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Chemical biology encompasses the study and manipulation of biological system using chemistry, often by virtue of small molecules or unnatural amino acids. Much insight has been gained into the mechanisms of biological processes with regards to protein structure and function, metabolic processes and changes between healthy and diseased states. As an ever expanding field, developing new tools to interact with and impact biological systems is an extremely valuable goal. Herein, work is described towards the synthesis of a small library of heterocyclic-containing small molecules and the mechanistic details regarding the interesting and unexpected chemical compounds that arose; an alternative set of non-toxic copper catalyzed azide-alkyne click conditions for in vivo metabolic labelling; and the synthesis of an unnatural amino acid for further chemical modification via [3+2] cycloadditions with nitrones upon incorporation into a peptide of interest. Altogether, these projects strive to supplement pre-existing methodology for the synthesis of small molecule libraries and tools for metabolic labelling, and thus provide further small molecules for understanding biological systems.

Chemical biology encompasses the study and manipulation of biological system using chemistry, often by virtue of small molecules or unnatural amino acids. Much insight has been gained into the mechanisms of biological processes with regards to protein structure and function, metabolic processes and changes between healthy and diseased states. As an ever expanding field, developing new tools to interact with and impact biological systems is an extremely valuable goal. Herein, work is described towards the synthesis of a small library of heterocyclic-containing small molecules and the mechanistic details regarding the interesting and unexpected chemical compounds that arose; an alternative set of non-toxic copper catalyzed azide-alkyne click conditions for in vivo metabolic labelling; and the synthesis of an unnatural amino acid for further chemical modification via [3+2] cycloadditions with nitrones upon incorporation into a peptide of interest. Altogether, these projects strive to supplement pre-existing methodology for the synthesis of small molecule libraries and tools for metabolic labelling, and thus provide further small molecules for understanding biological systems.

Chemical biology encompasses the study and manipulation of biological system using chemistry, often by virtue of small molecules or unnatural amino acids. Much insight has been gained into the mechanisms of biological processes with regards to protein structure and function, metabolic processes and changes between healthy and diseased states. As an ever expanding field, developing new tools to interact with and impact biological systems is an extremely valuable goal. Herein, work is described towards the synthesis of a small library of heterocyclic-containing small molecules and the mechanistic details regarding the interesting and unexpected chemical compounds that arose; an alternative set of non-toxic copper catalyzed azide-alkyne click conditions for in vivo metabolic labelling; and the synthesis of an unnatural amino acid for further chemical modification via [3+2] cycloadditions with nitrones upon incorporation into a peptide of interest. Altogether, these projects strive to supplement pre-existing methodology for the synthesis of small molecule libraries and tools for metabolic labelling, and thus provide further small molecules for understanding biological systems.

Les bicycles imidazo-imidazoles constituent une classe de composés hétérocycliques intéressants tant sur le plan chimique que pharmaceutique. Ils jouent un rôle très important dans la synthèse et la fonctionnalisation des composés à visé thérapeutique. Dans le cadre de la recherche de nouveaux candidats inhibiteurs de kinases, nous avons développé une voie de synthèse des imidazo[1,2-a]imidazoles mono- et bifonctionnalisés. Par la suite, nous avons mis au point une stratégie de synthèse rapide et efficace de bicycles imidazo[1,5-a]imidazolin-2-one et imidazo[1,5-a]imidazole. En outre, nous avons développé deux stratégies de fonctionnalisation via des réactions de couplage pallado-catalysées. Finalement nous avons synthétisé le motif imidazo[1,5-a]imidazole via la réaction de Groebke-Blackburn-Bienaymé (GBB). La potentialité de cette réaction a été exploitée dans des réactions decyclisation intramoléculaire! afin de préparer une nouvelle chimiothèque de composés polyhétérocycliques azotés. / The imidazo-imidazoles bicycles have received special attention among other nitrogen cycles due to their biologically interesting properties exploited in the medicine manufacturing. The imidazo-imidazole scaffold is one of the most representative nitrogen containing heterocycle, as it plays a significant role and possesses a major interest in drug synthesis and functionalization. In this work we report firstly a synthetic pathway to novel imidazo[1,2-a]imidazoles candidates for CKD inhibitors. Secondly we develop two strategies to prepareimidazo[1,5-a]imidazoles and their reactivity via pallado-catalyzed reactions. Finally, we disclose a fast and an efficient access to imidazo[1,5-a]imidazoles by using the Groebke-Blackburn-Bienaymé reaction (GBB), followed by a palladium catalysed intramolecular cyclization, affording thus new tetracyclic products with an elevated degree of molecular diversity.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-05-13T18:09:13Z No. of bitstreams: 1 fabiodesouzafernandes.pdf: 24065820 bytes, checksum: da2a7ed64d78294c49d6e226495eda40 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2016-06-27T21:20:25Z (GMT) No. of bitstreams: 1 fabiodesouzafernandes.pdf: 24065820 bytes, checksum: da2a7ed64d78294c49d6e226495eda40 (MD5) / Made available in DSpace on 2016-06-27T21:20:25Z (GMT). No. of bitstreams: 1 fabiodesouzafernandes.pdf: 24065820 bytes, checksum: da2a7ed64d78294c49d6e226495eda40 (MD5) Previous issue date: 2016-02-29 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Na Química Medicinal, dentre as várias técnicas de planejamento racional para a síntese de novas moléculas bioativas, a hibridação é umas das mais usadas. A união de dois ou mais compostos biologicamente ativos, no intuito de se criar um novo fármaco que conserve as propriedades biológicas das moléculas base e/ou crie uma nova atividade biológica para o composto híbrido, faz desta técnica um caminho rápido, eficaz e oportuno no descobrimento de novos candidatos a fármacos. Sinteticamente, dentre os vários métodos de junção de duas ou mais moléculas a Reação de Mannich está entre as metodologias aplicadas para isto. Este primeiro capítulo trata da síntese N-bases de Mannich derivadas da pirazinamida, que resultou na obtenção de dezenove compostos inéditos. Em um primeiro momento, foi realizada a tentativa de síntese de N-bases de Mannich derivadas da pirazinamida, utilizando três diferentes aminoálcoois Nalquilados. O desenvolvimento da metodologia mostrou que a reação era dependente do pH, tendo este que ser básico. No entanto, a baixa conversão da reação, juntamente com a difícil purificação do produto, uma vez que o mesmo apresentava o mesmo fator de retenção da pirazinamida e alta instabilidade impedindo qualquer funcionalização in situ inviabilizou qualquer possibilidade de continuação desta síntese. Desta forma, foi feita a substituição dos aminoálcoois N-aquilados por piperazinas N-substituídas, contendo cadeias lipofílicas, uma porção D-galactose, amidas lipofílicas, aminoalcoóis aromáticos e heteroaromáticos, sendo sintetizados 5 derivados inéditos da piperazina. A partir da reação de Mannich das piperazinas Nsubstituídas com a pirazinamida foram obtidas quatorze N-Bases de Mannich inéditas. Tanto as piperazinas N-substituídas como as N-bases de Mannich sintetizadas, foram submetidas à avaliação de suas atividades antibacterianas, antibiofilme e antituberculose, sendo que os resultados para atividade antibiofilme apresentaram bastante promissores. As lactamas são amidas cíclicas presentes em vários produtos naturais e em compostos sintéticos com atividade biológica. Devido a esta importância dentro da química medicinal, várias são as estratégias desenvolvidas para a síntese destes anéis heterocíclicos, com o objetivo de se conseguir uma síntese rápida, eficiente, estereoseletiva e utilizando a química verde para destes compostos. Dentre as várias metodologias sintéticas que permitem a obtenção estereoseletiva de Lactamas está à reação de Mannich-Acilação, inicialmente desenvolvida por Castagnoli em 1969 e aperfeiçoada recentemente pelo grupo de pesquisa do Professor Dr. Jared Shaw. Sendo assim, o segundo capítulo aborda desenvolvimento de uma metodologia a paritr da reação de Mannich-Acilação para a síntese de δ-lactamas como suporte para um estudo computacional sobre o mecanismo e estereoseletividade da reação. Para isso, a síntese do anidrido altamente reativo α-ciano glutárico, bem como, dos anidridos α- ciano glutárico substituídos com grupos metila ou fenila nas posições β ou γ foram realizadas. O escopo e as limitações da reação imina-anidrido com uma ampla variedade de iminas também foi investigada. As reações contendo aminas substituídas por grupos alquil volumosos e aromáticos foram mais diastereoseletivas. Já as reações envolvendo o uso dos anidridos α-ciano glutáricos não substituídos e contendo os grupos metila e fenila na posição β mostraram-se altamente diastereoseletivas, enquanto que para as reações envolvendo o anidrido α-ciano glutárico substituídos na posição γ houve uma perda da seletividade. Os estudos computacionais mostraram que a origem do estereocontrole da reação se dá na etapa de acilação, onde efeitos estéreos e trans anulares para o estado de transição na forma eclipsada justificam a formação do produto majoritário tendo uma relação syn entre os grupos carboxilato e fenil. Neste capítulo também foram exploradas algumas aplicações, no que diz respeito à utilização das δ-lactamas como possíveis inibidores da proteína FtsZ, em um estudo onde as δ-lactamas serviram como substratos na reação clássica de descarboxilação alilativa e na síntese dos produtos naturais Gelsidilam e Gelgamina B tendo a reação de Mannich-Acilação desenvolvida neste capítulo como uma das etapas chave. / In the Medicinal Chemistry, there are many techniques for development of new bioactive molecules. One way to do a rational planning of new drugs is using the molecular hybridization technique. In the molecular hybridization, the combination of two or more biologically active compounds in order to create a new pro-drug that preserves the biological properties or improve efficacy when compared to the parent drugs, makes this technique a quick way, effective and timely in the discovery of new drug candidates. Mannich reaction can be applicable to combine two or more fragments of drugs with biological activity. The first chapter will show the synthesis of new N-Mannich bases derived from pyrazinamide, which resulted in the synthesis of nineteen novel compounds. First of all, we tried to make the synthesis of new N-Mannich bases from of reaction between pyrazinamide, formaldehyde and N-alkylated amino alcohols. The development of this methodology showed that the reaction was pH dependent and it had to be basic. So we tried to control the pH of reaction using some bases, but the lower conversion of reaction together with the difficult purification of the product and the high instability led to an unsuccessful planning to get the products desired. Because of this, was made replacing of N-alkylated amino alcohols by N-substituted piperazines having lipophilic chain, D-galactose moiety, lipophilic amides, aromatic and heteroaromatic amino alcohols. With these new components we ran the Mannich reactions and was possible to synthesize fourteen novel N-Mannich bases. The N-substituted piperazines and N-Mannich bases synthesized were evaluated by antibacterial, antibiofilm and antituberculosis activities. The results of antibiofilm and antibacterial activity for some hybrids were very promising. In the second chapter, was developed a methodology to the synthesis of δ- lactams from cycloaddition between imines and cyano glutaric anhydrides like a support to mechanism and diastereoselectivity study of reaction. For this was made the synthesis of β, γ-substituted and unsubstituted cyano anhydrides. The scope of reaction was studied using differents amines and aldehydes. The reactions that were ran with bulky alkyl-substituted amines or aromatic amines were more selective than methylamine. The reactions involving the use of α-cyano-glutaric anhydrides unsubstituted or containing methyl groups and phenyl in the β position showed high diastereoselectivity. Reactions using the γ substituted anhydrides had a poor diastereoselectivity. Computational studies showed that acylation step is a determinant factor to diastereoselectivity, where the eclipsed transition state to anti product has steric and trans anular effects. Some applications of -lactams were made in other studies involving Tethering technique, decarboxylative allylation and total synthesis of Gelsedilam and Gelegamine B.

Chemical biology encompasses the study and manipulation of biological system using chemistry, often by virtue of small molecules or unnatural amino acids. Much insight has been gained into the mechanisms of biological processes with regards to protein structure and function, metabolic processes and changes between healthy and diseased states. As an ever expanding field, developing new tools to interact with and impact biological systems is an extremely valuable goal. Herein, work is described towards the synthesis of a small library of heterocyclic-containing small molecules and the mechanistic details regarding the interesting and unexpected chemical compounds that arose; an alternative set of non-toxic copper catalyzed azide-alkyne click conditions for in vivo metabolic labelling; and the synthesis of an unnatural amino acid for further chemical modification via [3+2] cycloadditions with nitrones upon incorporation into a peptide of interest. Altogether, these projects strive to supplement pre-existing methodology for the synthesis of small molecule libraries and tools for metabolic labelling, and thus provide further small molecules for understanding biological systems.

L’accumulation excessive de leucocytes conduisant à un dysfonctionnement de la réponse immunitaire est caractéristique de plusieurs maladies inflammatoires. La première étape du recrutement des leucocytes aux sites d’inflammation est tributaire de l’interaction entre le tétrasaccharide sialyl LewisX (sLeX) et les protéines d’adhésion sélectines P et E, qui sont exprimés sur les cellules endothéliales des parois vasculaires. Par conséquent, les sélectines sont des cibles thérapeutiques importantes. Ainsi, la conception d’antagonistes des sélectines est une stratégie prometteuse pour traiter l'inflammation aiguë. Par exemple, l’administration d’analogues du sLeX chez les patients hospitalisés souffrant de crises vaso-occlusives ou de syndrome de détresse respiratoire aiguë (SDRA) peut atténuer les enjeux d'accumulation de cellules immunitaires. Tout en se basant sur la première génération d'antagonistes des sélectines développées par notre laboratoire, l’objectif de ce travail était de synthétiser et d'évaluer l’activité biologique d’une nouvelle série d’analogues du sLeX ciblant l'inflammation aiguë. Ce travail établit deux nouvelles stratégies qui permettent d'accéder à des analogues du sLeX incorporant un motif galactopyranoside bicyclique avec une fonctionnalité carboxylate ayant une conformation restreinte. Dans la première approche, l’intermédiaire bicyclique clé est formé en 13 étapes à partir du D-galactose pentaacétate avec un rendement global de 19 %. Indépendamment de la stéréochimie des précurseurs, une réaction de cyclisation intramoléculaire a permis de générer l’intermédiaire clé avec le carboxylate en position axiale. Un contrôle cinétique Curtin-Hammett serait à l'origine de la stéréosélectivité, une hypothèse supportée par une étude expérimentale et par calculs théoriques DFT. La série des carboxylates équatoriales a également été préparée par une stratégie de désilylation basée sur la migration d'un ester β,γ-insaturé. La deuxième approche implique une stratégie de double glycosidation orthogonale qui est influencée par la conformation restreinte du bicycle. L'intermédiaire bicyclique, portant un groupement nitrile en C9 (alpha), a été préparé en 12 étapes avec un rendement global de 53 %. Cette approche a mené à une série d'antagonistes des sélectines incorporant des modifications d'amide, d'amine et de tétrazole, ainsi qu'un analogue incorporant un C6-benzamide. Cette approche modulaire peut être exploitée pour préparer d’autres isostères d'acide carboxylique. Un analogue hybride a été préparé en combinant le galactopyranoside bicyclique avec la fonctionnalisation de la chaîne latérale qui se retrouve sur l’espaceur à base de tartrate. Cette voie de synthèse a également été conçue afin d'accéder aux analogues du sLeX portant une sonde de photoaffinité. Cet analogue servira comme outil dans le marquage par photoaffinité des sélectines pour élucider les résidus clés du site actif. Les analogues de la deuxième génération ont été évalués pour leur capacité à se lier aux sélectines et d’empêcher les cellules immunitaires d’adhérer. Une méthode qualitative permettant de classer l’affinité de nos composés aux sélectines à l'aide de la spectroscopie SPR ainsi qu'une expérience préliminaire d'inhibition compétitive en solution ont été développées. Les principaux composés ont également été évalués à l'aide de tests in vitro d'adhésion de cellules HL-60 et de roulement par imagerie des cellules vivantes. Un essai de migration cellulaire par lavage péritonéal in vivo a été utilisé pour valider l’activité de nos composés principaux et leur capacité à inhiber le recrutement des neutrophiles dans un modèle d'inflammation aiguë. Nos résultats démontrent l’augmentation de la puissance et de l’activité de nos analogues de deuxième génération comparativement à la première. La série de galactopyranosides a démontré une spécificité pour l'inhibition de la P-sélectine, alors que la série des arabinopyranosides, incorporant un motif tétrazole, a démontré une activité remarquable vers la E-sélectine. La combinaison des deux modifications ont produit une activité pan-sélectines exceptionnelle qui justifie une enquête plus approfondie. / The first step for leukocyte adhesion and rolling along the vascular endothelium during the immune system inflammatory response involves the recognition of the tetrasaccharide sialyl LewisX (sLeX) by selectin glycoproteins. Dysfunction of the immune response, a consequence of several pathologies of inflammatory disease, leads to an excessive influx of leukocytes that necessitates therapeutic intervention. The development of glycomimetics, small molecule therapeutics that imitate complex glycans, is a promising strategy for treating inflammation. Specifically, a targeted approach amenable to severe acute inflammation, such as in hospitalized patients suffering from vaso-occlusive crises (VOC) or acute respiratory distress syndrome (ARDS). Building off the first generation of selectin antagonists developed by our laboratory, the aim of this work was to synthesize and evaluate the potency of a new class of sLeX glycomimetics for use as selectin antagonists targeting acute inflammation. This work describes the development of two novel strategies for sLeX glycomimetics incorporating a challenging trans-bicyclo[4.4.0] 3-O,4-C-fused galactopyranoside scaffold with a conformationally restricted carboxylate moiety. In the first approach, the key bicyclic galactopyranoside intermediate was accessed through a 13-step sequence with 19% overall yield from D-galactose pentaacetate. An unprecedented intramolecular cyclization reaction provided the desired axially configured bicyclic intermediate independent of the precursor stereochemistry. The origin of stereoselectivity was proposed to be under Curtin-Hammett kinetic control; a hypothesis supported by an experimental study and theoretical DFT calculations. The equatorial carboxylate series was also prepared using a desilylation strategy capitalizing on the migration of an β,γ-unsaturated ester. The second approach is highlighted by an orthogonal dual-glycosidation strategy that takes advantage of the conformationally restricted scaffold. The key bicyclic intermediate, bearing an α-configured C9 nitrile moiety, was prepared in 12 steps with a 53% overall yield. This approach led to a series of selectin antagonists incorporating axially-locked amide, amine, and tetrazole modifications at the C9 position, as well as an analogue incorporating a C6-benzamide. The modular galactopyranoside framework achieved using this approach can be exploited to prepare additional carboxylic acid bioisosteres for future SAR studies. A hybrid analogue was prepared, that combines the bicyclic galactopyranoside scaffold and a synthetic approach to selectin antagonists incorporating sidechain modifications to the first-generation tartrate diester. This synthetic route was also elaborated to access sLeX glycomimetics bearing a benzophenone-based photoaffinity probe. This analogue will serve as a valuable tool in the photoaffinity labeling of selectin proteins to elucidate key active site residues. The second-generation analogues were evaluated for their ability to inhibit selectin adhesion. A qualitative method to rank the binding strength towards recombinant P- and E-selectin proteins using SPR biosensor technology was developed, as well as a preliminary competitive inhibition in solution experiment with immobilized PSGL-1. Several compounds were also evaluated using an in vitro HL-60 cell adhesion assay, and a live-cell imaging experiment. An in vivo peritoneal lavage cellular migration assay was used to validate the potency of our lead compounds at inhibiting neutrophil recruitment in an acute inflammation model. Key results from the biological evaluations include an improvement in activity by restricting the conformation of the carboxylate moiety to the axial configuration, as well as an enhancement in potency over the lead compound from the first-generation series. Remarkably, specificity for P-selectin inhibition was observed with the galactopyranoside series, while the arabinopyranoside series, incorporating a tetrazole bioisostere, displayed significant activity towards E-selectin. The combination of the two modifications yielded remarkable pan-selectin activity that warrants further investigation.