Non-classical inhibitors of dihydrofolate reductase

This thesis comprises two main objectives. The first objective involved the stereochemical studies of chiral 4,6-diamino-1-aryl-1,2-dihydro-s-triazines and an investigation on how the different conformations of these stereoisomers may affect their binding affinity to the enzyme dihydrofolate reductase (DHFR). The ortho-substituted 1-aryl-1,2-dihydro-s-triazines were synthesised by the three component method. An ortho-substitution at the C6' position was observed when meta-azidocycloguanil was decomposed in acid. The ortho-substituent restricts free rotation and this gives rise to atropisomerism. Ortho-substituted 4,6-diamino-1-aryl-2-ethyl-1,2-dihydro-2-methyl-s-triazine contains two elements of chirality and therefore exists as four stereoisomers: (S,aR), (R,aS), (R,aR) and (S,aS). The energy barriers to rotation of these compounds were calculated by a semi-empirical molecular orbital program called MOPAC and they were found to be in excess of 23 kcal/mol. The diastereoisomers were resolved and enriched by C18 reversed phase h.p.l.c. Nuclear overhauser effect experiments revealed that (S,aR) and (R,aS) were the more stable pair of stereoisomers and therefore existed as the major component. The minor diastereoisomers showed greater binding affinity for the rat liver DHFR in in vitro assay. The second objective entailed the investigation into the possibility of retaining DHFR inhibitory activity by replacing the classical diamino heterocyclic moiety with an amidinyl group. 4-Benzylamino-3-nitro-N,N-dimethyl-phenylamidine was synthesised in two steps. One of the two phenylamidines indicated weak inhibition against the rat liver DHFR. This weak activity may be due to the failure of the inhibitor molecule to form strong hydrogen bonds with residue Glu-30 at the active site of the enzyme.

T-cell epitope prediction and immune complex simulation using molecular dynamics:state of the art and persisting challenges

Atomistic Molecular Dynamics provides powerful and flexible tools for the prediction and analysis of molecular and macromolecular systems. Specifically, it provides a means by which we can measure theoretically that which cannot be measured experimentally: the dynamic time-evolution of complex systems comprising atoms and molecules. It is particularly suitable for the simulation and analysis of the otherwise inaccessible details of MHC-peptide interaction and, on a larger scale, the simulation of the immune synapse. Progress has been relatively tentative yet the emergence of truly high-performance computing and the development of coarse-grained simulation now offers us the hope of accurately predicting thermodynamic parameters and of simulating not merely a handful of proteins but larger, longer simulations comprising thousands of protein molecules and the cellular scale structures they form. We exemplify this within the context of immunoinformatics.

Glutamatergic input-output properties of thalamic astrocytes

Astrocytes in the somatosensory ventrobasal (VB) thalamus of rats respond to glutamatergic synaptic input with metabotropic glutamate receptor (mGluR) mediated intracellular calcium ([Ca²?](i)) elevations. Astrocytes in the VB thalamus also release the gliotransmitter (GT) glutamate in a Ca²?-dependent manner. The tripartite synapse hypothesis posits that astrocytic [Ca²?](i) elevations resulting from synaptic input releases gliotransmitters that then feedback to modify the synapse. Understanding the dynamics of this process and the conditions under which it occurs are therefore important steps in elucidating the potential roles and impact of GT release in particular brain activities. In this study, we investigated the relationship between VB thalamus afferent synaptic input and astrocytic glutamate release by recording N-methyl-D-aspartate (NMDA) receptor-mediated slow inward currents (SICs) elicited in neighboring neurons. We found that Lemniscal or cortical afferent stimulation, which can elicit astrocytic [Ca²?](i) elevations, do not typically result in the generation of SICs in thalamocortical (TC) neurons. Rather, we find that the spontaneous emergence of SICs is largely resistant to acute afferent input. The frequency of SICs, however, is correlated to long-lasting afferent activity. In contrast to short-term stimulus-evoked GT release effects reported in other brain areas, astrocytes in the VB thalamus do not express a straightforward input-output relationship for SIC generation but exhibit integrative characteristics.

Proteomic analysis of a noninvasive human model of acute inflammation and its resolution:the twenty-one day gingivitis model

The 21-day experimental gingivitis model, an established noninvasive model of inflammation in response to increasing bacterial accumulation in humans, is designed to enable the study of both the induction and resolution of inflammation. Here, we have analyzed gingival crevicular fluid, an oral fluid comprising a serum transudate and tissue exudates, by LC-MS/MS using Fourier transform ion cyclotron resonance mass spectrometry and iTRAQ isobaric mass tags, to establish meta-proteomic profiles of inflammation-induced changes in proteins in healthy young volunteers. Across the course of experimentally induced gingivitis, we identified 16 bacterial and 186 human proteins. Although abundances of the bacterial proteins identified did not vary temporally, Fusobacterium outer membrane proteins were detected. Fusobacterium species have previously been associated with periodontal health or disease. The human proteins identified spanned a wide range of compartments (both extracellular and intracellular) and functions, including serum proteins, proteins displaying antibacterial properties, and proteins with functions associated with cellular transcription, DNA binding, the cytoskeleton, cell adhesion, and cilia. PolySNAP3 clustering software was used in a multilayered analytical approach. Clusters of proteins that associated with changes to the clinical parameters included neuronal and synapse associated proteins.

Astrocyte plasticity:implications for synaptic and neuronal activity

Astrocytes are increasingly implicated in a range of functions in the brain, many of which were previously ascribed to neurons. Much of the prevailing interest centers on the role of astrocytes in the modulation of synaptic transmission and their involvement in the induction of forms of plasticity such as long-term potentiation and long-term depression. However, there is also an increasing realization that astrocytes themselves can undergo plasticity. This plasticity may be manifest as changes in protein expression which may modify calcium activity within the cells, changes in morphology that affect the environment of the synapse and the extracellular space, or changes in gap junction astrocyte coupling that modify the transfer of ions and metabolites through astrocyte networks. Plasticity in the way that astrocytes release gliotransmitters can also have direct effects on synaptic activity and neuronal excitability. Astrocyte plasticity can potentially have profound effects on neuronal network activity and be recruited in pathological conditions. An emerging principle of astrocyte plasticity is that it is often induced by neuronal activity, reinforcing our emerging understanding of the working brain as a constant interaction between neurons and glial cells. © The Author(s) 2013.

Self-Learning Fuzzy Spiking Neural Network as a Nonlinear Pulse-Position Threshold Detection Dynamic System Based on Second-Order Critically Damped Response Units

Architecture and learning algorithm of self-learning spiking neural network in fuzzy clustering task are outlined. Fuzzy receptive neurons for pulse-position transformation of input data are considered. It is proposed to treat a spiking neural network in terms of classical automatic control theory apparatus based on the Laplace transform. It is shown that synapse functioning can be easily modeled by a second order damped response unit. Spiking neuron soma is presented as a threshold detection unit. Thus, the proposed fuzzy spiking neural network is an analog-digital nonlinear pulse-position dynamic system. It is demonstrated how fuzzy probabilistic and possibilistic clustering approaches can be implemented on the base of the presented spiking neural network.

Direct observation of morphological development during the spin-coating of polystyrene-poly(methyl methacrylate) polymer blends

We present results of the direct observation, in real-space, of the phase separation of high molecular weight polystyrene and poly(methyl methacrylate) from ortho-xylene using our newly developed technique of high speed stroboscopic interference microscopy. Taking a fixed concentration (3 wt % in o-xylene) at a fixed composition (1:4 by weight) and by varying the rotational rate during the spin-coating process, we are able to observe the formation of a range of phase separated bicontinuous morphologies of differing length-scales. Importantly, we are able to show that the mechanism by which the final phase separated structure is formed is through domain coarsening when rich in solvent, before vitrification occurs and fixes the phase separated structure. The ability to directly observe morphological development offers a route toward controlling the length-scale of the final morphology through process control and in situ feedback, from a single stock solution. © 2013 Wiley Periodicals, Inc.

Photocatalytic decomposition of organophosphonates and fluorophenols in irradiated titanium dioxide suspensions

Dimethyl methyl phosphonate (DMMP), diethyl methyl phosphonate (DEMP), and fluorophenols undergo rapid decomposition upon TiO$\sb2$ catalyzed photooxidation in air saturated aqueous solution. The degradation rates of DMMP were determined over a range of temperatures, under solar and artificial irradiation with and without simultaneous sonication. Solar illumination is effective for the degradation and the use of low energy of sonication increases the rate of mineralization. The surface area and the type of TiO$\sb2$ dramatically affect the photoactivity of the catalyst. A number of intermediate products are formed and ultimately oxidized to phosphate and carbon dioxide. Possible reaction mechanisms and pathways for DMMP and DEMP are proposed. The Langmuir-Hinshelwood kinetic parameters for the photocatalysis of fluorophenols suggest modestly different reactivity for each isomer. The adsorption constant is largest for the ortho isomer consistent with the adsorption onto TiO$\sb2$ through both hydroxyl and fluoride groups to form a chelated type structure. ^

Black band disease of corals: Ecology and physiology of Phormidium corallyticum

Black band disease of corals consists of a microbial community dominated by the cyanobacteriurn Phormidium corallyticum. The disease primarily affects reef-framework coral species, Active black band disease continually opens up new substrate in reef environments by destroying coral tissue as the disease line advances across the surface of infected colonies. A field study was carried out to determine the abundance and distribution of black band disease on the reef building corals in the Florida Keys. During July of 1992 and 1993, up to 0.72% of coral colonies were infected with black band disease. Analysis of the distribution showed that the disease was clumped. Seasonal patters varied, with some coral colonies infected year round, others exhibiting reinfection from summer 1992 to summer 1993, and some colonies infected for one year only. Statistical analysis of black band disease incidence in relation to various environmental parameters revealed that black band disease was associated with relatively shallow water depths, higher temperatures, elevated nitrite levels, and decreased ortho-phosphate levels. Additional field studies determined recovery of scleractinian coral colonies damaged or killed through the activities of black band disease over a five-year period. These studies determined if the newly exposed substrate was recolonized through scleractinian recruitment, if there was overgrowth of the damaged areas by the formerly diseased colony, or if coral tissue destruction continued after the cessation of black band disease activity. Tissue loss continued on all coral colonies with only one colony exhibiting new tissue growth. The majority of recolonization was by non-reef-framework corals and octocorallians, limited recruitment by framework species was observed. Physiological studies of P. corallyticum were carried out to investigate the photosynthetic capacity of this cyanobacterium, and to determine if this species has the ability to fix dinitrogen. The results of this research demonstrated that P. corallyticum reaches maximum photosynthetic rates at very low light intensities (27.9 μE/m/sec), and that P. corallyticum is able to carry out oxygenic photosynthesis in the presence of sulfide, an ability that is uncommon in prokaryotic organisms. ^

Advanced oxidation of arsenic species in aqueous solutions

Ingestion of arsenic from contaminated water is a serious problem and affects the health of more than 100 million people worldwide. Traditional water purification technologies are generally not effective or cost prohibitive for the removal of arsenic to acceptable levels (≤10 ppb). Current multi-step arsenic removal processes involve oxidation, precipitation and/or adsorption. Advanced Oxidation Technologies (AOTs) may be attractive alternatives to existing treatments. The reactions of inorganic and organic arsenic species with reactive oxygen species were studied to develop a fundamental mechanistic understanding of these reactions, which is critical in identifying an effective and economical technology for treatment of arsenic contaminated water. ^ Detailed studies on the conversion of arsenite in aqueous media by ultrasonic irradiation and TiO2 photocatalytic oxidation (PCO) were conducted, focusing on the roles of hydroxyl radical and superoxide anion radical formed during the irradiation. ·OH plays the key role, while O2 -· has little or no role in the conversion of arsenite during ultrasonic irradiation. The reaction of O2-· does not contribute in the rapid conversion of As(III) when compared to the reaction of As(III) with ·OH radical during TiO2 PCO. Monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA) are readily degraded upon TiO2 PCO. DMA is oxidized to MMA as the intermediate and arsenate as the final product. For dilute solutions, TiO2 also may be applicable as an adsorbent for direct removal of arsenic species, namely As(III), As(V), MMA and DMA, all of which are strongly adsorbed, thus eliminating the need for a multi-step treatment process. ^ Phenylarsonic acid (PA) was subjected to gamma radiolysis under hydroxyl radical generating conditions, which showed rapid degradation of PA. Product analysis and computational calculation both indicate the arsenate group is an ortho, para director. Our results indicate · OH radical mediated processes should be effective for the remediation of phenyl substituted arsonic acids. ^ While hydroxyl radical generating methods, specifically AOTs, appear to be promising methods for the treatment of a variety of arsenic compounds in aqueous media, pilot studies and careful economic analyses will be required to establish the feasibility of AOTs applications in the removal of arsenic. ^

Synthesis of aromatic monothiols and aromatic dithiols to increase the folding rate and yield of disulfide containing proteins

Most pharmaceutically relevant proteins and many extracellular proteins contain disulfide bonds. Formation of the correct disulfide bonds is essential for stability in almost all cases. Disulfide containing proteins can be rapidly and inexpensively overexpressed in bacteria. However, the overexpressed proteins usually form aggregates inside the bacteria, called inclusion bodies, which contains inactive and non-native protein. To obtain native protein, inclusion bodies need to be isolated and resolubilized, and then the resulting protein refolded in vitro. In vitro protein folding is aided by the addition of a redox buffer, which is composed of a small molecule disulfide and/or a small molecule thiol. The most commonly used redox buffer contains reduced and oxidized glutathione. Recently, aliphatic dithiols and aromatic monothiols have been employed as redox buffers. Aliphatic dithiols improved the yield of native protein as compared to the aliphatic thiol, glutathione. Dithiols mimic the in vivo protein folding catalyst, protein disulfide isomerase, which has two thiols per active site. Furthermore, aromatic monothiols increased the folding rate and yield of lysozyme and RNase A relative to glutathione. By combining the beneficial properties of aliphatic dithiols and aromatic monothiols, aromatic dithiols were designed and were expected to increase in vitro protein folding rates and yields. Aromatic monothiols (1-4) and their corresponding disulfides (5-8), two series of ortho- and para-substituted ethylene glycol dithiols (9-15), and a series of aromatic quaternary ammonium salt dithiols (16-17) were synthesized on a multigram scale. Monothiols and disulfides (1-8) were utilized to fold lysozyme and bovine pancreatic trypsin inhibitor. Dithiols (11-17) were tested for their ability to fold lysozyme. At pH 7.0 and pH 8.0, and high protein concentration (1 mg/mL), aromatic dithiols (16, 17) and a monothiol (3) significantly enhanced the in vitro folding rate and yield of lysozyme relative to the aliphatic thiol, glutathione. Additionally, aromatic dithiols (16, 17) significantly enhance the folding yield as compared to the corresponding aromatic monothiol (3). Thus, the folding rate and yield enhancements achieved in in vitro protein folding at high protein concentration will decrease the volume of renaturation solution required for large scale processes and consequently reduce processing time and cost.

Photocatalytic decomposition of organophosphonates fluorophenols in irradiated titanium dioxide suspensions

Dimethyl methyl phosphonate (DMMP), diethyl methyl phosphonate (DEMP), and fluorophenols undergo rapid decomposition upon TiO2 catalyzed photooxidation in air saturated aqueous solution. The degradation rates of DMMP were determined over a range of temperatures, under solar and artificial irradiation with and without simultaneous sonication. Solar illumination is effective for the degradation and the use of low energy of sonication increases the rate of mineralization. The surface area and the type of TiO2 dramatically affect the photoactivity of the catalyst. A number of intermediate products are formed and ultimately oxidized to phosphate and carbon dioxide. Possible reaction mechanisms and pathways for DMMP and DEMP are proposed. The Langmuir- Hinshelwood kinetic parameters for the photocatalysis of fluorophenols suggest modestly different reactivity for each isomer. The adsorption constant is largest for the ortho isomer consistent with the adsorption onto TiO2 through both hydroxyl and fluoride groups to form a chelated type structure.

Obtenção de organovermiculitas utilizando tensoativos e microemulsões e suas aplicações na separação de isômeros do Xileno

Surfactants are versatile organic compounds that have, in a single molecule, double chemical affinity. The surfactant molecule is composed by a hy drophobic tail group, a hydrocarbon chain (linear, branched, or mixed), and by a hydrophilic head group, which contains polar groups that makes it able to be applied in the organophilization process of natural clays. Microemulsions are microheterogeneous b lends composed by: a surfactant, an oily phase (non - polar solvent), an aqueous phase, and, sometimes, a co - surfactant (short - chain alcohol). They are systems with thermodynamic stability, transparent, and have high solubility power. Vermiculite is a clay m ineral with an expandable crystalline structure that has high cation exchange capacity. In this work vermiculite was used to obtain organoclays. The ionic surfactants dodecyl ammonium chlori de (DDAC) and cetyltrimethylammonium bromide (C 16 TAB) were used in the organophilization process. They were used as surfactant aqueous solutions and, for DDAC, as a microemulsion system. The organoclays were used to promote the separation of binary mixtures of xylene isomers (ortho - and meta - xylene). Dif ferent analytical techniques were used to characterize microemulsion systems and also the nanoclays. It was produced a water - rich microemulsion system with 0.92 nm droplet average diameter. The vermiculite used in this work has a cationic exchange capacity of 172 meq/100g and magnesium as main cation (24.25%). The basal spacing of natural vermiculite and organo - vermiculites were obtained by X - ray Diffraction technique. The basal spacing was 1.48nm for natural vermiculite, 4.01nm for CTAB - vermiculite (CTAB 4 ) , and 3.03nm for DDAC - vermiculite (DDAC M1A), that proves the intercalation process. Separation tests were carried out in glass columns using three binary mixtures of xylene (ortho - xylene and meta - xylene). The results showed that the organovermiculite pre sented an enhanced chemical affinity by the mixture of hydrocarbons, when compared with the natural vermiculite, and also its preference by ortho - xylene. A factorial experimental design 2 2 with triplicate at the central point was used to optimize the xylen e separation process. The experimental design revealed that the initial concentration of isomers in the mixture and the mass of organovermiculite were the significant factors for an improved separation of isomers. In the experiments carried out using a bin ary mixture of ortho - xylene and meta - xylene (2:1), after its percolating through the organovermiculite bed (DDAC M1), it was observed the preference of the organoclay by the ortho - xylene isomer, which was retained in greater quantity than the meta - xylene o ne. At the end of the treatment, it was obtained a final concentration in meta - xylene of 47.52%.

Modelos de condutividade térmica em rochas silicáticas, com ênfase em rochas da província Borborema, NE do Brasil

A practical approach to estimate rock thermal conductivities is to use rock models based just on the observed or expected rock mineral content. In this study, we evaluate the performances of the Krischer and Esdorn (KE), Hashin and Shtrikman (HS), classic Maxwell (CM), Maxwell-Wiener (MW), and geometric mean (GM) models in reproducing the measures of thermal conductivity of crystalline rocks.We used 1,105 samples of igneous and metamorphic rocks collected in outcroppings of the Borborema Province, Northeastern Brazil. Both thermal conductivity and petrographic modal analysis (percent volumes of quartz, K-feldspar, plagioclase, and sum of mafic minerals) were done. We divided the rocks into two groups: (a) igneous and ortho-derived (or meta-igneous) rocks and (b) metasedimentary rocks. The group of igneous and ortho-derived rocks (939 samples) covers most the lithologies de_ned in the Streckeisen diagram, with higher concentrations in the fields of granite, granodiorite, and tonalite. In the group of metasedimentary rocks (166 samples), it were sampled representative lithologies, usually of low to medium metamorphic grade. We treat the problem of reproducing the measured values of rock conductivity as an inverse problem where, besides the conductivity measurements, the volume fractions of the constituent minerals are known and the effective conductivities of the constituent minerals and model parameters are unknown. The key idea was to identify the model (and its associated estimates of effective mineral conductivities and parameters) that better reproduces the measures of rock conductivity. We evaluate the model performances by the quantity  that is equal to the percentage of number of rock samples which estimated conductivities honor the measured conductivities within the tolerance of 15%. In general, for all models, the performances were quite inferior for the metasedimentary rocks (34% <  < 65%) as compared with the igneous and ortho-derived rocks (51% <  < 70%). For igneous and ortho-derived rocks, all model performances were very similar ( = 70%), except the GM-model that presented a poor performance (51% <  < 65%); the KE and HS-models ( = 70%) were slightly superior than the CM and MW-models ( = 67%). The quartz content is the dominant factor in explaining the rock conductivity for igneous and ortho-derived rocks; in particular, using the MW-model the solution is in practice vi UFRN/CCET– Dissertação de mestrado the series association of the quartz content. On the other hand, for metasedimentary rocks, model performances were different and the performance of the KEmodel ( = 65%) was quite superior than the HS ( = 53%), CM (34% <  < 42%), MW ( = 40%), and GM (35% <  < 42%). The estimated effective mineral conductivities are stable for perturbations both in the rock conductivity measures and in the quartz volume fraction. The fact that the metasedimentary rocks are richer in platy-minerals explains partially the poor model performances, because both the high thermal anisotropy of biotite (one of the most common platy-mineral) and the difficulty in obtaining polished surfaces for measurement coupling when platyminerals are present. Independently of the rock type, both very low and very high values of rock conductivities are hardly explained by rock models based just on rock mineral content.

Preliminary identification of dehalogenation specificities exhibited by dehalorespiring bacteria from a marine microbial community

The ability of a previously PCB-enriched microbial culture from Venice Lagoon marine sediments to dechlorinate pentachlorophenol (PCP) and 2,3,5-trichlorophenol (2,3,5-TCP) was confirmed under anaerobic conditions in microcosms consisting of site water and sediment. Dechlorination activities against Aroclor 1254 PCB mixture were also confirmed as control. Pentachlorophenol was degraded to 2,4,6-TCP (75.92±0.85 mol%), 3,5-DCP (6.40±0.75 mol%), and phenol (15.40±0.87 mol%). From the distribution of the different dechlorination products accumulated in the PCP-spiked cultures over time, two dechlorination pathways for PCP were proposed: (i) PCP to 2,3,4,6-TeCP, then to 2,4,6-TCP through the removal of both meta double-flanked chlorine substituents (main pathway); (ii) alternately, PCP to 2,3,5,6-TeCP, 2,3,5-TCP, 3,5-DCP, then phenol, through the removal of the para double-flanked chlorine, followed by ortho single-flanked chlorines, and finally meta unflanked chlorines (minor pathway). Removal of meta double-flanked chlorines is thus preferred over all other substituents. 2,3,5-TCP, that completely lacks double-flanked chlorines, was degraded to 3,5-DCP through removal of the ortho single-flanked chlorine, with a 99.6% reduction in initial concentration of 2,3,5-TCP by week 14. 16S rRNA PCR-DGGE using Chloroflexi-specific primers revealed a different role of the two microorganisms VLD-1 and VLD-2, previously identified as dechlorinators in the Aroclor 1254 PCB-enriched community, in the dehalogenation of chlorophenols. VLD-1 was observed both in PCP- and TCP-dechlorinating communities, whereas VLD-2 only in TCP-dechlorinating communities. This indicates that VLD-1 and VLD-2 may both dechlorinate ortho single-flanked chlorines, but only VLD-1 is able to remove double-flanked meta or para chlorines.