A cruzaína, principal cisteíno protease do Trypanosoma cruzi, é um alvo terapêutico validado para o tratamento da doença de Chagas. Grande parte dos inibidores desta enzima é constituída de peptídeo-miméticos do tipo covalente irreversível cujo desenvolvimento, entretanto, tem sido evitado devido ao potencial efeito off target e ao perfil farmacocinético indesejável. O grupo de química medicinal NEQUIMED/ IQSC/USP vêm utilizando métodos avançados em quimioinformática para a identificação de inibidores reversíveis da cruzaína e de outras cisteíno proteases. Contudo, para que estes inibidores se desenvolvam a compostos matrizes mais eficientes, informações computacionais e estruturais de seus Modos de Interação (MOB) com a proteína alvo tornam-se fundamentais. Neste trabalho, a cristalografia de raios X foi utilizada para descrever em detalhes o MOB de três importantes inibidores reversíveis da cruzaína identificados pelo NEQUIMED: a dipeptidil-nitrila Neq0409 e os dois fragmentos moleculares Neq0147 e Neq0176. De modo a evitar a auto-proteólise experimentada pela cruzaína nativa que torna desafiadora a cristalização com inibidores de baixa afinidade como os fragmentos reversíveis, duas novas construções mutantes e inativas da cruzaína (a C25A e a C25S) foram desenvolvidas. A C25S foi validada como modelo cristalográfico representativo dado a coerência do MOB elucidado nesta enzima mutante e na cruzaína nativa para o inibidor mais estudado da cruzaína, o K777. A descrição da presença, orientação, conformação e modo de ação no sítio, além do completo padrão de interações fornecidos por estas estruturas cristalinas, validaram ortogonalmente os MOB preditos e os métodos de planejamento in silico usados no NEQUIMED, permitindo a identificação de inibidores muito mais potentes análogos ao Neq0147 e ao Neq0409. O grupo 2-acetamidotiofeno-3-carboxamida do Neq0176 e o anel heterocíclico de cinco membros baseado no 1,3,4-oxadiazol do Neq0147 foram identificados como alternativos aos tradicionais esqueletos peptídeo-miméticos. O impacto do efeito proteolítico na qualidade e na resolução de estruturas cristalográficas na cruzaína foi melhor compreendido a partir de duas estruturas de alta resolução obtidas para a cruzaína nativa em complexo com o metanotiossulfonato de metila (MMTS) e a iodoacetamida. Estes resultados permitiram compreender as bases experimentais para a cristalização de inibidores reversíveis de baixa afinidade. Todos os resultados estruturais obtidos via cristalografia de raios X neste trabalho são úteis para mapear as bases estruturais essenciais para o planejamento de futuros inibidores mais potentes e seletivos da cruzaína. / Cruzain, the major Trypanosoma cruzi cysteine protease, is a validated therapeutic target for the search of new medicines for the treatment of Chagas disease. A myriad of inhibitors of this enzyme consists of covalent irreversible peptidomimetics whose development has been impaired due to potential off target effect and undesirable pharmacokinetic profile. Modern cheminformatic methods employed by The Medicinal Chemistry Group (NEQUIMED/IQSC/USP) were used to identify cruzain reversible inhibitors. Their optimization for more efficient compounds can be accomplished by the use of data and information gathered from computational and structural modes of interaction (MOB). In this doctoral thesis, the X-ray crystallography was used to describe in detail the MOB of three important new cruzain reversible inhibitors: the dipeptidil-nitrile Neq0409 and the two molecular fragmentos Neq0147 and Neq0176. In order to avoid cruzain self-proteolysis during crystallization with low affinity reversible inhibitors such as the identified fragments, two new mutant and inactive constructs of cruzain (the C25S and C25A) were designed to upholding the same properties of the wild type catalytic site. The C25S was validated as representative crystallographic model given the coherence of the MOB elucidated for the best-known and studied cruzain inhibitor, the K777. The description of the presence, orientation, conformation and mode of action at the site, besides the complete pattern of bimolecular interactions, provided by these crystalline structures, orthogonally validated the predicted in silico MOB and allowed the identification of other potent inhibitors analogous to the Neq0147 and the Neq0409. The 2-acetamidothiophene-3-carboxamide moiety (Neq0176) and heterocyclic five-membered ring based on the 1,3,4-oxadiazole (Neq0147) were thereby identified as attractive alternatives to traditional peptidomimetics. The impact of proteolytic effect on the quality and resolution of crystallographic structures in cruzain was best understood from two high-resolution structures obtained for the native cruzain in complex with methyl methanethiolsulfonate (MMTS) and iodoacetamide. These results allow the understanding of experimental basis for the crystallization with reversible inhibitors of low affinity such as fragments. All structural results obtained by X-ray crystallography together with the catalytic site depiction using GRID and SuperStar methods are useful for mapping the essential structural basis for the design of future more potent and selective cruzain inhibitors.

A Doença de Alzheimer (DA) é um transtorno progressivo que acomete o Sistema Nervoso Central, causando demência em idosos. A doença leva a uma diminuição da memória, dificuldade no raciocínio e pensamento e alterações comportamentais. A fisiopatologia da doença corresponde ao aumento na concentração do peptídeo -amilóide com consequente deposição e formação da placa amiloide; e também ao aparecimento dos emaranhados neurofibrilares, que são agregados de proteína tau hiperfosforilada. A enzima glicogênio sintase cinase 3 beta (GSK-3) está diretamente envolvida nos dois processos e, por isso, a busca por novos inibidores dessa enzima é uma importante estratégia terapêutica para o tratamento da doença. Neste trabalho utilizou-se a triagem virtual em 7 bancos de dados de moléculas aplicando cinco diferentes estratégias in silico, através de planejamento de fármacos baseado em ligantes e baseado em estrutura, combinada com estudos in silico de farmacocinética, toxicidade e atividade biológica, seguido de posteriores ensaios de inibição enzimática in vitro. Obteve-se três compostos pela metodologia de farmacóforo, (Estratégia 3) dos quais dois deles demonstraram atividade inibitória interessante para GSK-3, na faixa de micromolar. A partir das outras quatro estratégias foram selecionados 16 compostos que futuramente serão também testados utilizando o mesmo protocolo de ensaio in vitro aqui utilizado. / Alzheimer\'s disease (AD) is a progressive disorder that affects the Central Nervous System, causing dementia in the elderly. The disease leads to decreased memory, difficulty in reasoning and thinking, and behavioral changes. The pathophysiology of the disease corresponds to the increase in -amyloid peptide concentration with consequent deposition and formation of the amyloid plaque and to the appearance of neurofibrillary tangles, which are aggregates of hyperphosphorylated tau protein. The enzyme glycogen synthase kinase-3 beta (GSK-3) is directly involved in both processes and, therefore, the search for new inhibitors of this enzyme is an important therapeutic strategy for the treatment of the disease. In this work, we used virtual screening in 7 molecule databases applying five different in silico strategies, using the ligand-based and structure-based drug design methodologies, combined with in silico studies of pharmacokinetics, toxicity and biological activity, followed by subsequent assays enzymatic inhibition in vitro. We obtained three compounds by the pharmacophore methodology (Strategy 3) of which two of them demonstrated interesting inhibitory activity for GSK-3 in the micromolar range. From the other four strategies, 16 compounds were selected which in future will also be tested using the same in vitro assay protocol used here.

O Projeto Genoma Humano do Câncer (PGHC), financiado pela FAPESP e pelo Instituto Ludwig de Pesquisa sobre o câncer, buscou identificar os genes expressos nos tipos mais comuns de câncer no Brasil. Tal projeto conseguiu identificar aproximadamente um milhão de seqüências de genes de tumores freqüentes no Brasil. A contribuição brasileira foi maior para tumores de cabeça e pescoço, mama e cólon. Uma das iniciativas mais recentes e estimuladas pelo PGHC é o projeto Genoma Clínico, o qual visa desenvolver novas formas de diagnóstico e tratamento do câncer através do estudo de genes expressos. A partir da análise molecular de tecidos saudáveis e neoplásicos em diferentes estágios, é possível identificar marcadores de prognóstico, permitindo escolhas de terapias mais adequadas e eficientes. A proteína hnRNP K foi identificada como um desses marcadores, em neoplasias da região da cabeça e pescoço, sendo objetivo deste estudo a aplicação de técnicas de bioinformática e modelagem molecular no planejamento baseado em estrutura de candidatos a fármacos antineoplásicos que bloqueiem a atividade da proteína. A proteína hnRNP K apresenta diversas funções e é encontrada nos mais diversos compartimentos celulares, interferindo, basicamente, no sistema de expressão gênica. Essa proteína apresenta 3 domínios KH, os quais são responsáveis por sua ligação à moléculas de DNA e RNA. Modelos de boa qualidade dos domínios KH foram construídos através da estratégia de modelagem molecular por homologia estrutural. Após screening virtual em bases de dados de compostos (330.000 aproximadamente) com propriedades drug-like, 15 compostos com potencial de interação com o domínio KH3 foram selecionados. Os modos de ligação para cada um dos mesmos no sítio ligante do domínio KH3 foram sugeridos por simulações de docking e apresentaram um bom encaixe espacial com os sítios receptores virtuais calculados pelos campos de interação molecular. Simulações de dinâmica molecular foram realizadas com o intuito de avaliar a estabilidade dos compostos selecionados, que também foram avaliados quanto à presença de grupamentos toxicofóricos em sua estrutura. / The Brazilian Project Genoma Câncer (PGHC) supported by FAPESP and the Ludwig Institute for Cancer Research, intended to identify the genes involved in the most common cases of cancer in Brazil. In this project about a million of gene sequences were identified. The major contribution was made in breast, colorectal and head and neck cancers. The results obtained stimulated the creation of another project, called Genoma Clínico, which intend to develop new trends in treatments and diagnosis of cancer based on the study of expressed genes. Analyzing healthy and neoplasic tissues in different stages, it is possible to identify molecular markers related to the prognosis of cancer, allowing the use of more efficient therapies. The hnRNP K protein was identified as a molecular marker in head and neck cancer, where the objective of this work lies in the application of bioinformatics and molecular modeling strategies by structure-based drug design to identify potential antineoplasic drug candicates that could act against hnRNP K protein. The hnRNP K protein is encountered in all cellular compartments and act, basically, in the gene expression pathways. Its structure is composed by three KH domains that mediate interactions with DNA and RNA molecules. High quality models of KH domains were built by homology modeling. After the virtual screening simulations performed with drug-like compound databases, containing approximately 330.000 compounds, 15 were selected as potential ligands of KH3 domain of hnRNP K. The binding modes suggested for these compounds, by docking simulations, presented a good spatial fit when compared with the virtual receptor sites calculated by molecular interaction fields. Molecular dynamics simulations were performed in order to evaluate de stability of the binding modes suggested. The potential ligands were also evaluated to identify toxicophoric features in its chemical structures.

differential scanning calorimetric profile and the generation of much less intense and broader peaks in the powder X-ray diffraction pattern compared to beta-CD. FTIR analysis revealed significant physical interactions between CX oil and beta-CD in the granules, possibly due to complexation. Results from phase solubility measurements and proton nuclear magnetic resonance ( 1H-NMR) analysis of pure 3-butylidenephthalide (3-BDPH), a representative CX component, lend some support for the formation of a 1:1 stoichiometric inclusion complex between 3-BDPH and beta-CD. / Rhizoma chuanxiong (CX), the dried rhizome of Ligusticum Chuangxiong Hort. (Umbelliferae), has been extensively used in mainland China as a traditional herbal medicine for treating cardio-/cerebrovascular diseases and gynecological disorders. However, the active components in CX, which are predominantly essential oils, generally exhibit poor stability (mostly photo-oxidation), high volatility, low aqueous solubility, and extensive gut/hepatic metabolism, all of which can significantly reduce their oral bioavailability and therapeutic efficacy. The present project has investigated the feasibility of utilizing three formulation approaches to circumvent the aforementioned problems associated with the peroral delivery of CX (as crude oil mixture or individual components). / The first approach involved inclusion of CX oil in beta-cyclodextrin (beta-CD) as solid granules using a coprecipitation method optimized with the aid of an orthogonal study design. The resulting CX oil granules were colorless and odorless with a median particle size of 11.38mum; were stable to heat, light and moisture, and readily soluble in simulated gastric and intestinal fluids. The granules were largely amorphous, as evidenced by an absence of the melting endotherm for beta-CD in the formulation could be largely explicated by the complexation behavior and hydration properties of the two polymers blended in different weight percentages, as substantiated by turbidity measurement, viscosity determination and FTIR analysis of the pure polymer mixtures as well as swelling measurement of the formulated tablets. The sustained release behavior of 3-BDPH from the tablet was dependent on the relative proportion of the two polymers present, and could be similarly explained by the changes in hydration and complexation behavior of the polymers during the penetration of aqueous fluid into the tablet matrix. / The second approach involved incorporation of CX oil into surfactant micelles and liquid crystals as a self-emulsifying drug delivery system (SEDDS). An optimal formulation was developed through a judicial choice of excipients (lipids and surfactants/cosurfactant) and their proper combination in the correct proportions, as determined by the spontaneity of the emulsification process and the change in emulsion droplet size. The formulation was readily dispersible in water upon mild agitation, free from unpleasant odor, and stable in soft gelatin capsules for a storage period of at least 12 months under ambient condition. The optimal utilization of the lipid and surfactant blends in defined proportions in the formulation was further substantiated by interfacial tension determination and equilibrium phase analysis. / The third approach involved formulation of 3-BDPH (or crude CX oil) into a sustained-release buccoadhesive tablet, based on a systematic evaluation of the adhesive properties of two polymers (Carbopol 974P and hydroxypropyl methylcellulose K4M) used in the formulation. The adhesive properties of the formulation could be largely explicated by the complexation behavior and hydration properties of the two polymers blended in different weight percentages, as substantiated by turbidity measurement, viscosity determination and FTIR analysis of the pure polymer mixtures as well as swelling measurement of the formulated tablets. The sustained release behavior of 3-BDPH from the tablet was dependent on the relative proportion of the two polymers present, and could be similarly explained by the changes in hydration and complexation behavior of the polymers during the penetration of aqueous fluid into the tablet matrix. / Gao Yuan. / "April 2005." / Adviser: Albert H. L. Chow. / Source: Dissertation Abstracts International, Volume: 68-03, Section: B, page: 1585. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (p. 193-223). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

La méthode de conception de médicaments à partir de molécules « fragments » (connue sous le nom de « Fragment-Based Drug Design ») a été proposée au milieu des années 90, et a depuis été reconnue comme une alternative tangible aux techniques plus classiques de recherche de médicaments telles que le criblage à haut débit par exemple. La méthode des fragments consiste à cribler un petit nombre (< 10000) de composés organiques de faible poids moléculaire (< 300 Da) afin de détecter ceux qui se lient à la cible (protéine ou acides nucléiques). Du fait de leur faible complexité, les fragments présentent une affinité faible pour la cible, et la détection s'effectue généralement grâce à une technique biophysique (en particulier, résonance magnétique nucléaire (RMN), cristallographie aux rayons X, résonance plasmonique de surface). Les fragments « hits » sont ensuite modifiés par addition de nouvelles fonctions chimiques, ou par liaison de deux fragments, afin d'élaborer, étape par étape, une molécule capable d'établir des interactions plus nombreuses avec la cible, et d'améliorer ainsi l'affinité. Comparée aux méthodes classiques de criblage haut débit, la méthode des fragments offre divers avantages, notamment une meilleure exploration de l'espace chimique, une meilleure efficacité de liaison des molécules « hits », et une plus grande facilité d'optimisation des hits en molécules plus affines. Dans le cadre de ce projet de thèse, plusieurs aspects de la méthode des fragments ont été abordés : dans une première partie, nous étudions un cas concret d'application de la méthode des fragments à la recherche d'un inhibiteur de la peroxiredoxine 5 humaine, en utilisant la RMN comme outil de criblage des fragments ainsi que comme outil d'étude des interactions protéine-fragment. La découverte d'un inhibiteur de cette enzyme représente une avancée importante, qui devrait permettre de mieux comprendre son fonctionnement. Les autres parties de ce projet de thèse abordent des aspects plus méthodologiques de la méthode des fragments : les fragments conservent-ils leur site de liaison, leur efficacité de liaison et leur mode d'interaction au cours de leur élaboration en inhibiteur ? Les fragments peuvent-ils être spécifiques d'une protéine ? D'un site de liaison particulier ? Ces questions, rarement traitées, sont pourtant essentielles à la compréhension du comportement des molécules fragments, et sont abordées d'une part en défragmentant plusieurs inhibiteurs de la protéine Bcl-xL et en étudiant par RMN le comportement de ces fragments vis-à-vis de la protéine en termes d'affinité et de site de liaison, d'autre part en réalisant le criblage par RMN d'une série de fragments sur cinq protéines différentes (peroxiredoxine 5 humaine, sérum albumine humaine et trois protéines homologues de la famille Bcl-2). De manière générale, ce projet de thèse vise à étudier des aspects peu abordés de la méthode des fragments et à proposer des pistes permettant de mieux comprendre le comportement des fragments vis-à-vis de leur cible, au cours du criblage initial comme lors de leur optimisation / Fragment-Based Drug Design (FBDD) has been proposed in 1996 and has since been recognized as a tangible alternative to the more classical drug discovery methods such as High-Throuput Screening. FBDD consists of screening a small number (< 10 000) of low-molecular weight (< 300 Da) compounds and detect those that bind to the target (protein or nucleic acids). Because of their low complexity, fragment molecules usually display low affinities for their target, hence detecting fragment-protein interactions is mostly achieved using a biophysical technique (mostly Nuclear Magnetic Resonance (NMR), X-ray crystallography or Surface Plasmon Resonance). “Hit” fragments are then modified by addition of chemical substituents, or linked together, so as to elaborate a more complex molecule, forming more interactions with the target and hence displaying an improved affinity. As compared to the more classical High Throughput Screening method, fragment screening provides several advantages, including a better exploration of chemical space, highly ligand-efficient hits and easier optimization of the hits into more affine molecules. In this PhD project, several aspects of FDBB have been addressed : first, FBDD approaches were applied to the research of an inhibitor of the human peroxiredoxin 5 protein, using NMR not only as a screening method but also for the characterization of the protein-fragment interactions. The discovery of an inhibitor against this enzyme would allow to better understand its function. Next, methodological aspects of the FBDD method were addressed : Do fragments conserve their binding site, binding efficiency and mode of interaction upon optimization? Can the fragments display specificity towards a given target? Towards a given binding site? These issues, rarely studied, are yet essential to the understanding of the behavior of fragment molecules, and will be addressed firstly by defragmentating several Bcl-xL inhibitors into fragments and studying their behavior towards the protein in terms of a_nity and binding mode, secondly by screening a set of fragments against five different proteins (human peroxiredoxin 5, human serum albumin and three homologous proteins of the Bcl-2 family of proteins). More generally, this PhD project aims at studying less characterized aspects of the fragment methodology and proposing answers to better understand the behavior of fragment molecules towards their targets, both in the initial screening step and then during their optimization

A cruza&iacute;na, principal ciste&iacute;no protease do Trypanosoma cruzi, &eacute; um alvo terap&ecirc;utico validado para o tratamento da doen&ccedil;a de Chagas. Grande parte dos inibidores desta enzima &eacute; constitu&iacute;da de pept&iacute;deo-mim&eacute;ticos do tipo covalente irrevers&iacute;vel cujo desenvolvimento, entretanto, tem sido evitado devido ao potencial efeito off target e ao perfil farmacocin&eacute;tico indesej&aacute;vel. O grupo de qu&iacute;mica medicinal NEQUIMED/ IQSC/USP v&ecirc;m utilizando m&eacute;todos avan&ccedil;ados em quimioinform&aacute;tica para a identifica&ccedil;&atilde;o de inibidores revers&iacute;veis da cruza&iacute;na e de outras ciste&iacute;no proteases. Contudo, para que estes inibidores se desenvolvam a compostos matrizes mais eficientes, informa&ccedil;&otilde;es computacionais e estruturais de seus Modos de Intera&ccedil;&atilde;o (MOB) com a prote&iacute;na alvo tornam-se fundamentais. Neste trabalho, a cristalografia de raios X foi utilizada para descrever em detalhes o MOB de tr&ecirc;s importantes inibidores revers&iacute;veis da cruza&iacute;na identificados pelo NEQUIMED: a dipeptidil-nitrila Neq0409 e os dois fragmentos moleculares Neq0147 e Neq0176. De modo a evitar a auto-prote&oacute;lise experimentada pela cruza&iacute;na nativa que torna desafiadora a cristaliza&ccedil;&atilde;o com inibidores de baixa afinidade como os fragmentos revers&iacute;veis, duas novas constru&ccedil;&otilde;es mutantes e inativas da cruza&iacute;na (a C25A e a C25S) foram desenvolvidas. A C25S foi validada como modelo cristalogr&aacute;fico representativo dado a coer&ecirc;ncia do MOB elucidado nesta enzima mutante e na cruza&iacute;na nativa para o inibidor mais estudado da cruza&iacute;na, o K777. A descri&ccedil;&atilde;o da presen&ccedil;a, orienta&ccedil;&atilde;o, conforma&ccedil;&atilde;o e modo de a&ccedil;&atilde;o no s&iacute;tio, al&eacute;m do completo padr&atilde;o de intera&ccedil;&otilde;es fornecidos por estas estruturas cristalinas, validaram ortogonalmente os MOB preditos e os m&eacute;todos de planejamento in silico usados no NEQUIMED, permitindo a identifica&ccedil;&atilde;o de inibidores muito mais potentes an&aacute;logos ao Neq0147 e ao Neq0409. O grupo 2-acetamidotiofeno-3-carboxamida do Neq0176 e o anel heteroc&iacute;clico de cinco membros baseado no 1,3,4-oxadiazol do Neq0147 foram identificados como alternativos aos tradicionais esqueletos pept&iacute;deo-mim&eacute;ticos. O impacto do efeito proteol&iacute;tico na qualidade e na resolu&ccedil;&atilde;o de estruturas cristalogr&aacute;ficas na cruza&iacute;na foi melhor compreendido a partir de duas estruturas de alta resolu&ccedil;&atilde;o obtidas para a cruza&iacute;na nativa em complexo com o metanotiossulfonato de metila (MMTS) e a iodoacetamida. Estes resultados permitiram compreender as bases experimentais para a cristaliza&ccedil;&atilde;o de inibidores revers&iacute;veis de baixa afinidade. Todos os resultados estruturais obtidos via cristalografia de raios X neste trabalho s&atilde;o &uacute;teis para mapear as bases estruturais essenciais para o planejamento de futuros inibidores mais potentes e seletivos da cruza&iacute;na. / Cruzain, the major Trypanosoma cruzi cysteine protease, is a validated therapeutic target for the search of new medicines for the treatment of Chagas disease. A myriad of inhibitors of this enzyme consists of covalent irreversible peptidomimetics whose development has been impaired due to potential off target effect and undesirable pharmacokinetic profile. Modern cheminformatic methods employed by The Medicinal Chemistry Group (NEQUIMED/IQSC/USP) were used to identify cruzain reversible inhibitors. Their optimization for more efficient compounds can be accomplished by the use of data and information gathered from computational and structural modes of interaction (MOB). In this doctoral thesis, the X-ray crystallography was used to describe in detail the MOB of three important new cruzain reversible inhibitors: the dipeptidil-nitrile Neq0409 and the two molecular fragmentos Neq0147 and Neq0176. In order to avoid cruzain self-proteolysis during crystallization with low affinity reversible inhibitors such as the identified fragments, two new mutant and inactive constructs of cruzain (the C25S and C25A) were designed to upholding the same properties of the wild type catalytic site. The C25S was validated as representative crystallographic model given the coherence of the MOB elucidated for the best-known and studied cruzain inhibitor, the K777. The description of the presence, orientation, conformation and mode of action at the site, besides the complete pattern of bimolecular interactions, provided by these crystalline structures, orthogonally validated the predicted in silico MOB and allowed the identification of other potent inhibitors analogous to the Neq0147 and the Neq0409. The 2-acetamidothiophene-3-carboxamide moiety (Neq0176) and heterocyclic five-membered ring based on the 1,3,4-oxadiazole (Neq0147) were thereby identified as attractive alternatives to traditional peptidomimetics. The impact of proteolytic effect on the quality and resolution of crystallographic structures in cruzain was best understood from two high-resolution structures obtained for the native cruzain in complex with methyl methanethiolsulfonate (MMTS) and iodoacetamide. These results allow the understanding of experimental basis for the crystallization with reversible inhibitors of low affinity such as fragments. All structural results obtained by X-ray crystallography together with the catalytic site depiction using GRID and SuperStar methods are useful for mapping the essential structural basis for the design of future more potent and selective cruzain inhibitors.

Including inherited genetic diseases, like lipoprotein lipase deficiency, and acquired diseases, such as cancer and HIV, gene therapy has the potential to treat or cure afflicted people by driving an affected cell to produce a therapeutic protein. Using primarily viral vectors, gene therapies are involved in a number of ongoing clinical trials and have already been approved by multiple international regulatory drug administrations for several diseases. However, viral vectors suffer from serious disadvantages including poor transduction of many cell types, immunogenicity, direct tissue toxicity and lack of targetability. Non-viral polymeric gene delivery vectors (polyplexes) provide an alternative solution but are limited by poor transfection efficiency and cytotoxicity. Microfluidic (MF) nano-precipitation is an emerging field in which researchers seek to tune the physicochemical properties of nanoparticles by controlling the flow regime during synthesis. Using this approach, several groups have demonstrated the successful production of enhanced polymeric gene delivery vectors. It has been shown that polyplexes created in the diffusive flow environment have a higher transfection efficiency and lower cytotoxicity. Other groups have demonstrated that charge-stabilizing polyplexes by sequentially adding polymers of alternating charges improves transfection efficiency and serum stability, also addressing major challenges to the clinical implementation of non-viral gene delivery vectors. To advance non-viral gene delivery towards clinical relevance, we have developed a microfluidic platform (MS) that produces conventional polyplexes with increased transfection efficiency and decreased toxicity and then extended this platform for the production of ternary polyplexes. This work involves first designing microfluidic devices using computational fluid dynamics (CFD), fabricating the devices, and validating the devices using fluorescence flow characterization and absorbance measurements of the resulting products. With an integrated separation mechanism, excess polyethylenimine (PEI) is removed from the outer regions of the stream leaving purified polyplexes that can go on to be used directly in transfections or be charge stabilized by addition of polyanions such as polyglutamic acid (PGA) for the creation of ternary polyplexes. Following the design portion of the research, the device was used to produce binary particle characterization was carried out and particle sizes, polydispersity and zeta potential of both conventional and MS polyplexes was compared. MS-produced polyplexes exhibited up to a 75% reduction in particle size compared to BM-produced polyplexes, while exhibiting little difference in zeta potential and polydispersity. A variety of standard biological assays were carried out to test the effects of the vectors on a variety of cell lines – and in this case the MS polyplexes proved to be both less toxic and have higher transfection efficiency in most cell lines. HeLa cells demonstrated the highest increase in transgene expression with a 150-fold increase when comparing to conventional bulk mixed polyplexes at the optimum formulation. A similar set of experiments were carried out with ternary polyplexes produced by the separation device. In this case it was shown that there were statistically significant increases in transfection efficiency for the MS-produced ternary polyplexes compared to BM-produced poyplexes, with a 23-fold increase in transfection activity at the optimum PEI/DNA ratio in MDAMB-231 cells. These MS-produced ternary polyplexes exhibited higher cell viability in many instances, a result that may be explained but the reduction in both free polymer and ghost particles.

The extensive and sometimes incorrect and noncompliant use of various types of antimicrobial agents has accelerated the development of antimicrobial resistance (AMR). In fact, AMR has become one of the greatest global threat to human health in this era. The broad-spectrum antibiotics aminoglycosides (AGs) display excellent potency against most Gram-negative bacteria, mycobacteria, and some Gram-positive bacteria, such as Staphylococcus aureus. The AG antibiotics amikacin, gentamicin, kanamycin, and tobramycin are still commonly prescribed in the U.S.A. for the treatment of serious infections. Unfortunately, bacteria evolve to acquire resistance to AGs via four different mechanisms: i) changing in membrane permeability to resist drugs from entering, ii) upregulating efflux pumps for active removal of intracellular AGs, iii) modifying the antimicrobial target(s) to prevent drugs binding to their targets, and iv) acquiring resistance enzymes to chemically inactivate the compounds. Amongst all, the acquisition of resistance enzymes, AG-modifying enzymes (AMEs), is the most common resistance mechanism identified. Depending on the chemistry each enzyme catalyzes, AMEs can be further divided into AG N-acetyltransferases (AACs), AG O-phosphotransferases (APHs), and AG O-nucleotidyltransferases. To overcome AME-related resistance, we need to better understand these resistance enzymes and further seek ways to either escape or inhibit their actions. In this dissertation, I summarized my efforts to characterize the AAC(6') domain and its mutant enzymes from a bifunctional AME, AAC(6')-Ie/APH(2")-Ia as well as another common AME, APH(3')-IIa. I also explained my attempt to inhibit the action of various AAC enzymes using metal salts. In an effort to explore the current resistance epidemic, I evaluated the resistance against carbapenem and AG antibiotics and the correlation between the resistance profiles and the AME genes in a collection of 122 Pseudomonas aeruginosa clinical isolates obtained from the University of Kentucky Hospital System. Besides tackling the resistance mechanisms in bacteria, I have also attempted to explore a new antifungal option by repurposing an existing antipsychotic drug, bromperidol, and a panel of its derivatives into a combination therapy with the azole antifungals against a variety of pathogenic yeasts and filamentous fungi.

An estimated 13.9% of Americans currently meet criteria for an alcohol (ethanol; EtOH) use disorder (AUD). While there are 4 medications approved by the Food and Drug Administration (FDA) to treat AUD, these treatments have demonstrated poor clinical efficacy. Our ongoing research program encompasses a multi-tiered screening of a natural product library and validation process to provide novel information about the mechanisms underlying EtOH-induced changes in neurobiology and to identify novel chemical scaffolds to be exploited in the development of pharmacological treatments for AUD in a rodent organotypic hippocampal slice culture model. Initial screens of several natural product compounds identified 3 compounds which attenuate 48 h EtOH-induced cytotoxicity in vitro. As analogs of natural products can be developed to have enhanced therapeutic potential over parental structures, Study 1 sought to extend on prior findings via the screening of several natural product analogs for their ability to attenuate EtOH-induced cytoxicity. Nine natural produce analogs demonstrated potent cytoprotective effects against EtOH-induced toxicity at 48 h. Several reports suggest EtOH-induced neurotoxicity may be secondary to the induction of persistent neuroimmune activation, and isoflavonoids have been shown to have effects on neuroimmune signaling. Thus, Study 2 compared the effects of compound 9b, an isoflavonoid analog identified in Study 1, to daidzein (DZ), a prototypical isoflavonoid, in the same 48 h model, with the addition of a neuroimmune component. Specifically, culture media was collected to assess for the release of the neuroimmune mediators HMGB1, TNF-α, IL-6, and IL-10 via ELISA. Compound 9b and DZ protected against EtOH-induced cytotoxicity at 48 h. EtOH exposure significantly increased secretion of HMGB1 and IL-6 into culture media at 48h. Compound 9b and DZ attenuated these increases at all concentrations tested. These results suggest potential neuroimmune modulating properties of isoflavonoids which may contribute to their neuroprotective effects against EtOH in vitro. These findings highlight the potential applications DZ and the novel isoflavonoid analog 9b for use in the treatment of AUD.

Introduction: Myocardial infarction (MI) remains the leading cause of morbidity and mortality worldwide. Induced by cardiomyocyte death, MI initiates a prolonged and uncontrolled inflammatory response which impairs the healing process. Immune cells, such as macrophages, play a central role in organizing the early post-MI inflammatory response and the subsequent repair phase. Two activation states of macrophages have been identified with distinct and complementary functions (inflammatory vs. reparatory). This bimodal pattern of macrophage activation is an attractive therapeutic target to favorably resolve post-MI inflammation and enhance recovery. It has been demonstrated that azithromycin (AZM), a commonly used antibiotic with immunomodulatory effects, polarizes macrophages towards the reparatory phenotype. AZM has an excellent safety profile and has been approved for human use. We hypothesize that AZM reduces inflammation and improves heart function in MI. Methods and results: In our initial studies, we demonstrated that oral free AZM (160 mg/kg daily for 7 days), initiated 3 days prior to MI, enhances post-MI cardiac recovery as a result of shifting macrophages to the reparatory state. We observed a significant reduction in mortality with AZM therapy. AZM-treated mice showed a significant decrease in pro-inflammatory and an increase in reparative macrophages, decreasing the pro-inflammatory/reparative macrophage ratio. Macrophage changes were associated with a significant decline in pro- and an increase in anti-inflammatory cytokines. Additionally, AZM treatment was correlated with a distinct decrease in neutrophil count due to apoptosis, a known signal for shifting macrophages towards the reparative phenotype. Finally, AZM treatment improved cardiac recovery, scar size, and angiogenesis. We designed this proof of concept study using pre-MI AZM therapy to achieve steady state levels prior to injury. Therefore, in our follow-up studies we targeted inflammatory macrophages using a non-Pegylated liposomal formulation of AZM (Lazm) which has been shown in multiple studies to promote drug efficacy and minimize off-target effects. To test the hypothesis that Lazm is more effective and safer than free AZM, low doses of free/liposomal AZM (10 or 40 mg/kg, administered intravenously) were initiated immediately after MI. We observed that Lazm induces early resolution of the post-MI inflammatory response as evidenced by switching of the activation state of monocytes/macrophages towards the reparatory phenotype. Neutrophils were substantially decreased, particularly pro-inflammatory neutrophils. Cytokine profiles were also shifted to the anti-inflammatory status with Lazm therapy. Taken together, AZM treatment resulted in a significant shift in macrophage activation towards the reparatory state. The shift in inflammatory state was accompanied by a decrease in apoptosis and infarct size in the injured heart, as well as enhanced angiogenesis and LV functional recovery in our long-term studies. In addition, Lazm was protective against off-target effects of AZM on the heart. Conclusion: This is the first evidence of a novel and clinically-relevant therapeutic strategy to modulate post-MI inflammation. We found that AZM reduces cardiac inflammation and improves adverse cardiac remodeling after infarction via promoting a shift of macrophage activation state. The overarching significance of this work is the modulation of sterile inflammation, which can be a viable therapeutic target in many conditions including stroke and heart attack. Additionally, this is the first study to demonstrate the immune modulation properties of liposomal AZM, which has wide potential therapeutic applications beyond the cardiovascular field. Importantly, liposomal formulation of AZM is protective from its cardiac off-target effects. Our findings strongly support clinical trials using AZM as a novel and clinically relevant therapeutic target to improve cardiac recovery and reduce heart failure post-MI in humans.