Thesis (Ph.D.)--Uniformed Services University of the Health Sciences, 2006 / Typescript (photocopy)

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Non-Saccharomyces yeasts of oenological origin have previously been associated with spoilage or regarded as undesired yeasts in wine. However, these yeasts have recently come under investigation for their positive contribution towards wine aroma especially when used in sequential or co-inoculated fermentations with Saccharomyces cerevisiae. These yeasts are also known to secrete a number of enzymes that could be applicable in wine biotechnology. Amongst these enzymes are aspartic proteases. The secreted proteases from some non-Saccharomyces yeast may play a role in protein haze reduction, as demonstrated by some authors, while simultaneously increasing the assimilable nitrogen content of the wine for the utilization and growth of fermentative microorganisms. Moreover, the proteases may have an indirect effect on wine aroma by liberating amino acids that serve as aroma precursors. Although many screenings have been performed detecting protease activity in non-Saccharomyces yeasts, no attempts have been made to characterize these enzymes. This study set out to isolate and characterize genes encoding extracellular aspartic proteases from non-Saccharomyces yeasts. An enzymatic activity screening of a collection of 308 Saccharomyces and non-Saccharomyces yeasts, isolated from grape must, was performed. The aspartic protease-encoding genes of two non- Saccharomyces yeasts, which showed strong extracellular proteolytic activity on plate assays, were isolated and characterized by in silico analysis. The genes were isolated by employing degenerate and inverse PCR. One gene was isolated from Metschnikowia pulcherrima IWBT Y1123 and named MpAPr1. The other putative gene was isolated from Candida apicola IWBT Y1384 and named CaAPr1. The MpAPr1 gene is 1137 bp long, encoding a 378 amino acid putative protein with a predicted molecular weight of 40.1 kDa. The CaAPr1 putative gene is 1101 bp long and encodes a 367 amino acid putative protein with a predicted molecular weight of 39 kDa. These features are typical of extracellular aspartic proteases. The deduced protein sequences showed less than 40% homology to other yeast extracellular aspartic proteases. By heterologous expression of MpAPr1 in S. cerevisiae, it was confirmed that the gene encodes an extracellular acid protease. The expression of MpAPr1 was shown to be induced in media containing proteins as sole nitrogen source and repressed when a preferred nitrogen source was available. The gene was expressed in the presence of casein, bovine serum albumin (BSA) and grape juice proteins and repressed in the presence of ammonium sulphate. Expression was most induced in the presence of grape juice proteins, which was expected since these proteins are present in the natural habitat of the yeast. A genetic screening confirmed the presence of the MpAPr1 gene in 12 other M. pulcherrima strains isolated from grape juice. The extracellular protease activity of the strains was also visualized on plates. As far as we know, this is the first report on the genetic characterization of secreted aspartic proteases from non-Saccharomyces yeasts isolated from grape must and provides the groundwork for further investigations. / AFRIKAANSE OPSOMMING: Nie-Saccharomyces giste is voorheen met wynbederf geassosieer en hul teenwoordigheid in wyn is ongewens. Hierdie giste is onlangs ondersoek vir hulle positiewe bydrae tot wyn aroma, in veral sekwensiële en ko-inokulerings met Saccharomyces cerevisiae. Sommige van die nie-Saccahromyces giste skei ‘n verskeidenhied ensieme af wat moontlik vir die wynmaker van nut kan wees. Een groep van hierdie ensieme is die aspartiese suurproteases. Soos deur sommige navorsers aangetoon word, kan die proteases die vorming van proteïenwaasverlaging, terwyl dit terselfdertyd die assimilerende stikstofinhoud van die wyn vir die gebruik en groei van fermentasie-mikroörganismes verhoog. Die proteases kan moontlik ook ‘n indirekte uitwerking op die aromaprofiel van die wyn hê deur die vrystelling van aminosure wat as aromavoorlopers dien. Alhoewel baie studies gedoen is wat die ekstrasellulêre teenwoordigheid van proteases bevestig in nie-Saccharomyces giste wat van druiwesap/wyn afkoms is, is daar geen dokumentasie oor die genetiese karakterisering van hierdie ensieme beskikbaar nie. Die doel van hierdie studie was om gene wat aspartiese proteases in nie-Saccharomyces giste enkodeer, te isoleer en gedeeltelik te karakteriseer. ‘n Versameling van 308 Saccharomyces en nie-Saccharomyces giste wat uit druiwe sap geïsoleer is, is gesif vir ensiematiese aktiwiteit deur plaattoetse uit te voer. Twee gene wat aspartiese protease enkodeer, is geïsoleer van twee nie-Saccharomyces giste. Dit hetpositief gedurende die aktiwiteitstoetse getoets en is deur in silico–analise gekarakteriseer. Die gene is deur die uitvoering van gedegenereerde en inverse PKR geïdentifiseer. Een geen is vanaf Metschnikowia pulcherrima IWBT Y1123 geïsoleer en is MpAPr1 genoem, terwyl die ander van Candida apicola IWBT Y1384 geïsoleer en CaAPr1 genoem is. Die MpAPr1-geen is 1137 bp lank en enkodeer ‘n proteïen wat uit 378 aminosure bestaan met ‘n voorspelde molekulêre massa van 40.1 kDa. Daar teenoor is die CaAPr1-geen 1101 bp lank en enkodeer vir ‘n proteïen wat uit 367 aminosure met ‘n molekulêre massa van 39 kDa bestaan. Hierdie eienskappe is kenmerkend van aspartiese protease. Die afgeleide proteïenvolgorde het minder as 40% homologie met ander ekstrasellulêre aspartiese proteases vertoon, wat dui op die nuwigheid van hierdie ensieme. Die MpAPr1-geen is heterologies in S. cerevisiae YHUM272 uitgedruk en dit het bevestig dat die geen inderdaad ‘n ekstrasellulêre aspartiese protease enkodeer. Die MpAPr1-geen is uitgedruk in media wat alleenlik proteïen as stikstofbron bevat het, terwyl dit onderdruk is in gevalle waar ‘n verkose stikstofbron beskikbaar was. Die geen is uitgedruk in die teenwoordigheid van kaseïen, BSA en proteïene afkomstig vanaf druiwesap en in die teenwoordigheid van ammoniumsulfaat onderdruk. Die hoogste uitdrukking was in die teenwoordigheid van druifproteïene. Hierdie proteïene is teenwoordig in die natuurlike habitat van die gis en is dus dalk ‘n bekende stikstofbron vir die gis. ‘n Genetiese sifting het die teenwoordigheid van die MpAPr1-geen in 12 ander M. pulcherrima–rasse, wat ook van wynkundige oorsprong is, bevestig. Die aspartiese protease-aktiwiteit van die 12 rasse is ook op agarplate waargeneem. Na ons wete, is dit die eerste verslag oor die genetiese karakterisering van afgeskeide aspartiese proteases van nie- Saccharomyces giste van wynkundige oorsprong en verskaf die grondslag vir verdere ondersoek.

The concerns of the present study were to determine 1) the conditions necessary to measure displaceable [³H] L-aspartate binding to membrane fractions of the rat brain, 2) whether the binding demonstrated the charcteristics of the site which is active in vivo, and 3) whether the acidic amino acid neurotransmitters aspartate and glutamate bind to identical or different sites by comparing the pharmacological specificities of the [³H] L-aspartate binding with that of [³H] L-glutamate. The conditions of the [³H] L-aspartate binding assay were determined in synaptosomal and total particulate fractions of whole rat brain. The reaction mixture which included the membrane fraction suspended in Tris-HCl buffer (pH 7.4) in the presence or absence of the compound under test, was incubated at 37°C for 30 minutes. The reaction was stopped by centrifugation and the radioactivity in the pellet counted by liquid scintillation spectrometry. The [³H] L-aspartate binding was characterized in total particulate fractions of rat cerebellum. The apparent dissociation constant (K[sub=D]) and maximum binding (Bmax), as determined by Scatchard analysis, are 1.64 ± 0.34 μM and 7711 ± fmol/mg protein respectively. The displaceable binding is reversible, saturable, independent of the presence of NA⁺, has an affinity in the range where the neurotransmitter is active in vivo, and demonstrates a pharmacological specificity which includes stereospecificity. The compounds tested to demonstrate the pharmacological specificity were L-aspartate (IC[sub=50] = 1.81 μM), D-aspartate (IC[sub=50] = 46.6 μM), L-glutamate (IC[sub=50] = 1.24 μM), N-methyl-DL-aspartate (inactive), kainate (inactive), D-alpha-aminoadipate (inactive), and L-alpha-aminoadipate (IC[sub=50] =7.12 μM). The pharmacological specificity of [³H] L-aspartate binding was different from that of [³H] L-glutamate. When the binding data only are considered, therefore, separate receptors for aspartate and glutamate are indicated. The pharmacological specificity of the [³H] L-aspartate binding, that is the affinity of the binding site for N-methyl-DL-aspartate, D- and L-alpha-aminoadipate, however, does not correlate with the potency of these compounds derived from iontophoretic studies. L-alpha-aminoadipate is very effective while N-methyl-DL-aspartate and D-alpha-aminoadipate do not displace the [³H] L-aspartate binding. In iontophoretic studies, N-methyl-D-aspartate and D-alpha-aminoadipate are very potent as compared to aspartate while L-alpha-aminoadipate Is inactive. The [³H] L-aspartate binding then may not represent the site which is active in vivo. The characteristics of the aspartate site in vivo, however, may not be truely represented in iontophoretic studies because of, for example, uptake of the compounds. The aspartate binding site, therefore, must be identified as that which is activated in vivo. The question of separate receptors for aspartate and glutamate then must still be resolved. / Science, Faculty of / Zoology, Department of / Graduate

Novel terpolymers of leucine (L), aspartic acid (D), and valine (V) were developed as targeting drug delivery carriers that specifically interact with the α 4 β 1 integrin, which is over-expressed in human malignant melanoma cells. As such, copolymerization and terpolymerization of leucine-N-carboxyanhydride (NCA), β-benzyl-aspartate-NCA, and valine-NCA, in dioxane, initiated with triethylamine, were investigated to determine the random nature of the terpolymer composition, for potential application as a targeting drug delivery carrier. The reactivity ratio of each monomer was determined by using Fineman-Ross, Kelen-Tüdös, and nonlinear least-squares curve fitting methods. The product of the estimated reactivity ratios from the monomers in the binary copolymerizations indicated that random polymers were predominantly formed. Based on the reactivity ratios determined from the binary copolymers, Alfrey-Goldfinger equations were used to estimate the composition of the terpolymers. There was no statistical difference between the actual monomer compositions and the calculated compositions of the terpolymers, which validate the randomness of the terpolymers. Therefore, the poly (Leucine-Aspartate-Valine) synthesized in this study is primarily a random terpolymer. The probability of the appearance of LDV sequences occurring within the random polymers were assessed by analyzing the influence of tacticity on the 13 C NMR signals of LDV terpolymers, a statistical method based on the terminal terpolymerization model, and the Poisson distribution, with the highest probability (∼13%) of LDV occurring in a random terpolymer of LDV to be approximately 8 to 9 triad units. Poly (LDV) polymers were shown to exhibit strong binding affinity for A-375 human malignant melanoma cells. The effectiveness of poly (LDV) to target malignant melanoma was evaluated and it showed that 21.3 ± 2.10% of melanoma cells adhered to poly (LDV) films compared to 39.0 ± 3.90% with the positive control fibronectin, whereas binding to HTB-129 human breast carcinoma cells and NHEK normal human keratinocytes were not significant. Poly (LDV)-doxorubicin conjugates displayed excellent selectivity and cytotoxicity in the delivery of doxorubicin. It was shown that the poly (LDV)doxorubicin conjugates exhibited cytotoxicity toward human malignant melanoma cells, but were less toxic than free doxorubicin. In addition, poly (LDV)-doxorubicin conjugates displayed a substantial reduction in toxicity per mole of doxorubicin against normal human keratinocyte cells when compared to free doxorubicin. Fluorescence microscopy showed poly (LDV)-FITC conjugates bound to the A-375 cells and were internalized within 30 minutes. Scatchard plots of poly (LDV)-doxorubicin conjugates were generated, which determined the association constants and established that there is one class of binding sites. It was shown that poly (LDV) could be internalized in a target specific manner by human malignant melanoma cells, which is dependent on the number of LDV targeting moieties in the polymer. These results established that poly (LDV) could be used as a drug delivery carrier that specifically targets the α 4 β 1 integrin.

No description available.

This thesis is focused on enzymatic studies of the secreted aspartic proteases (Saps) from Candida albicans as a tool for discovery of anti-candida drugs. C. albicans causes infections in a number of different locations, which differ widely in the protein substrates available and pH. Since C. albicans needs Saps during virulent growth, these enzymes are good targets for drug development. In order to investigate the catalytic characteristics of Saps and their inhibitor affinities, substrate-based kinetic assays were developed. Due to the low sensitivity of these assays, especially at the sub-optimal pH required to mimic the different locations of infections, these assays were not satisfactory. Therefore, a biosensor assay was developed whereby, it was possible to study interaction between Saps and inhibitors without the need to optimise catalytic efficacy. Furthermore, the biosensor assay allowed determination of affinity, as well as the individual association and dissociation rates for inhibitor interactions. Knowledge about substrate specificity, Sap subsite adaptivity, and the pH dependencies of catalytic efficacy has been accumulated. Also, screening of transition-state analogue inhibitors designed for HIV-1 protease has revealed inhibitors with affinity for Saps. Furthermore, the kinetics and pH dependencies of their interaction with Saps have been investigated. One of these inhibitors, BEA-440, displayed a complex interaction with Saps, indicating a conformational change upon binding and a very slow dissociation rate. A time dependent interaction was further supported by inhibition measurements. The structural information obtained affords possibilities for design of new more potent inhibitors that might ultimately become drugs against candidiasis. The strategy to combine substrate specificity studies with inhibitor screening has led to complementary results that generate a framework for further development of potent inhibitors.

Sabe-se que a hemoglobina é uma rica fonte de peptídeos antimicrobianos (hemocidinas). A primeira hemocidina derivada da hemoglobina bovina caracterizada em carrapatos foi o peptídeo Hb33-61, que é ativo contra bactérias gram-positivas e fungos. Acredita-se que tais hemocidinas sejam geradas proteoliticamente no intestino do carrapato. Neste trabalho nós caracterizamos bioquimicamente uma catepsina D, designada BmAP. A análise da expressão gênica por qPCR mostrou que ela é expressa predominantemente no intestino. Através de LC-MS/MS, determinamos a especificidade de clivagem da BmAP utilizando Hb bovina, e verificamos que resíduos hidrofóbicos foram preferencialmente clivados nos subsítios P1 e P1. Também investigamos a especificidade de clivagem da catepsina L intestinal BmCL1, utilizando uma biblioteca combinatória de tetrapeptídeos e através de hemoglobinólise in vitro. A BmCL1 preferiu resíduos alifáticos no P2 e polares no P1 e P1. Além disso, hidrolisou a cadeia da Hb bovina entre A63/A64, gerando peptídeos com estrutura primária similar ao Hb 33-61. A hemoglobinólise com a BmAP e/ou BmCL1 resultou na formação de algumas hemocidinas, corroborando a hipótese do seu envolvimento na geração endógena de peptídeos antimicrobianos. / It is known that hemoglobin is a rich source of antimicrobial peptides (hemocidins). The first hemoglobin-derived hemocidin characterized in ticks was the peptide Hb33-61, which is active against Gram-positive bacteria and fungi. It is believed that hemocidins are endogenously generated in the tick gut. In this work we biochemically characterized a cathepsin D, designated BmAP. Expression analysis by qRT-PCR showed that it is expressed predominantly in the gut. Through LC-MS/MS, we determined the cleavage specificity of BmAP using bovine hemoglobin, and we verified that hydrophobic residues were preferentially cleaved at the subsites P1 and P1. We also investigated the cleavage specificity of the intestinal cathepsin L BmCL1, using a positional scanning synthetic combinatorial library and through in vitro hemoglobinolysis. BmCL1 preferred aliphatic residues at P2 and polar residues at P1 and P1. Also, it hydrolysed the subunit of bovine hemoglobin at A63/A64, generating peptides with a primary structure similar to Hb 33-61. Hemoglobinolysis with BmAP and/or BmCL1 resulted in the formation of some hemocidins, corroborating the hypothesis that these proteinases are involved in the endogenous generation of antimicrobial peptides

Hidróxidos Duplos Lamelares (HDLs), são materiais lamelares constituídos de camadas positivamente carregadas de um hidróxido misto de dois metais (um di e um trivalente), com ânions hidratados no domínio interlamelar. Apesar de serem potenciais adsorventes, o estudo da adsorção de aminoácidos sobre estes sólidos ainda não foi realizado. Este é importante, pois abre caminho para a aplicação de HDLs na remoção e recuperação de aminoácidos de soluções aquosas, provenientes de processos industriais. Este trabalho teve por objetivo estudar a adsorção e a sorção dos aminoácidos: Ácido Aspártico (Asp), Ácido Glutâmico (Glu) e Fenilalanina (Phe), a partir de soluções aquosas, em HDLs do sistema [Mg-Al-CO3], verificando o efeito de variáveis como temperatura, pH e força iônica (FI) do meio. O adsorvente foi preparado pelo método de coprecipitação a pH variável e caracterizado quanto à composição, organização estrutural, textura e morfologia. A adsorção de Asp, Glu e Phe no HDL não calcinado indicaram que não ocorre a substituição do ânion interlamelar (CO32-), mas sim a adsorção por interação do aminoácido com as cargas residuais na superfície do HDL. O processo mostrou uma grande dependência das variáveis estudadas. A adsorção de Asp e Glu tem comportamento semelhante, embora o aumento da força iônica, seja mais pronunciado em pH 7 para o Asp, e em pH 10 para o Glu. Sem aumento da força iônica, as isotermas atingem ou se aproximam do patamar de adsorção destes aminoácidos, e o aumento na temperatura diminui a quantidade máxima adsorvida. A adsorção de Phe apresentou comportamento similar aos anteriores, exceto pelo fato do aumento da força iônica causar uma diminuição na adsorção. Os resultados obtidos para a sorção no HDL calcinado mostraram que inicialmente o HDL é reconstituído contendo ânions OH- intercalados que são deslocados pelo aminoácido conforme a concentração deste aumenta. Neste caso, Asp e Glu também apresentaram comportamentos semelhantes: as isotermas atingem um patamar onde a sorção torna-se constante e o aumento da temperatura diminui a quantidade sorvida. Para a Phe, a quantidade sorvida é muito maior que para os demais e não se observa o patamar de sorção constante. A temperatura não causa alteração significativa na quantidade sorvida. Os resultados de remoção dos aminoácidos, obtidos para o HDL calcinado se mostraram mais eficientes do que àqueles observados no HDL não calcinado. / Layered Double Hydroxides (LDHs), are lamellar materials constituted of positively charged layers of two cations mixed hydroxide (a bi and a trivalent one), with hydrated anions in the interlayer domain. In spite of they being potential adsorbents, the study of the adsorption of amino acids on these solids has not been done yet. This is important, because it opens the perspective for the application of LDHs to remove and to recover amino acids from aqueous solutions, resultant from industrial processes. The aim of this work was to study the adsorption and the sorption of the amino acids: Aspartic Acid (Asp), Glutamic Acid (Glu) and Phenylalanine (Phe), from aqueous solutions, in [Mg-Al-CO3] LDHs, verifying the effect of the variables: temperature, pH and ionic strength of the medium. The adsorbent was prepared by the coprecipitation method and characterized with respect to their composition, structural organization, texture and morphology. The adsorption of Asp, Glu and Phe in LDH indicated that the substitution of the interlayer anion (CO32-) doesn\'t occur, but the adsorption process occurs by the interaction of the amino acid with the residual charges on the LDH surface. The process showed a dependence on the parameters studied. The adsorption of Asp and Glu presented similar behavior, although the ionic strength effect is more pronounced in pH 7 for Asp, and in pH 10 for Glu. Without the increase in ionic strength, the isotherms reach or approach a plateau, and the increasing in the temperature reduces the maximum amount adsorbed. The adsorption of Phe has similar behavior to the previous ones, except at higher ionic strength, in which a decrease in the adsorption was observed. The results for the sorption in calcined LDH showed that the LDH are reconstituted with the OH- anions intercalated at low amino acid concentrations. The intercalation of amino acid becomes important as their concentration increase. In this case, Asp and Glu also presented similar behaviors: the isotherms reach a plateau where the sorption becomes constant and the increase of the temperature reduces the amount of sorbed amino acid. For Phe, the amount sorbed is higher than those for the others amino acids and the plateau of constant sorption was not observed. The temperature doesn\'t cause any significant alteration in the sorbed amount. The results of removing the amino acids on calcined LDH showed to be more efficient than those observed for the adsorption in LDH.

<p>This thesis describes the design and synthesis of compounds that are</p><p>intended to inhibit serine and aspartic proteases. The first part of the text deals with preparation of inhibitors of the hepatitis C virus (HCV) NS3 serine protease. Hepatitis C is predominantly a chronic disease that afflicts about 170 million people worldwide. The NS3 protease, encoded by HCV, is essential for replication of the virus and has become one of the main targets when developing drugs to fight HCV. The inhibitors discussed here constitute surrogates for the widely used <em>N</em>-acyl-hydroxyproline isostere designated 4-hydroxy-cyclopentene. The stereochemistry of the 4-hydroxy-cyclopentene scaffold was determined by nuclear overhauser effect spectroscopy (NOESY) and the regiochemistry by heteronuclear multiple bond correlation (HMBC). The scaffold was decorated with different substituents to obtain both linear and macrocyclic HCV NS3 protease inhibitors that display low nanomolar activity. The second part of the thesis describes the design and synthesis of potential aspartic protease inhibitors. The hydroxyethylene motif was used as a noncleavable transition state isostere. The synthetic route yielded a pivotal intermediate with excellent stereochemical control, which was corroborated by NOESY experiments. This intermediate can be diversified with different substituents to furnish novel aspartic protease inhibitors.</p> / Report code: LIU-TEK-LIC-2006:45

<p>Ten years ago, the first protease inhibitor targeting the human immunodeficiency virus (HIV) was approved for clinical use. Highly active antiretroviral therapy (HAART), which combined protease and reverse transcriptase inhibitors, quickly became the standard therapy for treating patients infected with HIV and Acquired Immune Deficiency Syndrome (AIDS). Nevertheless, last year the AIDS pandemic reached its highest level ever. Many infected patients, mainly in the developing countries, are still without treatment. Among those patients who receive treatment, an increase in drug resistance and new-infection with drug-resistant strains are seen. To come to terms with these problems, new drugs that are efficient against resistant strains and can be produced at low cost are needed.</p><p>In this study, we have focused our research efforts on cyclic sulfamides active as HIV-1 protease inhibitors. Distinctive to this compound class, as compared to the inhibitors so far approved for clinical use, was the incorporation of a water mimic that displaces the structural water (W301) observed in the X-ray crystal co-complexes. The first part of the study was aimed at understanding the rationale behind the nonsymmetric binding mode that the inhibitor adopted when bound to the enzyme. Symmetric and nonsymmetric inhibitors were synthesized and the structure-activity relationships and preferable binding modes were rationalized with the help of Comparative Molecular Field Analysis (CoMFA).</p><p>In the second part of the study, an attempt was made to reduce the size of these inhibitors. As a result, the traditional P1/P1' substituents were removed, while the P2/P2' substituents were elongated in an attempt to reach between the binding sites. The design hypothesis was shown to be successful and inhibitors possessing nanomolar activity were identified.</p>