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Dissertations / Theses on the topic 'Natural molecules'

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Published: 4 June 2021
Last updated: 15 February 2022

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1

Camou-Arriola, Fernando Alberto Josue. "Structure determinations of natural products and related molecules." Diss., The University of Arizona, 1989. http://hdl.handle.net/10150/184773.

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Structures were determined for 48 new natural products and several related compounds by NMR methods. One new natural product and two unnatural product structures were determined by X-ray diffraction. Molecular mechanics calculations on two indoles related to the neurotransmitter serotonin and on some synthetic cyclophanes were used to gain information about their preferred conformations. Considerable time is wasted redetermining the structures of known natural products when they are encountered in new sources. To help alleviate this problem, a database which searches on proton NMR chemical shifts was developed.
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2

O'Leary-Steele, Catherine Ann. "The synthesis of skeletally diverse, natural product-like small molecules." Thesis, University of Leeds, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.496526.

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3

Tang, Lam T. "New routes to heterocyclic product families." Thesis, University of Oxford, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.365338.

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4

Goté, Lisa R. "Alternate pathways of cytotoxic T lymphocyte and natural killer cell activation." Thesis, Virginia Tech, 1995. http://hdl.handle.net/10919/43130.

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CD44 is a transmembrane glycoprotein found on a variety of cells including those of myeloid and lymphoid origin. CD44 is highly conserved among various species and is involved in the homing of lymphocytes and monocytes to lymph nodes, Peyer's patches, and sites of inflammation. In the present study, we demonstrate that monoclonal antibody (mAb) 9F3, directed against murine CD44 expressed on cytotoxic T lymphocytes (CTls), can trigger the lytic activity of CTls and redirect CTl-mediated lysis to antigen-negative Fc receptor-positive target cells. Similar redirected lysis was also inducible using mAb MEL - 14, directed against the lymphocyte homing receptor for endothelium (gp - 90MEL-14). The redirected lysis induced by mAbs 9F3 and MEl-14 in the CTL was similar to that induced by mAbs against the aβ T-cell receptor or CD3. In contrast, mAbs directed against CDS, CD45R, and CD11a (LFA-1, lymphocyte function-associated antigen 1) failed to evoke lytic activity. Furthermore, CD44 and MEl-14 mAbs were able to mediate NK cell lysis of the NK-resistant tumor PS15. The current study demonstrates that CD44 and gp_90MEL-14 molecules, in addition to participating in T-cell homing and adhesion, may play a major role in delivering the transmembrane signal to the CTl that triggers the lytic activity, even when the T cell receptor is not occupied. The alternate pathway of CTL activation characterized in this study may exhibit both beneficial and deleterious effects on the host. On one hand, this property may enable CTL to kill cancer cells or virally-infected cells which may fail to express major histocompatibility complex (MHC)-encoded antigens. On the other hand, this alternate pathway may contribute to nonspecific tissue damage seen at sites of inflammation.


Master of Science
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5

Wang, Siyuan. "Engineering of polyketide biosynthetic pathways for bioactive molecules." DigitalCommons@USU, 2016. https://digitalcommons.usu.edu/etd/4684.

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Polyketides are a large group of structurally diverse natural products that have shown a variety of biological activities. These molecules are synthesized by polyketide synthases (PKSs). PKSs are classified into three types based on their sequence, primary structure, and catalytic mechanism. Because of the bioactivities of polyketide natural products, this study is focused on the engineering of PKS pathways for efficient production of useful bioactive molecules or structural modification to create new molecules for drug development. One goal of this research is to create an efficient method to produce pharmaceutically important molecules. Seven biosynthetic genes from plants and bacteria were used to establish a variety of complete biosynthetic pathways in Escherichia coli to make valuable plant natural products, including four phenylpropanoid acids, three bioactive natural stilbenoids, and three natural curcuminoids. A curcumin analog dicafferolmethane was synthesized by removing a methyltransferase from the curcumin biosynthetic pathway. Furthermore, introduction of a fungal flavin-dependent halogenase into the resveratrol biosynthetic pathway yielded a novel chlorinated molecule 2-chloro-resveratrol. This demonstrated that biosynthetic enzymes from different sources can be recombined like legos to make various plant natural products, which is more efficient (2-3 days) than traditional extraction from plants (months to years). Phenylalanine ammonia-lyase (PAL) is a key enzyme involved in the first biosynthetic step of some plant phenylpropanoids. Based on the biosynthetic pathway of curcuminoids, a novel and efficient visible reporter assay was established for screening of phenylalanine ammonia-lyase (PAL) efficiency in Escherichia coli. The other goal of this research is to characterize and engineer natural product biosynthetic pathways for new bioactive molecules. The biosynthetic gene cluster of the antibacterial compound dutomycin was discovered from Streptomyces minoensis NRRL B-5482 through genome sequencing. Confirmation of the involvement of this gene cluster in dutomycin biosynthesis and creation of a series of new molecules were successfully conducted by rationally modifying the biosynthetic pathway. More importantly, a new demethylated analog of dutomycin was found to have much higher antibacterial activity against Staphylococcus aureus and methicillin-resistant Staphylococcus aureus.
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6

Süß, Barbara [Verfasser]. "Taste Molecules and Taste Modulators Generated by Targeted Natural Product Transformation / Barbara Süß." München : Verlag Dr. Hut, 2013. http://d-nb.info/1042307873/34.

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7

Rhys, Natasha Hazel. "Exploring the structural properties of natural and synthetic biological molecules in aqueous solution." Thesis, University of Leeds, 2015. http://etheses.whiterose.ac.uk/11248/.

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Peptoids are synthetic mimics of naturally-occurring peptides (the natural building blocks of proteins). These interesting building blocks are more resistant to temperature, pH and solvent denaturation, and possess a more exible backbone compared to their peptide counterparts. As a result, peptoids are emerging as promising biomimetic materials for a range of applications. Despite this potential, very little is known about the intermolecular interactions which determine their stability and solubility, including hydrogen-bonding, hydrophobic interactions and hydration properties, as well the structural properties of the individual imino acid blocks that make them. This thesis presents neutron diffraction experiments coupled with isotopic substitution and computational modelling to complete a structural study on a model imino acid in aqueous solution. The focus here has been on glutamine, a molecule that is capable of forming multiple hydrogen bonds and is thought to self-assemble through preferential side-chain hydrogen bond interactions, making it an interesting model system. Furthermore, glutamine is important in many biochemical processes and its presence has been associated with a number of neurodegenerative diseases. By probing the structural properties of the model system in aqueous solution and of its amino acid equivalent, L-glutamine, it has been possible to uncover details of important intermolecular interactions that govern the properties of these biomolecules. The interactions of the model imino acid have also been observed with respect to temperature and concentration and compared to a naturally-occurring imino acid, sarcosine, to determine the impact of side chain on imino acid interactions. This work also serves as a reference for completing structural studies on such biomolecules, covering methodological benefits and limitations. This is the necessary first step in building a framework to understand the self-assembly and driving forces in more complex peptoid and peptide structures and serves as a reference for completing neutron studies on natural and synthetic biomolecules.
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8

Backström, Eva. "Expression of stimulatory and inhibitory molecules in interactions between natural killer cells and neurons /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-516-6.

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9

De, Ghellinck D'Elseghem Alexis. "Natural and model membranes: structure and interaction with bio-active molecules via neutron reflection." Doctoral thesis, Universite Libre de Bruxelles, 2013. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209550.

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Dans cette thèse de doctorat, la structure de membranes naturelles et modèles et leurs interactions avec des molécules biologiquement actives ont été étudiées au moyen de la réflectométrie de neutrons. Les lipides naturels ont été extraits de la levure Pichia pastoris, poussée en milieux deutéré et hydrogéné. L’analyse a montré que la quantité relative de phospholipides n’est pas affectée par le changement en composition isotopique du milieu de croissance. Cependant, les cellules de levures deutérées contiennent principalement des acides gras C18 :1 alors que le degré d’insaturation est plus élevé chez les levures hydrogénés. Diminuer la température du milieu de croissance permet d’augmenter le degré d’insaturation des acides gras chez les levures deutérées. Une analyse qualitative des sphingolipides a été réalisée et un protocole pour séparer les fractions phosphocholines et phosphoethanolamine a été établi.

La structure de bicouches composées des lipides de levures a été étudiée par réflectivité de neutrons. La bicouche composée de lipides deutérés polaires a une épaisseur similaire aux bicouches faites de phosphocholines C18:1 synthétiques. En présence de stérols, la rugosité aux interfaces entre les têtes polaires et les chaînes augmente. La bicouche composée de lipides polaires hydrogénés est plus mince que celle deutérée. Ceci est dû à la composition en acides gras beaucoup plus variée et du plus grand nombre d’insaturations. En présence de stérols, l’épaisseur de la bicouche hydrogénée augmente.

L’interaction de ces bicouches avec l’amphotéricine B (AmB) a été étudiée. L’AmB est un antifongique qui interagit fortement avec les membranes contenant de l’ergostérol et moins fortement avec des membranes contenant du cholestérol. Dans tous les cas, les molécules d’AmB forment une couche épaisse et diluée au dessus de la bicouche lipidique. En présence de stérols, les molécules d’AmB pénètrent dans la bicouche et change sa structure selon la composition en acide gras.

La structure de bicouches lipidiques de plante et leurs interactions avec des intermédiaires de synthèse ont aussi été étudiées par réflectivité de neutrons. Des mélanges ternaires de plantes étaient déposés sur silicium et des mélanges quaternaires sur saphir. L’épaisseur de la bicouche composée de mélange ternaire est de 38 Å, tandis que celle du mélange ternaire est de 28 Å, la différence venant probablement d’un effet de substrat. La présence de diacylglycérol (DAG) a comme conséquence d’augmenter l’aire par lipide, et ainsi de changer la conformation des têtes polaires. L’interaction des bicouches de lipide de plante avec l’acide phosphatidique (PA) dans le but d’observer un flip-flop possible a aussi été étudiée mais le PA a tendance à désorbé les bicouches du substrat et aucun mécanisme de flip flop n’a été détecté.

Finalement, la localisation d’une petite molécule, le resvératrol, dans des bicouches modèles a été étudiée. Le resvératrol est connu pour être responsable du « paradoxe français » qui est une corrélation inverse entre la consommation d’aliment gras et un faible taux de maladie cardiaque. Quand le resvératrol est adsorbé à partir de la phase liquide, il induit une réorganisation des têtes polaires. Quand il est déposé sur le substrat en présence des lipides, il est présent à l’interface entre les têtes polaires et les chaines.


Doctorat en Sciences
info:eu-repo/semantics/nonPublished

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10

Morita, Masaki. "Synthesis of Cage-Shaped Molecules of Physalins for Biological Evaluations." 京都大学 (Kyoto University), 2014. http://hdl.handle.net/2433/188511.

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11

Lindgren, Anders. "Synthesis of Small Molecules Targeting ADP-Ribosyltransferases and Total Synthesis of Resveratrol Based Natural Products." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-108010.

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Diphtheria Toxin-like ADP-Ribosyltransferases The Human ADP-ribosyl transferases (ARTDs) are a group of poorly studied enzymes which are believed to be involved in e.g. DNA repair, protein degradation, transcription regulation and cell death. Medicinal chemistry programmes aimed at developing selective inhibitors of these ARTDs were initiated. A suitable starting compound for one of these enzymes, ARTD3, was found by screening a library of NAD-mimics using a thermal shift assay. A virtual screening protocol was instead developed in order to find novel inhibitors of ARTD7, 8, and 10. The hit compounds were then further developed into selective inhibitors of the corresponding ARTDs by systematically varying different structural features using a combination of synthetic organic chemistry, computational chemistry and structural biology. Compounds were initially characterized using differential scanning fluorimetry which was later replaced with an enzymatic assay to obtain IC50 values. Biotinylated analogs were also synthesized in an attempt to develop an AlphaScreen assay. A selective ARTD3 inhibitor was ultimately identified and found to delay DNA repair in cells after γ-irradiation. These compounds are potentially valuable tools for elucidating the biological role of the poorly characterized ARTD-family of proteins. Total Synthesis of Resveratrol Based Natural Products The polyphenolic natural product (-)-hopeaphenol was found to inhibit the type III secretion system present in certain gram-negative bacteria. (-)-Hopeaphenol is a tetramer of resveratrol and in order to investigate whether the entire structure was essential for inhibition two resveratrol dimers, ε-viniferin and ampelopsin B, were synthesized using a flexible and divergent synthetic route. Highlights of the synthetic strategy include the use of cyclopropylmethyl protecting groups, allowing an acid mediated three-step-one-pot deprotection-epimerization-cyclization of an advanced intermediate to form ampelopsin B. All previously reported syntheses of these two natural products include a dimerization of resveratrol which severly limits the possibilities to synthesize structural analogs. This new strategy enables the synthesis of a wide variety of analogs to ε-viniferin and ampelopsin B.
Populärvetenskaplig sammanfattning Små molekyler för att identifiera proteiners funktion Vår arvsmassa innehåller cirka 24000 gener som i sin tur innehåller information för hur de tusentals proteiner vi är uppbyggda av ska framställas. Många läkemedel fungerar genom att en molekyl interagerar med ett av dessa proteiner och hämmar dess funktion för att på så sätt framkalla en önskad effekt. Vi vet dock inte vilken funktion många av våra proteiner fyller vilket ofta gör utvecklingen av nya läkemedel svår eller omöjlig. Den första delen av denna avhandling beskriver en grupp proteiner kallade ARTDs och hur små molekyler kan framställas och systematiskt förbättras för att till slut helt kunna slå ut vissa av dessa ARTDs. Genom att sedan studera vilka effekter detta medför kan man ta reda på vilken funktion proteinet fyller. På längre sikt skulle denna kunskap sedan kunna användas för att utveckla nya läkemedel genom att till exempel slå ut de proteiner som orsakar en sjukdom. Totalsyntes av naturprodukter Naturprodukter defineras inom kemin som naturligt förekommande molekyler som produceras av levande organismer. De kan hittas i allt från mikroorganismer och växter till djur och kan vara en del av deras ämnesomsättning, en restprodukt eller ha någon annan funktion, känd eller okänd. Människor, och i vissa fall även andra djur, har sedan urminnes tider ovetandes använt dessa molekyler för en mängd olika syften, som gifter, färgämnen eller läkemedel. Penicillin är en av de mest kända, men mer än hälften av de nya läkemedel som godkänts de senaste trettio åren bygger på naturprodukter eller har inspirerats av dessa. De fortsätter således att vara viktiga för utvecklingen av nya läkemedel trots att vi idag har möjligheten att utveckla sådana från grunden. Att framställa naturprodukter på konstgjord väg kallas totalsyntes och är ofta en mycket svår och tidskrävande process. Vanligtvis rör det sig om mycket stora och komplexa molekyler och det finns sällan ett uppenbart sätt att genomföra totalsyntesen. För att bättre klara av detta måste nya metoder utvecklas. Den andra delen av denna avhandling beskriver nya metoder för att framställa komplexa molekyler kallade polyfenoler. Målet var att dessa metoder skulle vara så pass flexibla att de även kan användas för att framställa nya polyfenoler som aldrig tidigare existerat men som har förbättrade egenskaper.
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12

He, Wei. "Application of (3,3)-sigmatropic rearrangements to the rapid elaboration of complex molecules including natural products /." The Ohio State University, 1991. http://rave.ohiolink.edu/etdc/view?acc_num=osu1341508945.

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13

Assarsson, Erika. "Acquisition and function of NK cell-associated molecules on T cells /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-487-9/.

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14

Sundbäck, Jonas. "NK cell inhibitory receptor interactions with MHC class I molecules /." Stockholm, 2001. http://diss.kib.ki.se/2001/91-628-4819-4/.

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15

Fastus, Karola [Verfasser]. "Natural products from tobacco (Nicotiana Tabacum) and thermally generated taste molecules in tobacco smoke / Karola Fastus." München : Verlag Dr. Hut, 2014. http://d-nb.info/105932976X/34.

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16

Maki, Guitta. "Mechanism of leukemic cell killing by IL-2 activated natural killer cells : role of cell adhesion molecules." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/nq25105.pdf.

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17

Telford, Erica. "Dual role of three natural molecules in regulating the expression of β-defensin-3 and pro-inflammatory mediators." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC273.

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Les peptides antimicrobiens (PAMs) sont des effecteurs de la réponse innée produits et sécrétés par les cellules épithéliales intestinales. A l’interface entre l’épithélium et les microbes, ils représentent un élément important de la barrière muqueuse. Certains PAMs, tels que la bêta-défensine humaine 1 (BDH-1), sont exprimés de manière constitutive, tandis que d'autres PAMs, dont la BDH-2 et la BDH-3, sont induits par des signaux dérivés des microbes et de l'hôte. Les PAMs contrôlent la densité des bactéries commensales dans la lumière intestinale ainsi que la capacité invasive des agents pathogènes. En effet, les PAMs jouent un rôle majeur dans l’induction des réponses immunitaires innée et adaptative. Ainsi, outre leurs effets antimicrobiens et immunorégulateurs, les PAMs ont également une fonction angiogénique et anti-tumorale, entre autres. Il y a peu d’études sur la régulation des PAMs. Cependant, leur dérégulation a été associée à plusieurs pathologies humaines, notamment aux maladies inflammatoires chronique de l’intestin, ce qui souligne leur rôle majeur dans le maintien de l'homéostasie. Grâce à leurs effets multiples, les PAMs constituent une cible thérapeutique intéressante pour développer des solutions alternatives ou complémentaires aux antibiotiques afin de mieux faire face à l'émergence de maladies infectieuses et à la résistance aux antibiotiques. Enfin, les PAMs pourraient aider à rétablir l'homéostasie dans les maladies inflammatoires.À la suite d’un criblage d’une banque de molécules naturelles, notre équipe a identifié trois cibles prometteuses, l'andrographolide (AND), l'isoliquiritigénine (ISL) et l'oridonine (ORD), qui augmentent l'expression de BDH-3 sans induire celle de gènes pro-inflammatoires. Au cours de ce projet, nous avons étudié précisément l'effet de l'AND, de l'ISL et de l'ORD sur l'induction de l'expression de BDH-3 dans un modèle in vitro de cellules épithéliales intestinales. Ces molécules ont un effet inducteur non seulement individuellement mais également de manière synergique puisque la combinaison de ces molécules augmente fortement l’expression de BDH-3. En outre, AND, ISL et ORD ont réduit l'expression des gènes pro-inflammatoires IL-1β, IL-6, IL-8 et TNF-α lorsque celle-ci était induite par des stimuli inflammatoires endogènes ou bactériens. D’autres études menées par le groupe ont pour but de définir in vitro et ex vivo l’activité de ces composés et de déterminer leurs mécanismes d’actions en étudiant les voies intracellulaires impliquées.En conclusion, l’AND, l’ISL et l’ORD représentent des outils prometteurs pour étudier la régulation des PAMs et pourraient devenir des candidats thérapeutiques pour les pathologies nécessitant un renforcement de la barrière muqueuse tout en réduisant l'inflammation
Antimicrobial peptides (AMPs) are innate immune effectors produced and secreted by intestinal epithelial cells at the microbe-epithelium interface, where they represent an important component of the mucosal barrier. Some AMPs, such as human beta defensin (HBD)-1, are constitutively expressed, while others, including HBD-2 and HBD-3, are induced by a broad range of microbial- and host-derived signals. AMPs control the density of luminal commensal bacteria and invasive capacities of pathogens and have a role in perpetuating the innate immune response and inducing the adaptive response. Indeed, they present antimicrobial, immunoregulatory, angiogenic and anti-tumor effects, among the others. Little is known about regulation of AMP expression, but its deregulation has been associated with several human pathologies, including inflammatory bowel diseases, highlighting their crucial role in maintaining the homeostasis. Due to their multifaceted activities, AMPs represent an appealing therapeutic target for developing novel or complementary solutions to antibiotics, to face the emergence of infectious diseases in public health and the crisis of antimicrobial resistance, and to help re-establishing homeostasis in inflammatory diseases.By screening a bank of natural molecules, our team identified three promising targets, andrographolide (AND), isoliquiritigenin (ISL) and oridonin (ORD), which increase the expression of HBD-3 without inducing pro-inflammatory genes. This project thoroughly studied the effect of AND, ISL and ORD on inducing expression of HBD-3 in an in vitro model of intestinal epithelial cells. These molecules not only produced this effect when used alone, but also acted synergistically, highly inducing the expression of HBD-3 when used in combination. Moreover, AND, ISL and ORD hindered the expression of the pro-inflammatory genes IL-1β, IL-6, IL-8 and TNF-α upon stimulation of cells with endogenous or bacterial inflammatory stimuli. Further studies conducted by the group aimed at characterizing the activity of the compounds in vitro and ex vivo and unravelling their mechanisms of action by studying the intracellular pathways involved.In conclusion, AND, ISL and ORD represent useful tools to study the regulatory network controlling expression of AMPs and might develop to be candidate drugs for pathologic conditions in which strengthening the mucosal barrier, while reducing inflammation, is needed
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18

Sugimoto, Naoshi. "Foxp3-dependent and -independent molecules specific for CD25[+]CD4[+] natural regulatory T cells revealed by DNA microarray analysis." Kyoto University, 2007. http://hdl.handle.net/2433/135673.

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19

Chakraborty, Sourav. "Molecular Probes for Biologically Important Molecules: A Study of Thiourea, Hydroxyl radical, Peroxynitrite and Hypochlorous acid." ScholarWorks@UNO, 2010. http://scholarworks.uno.edu/td/1132.

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Numerous chemical species are important to the health of biological systems. Some species can be beneficial at low doses and harmful at high doses. Other species are highly reactive and trigger serious cell damage. Improved methods to detect the presence and activity of such species are needed. In this work, several biologically important species were studied using appropriate analytical techniques. Fluoride is an important species in human physiology. It strengthens teeth and gives protection against dental caries. However, elevated concentrations of fluoride in the body can lead to health problems such as dental and skeletal fluorosis. Reported fluoride sensors used fluorescence quenching methods in determining fluoride concentration. Our study explored synthesis and characterization of 1,8-bis(phenylthioureido) naphthalene (compound 1) as a fluoride sensing molecule. Compound 1 showed a remarkable 40 fold enhancement in fluorescence with 5 eq of fluoride addition. Compound 1 also showed possibility of visual colorimetric sensing with fluoride. Free radical mediated oxidations of biomolecules are responsible for different pathological conditions in the human body. Superoxide is generated in cells and tissues during oxidative burst. Moderately reactive superoxide is converted to peroxyl, alkoxyl and hydroxyl radicals by various enzymatic, chemical, and biochemical processes. Hydroxyl radical imparts rapid, non specific oxidative damage to biomolecules such as proteins and lipids. Superoxide also reacts with nitric oxide in cells to yield peroxynitrite, which is highly reactive and damages biomolecules. Both hydroxyl radical and peroxynitrite readily react with amino acids containing aromatic side chains. Low density lipoprotein (LDL) carries cholesterol in the human body. Elevated concentration of LDL is a potential risk factor for atherosclerosis. Previous research drew a strong correlation between oxidized low density lipoprotein (ox-LDL) and plaque formation in the arterial wall. More importantly, oxidative damage causes structural changes to the LDL protein (apo B-100) which might facilitate the uptake of LDL by macrophages. In this study LDL was exposed to various concentrations of hydroxyl radical peroxynitrite and hypochlorite. Thereafter oxidized amino acid residues in apo B-100 were mapped by LC-MS/MS methods. We found widely distributed oxidative modifications in the apo B-100 amino acid sequence.
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20

Antonova, Elena S. "The regulatory network controlling natural competence for DNA uptake in Vibrio cholerae." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/47626.

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The bacterial pathogen Vibrio cholerae is responsible for ongoing cholera outbreaks in Haiti and elsewhere. Association of V. cholerae with the human host is responsible for fatal disease, but the bacteria also reside as natural inhabitants of aquatic environments, commonly attaching as biofilms to chitinous surfaces of copepods and crabs. Prior studies in V. cholerae demonstrated that competence for genetic transformation, a mechanism of horizontal gene transfer (HGT), requires the TfoX regulator protein that is triggered by chitin, and the HapR transcription factor that is made in response to quorum sensing (QS) signals produced by V. cholerae and Vibrios. To define regulatory components connecting extracellular signals to natural competence, I first demonstrated that QS molecules produced by Vibrios within multi-species chitinous biofilms are required for DNA uptake by V. cholerae, confirming the critical role of QS signals in HGT. Second, I identified by transposon-mutagenesis a new positive regulator of competence, CytR (cytidine repressor), only studied prior in E. coli as a regulator of nucleoside scavenging. Specific mutations in V. cholerae CytR impaired expression of competence genes and halted DNA uptake; and the addition of exogenous cytidine had similar affects as predicted in E. coli. V. cholerae and other competent Vibrios encode TfoX, HapR, and CytR, although none of these regulators directly controls genes coding for the DNA uptake apparatus. Thus, these results have uncovered a regulatory network, likely used by many Vibrios, that contains additional factors linking several extracellular chemical molecules (cytidine, chitin, and QS signals) to DNA uptake. My study has begun to define a molecular mechanism by which both environment and genetics contribute to genome evolution for this important marine pathogen.
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21

Zetterström, Caroline E. "Small Molecules as Tools in Biological Chemistry : Effects of Synthetic and Natural Products on the Type III Secretion System." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-70281.

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The increasing use of antibiotics has led to a huge problem for society, as some bacteria have developed resistance towards many of the antibiotics currently available. To help find solutions to this problem we studied small molecules that inhibit bacterial virulence, the ability to cause disease. The type III secretion system (T3SS) is a conserved virulence system found in several gram-negative bacteria, including human and plants pathogens, such as Yersinia spp., Pseudomonas aeruginosa, Chlamydia spp., Salmonella spp., Shigella spp, enteropathogenic Escherichia coli (EPEC), enterohemorrhagic Escherichia coli (EHEC), and Erwinia spp. One class of virulence-blocking compounds is the salicylidene acylhydrazides. They were first identified in a screen towards the T3SS in Yersinia pseudotuberculosis and have since been shown to block the T3SS in a panel of gram-negative bacteria such as Chlamydia spp. Salmonella enterica, Shigella flexneri and EPEC. We designed and synthesized a library of 58 salicylidene acylhydrazides and evaluated their activity as virulence-blocking compounds in Y. pseudotuberculosis followed by calculations of quantitative structure activity relationships (QSARs). Four QSAR models were calculated, and when used in consensus they correctly classified between five out of eight compounds for Y. pseudotuberculosis as active or inactive and six out of eight compounds for C. trachomatis. Since the target and mode of action of the salicylidene acylhydrazides were unknown, we used solution and solid phase synthesis to synthesize three different affinity reagents. One of these affinity reagents was used in affinity chromatography experiments, where 19 putative target proteins from an E. coli O157 bacterial lysate were identified. We studied four of the proteins, Tpx, WrbA, FolX, and AdhE, in more detail in Y. pseudotuberculosis and E. coli O157. We believe that the salicylidene acylhydrazides act on multiple targets that together result in down-regulation of T3SS functions. A knockout of AdhE in E. coli O157 showed a similar phenotype as salicylidene acylhydrazide treated E. coli, suggesting that this protein may be particularly interesting as a drug target. Many of the antibiotics used today originate form natural sources. In contrast, most virulence-blocking compounds towards the T3SS are small synthetic organic molecules. Therefore, a prefractionated natural product library with marine and terrestrial biota samples was screened towards the T3SS in Y. pseudotuberculosis. Neohopeaphenol A was identified as a hit and shown to have micromolar activity towards Y. pseudotuberculosis and P. aeruginosa in cell-based infection models.
Det ökande användandet av antibiotika har lett till stora problem för samhället. Många bakterier har utvecklat resistens mot de antibiotika som finns tillgängliga. För att försöka hitta en möjlig lösning på detta problem, arbetar vi med en strategi där vi med hjälp av små organiska molekyler inhiberar bakteriernas virulenssystem, deras förmåga att orsaka sjukdom. Traditionella antibiotika är antingen, bakteriocida, avdödande eller bakteriostatiska, tillväxthämmande. Bakteriernas enda sätt för att överleva antibiotikabehandlingen är att utveckla resistens. Forskarvärlden tror att molekyler som inhiberar bakteriernas virulenssystem, leder till ett minskat tryck att utveckla resistens mot dessa molekyler, eftersom de inte dödar eller hämmar bakterietillväxten, utan bara avväpnar bakterierna. Typ III sekretionssystemet är ett virulenssystem som finns i många gram-negativa bakterier, t.ex., Yersinia spp., Pseudomonas aeruginosa, Chlamydia spp., Salmonella spp., Shigella spp, enteropatogena Escherichia coli (EPEC) och Erwinia spp. Salicylidenacylhydraziderna är en substansklass virulensblockare som inhiberar typ III sekretionssystemet i de ovan nämnda bakterierna. I denna avhandling har vi designat och syntetiserat ett bibliotek med 58 salicylidenacylhydrazider och utvärderat deras biologiska aktivitet som virulensblockare i Y. pseudotuberculosis. Vi relaterade den biologiska aktiviteten till de kemiska egenskaperna hos salicylidenacylhydraziderna i kvantitativa strukturaktivitetssamband. Med hjälp av dessa samband kunde vi prediktera och validera aktiviteten till aktiv eller inaktiv för fem av åtta nya salicylidenacylhydrazider i Y. pseudotuberculosis och sex av åtta i C. trachomatis. Eftersom verkningsmekanismen för salicylidenacylhydraziderna var okänd, så syntetiserade vi tre olika affinitetsmolekyler med kombinerad lösnings- och fastfas-syntes. En av affinitetsmolekylerna användes sedan för att ”fiska ut” och identifiera 19 potentiella målproteiner i ett bakterielysat från E. coli. Fyra av dessa proteiner, TpX, WrbA, FolX och AdhE har vi studerat vidare i Y. pseudotuberculosis och E. coli. Utifrån resultaten tror vi att salicylidenacylhydraziderna interagerar med flera proteiner som tillsammans resulterar i en nedreglering av type III sekretionssystemen. Vår samarbetspartner, Andrew Roe och hans forskargrupp (Universitetet i Glasgow), har studerat AdhE i E. coli.  De har visat att E. coli som saknar genen för proteinet AdhE, har samma fenotyp som E. coli behandlad med salicylidenacylhydraziderna, d.v.s. ett nedreglerat T3SS, vilket gör AdhE till ett speciellt intressant målprotein. I jämförelse med många av våra nuvarande antibiotika som har ett naturligt ursprung så är de flesta studerade virulensblockare små syntetiska organiska molekyler. Därför testades en stor kollektion av naturprodukter från marina och landlevande växter och invertebrater från Sydostasien, för att hitta nya inhibitorer mot typ III sekretionssystemet i Y. pseudotuberculosis. Neohopeaphenol A som kommer från barken på Hopea hainanensis, ett träd som växer i sydostasiens regnskogar, identifierades som en ny virulensblockare. Neohopeaphenol A visade sig vara en potent virulensblockare i in vitro infektionsförsök med Y. psudotuberkulosis eller Pseudomonas aeruginosa. Forskningen i denna avhandling visar att virulensblockare kan hjälpa oss att förstå hur bakterier orsakar sjukdom. Förhoppningsvis kan det i framtiden leda till nya typer av läkemedel mot infektionssjukdomar.
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Maddirala, Amarendar Reddy. "Applications of Ugi Four Component Cascade Coupling Reactions for the Synthesis of Bioactive Diverse Heterocyclic Molecules and Natural Products." University of Toledo / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1461775415.

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Calla-Magariños, Jacqueline. "Bioactive leishmanicidal alkaloid molecules from Galipea longiflora Krause with immunomodulatory activity." Doctoral thesis, Stockholms universitet, Wenner-Grens institut, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-81439.

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According to WHO, leishmaniasis is endemic in 98 countries, and has been placed ninth in a global analysis of infectious diseases. Treatment of leishmaniasis is based on pentavalent antimonials but toxicity and developing resistance have been reported. Traditional medicine and scientific studies have shown that the extract of Galipea longiflora Krause (Evanta) exhibits antileishmanial activity. We hypothesized that the healing observed when using this plant might not only be due to the direct action on the parasite, but possibly to a parallel effect on the host immune response. We found that an alkaloid extract of Evanta (AEE) inhibited the growth of Leishmania braziliensis promastigotes while viability of eukaryotic cells was practically not affected. We also found that AEE interfered with polyclonal activation or Leishmania-specific re-stimulation of lymphocytes, as revealed by a reduction of in vitro cellular proliferation and IFN-g production. More important, AEE treatment of mice hosting L. braziliensis showed that AEE is able to control both inflammation and parasite load. Additionally, the healing process was improved when AEE and meglumine antimoniate were administered simultaneously. Dendritic cells (DCs) play a pivotal role in T-cell stimulation and polarization of naïve T cells. Therefore, we investigated if AEE could alter the activation of DCs and if allostimulatory DCs properties were altered if activated in the presence of AEE. DCs activated in the presence of AEE reduced the production of IL-12p40 and IL-23. When we analyzed the allostimulatory capacity of AEE-treated DCs, we found that allogeneic CD4+ T-cells secreted lower levels of IFN-γ. In conclusion, this thesis provides valuable insight into the effects of Evanta derived extract. The dual effect found for AEE, on Leishmania parasite and on the immune response, suggests that AEE may be useful in controlling the parasite burden and preventing over-production of inflammatory mediators and subsequently avoiding tissue damage.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Accepted. Paper 3: Submitted.

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Marginean, Denisse, and Ebba Hellstrand. "Fluorescent molecules as probes for characterization of amyloid β fibrils." Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-178005.

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Alzheimer’s Disease (AD) is the leading cause of dementia in the world and the World Health Organization has recognized AD as a global public health priority. One of the pathological hallmarks of AD is amyloid plaques formed from amyloid β (Aβ) fibrils. Aβ is formed when amyloid precursor protein is cleaved by secretase enzymes. Cleavage by different secretases causes Aβ to occur in different forms, mainly as 40 and 42 residue long proteins, called Aβ1-40 and Aβ1-42, where Aβ1-42 is more likely to form amyloid fibrils and is therefore considered more harmful. Fluorescent probes are currently used to stain Aβ fibrils for their detection and characterization.  We performed a literature study analysing which fluorescent probes are used for imaging of amyloid fibrils and present both the most commonly used probes but also newer probes that have been recently synthesized. Fluorescence spectra of a selection of probes were analysed in order to suggest some new combinations of probes for double-staining with the aim to be able to distinguish between Aβ1-40 and Aβ1-42. Microscopy images of the probe combinations were obtained in order to analyse the double staining results and the fluorescence intensities of the probes were plotted in different ways. All selected combinations were able to distinguish between Aβ1-40 and Aβ1-42, because of differently stained fibrils, and also displayed differences in fluorescence intensity at peak emission wavelength. The obtained results show that double-staining of amyloid fibrils with fluorescent probes can give additional information compared to staining fibrils with only one probe.
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Montanari, Serena <1986&gt. "Cannabinoid system combined to classic targets for a new MTDL strategy: design and synthesis of natural inspired molecules for Alzheimer's disease." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/6903/.

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In this thesis is described the design and synthesis of potential agents for the treatment of the multifactorial Alzheimer’s disease (AD). Our multi-target approach was to consider cannabinoid system involved in AD, together with classic targets. In the first project, designed modifications were performed on lead molecule in order to increase potency and obtain balanced activities on fatty acid amide hydrolase and cholinesterases. A small library of compounds was synthesized and biological results showed increased inhibitory activity (nanomolar range) related to selected target. The second project was focused on the benzofuran framework, a privileged structure being a common moiety found in many biologically active natural products and therapeutics. Hybrid molecules were designed and synthesized, focusing on the inhibition of cholinesterases, Aβ aggregation, FAAH and on the interaction with CB receptors. Preliminary results showed that several compounds are potent CB ligands, in particular the high affinity for CB2 receptors, could open new opportunities to modulate neuroinflammation. The third and the fourth project were carried out at the IMS, Aberdeen, under the supervision of Prof. Matteo Zanda. The role of the cannabinoid system in the brain is still largely unexplored and the relationship between the CB1 receptors functional modification, density and distribution and the onset of a pathological state is not well understood. For this reasons, Rimonabant analogues suitable as radioligands were synthesized. The latter, through PET, could provide reliable measurements of density and distribution of CB1 receptors in the brain. In the fifth project, in collaboration with CHyM of York, the goal was to develop arginine analogues that are target specific due to their exclusively location into NOS enzymes and could work as MRI contrasting agents. Synthesized analogues could be suitable substrate for the transfer of polarization by p-H2 molecules through SABRE technique transforming MRI a more sensitive and faster technique.
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Lu, Zhen. "DEVELOPMENT OF HIGH LEVEL AB INITIO METHODS TO DESCRIBE NONADIABATIC EVENTS AND APPLICATIONS TO THE EXCITED STATES OF SMALL BIOLOGICAL MOLECULES." Diss., Temple University Libraries, 2015. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/320918.

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Chemistry
Ph.D.
The development of quantum mechanics has historically allowed researchers to theoretically explore the fundamental physical properties of atoms and molecules. Although quantum mechanics has been around for almost a century, its use was largely limited by the computational complexity it demanded. In the past decade, computer technology has evolved to the point where it is possible to perform calculations on biologically relevant systems. This has allowed us to corroborate results obtained from experiment as well as predict and explain phenomena that experiment cannot. Unfortunately, the field as a whole has not progressed to the point where high level methods, such as Multi-Reference Configuration Interaction (MRCI), are applicable to large molecular systems. Thus, to effectively study these systems, compromises must be made. In this work, two different approaches are taken to study the photophysical properties of systems such as DNA. In the first approach, a model system is formulated and studied in lieu of the larger target system. The excited state dynamics of 8-oxoguanine (8-oG) and its anion are studied in order to assess the possibility of taking part in an electron transfer mechanism to repair a nearby cyclobutane pyrimidine dimer (CPD). It is found that barriers on the anion S1 excited state surface prohibits easy access to conical intersections with the ground state, causing the anion to have a much longer excited state lifetime than the neutral form. Although much insight can be gained by this method, it is not uncommon for crucial interactions to be lost through simplification. In this case, when 8-oG is placed in an adenine dinucleotide, the π stacking interaction allows it to form a long lived radical base pair, which may be fundamental to its role in CPD repair. Unfortunately, it is impossible to carry out the same excited state calculations for the 8-oG/adenine dinucleotide due to computational cost. For reasons such as these, we also implement and benchmark a new approach to carrying out high level configuration interaction calculations in which the MRCI is expanded in the basis of high multiplicity natural orbitals (HMNOs). Specifically, the HMNO approach is implemented by expanding the MRCI wavefunction in the basis of natural orbitals generated from a ground state high multiplicity Configuration Interaction Singles and Doubles (CISD) calculation. Excited state calculations both at and away from the Franck-Condon region were performed to benchmark the ability of the HMNO approach using CISD and MRCI to reproduce standard MRCI energies. The ability of the HMNOs to be truncated was also explored, yielding efficient truncation criteria and guidelines for choosing the best basis set. It is found that the MRCI/HMNO approach yields energies that are in excellent agreement with standard MRCI while only requiring a fraction of the computational effort, possibly allowing it to be applied to larger systems such as nucleotide dimers.
Temple University--Theses
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Cockroft, Nicholas T. "Applications of Cheminformatics for the Analysis of Proteolysis Targeting Chimeras and the Development of Natural Product Computational Target Fishing Models." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu156596730476322.

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Gannon, Gregory Allan. "Peripheral blood lymphocyte trafficking and natural killer cell cytolytic activity during prolonged, exhaustive aerobic exercise, a focus on cell adhesion molecules and ß-endorphin." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape17/PQDD_0002/NQ35159.pdf.

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Tay, Chin Hun. "In Vivo Regulation of Murine Cytomegalovirus Infections: The Role of Cell Surface Molecules and Mechanisms of Control by Natural Killer Cells: A Dissertation." eScholarship@UMMS, 1997. https://escholarship.umassmed.edu/gsbs_diss/64.

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The overall aim of this thesis was to determine how natural killer (NK) cells regulate virus infections in vivo. Anti-viral mechanisms by which NK cells control murine cytomegalovirus (MCMV) infection in the spleens and livers of adult C57BL/6 mice were first studied, revealing different mechanisms of control in different organs. Three days post-infection, MCMV titers in the spleens of perforin-deficient (perforin 0/0) mice were higher than in wild type controls, but no elevation of liver titers was found in perforin 0/0 mice. NK cell depletion in MCMV-infected perforin 0/0 mice resulted only in an increase in liver viral titers but not in spleen titers. Depletion of IFN-γ in adult C57BL/6 mice by injections with mAbs to IFN-γ resulted in an increase in viral titers in the liver but not in the spleen. Analyses using IFN-γ-receptor-deficient (IFN-γR0/0) mice, rendered chimeric with C57BL/6 bone marrow cells, indicated that even though the donor spleen cells could respond to IFN-γ, the depletion of NK cells in a recipient environment where the host cells could not respond to IFN-γ caused an increase in MCMV titers in the spleens but had little effect in the liver. IFN-γ has the ability to induce a variety of cells to produce nitric oxide (NO), and administrating the nitric oxide synthase (NOS) inhibitor Nω-monomethyl-L-arginine (L-NMA) into MCMV-infected adult C57BL/6 mice resulted in MCMV titer increases in the liver but not in the spleen. These data indicate that in adult C57BL/6 mice, there is a dichotomy in the mechanisms utilized by NK cells in the regulation of MCMV in different organs. In the spleen NK cells exert their effects in a perforin-dependent manner, suggesting a cytotoxic mechanism, whereas in the liver the production of IFN-γ by NK cells may be a predominant mechanism in the regulation of MCMV synthesis. These results may explain why the Cmv-1r (Cmv-1-resistant) locus, which maps closely to genes regulating NK cell cytotoxic function, confers an NK cell-dependent resistance to MCMV infection in the spleen but not in the liver. The ability of adoptively transferred cells to protect suckling mice from MCMV was another model used to study the mechanisms utilized by NK cells in the regulation of MCMV. Adoptive transfers of 129, C57BL/6 and perforin 0/0 spleen cells or lymphokine-activated killer (LAK) cells into 4 - 6 day old MCMV-infected C57BL/6 suckling mice significantly lowered the splenic MCMV titers in these mice compared to the infected controls. Adoptive transfers of C57BL/6 spleen cells into MCMV-infected 129 suckling mice also decreased the amount of MCMV in the 129 suckling mice, but C57BL/6 spleen cells could not regulate MCMV synthesis when adoptively transferred into 129/IFN-γR0/0 suckling mice. These results suggest that, in the suckling mouse model, the regulation of MCMV by the adoptively transferred NK cells is via an IFN-γ-dependent, perforin-independent, Cmv-1-independent mechanism. The Cmv-1 gene locus resides within the NK gene complex, in close proximity to the Ly49 NK cell receptor family. Analyses were carried out to determine if any of the 4 known Ly49 NK cell receptors (Ly49A, C, D and G2) played a role in the control of MCMV synthesis by NK cells. Studies comparing the expression of the different Ly49 NK cell subsets in the spleen and the peritoneal cavity revealed that there were differences in the distribution of the Ly49 receptors on NK1.1+ cells. Three days post-MCMV infection, the percentage of NK1.1+- Ly49+ NK cells in the spleen and the peritoneal cavity were different than in naive controls. Within the splenic NK1.1+ population, increases in NK1.1+ -Ly49A+ and NK1.1+-Ly49G2+ cells but decreases in NK1.1+-Ly49C+ and NK1.1+-Ly49D+ cells were observed. These changes in the spleen were accompanied by a concomitant decrease in NK1.1+ - Ly49A+ cells and increases in NK1.1+-Ly49C+, NK1.1+-Ly49D+ and NK1.1+-Ly49G2+ cells within the NK1.1+ population in the peritoneal cavity. These data suggest that 3 days post-MCMV infection, there may be movement of NK cells between the different organs. The role of Ly49 NK cell receptors in the regulation of MCMV was tested using adult C57BL/6 mice depleted of single or multiple Ly49 NK cell subsets. These in vivo depletions did not affect the ability of the residual NK cells to regulate MCMV synthesis. LAK cells sorted into the different Ly49 NK cell subsets and adoptively transferred into C57BL/6 suckling mice lowered the splenic MCMV titers in these mice. Together, these results indicate that even though there is a redistribution of the Ly49 NK cell subsets during MCMV infection, the presence or absence of anyone of the 4 tested Ly49 NK cell receptors does not affect the regulation of MCMV by NK cells. However, there remain a possibility that one of the undefined Ly49 receptors or an untested NK cell receptor may be important in the control ofMCMV. Most of the cloned NK cell receptors have been shown to bind to MHC class I molecules, and MHC class I antigens have been implicated as modulators of target cell sensitivity to NK cell-mediated lysis. The regulation of virus infections and the fate of NK cells and their natural targets was examined in β2-microglobulin-deficient mice [β2m (-/-)], which have defective MHC class I expression. Infections with either the NK cell-sensitive MCMV or the NK cell-resistant lymphocytic choriomeningitis virus (LCMV) significantly augmented NK cell activity in either C57BL/6 or β2m (-/-) mice. Depletion of NK cells in vivo with antiserum to asialo GM1 markedly enhanced the synthesis of MCMV but had no effect on the synthesis of LCMV in either strain of mouse. Adoptively transferred β2m (-/-) spleen cells lowered splenic MCMV titers in C57BL/6 suckling mice, not unlike adoptively transferred C57BL/6 spleen cells. Analysis of naturally NK cell-sensitive thymocyte targets from these virus-infected β2m (-/-) mice revealed no cell surface expression of class I MHC detectable by conformation-dependent or -independent antibodies, but the virus infections enhanced class I expression on thymocytes from C57BL/6 mice. The sensitivity of C57BL/6 thymocytes to NK cell-mediated lysis was markedly reduced after in vivo poly inosinic:cytidylic (poly I:C) treatment or viral infection; in contrast, the sensitivity of the β2m (-/-) thymocytes was significantly less affected by poly I:C or viral infection. These data indicate that the normal expression of MHC class I antigens on NK cells or their targets is not required for the anti-viral functions of NK cells against an NK-sensitive virus (MCMV) nor do they protect an NK-resistant virus (LCMV) from the anti-viral activity of NK cells. Together, the data presented in this thesis help to further our understanding of the mechanisms utilized by NK cells in the control ofMCMV in both adult and suckling mice, and also help clarify the roles played by Ly49 NK cell receptors and MHC class I molecules in the regulation of MCMV.
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Wahlström, Rickard. "Validation of docking performance in the context of a structural water molecule using model system." Thesis, Department of Physics, Chemistry and Biology, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-19525.

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In silico ligand docking is a versatile and common technique when predicting ligands and inhibitors for protein binding sites. The various docking programmes aim to calculate binding energies and to predict interactions, thus identifying potential ligands.The currently available programmes lack satisfying means by which to account for structural water molecules which can either mediate protein-ligand contacts or be displaced upon ligand binding. The present project aims to generate data to facilitate the global work of developing scoring functions in docking programmes to account for structural water molecules contribution to ligand binding to fill the said void. This is done by validating the performance of docking using a simple model system (cytochrome C peroxidase (CCP) W191G) containing four well ordered, deeply buried structural water molecules which are known to either interact with a ligand or to be displaced upon ligand binding.Known ligands were docked into eight (crystallographically determined) receptor set-ups comprising the receptor and no, one or two of the water molecules. The performance was validated by comparison of the binding modes of the docked ligands and the crystal structures, comparison of docking scores of the ligands in the different set-ups, enrichment of the ligands from a database of decoys and finally by predicting new ligands from the decoy database. In addition a high resolution crystal structure of CCP W191G in complex with 3-aminopyridine (3AP) was determined in order to resolve ambiguities in the binding mode of this ligand.

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Palierse, Estelle. "Development of a hybrid coating associating biomimetic hydroxyapatite and natural antibiotics with antibacterial properties." Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS316.

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Cette thèse porte sur l’élaboration de revêtements de surface hybrides composés d’hydroxyapatite biomimétique et de molécules antibactériennes naturelles, dans le but d’ajouter des propriétés antibactériennes et d’améliorer l’ostéointégration d’implants en titane (Ti6Al4V). Quatre molécules naturelles biologiquement actives (MABs) ont été étudiées : acide rosmarinique, acide chlorogénique, baicaline et baicaléine. Pour comprendre l’interaction entre ces molécules et l’hydroxyapatite, nous présentons trois études complémentaires : en solution avec l’ion calcium, avec des nanoparticules d’hydroxyapatite et avec un revêtement de surface d’hydroxyapatite biomimétique sur alliage de titane. En solution, le pH influence la complexation entre les MABs et le calcium. Les MABs inhibent la formation de l’hydroxyapatite lorsqu’elles sont incorporées pendant sa synthèse, sous forme de nanoparticules ou de revêtements. Elles peuvent cependant être efficacement adsorbées à la surface de particules ou de revêtements pré-synthétisés. Enfin, nous présentons les propriétés biologiques des nanoparticules et de revêtements avec la baicaléine adsorbée. Les nanoparticules hybrides sont de potentiels agents antioxydants, mais n’ont pas d’activité antibactérienne. Les revêtements de surface hybrides sont quant à eux efficaces pour limiter la croissance bactérienne de Staphylococcus epidermidis CIP 105.777. L’originalité de ce travail repose sur l’utilisation de molécules antibactériennes naturelles, mais nous soulignons la difficulté de les utiliser de par leur faible solubilité et stabilité à pH physiologique, ce qui devra être considéré pour une utilisation dans des applications biomédicales
This thesis aims to develop a hybrid coating based on biomimetic hydroxyapatite and natural antibacterial molecules, with the goal to add antibacterial properties and enhance the osseointegration of titanium (Ti6Al4V) implants. Four natural biologically active molecules (BAMs) were tested, rosmarinic acid, chlorogenic acid, baicalin and baicalein. To understand the interaction between those molecules and hydroxyapatite, we present here three complementary studies: in solution with calcium ion, with hydroxyapatite nanoparticles and with biomimetic hydroxyapatite coatings on titanium alloy. The complexation between BAMs and calcium ion in solution is highly pH-dependent. When incorporated within hydroxyapatite nanoparticles or coatings during synthesis, BAMs inhibit the formation of the mineral phase. On the contrary, they can be efficiently adsorbed on pre-synthesized particles. Finally, we present the biological properties of hydroxyapatite nanoparticles and coatings with adsorbed baicalein. Hybrid nanoparticles are potent antioxidant agents, but they do not exhibit any antibacterial activity, whereas hybrid coatings have a significant effect on the bacterial growth of Staphylococcus epidermidis CIP 105.777. This work originality stands on the use of natural antibacterial molecules, but we highlight the difficulty to handle them, due to their poor solubility and stability in physiological pH, which should be considered for further use in biomedical applications
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Northrop, Brian Hale. "Quantum mechanical investigations of reactions involved in natural products and organic materials formation, synthetic and theoretical studies of the formation and dynamic properties of mechanically interlocked molecules." Diss., Restricted to subscribing institutions, 2006. http://proquest.umi.com/pqdweb?did=1260800431&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.

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Hoepfner, Narenda. "An investigation into how two Natural Science teachers in the Khomas region mediate learning of the topic of atoms and molecules in Grade 7 : a case study." Thesis, Rhodes University, 2015. http://hdl.handle.net/10962/d1017342.

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The teaching of abstract concepts requires higher cognitive thinking skills and thus presents a challenge for most subjects in the curriculum, in particular, science subjects. Teachers often complain that they struggle to develop higher cognitive skills in learners in such topics. As a result, learners fail to understand science concepts and then complain that science is boring and hence lose interest in the subject. The main reason for this study was to investigate how Grade 7 Natural Science teachers mediate the learning of abstract topics, in particular, atoms and molecules which are regarded as the building blocks in chemistry. This study further sought to develop a teaching unit of work on atoms, molecules and the Periodic Table in partnership with the participating teachers, in order to help improve teaching and learning of the topic. The study is located within an interpretive paradigm. Within this paradigm, a qualitative case study approach was adopted whereby two Grade 7 Natural Science teachers in the Khomas Region were the research participants. This approach enabled me to seek for answers beyond the obvious classroom experiences by using document analysis, semi-structured interviews and classroom observation (which were video-taped and transcribed). The theoretical frameworks underpinning this study focused on mediation of learning and social constructivism as expounded by Vygotsky, in conjunction with Shulman’s pedagogical content knowledge. Hence, emphasis was placed on the teaching strategies used by teachers, such as elicitation of prior knowledge during the lessons, language used, interaction of learners and ways how teachers deal with the challenges faced by them in the mediation of learning. An inductive analysis to discover patterns and themes was applied during the data analysis process. The themes were further turned into analytical statements to interpret the data. The validation process was achieved by using a variety of data gathering techniques. I watched the videotaped lessons with the observed teachers and I made use of member checking in the form of stimulated recall interviews and transcripts of the interviews. Thus, a summary of discussions were given back to the respondents to verify their responses and check for any misinterpretations. Different chapters of my study were given to colleagues to read through as a means of the validation process. Herein lies the importance of a critical friend in qualitative research. The findings of the study revealed that concepts of high cognitive demand should not be oversimplified when introduced to learners, as learners might find it difficult to define and conceptualise concepts as they do not have proper insights into the concepts. The findings further illuminated that teachers should develop a strong subject content knowledge as well as pedagogical content knowledge to have the best strategies in place to mediate learning of this topic. The study concludes, with Phase 2, that the exposure of and cooperation between teachers plays an indispensable role in their professional development. Essentially, this enables teachers to make use of different teaching styles as they scaffold learners in the process of making sense of, in particular, abstract science concepts. Finally, this study recommends that teachers need to engage in on-going professional development opportunities and be equipped with suitable learning support and other necessary physical resources, as a way of motivation and to be in a position to deal with all the many challenges they have to face during the mediation of learning.
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34

Lima, Rebeca Larangeira de. "Perfil sazonal da atividade de antioxidante in vitro de algas da famÃlia Caulerpaceae." Universidade Federal do CearÃ, 2015. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=15354.

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Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico
As macroalgas sÃo fontes de molÃculas bioativas com propriedades antioxidantes, muitas das quais apresentam variaÃÃes ao longo do ano. Cinco algas verdes do gÃnero Caulerpa (C. cupressoides, C. mexicana, C. prolifera, C. racemosa e C. sertularioides) foram coletadas mensalmente na Praia do Pacheco, de janeiro a dezembro de 2006. ApÃs as coletas, elas foram transportadas para o laboratÃrio, lavadas com Ãgua corrente para retirada de impurezas e epÃfitas e liofilizadas. Os extratos algÃceos foram preparados em metanol (MeOH) na proporÃÃo 1:20 (p:v) sob agitaÃÃo por 1 h a 20ÂC em um agitador orbital, em seguida, filtrados, e os resÃduos submetidos a mais duas extraÃÃes sucessivas. O material das trÃs extraÃÃes metanÃlicas foi reunido e concentrado em um evaporador rotativo. PorÃÃes de 10 mg do extrato concentrado foram suspensas em 10 mL de MeOH (50%). Esse extrato (1 mg/mL) foi utilizado para a determinaÃÃo do conteÃdo fenÃlico total (CFT). A atividade antioxidante in vitro foi medida atravÃs da capacidade de sequestrar o radical DPPH, do poder de reduÃÃo de Ãons fÃrricos (FRAP), do branqueamento do β-caroteno (BCB) e da habilidade de quelaÃÃo de Ãons ferrosos (FIC), nas concentraÃÃes 5, 50, 500 e 1.000 Âg/mL, preparadas a partir do extrato. O quelante de metais EDTA foi utilizado como controle positivo no FIC, e o antioxidante sintÃtico BHA, nas demais determinaÃÃes. Os valores de CFT foram maiores no segundo semestre do ano e variaram de 4 a 32 mg AGE/g extrato. Os resultados do sequestro do radical DPPH, do BCB e do FIC nÃo exibiram padrÃo de variaÃÃo e apresentaram atividades superiores a 25%, 70% e 10%, respectivamente. O FRAP nos extratos de C. cupressoides, C. racemosa e C. serlularioides foi maior no segundo semestre do ano, no de C. mexicana o maior valor ocorreu no primeiro semestre e no de C. prolifera, as variaÃÃes ao longo do ano nÃo obedeceram a um padrÃo como nos demais. Em todas as metodologias as atividades dos extratos algÃceos foram inferiores Ãquelas dos controles positivos. As cinco espÃcies de Caulerpa podem ser consideradas fonte de potenciais antioxidantes, com possÃveis usos, como na indÃstria alimentÃcia, nÃo requisitando de um perÃodo do ano especÃfico para a extraÃÃo desses compostos antioxidantes, jà que embora haja variaÃÃo ao longo do ano, ela nÃo à muito pronunciada.
Macroalgae are sources of bioactive molecules with antioxidant properties, many of which present seasonal variation. Five green algae of the genus Caulerpa (C. cupressoides, C. mexicana, C. prolifera, C. racemosa and C. sertularioides) were collected monthly at Pacheco Beach, from January to December 2006. After collection, they were transported to the laboratory, washed under running water to remove impurities and epiphytes, and freeze-dried. The algae extracts were prepared in methanol (MeOH) in the proportion 1:20 (w:v) under stirring for 1 h at 20ÂC in an orbital shaker followed by filtration, and the residues were submitted to two further successive extractions. The filtrate from the three methanolic extractions was gathered and concentrated in a rotary evaporator. Portions of the concentrated extract (10 mg) were suspended in 10 mL MeOH (50%). This extract (1 mg/mL) was used in the determination of the total phenolic content (TPC). In vitro antioxidant activity was measured by DPPH radical scavenging, ferric-reducing antioxidant power (FRAP), β-carotene bleaching (BCB), and ferrous ion chelating (FIC), at the concentrations 5, 50, 500 and 1000 Âg/mL, prepared from the extract. The metal chelator EDTA was used as a positive control in FIC, while the remaining essays used the synthetic antioxidant BHA. The TPC values were higher in the second semester of the year and varied from 4 to 32 mg GAE/g extract. The DPPH radical scavenging, BCB and FIC results did not exhibit variation patterns and presented activities greater than 25%, 70% and 10%, respectively. FRAP in the extracts of C. cupressoides, C. racemosa and C. sertularioides was higher in the second half of the year, while for C. mexicana the largest value was found in the first half of the year, and for C. prolifera variations during the year did not obey a pattern similar to the others. In all methodologies the activities of the alga extracts were inferior to the positive controls. The five species of Caulerpa can be considered potential sources of antioxidants with possible uses, such as in the food industry, not requiring a specific annual period for the extraction of these antioxidant compounds, as though there is variation across the year, it is not highly pronounced.
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35

Rego, Adriana Isabel Correia. "Exploring Polar Microbiomes as Source of Bioactive Molecules." Dissertação, 2017. https://hdl.handle.net/10216/110558.

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36

Loureiro, Joana Cristina Barbosa. "Reactivation of p53: Searching for new small molecules anticancer candidates." Dissertação, 2016. https://repositorio-aberto.up.pt/handle/10216/90987.

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37

Rego, Adriana Isabel Correia. "Exploring Polar Microbiomes as Source of Bioactive Molecules." Master's thesis, 2017. https://hdl.handle.net/10216/110558.

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38

Loureiro, Joana Cristina Barbosa. "Reactivation of p53: Searching for new small molecules anticancer candidates." Master's thesis, 2016. https://repositorio-aberto.up.pt/handle/10216/90987.

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39

Chen, Erh-Hao, and 陳邇浩. "The Natural Bond Orbital Anaiysis of the Canonical Molecular Orbital for Some Simple Molecules." Thesis, 1998. http://ndltd.ncl.edu.tw/handle/90142115723985060499.

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40

Ramos, Ana Sofia Ferreira de Almeida. "Exploiting the bioactive potential of microbial small molecules for the development of next generation antimicrobials." Dissertação, 2018. https://hdl.handle.net/10216/118830.

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41

Glendening, Eric David. "Natural resonance theory and studies of electronic delocalization in molecules." 1991. http://catalog.hathitrust.org/api/volumes/oclc/24259097.html.

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Thesis (Ph. D.)--University of Wisconsin--Madison, 1991.
Vita. Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references.
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42

Ramos, Ana Sofia Ferreira de Almeida. "Exploiting the bioactive potential of microbial small molecules for the development of next generation antimicrobials." Master's thesis, 2018. https://hdl.handle.net/10216/118830.

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43

Kant, Rajni, and 康竣磊. "Identification of small molecules/natural compounds for therapeutic/preventive uses in liver cancer." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/2wnyeg.

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44

Humason, Alan Wilfred. "A search for multi-drug resistance pump inhibitor molecules by isolation of natural products." 2005. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:1430987.

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45

"Design and Synthesis of Artificial Photosynthetic Molecules to Mimic Aspects of Natural Photosynthetic Mechanisms." Doctoral diss., 2011. http://hdl.handle.net/2286/R.I.9419.

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abstract: Natural photosynthesis features a complex biophysical/chemical process that requires sunlight to produce energy rich products. It is one of the most important processes responsible for the appearance and sustainability of life on earth. The first part of the thesis focuses on understanding the mechanisms involved in regulation of light harvesting, which is necessary to balance the absorption and utilization of light energy and in that way reduce the effect caused by photooxidative damage. In photosynthesis, carotenoids are responsible not only for collection of light, but also play a major role in protecting the photosynthetic system. To investigate the role of carotenoids in the quenching of the excited state of cyclic tetrapyrroles, two sets of dyads were studied. Both sets of dyads contain zinc phthalocyanine (Pc) covalently attached to carotenoids of varying conjugation lengths. In the first set of dyads, carotenoids were attached to the phthalocyanine via amide linkage. This set of dyads serves as a good model for understanding the molecular "gear-shift" mechanism, where the addition of one double bond can turn the carotenoid from a nonquencher to a very strong quencher of the excited state of a tetrapyrrole. In the second set of dyads, carotenoids were attached to phthalocyanine via a phenyl amino group. Two independent studies were performed on these dyads: femtosecond transient absorption and steady state fluorescence induced by two-photon excitation. In the transient absorption study it was observed that there is an instantaneous population of the carotenoid S1 state after Pc excitation, while two-photon excitation of the optically forbidden carotenoid S1 state shows 1Pc population. Both observations provide a strong indication of the existence of a shared excitonic state between carotenoid and Pc. Similar results were observed in LHC II complexes in plants, supporting the role of such interactions in photosynthetic down regulation. In the second chapter we describe the synthesis of porphyrin dyes functionalized with carboxylate and phosphonate anchoring groups to be used in the construction of photoelectrochemical cells containing a porphyrin-IrO2·nH2O complex immobilized on a TiO2 electrode. The research presented here is a step in the development of high potential porphyrin-metal oxide complexes to be used in the photooxidation of water. The last chapter focuses on developing synthetic strategies for the construction of an artificial antenna system consisting of porphyrin-silver nanoparticle conjugates, linked by DNA of varied length to study the distance dependence of the interaction between nanoparticles and the porphyrin chromophore. Preliminary studies indicate that at the distance of about 7-10 nm between porphyrin and silver nanoparticle is where the porphyrin absorption leading to fluorescence shows maximum enhancement. These new hybrid constructs will be helpful for designing efficient light harvesting systems.
Dissertation/Thesis
Ph.D. Chemistry 2011
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46

Moreira, Sara Gomes. "Drugging p53 - impaired tumors: impact of new small molecules targeting p73 and mutant p53." Tese, 2019. https://hdl.handle.net/10216/122966.

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47

Moreira, Sara Gomes. "Drugging p53 - impaired tumors: impact of new small molecules targeting p73 and mutant p53." Doctoral thesis, 2019. https://hdl.handle.net/10216/122966.

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48

Jesus, Rita Rodrigues Fernandes de. "Natural inspired small organic molecules for targeting aquaporins as a novel therapeutic approach to pancreatic cancer." Master's thesis, 2021. http://hdl.handle.net/10362/117540.

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Exploration of natural products for potential therapeutic use and asymmetric organic synthesis is an interesting approach for natural product valorisation. Therefore, in the present work, two projects were investigated: discovery of novel pharmacological agents for cancer treatment and development of a new series of asymmetric catalysts. Aquaporins (AQPs) are transmembrane proteins involved in metastatic and tumour growth processes. Thus, their potential as a novel druggable cancer target prompted the study of AQPs modulators, from natural sources. In this first project, two labdane diterpenes present in Cistus Ladaniferus — Labdanolic acid (LA) and 6-oxocativic acid (OA) — were isolated and their biological activity was studied in three different AQPs (AQP1, AQP3, AQP5), aiming to unleash a new therapeutic application for cancer treatment. Through AQPs permeability assays using the stopped flow technique, results indicated that both compounds were not promising for cancer treatment, since a decrease in permeability is not depicted in any of the AQPs under study. In addition, a linear total synthesis of OA from LA was investigated but without promising results. Using another natural source —Lupinus albus L. — another family of natural products is encountered: quinolizidine alkaloids. Lupanine and Sparteine are members of this family with known pharmacological activity. Sparteine is mostly known for its use in asymmetric catalysis as a chiral base. Considering the possibility of developing a new series of asymmetric catalysts with increased enantioselectivity comparing to the already known chiral base sparteine, and based on studies previously developed in our group, in this second project we envisioned the development of a new series of asymmetric catalysts via functionalization of lupanine with a nitrile functional group, through a yet unreported C-H activation electrochemical approach. In batch, 17-cyano rac-lupanine was obtained in high yield and selectivity, whereas in flow, further studies need to be performed to improve reaction selectivity. Additionally, derivatizations of 17-cyano-rac lupanine and 17-cyano-rac-sparteine were investigated, yielding new synthetically useful products. In the context of finding novel AQPs inhibitors, 17-cyano-rac-lupanine, 17-cyano-rac sparteine and the derivatives synthetized throughout this work were studied in three different AQPs (AQP1, AQP3, AQP5) using the stopped flow technique. No promising results in regard to cancer treatment were obtained. Both projects will add insight to natural product utility.
O aproveitamento de productos naturais para uma potencial aplicação terapêutica e/ou catálise assimétrica é uma abordagem interessante para a valorização de produtos naturais. Assim sendo, neste trabalho dois projetos foram estudados: descoberta de novos agentes farmacológicos para o tratamento do cancro, e desenvolvimento de uma nova série de catalisadores assimétricos. As aquaporinas (AQPs) são proteínas transmembranares envolvidas em processos metastáticos e de crescimento tumoral. Deste modo, o seu potencial como alvos terapêuticos levou ao estudo de moduladores de AQPs a partir de fontes naturais. Neste primeiro projeto, dois diterpenos do tipo lábdano presentes na planta Cistus Ladaniferus – ácido labdanólico a ácido-6-oxocativico – foram isolados e a sua atividade biológica estudada em três diferentes AQPs (AQP1, AQP3 e AQP5), com o objetivo de descobrir uma terapia inovadora para o tratamento do cancro. Através de estudos de permeabilidade usando a técnica de stopped flow, foi possível concluir que ambos os compostos não são promissores para o tratamento do cancro, visto que não é observado em nenhuma das AQPs em estudo uma diminuição da permeabilidade. Paralelamente, síntese do ácido-6-oxocativico partindo do ácido labdanólico foi desenvolvida, mas sem resultados promissores. Tirando partido de outra planta — Lupinus albus L. — outra família de productos naturais é encontrada: alcalóides quinolizidínicos. A lupanina e a esparteina são compostos com conhecida atividade farmacológica e membros desta família de compostos. A esparteina é conhecida principalmente como base quiral em catálise assimétrica. Tendo em conta a possibilidade de desenvolver uma nova série de catalisadores assimétricos com uma enantiosselectividade superior á já conhecida esparteína, e com base em estudos previamente desenvolvidos no nosso grupo, neste segundo projeto foi iniciado o desenvolvimento de uma nova série de catalisadores assimétricos com base na funcionalização C-H eletroquímica da lupanina com um grupo nitrilo numa abordagem que até hoje não está reportada na literatura. Em batch, 17-ciano-rac-lupanina foi obtida com elevada seletividade e rendimento, enquanto que em química de fluxo, estudos adicionais devem ser efetuados para melhorar a seletividade da reação. Paralelamente, derivatizações foram efetuadas na 17-ciano-rac-lupanina e 17-ciano-rac-esparteina, levando à formação de produtos sinteticamente úteis. No âmbito de descobrir novos inibidores de aquaporinas, 17-ciano-rac-lupanina, 17-ciano-rac-esparteina e os derivados sintetizados ao longo deste trabalho foram estudados em três diferentes AQPs (AQP1, AQP3 e AQP5) usando a técnica de stopped flow. Os resultados indicam que todos os compostos em estudo não são promissores para o tratamento do cancro. Ambos os projetos têm com objetivo valorizar a aplicação dos produtos naturais
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49

Bohmann, Jonathan Andrew. "Ab initio calculations of nuclear magnetic shielding tensors in small molecules and their interpretation using natural chemical shielding analysis." 1996. http://catalog.hathitrust.org/api/volumes/oclc/36561966.html.

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50

Sunagar, Kartik. "Molecular Evolution of Animal Venom." Tese, 2013. https://repositorio-aberto.up.pt/handle/10216/70349.

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