfection methods. Sporicidal activity was calculated as log reduction in CFU. Of the biocides tested, 6% hydrogen peroxide and a quaternary ammonium compound/chlorine dioxide combination were most effective compared to a Quat/biguanide, amphoteric surfactant, 70% v/v ethanol in deionised water and isopropyl alcohol in water for injection. Of the different application methods tested, spraying followed by wiping was the most effective, followed closely by wiping alone. Spraying alone was least effective.

Guiding local regression using visualisation

Solving many scientific problems requires effective regression and/or classification models for large high-dimensional datasets. Experts from these problem domains (e.g. biologists, chemists, financial analysts) have insights into the domain which can be helpful in developing powerful models but they need a modelling framework that helps them to use these insights. Data visualisation is an effective technique for presenting data and requiring feedback from the experts. A single global regression model can rarely capture the full behavioural variability of a huge multi-dimensional dataset. Instead, local regression models, each focused on a separate area of input space, often work better since the behaviour of different areas may vary. Classical local models such as Mixture of Experts segment the input space automatically, which is not always effective and it also lacks involvement of the domain experts to guide a meaningful segmentation of the input space. In this paper we addresses this issue by allowing domain experts to interactively segment the input space using data visualisation. The segmentation output obtained is then further used to develop effective local regression models.

Remote-controlled experiments with cloud chemistry

Developing cleaner chemical processes often involves sophisticated flow-chemistry equipment that is not available in many economically developing countries. For reactions where it is the data that are important rather than the physical product, the networking of chemists across the internet to allow remote experimentation offers a viable solution to this problem.

Dificuldades de aprendizagem do conteúdo de soluções: proposta de ensino contextualizada

The study of solutions is considered very important to chemist’s education because most of the chemical reactions occur in aqueous medium, being also required to understand other subject such as chemical changes, electrochemical and chemical balance. Nevertheless, it is noticed that many students indicate learning difficulties related to the content of solutions, how to pass among the macro-submicroscopic knowledge levels, and how to solve quantitative problems that demanding the establishment of a stoichiometric ratios. This thesis defended considers the use of contextualized teaching strategies about some subject associated to the study of solution, can foster student learning through reflection and understanding of their own difficulties, besides to provide motivation and active participation. The target group is formed by students of the undergraduate distance education with major in chemistry education of the Universidade Federal do Rio Grande do Norte (UFRN), and they were chosen because this education system is expanding and its learning difficulties publications number is reduced as well. Thus, the first methodological stage was to identify the student’s main learning difficulties associated to the study of solutions through literature sources. Next, using an adapted script of the Plano Nacional do Livro Didático para o Ensino Médio (PNLEM, Textbook National Plan for High School), the approach of the content of solutions printed in educational materials used by the target group was analyzed. Afterward, a teaching unit was planned in the last methodological stage and, finally, a new teaching unite was given with a sequence of contextualized activities such as video presentation, dialogued lecture, questionnaires application, exercises, and an experiment, where the target group’s main difficulties related to learning of solution were identified. The participants of the teaching unit activities had some learning difficulties in understand concepts of compound, ion, charge, entropy and solubility, as well as to identify the ion charge, interpret statements, decode tables, use the chemical language, perform mathematical calculations and use concentration units, similar results raised in the literature sources. In order to work on these difficulties, these students were encouraged to expose, question and test their ideas about the phenomenon under study, allowing learn from their mistakes and reflect on the organization strategy of scientific explanatory models they use. Therefore, activities and information about learning difficulties presented in this thesis need to be critical reflection object, because it can help both students in the process of acquiring knowledge about the content of solutions and professors in the planning of their lessons.

Computer assisted synthesis and in-vitro cytotoxic evaluation of new pyrazole-fused isoquinolinoquinones derivatives as PI3K receptor antagonist with promising antitumoral activity

The importance of pyrazole and isoquinoline-5,8-dione scaffolds in medical chemistry is underlined by the high number of drugs currently on trading that contains these active ingredients. Due to their cytotoxic capability, the interest of medicinal chemists in these heterocyclic rings has grown exponentially especially, for cancer therapy. In this project, the first synthesis of pyrazole-fused isoquinoline-5,8-diones has been developed. 1,3-Dipolar cycloaddition followed by oxidative aromatization, established by our research group, has been employed. Screening of reaction conditions and characterization studies about the regioselectivity have been successfully performed. A remote control of regioselectivity, to achieve the two possible regioisomers has been accomplished. Through Molecular Docking studies, Structure-Activity relationship of differently substituted scaffolds containing our central core proved that a family of PI3K inhibitors have been discovered. Finally, in order to verify the promising antitumor activity, a first test of cell viability in vitro on T98G cell line of a solid brain tumor, the Glioblastoma Multiforme, showed cytotoxic inhibition comparable to currently trade anticancer drugs.

Ion-mediated conformational switches

Molecular switches are ubiquitous in Nature and provide the basis of many forms of transport and signalling. Single synthetic molecules that change conformation, and thus function, reversibly in a stimulus-dependent manner are of great interest not only to chemists but society in general; myriad applications exist in storage, display, sensing and medicine. Here we describe recent developments in the area of ion-mediated switching.

Catalytic Processes Mediated by Metal−Organic Frameworks : Reactivity and Mechanistic Studies

The present thesis describes the development of heterogeneous catalytic methodologies using metal−organic frameworks (MOFs) as porous matrices for supporting transition metal catalysts. A wide spectrum of chemical reactions is covered. Following the introductory section (Chapter 1), the results are divided between one descriptive part (Chapter 2) and four experimental parts (Chapters 3–6). Chapter 2 provides a detailed account of MOFs and their role in heterogeneous catalysis. Specific synthesis methods and characterization techniques that may be unfamiliar to organic chemists are illustrated based on examples from this work. Pd-catalyzed heterogeneous C−C coupling and C−H functionalization reactions are studied in Chapter 3, with focus on their practical utility. A vast functional group tolerance is reported, allowing access to substrates of relevance for the pharmaceutical industry. Issues concerning the recyclability of MOF-supported catalysts, leaching and operation under continuous flow are discussed in detail. The following chapter explores puzzling questions regarding the nature of the catalytically active species and the pathways of deactivation for Pd@MOF catalysts. These questions are addressed through detailed mechanistic investigations which include in situ XRD and XAS data acquisition. For this purpose a custom reaction cell is also described in Chapter 4. The scope of Pd@MOF-catalyzed reactions is expanded in Chapter 5. A strategy for boosting the thermal and chemical robustness of MOF crystals is presented. Pd@MOF catalysts are coated with a protecting SiO2 layer, which improves their mechanical properties without impeding diffusion. The resulting nanocomposite is better suited to withstand the harsh conditions of aerobic oxidation reactions. In this chapter, the influence of the nanoparticles’ geometry over the catalyst’s selectivity is also investigated. While Chapters 3–5 dealt with Pd-catalyzed processes, Chapter 6 introduces hybrid materials based on first-row transition metals. Their reactivity is explored towards light-driven water splitting. The heterogenization process leads to stabilized active sites, facilitating the spectroscopic probing of intermediates in the catalytic cycle.

Tackling Ageing Continence through Theory, Tools & Technology (TACT3)

The complexity of issues surrounding continence management, have been investigated by a UK multi-disciplinary research team working under the project title Tackling Ageing Continence through Theory Tools and Technology (TACT3). The team comprising engineers, chemists, health researchers, designers and social anthropologists is funded by the New Dynamics of Ageing Programme, ‘a seven year multidisciplinary research initiative with the ultimate aim of improving quality of life of older people. The programme is a unique collaboration between five UK Research Councils , and is the largest and most ambitious research programme on ageing ever mounted in the UK’ (www.newdynamics.group.shef.ac.uk). The TACT3 project comprises four work packages that are individually managed by members of the research team. One work package focuses solely on knowledge transfer of the research outputs and the management of the overall project. Another work package, entitled ‘Challenging Environmental Barriers’ has focused on the barriers in the built environment that prevent older people with continence concerns from participating in wider social life, namely access to publicly available toilet facilities. We also have a work package entitled ‘Improving Continence Interventions and Services’ which is exploring patient, carer and service providers experiences in receiving and delivering National Health Service (NHS) continence management treatments. The fourth workpackage ‘Developing Assistive Technologies’ has worked with users to develop devices that promote confidence, improve health and therefore may facilitate greater social interaction for older people with continence management concerns.

Jaquard Laquer

In 2010 Avella worked with the Yves St Laurent (YSL) textiles research team to find elements for a coating that could be applied to weave surfaces in the form of a ‘laquer’ finish. Working with industrial chemists, Avella designed a Jaquard weave pattern to function as substrate for this laquer coating. Successfully used to make womenswear with a high gloss finish, this textile was patented before being displayed in 2010 and much imitated in other collections. Continuing this research for the following collection Avella pursued experiments in laboratory-based industrial chemistry to find a liquid coating that could, like ‘laquer’, be applied as a surface finish to textiles. The resulting metallic iridescent surface was first used in the 20?? Collection (Intellectual Property YSL). Whilst the culture of neophilia in Womenswear fashion at YSL demands permanent innovation for stylistic rather than functional reasons, the innovations in the surface coatings of textiles has potential instrumentality which Avella brings to the resources of the RCA Materials For Living Research Hub and its Inspiring Matter Biennial Conference (2012). Cross disciplinary knowledge transfer between design practices is fundamental to research as process in the School of Material, and textile, as medium, has particularly conformable properties which are especially valuable to this. Anthropologist Susanne Kuechler describes woven textiles as having ’profound meaning as agents of boundary creation’, and Avella’s textiles innovations explore the complexity of the garment as boundary between ‘inside’ and ‘outside’.

Exploring redox-driven self-assembly of mixed metal polyoxometalates

How can we control the experimental conditions towards the isolation of specific structures? Why do particular architectures form? These are some challenging questions that synthetic chemists try to answer, specifically within polyoxometalate (POM) chemistry, where there is still much unknown regarding the synthesis of novel molecular structures in a controlled and predictive manner. This work covers a wide range of POM chemistry, exploring the redox self-assembly of polyoxometalate clusters, using both “one-pot”, flow and hydrothermal conditions. For this purpose, different vanadium, molybdenum and tungsten reagents, heteroatoms, inorganic salts and reducing agents have been used. The template effect of lone-pair containing pyramidal heteroatoms has been investigated. Efforts to synthesize new POM clusters displaying pyramidal heteroanions (XO32-, where X= S, Se, Te, P) are reported. The reaction of molybdenum with vanadium in the presence of XO32- heteroatoms is explored, showing how via the cation and experimental control it is possible to direct the self-assembly process and to isolate isostructural compounds. A series of four isostructural (two new, namely {Mo11V7P} and {Mo11V7Te} and two already known, namely {Mo11V7Se} and {Mo11V7S} disordered egg-shaped Polyoxometalates have been reported. The compounds were characterized by X-ray structural analysis, TGA, UV-Vis, FT-IR, Elemental and Flame Atomic Absorption Spectroscopy (FAAS) analysis and Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES). Cyclic Voltammetry measurements have been carried out in all four compounds showing the effect of the ionic density of the heteroatom on the potential. High-Resolution ESI-MS studies have revealed that the structures retain their integrity in solution. Efforts to synthesize new mixed-metal compounds led to isolation, structural, and electronic characterization of the theoretically predicted, but experimentally elusive δ-isomer of the Keggin polyoxometalate cluster anion, {H2W4V9O33(C6H13NO3)}, by the reaction of tungstate(VI) and vanadium(V) with triethanolammonium ions (TEAH), acting as a tripodal ligand grafted to the surface of the cluster. Control experiments (in the absence of the organic compound) have proven that the tripodal ligand plays crucial role on the formation of the isomer. The six vanadium metal centres, which consist the upper part of the cluster, are bonded to the “capping” TEA tripodal ligand. This metal-ligand bonding directs and stabilises the formation of the final product. The δ-Keggin species was characterized by single-crystal X-ray diffraction, FT-IR, UV-vis, NMR and ESI-MS spectrometry. Electronic structure and structure-stability correlations were evaluated by means of DFT calculations. The compounds exhibited photochromic properties by undergoing single-crystal-to-single-crystal (SC-SC) transformations and changing colour under light. Non-conventional synthetic approaches are also used for the synthesis of the POM clusters comparing the classical “one-pot” reaction conditions and exploring the synthetic parameters of the synthesis of POM compounds. Reactions under hydrothermal and flow conditions, where single crystals that depend on the solubility of the minerals under hot water and high pressure can be synthesized, resulted in the isolation of two isostructural compounds, namely, {Mo12V3Te5}. The compound isolated from a continuous processing method, crystallizes in a hexagonal crystal system, forming a 2D porous plane net, while the compound isolated using hard experimental conditions (high temperature and pressure) crystallizes in monoclinic system, resulting in a different packing configuration. Utilizing these alternative synthetic approaches, the most kinetically and thermodynamically compounds would possibly be isolated. These compounds were characterised by single-crystal X-ray diffraction, FT-IR and UV-vis spectroscopy. Finally, the redox-controlled driven oscillatory template exchange between phosphate (P) and vanadate (V) anions enclosed in an {M18O54(XO4)2} cluster is further investigated using UV-vis spectroscopy as a function of reaction time, showed that more than six complete oscillations interconverting the capsule species present in solution from {P2M18} to {V2M18} were possible, provided that a sufficient concentration of the TEA reducing agent was present in solution. In an effort to investigate the periodicity of the exchange of the phosphate and vanadate anions, time dependent Uv-vis measurements were performed for a period at a range of 170-550 hours. Different experimental conditions were also applied in order to investigate the role of the reducing agent, as well as the effect of other experimental variables on the oscillatory system.

Synthesis of porous graphene/TiO2 by use of recycled graphite

Graphene-based nanomaterials are a kind of new technological materials with high interest for physicists, chemists and materials scientists. Graphene is a two-dimensional (2-D) sheet of carbon atoms in a hexagonal configuration with atoms bonded by sp2 bonds. These bonds and this electron configuration provides the extraordinary properties of graphene, such as very large surface area, a tunable band gap, high mechanical strength and high elasticity and thermal conductivity [1]. Graphene has also been investigated for preparation of composites with various semiconductors like TiO2, ZnO, CdS aiming at enhanced photocatalytic activity for their use for photochemical reaction as water splitting or CO2 to methanol conversion [2-3]. In this communication, the synthesis of porous graphene@TiO2 obtained from a powder graphite recycled, supplied by ECOPIBA, is presented. This graphite was exfoliated, using a nonionic surfactant (Triton X-100) and sonication. Titanium(IV) isopropoxide was used as TiO2 source. After removing the surfactant with a solution HCl/n-propanol, a porous solid is obtained with a specific area of 358 m2g-1. The solid was characterized by XRD, FTIR, XPS, EDX and TEM. Figure 1 shows the graphene 2D layer bonded with nanoparticles of TiO2. When a water suspension of this material is exposed with UV-vis radiation, water splitting reaction is carried out and H2/O2 bubbles are observed (Figure 2)