Since its emergence in December 2019, SARS-CoV-2 has infected over 200 million people globally. SARS-CoV-2 spike (S) decorates the viral envelope and is responsible for facilitating viral entry into the host cell. To mediate membrane fusion, S must be proteolytically cleaved. For the closely related SARS-CoV S, cleavage at the host cell surface must be facilitated by the serine protease TMPRSS2. We demonstrated that SARS-CoV-2 S can facilitate fusion independent of TMPRSS2 and sought to identify other proteases capable of driving SARS-CoV-2 S-mediated fusion. We show that the ADAMs and MMP inhibitor GI 254023X is capable of substantially reducing SARS-CoV-2 S-mediated syncytium formation. Additionally, we identified MMP-9, a protein target of GI 254023X, as a host protease capable of enhancing SARS-CoV-2 lentivirus entry in HEK293T-ACE2 cells. These results implicate ADAM and MMP proteases, in particular MMP-9, as potential antiviral drug targets against COVID-19 pathogenesis.

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Thesis Title Exploring new methodologies to identify disease-associated variants in African populations through the integration of patient genotype data and clinical phenotypes derived from routine health data: A case study for Type 2 Diabetes Mellitus patients in the Western Cape Province, South Africa. Abstract Introduction There is poor knowledge on the genetic drivers of disease in African populations and this is largely driven by the limited data for human genomes from sub-Saharan Africa. While the costs of generating human genomic data have gone down significantly, they are still a barrier to generating large scale African genomic data. This project is therefore a proof-of-concept pilot study that demonstrates the implementation of a cost-effective, scalable genotyped virtual cohort that can address population level genomic questions. Methods We optimised a tiered informed consent process that is suitable for the cohort study design and adapted it to conducting human genomic research in the African context. We used an existing dataset to explore statistical methods for modelling longitudinal routine health data into a standardised phenotype for genome wide association studies (GWAS). We then conducted a feasibility study and piloted the tiered informed consent process, DNA collection by buccal swab and DNA extraction from buccal swabs and peripheral blood samples. DNA samples were genotyped for approximately 2.2 million variants on the Infinium™ H3Africa Consortium Array V2. Genotyping quality control (QC) was done in Plink 1.9 and genome wide imputation on the Sanger Imputation Service. We demonstrated successful variant calling and provide aggregate statistics for known aetiological variants for type 2 diabetes and severe COVID-19 as well as demonstrating the feasibility of running nested case-control GWAS with these data. Results We demonstrate the use of routine health data to provide complex phenotypes to link to genotype data for both non-communicable diseases (diabetes) and infectious diseases (Tuberculosis, HIV and COVID-19). 459 participants consented to providing a DNA sample and access to their routine health data and were included in the feasibility study. A total of 343 DNA samples and 1782023 genotyped variants passed quality control and were available for further analysis. While most of the cohort population clustered with the 1000 genomes African population, principal component analysis showed extensive population admixture. For the COVID-19 analysis, we identified 63 cases of severe COVID-19 and 280 controls, and for the type 2 diabetes analysis we identified 93 cases and 250 controls using the routine health data of participants in the cohort. While the sample sizes were insufficient for a GWAS we were able to evaluate known type 2 diabetes mellitus and COVID-19 variants in the study population. Conclusion We have described how we conceptualised and implemented a genotyped virtual population cohort in a resource constrained environment, and we are confident that this design and implementation are appropriate to scale up the cohort to a size where novel health discoveries can be made through nested case-control studies. In the interim we demonstrate the analysis and validation of aetiological variants identified in other studies and populations.

Introduction: Alpha-2-macroglobulin (α2m) is a plasma glycoprotein serine protease inhibitor. Previous studies have shown that coagulation factor concentrations are highly variable with age and α2m levels have been found to be twice as high in newborns compared to adults. This may contribute to a resistance towards thrombotic events observed in young populations. Protein glycosylation is known to affect protein activity and the glycosylation profile of adult α2m has previously been analyzed. Information regarding glycosylation of α2m in other age groups has yet to be elucidated. Therefore, the purpose of this study is to examine the differences in the glycosylation profiles between newborn and adult α2m. Methods: To evaluate glycan macroheterogeneity, plasma samples were enzymatically deglycosylated by PNGaseF, followed by SDS PAGE and western blotting (WB) to detect α2m. To evaluate microheterogeneity, plasma samples were incubated with Neuraminidase (Clostridium perfringens) followed by native PAGE and WB to determine sialic acid content. To detect non-sialylated terminal galactose residues, plasma samples were incubated with immobilized RCA120, and lectin-bound molecules were separated from unbound molecules. Additionally, the affinity of α2m for ricin was evaluated by eluting bound proteins with increasing concentrations of galactose. All fractions were subjected to SDS-PAGE and WB to detect α2m. 2D gel electrophoresis was completed to examine differences in pI and molecular weight of α2m in both age groups. Purification by immunoprecipitation was also performed and eluted α2m was analyzed by fluorescence-assisted carbohydrate electrophoresis (FACE) to determine the glycan fingerprint in the two populations. Results: Deglycosylation of both newborn and adult α2m with PNGaseF resulted in a change in migration and apparent molecular weight, however no statistically significant difference was found between newborn and adult. On native PAGE following treatment with neuraminidase, newborn α2m exhibited a statistically significant change in migration compared to adult. Additionally, newborn α2m exhibited a higher percentage of molecules bound to RCA120 than adult (no statistical difference) and elution of α2m from RCA120 with a galactose step gradient produced similar profiles for newborn and adult molecules. 2D electrophoresis and WB revealed a difference in pI of α2m in newborns as compared to adults. Finally, purified newborn and adult α2m were analyzed by FACE and quantification of prominent fluorescent bands revealed a higher secondary:primary band ratio in newborns when compared to adults. Conclusions: To our knowledge, this is the first study investigating glycosylation differences between newborn and adult α2m molecules. The results from PNGaseF analyses indicate no significant difference in total N-glycan content. Neuraminidase results suggest significantly greater sialic acid presence on newborn α2m, however there was no significant difference in galactose content. 2D electrophoresis revealed a difference in pI as well as the way in which newborn and adult α2m degrade when exposed to experimental conditions. A2m was successfully purified from both newborn and adult plasma, and FACE results indicate that the proportion of more branched glycans present in the two major fluorescent bands are of higher quantity in newborns than adults. / Thesis / Master of Science (MSc)

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No description available.

Le neutrophile est un type cellulaire de l'immunité innée essentiel à la gestion de perturbations homéostatiques impliquant des agents pathogènes. Il nettoie le site d'une réaction inflammatoire de ses débris et y combat les agents infectieux via la phagocytose, la dégranulation et l'explosion oxydative. De plus, il peut produire et relâcher une quantité importante de médiateurs lipidiques et peptidiques. Ces molécules ont pour rôle la génération d'un environnement inflammatoire propice à la résolution d'une perturbation homéostatique, ce qui inclut l'activation et le recrutement d'autres types cellulaires du système immunitaire. Parmi les médiateurs lipidiques que le neutrophile peut produire, on retrouve les prostanoïdes, qui sont issus d'une cascade de synthèse initiée par une enzyme appelée cyclooxygénase (COX). Récemment, un partenaire d'interaction fut trouvé pour la COX. À l'aide du test de levures à double hybride, il fut démontré qu'une protéine appelée nucléobindine (Nue) pouvait interagir avec les deux isoformes de cyclooxygénase existants (la COX-1 et la COX-2). La Nue est une protéine potentiellement multifonctionnelle dont le rôle n'est pas encore établi. La présente étude vise à déterminer si une interaction COX2/Nuc est possible en milieu intracellulaire et, advenant le cas, à en préciser la fonction. / The neutrophil is a cell type of innate immunity that is essential in the management of homeostatic imbalances involving pathogens. It cleans the site of an inflammatory reaction of its debris and gets rid of infectious material via phagocytosis, degranulation and oxydative burst. Moreover, it can release an important quantity of bioactive lipids and peptide mediators which ail have for common objective the creation of an inflammatory environment conducive to the resolution of a homeostatic perturbation. In fulfilling their duty, these molecules will, amongst other things, recruit and activate other cell types of the immune System. The bioactive lipid class of mediators includes the prostanoïd family generated from an enzymatic cascade initiated by an enzyme called cyclooxygenase (COX). Recently, an interaction partner was found for COX. The yeast two-hybrid assay, revealed that a protein named nucleobindin (Nue) could interact with both isoforms of cyclooxygenase (COX-1 and COX-2). Nue is a potentially multifunctional protein that has yet to be assigned a definitive role. Using the human neutrophil as an experimental model, the present study assesses the possibility and consequences of a COX-2/Nuc interaction in the intracellular environment.

Throughout many parts of the world house dust mites (HDM) are considered as a major source of indoor aeroallergens and they are powerful inducers of allergic diseases. Proteolytic HDM allergens are recognised as being able to directly activate respiratory epithelial cells and thereby actively participate in innate immune responses. Although several major HDM allergens lack proteolytic activity, their possible ability to similarly interact with epithelial cells is not known. The overall aim of this thesis was therefore to elucidate if and how major non-proteolytic group 2 allergens from different mite species interact with respiratory epithelial cells. The effects of the structurally related Der p 2, Der f 2 and Eur m 2 from different HDM species as well as the storage mite allergen Lep d 2 were studied in vitro using human respiratory epithelial cells. Also the non-proteolytic, but structurally dissimilar, Fel d 1 from cat, Can f 2 from dog, Bet v 1 from birch and Phl p 5a from timothy were studied. In this thesis evidence that major group 2 mite allergens activate bronchial epithelial cells is presented. Following allergen exposure the secreted amount of the inflammatory mediators G-CSF, GM-CSF, IL-6, IL-8, MCP-1, MIP-3α and sICAM-1 was increased. Surface expression of ICAM-1 was also increased following allergen exposure. Moreover, Fel d 1 and Can f 2 induced secretion of the same mediators from bronchial epithelial cells, representing two additional protein structures being able to directly induce cell activation. In experiments using specific inhibitors and siRNA transfection, it was shown that the mite allergens engage TLR4 and activation through MyD88, MAPK and NF-κB signal transduction pathways. In conclusion, the novel findings in this thesis provide knowledge on how major aeroallergens, in addition to their ability to provoke specific adaptive immune responses, may aggravate a respiratory airway disease by adjuvant-like activation of inflammatory responses in bronchial epithelial cells. This differs from previously reported allergen-induction of epithelial cells by the clear independency of proteolytic activation.

O objetivo deste trabalho foi investigar o uso de NbCl5 como ácido de Lewis em reações de cicloadição. Foram estudadas algumas reações de cicloadição [2 + 2], Reações de Diels-Alder entre enonas e ciclopentadieno e Reações da aza-Diels-Alder com bases de Schiff, avaliando o efeito da temperatura e da concentração molar do NbCl5. A comparação dos rendimentos, dos produtos formados e do tempo de reação com NbCl5, também foi um ponto fundamental da pesquisa. As reações de cicloadição [2 + 2] foram realizadas entre ésteres propiólicos e diferentes tipos de alcenos (éteres enólicos de silício e alcenos alifáticos). Nas reações com os éteres enólicos de silício não foi verificada a formação dos respectivos adutos de ciclobuteno, pois o NbCl5 promove a quebra da ligação oxigênio-silício, não levando à formação do produto desejado. Nas reações com os alcenos alifáticos foi possível obter o respectivo aduto, porém com rendimentos menores que com outros ácidos de Lewis. Quanto às reações de Diels-Alder, foram investigadas as reações entre diferentes ciclo-enonas (dienófilos de baixa reatividade) com ciclopentadieno (dieno) na presença de NbCl5. Os resultados obtidos indicam que o NbCl5 é um bom ácido de Lewis para ativar reações de Diels-Alder, apresentando tempos reacionais menores e alta diastereosseletividade a temperaturas mais baixas, quando comparado com outros ácidos de Lewis. A possibilidade de efetuar reações do Diels-Alder a -78 0C é um dos aspectos de destaque neste trabalho, pois, além de demonstrar a forte ativação do sistema enona exercido pelo NbCl5, possibilita obter produtos com alta seletividade. Paralelamente aos estudos de sistemática reacional foram realizados estudos de elucidação estrutural completa de alguns dos compostos sintetizados, utilizando-se diversas técnicas de RMN (uni e bidimensionais), e o auxílio de cálculos teóricos. Nas reações de aza-Diels-Alder entre bases de Schiff e di-hidropirano, o NbCl5 se mostrou um ótimo catalisador para a síntese de derivados de piranoquinolinas. Estes derivados formam uma importante classe de produtos naturais que apresentam ampla atividade biológica. As reações foram conduzidas com baixas concentrações de nióbio e em tempos relativamente curtos, obtendo-se rendimentos variando de 72 a 96 %. Outro fator a se destacar é a alta diastereosseletividade encontrada nestas reações. Também foram realizados estudos da atividade tripanocida dos derivados de piranoquinolinas preparados através das reações de aza-Diels-Alder catalisadas por NbCl5. / The aim of this work was to investigate the use of NbCl5 as Lewis acid in cycloadittion reactions. We have studied [2 + 2] cycloaddition reactions, Diels-Alder reactions between enonas and cyclopentadiene and aza-Diels-Alder reactions with Schiff bases. The effects of the temperature and of the molar concentration of NbCl5 were also evaluated. Comparasion of reaction yields, obtained products as well as reation time with NbCl5 were also a key point on this work. The [2 + 2] cycloaddition reactions were performed using propiolic ester and different types of alkenes (silyl enol ethers and aliphatic alkenes). In the reactions with silyl enol ethers, formation of the corresponding cyclobutene aductts was not verified, since the NbCl5 promotes the rupture of oxygen-silicon bonds, and the desired product is not obtained. In the reactions with aliphatic alkenes, it was possible to obtain the adduct, however, in lower yields as compared to those obtained with others Lewis acids. Regarding the Diels-Alder reactions, we have investigated reactions using different cycloenones (dienophiles of low reactivity) with cyclopentadiene (diene) with NbCl5. The obtained results indicate that NbCl5 is a good Lewis acid to activate these Diels-Alder reactions, resulting in shorter reaction times and higher diastereoselectivity at lower temperatures than other Lewis acids. The possibility of carrying out Diels-Alder reaction at -78 0C is another remarkable aspect of this work. Besides demonstrating the strong activation of the enone system by NbCl5, it opens the possibility of obtaining high stereoselectivity. We have also performed studies of complete structural elucidation of some compounds by using different NMR techniques (uni and bidimensional), with the help of theoretical calculations. In the aza-Diels-Alder reactions between Schiff bases and dihydropyran, the NbCl5 was an excellent catalyst for the synthesis of pyranoquinoline derivatives. These derivatives are an importante class of natural products that exhibit wide range of biological activity. The reactions were carried out at low concentration of niobium and in relatively short times, resulting in yields varying from 72 to 96 %. Another aspect that should be remarked is the high diastereoselectivity found in these reactions. We have also carried out studies of tripanocydal activity of pyranoquinoline derivatives prepared through aza-Diels-Alder reactions catalyzed by NbCl5.

La síntesi i caracterització estructural d'un nou tipus de macrocicles nitrogenats de 15, 20 i 25 membres, els quals contenen triples i dobles enllaços i diferents unitats aríliques a la seva estructura, ha estat estudiada. S'han preparat els complexos de pal·ladi(0) dels corresponents macrocicles poliinsaturats de 15 membres, els quals són estables a l'aire i a la humitat i en alguns casos presenten quiralitat. La seva caracterització completa s'ha portat a terme mitjançant RMN i difracció de raigs-X. S'ha estudiat també la reacció de cicloisomerització d'aquests macrocicles emprant diferents catalitzadors basats en metalls de transició, observant-se que el catalitzador de Wilkinson, de rodi(I), és el que ha donat més bons resultats. Finalment, s'ha realitzat una introducció a l'estudi del mecanisme d'aquest tipus de reaccions mitjançant ESI-MS, així com també un estudi inicial de la reacció de cicloisomerització enantioselectiva. / The synthesis and structural analysis of a new type of 15-, 20- and 25-membered nitrogen-containing polyunsaturated macrocycles has been carried out. Palladium(0) complexes of 15-membered polyunsaturated azamacrocycles, which are air and moisture stable and in some cases present chirality, has been prepared and fully caracterized by means of NMR spectroscopy and X-ray diffraction. The cycloisomerization reaction of these macrocycles using different catalysts based in different transition metals has been studied. It was observed that Wilkinson's catalyst (rhodium(I) catalyst) gave the best results. A brief look at the mechanism of cyclotrimerization reaction by means of ESI-MS has been carried out. Finally, an introduction in the study of the enantioselective cycloisomerization reaction of these macrocycles has been done.