The Kingston group's engagement in an International Cooperative Biodiversity Group (ICBG) program and a collaborative research project established between Virginia Tech and the Institute for Hepatitis and Virus Research (IHVR) has focused on the search for bioactive natural products from tropical forests in both Madagascar and South Africa. As a part of this research, a total of four antiproliferative extracts were studied, leading to the isolation of fourteen novel compounds with antiproliferative activity against the A2780 human ovarian cancer line. One extract with antimalarial activity was studied, which led to the isolation of two new natural products with antiplasmodial activity against a drug-resistant Dd2 strain of Plasmodium falciparum. The plants and their secondary metabolites are discussed in the following order: two new antiproliferative acetogenins from a Uvaria sp. (Annonaceae); two new antiproliferative calamenene-type sesquiterpenoids from Sterculia tavia (Malvaceae); two new antiproliferative triterpene saponins from Nematostylis anthophylla (Rubiaceae); six new antiproliferative homoisoflavonoids and two new bufatrienolides from Urginea depressa (Asparagaceae); and two new antiplasmodial anthraquinones from Kniphofia ensifolia (Asphodelaceae). The structures of all these compounds were determined by analysis of their mass spectrometric, 1D and 2D NMR, UV and IR spectroscopic and optical rotation data. Other than structural elucidation, this work also involved bioactivity evaluations of all the isolates, as well as total synthesis of the two antiproliferative sesquiterpenoids, and a structure-activity relationship (SAR) studies on the antiplasmodial anthroquinones. / Ph. D.

The work in the dissertation expands the applications of DIEF and describes the development of incorporating DIEF in a microfluidic chip to create a comprehensive proteomics tool. Proof-of-concept DIEF experiments have been done previously, so the focus of this work is to explore the capabilities of DIEF. Dynamic isoelectric focusing (DIEF) is a separation technique invented by Dr. Luke Tolley. It is similar to capillary isoelectric focusing except it uses four high voltage electrodes to form a pH gradient instead of only two. The additional two electrodes are able to manipulate the pH gradient resulting in selection of the region and of the range of pH within a pre-defined sampling or extraction point. One of the first applications described for DIEF was to isolate a single protein from a complex mixture. The protein isolated was a cellulase enzyme capable of degrading multiple cellulose materials over a wide range of environmental conditions. DIEF did isolate the protein in a pH span of 0.005 which is equivalent to 0.075% of the total pH range. Fractions were collected for sequencing analysis, but the fractions were contaminated with keratin both times. DIEF was also successfully performed in an open air channel. Though other electromigration techniques have been successfully done in open air channels, these techniques were severely time and pH limited. In contrast, DIEF in an open air channel is capable of using the entire 3-10 pH range and can perform isolations until the proteins are completely separated. The device developed was also an improvement on increasing sample capacity. The channel was significantly bigger than the traditional glass capillaries used. Since the channel was open, fraction collection was made simpler by collecting using a pipette. This work also demonstrated that DIEF can be made through the use of silicone molding compounds and polyurethane. The amount of milling needed is reduced, the pieces are produced quickly, and a single mold can produce several pieces. Machining pieces with fragile bits is not needed to be done as much since only one acrylic piece is required produce a mold. The mold can produce several polyurethane pieces. This fabrication method has proven useful for making DIEF holders. The next step was to make DIEF a truly comprehensive proteomic tool by incorporating it into a microfluidic chip. Multiple sample fractions are rapidly generated on chip through the use of multiple bubbles simultaneously injected into the separation channel. This stops the separation and, since each droplet is isolated from others by a bubble on each side, the protein peaks are not able to broaden. This novel use of digital microfluidics is still a work in progress, but the fundamentals have been demonstrated. The fabrication protocol for making molds and PDMS casts was developed using materials and procedures that can be done in a common laboratory environment. DIEF is a separation technique still in its infancy, with a wide variety of available applications. DIEF will continue to be tested in other areas and developed into a comprehensive proteomic tool.

This thesis examined the antimicrobial activity of select neotropical plants from Costa Rica and traditional Q’eqchi Maya medicines from Belize. In particular the potential for interference with bacterial quorum sensing (QS) and biofilm formation as well as fungal growth were assessed. Of one hundred and twenty six extracts collected from Costa Rica, one third showed significant QS inhibition while 13 species displayed more biofilm inhibitory activities than the positive control allicin. The active species belonged to the Lepidobotryaceae, Melastomataceae, Meliaceae, Sapindaceae, and Simaroubaceae. Twelve Marcgraviaceae species were tested for the same biological activities; of these, three showed similar QS inhibition to that of the positive control Delisea pulchra (Greville) Montagne and five with at least 30% biofilm inhibition. Only one species inhibited fungal growth – Marcgravia nervosa Triana & Planch. Bioassay-guided isolation of this plant resulted in the identification of the active principle as a naphthoquinone, with a minimum inhibitory concentration (MIC) ranging from 85 to 100 μM against Saccharomyces cerevisiae. Similarly, sixty one Q’eqchi’ Maya medicinal plant species were evaluated for their antimicrobial activities. Of these, four species showed more QS inhibition than D. pulchra, seven with comparable biofilm inhibitory activities that of allicin, and two with similarly antifungal activity to berberine. Two spirostanol saponins were isolated from Cestrum schlechtendahlii G.Don, an active antifungal plant. The major saponin showed growth inhibition against Saccharomyces cerevisiae and Fusarium graminearum, with MICs of 16.5 μM and 132 μM, respectively. Further analyses of this compound using chemical genomics suggested that its antifungal mechanism of action is pleiotropic, affecting multiple targets. Taken together, these findings showed that neotropical plants and traditional Q’eqchi’ Maya medicines contain phytochemicals that interfere with bacterial biofilm formation and quorum sensing as well as fungal growth.

>Magister Scientiae - MSc / The high rate of rediscovery of known compounds has led to a decline in the discovery of novel natural products. The high biodiversity of organisms growing in extreme conditions such as oceans has led to the increased interest by researchers for their use as a source of novel natural products. Marine bacteria are known for their extensive biosynthetic capacity to produce diverse natural products, which are suitable for various biotechnology applications such as in agriculture, for treatment of fungal plant pathogens, and as antibiotics, for treatment of bacterial infections. This study aimed at discovering novel secondary metabolites from marine bacteria previously associated with novel marine invertebrate species endemic to the South African coast. The methodologies used in this study included a bioassay guided fractionation coupled to genome sequencing and mining. For the bioassay guided fractionation approach, the study first focused on screening marine bacteria for antimicrobial activity when cultured on 4 different media, against fungal strains previously shown to be virulent olive trunk pathogens. In parallel, the bacterial isolates with the most inhibitory activity against the fungal pathogens were also screened for antimicrobial activity against 4 indicator strains including Gram-negative Escherichia coli 1699 (E. coli), Pseudomonas putida, and Gram-positive Staphylococcus epidermidis ATCC14990, and Bacillus cereus ATCC10702. One of the marine bacterial isolates, PE6-126, showed diverse antimicrobial activity including antibacterial and antifungal activity against the tested strains. The genome sequencing data revealed that this isolate was B. cereus based on the average nucleotide identity (ANI) (>99%) to reference strains. antiSMASH analysis of the genome revealed nine predicted secondary metabolite clusters including bacteriocins (2), non-ribosomal peptide synthetase (NRPS) (2), siderophore (1), sactipeptide (1), betalactone (1), linear azol(in)e-containing peptides (LAP) - bacteriocin (1) and a terpene (1). Some of these pathways had low to no sequence similarity to known pathways, indicating the potential of these pathways to produce novel compounds. One of the pathways showed very high sequence similarity to the thuricin CD pathway in Bacillus thuringiensis. Considering that thuricin CD has been reported to have antimicrobial activity against B. cereus (ATCC1072), it was hypothesised that it could also be produced by PE6-126. However, the antimicrobial extract from PE6-126 was tested for sensitivity to proteinase K and heat treatment, which thuricin CD is known to be sensitive to. The results revealed that the antimicrobial activity was not lost after treatment, implying that a different metabolite could be responsible for the anti-B. cereusactivity. In addition, PE6-126 initially displayed antimicrobial activity against a multi-drug resistant E. coli 1699, suggesting some of the antimicrobial compound/(s) produced by this strain could potentially be novel. The bioassay-guided fractionation approach coupled to Liquid Chromatography Mass Spectrometry (LC-MS) did not lead to identification of the antimicrobial compound/(s), therefore it remains a question whether the secondary metabolite pathways predicted by antiSMASH lead to the production of the active compound/(s).The results from this study showed that even well studied species have the potential to synthesize as yet undescribed compounds, based on the novelty of some of the pathways. This study highlights the importance of employing a genome-guided approach in drug discovery, as there may be many novel compounds to discover from biosynthetic pathways that have not yet been characterised. Further research is needed to identify the antimicrobial compound/(s) produced by PE6-126.

Philosophiae Doctor - PhD / bioassay guided isolation approach was then used to isolate the high molecular weight antibacterial compound (50kDa-100kDa) from T. actiniarum fermentations. With common protein isolation, purification and detection methods failing to provide insight into the nature of the antibacterial compound, we hypothesized that the active agent is not proteinaceous in nature and may be a high molecular weight exopolysaccharide. Extraction and antibacterial screening of the exopolysaccharide fraction from T. actiniarum showed antibacterial activity as well as lytic activity when subjected to a zymography assay using Pseudomonas putida whole cells as a substrate. Additionally, the biosynthetic pathways for the production of poly-β-1, 6-N-acetyl-glucosamine (PNAG), an exopolysaccharide involved in biofilm formation and chondroitin sulfate, a known and industrially important glycosaminoglycan with antibacterial and anti-inflammatory activity was identified and the mechanism may be novel. Genome mining identified a variety of novel secondary metabolite gene clusters which could potentially encode other novel bioactivities. Therefore a bioassay guided isolation, focused on the small (<3kDa) molecules, was pursued. Secondary metabolites were extracted, fractionated and screened for biofilm inhibition, antibacterial and anticancer activity and activity was observed in all assays. Active fractions were dereplicated by UHPLC-QToF-MS and compounds of interest were isolated using mass guided preparative HPLC. The purity of the isolated compounds was assessed using UHPLC-QToF-MS and NMR and the structure of the target compounds elucidated. Structures that could be determined were the bile acids cholic acid and 3-oxo cholic acid and although not responsible for the observed activities, this is the first report of bile acid production for this genus. This is the first study investigating the bioactive potential of the strain and the first demonstrating that T. actiniarum is a promising source of potentially novel pharmaceutically relevant natural products depicted through both culture-dependent and culture-independent approaches.

Made available in DSpace on 2015-05-14T13:00:09Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 6176997 bytes, checksum: 84882ba9517a6db053cc7c655b0e9d39 (MD5) Previous issue date: 2014-08-25 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Propolis is an heterogeneous mixture of substances, produced by melliferous bees from plants in close proximity with the bee´s hives. It is usually classified according to its botanical origin and chemical composition that vary according to geographical origin. Studies have shown that red propolis have physicochemical and biological properties that are diverse from other propolis types. There is a scarcety of studies with Brazilian red propolis, and no study with the red propolis from Igarassu (PE, Brazil), and thus its botanical origin, chemical characterization, and pharmacological activities have not been determined. The aim of this study was to perform a bioassay-guided fractionation of two propolis samples, collected from Igarassu, in order to determine the substances responsible for its antimicrobial, antioxidant, antileukemic and leishmanicidal activities, as well as its palynological profile. The samples of propolis were collected in Igarassu-PE, in natura, in May 2012 in two apiaries. They were submitted to palynological analyses to identify the pollen types and their frequency in the samples. Then, samples in natura were powdered, extracted with 96% ethanol and concentrated to obtain the crude ethanol extract. This extract was dissolved in a mixture of methanol:water (1:1, v/v) and partitioned with hexane and ethyl acetate, obtaining the hexane, ethyl acetate and hydroalcoholic fractions. The acetate fraction was submitted to column chromatography with Sephadex LH20 for isolation of the compounds. The propolis in natura was subjected to preliminary phytochemical screening. The ethanol extract was evaluated for identification of compounds by HPLC-MS. The propolis in natura, ethanol extract, hexane fraction, ethyl acetate and hydroalcoholic were submitted to HPLC analysis for identification and quantification of phenolic compounds. A total of 28 different pollen types belonging to 16 families and 30 genera were found in the samples. The most frequent were: Serjania and Dalbergia (sample 1 April 2011), Fabaceae 1 and Dalbergia (sample 2 April 2011), Stigmaphyllon (sample 1 and 2 May 2012). It was found the presence of flavonoids and steroids in propolis in natura. Twenty five compounds were identified in the crude ethanol extract of the samples 1 and 2. The major compounds belong to the class of flavonols, flavanas, isoflavones and prenylated benzophenones pterocarpans, demonstrating the usefulness of the technique of LC - Orbitrap - FTMS. The chemical profile of samples 1 and 2 of propolis are characterized by the presence of benzophenone. In propolis in natura, ethanol extract, hexane fraction, ethyl acetate and hydroalcoholic, we were able to identify and quantify 8 substances, 1 phenolic acid and 7 flavonoids. In the ethyl acetate fraction of sample 1 the isoflavone formononetin was isolated. It is observed that during the fractionation, starting from propolis in natura crushed to formononetin isolated substance, there was an increase in fungistatic power. It is observed that with fractionation, starting from propolis in natura to formononetin isolated substance, there was an increase in fungistatic power. Regarding antioxidant activity against DPPH radical, it was observed that all samples showed antioxidant power, with the exception of isolated formononetin. In descending order, in relation to antioxidant power, the most nonpolar samples had higher activity than polar samples. Both propolis in natura as crude ethanol extract showed strong activity against Leishmania promastigotes of L. amazonensis. The antileukemic activity on the cell line HL- 60 also increased with fractionation. / A própolis é uma mistura heterogênea de compostos e é produzida por abelhas a partir de vegetais encontrados próximos às colmeias. É classificada de acordo com a origem botânica e a composição química que pode variar entre as regiões. Estudos têm demonstrado que a própolis vermelha possui características físico-químicas e biológicas diferenciadas. No estado de Pernambuco, até o momento são poucos os trabalhos realizados com a própolis vermelha, e não há na literatura estudos com a própolis vermelha de Igarassu PE, com isso sua origem botânica, caracterização química e suas atividades farmacológicas, ainda não estão definidas. O objetivo deste estudo foi realizar um fracionamento biomonitorado de duas amostras de própolis vermelha, coletadas em Igarassu PE, a fim de determinar os compostos responsáveis pelas atividades antimicrobiana, antioxidante, antileucêmica e antileishmania, além de traçar um perfil palinológico. As amostras de própolis vermelha foram coletadas em Igarassu-PE, na forma in natura, em maio de 2012, em dois apiários. Foram submetidas à análise palinológica, para identificação dos grãos de pólen e dos tipos polínicos presentes. Em seguida, as amostras in natura foram trituradas, extraídas em etanol 96% e concentradas obtendo-se o extrato etanólico bruto seco. Esse extrato foi suspenso em uma mistura de metanol-água (1:1) e fracionado por separação líquido-líquido com hexano e acetato de etila, obtendo-se as frações hexânica, acetato de etila e hidroalcoólica. A fração acetato foi refracionada em coluna de Sephadex LH-20 para isolamento dos compostos. A própolis in natura foi submetida ao screening fitoquimico preliminar. O extrato etanólico foi avaliado para identificação dos compostos por CLAE-EM. A própolis in natura, extrato etanólico, frações hexânica, acetato de etila e hidroalcoólica foram submetidas a análise do perfil cromatográfico por CLAE, análise do perfil fenólico, identificação e quantificação de compostos fenólicos e avaliação das atividades farmacológicas. Nas amostras in natura, foram encontrados 28 tipos polínicos, pertencentes a 16 famílias e 30 gêneros botânicos. Os tipos polínicos que apareceram em maior frequência foram: Serjania e Dalbergia (amostra 1- abril de 2011), Fabaceae 1 e Dalbergia (amostra 2-abril de 2011), Stigmaphyllon (amostra 1 e 2-maio de 2012). Verificou-se a presença de flavonoides e esteroides na própolis in natura. Foram identificados 25 compostos no extrato etanólico bruto das amostras 1 e 2 de própolis vermelha, onde as principais substâncias identificadas pertencem à classe dos flavonols, flavanas, isoflavonas, pterocarpanos e benzofenonas preniladas, demonstrando a utilidade da técnica de LC - Orbitrap - FTMS. O perfil químico das amostras 1 e 2 de própolis vermelha são caracterizados pela presença de benzofenonas. Na própolis in natura, extrato etanólico, frações hexânica, acetato de etila e hidroalcoólica, foram identificadas e quantificadas 8 substâncias, sendo 1 ácido fenólico e 7 flavonoides. Na fração acetato de etila da amostra 1, foi isolada a isoflavona formononetina. Observa-se que ao longo do fracionamento, partindo da própolis in natura triturada até a substância isolada formononetina, houve um aumento no poder fungistático. Em relação a atividade antioxidante, medida pelo método de DPPH, observou-se que todas as amostras apresentaram poder antioxidante, com exceção da substância isolada. Em ordem decrescente, em relação ao poder antioxidante, as amostras mais apolares tiveram maior atividade que as amostras polares. Tanto a própolis in natura triturada assim como o extrato etanólico bruto apresentaram forte atividade antileishmania sobre as formas promastigotas de L. amazonensis. A atividade antileucêmica também aumentou ao longo do fracionamento, sobre a linhagem celular HL-60.

>Magister Scientiae - MSc / The high rate of rediscovery of known compounds has led to a decline in the discovery of novel natural products. The high biodiversity of organisms growing in extreme conditions such as oceans has led to the increased interest by researchers for their use as a source of novel natural products. Marine bacteria are known for their extensive biosynthetic capacity to produce diverse natural products, which are suitable for various biotechnology applications such as in agriculture, for treatment of fungal plant pathogens, and as antibiotics, for treatment of bacterial infections. This study aimed at discovering novel secondary metabolites from marine bacteria previously associated with novel marine invertebrate species endemic to the South African coast. The methodologies used in this study included a bioassay guided fractionation coupled to genome sequencing and mining. For the bioassay guided fractionation approach, the study first focused on screening marine bacteria for antimicrobial activity when cultured on 4 different media, against fungal strains previously shown to be virulent olive trunk pathogens. In parallel, the bacterial isolates with the most inhibitory activity against the fungal pathogens were also screened for antimicrobial activity against 4 indicator strains including Gram-negative Escherichia coli 1699 (E. coli), Pseudomonas putida, and Gram-positive Staphylococcus epidermidis ATCC14990, and Bacillus cereus ATCC10702. One of the marine bacterial isolates, PE6-126, showed diverse antimicrobial activity including antibacterial and antifungal activity against the tested strains. The genome sequencing data revealed that this isolate was B. cereus based on the average nucleotide identity (ANI) (>99%) to reference strains. antiSMASH analysis of the genome revealed nine predicted secondary metabolite clusters including bacteriocins (2), non-ribosomal peptide synthetase (NRPS) (2), siderophore (1), sactipeptide (1), betalactone (1), linear azol(in)e-containing peptides (LAP) - bacteriocin (1) and a terpene (1). Some of these pathways had low to no sequence similarity to known pathways, indicating the potential of these pathways to produce novel compounds. One of the pathways showed very high sequence similarity to the thuricin CD pathway in Bacillus thuringiensis. Considering that thuricin CD has been reported to have antimicrobial activity against B. cereus (ATCC1072), it was hypothesised that it could also be produced by PE6-126. However, the antimicrobial extract from PE6-126 was tested for sensitivity to proteinase K and heat treatment, which thuricin CD is known to be sensitive to. The results revealed that the antimicrobial activity was not lost after treatment, implying that a different metabolite could be responsible for the anti-B. cereus activity. In addition, PE6-126 initially displayed antimicrobial activity against a multi-drug resistant E. coli 1699, suggesting some of the antimicrobial compound/(s) produced by this strain could potentially be novel. The bioassay-guided fractionation approach coupled to Liquid Chromatography Mass Spectrometry (LC-MS) did not lead to identification of the antimicrobial compound/(s), therefore it remains a question whether the secondary metabolite pathways predicted by antiSMASH lead to the production of the active compound/(s). The results from this study showed that even well studied species have the potential to synthesize as yet undescribed compounds, based on the novelty of some of the pathways. This study highlights the importance of employing a genome-guided approach in drug discovery, as there may be many novel compounds to discover from biosynthetic pathways that have not yet been characterised. Further research is needed to identify the antimicrobial compound/(s) produced by PE6-126.

No description available.

No description available.

Da fração hexânica do extrato metanólico das folhas de Guarea guidonia (Meliaceae), foram isolados os diterpenos: [11S-(1&#945;,2E,6E,10&#945;)]-3,7,11-trimetil-11-(4-metil-pent-3-en-1-i1)biciclo[8.1.0]undeca-2,6-dieno e [1S(1a&#946;,4a&#945;,7a&#946;,7b&#946;)]-decaidro-1,7-dimetil-1-(4-metil-pent-3-en-1-il)-4-metilen-1H-cicloprop[e]azulen-7-ol, já descritos na literatura, além de dois novos isômeros de [1S-(1a&#946;,4a&#945;,7a&#946;, 7a&#946;)]-decaidro-1,7-dimetil-1-(2-hidroxi-4-metil-pent-3-en-1-il)-4metilen-1H-cicloprop[e]azulen-7-ol. No óleo essencial obtido das folhas do mesmo espécimen foram identificados, através da análise dos dados espectroscópicos (RMN 13C, RMN 1H e EM), os sesquiterpenos: eudesma-5,7-dieno, 5&#945;,6&#945;-epoxi-eudesm-7-eno, eudesma-5,7-dien-2&#945;-ol, 5&#945;,6&#945;-epoxi-eudesm-7-en-9-ol e guaia-6-en-10-ol, ainda não descritos na literatura, além de eudesma-4(15), 11(13)-dieno, eudesm-6-em-4&#945;-ol, eudesma-4,11-dieno e 5&#945;,6&#945;,7&#945;,8&#945;-diepoxieudesmano. Diversos extratos vegetais assim como substâncias puras e misturas de composições conhecidas foram testadas com a finalidade de se detectarem substâncias com atividade anticancerígena. Para tal, empregou-se o bioensaio com linhagens mutantes do fungo Saccharomyces cerevisiae, utilizados pelo grupo do Prof. Dr. David Kingston, do Virgínia Tech Institute. Também foi realizado um estudo químico biomonitorado por aquele bioensaio. / From the hexanic extract of the dry leaves of Guarea guidonia (Meliaceae) two new isomers of decahydro-1,7-dimethyl-1-(2-hydroxy-4-methyl-pent-3-en-1-yl)4- methylen-1H-cycloprop[e]azulen-7-ol were isolated together with the known diterpenes [11S-(1&#945;,2E,6E,10&#945;)]-3,7,11-trimethyl-11-(4-methyl-pent-3-en-1yl) bicyclo[8.1.0]undeca-2,6-dien and [1S-(1a&#946;,4a&#945;,7a&#946;,7bJ3)]-decahydro-1,7dimethyl- 1-(4-methyl-pent-3-en-1-yl)-4-methylen-1H-cycloprop[e]azulen-7-ol. The essential oil from the leaves of the same plant afforded the sesquiterpenes eudesma-5,7-diene, 5&#945;,6&#945;-epoxy-eudesm-7-ene, eudesma-5,7-dien-2&#945;-ol, 5&#945;,6&#945;-epoxy-eudesm-7-en-9-ol and guaia-6-en-10-ol not previouly described, besides eudesma-4(15),11 (13)-diene, eudesm-6-en-4&#945;-ol, eudesma-4,11-diene and 5&#945;,6&#945;,7&#945;,8&#945;-bisiepoxy-eudesmane. All of these compounds were identified through 13C and 1H NMR spectroscopy as well as MS. Several plant extracts and pure compounds were tested in the search for potential anticancer agents, through the mechanism-based yeast bioassay, utilizing mutants of the yeast Saccharomyces cerevisiae. The screening of those plant materials and a bioassay-guided fractionation of an active extract were both carryed out in the laboratories of Professor David G.I. Kingston at Virginia Tech Institute.