Submitted in fulfillment of the requirements for the Doctor of Philosophy degree in Chemistry, Durban University of Technology, Durban, South Africa, 2016. / In drug discovery and development projects, metabolism of new chemical entities (NCEs) is a major contributing factor for the withdrawal of drug candidates, a major concern for other chemical industries where chemical-biological interactions are involved. NCEs interact with a target macro-molecule to stimulate a pharmacological or toxic response, known as pharmacodynamics (PD) effect or through the Adsorption, Distribution, Metabolism, and Excretion (ADME) process, triggered when a bio-macromolecule interacts with a therapeutic drug. Therefore, the drug discovery process is important because 75% of diseases known to human kind are not all cured by therapeutics currently available in the market. This is attributed to the lack of knowledge of the function of targets and their therapeutic use in order to design therapeutics that would trigger their pharmacological responses. Accordingly, the focus of this work is to develop cost saving strategies for medicinal chemists involved with drug discovery projects. Therefore, studying the synergy between in silico and in vitro approaches maybe useful in the discovery of novel therapeutic compounds and their biological activities. In this work, in silico methods such as structure-based and ligand-based approaches were used in the design of the pharmacophore model, database screening and flexible docking methods. Specifically, this work is presented by the following case studies: The first involved molecular docking studies to predict the binding modes of catechin enantiomer to human serum albumin (HSA) interaction; the second involved the use of docking methods to predict the binding affinities and enantioselectivity of the interaction of warfarin enantiomers to HSA. the third case study involved a combined computational strategy in order to generate information on a diverse set of steroidal and non-steroidal CYP17A1 inhibitors obtained from literature with known experimental IC50 values. Finally, the fourth case study involved the prediction of the site of metabolisms (SOMs) of probe substrates to Cytochrome P450 metabolic enzymes CYP 3A4, 2D6, and 2C9 making use of P450 module from Schrödinger suite for ADME/Tox prediction. The results of case study I were promising as they were able to provide clues to the factors that drive the synergy between experimental kinetic parameters and computational thermodynamics parameters to explain the interaction between drug enantiomers and thetarget protein. These parameters were correlated/converted and used to estimate the pseudo enantioselectivity of catechin enantiomer to HSA. This approach of combining docking methodology with docking post-processing methods such as MM-GBSA proved to be vital in estimating the correct pseudo binding affinities of a protein-ligand complexes. The enantioselectivity for enantiomers of catechin to HSA were 1,60 and 1,25 for site I and site II respectively. The results of case study II validates and verifies the preparation of ligands and accounting for tautomers at physiological pH, as well as conformational changes prior to and during docking with a flexible protein. The log KS = 5.43 and log KR = 5.34 for warfarin enantiomer-HSA interaction and the enantioselectivity (ES = KS/KR) of 1.23 were close to the experimental results and hence referred to as experimental-like affinity constants which validated and verified their applicability to predict protein-ligand binding affinities. In case study III, a 3D-QSAR pharmacophore model was developed by using 98 known CYP17A1 inhibitors from the literature with known experimental IC50 values. The starting compounds were diverse which included steroidal and non-steroidal inhibitors. The resulting pharmacophore models were trained with 69 molecules and 19 test set ligands. The best pharmacophore models were selected based on the regression coefficient for a best fit model with R2 (ranging from 0.85-0.99) & Q2 (ranging from 0.80-0.99) for both the training and test sets respectively, using Partial Least Squares (PLS) regression. On the other hand, the best pharmacophore model selected was further used for a database screening of novel inhibitors and the prediction of their CYP17A1 inhibition. The hits obtained from the database searches were further subjected to a virtual screening workflow docked to CYP17A1 enzyme in order to predict the binding mode and their binding affinities. The resulting poses from the virtual screening workflow were subjected to Induced Fit Docking workflow to account for protein flexibility during docking. The resulting docking poses were examined and ranked ordered according to the docking scores (a measure of affinity). Finally, the resulting hits designed from an updated model from case study III were further synthesized in an external organic chemistry laboratory and the synthetic protocols as well as spectroscopic data for structure elucidation forms part of the provisional patent specification. A provisional patent specification has been filed (RSA Pat. Appln. 2015/ 07849). The case studies performed in this thesis have enabled the discovery of non-steroidal CYP17A1 inhibitors. / D

This study had a twofold purpose. First, the usefulness of the simplex algorithm as a short method of optimization in high performance liquid chromatographic separations was investigated. The second was to test a modified simplex method. The volume fractions of mobile phase components were chosen as the variable factors in the optimization process. Four test cases were performed which included separation of cholesterol esters, naphthalene and its derivatives, polycyclic aromatic compounds, and the thiane compounds. The standard for accepting an optimum was based on the baseline separation of two adjacent peaks and the analysis time. In addition to successful separations, the correlation between the separation and the chemical characteristics of mobile phase compositions was calculated and this could then be used for further modification of simplex search strategy.

Orientador: Marcos Fernando de Souza Teixeira / Banca: Luiz Henrique Dall'Antonia / Banca: Maria Valnice Zanoni / Resumo: A presente dissertação de mestrado apresenta o estudo da eletropolimerização de monômeros à base de Schiff na ausência de cátions metálicos (N,N'-bis(5-aminosalicilidenoimina) - NH2 -salen) e do monômero a base de Schiff contendo níquel como cátion metálico no centro ligante tetradentado (N,N',N'',N'''-tetrabis(salicilideno)3,3',4,4'-bifenileno tetramino de níquel (II)) - Ni2 (Bisalphen). A obtenção do monômero NH 2 -salen foi realizada pela redução metálica em meio ácido do monômero NO 2 -salen (N,N'-bis(5-nitrosalicilidenoimina)), sendo confirmada pela técnica de espectroscopia no infravermelho (FTIR), espectrofotometria na região de UV-vís e por espectroscopia de massa (MS-EI). As análises dos voltamogramas de eletropolimerização, e dos perfis voltamétricos em solução aquosa, demonstram um mecanismo de por acoplamento C-N. O mecanismo foi confirmado pelo estudo de velocidade de varredura e número de ciclos de potenciais, como também pela caracterização por espectroscopia Raman. Em solução aquosa o filme de poli(NH-salen) apresentou um único par redox na ausência de oxigênio molecular, atribuído ao par redox R 1 -NH-C-R 2 /R 1 -N=C-R 2 , onde um aumento da concentração de espécie eletroativa foi obtida em função do aumento da razão [carga do íon]/[raio iônico] dos ânions presentes em solução, que pode ser atribuído a necessidade da difusão dos ânions no processo de transferência eletrônica. Para comparação dos mecanismos de formação, a obtenção do filme polimérico do complexo metálico Ni 2 (Bisalphen) foi realizada de modo semelhante, modificando apenas o solvente e eletrólito suporte utilizado. Na etapa de eletropolimerização, os resultados foram satisfatórios somente em solvente THF contendo... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: This dissertation presents the study of electropolymerization of monomers to the Schiff base in the absence of metal cations (N, N'-bis (5-amine-salicylideneimine) - NH2 -salen) and the Schiff base monomer containing nickel as metallic cation in the tetradentate center (N,N',N'',N'''-tetrabis(salicylidene) 3,3',4,4'-biphenylene-tetramine of nickel (II) - Ni2 (Bisalphen)). The NH 2 -salen monomer synthesis was realized by metallic reduction in acid medium from NO2 -salen (N,N'-bis(5-nitro-salicylideneimine)), being confirmed by the infrared spectroscopy (FTIR), UV-Vis spectrophotometry, and mass spectroscopy of electronic impact (MS-EI). The voltammetric profiles obtained on electropolymerization stage and in aqueous solution show the mechanism formation based on C-N coupling. This mechanism was confirmed by scan rate, potential cycle number study, and by the Raman characterization. In aqueous solution the poli(NH-salen) film showed one redox couple in absence of molecular oxygen, which was ascribed to R 1 -NH-C-R 2 /R 1 -N=C-R 2 redox couple. The increase of surface coverage was obtained in function of [ion charge]/[ionic radius] ratio of the anions present in aqueous solution, which can be ascribed to necessity of anion diffusion on electronic transfer. In order to compare the electropolymerization mechanism, the polymeric film of Ni2 (Bisalphen) was also obtained by electropolymerization technique. However, the solvent and supporting electrolyte were different. In the electropolymerization stage, the results were satisfactory only in THF solvent using the TBAP as supporting electrolyte, which can be ascribed to low solubility of complex in other solvents, as well as the low dipole value, necessary to propagation of the reaction. Due to presence of the metallic cation on monomer structure, the electropolymerizatiom... (Complete abstract click electronic access below) / Mestre

Thesis (Ph.D.)--Drexel University, 2009. / Includes abstract and vita. Includes bibliographical references (leaves 204).

Thesis (Ph. D.)--University of Missouri-Columbia, 2001. / Typescript. Vita. Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2001. / Typescript. Vita. Includes bibliographical references. Also available on the Internet.

Dissertation submitted in partial compliance with the requirements of the Masters Degree in Technology: Chemistry, in the Faculty of Applied Sciences at the Durban University of Technology, 2008. / In this work, a holistic approach to validate analytical methods was assessed by virtue of Monte Carlo simulations. This approach involves a statement of the methodsâ s scope (i.e. analytes, matrices and concentration levels) and requisites (internal or external); selection of the methodâ s (fit-for-purpose) features; pre-validation and validation of the intermediate accuracy and its assessment by means of Monte Carlo simulations. Validation of the other methodâ s features and a validity statement in terms of a â fit-for-purposeâ decision making, harmonized validation-control-uncertainty statistics and short-term routine work with the aim of proposing virtually â ready-to-useâ methods. The protocol could be transferred to other methods. The main aim is to harmonize the work to be done by research teams and routine laboratories assuming that different aims, strategies and practical viewpoints exist. As a result, the recommended protocol should be seen as a starting point. It is necessary to propose definitive (harmonized) protocols that must be established by international normalisation/accreditation entities. The Quality Assurance (Method verification and Internal Quality Control, IQC) limits, as well as sample uncertainty were estimated consistently with the validated accuracy statistics i.e. E U (E) and RSDi + U (RSDi). Two case studies were used to assess Monte Carlo simulation as a tool for method validation in analytical laboratories, the first involves an indirect polarographic method for determining nitrate in waste water and the second involves a direct determination of heavy metals in sea water by differential pulse anodic stripping voltammetry, as an example of the application of the protocol. In this sense the uncertainty obtained could be used for decision making purposes as it is very tempting to use uncertainty as a commercial argument and in this work it has been shown that the smaller the uncertainty, the better the measurement of the instrument or the laboratoryâ s reputation.

The objective of this thesis is to categorize carpet types according to their XRF spectra and verify if further classification of carpets is possible for use of an XRF analysis system in the carpet manufacturing line. This thesis consists of (1) implementing and studying effective algorithms for automated analysis of X-ray spectra, (2) comparing known algorithms for X-ray spectra analysis, and (3) implementing our own algorithm for classification of carpets spectra obtained for further fluorine online analysis of XRF inspected carpets. This research is intended for quick and accurate automated analysis of raw XRF spectra and matching analysis results to a database of XRF spectra of raw carpets. The research uses spectrum signal processing and spectrum analysis regarding efficacy of combined methods for XRF inspected carpets. X-Ray Fluorescence is a key technology for detection of chemical elements. Fluorine is a key element for carpet's quality. XRF has been chosen to be a potential candidate to measure fluorine since it is a versatile tool for low concentration element detection. Due to specific XRF background spectrum for each different carpet type, carpet samples may need specific calibrations for further computation of carpet fluorine concentration. Automating the detection of the carpet type is intended to help in automating the XRF calibration.

Thesis (Ph. D.)--University of Washington, 1991. / Vita. Includes bibliographical references (leaves [131]-137).

Thesis (M.Sc.) - Carleton University, 2006. / Includes bibliographical references (p. 85-86). Also available in electronic format on the Internet.