Tuberculosis, caused by the pathogenic bacteria Mycobacterium tuberculosis, is one of the most widespread and deadly infectious diseases today. Treatment of tuberculosis relies on antibiotics that were developed more than 50 years ago. These are now becoming ineffective due to the emergence of antibiotic resistant strains of the bacteria. The aim of the research in this thesis was to develop new antibiotics for tuberculosis treatment. To this end, we targeted enzymes from two essential biosynthetic pathways in M. tuberculosis for drug development. The methylerythritol phosphate (MEP) pathway synthesizes a group of compounds called isoprenoids. These compounds have essential roles in all living organisms. The fact that humans utilize a different pathway for isoprenoid synthesis makes the MEP pathway enzymes attractive targets for drug development. We have determined the structures of two essential enzymes from this pathway by X-ray crystallography: 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) and 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD). These are the first structures of these enzymes from M. tuberculosis. Additionally, structures of the IspD enzyme from the related bacteria Mycobacterium smegmatis were determined. We have characterized these enzymes and evaluated the efficiency of a number of inhibitors of the DXR enzyme by biochemical methods. Crystal structures of DXR in complex with some of these inhibitors were also determined. The second pathway of interest for drug development is the universal pathway for Coenzyme A biosynthesis. Enzymes in this pathway have essential roles in all living organisms. However, the bacterial enzymes have little similarity to the human homologues. We have determined a number of structures of the M. tuberculosis pantothenate kinase (PanK), the regulatory enzyme of this pathway, in complex with two new classes of inhibitory compounds, and evaluated these by biochemical methods. The structures and biochemical characterization of these enzymes provide us with detailed information about their functions and broadens our knowledge of these bacteria. Biochemical and structural information about new inhibitors of these enzymes serve as a starting point for future development of antibiotics against tuberculosis.

Acute myeloid leukemia (AML) is a life-threatening malignant disorder with dismal prognosis. AML is characterized by frequent genetic changes involving tyrosine kinases, normally acting as important mediators in many basic cellular processes. Due to the overexpression and frequent mutations of the FMS-like receptor tyrosine kinase 3 (FLT3) in AML, this tyrosine kinase receptor has become one of the most sought after targets in AML drug development. In this thesis, we have used a combination of high-throughput screens, direct target interaction assays and sequential cellular screens, including primary patient samples, as an approach to discover new targeted therapies. Gefitinib, a previously known inhibitor of epidermal growth factor receptor and the two novel tyrosine kinase inhibitors AKN-032 and AKN-028, have been identified as compounds with cytotoxic activity in AML. AKN-028 is a potent inhibitor of FLT3 with an IC50 value of 6 nM in an enzyme assay, but also displaying in vitro activity in a variety of primary AML samples, irrespective of FLT3 mutation status or quantitative FLT3 expression. AKN-028 shows a sequence dependent in vitro synergy when combined with standard cytotoxic agents cytarabine or daunorubicin, with better efficacy when cells are exposed to standard chemotherapy simultaneously or for 24 hours prior to adding AKN-028. Antagonism is observed when cells are pre-treated with AKN-028, possibly explained by the cell cycle arrest induced by the compound. In vivo cytotoxic activity and good oral bioavailability have made AKN-028 a candidate drug for clinical studies and the compound is presently investigated in an international two-part multicenter phase I/II study. Results from microarray studies performed to further elucidate the mechanism of action of AKN-028, revealed significantly altered gene expression induced by AKN-028 in both AML cell lines and in primary AML cells, with an enrichment of the Myc pathway among the downregulated genes. Furthermore, tyrosine kinase activity profiling shows a dose-dependent kinase inhibition by AKN-028 in all AML samples tested. Interestingly, cells with a high overall kinase activity were more sensitive to AKN-028. Provided conformation in a larger set of samples, kinase activity profiling may give useful information in individualizing treatment of patients with AML.

Thesis (Ph. D.)--Ohio State University, 2007. / Title from first page of PDF file. Includes bibliographical references (p. 154-175).

Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.

Thesis (Ph.D.)--Pardee Rand Graduate School, 2009. / Title from PDF t.p. Includes bibliographical references.

Thesis (M.S.)--Oregon State University, 2011. / Printout. Includes bibliographical references (leaves 58-59). Also available on the World Wide Web.

Orientador: Jean Leandro dos Santos / Banca: Carolina Lanaro / Banca: Magnun Nueldo Nunes dos Santos / Banca: Rafael Victorio Carvalho Guido / Banca: Jeanine Giarolla Vargas / Resumo: A Anemia Falciforme (AF) é uma anemia hemolítica genética caracterizada por uma mutação no gene da globina beta. Além do quadro vaso-oclusivo, os pacientes com AF apresentam processo inflamatório crônico caracterizado pelo aumento de diversas citocinas pró-inflamatórias, a exemplo do Fator de Necrose Tumoral alfa (TNF-α). Atualmente, a hidroxiureia (HU) é o único fármaco disponível para o tratamento e seus efeitos benéficos estão associados ao óxido nítrico (NO), gerado após biotransformação. O NO desempenha efeitos benéficos na doença tais como: vasodilatação, inibição da agregação plaquetária e aumento na produção de hemoglobina fetal (HbF). Nesse contexto, foram sintetizados os compostos 3(a-b); 4(a-b) e 5(a-b) obtidos através da estratégia de hibridação molecular da subunidade inibidora de TNF-α presente na pomalidomida com o núcleo furoxânico (1,2,5-oxadiazol-2-N-óxido) com propriedades doadores de NO. Os compostos sintetizados foram obtidos em rendimentos que variaram entre 13 e 30%. As moléculas do estudo demonstraram capacidade de liberar NO em níveis que variaram entre 1 e 30%. Em cultura de células CD34+, o composto 4b (2,5 μM) foi capaz de induzir gobina γ, enquanto HU foi ativa apenas em concentrações 4 vezes superiores (10 μM). Estudos preliminares do possível mecanismo de ação mostraram que o composto 4b não interefe na expressão de fatores de transcrição a exemplo do BCL11A, IKAROS, LRF e nos níveis de acetilação de histona H3. O composto 4b foi capaz de induzi... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Sickle Cell Anemia is a genetic blood disease in which there is a mutation in the β-hemoglobin gene. This mutation promotes polymerization of hemoglobin molecules that change the structure of the erythrocyte cytoskeleton promoting sickling of the cell. Moreover, there is increased adhesion of blood cells in the vessel contributing to the increasement of the vaso-occlusive process, the main characteristic of the disease. It is further known that the chronic inflammation associated with the disease contributes to a number of complications and among the process responsible for this proinflammatory cytokine is TNF-α, which is an important target for therapeutic intervention. Hydroxyurea (HU) is the only available drug for treatment and its beneficial effects are associated with the same capacity biotransformation of nitric oxide. The NO plays beneficial effects such as vasodilation, inhibition of platelet aggregation and production of fetal hemoglobin (Hb F), latter has the function of decreasing polymerization of hemoglobin. In this context, continuing the research line that aims at planning, synthesis and pharmacological evaluation of new prototypes drug candidates for the treatment of sickle cell anemia complications, in this work have synthesized a series of four new hybrid compounds ( I- IV) containing the phtalimide (TNF-alfa inhibitory subunit) and furoxan subunits ( nitric oxide donors) according to structural design. The compounds were presented as NO donors. Compounds I-IV were shown to be inhibitors of TNF-α in the immunoassay of this cytokine assay and the compound IV is the most promising inhibiting between 65% in smaller concentrations than the other. In the assay of ADP-induced platelet aggregation, compounds III and IV were able to inhibit platelet aggregation sigficantily. In addition, the compound I after 72 hours was... (Complete abstract click electronic access below) / Doutor

Malaria is an infectious disease caused by parasites of the Plasmodium genus with mortality rates of more than a million annually, hence a major global public health concern. Plasmodium falciparum (P. falciparum) accounts for over 90% of malaria incidence. Increased resistance to antimalarial drugs by the Plasmodium parasite, coupled with the lack of an effective malaria vaccine necessitates the urgent need for new research avenues to develop novel and more potent antimalarial drugs. This study focused on falcipains, a group of P. falciparum cysteine proteases that belong to the clan CA and papain family C1, that have emerged as potential drug targets due to their involvement in a range of crucial functions in the P. falciparum life cycle. Recently, falcipain-2 has been validated as a drug target but little is known of its Plasmodium orthologs. Currently, there are several falcipain inhibitors that have been identified, most of which are peptide based but none has proceeded to drug development due to associated poor pharmacological profiles and susceptibility to degradation by host cysteine proteases. Non-peptides inhibitors have been shown to be more stable in vivo but limited information exists. In vivo studies on falcipain-2 and falcipain-3 inhibitors have also been complicated by varying outcomes, thus a good understanding of the structural variations of falcipain Plasmodium orthologs at the active site could go a long way to ease in vivo results interpretation and effective inhibitor design. In this study, we use bioinformatics approaches to perform comparative sequence and structural analysis and molecular docking to characterize protein-inhibitor interactions of falcipain homologs at the active site. Known FP-2 and FP-3 small molecule nonpeptide inhibitors were used to identify residue variations and their effect on inhibitor binding. This was done with the aim of screening a collection of selected non-peptide compounds of South African natural origin to identify possible new inhibitor leads. Natural compounds with high binding affinities across all Plasmodium orthologs were identified. These compounds were then used to search the ZINC database for similar compounds which could have better binding affinities across all selected falcipain homologs. Compounds with high binding affinities across all Plasmodium orthologs were found.

Radiotherapy is second only to surgery in the curative management of patients with cancer, and yet the molecular mechanisms that determine the sensitivity of tumours to radiation remain largely unclear. A high-throughput radiosensitivity screening method based on clonogenicity was developed and a siRNA library against kinase targets was screened. The gold standard colony formation endpoint was chosen for determining reproductive cell death after radiation treatment, since effects on proliferation often do not reflect survival. Thiamine pyrophosphokinase-1 (TPK1), a key component of Vitamin B1/thiamine metabolism, was identified as a target for radiosensitisation. TPK1 knockdown caused significant radiosensitisation in cancer but not normal tissue cell lines. Other means of blocking this pathway such as knockdown of thiamine transporter-1 (THTR1) or treatment with the thiamine analogue pyrithiamine hydrobromide (PyrH) caused significant tumour specific radiosensitisation. There was persistent DNA damage in cells irradiated after TPK1 and THTR1 knockdown or PyrH treatment. Thus this screen allowed the identification of thiamine metabolism as a novel radiosensitisation target that affects DNA repair. Short-term modulation of thiamine metabolism could be a clinically exploitable strategy to achieve tumour specific radiosensitisation. Three additional genes, signal recognition particle-72 kDa (SRP72), glycogen synthase 3-beta (GSK3β) and MAP/Microtubule Affinity-Regulating Kinase 2 (MARK2) were also investigated. Knockdown of these genes radiosensitised both tumour and normal tissue cell lines and expression of two of them, GSK3β and SRP72 were found to be associated with poor recurrence-free survival in early breast cancer patients.