Chapter 1 gives an introduction on the physical and electronic properties of fluorine and the C-F bond. The application of fluorine in organic chemistry, which is mainly attributed to the electronic properties of fluorine is described. The role of fluorine in neuropsychiatric drug development and for influencing the conformational study of bioactive amines is also illustrated. Chapter 2 of the thesis describes the synthesis of the two fluorinated stereoisomers (2R, 3S) and (2S, 3S) 3-fluoro N-methyl–D-aspartate (NMDA). These were prepared as analogues to study the binding conformation of NMDA on the glutameric NMDA receptor. The (2S, 3S)-3-fluoro NMDA D-72 was successfully prepared from diethyl D-tartrate. The (2S,3R)- stereoisomer was prepared by separation of diastereoisomers generated by reaction of a meso- epoxide with an enantiomerically pure amine, followed by fluorination. Both the (2S,3R)- and (2R,3S)- enantiomers were prepared separately, however assignment of the absolute configuration to each enantiomer could not be unambiguously proven. The fluorinated 3F-NMDA stereoisomers were assessed by dose response analysis and TEVC analysis in the rat glutamate receptor. The biological results show that the (2S, 3S)-3F NMDA D-72 is a good agonist, whereas (2R, 3S)- and (2S, 3R)-3-fluoro NMDA are inactive stereoisomers. The result of this study indicates that (2S, 3S)-3F NMDA D-72 is the only relevant agonist that can access a conformation for binding to NMDA receptor. Chapter 3 describes the preparation of fluorinated analogues of the calcium receptor agonist Cinacalcet. The (2R,1’R)-123 and (2S,1’R)-124 fluoro Cinacalcet diastereoisomers were prepared from 3’-(trifluoromethyl)cinnamic acid and 3’’-SF₅-137 Cinacalcet was synthesized from pentafluorosulfanyl benzyl alcohol. The biological assessment in the calcium receptor (CaR) revealed that both (2R,1’R)-123 and (2S,1’R)-124 fluoro Cinacalcet is slightly lower in potency compared to the non-fluorinated Cinacalcet 117. This suggests that the Cinacalcet 117 adopts an extended conformation when bound to the receptor. The 3’’-SF₅-137 Cinacalcet possesses equipotent activity with Cinacalcet 117.

Chagas disease, is caused by the protozoan Trypanosoma cruzi. The available chemotherapy is restricted to two compounds: Nifurtimox and Benzonidazol. The T. cruzi life cycle occurs among invertebrate and vertebrate hosts and its survival strongly depends on its ability to catabolise both, carbohydrates and amino acids to obtain energy. The amino acids have an important role in several biological processes in this parasite. In this context, we studied the L-asparagine (Asn) relevance in the metabolism, differentiation and stress resistance of the T cruzi. Our results have shown that epimastigotes use Asn as carbon source, and contributes with the resistance to nutritional and oxidative stress. The Asn also showed a positive influence in metacyclogenesis and supported the ATP synthesis. Finally, the absence of Asn interfered with the proliferation of the replicative forms of T. cruzi. Taken together, our results suggest the involvement of the Asn metabolism in the protection of T. cruzi when submitted to different stress conditions. / Chagas disease, is caused by the protozoan Trypanosoma cruzi. The available chemotherapy is restricted to two compounds: Nifurtimox and Benzonidazol. The T. cruzi life cycle occurs among invertebrate and vertebrate hosts and its survival strongly depends on its ability to catabolise both, carbohydrates and amino acids to obtain energy. The amino acids have an important role in several biological processes in this parasite. In this context, we studied the L-asparagine (Asn) relevance in the metabolism, differentiation and stress resistance of the T cruzi. Our results have shown that epimastigotes use Asn as carbon source, and contributes with the resistance to nutritional and oxidative stress. The Asn also showed a positive influence in metacyclogenesis and supported the ATP synthesis. Finally, the absence of Asn interfered with the proliferation of the replicative forms of T. cruzi. Taken together, our results suggest the involvement of the Asn metabolism in the protection of T. cruzi when submitted to different stress conditions.

Thesis advisor: Evan R. Kantrowitz / The enzyme aspartate transcarbamoylase (ATCase) is an enzyme in the pyrimidine nucleotide biosynthetic pathway. It was once an attractive target for anti-proliferation drugs but has since become a teaching model due to kinetic properties such as cooperativity and allostery exhibited by the Escherichia coli form of the enzyme. ATCase from E. coli has been extensively studied over that last 60 years and is the textbook example of allosteric enzymes. Through this past research it is understood that ATCase is allosterically inhibited by CTP, the end product of pyrimidine biosynthesis, and allosterically activated by ATP, the end product of the parallel purine biosynthetic pathway. Part of the work discussed in this dissertation involves further understanding the catalytic properties of ATCase by examining an unregulated trimeric form from Bacillus subtilis, a bacterial ATCase that more closely resembles the mammalian form than E. coli ATCase. Through X-ray crystallography and molecular modeling, the complete catalytic cycle of B. subtilis ATCase was visualized, which provided new insights into the manifestation of properties such as cooperativity and allostery in forms of ATCase that are regulated. Most of the work described in the following chapters involves understanding allostery in E. coli ATCase. The work here progressively builds a new model of allostery through new X-ray structures of ATCase*NTP complexes. Throughout these studies it has been determined that the allosteric site is bigger than previously thought and that metal ions play a significant role in the kinetic response of the enzyme to nucleotide effectors. This work proves that what is known about ATCase regulation is inaccurate and that currently accepted, and taught, models of allostery are wrong. This new model of allostery for E. coli ATCase unifies all old and current data for ATCase regulation, and has clarified many previously unexplainable results. / Thesis (PhD) — Boston College, 2013. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Chagas disease, is caused by the protozoan Trypanosoma cruzi. The available chemotherapy is restricted to two compounds: Nifurtimox and Benzonidazol. The T. cruzi life cycle occurs among invertebrate and vertebrate hosts and its survival strongly depends on its ability to catabolise both, carbohydrates and amino acids to obtain energy. The amino acids have an important role in several biological processes in this parasite. In this context, we studied the L-asparagine (Asn) relevance in the metabolism, differentiation and stress resistance of the T cruzi. Our results have shown that epimastigotes use Asn as carbon source, and contributes with the resistance to nutritional and oxidative stress. The Asn also showed a positive influence in metacyclogenesis and supported the ATP synthesis. Finally, the absence of Asn interfered with the proliferation of the replicative forms of T. cruzi. Taken together, our results suggest the involvement of the Asn metabolism in the protection of T. cruzi when submitted to different stress conditions. / Chagas disease, is caused by the protozoan Trypanosoma cruzi. The available chemotherapy is restricted to two compounds: Nifurtimox and Benzonidazol. The T. cruzi life cycle occurs among invertebrate and vertebrate hosts and its survival strongly depends on its ability to catabolise both, carbohydrates and amino acids to obtain energy. The amino acids have an important role in several biological processes in this parasite. In this context, we studied the L-asparagine (Asn) relevance in the metabolism, differentiation and stress resistance of the T cruzi. Our results have shown that epimastigotes use Asn as carbon source, and contributes with the resistance to nutritional and oxidative stress. The Asn also showed a positive influence in metacyclogenesis and supported the ATP synthesis. Finally, the absence of Asn interfered with the proliferation of the replicative forms of T. cruzi. Taken together, our results suggest the involvement of the Asn metabolism in the protection of T. cruzi when submitted to different stress conditions.

Este trabalho teve por finalidade a implementação e desenvolvimento de novos métodos para a análise de curvas de espalhamento de raios X a baixo ângulo por sistemas monodispersos. O resultado básico final deste trabalho foi a confecção de três programas de computador e suas aplicações em proteínas de interesse biológico. ELLFIT é um programa de computador que encontra o elipsóide cuja curva de SAXS melhor se ajusta a uma dada curva experimental. Para casos favoráveis este programa é capaz de determinar a dimensão máxima e algumas características básicas do formato da partícula. CRYSOL é um programa para a avaliação de curvas de espalhamento em solução para proteínas com estrutura atômica conhecida. O programa usa a expansão de multipolos para o cálculo rápido da promediação espacial e simula uma camada de hidratação ao redor da proteína. CRYSOL pode predizer a curva de SAXS de uma determinada proteína e compará-la com dados experimentais. HOMDIM é um programa para a determinação da posição das sub-unidades de um homodímero no caso de ser conhecida somente a estrutura da sub-unidade sozinha. Dada a curva experimental e a amplitude da sub-unidade, HOMDIM procura os parâmetros posicionais que descrevem o homodímero. Estes e outros programas foram aplicados a várias proteínas. O método da expansão de multipolos foi usado na determinação do envelope molecular de uma inibidora de ALPHA-amilase. O programa CRYSOL foi utilizado para resolver uma ambiguidade na estrutura quatemária cristalina da hexocinase e o programa HOMDIM para a proposição de um novo modelo para a estrutura quatemária da aspartato transcarbamilase no estado R em solução / This work was aimed at the implementation and development of new methods for solution scattering analysis of monodisperse systems. The basic final result of this work was the development of three programs and their applications to proteins of biological interest. ELLFIT is a computer program, which finds the elipsoid whose SAXS curve has the best fit to a given experimental curve. In favorable cases, this program is able to determine the maximum dimension and some basic characteristic of the particle shape. CRYSOL is a program for evaluating the solution scattering from, proteins of known structure. The program uses multipole expansion for fast calculation of the spherically averaged scattering pattern and takes into account the hydration shell. Given the atomic coordinates it can predict the solution scattering curve and compare it with the experimental scattering curve. HOMDIM is a program to determine the position of both subunits of a homodimer when only one sub-unit structure is known. Given the experimental curve of the homodimer and the subunit scattering amplitudes. HOMDIM searches for the positional parameters, which describe the homodimer. These and other programs were used to study several proteins. The multipole expansion method was used in the shape determination of an ALPHA-amylase inhibitor. The program CRYSOL was used to solve the ambiguity in the hexokinase quaternary crystal structures and the program HOMDIM was utilized for the quaternary structure modeling of the R-state of the aspartate transcarbamilase in solution

Doctor of Philosophy (Medicine) / Glutamate transporters play a role in removing extracellular excitatory neurotransmitter, L-glutamate into the cells. The rate of the uptake depends on the density of the transporters at the membrane. Some studies claimed that glutamate transporters could transit between the cytoplasm and the membrane on a time-scale of minutes. The present study examined the distribution of glutamate transporter GLAST predominantly expressed in rat cortical cultured astrocytes between the membrane and the cytoplasm by using deconvolution microscopy and then analyzing the images. The regulation of the distribution of GLAST was studied in the presence of glutamate transporter substrate (D-aspartate), purinergic receptor activators (α,β-methylene ATP, adenosine), neuroleptic drugs (clozapine, haloperidol), ammonia (hyperammonia) and Na+/K+-ATPase inhibitors (ouabain, digoxin and FCCP). It was demonstrated that the translocation of GLAST towards the plasma membrane was induced by D-aspartate, α,β-methylene ATP, adenosine, clozapine and ammonia (at 100 μM and very high concentrations of 10 mM). However, the inhibition of Na+/K+-ATPase activity had an opposite effect, resulting in redistribution of GLAST away from the membrane. It has previously been claimed that the membrane-cytoplasm trafficking of GLAST was regulated by phosphorylation catalysed by protein kinase C delta (PKC-delta). Involvement of this mechanism has, however, been put to doubt when rottlerin, a PKC-delta inhibitor, used to test the hypothesis showed to inhibit Na+/K+-ATPase-mediated uptake of Rb+, suggesting that rottlerin influenced the activity of Na+/K+-ATPase. As Na+/K+-ATPase converts ATP to energy and pumps Na+, K+ ions, thus helping to maintain normal electrochemical and ionic gradients across the cell membrane. Its inhibition also reduced D-aspartate transport and could impact on the cytoplasm-to-membrane traffic of GLAST molecules. Furthermore, rottlerin decreased the activity of Na+/K+-ATPase by acting as a mitochondrial inhibitor. The present study has focused on the inhibition of Na+/K+-ATPase activity by rottlerin, ouabain and digoxin in homogenates prepared from rat kidney and cultured astrocytes. The activity of Na+/K+-ATPase was measured by the absorption of inorganic phosphate product generated from the hydrolysis of ATP and the fluorescent transition of the dye RH421 induced by the movement of Na+/K+-ATPase. This approach has a potential to test whether the rottlerin effect on Na+/K+-ATPase is a direct inhibition of the enzyme activity. Rottlerin has been found to block the activity of Na+/K+-ATPase in a dose-dependent manner in both rat kidney and astrocyte homogenates. Therefore, rottlerin inhibited the activity of Na+/K+-ATPase directly in a cell-free preparation, thus strongly indicating that the effect was direct on the enzyme. In parallel experiments, ouabain and digoxin produced similar inhibitions of Na+/K+-ATPase activity in rat kidney while digoxin blocked the activity of Na+/K+-ATPase to a greater extent than ouabain in rat cortical cultured astrocytes. In a separate set of experiments, Na+/K+-ATPase in the astrocytic membrane was found to be unsaturated in E1(Na+)3 conformation in the presence of Na+ ions and this could explain the differences between the effects of digoxin and ouabain on the activity of Na+/K+-ATPase in rat astrocytes. In addition, it was found that at low concentrations of rottlerin, the activity of Na+/K+-ATPase was increased rather than inhibited. This effect was further investigated by studying rottlerin interactions with membrane lipids. The activity of Na+/K+-ATPase has been reported to be regulated by membrane lipids. The enzyme activity can be enhanced by increasing fluidity of the lipid membrane. I have, therefore, proposed that rottlerin binds to the membrane lipids and the effects of rottlerin on Na+/K+-ATPase are mediated by changes in the properties (fluidity) of the membrane. The hypothesis was tested by comparing rottlerin and a detergent, DOC (sodium deoxycholate), for their binding to the lipids by using a DMPC (1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine) monolayer technique. DOC has been shown to both increase and inhibit activity of Na+/K+-ATPase in a manner similar to that displayed by rottlerin. The effects of rottlerin and DOC on the DMPC monolayers were studied by measuring the surface pressure of DMPC monolayers and surface area per DMPC molecule. I established that both rottlerin and DOC decreased the surface pressure of DMPC monolayers and increased the surface area per DMPC molecule. This indicates that both rottlerin and DOC penetrated into the DMPC monolayers. If rottlerin can interact with the lipids, changes in fluidity of the lipid membrane cannot be ruled out and should be considered as a possible factor contributing to the effects of rottlerin on the activity of Na+/K+-ATPase. Overall, the study demonstrates that rottlerin is not only a PKC-delta inhibitor but can have additional effects, both on the enzyme activities (Na+/K+-ATPase) and/or on lipid-containing biological structures such as membranes. The findings have implication not only for studies where rottlerin was used as a supposedly specific PKC-delta inhibitor but also for mechanisms of its toxicity.

The members of the genus Streptomyces are well-known for their capacity to synthesize a vast repertoire of secondary metabolites, including many useful antibiotics and proteins. Streptomyces clavuligerus is the producer of the medically important &amp / #946 / -lactam antibiotics such as cephamycin C and the potent &amp / #946 / -lactamase inhibitor clavulanic acid. The aspartate pathway of S. clavuligerus is an important primary metabolic pathway providing substrates for &amp / #946 / -lactam synthesis. This pathway uses L-aspartic acid as the precursor for the biosynthesis of the amino acids L-lysine, L-methionine, L-isoleucine, L-threonine and several important metabolic intermediates. L-&amp / #945 / -aminoadipic acid (&amp / #945 / -AAA) required for &amp / #946 / -lactam synthesis is a catabolic product of L-lysine produced from the lysine branch of the aspartate pathway. The carbon flow through the L-lysine-specific branch of aspartate pathway is limiting for the formation of cephamycin C. Formation of L-homoserine from aspartate semialdehyde (ASA) is the first step of the other branch of the aspartate pathway leading to L-threonine, L-isoleucine and L-methionine synthesis and is catalyzed by homoserine dehydrogenase (HSD, EC 1.1.1.3). Regulation of the activity or biosynthesis of the HSD of S. clavuligerus determines the availability of ASA for the biosynthesis of L-lysine and &amp / #945 / -AAA. The gene encoding for homoserine dehydrogenase (hom) was previously cloned from S. clavuligerus NRRL 3585 and characterized in our laboratory. In this study, the hom gene was disrupted via insertion of a kanamycin resistance cassette into this gene which was subsequently transferred to S. clavuligerus cells using the Streptomyces plasmid vector pIJ486. A hom mutant of S. clavuligerus (AK39) was formed through integration into the chromosome by double crossing over and the effects of hom disruption on cephamycin C yields were investigated. Disruption of hom gene resulted in a 1.7 to 2.0 fold increase in specific cephamycin C production in chemically defined medium (CDM).

No description available.

N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated ionotropic receptors. When activated, NMDARs let extracellular sodium and calcium ions enter neurons. This calcium influx, depending on its duration, intensity and the presence of nearby signalling proteins can signal to synaptic plasticity. Additionally, physiological NMDAR activity promotes pro-survival cascades and gene transcription, whereas both lack of activation and overactivation of these receptors trigger pro-death signals. Several neurodegenerative pathologies such as stroke/ischemia and Alzheimer’s disease are thought to involve NMDAR overactivation, so-called “excitotoxicity”, but since NMDARs are important for normal neuronal physiology, potential therapeutical approaches needs to go beyond simple antagonism. Here, we studied the receptor subunit composition and the molecular cascades downstream of the receptor activation to try and isolate the pro-death pathways in NMDAR-mediated excitotoxicity. We found that the NR2 subunit composition did not dictate the type of NMDAR-mediated signals, as receptors comprised of NR2B subunits were able to signal to death, survival and plasticity. However, we also found that the intracellular tail of the NR2B subunit was more efficient at triggering neuronal death compared to the NR2A C-terminus, which suggests that different pro-death signalling complexes are associated to each subunit. Two pro-death signals, the p38 and c-Jun N-terminal kinase (JNK) cascades, are key mediators of neuronal excitotoxicity. In a non-neuronal cell line, NMDAR-mediated cell death could be reconstituted but was found to rely solely on JNK and not p38. This was due to the lack of pro-death signals from the NR2B-PDZ domain, a cytoplasmic interacting domain which forms a signalling cassette with the neuronal proteins PSD-95 and neuronal nitric oxide synthase. This PDZ-ligand recruits the p38 cascade in neurons, but was absent in non-neuronal cells. The pro-death p38 pathway could be inhibited in neurons by disrupting the PDZ domain interactions, which protects against excitotoxicity. This disruption was not affecting normal synaptic transmission, potentiation or survival signalling, suggesting that this could be a therapeutically viable avenue. Thus, this work has expanded the understanding of how NMDAR subunits and their cytoplasmic domains mediate signalling leading to a variety of cellular outcomes; a crucial point for the development of a strategy specifically targeting NMDAR- mediated pro-death signalling.

Streptomyces clavuligerus is a gram-positive filamentous bacterium well known for its ability to produce an array of &amp / #61538 / -lactam compounds (secondary metabolites) including cephamycin C, clavulanic acid and other structurally related clavams. Of these, cephamycin C is a second generation cephalosporin antibiotic having great medical significance. Biosynthesis of the &amp / #946 / -lactam nucleus begins with the non-ribosomal condensation of L-&amp / #945 / -aminoadipic acid (&amp / #945 / -AAA), L-cysteine and L-valine to form the tripeptide &amp / #945 / -aminoadipiyl-cysteinyl-valine (ACV). In Streptomyces clavuligerus, &amp / #945 / -aminoadipic acid (&amp / #945 / -AAA) is a catabolic product of L-lysine produced from the lysine branch of the aspartate pathway and its biosynthesis represents a key secondary metabolic regulatory step in carbon flow to &amp / #946 / -lactam synthesis through this core pathway. The ask (aspartokinase)-asd (aspartate semialdehyde dehydrogenase) gene cluster which encodes for the first key enzymes of aspartate pathway has already been cloned from S. clavuligerus, characterized and heterologously expressed for the first time in our laboratory. Amplification of ask-asd cluster or ask gene alone in a multi-copy Streptomyces plasmid vector and determination of the effects of multiple copies on cephamycin C biosynthesis were the goals of the present study. For this purpose, three different strategies were employed. Of these, two strategies involving the use of vector pIJ702 did not work because of the instability of resulting recombinant plasmids. In the third and last strategy, we used another multicopy Streptomyces vector, pIJ486, which we showed in this study to be very stable for the same purpose. Meanwhile, an efficient protoplast transformation protocol was developed in our laboratory. Ask gene was cloned into this vector and S. clavuligerus protoplasts were efficiently transformed with the recombinant plasmid (pTB486) using the newly-developed protocol. After stable recombinants were obtained, the effects of the multiple copies of ask gene on cephamycin C biosynthesis were determined. There was a profound reduction in the rate and extent of growth of Ask overproducers, as experienced by testing two independent ask-multicopy recombinants. Although one such recombinant strain (designated S. clavuligerus TB 3585) had a 5.5 fold increased level of Ask activity as compared to the parental strain, it displayed only a 1.1 fold increase in specific production of cephamycin C.