Thesis (M.S.)--Rutgers University, 2008. / "Graduate Program in Medicinal Chemistry." Includes bibliographical references (p. 102-113).

Thesis (Ph. D.)--University of Texas at Austin, 1998. / Vita. Includes bibliographical references (leaves 378-392). Available also in a digital version from Dissertation Abstracts.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1943. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Bibliographies: leaves 60-89, 126-135.

As ferramentas computacionais de modelagem molecular e de QSAR estão integradas ao processo de planejamento de fármacos na busca inesgotável por novas moléculas bioativas de elevado interesse terapêutico. O trabalho em Química Medicinal realizado nesta dissertação de mestrado envolveu o estudo das relações entre a estrutura e atividade de inibidores da enzima purina nucleosídeo fosforilase (PNP) bovina e de Schistosoma mansoni. A potência de uma série de inibidores da PNP de S. mansoni foi determinada experimentalmente através da medida de valores de 1C50, empregando um ensaio cinético padronizado e validado. Conjuntos de dados padrões para inibidores da enzima PNP bovina e de S. mansoni foram organizados, contendo os dados de estrutura e atividade correspondentes. Estes conjuntos formaram a base científica para o desenvolvimento dos modelos preditivos de QSAR 2D, empregando o método holograma QSAR. Os modelos finais de HQSAR desenvolvidos possuem alta consistência interna e externa, apresentando bom poder preditivo. Estes modelos, em conjunto com as informações obtidas dos mapas de contribuição de HQSAR, são guias químico-medicinais importantes no planejamento de inibidores mais potentes e seletivos, candidatos a protótipos de novos fármacos na quimioterapia segura das doenças alvo deste trabalho / Computational tools for molecular modeling and QSAR are well-integrated into the drug design process in the search for new bioactive molecules of significant therapeutic interest. The Medicinal Chemistry work done in this dissertation involved structure-activity studies of inhibitors of bovine and Shistosoma mansoni purine nucleoside phosphorylase (PNP). The potency of a series of S. mansoni inhibitors was experimentally determined through measurements of IC50 values, employing a standard validated kinetic assay. Data sets for bovine and S. mansoni PNP were organized, encompassing the structural information and corresponding biological data. These data sets established the scientific basis for the development of the predictive QSAR models using the hologram QSAR method. The final HQSAR models generated possess both good internal and external consistency with good correlative and predictive power. These models and the information obtained from the HQSAR contribution maps should be useful in guiding future medicinal chemistry efforts designed to discover novel potent and selective inhibitors as drug candidates for the chemotherapy of the target diseases of this work

Submitted by Franciele Moreira (francielemoreyra@gmail.com) on 2018-11-05T13:39:32Z No. of bitstreams: 2 Dissertação - Luciana Oliveira Barateli - 2018.pdf: 3641421 bytes, checksum: a96d12f5fce8d5c02a9793dec50ebfbf (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-11-05T14:49:58Z (GMT) No. of bitstreams: 2 Dissertação - Luciana Oliveira Barateli - 2018.pdf: 3641421 bytes, checksum: a96d12f5fce8d5c02a9793dec50ebfbf (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-11-05T14:49:58Z (GMT). No. of bitstreams: 2 Dissertação - Luciana Oliveira Barateli - 2018.pdf: 3641421 bytes, checksum: a96d12f5fce8d5c02a9793dec50ebfbf (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2018-08-27 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Stryphnodendron adstringens presents a wide geographical distribution, being predominant in regions of Cerrado sensu stricto and is popularly known as "barbatimão". It is a species widely used in herbal medicine because of its anti-inflammatory, antibacterial and antiulcerogenic potential. The Cerrado’s removal of vegetation cover reduces significantly the number of several native species, among them S. adstringens. Thus, it is important that efficient strategies for the use and conservation of this species are drawn. In order to provide molecular tools for studies of genetic diversity and conservation of S. adstringens, the present work had the objective of developing microsatellite markers for the species. Genomic DNA was obtained from leaf tissue using the CTAB protocol. The identification of the microsatellite regions and the design of the primers were performed using the QDD program modules. From the identified microsatellite regions, 20 pairs of primers were designed, 14 of which flank microsatellite regions composed of dinucleotides, four by tetranucleotides and two by pentanucleotides. Initially, four individuals were used for the standardization tests of the PCR protocol and annealing temperatures. Subsequently, 48 individuals were selected, distributed in three populations, to evaluate polymorphism via 6% polyacrylamide gel. Of the 20 pairs of primers evaluated, 16 presented polymorphic amplification products and four monomorphic amplification products. Considering the 16 polymorphic markers, the number of alleles varied between two (SadH19) and 13 (SadH13), with a mean of seven alleles per locus. The observed heterozygosity (Ho) and expected (He) and PIC values were 0.506, 0.543, 0.635, respectively. The mean Hmax value founded (65,519) indicates values of genetic diversity that can be considered medians for this set of loci evaluated in three populations of S. adstringens. On the other hand, although genetic diversity is median, this set of 16 polymorphic markers exhibited a ombined probability of paternity exclusion high (0.9999983) and combined probability of genetic identity low (3,49x10-15). The analysis of variance of allelic frequencies presented significant values for two of the three estimated statistics with f not significant 0.050, significant θ equal to 0,329 and F in the overall value also significant 0.360. Thus, it can be concluded that the panel of polymorphic markers developed for S. adstringens is highly informative and indicated for population genetic studies for the species. Another important factor is that these markers can be tested in other evolutionarily close species for the availability of microsatellite markers, without the need to develop new primers. / Stryphnodendron adstringens apresenta ampla distribuição geográfica, sendo predominante em regiões de Cerrado stricto sensu e é conhecida popularmente como “barbatimão”. É uma espécie utilizada na medicina fitoterápica por seu potencial anti-inflamatório, antibacteriano e antiulcerogênico. A retirada de cobertura vegetal do Cerrado diminui significativamente o número de diversas espécies nativas, dentre elas S. adstringens. Dessa forma, é importante que sejam traçadas estratégias eficientes para o uso e a conservação dessa espécie. A fim de disponibilizar ferramentas moleculares para estudos de diversidade genética e conservação de S. adstringens, o objetivo desse estudo foi desenvolver marcadores microssatélites e estimar o potencial informativo desses marcadores para subsidiar estudos de genética populacional da espécie. A identificação das regiões microssatélites e o desenho dos primers foram realizados usando o programa QDD. Inicialmente, foram utilizados quatro indivíduos para os testes de padronização do protocolo de PCR e temperaturas de anelamento. Posteriormente, foram selecionados 48 indivíduos, provenientes de três populações, para avaliação de polimorfismo via gel de poliacrilamida a 6%. A partir das regiões microssatélites identificadas, foram desenhados 20 pares de primers, sendo que 14 flanqueiam regiões microssatélites compostas por dinucleotídeos, quatro por tetranucleotídeos e dois por pentanucleotídeos. Dos 20 pares de primers avaliados, 16 apresentaram produtos de amplificação polimórficos e quatro monomórficos. Considerando os 16 marcadores polimórficos, o número de alelos variou entre dois (SadH19) e 13 (SadH13), com uma média igual a sete alelos por loco. Os valores das médias da heterozigosidade observada (Ho) e esperada (He) e do PIC foram iguais a 0,506, 0,543, 0,635 respectivamente. A proporção da diversidade máxima encontrada foi de 65%, o que indica valores de diversidade genética que podem ser considerados medianos para esse conjunto de locos avaliados em três populações de S. adstringens. Por outro lado, embora a diversidade genética seja mediana, esse conjunto de 16 marcadores polimórficos exibiu uma probabilidade de exclusão de paternidade combinada alta (0,999983) e uma probabilidade de identidade combinada baixa (3,49x10-15). A análise de variância das frequências alélicas apresentou valores significativos para duas das três estatísticas estimadas com f não significativo 0,050, θ significativo igual a 0,329 e F no valor global também significativo 0,360. Assim, pode-se concluir que o painel de marcadores polimórficos desenvolvidos para S. adstringens é altamente informativo e indicado para estudos genéticos populacionais para a espécie. Outro fator importante é que esses marcadores podem ser testados em outras espécies próximas evolutivamente para possível disponibilização de marcadores microssatélites, sem a necessidade de desenvolvimento de novos primers.

Submitted by (edna.saturno@ufrpe.br) on 2016-06-14T14:18:23Z No. of bitstreams: 1 Alejandro Lozano Balcazar.pdf: 872682 bytes, checksum: e3abd135cdb60662dc0bab0b46db32ec (MD5) / Made available in DSpace on 2016-06-14T14:18:23Z (GMT). No. of bitstreams: 1 Alejandro Lozano Balcazar.pdf: 872682 bytes, checksum: e3abd135cdb60662dc0bab0b46db32ec (MD5) Previous issue date: 2009-06-15 / This search analyzes a pharmacopoeia under the optics of the apparency hypothesis. This hypothesis divides plants into apparent and not apparent ones, being the first, in a simple way, perennial woody plants, and the second herbaceous with short life cycle. The apparency hypothesis, when facing the ethnobotany, proposes a positive relationship between the availability of species (usually measured by phytosociological parameters) and its use value for people (calculated through ethnobotanical information). In the community of Caçimbas, settlement which uses plant resources from the Cerrado of the Araripe National Forest (FLONA-Araripe) in the State of Ceará, semi-structured interviews were used to obtain the inventory of medicinal plants, their collection site, diseases for which they are indicated, and calculate its use value, as well as their commercial and practical importance. During the process of botanical collections was set the habit of the plants and they also were featured into woody and non woody ones. The herbaceous habit and the woody plants had the greatest richness of etnoespécies, the herbaceous and non woody ones had the highest practical value, and anthropogenic areas resulted to be the main source of medicinal plants; herbs and trees had equal versatility in the treatment of diseases and they do not differ in regards to the use value. The trees stood out as the most commercially important. In addition, two vegetation plots were held at FLONA to test the relationship between phytosociological parameters and the use and commercial value of the medicinal plants. The commercial and use value were not correlated with the abundance, frequency or ecological importance index of the plants. This study provides information for the development and management plan of the Araripe National Forest, indicating how is the dynamic of use of medicinal plants resources by a nearby community, and allowing the analysis of the role of the FLONA in the cultural, practical and commercial dynamics of use of medicinal plants. This survey provides data on the use of medicinal plants in Brazilian semiarid, arriving with information about the application of the apparency hypothesis in understanding the dynamics of use of these resources. / Esta pesquisa foi baseada na análise de uma farmacopéia sob a ótica da hipótese da aparência. Esta hipótese divide as plantas em aparentes e não aparentes, sendo, simplificadamente, as primeiras lenhosas perenes e as segundas herbáceas de ciclo de vida curto. A hipótese da aparência, quando virada para a etnobotánica, propõe uma relação positiva entre a disponibilidade das espécies (usualmente medida por parâmetros fitossociológicos) e o seu valor de uso para as pessoas (calculado por meio de informações etnobotânicas). Na comunidade de Caçimbas, povoado que utiliza recursos vegetais no cerrado da Floresta Nacional do Araripe (FLONA-Araripe) estado do Ceará, foram utilizadas entrevistas semiestruturadas para obter o inventário das plantas medicinais, seu local de coleta, doenças para as que são indicadas, e calcular seu valor de uso, valor comercial e importância prática. Durante coletas botânicas foi definido o hábito das plantas e também foram caracterizadas em lenhosas e não lenhosas. O hábito herbáceo e as lenhosas tiveram a maior riqueza de etnoespécies, as não lenhosas herbáceas são as de maior valor prático, e as zonas antropogênicas resultaram ser a principal fonte de plantas medicinais; ervas e árvores resultaram igualmente versáteis no tratamento de doenças e não se diferenciaram quanto ao valor de uso. As árvores se destacaram como as de maior importância comercial. Além disso, duas parcelas de vegetação foram realizadas na FLONA para testar a relação entre parâmetros fitossociológicos e o valor de uso e valor comercial das plantas medicinais. O valor de uso e valor comercial não se correlacionaram com a abundancia, freqüência e índice de valor de importância ecológico das plantas medicinais. O presente estudo fornece informação para o desenvolvimento do plano de manejo da Floresta Nacional do Araripe (FLONA-Araripe) indicando como é a dinâmica de uso de plantas medicinais por uma comunidade adjacente, e possibilitando a análise do papel da FLONA no valor cultural e importância prática e comercial das plantas medicinais. Esta pesquisa fornece dados sobre o uso de plantas medicinais no semiárido brasileiro, aportando com informações sobre a aplicação da hipótese da aparência na compreensão da dinâmica de uso desses recursos.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-04-29T14:00:29Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Minha dissertação final para biblioteca.pdf: 6771552 bytes, checksum: cc238895a0629230ce30655a760f5a10 (MD5) / Made available in DSpace on 2016-04-29T14:00:29Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Minha dissertação final para biblioteca.pdf: 6771552 bytes, checksum: cc238895a0629230ce30655a760f5a10 (MD5) Previous issue date: 2015-02-19 / CAPEs / Estima-se que até 2030 o câncer será responsável por até 12 milhões de óbitos. Tendo em vista a necessidade de novos tratamentos para o câncer, este trabalho tem como objetivo sintetizar, caracterizar estruturalmente e avaliar a atividade anticâncer de sete novos derivados tiazacridínicos (LPSF AA-56, LPSF AA-57, LPSF AA-59, LPSF AA-60, LPSF AA-61, LPSF AA-62, LPSF AA-63). Estes derivados provém da hibridização molecular dos núcleos de tiazolidina e de acridina. As sínteses para obtenção destes compostos foram otimizadas para obtenção de um melhor rendimento. A síntese da tiazolidina-2,4-diona (TZD) foi feita por reação de ciclização. Uma posterior N-alquilação da TZD em presença de uma base e da 9-(bromo-metil)acridina, conduziu a formação do intermediário LPSF AA-1A. Os intermediários ésteres de Cope (IPs) foram obtidos a partir de uma reação de condensação Knoevenagel. A última etapa ocorreu por uma reação de adição de Michael através de reação entre a TZD N-alquilada com os ésteres de Cope, formando os derivados tiazacridínicos substituídos. A pureza e comprovação estrutural das moléculas sintetizadas foram obtidas através de cromatografia líquida acoplada a espectrômetro de massa (LC-MS), infravermelho (IV) e ressonância magnética nuclear (RMN) de hidrogênio. Ensaios de citotoxicidade dos derivados sintetizados foram realizados em células leucêmicas, fígado e próstata. Entre os compostos sintetizados, o LPSF AA-57 exibiu a atividade anti-cancerígena mais potente contra as linhagens celulares Jurkat (6,63 ± 2,65 μM), HL-60 (6,51 μM), K562 (3,97 ± 1,36 μM) e o LPSF AA-60 exibiu a atividade anti-cancerígena mais potente contra DU 145 (7,22 ± 3,12 μM). / It is estimated that cancer will be responsible for up to 12 million deaths by 2030. Given the need for new treatments for cancer this work aims to synthesize, characterize structurally and evaluate the anti-cancer activity of seven new thiazacridines derivatives (LPSF AA-56, LPSF AA-57, LPSF AA-59, LPSF AA-60, LPSF AA-61, LPSF AA-62, and LPSF AA-63). These derivatives derived of molecular hybridization from nucleus of thiazolidine and acridine. The syntheses for obtaining these compounds were optimized to obtain the best performance. Synthesis of thiazolidine-2,4-dione (TZD) was carried out by cyclization reaction. A further N-alkylation of the TZD in the presence of a base and 9-(bromomethyl)acridine, leading to formation of intermediate LPSF AA-1A. Intermediate esters of Cope (IPs) were obtained from a Knoevenagel condensation reaction. The last step was by a Michael addition, reaction between the N-alkylated TZD with ester of Cope, forming substituted thiazacridines derivatives. The purity and structural confirmation of the synthesized molecules were obtained from liquid chromatography coupled to mass spectrometry (LC-MS), infrared (IR) and Proton nuclear magnetic resonance (NMR). Assays of cytotoxicity of the synthesized products was conducted in leukemic cells, liver and prostate. Among the synthesized compounds, the LPSF AA-57 exhibited the most potent anti-cancer activity against cell lines Jurkat (6,63 ± 2,65 μM), HL-60 (6,51 μM), K562 (3,97 ± 1,36 μM) and the LPSF AA-60 exhibited the most potent anti-cancer activity against DU 145 (7,22 ± 3,12 μM).

<p>  Acute myeloid leukemia (AML) is a devastating cancer with an overall 5-year survival rate of approximately 30%, despite efforts to develop therapeutics to combat this disease. AML is caused by various mutations, and frequent genetic errors found in 30% of AML patients are mutations in the FMS-like tyrosine kinase 3 (FLT3). Recently two FLT3 drugs for AML, Midostaurin and Gilteritinib, have been approved by the FDA, but resistance to these drugs, such as FLT3D835Y/V and F691L, mutations have limited the efficacies of both of these drugs. Thus, there is a need for newer generation FLT3 inhibitors that cover mutations encountered in the clinic. The Sintim laboratory has developed a FLT3 inhibitor, HSN748, which has shown remarkable efficacies against the majority of the FLT3 mutants. Pre-IND studies are now ongoing to support a potential clinical trial of HSN748 for AML treatment that is resistant to the approved therapeutics midostaurin and gilteritinib. The characterization of HSN748 on the proteome and phosphoproteome level was undertaken to provide a more granular view on how this potential AML therapeutic affects key cellular processes. Global proteomic and phosphoproteomic analysis revealed that HSN748 may play a role in cell cycle regulation, spindle formation, leukemic stem cell maintenance, and transcription and confirmed previous in vitro studies that showed inhibition of other kinases relevant to AML treatment, such as AURKB and Raf-1.</p> <p>Recently, there have been efforts to improve the timespan of therapeutic efficiency of FLT3 inhibitors by combining FLT3 inhibitors with other drugs that target other processes essential to AML. Clinical trials (e.g. NCT03735875) are ongoing to evaluate FLT3 inhibitors combined with venetoclax against AML. The second part of this thesis project evaluated the combination of HSN748 analogs with venetoclax and discovered that the combinations synergize to increase apoptotic activity in AML cells harboring FLT3-ITD with secondary mutations D835Y or F691L, which are two clinically important genetic alterations that lead to drug resistance against current FLT3 inhibitors. We determined that the nicotinamide analog, HSL468, synergized with venetoclax with a coefficient of inhibition of 0.23 for the combination with HSL468 at 1.25 nM and venetoclax at 80 nM against an AML cell line that has both the FLT3-ITD and F691L mutations, which are responsible for resistance to most current FLT3-targeted AML therapeutics, including the combination therapy of gilterinitib and venetoclax.</p>

<p>  </p> <p>Using a version of the Povarov-Doebner reaction, we were able to identify and develop a novel kinase inhibitor scaffold that is tunable, selective, and able to target drug-resistant mutant kinases. The 3H-pyrazolo[4,3-f]quinoline moiety was shown to be a privileged kinase inhibitor scaffold with a strong inhibition several different kinases. Herein, various 3H-pyrazolo[4,3-f]quinoline-containing compounds were synthesized quickly via the Povarov-Doebner multicomponent reaction. Our scaffold has demonstrated to potently inhibit FLT3 and CDK2 with nanomolar IC50 values. These FLT3 inhibitors were also shown to inhibit leukemic cell growth in a mouse disseminated AML model, establishing these 3H-pyrazolo[4,3-f]quinoline-containing compounds as lead compounds to develop into anti-cancer agents. The 3H-pyrazolo[4,3-f]quinoline moiety has potently inhibited ROCK1/2 with single digit nanomolar IC50 values, newly synthesized analogs with replacement of the boronic acid moiety with an amide also displayed inhibition of ROCK1/2. The most active compound (<strong>HSH3107</strong>) potently inhibits ROCK1/2 and although it did not display any antiproliferative effects against MDA-MB-231 (triple negative breast cancer cell line) at 1 µM, it did slow cell migration for up to 48 hours compared to DMSO control and Fasudil. Acyclic amide analogs of this scaffold have also led to the discovery of CDK12 and CDK13 inhibitors which can serve as a potential therapeutic in cancers where there may be no treatment strategy available or where resistance has emerged.</p>

<p>This thesis describes the initial steps towards the use of dipeptidyl acyloxymethyl ketones as a platform to develop molecular imaging (MI) probes for cancer. Initially the synthesis of an AOMK was performed following a literature procedure which resulted in an epimerized product. This issue was addressed by optimizing an alternative method yielding all intermediates in yields similar or better to those reported in the literature (final product yield of 67%). An AOMK derivative that can be used to evaluate target expression levels was synthesized by linking a fluorescent dye to the ε-amine group of lysine in accordance to a literature procedure describing the synthesis of an optical imaging probe in 24% yield. A second generation derivative AOMK was prepared by linking 4-fluoro-benzoic acid to the same amino group yielding a model of a PET MI probe.</p> <p>An endpoint colorimetric assay was developed and optimized to test cathepsin B inhibitors. Due to the fact that the AOMKs exhibit time-dependent inhibition these assay conditions did not prove to be adequate for the assessment of the cathepsin B binding. Steps toward developing a continuous assay that would be better suited for these compounds were achieved. Factors such as the relationship between the formation of the assay product vs enzyme concentration and determination of the Michelis-Menten constant (K_m = 390 ± 30 nM) were established. These parameters can be used to determine the optimal enzyme and substrate concentration that should be used to test the AOMK based probes.</p> / Master of Science (MSc)