Previously, gp16, the ATPase protein of phi29 DNA packaging motor, was an enigma due to its tendency to form multiple oligomeric states. Recently we employed new methodologies to decipher both its stoichiometry and also the mechanism in which the protein functions to hydrolyze ATP and provide the driving force for DNA packaging. The oligomeric states were determined by biochemical and biophysical approaches. Contrary to many reported intriguing models of viral DNA packaging, it was found that phi29 DNA packaging motor permits the translocation of DNA unidirectionally and driven cooperatively by three rings of defined shape. The mechanism for the generation of force and the role of adenosine and phosphate in motor motion were demonstrated. It was concluded that phi29 genomic DNA is pushed to traverse the motor channel section by section with the aid of ATPase gp16, similar to the hexameric AAA+ family in the translocation of dsDNA. A new model of "Push through a One-way Valve" for the mechanism of viral DNA packaging motor was coined to describe the coordinated interaction among the hexameric packaging ATPase gp16 and the revolution mechanism of the dodecameric channel which serves as a control device to regulate the directional movement of dsDNA.

<p>Artemisia Afra, a popular South African traditional herbal medicine is commonly administered as a tea infusion of the leaves. However, clinical trials proving it safety and efficacy are lacking mainly due to the absence of good quality dosage forms and credible placebos for the plant. The objectives of this study were to prepare a standardized preparation of the plant leaves and freeze-dried aqueous extract powder of the leaves, in a tea bag dosage form and to design and prepare credible placebos for these plant materials.</p>

The enzyme 11β-Hydroxysteroid Dehydrogenase 1 (11β-HSD1) catalyses the intracellular biosynthesis of the active glucocorticoid cortisol. Tissue specific dysregulation of the enzyme has been implicated in the development of metabolic syndrome and other associated diseases. Experiments with transgenic mice and prototype inhibitors show that inhibition of 11β-HSD1 in visceral adipose tissue and liver leads to a resistance of diet-induced hyperglycemia and a favourable lipid and lipoprotein profile as compared to controls. 11β-HSD1 inhibition has thus been proposed as an effective strategy to decrease intracellular glucocorticoid levels without affecting circulating glucocorticoid levels that are essential for stress responses. The clinical development of selective and potent drugs has therefore become a priority. In this research, a process of virtual screening employing the novel algorithm UFSRAT (Ultra Fast Shape Recognition with Atom Types) was used to discover compounds which had specific physicochemical and spatial atomic parameters deemed essential for inhibition of 11β-HSD1. The top scoring compounds were assayed for inhibitory activity against recombinant human and mouse enzyme, using a fluorescence spectroscopy approach. In addition, HEK-293 cell based assays with either human, mouse or rat enzymes were carried out using a scintillation proximity assay (SPA). The most potent compound competitively inhibited human 11β-HSD1 with a Kiapp value of 51 nM. Recombinant mouse and human enzyme were expressed, purified and characterised and used in a series of ligand binding assays. Further to this, an X-ray crystal structure of mouse 11β-HSD1 in complex with a tight binding inhibitor – carbenoxolone was solved.

<p>This thesis focuses on the development of algorithms that will allow protein design calculations to incorporate more realistic modeling assumptions. Protein design algorithms search large sequence spaces for protein sequences that are biologically and medically useful. Better modeling could improve the chance of success in designs and expand the range of problems to which these algorithms are applied. I have developed algorithms to improve modeling of backbone flexibility (DEEPer) and of more extensive continuous flexibility in general (EPIC and LUTE). I’ve also developed algorithms to perform multistate designs, which account for effects like specificity, with provable guarantees of accuracy (COMETS), and to accommodate a wider range of energy functions in design (EPIC and LUTE).</p> / Dissertation

This dissertation aimed at developing an inhibitor strategy to improve the oral bioavailability (Foral) and systemic exposure (AUC∞) of buprenorphine (BUP) as well as reduce the variability associated with them. Twenty-seven generally recognized as safe (GRAS) compounds or dietary substances were evaluated for their potential to inhibit the oxidative and conjugative metabolism of BUP, using pooled human intestinal and liver microsomes. In both the organs, oxidation appeared to be the major metabolic pathway with a 6 fold (intestine) and 4 fold (liver) higher intrinsic clearance than glucuronidation. Buprenorphine was predicted to show low and variable Foral, AUC∞, and a large total clearance. The biorelevant solubilities of 5 preferred inhibitors were incorporated in the final model. An inhibitor dosing strategy was identified to increase Foral and reduce the variability in oral BUP AUC∞. These results demonstrate the feasibility of the approach of using GRAS or dietary compounds to inhibit the presystemic metabolism of buprenorphine and thus improve its oral bioavailability. This inhibitor strategy has promising applicability to a variety of drugs suffering from low and variable oral bioavailability due to extensive presystemic oxidative and conjugative metabolism.

The overall aim of the research is to develop a computational platform based on HINT paradigm for manipulating, predicting and analyzing biomacromolecular-ligand structure. A second synergistic goal is to apply the above methodology to design novel and potent anti-cancer agents. The crucial role of the microtubule in cell division has identified tubulin as an interesting target for the development of therapeutics for cancer. Pyrrole-containing molecules derived from nature have proven to be particularly useful as lead compounds for drug development. We have designed and developed a series of substituted pyrroles that inhibit growth and promote death of breast tumor cells at nM and μM concentrations in human breast tumor cell lines. In another project, stilbene analogs were designed and developed as microtubule depolymerizing agents that showed anti-leukemic activity. A molecular modeling study was carried out to accurately represent the complex structure and the binding mode of a new class of tubulin inhibitors that bind at the αβ-tubulin colchicine site. These studies coupled with HINT interaction analyses were able to describe the complex structure and the binding modes of inhibitors. Qualitative analyses of the results showed general agreement with the experimental in vitro biological activity for these derivatives. Consequently, we have been designing new analogs that can be synthesized and tested; we believe that these molecules will be highly selective against cancer cells with minimal toxicity to the host tissue. Another goal of our research is to develop computational tools for drug design. The development and implementation of a novel cavity detection algorithm is also reported and discussed. The algorithm named VICE (Vectorial Identification of Cavity Extents) utilizes HINT toolkit functions to identify and delineate a binding pocket in a protein. The program is based on geometric criteria and applies simple integer grid maps to delineate binding sites. The algorithm was extensively tested on a diverse set of proteins and detects binding pockets of different shapes and sizes. The study also implemented the computational titration algorithm to understand the complexity of ligand binding and protonation state in the active site of HIV-1 protease. The Computational titration algorithm is a powerful tool for understanding ligand binding in a complex biochemical environment and allows generating hypothesis on the best model for binding.

Phenylephrine (PE) is the most commonly used over-the-counter nasal decongestant. The problem associated with phenylephrine is that it undergoes extensive first pass metabolism in the intestinal gut wall leading to its poor and variable oral bioavailability. This research project aims at developing strategies in order to increase the oral bioavailability of PE by co-administration of GRAS compounds. A HILIC assay method was developed to detect the parent drug, phenylephrine (PE) and its sulfate metabolite (PES).The enzyme kinetic studies were done with phenolic dietary or GRAS compounds using LS180 human intestinal cell model, recombinant SULT enzymes and human intestinal cytosol (HIC). From the screening studies done, one inhibitor was selected in order to study the mechanism of inhibition. In conclusion the studies done in vitro provided a basis in order to predict in vivo intrinsic clearance through the sulfation pathway.

Arf1 est une petite protéine G (pG), essentiellement impliquée dans le trafic vésiculaire. Arf1 oscille entre deux conformations, l'une active liée au GTP et l'autre inactive associée au GDP. Arno est un des facteurs d'échange (GEF) capable d'activer Arf1 en stimulant l'échange GDP/GTP. Suractivée dans les cellules invasives du cancer du sein, Arf1 joue un rôle important dans la migration et la prolifération des cellules cancéreuses.Le but de ma thèse s'inscrit dans l'étude et la modulation de l'interaction pG-GEF, et plus spécifiquement, le couple Arf1-Arno. Mon travail a été planifié autour de deux axes: (1) L'étude fine de l'interaction entre Arf1 et Arno, et sa modulation avec un inhibiteur connu la Bréféldine A (BFA). (2) La mise en place d'une stratégie de conception d'inhibiteurs de l'interaction protéine-protéine du couple Arf1-Arno.Dans un premier temps, nous avons mis en place une méthode basée sur la résonance plasmonique de surface (SPR) permettant la détermination des paramètres cinétiques de l'interaction entre Arf1 et Arno. Nous avons précisé aussi les conséquences des partenaires allostériques (GDP, GTP, et Mg2+) et de la BFA sur les paramètres cinétiques de l'interaction. Ceci a permis une analyse fine de la régulation allostérique et du mode d'action de la BFA. Appliquée à d'autres inhibiteurs, cette méthode permettra d'examiner leur mécanisme d'inhibition.Dans la deuxième partie j'expose, la stratégie que nous avons utilisé pour la conception rationnelle d'inhibiteur de l'interaction entre Arf1 et Arno. Elle est basée sur le criblage virtuel de fragments au niveau des résidus clé « hotspots » de l'interaction, la validation des molécules-touches par des techniques biophysiques, et l'élimination de molécules artefacts. Les structures des complexes fragments-Arno ont été résolues, ce qui confirme la validité de cette stratégie ouvrant la voie vers l'optimisation moléculaire pour obtenir des inhibiteurs plus efficaces. / Arf1 is a small GTPases, essentially involved in the vesicular traffic. Arf1 switch between two conformations, an active form bound to GTP and an inactive form bound to GDP. Arno is one of the exchange factors (GEF) that can activate Arf1, through its catalytic Sec7 domain, promoting the exchange of GDP by GTP. Activated in breast cancer cells, Arf1 plays an important role in the migration and proliferation of cancer cells.The aim of my thesis was the study and the modulation of the interaction between small G proteins and their GEFs, more precisely the Arf1-Arno interaction. My work has been planned around two axes: (1) the study of the interaction between Arf1 and Arno, and its modulation with a known inhibitor Brefeldin A (BFA). (2) The development of a rational strategy for designing inhibitors of protein-protein interaction for the Arf1-Arno complex.In the first part of my PhD work, we set up a Surface Plasmon Resonance (SPR) method allowing to determine the kinetic parameters of the interaction between Arf1 and Arno. We also studied the effects of allosteric partners such as GDP, GTP and Mg2+ as well as the known uncompetitive inhibitor (Brefeldin A). This SPR approach allowed a very informative analysis at qualitative and quantitative levels of the various complexes taking place during the exchange reaction that should help to solve the inhibitory mechanism for the known inhibitors reported in the literature. In the second part of my thesis, we propose a strategy for targeting the interaction between Arf1and Arno. This approach is based on virtual screening of fragments at hotspot regions. Using biophysical techniques such fluorescence techniques, SPR, NMR and X-Ray crystallography, we identified and validated Hits, showing by crystallographic structural data their modes of interaction with the target protein Arno. A fluorescence polarization test was also developed to identify false positive fragments to eliminate promiscuous aggregators. Taken together, our work proposes a method based on SPR allowing the study of known inhibitors of GEFs, understanding at molecular level their mode of action. We also propose a general strategy for finding Hit fragments that designing competitive inhibitor of the interaction small G protein with its GEFs, that can be the scaffold for designing more powerful inhibitors.

A malária, doença causada pelo protozoário do gênero Plasmodium, está entre as doenças que mais causam mortes os países subdesenvolvidosn. O hospedeiro é infectado por meio da picada do mosquito do gênero Anopheles, que introduz o parasita durante a hematofagia. As formas mais graves são causadas pelo Plasmodium vivax e o Plasmodium falciparum. As regiões mais afetadas por estas formas são África Subsaariana, Ásia, América Central e Sul. Desde o começo do século XXI, a Organização Mundial de Saúde (OMS) busca erradicar a doença, porém o P.falciparum se mostrou resistente aos fármacos antimaláricos existentes, dificultando a eficácia do tratamento. Isto, entre outros fatores, como mortalidade e alto índice de infecção, tornam necessárias novas pesquisas para a descoberta de novos fármacos mais seguros e eficazes contra a malária. Estudos têm mostrado como um alvo promissor para a criação de novos antimaláricos, a cisteína protease falcipaína, a qual se apresenta em três isoformas no parasita, sendo elas, falcipaína 1, 2 e 3. A falcipaína 2 está ligada com a hidrólise da hemoglobina, e seus inibidores vem sendo estudados como alternativas na busca de agentes antimaláricos. Derivados de semicarbazona, tais como o nitrofural e o hidroximetilnitrofural demonstraram atividade inibitória de cisteíno proteases parasitárias. Utilizando estratégias modernas de planejamento de fármacos e por meio da integração entre técnicas computacionais e experimentais, realizou-se o planejamento, síntese e avaliação biológica de compostos derivados dos ditiocarbazatos e tiossemicarbazonas, bioisosteros de semicarbazona, como inibidores da cisteíno protease falcipaína 2, no intuito de obter novos antimaláricos. Aplicaram-se técnicas de modelagem molecular em três séries de compostos (A, B e C), sendo a A e B derivados dos ditiocarbazatos e a C das tiossemicarbazonas. Estes estudos sugerem, três compostos da série A, quatro na série B e três na C com maior potencial para inibição da falcipaína 2. Isso devido aos resultados teóricos indicarem condições favoráveis ao ataque nucleofílico da cisteína 42 catalítica da falcipaína 2 às tiocarbonilass presentes nos compostos planejados. Estes derivados foram sintetizados, analisados por espectroscopia de ressonância magnética de 1H e 13C, espectroscopia de IV, ponto de fusão e pureza caracterizando sua formação. Após a obtenção, os compostos foram enviados para ensaios biológicos frente ao parasita P. falciparum. Os compostos testados não apresentaram inibição, porém é sabido que muitos inibidores enzimáticos não são ativos contra o parasita mesmo tendo alta potência contra a enzima, isto devido às barreiras a serem ultrapassadas até chegar ao alvo bioquímico, deste modo faz-se necessário ensaios contra a enzima para validar nossa hipótese. / Malaria, a disease caused by the protozoan of the genus Plasmodium, is among the most deadly diseases in poor countries. The host is infected through the bite of the mosquito of the genus ,i>Anopheles, which introduces the parasite during hematophagy. The most severe forms are caused by Plasmodium vivax and Plasmodium falciparum. The regions most affected by these forms are Sub-Saharan Africa, Asia, Central and South America. Since the beginning of the 21st century, the World Health Organization (WHO) has sought to eradicate the disease, but P. falciparum has been resistant to antimalarial drugs treatment. Among other factors, such as mortality and high infection rates, new research is needed to find new, safer and more effective drugs against malaria. Studies have shown as a promising target for the creation of new antimalarial drugs, the cysteine protease falcipain, which is present in three isoforms in the parasite: falcipain 1, 2 and 3. Falcipain 2 is linked to the hydrolysis of hemoglobin, and its inhibitors have been studied as alternatives in the search for antimalarial agents. Derivatives of semicarbazone such as nitrofural and hydroxymethylnitrofural demonstrated inhibitory activity of parasitic cysteine proteases. Using modern strategies for drug design and the integration of computational and experimental techniques, the design, synthesis and biological evaluation of compounds derived from dithiocarbazates and thiossemicarbazones, semicarbazone biosynthesis as inhibitors of cysteine protease falcipain 2 were carried out in order to new antimalarials. Molecular modeling studies were performed in three series of compounds (A, B and C), with A and B being derived from dithiocarbazates and C from thiossemicarbazones. These studies suggest three compounds in the A series, four in the B series, and three in the C group with the greatest potential for inhibition of falcipain 2. This is due to the theoretical results indicating favorable conditions for the nucleophilic attack of the catalytic cysteine of falcipain 2 on thionyls present in the compounds planned. These derivatives were synthesized, analyzed by 1H and 13C magnetic resonance spectroscopy, IR spectroscopy and melting point, characterizing their formation. After being obtained, the compounds were sent for biological assays against the P. falciparum parasite. The compounds tested did not show inhibition, but it is known that many enzyme inhibitors are not active against the parasite even though they have high potency against the enzyme, this is due to the barriers to be overcome until reaching the biochemical target, thus enzyme to validate our hypothesis.

A Doença de Chagas, endêmica na América Latina, é causada pelo parasito tripanossomatídeo Trypanosoma cruzi e atualmente já se espalha para o restante do mundo devido à migração humana. Os dois medicamentos disponíveis para o tratamento dessa doença, o Nifurtimox, (banido do Brasil), e o Benzonidazol, são eficazes somente na etapa aguda da doença e possuem efeitos colaterais severos. Recentemente, três novas substâncias para o tratamento chegaram à fase clínica de testes contra essa doença, mas ainda é necessária a pesquisa de novas moléculas contra esse parasito. A enzima Gliceraldeído-3-fosfato Desidrogenase (GAPDH) foi selecionada como alvo para busca de moléculas potencialmente tripanossomicidas. De forma a inibir essa enzima, a busca de moléculas baseou-se na abordagem de fragmentos moleculares para encontrar substâncias com elevada eficiência de ligante. A partir de um banco de dados comercial de 500 mil moléculas, filtros moleculares de solubilidade e da Regra dos Três foram aplicados para montar uma biblioteca focalizada de moléculas. Essa biblioteca foi submetida a estudos integrados baseados na estrutura do alvo macromolecular (docagem) e do substrato da enzima (similaridade química e eletrostática) e a inspeção visual dos fragmentos bem classificados em ambas técnicas foi realizada de modo a selecionar cinco compostos de classes químicas diversas. Essas substâncias foram submetidas a ensaios enzimáticos in vitro por meio de espectroscopia de fluorescência, sendo encontrado então um fragmento com Ki de (425 &plusmn; 53) &mu;M e eficiência de ligante de 0,33, valor bastante promissor para abordagem baseada em fragmentos moleculares. Estudos de simulação por Dinâmica Molecular (MD) foram feitos para as cinco moléculas adquiridas, com energia de interação ligante-enzima calculada usando o método MM-GB/SA. A classificação das moléculas por essa energia foi idêntica à obtida experimentalmente. Além disso, a MD possibilitou a predição de modo de interação dos fragmentos no sítio ativo da TcGAPDH e a identificação de uma nova cavidade passível de modulação de sua atividade. Uma segunda série de fragmentos foi selecionada baseada no fragmento ativo de modo a construir uma relação estrutura-atividade (SAR) teórica por MD. A SAR sugere que a presença de um átomo nitrogênio capaz de doar ligações de hidrogênio é importante para a interação, com o resíduo de aminoácido Asp210. Este resíduo de aminoácido desponta como um possível ponto de seletividade para a enzima humana, que possui uma leucina nessa posição. Além disso, a posição na substituição do anel central também está diretamente relacionada à interação da molécula com a enzima, com uma substituição 2,3 em um anel de cinco membros a mais favorável. Este trabalho identificou pela primeira vez um fragmento molecular com alta eficiência de ligante para a enzima TcGAPDH, com o auxílio do uso conjunto de técnicas baseadas na estrutura do ligante e do alvo, para seleção de moléculas, e espectroscopia de fluorescência para identificação de atividade inibitória frente à enzima. Método de simulação por MD conseguiu reproduzir os resultados experimentais e prover informações teóricas de SAR para o composto ativo. / Chagas disease is a parasitic illness endemic in Latin America caused by the trypanosomatid parasite Trypanosoma cruzi that spreads around the world due to people migration. Nowadays, Benznidazole and Nifurtimox (banned in Brazil), are used for the treatment of this disease but causes severe side effects to patients. Recently, three new molecules have reached clínical trials phase in the development of drugs against Chagas disease but it is still necessary to develop new drugs. In this studies, the enzyme Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) was used as a target for the search of new antitrypanosomatid molecules. It belongs to the glycolytic pathway, the major one for parasite\'s energy generation. With the aim searching a new molecule that inhibits this enzyme, the fragment-based approach guided the search of molecules with high ligand efficiency. A focused compound library was assembled from a database of 500,000 molecules using molecular and solubility filters and the Rule of Three. The integrated use of ligand (chemical and electrostatic similarity) and target (molecular docking) based drug design was carried out to rank the molecular fragments by a consensual score. Through visual inspection of the top 500 molecules five diverse fragments were selected for the in vitro enzymatic assays using fluorescence spectroscopy. One of these molecules shows a Ki equals to (425 &plusmn; 53) &mu;M and ligand efficiency equals to 0,33, a promising value for the fragment-based approach. Additionally, Molecular Dynamics simulations (MD) were carried out with these fragments and the predicted energy of interaction for fragment-enzyme complex was able to rank the molecules as using the experimental results. Furthermore, the MD was useful to predict the mode of interaction of the fragments in the active site of enzyme and to reveal a new cavity close to the substrate binding site. A second generation of compounds was selected based on the structure of the active fragment to construct theoretical structure-activity relationship (SAR) using MD. SAR indicates that the presence of a nitrogen with hydrogen-bond donor property is important to the interaction, making hydrogen-bonding with the amino acid residue Asp210. In addition, MD shows the influence of different substituent posítion in the central ring in the energy of the interaction, with a 2,3 substitution at five-atom ring the most favorable. This study identifies the first molecular fragment with high ligand efficiency for the enzyme TcGAPDH, with the combined use of ligand and target-based tools and fluorescence spectroscopy, for selection and identification of active compounds against the enzyme. MD was able to reproduce experimental results and generate theoretical information of SAR to the active molecular fragment.