MetaPrint2D, a new software tool implementing a data-mining approach for predicting sites of xenobiotic metabolism has been developed. The algorithm is based on a statistical analysis of the occurrences of atom centred circular fingerprints in both substrates and metabolites. This approach has undergone extensive evaluation and been shown to be of comparable accuracy to current best-in-class tools, but is able to make much faster predictions, for the first time enabling chemists to explore the effects of structural modifications on a compound’s metabolism in a highly responsive and interactive manner. MetaPrint2D is able to assign a confidence score to the predictions it generates, based on the availability of relevant data and the degree to which a compound is modelled by the algorithm. In the course of the evaluation of MetaPrint2D a novel metric for assessing the performance of site of metabolism predictions has been introduced. This overcomes the bias introduced by molecule size and the number of sites of metabolism inherent to the most commonly reported metrics used to evaluate site of metabolism predictions. This data mining approach to site of metabolism prediction has been augmented by a set of reaction type definitions to produce MetaPrint2D-React, enabling prediction of the types of transformations a compound is likely to undergo and the metabolites that are formed. This approach has been evaluated against both historical data and metabolic schemes reported in a number of recently published studies. Results suggest that the ability of this method to predict metabolic transformations is highly dependent on the relevance of the training set data to the query compounds. MetaPrint2D has been released as an open source software library, and both MetaPrint2D and MetaPrint2D-React are available for chemists to use through the Unilever Centre for Molecular Science Informatics website.

Fungi and Oomycetes represent the two most important groups of eukaryotic plant pathogens. Besides chemical and physical control of these pathogens, biological control is an approach enjoying increasingly more focus. One of the biological agents increasingly employed in biological control of plant pathogenic fungi is ironically the fungus Trichoderma, more specifically Trichoderma harzianum. Besides control of the fungal plant pathogens, another interesting aspect observed when plants are treated with Trichoderma harzianum are effects such as complete and even stand of plants, faster seed germination, increases in plant height and overall enhanced plant growth. Though there have been various studies on this effect, almost no research has yet been conducted to elucidate the mechanism by which these effects occur. In particular, effects such as faster seed germination suggest that Trichoderma harzianum produces a metabolite that may mimic the plant growth hormone gibberellic acid. Through an evaluation of the various metabolites produced by Trichoderma harzianum; gliotoxin seemed structurally most similar to gibberellic acid. To verify that gliotoxin can indeed serve as an analogue for gibberellic acid and elicit similar physiological responses in plants, a two–pronged approach was followed. Firstly, molecular similarity evaluation through common pharmacophore evaluation was conducted, followed by docking simulations into the recently discovered receptor for gibberellic acid. Common pharmacophore evaluation between gibberellic acid and gliotoxin showed successful alignment of gliotoxin into the gibberellic acid based pharmacophore space. Furthermore, docking simulations further strengthened this by the similarity in docking scores calculated and the similar poses of the ligands (gliotoxin and gibberellic acid) in the receptor space. However, similarity in pharmacophore alignment and docking simulation results only suggest that gliotoxin should be able to occupy the receptor space, but it is not a guarantee that similar physiological responses will be elicited. In the second part of the project, the ability of gliotoxin to elicit similar physiological responses in plants to gibberellic acid was investigated. For this, a–amylase induction; plant emergence and height; and chlorophyll fluorescence were compared for both gliotoxin and gibberellic acid treatments. In terms of a–amylase induction, gliotoxin was able to induce production of the enzyme as visualised by starch–containing native gel electrophoresis (zymograms). Gliotoxin induced the strongest response at a 10–6 M dilution which is typically the range expected for hormones in biological systems in de–embryonated seeds of Phaseolus vulgaris. Gibberellic acid was able to induce the strongest response at a 10–7 M dilution. In essence, similar physiological responses were observed. In terms of plant emergence and plant height, treatment with gliotoxin or gibberellic acid resulted in plant emergence a day earlier than the untreated control. However, even though there were slight differences in plant height favouring the gliotoxin or gibberellic acid treated plants, the differences were not statistically significant. Thus, in this regard similar responses were again observed for both gliotoxin and gibberellic acid treatments. In the final evaluation the effect of gliotoxin and gibberellic acid treatments on the chlorophyll fluorescence of mature plants was investigated. Overall, both gliotoxin and gibberellic acid elicited beneficial effects on plant vitality, expressed through PI(Abs) with the gliotoxin treatment performing better than the equivalent gibberellic acid treatment. Overall, the physiological tests demonstrated that gliotoxin can indeed elicit similar positive physiological responses to gibberellic acid in Phaseolus vulgaris. Furthermore the test used in this project can serve as a standard evaluation bench for screening for gibberellic acid analogues on a laboratory scale before larger scale field trials are considered. / Thesis (Ph.D. (Microbiology))--North-West University, Potchefstroom Campus, 2012.

Fungi and Oomycetes represent the two most important groups of eukaryotic plant pathogens. Besides chemical and physical control of these pathogens, biological control is an approach enjoying increasingly more focus. One of the biological agents increasingly employed in biological control of plant pathogenic fungi is ironically the fungus Trichoderma, more specifically Trichoderma harzianum. Besides control of the fungal plant pathogens, another interesting aspect observed when plants are treated with Trichoderma harzianum are effects such as complete and even stand of plants, faster seed germination, increases in plant height and overall enhanced plant growth. Though there have been various studies on this effect, almost no research has yet been conducted to elucidate the mechanism by which these effects occur. In particular, effects such as faster seed germination suggest that Trichoderma harzianum produces a metabolite that may mimic the plant growth hormone gibberellic acid. Through an evaluation of the various metabolites produced by Trichoderma harzianum; gliotoxin seemed structurally most similar to gibberellic acid. To verify that gliotoxin can indeed serve as an analogue for gibberellic acid and elicit similar physiological responses in plants, a two–pronged approach was followed. Firstly, molecular similarity evaluation through common pharmacophore evaluation was conducted, followed by docking simulations into the recently discovered receptor for gibberellic acid. Common pharmacophore evaluation between gibberellic acid and gliotoxin showed successful alignment of gliotoxin into the gibberellic acid based pharmacophore space. Furthermore, docking simulations further strengthened this by the similarity in docking scores calculated and the similar poses of the ligands (gliotoxin and gibberellic acid) in the receptor space. However, similarity in pharmacophore alignment and docking simulation results only suggest that gliotoxin should be able to occupy the receptor space, but it is not a guarantee that similar physiological responses will be elicited. In the second part of the project, the ability of gliotoxin to elicit similar physiological responses in plants to gibberellic acid was investigated. For this, a–amylase induction; plant emergence and height; and chlorophyll fluorescence were compared for both gliotoxin and gibberellic acid treatments. In terms of a–amylase induction, gliotoxin was able to induce production of the enzyme as visualised by starch–containing native gel electrophoresis (zymograms). Gliotoxin induced the strongest response at a 10–6 M dilution which is typically the range expected for hormones in biological systems in de–embryonated seeds of Phaseolus vulgaris. Gibberellic acid was able to induce the strongest response at a 10–7 M dilution. In essence, similar physiological responses were observed. In terms of plant emergence and plant height, treatment with gliotoxin or gibberellic acid resulted in plant emergence a day earlier than the untreated control. However, even though there were slight differences in plant height favouring the gliotoxin or gibberellic acid treated plants, the differences were not statistically significant. Thus, in this regard similar responses were again observed for both gliotoxin and gibberellic acid treatments. In the final evaluation the effect of gliotoxin and gibberellic acid treatments on the chlorophyll fluorescence of mature plants was investigated. Overall, both gliotoxin and gibberellic acid elicited beneficial effects on plant vitality, expressed through PI(Abs) with the gliotoxin treatment performing better than the equivalent gibberellic acid treatment. Overall, the physiological tests demonstrated that gliotoxin can indeed elicit similar positive physiological responses to gibberellic acid in Phaseolus vulgaris. Furthermore the test used in this project can serve as a standard evaluation bench for screening for gibberellic acid analogues on a laboratory scale before larger scale field trials are considered. / Thesis (Ph.D. (Microbiology))--North-West University, Potchefstroom Campus, 2012.

Virtual screening is a well-established part of computer-aided drug design, which heavily employs similarity search and similarity modeling methods. Most of the popular methods are target agnostic, leaving space for design of new methods that would take into account the specifics of the particular molecular target. Additionally, newly developed methods suffer from two related issues: benchmarking and availability. Benchmarking in the domain often suffers from the use of inappropriate reference methods, lack of reproducibility, and the use of nonstandard benchmark datasets. Although there have been several benchmarking studies in the domain that aim at addressing these issues, mainly by offering a standardized comparison, they often suffer from similar drawbacks. For these reasons, new methods fail to gain trust and therefore fail to become a part of the standard toolbox, which thus consists mostly of older methods. In this work, we address the above-described issues. First, we introduce new adaptive methods for virtual screening. Then, to make our and other newly developed methods readily available, we have designed and implemented a virtual screening tool. To address the benchmarking issue, we have compiled a publicly available collection of benchmarking datasets and proposed a platform offering a...

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Una de les àrees més prometedores en recerca biomèdica i farmacèutica és el disseny molecular computacional, que intenta establir relacions entre propietats físico-químiques i activitat biològica. L'èxit d'aquestes tècniques depen críticament de la qualitat de la descripció molecular. En aquest sentit, metodologies basades en potencials d'interacció molecular (MIP) són eines útils per la comparació de compostos que presenten comportaments biològics semblants. Aquest projecte desenvolupa eines per comparar molècules basades en la caracterització de llurs MIPs. El programa de similaritat molecular MIPsim ha estat desenvolupat i aplicat a diferents problemes biològics. Aquesta tesi consisteix en quatre estudis científics que mostren l'ús del MIPSim en aliniament molecular, catalisi enzimàtica, en acoratge de molècules dins el lligand i en estudis 3D-QSAR. / One of the most promising areas in biomedical and pharmaceutical research is computer assisted molecular design, which tries to stablish relationships between physicochemical properties and biological activity. The success of these techniques depends critically on the quality of the molecular description. In this sense, methodologies based on molecular interaction potentials (MIP) are useful tools for the comparison of compounds displaying related biological behaviours. This project aims to develop tools to compare 'molecules based on the characterization 'of their MIPs. To this end, the molecular similarity program MIPSim has been further developed and applied to different biological problems. This thesis consists on four scientific studies showing the use of MIPSim for molecular alignment, enzymatic catalysis, ligand-protein docking and 3D-QSAR analyses.

Made available in DSpace on 2016-06-02T19:22:07Z (GMT). No. of bitstreams: 1 4217.pdf: 3961717 bytes, checksum: 3053793c39a626c9cf9d5fb8f9c0fa21 (MD5) Previous issue date: 2011-02-18 / Universidade Federal de Sao Carlos / The ventricular myocardial contractility of the matrinxã teleost, Brycon amazonicus, was analysed in previous experimentation with isometric multicellular preparations, in time effect and force-frequency relationship experiments, with and without exposure to the alkaloid ryanodine, a sarcoplasmic reticulum (SR) Ca2+ release blocker. In this study, different methodological approaches were used, such as isometric stress (EI, mN.mm-2), that permitted to identify the sensitivity of the myocardium to ryanodine, with the majority contribution of Ca2+ from the SR. The use of time to peak tension and time to half relaxation parameters (TPT and THR, ms) were ineffective to evaluate the contraction and relaxation performances during time effect experiments. New approaches such as contraction rates and initial relaxation rates (TC and TIR, mN.mm-2.s-1) demonstrated directly the impairment of the myocardium exposed to ryanodine. The negative staircase effect, characteristic of the teleost s forcefrequency relationship was evidenced by EI. The maximum rates of contraction and maximum rates of relaxation (TMC and TMR, mN.mm-2.s-1) and the average rates of contraction and average rates of relaxation (TMedC and TMedR, mN.mm-2.s-1) showed the impairment of the myocardium contractility exposed to ryanodine as well as the low sensitivity of frequency increments on the contractility when considered the values of TPT and THR. The TMedC and TMedR values indicated a greater possibility of heart rate regulation than the TMC and TMR values, probably due to these estimates consider the amount of instantaneous rate changes of contraction wave on calculation instead of just one point on the curve. The cardiac pumping capacity (CBC, mN.mm2.min-1) showed that the optimal range of frequency for isometric contraction is narrow and that the myocardium of the species should be working on the limit at rest. The analyses of integral of isometric tension (ITI, mN.mm- 2.s), and integral of isometric tension per minute (ITIPM, mN.mm-2.min), showed that these were unsuitable indexes for the assessment of cardiac contractility in the way they were calculated, as inconsistent interpretations were generated, probably by using information from the curve of contraction irrelevant to the isometric preparation. The contractility index (IC, mN.mm-2) created in this work, suggested that the myocardium contractility of the species is more sensitive to increases in frequency. On the other hand, the contractility index per minute (ICPM, mN.mm-2) showed that the optimum range of frequencies for the B. amazonicus myocardial contraction can be much wider and could allow performance reserve, such as reported in other studies of cardiac function in teleosts. The protein expression of SERCA2a and phospholamban (PLB) were analysed by Western Blot technique and their expression supported the findings of the SR functionality. The comparative analysis of these proteins, using amino acid sequences available in public databases (GenBank and UniProt), revealed levels of similarity between the SERCA2a and PLB in fish and other vertebrates, strengthened the findings of studies with Western Blot experiments. Taken together, the results suggest that B. amazonicus myocardium is dependent on SR Ca2+ stores under physiological frequencies and, despite the negative staircase pattern, must possess a performance reserve at supraphysiologic frequencies. / A contratilidade do miocárdio ventricular do teleósteo matrinxã, Brycon amazonicus, foi analisada com dados de experimentos prévios, realizados com preparações isométricas multicelulares e protocolos de efeito do tempo e de relação forçafrequência, com e sem exposição ao alcalóide rianodina, bloqueador dos canais de liberação de Ca2+ do retículo sarcoplasmático (RS). Nesse estudo foram utilizadas diferentes abordagens metodológicas de tratamento de dados, como o estresse isométrico (EI, mN.mm-2), a partir do qual foi possível identificar a sensibilidade do miocárdio à rianodina, com contribuição majoritária do Ca2+ proveniente do RS. A utilização dos tempos para o pico de tensão e para metade do relaxamento (TPT e THR, ms), se mostraram ineficazes para avaliar o desempenho da contração e relaxamento no experimento do efeito do tempo. Novas abordagens na análise dos dados, como a taxa de contração e taxa inicial de relaxamento (TC e TIR, mN.mm- 2.s-1) demonstraram explicitamente o comprometimento do miocárdio durante a exposição à rianodina. O efeito escada negativo, característico da relação forçafrequência de teleósteos foi evidenciado pelo EI. As taxas máximas de contração e de relaxamento (TMC e TMR, mN.mm-2.s-1) e as taxas médias de contração e de relaxamento (TMedC e TMedR, mN.mm-2.s-1) além de demonstrarem o comprometimento da contratilidade durante exposição à rianodina, indicaram que existe um menor comprometimento da tensão durante elevação da frequência, quando comparados aos valores de TPT e THR. A TMedC e a TMedR apresentaram resultados relacionados a uma frequência cardíaca com maior possibilidade de ajustes do que a TMC e a TMR, provavelmente por considerarem o conjunto de variação das taxas instantâneas da contração e não somente um único ponto da curva. A capacidade de bombeamento cardíaco (CBC, mN.mm-2.min-1) mostrou que a faixa ótima de frequência para contração isométrica é estreita e que o miocárdio da espécie deve estar trabalhando no limiar na condição de repouso. As análises da integral da tensão isométrica (ITI, mN.mm-2.s), e da integral da tensão isométrica por minuto (ITIPM, mN.mm-2.min) mostraram-se inapropriadas para a avaliação da contratilidade cardíaca pelo modo como foram calculadas, uma vez que geraram interpretações incoerentes, provavelmente por utilizarem informações da curva de contração irrelevantes para a preparação isométrica. O índice de contratilidade (IC, mN.mm-2) criado nesse trabalho, sugere que o miocárdio da espécie é mais sensível às elevações de frequência. Por outro lado, o índice de contratilidade por minuto (ICPM, mN.mm-2) mostrou que a faixa ótima de frequências para a contração cardíaca de B. amazonicus pode ser mais ampla, o que permitiria uma reserva de desempenho, assim como observado para outros teleósteos. A expressão das proteínas SERCA2a e fosfolambano (PLB) foram analisadas pela técnica de Western Blot e sua expressão reforçaram os achados de funcionalidade do RS. A análise comparativa dessas proteínas utilizando sequências de aminoácidos disponíveis em bancos de dados públicos (GenBank e UniProt) revelou os níveis de similaridade entre a SERCA2a e PLB de peixes e mamíferos, reforçando os achados dos estudos com Western Blot. Em conjunto, os dados sugerem que o miocárdio do B. amazonicus, apresenta uma nítida dependência do RS em frequências fisiológicas e, apesar de exibir um claro padrão escada negativo, deve apresentar uma reserva de desempenho para frequências suprafisiológicas.