Structural investigations on two mycobacterial enzymes were carried out. Tuberculosis still remains a major threat to mankind even though drugs against it have been in use for many decades. The emergence of drug resistant strains of the bacteria calls for the identification of new targets based on which new drugs can be developed to combat the disease. A thorough understanding of the functioning of the target molecules is essential for this approach. We have taken up the structural studies on two such molecules, aspartic proteinases and adenylyl cyclases, of Mycobacterium tuberculosis with a view to obtain insights into their mechanisms of action at the atomic level. The work presented in the thesis includes (i) the identification, cloning, expression, purification and structure determination of a putative aspartic proteinase domain of M. tuberculosis and (ii) the crystal structure of an adenylyl cyclase of M. tuberculosis and its mutant; and also of an adenylyl cyclase from M. avium. Chapter 1 presents an overview of aspartic proteinases and nucleotide cyclases with an emphasis on their structural features. The methods employed during the course of the present work are described in Chapter 2. Work on the putative aspartic proteinase domain identified in M. tuberculosis is presented in Chapter 3. The structure of the aspartic proteinase domain is the first structural report of such domain from any bacteria. A search in the genome of M. tuberculosis showed a weak similarity to the HIV aspartic proteinase sequence. This region corresponds to the C-terminal domain of a PE family protein in M. tuberculosis. The presence of two signature motifs, DTG and DSG, of aspartic proteinases in the full sequence of this domain encouraged us to take up further studies on this domain. Previous reports identifying the protein as a surface antigen and our findings on the occurrence of similar domains in two other PE proteins of M. tuberculosis and also in other pathological strains of Mycobacteria indicated that these domains probably play an important role in infecting the host. The crystal structure of one of the domains showed that it has a pepsin-like fold and the catalytic site architecture of known aspartic proteinases. However, no proteolytic activity was detected. The size of the molecule is intermediate to eukaryotic pepsins and the homodimeric retroviral pepsins. A close examination of the binding site revealed subtle differences when compared to the active enzyme structures. Appropriate mutations of some of the residues in this region to convert it to an active enzyme did not make it active. Once the in vivo function of these putative aspartic proteinase domains is established, their potential to act as drug targets can be probed as the PE proteins are present exclusively in pathogenic Mycobacteria. As part of an ongoing project on adenylyl cyclases of Mycobacteria, we have taken up the structure analysis of the catalytic domains of two adenylyl cyclases; Rv1625c from M. tuberculosis and Ma1120 from M. avium. This work is described in Chapter 4. The wild-type of Rv1625c crystallized as a domain swapped head to head inactive dimer even though it is an active dimer in solution and expected to have a head to tail arrangement as in the previously reported structures of the active forms of the enzyme. Mutation of a phenylalanine residue presumed to occur at the subunit interface of the active dimeric structure of the enzyme to an arginine residue, a conserved residue of guanylyl cyclases, resulted in reduced adenylyl cyclase activity. This mutant crystallized as a monomer though it was expected to be an active dimer. Similarly, Ma1120 also has a monomeric structure in the crystal in spite of showing activity in solution. Though our aim was to capture the active dimers in the crystalline state we did not succeed in this effort in any of the three cases. The catalytic reaction probably takes place very rapidly with the formation of a transient active form of the dimer which cannot be easily crystallized. However, the analysis revealed new structures which are likely to represent the stable states of the enzyme when it is required to stay inactive in certain conditions. We have also established that the N-terminal segments of the enzyme, a loop at the dimeric interface and external factors like pH are involved in determining the oligomeric status of the enzyme thereby regulating its function. Publications 1 Crystal structure of a putative aspartic proteinase domain of the Mycobacterium tuberculosis cell surface antigen PE_PGRS16; Deivanayaga V. Barathy and K. Suguna; FEBS Open Bio (In Press) 2 New structural forms of mycobacterial adenylyl cyclases (in preparation)

In everybody’s lives, there are strong emotional or surprising events that, for being special, are vividly remembered for a lifetime. Sometimes, these memories include one-shot images or details of associated daily life events that, for being ordinary, should have been rapidly forgotten. Why and how does the brain form and retain detailed memories of trivial events? The synaptic tagging and capture (STC) hypothesis of memory formation (Frey & Morris, Nature 1997) provides a theoretical framework that might explain the formation of these flashbulb memories at a cellular level. The hypothesis suggests that strong events, producing long-lasting memories, might stabilise memory for weak events by up-regulating the synthesis of late-phase plasticity-related proteins in neurons encoding memory traces for both events. This thesis tests this prediction of the STC hypothesis during the formation of long-term place memory in rodents. First, two new behavioural tasks are developed which provide sensitive measures of rapidly acquired place memory persistence - a new one-trial place memory task in the “event arena” and a modified delayed matching-to-place (DMP) protocol in the watermaze. Persistence of place memory is assessed and compared in these tasks. Given the important role of NMDA receptor activation during STC mechanisms, the contribution of NMDA and AMPA receptor activation in the hippocampus for the encoding and retrieval of place memory, respectively, is also established. Finally, weak and strong encoding events, leading to the formation of either shortor long-lasting place memory in the watermaze DMP task, are characterized. A second series of experiments investigates the possibility of synergistic interactions between different encoding events that occur in two different watermazes. First, weak and strong encoding events are arranged to occur within a short time-window to test behavioural analogues of the “strong-before-weak” and “weak-before-strong” STC paradigms characterised in electrophysiological experiments in rat hippocampal slices (Frey and Morris, 1997, 1998b). Then, after establishing i) the time course and local specificity of protein synthesis inhibition by intra-hippocampal infusion of anisomycin in vivo, ii) the dependence of long-term memory for strong encoding events on protein synthesis in the hippocampus, and iii) the induction of transcriptional and translational mechanisms in the hippocampus by strong encoding events, a behavioural analogue of the “strong-before-strong” STC paradigm (Frey and Morris, 1997) is also investigated. The results of these experiments are supportive of i) a role for hippocampal NMDA receptor-mediated synaptic plasticity in the encoding of rapidly acquired place memory; ii) a role for hippocampal AMPA receptor-mediated synaptic transmission in both encoding and retrieval of memory; and iii) a role for transcriptional and translational mechanisms in the hippocampus in the stabilisation of place memory. However, no evidence could be found supporting the involvement of synaptic tagging and capture mechanisms during the formation of long-lasting place memory.

The hydrogenation of β-ketoesters over chirally modified Ni catalysts is a celebrated and thoroughly researched example of an enantioselective heterogeneous catalytic reaction. Enantioselective heterogeneous processes, although extremely attractive in terms of fewer complications in the separation of products from the catalyst, are hindered in their viability as industrial applications due to the lack of detailed knowledge on how chirality is conferred to the metal surface. Surface science techniques have afforded substantial progress into determining mechanisms between modifier, reactant and catalyst to explain the source of enantioselectivity of the system. In this study, a combination of solution and ultra-high vacuum (UHV)-based experiments allow a more realistic interpretation of the surface chemistry underpinning the catalytic reaction as the key step in achieving enantioselective performance is the adsorption of chiral modifiers from solution. The behaviour of (S)-aspartic acid and (S)-lysine on Ni{111} and their interaction with the prochiral β-ketoester methylacetoacetate is investigated in this study to understand their potential as chiral modifiers for the system. In UHV, scanning tunnelling microscopy (STM), reflection absorption infrared spectroscopy (RAIRS), and temperature programmed desorption (TPD) are used to analyse the conformation and order of the amino acids on the metal, and their thermal stability. Additionally, liquid-solid interface RAIRS and X-ray photoelectron spectroscopy (XPS) are used to examine the modified Ni surface, prepared under aqueous conditions, to give an accurate representation of the catalytic studies. It has been found highly likely that, for (S)-aspartic acid modified Ni{111}, enantioselective sites exist at step or step/kink defects, formed by corrosive leaching of the Ni substrate. Conversely, lysine appears to bind with a high sticking probability to Ni, in the form of lysine islands, and does not appear to etch the Ni chirally. Finally, similar experiments have been carried out on Au{111}, where lysine was found to chiral restructure the surface and form nanofingers, and 2D Ni clusters grown on Au{111} in order to investigate the formation of possible metal-organic frameworks.

The blood fluke Schistosoma mansoni and the hard tick Ixodes ricinus produce an aspartic protease cathepsin D which initiates degradation of hemoglobin, their key nutrient. First, in the presented work, the protocol for refolding and activation of the zymogen of cathepsin D from I. ricinus (IrCatD) was developed and optimized. In acidic pH the propeptide of IrCatD zymogen was removed by an auto-activation mechanism. Further, a kinetic assay with fluorogenic substrates was employed to study functional properties of IrCatD including pH optimum, substrate and inhibition specificities. Second, two isoforms of cathepsin D from S. mansoni (SmCatD) were produced using recombinant expression in E. coli. These recombinant proteases were isolated from inclusion bodies using affinity chromatography under denaturating conditions, and protocol for their refolding was developed and optimized. The studied aspartic proteases are pharmacological targets: inhibitors of SmCatD represent potential chemotherapeutics for the treatment of schistosomiasis, and IrCatD is a candidate antigen for the development of novel anti-tick vaccines.

La cardosine A est une protéase aspartique identifiée il y a plus de 20 ans dans les cellules du chardon Cynara cardunculus. Sa distribution dans tous les tissus de la plante et ses caractéristiques enzymatiques ont été caractérisées par approches biochimiques. La cardosine A a des fonctions essentielles dans la reproduction, la mobilisation de réserves protéiques, et le remaniement de membranes. Pour assumer ces différentes fonctions, la cardosine A doit pouvoir transiter et s’accumuler dans différents compartiments intracellulaires : vacuole de stockage, vacuoles lytiques, ou autres compartiments membranaires. Il n’y a cependant que très peu de données disponibles sur les mécanismes de biosynthèse, de tri, de transport et d’adressage aux différents compartiments cellulaires. De récents travaux suggèrent que l’expression en modèle hétérologue pourrait être utilisée pour une meilleure compréhension de la biologie intracellulaire de la cardosine A. Les résultats de cette étude montrent que l’expression transitoire de la cardosine A dans les feuilles de Nicotiana tabacum est un bon modèle expérimental pour explorer le transport de la cardosine A dans la cellule. En effet dans ce système les mécanismes de maturation et de transport de la protéine à la vacuole sont conservés. De plus, une lignée stable d’Arabidopsis thaliana exprimant la cardosine A sous promoteur inductible s’est également avérée un bon modèle d’étude du transport intracellulaire de la cardosine A. L’utilisation de ces systèmes hétérologues a permis de combiner l’expression de formes mutées de la cardosine A (dans lesquelles des séquences spécifiques ou des acides aminés avaient été tronqués ou modifiés) avec des approches de biochimie et d’imagerie cellulaire pour identifier des signatures moléculaires responsables de l’adressage vacuolaire de la protéine. Nos résultats montrent que la cardosine A a deux déterminants vacuolaires dans sa séquence protéique : le domaine “PSI”, qui définit un déterminant d’adressage vacuolaire original et propre à certaines protéases aspartiques, et un peptide C-terminal appartenant à la classe bien définie des ctVSD. De plus, les résultats montrent que la présence de ces deux déterminants illustre la capacité d’emprunter deux routes distinctes pour atteindre la vacuole : le domaine PSI peut permettre d’attendre la vacuole sans passer par le Golgi, tandis que le domaine C-ter négocie un transport classique Reticulum, Golgi, Prévacuole, Vacuole. Cette capacité à choisir deux routes différentes n’est pas observée pour la cardosine B, autre protéase aspartique du chardon présentant une haute homologie de séquence avec la cardosine A. Pour expliquer cette capacité de la cardosine A à emprunter deux routes vacuolaires différentes, l’hypothèse d’un rôle possible de la glycosylation dans le tri des protéines entre les deux routes vacuolaires est alors étudiée. L’expression de la cardosine A dans les graines en germination d’Arabidopsis thaliana révèle que la protéine peut s’accumuler d’une manière différentielle dans les graines en absence de germination ou pendant la germination, tout au long du système endomembranaire jusqu’à la vacuole de réserve ou dans les vacuoles lytiques en formation. Les expériences de blocage de transport du Reticulum au Golgi n’ont pas permis de conclure d’une manière certaine si les accumulations vacuolaires dérivaient d’un transport pouvant court-circuiter le Golgi comme dans les feuilles de Nicotiana. Au total, la cardosine A constitue une protéine modèle pour étudier les transports vacuolaires chez Nicotiana tabacum and Arabidopsis thaliana, deux systèmes hétérologues qui permettent de développer des méthodes complémentaires pour une exploration fonctionnelle des mécanismes impliqués. Cette étude permet de contribuer à une meilleure connaissance de la biologie des cardosines en particulier, et des protéases aspartiques en général. / The aspartic proteinase cardosin A is a vacuolar enzyme found to accumulate in protein storage vacuoles and lytic vacuoles in the flowers and in protein bodies in seeds of the native plant cardoon. Cardosin A has been first isolated almost two decades ago and has been extensively characterized since, both in terms of distribution within the tissues and of enzyme biochemistry. In the native system, several roles have been addressed to cardosin A in reproduction, mobilization of reserves and membrane remodeling. To participate in such diverse events, cardosin A must accumulate and travel to different compartments inside the cell: protein storage vacuoles, lytic vacuoles, cytoplasmic membrane (and eventually outside the cell). However, not much information is available regarding cardosin A biogenesis, sorting or trafficking to the different compartments. Recent studies have approached the expression of cardosin A in Arabidopsis thaliana and Nicotiana tabacum. These preliminary observations were the starting point of a detailed study of cardosin A expression, localisation, sorting and trafficking routes, resourcing to several and very different methods. It has been showed that transient expression of cardosin A in Nicotiana tabacum leaf is a good system to explore cardosin A trafficking inside the cell, as the protein is processed in a similar manner as the control and accumulates in the vacuole. Furthermore, an Arabidopsis thaliana line expressing cardosin A under an inducible promoter was explored to understand cardosin A dynamics in terms of vacuolar accumulation during seed germination events. Similarly to the Nicotiana tabacum one, this system was also validated for cardosin A expression and it allowed to conclude that the protein’s expression did not retrieved any phenotype to the cells or individuals. However, experiments conducted in BY-2 cells revealed to be inconclusive since cardosin A expression in this system is not predictable. The data obtained along this work using several cardosin A mutated forms, lacking specific domains or point-mutated, allowed to determine that cardosin A has two Vacuolar Sorting Determinants in its protein sequence: the PSI, an unconventional sorting determinant, and the C-terminal peptide, a C-terminus sorting determinant by definition. Furthermore, it was also demonstrated that each domain represents a different route to the vacuole: the PSI bypasses the Golgi Apparatus and the C-terminal peptide follows a classic Endoplasmic Reticulum-Golgi Apparatus-Prevacuole route to the vacuole. This difference in the trafficking routes is not observed for cardosin B sorting determinants as both the PSI and C-terminal peptide from cardosin B needs to pass the Golgi Apparatus to reach the vacuole. A putative role for glycosylation in the trafficking routes is further discussed as cardosin A PSI, contrary to cardosin B, is not glycosylated. The production of mutants affecting cardosin A glycosylation sites supported this idea. Moreover, cardosin A expression in germinating Arabidopsis thaliana seeds revealed a differential accumulation in non-germinated and germinated seedlings. Cardosin A was detected along the secretory pathway to the Protein Storage Vacuole in association with the Endoplasmic Reticulum, Golgi Apparatus, Prevacuole and newly formed Lytic Vacuoles. The drug Brefeldin A caused the protein to be retained in the Golgi Apparatus, despite some amount being still detected in the vacuole, not being clear if the Golgi Apparatus bypass observed in Nicotiana tabacum leaves occurs in this system. As a whole, cardosin A confirmed to be a good model to study vacuolar sorting in these two systems that complement each other in terms of approaches available. This study provided good results in order to understand in more detail cardosin A biology in particular and vacuolar trafficking of plant Aspartic Proteinases as a group.

Since the outbreak of the HIV/AIDS pandemic in the 1980s, the disease has cost the lives of over 30 million people, and a further 33 million are currently living with the HIV infection. With the appropriate treatment, HIV/AIDS can today be regarded as a chronic but manageable disease. However, treatment is not available globally and UNAIDS still estimates that there are currently 5000 AIDS-related deaths worldwide per day. HIV protease inhibitors (PIs) constitute one of the fundaments of HIV treatment, and are commonly used in so-called highly active antiretroviral therapy (HAART), together with reverse transcriptase inhibitors. Although there are ten PIs on the market, there is still a need for novel structures. The rapid development of resistant strains, due to the high frequency of mutations, together with the commonly observed adverse effects of the drugs available, illustrate the need to develop new potent structures. Two novel scaffolds were investigated in this work. A tertiary alcohol-containing scaffold comprising a three-carbon tether, and a β-hydroxy γ-lactam-based scaffold were designed, synthesized and evaluated using enzyme- and cell-based assays. X-ray analyses of inhibitors from each class provided information on inhibitor–protease interactions. The inhibitors containing the tertiary alcohol provided at best an enzymatic inhibition (Ki) of 2.3 nM, and an inhibition in the cell-based assay (EC50) of 0.17 µM. The γ-lactam-based inhibitors exhibited better inhibition than the first series; the best values being Ki = 0.7 nM and EC50 = 0.04 µM. The second part of these studies involved the evaluation of a novel non-resonance continuous-flow microwave instrument. The instrument was validated regarding heating capacity, temperature stability and temperature homogeneity. A number of model reactions were performed with low- and high-microwave-absorbing solvents. It was found that the microwave heating source allowed rapid temperature adjustment, together with easily regulated, flow-dependent reaction times, providing an efficient tool for reaction optimisation.

Malaria is one of the major public health problems in the world. Approximately 500 million people are afflicted and almost 3 million people die from the disease each year. Of the four causative species Plasmodium falciparum is the most lethal. Due to the rapid spread of parasite resistance there is an urgent need for new antimalarial drugs with novel mechanisms of action. Several promising targets for drug intervention have been revealed. This thesis addresses the parasitic aspartic proteases termed plasmepsins (Plm), which are considered crucial to the hemoglobin catabolism essential for parasite survival. The overall aim was to identify inhibitors of the P. falciparum Plm I, II, and IV. More specific objectives were to attain activity against P. falciparum in infected erythrocytes and selectivity versus the most homologous human aspartic protease cathepsin D (Cat D). To guide the design process the linear interaction energy (LIE) method was employed in combination with molecular dynamics. Initial investigations of the stereochemical requirements for inhibition resulted in identification of an L-mannitol derived scaffold encompassing a 1,2-dihydroxyethylene transition state isostere with affinity for Plm II. Further modifications of this scaffold provided inhibitors of all three target plasmepsins (Plm I, II, and IV). Apart from the stereochemical analysis three major kinds of manipulation were explored: a) P1/P1′ and P2/P2′ side chain alterations, b) replacement of amide bonds by diacylhydrazine, 1,3,4-oxadiazole, and 1,2,4-triazole, and c) macrocyclization. Several inhibitors of Plm I and II with Ki values below 10 nM were discovered and one Plm IV selective inhibitor comprising two oxadiazole rings was found which represents the most potent non-peptide Plm IV inhibitor (Ki = 35 nM) reported to date. Some of the identified plasmepsin inhibitors demonstrated significant activity against P. falciparum in infected erythrocytes and all inhibitors showed a considerable selectivity for the plasmepsins over the human Cat D.

published_or_final_version / Public Health / Master / Master of Public Health

Thesis (Ph. D.)--Case Western Reserve University, 2005. / [School of Medicine] Department of Genetics. Includes bibliographical references. Available online via OhioLINK's ETD Center.

Thesis--Catholic Univ. of America. / Includes bibliographical references (p. 70-73).