Cancer is a leading cause of death worldwide, accounting for around 13% of all death [1]. Traditional cancer therapeutics usually require careful selection of one or more intervention, such as surgery, radiotherapy, and chemotherapy, which have made momentous progress, but have ample limitations [2]. The next generation of cancer therapeutics will specifically target processes responsible for the growth and survival of cancer cells. Among the most promising of these molecularly-targeted therapeutics are short interfering RNAs (siRNAs). These siRNAs serve as the effectors of RNA interference, a naturally occurring and highly specific mechanism for regulating gene expression through sequence-specific degradation of messenger RNA. However, the native structure of RNA is plagued with undesirable chemical properties. For example, the sugar-phosphate backbone contains a negative charge which hinders its ability to cross the negatively charged lipid bilayer. Furthermore, the phosphodiester backbone is a substrate for nucleases, which catalytically cleaves the phosphate-oxygen bond, thus degrading the native RNA [3]. As such, there is widespread interest in chemically modifying the backbone of siRNAs in order to overcome some of the inherent problems with its native structure. There have been only two reports that have employed amide-bond linkages as phosphate replacements within siRNAs [4, 5]. In both of these studies, the amide bond containing monomer units were placed at the 3’-overhangs and not within the internal Watson-Crick region of the double stranded siRNA due to the limitation of standard solid-phase oligonucleotide synthesis. In this thesis, we proposed to utilize phosphoramidite chemistry to localize internal amide-bond modifications [6]. A practical synthesis of a peptide nucleic acid unit combined with an RNA nucleoside (PNA-RNA dimer, UaU) is reported [7]. Using this PNA-RNA dimer phosphoramidite allows us to control the site-specific location of the internal amide-bond modification throughout the desired RNA strand. Polyacrylamide gel (PAGE) and mass spectrometry analysis were performed to ensure the formation of full-length modified siRNA molecules. The effects of these modifications were explored with respect to the biophysical and biological properties of the modified siRNAs. The techniques used in this work included hybridization affinity assays (melting temperature), secondary structure determination (circular dichroism), cell-based luciferase assays, and nuclease stability assays. Melting temperature experiment reveals that localizing a UaU dimer unit within the RNA oligonucleotides has an overall destabilizing effect, whereas UaU modifications at the 3’-overhang positions show little change in thermal stability. Circular dichroism experimental results illustrate that all chemically modified siRNAs exhibit the standard A-form helix. In cell-based luciferase assays, we utilized two different target sequences and our results highlight the compatibility of utilizing a neutral amide-bond backbone within siRNAs. Specifically, the internal amide-bond modification is compatible within the RNAi machinery when placed at 3’-overhang position in the sense strand of the double-stranded siRNA. However, poor efficacy is observed when this unit is placed adjacent the Ago 2 cleavage site on the antisense strand. The nuclease stability assays reveal that the introduction of a PNA-RNA dimer at the 3’-end of the siRNA where the exonuclease cleaves the terminal nucleotide, increased markedly the resistance to serum-derived nucleases. To the best of our knowledge, this is the first report that involves amide-bonds as phosphate backbone replacements within the internal regions of siRNAs and thus opens the future possibility for examining and utilizing this modification in studying new structure-function relationships. / UOIT

No description available.

No / Mechanochemical chemoenzymatic peptide and amide bond formation catalysed by papain was studied by ball milling. Despite the high-energy mixing experienced inside the ball mill, the biocatalyst proved stable and highly efficient to catalyse the formation of α,α- and α,β-dipeptides. This strategy was further extended to the enzymatic acylation of amines by milling, and to the mechanosynthesis of a derivative of the valuable dipeptide L-alanyl-L-glutamine. / We thank RWTH Aachen University for support from the Distinguished Professorship Program funded by the Excellence Initiative of the German federal and state governments. EPSRC, grant no. EP/L019655/1.

Cross-coupling reactions, where a transition metal catalyst facilitates the formation of a new carbon-carbon or carbon-heteroatom bond between two coupling partners, has become one of the most widely used, reliable, and robust family of transformations for the construction of molecules. The Nobel Prize was awarded to pioneers in this field who primarily used aryl iodides, bromides, and triflates as electrophilic coupling partners. The expansion of the reaction scope to non-traditional electrophiles is an ongoing challenge to enable an even greater number of useful products to be made from simple starting materials. The major goal of this thesis research is to improve and expand upon this field by using esters as electrophiles via the activation of the strong C(acyl)−O bond. Esters are particularly robust in comparison to other carboxylic acid derivatives used in cross-coupling reactions. Success on the activation of such inert functional group using catalysis has both fundamental and practical value. By discovering new reaction modes of this abundant functional group, synthetic routes to access novel or industrially important molecules can be improved. Chapter 1 of this thesis describes a literature overview of what has been accomplished in the field of cross coupling reactions using carboxylic acid derivatives as electrophilic coupling partners. Chapter 2 discloses the first palladium Suzuki-Miyaura couplings of phenyl esters to produce ketones. The method is efficient and robust, giving good yields of useful products. The reaction is proposed to proceed via an oxidative addition to the strong C(acyl)−O bond of the ester. In contrast to previous efforts in this field that use traditional catalysts such as Pd(PPh3)4, the developed reaction requires use of an electron-rich, bulky N-heterocyclic carbene ligand, which facilitates the strong bond activation. Furthermore, a palladium-catalyzed cross-coupling between aryl esters and anilines is reported, enabling access to diverse amides. The reaction takes place via a similar activation of the C−O bond by oxidative addition with a Pd−NHC complex, which enables the use of relatively non-nucleophilic anilines that otherwise require stoichiometric activation with strong bases to react. Chapter 3 discloses a nickel-catalyzed amide bond formation using unactivated and abundant esters. In this transformation, an accessible nickel catalyst can facilitate the activation of diverse aliphatic and aromatic esters to enable direct amide bond formation with amines as nucleophiles. No stoichiometric base, acid, or other activating agent is needed, providing exceptional functional group tolerance and producing only methanol as a by-product. This reaction is of both fundamental and practical importance because it is the first to demonstrate that simple conditions can enable Ni to cleave the C–O bond of an ester to make an oxidative addition product, which can be subsequently coupled with amines. This discovery contrasts industrially-common and wasteful methods that still require stoichiometric activating agents or multistep synthesis. Chapter 4 describes the evaluation of different types of cross-coupling reactions using methyl esters as electrophilic coupling partner. A high-throughput screening technique has been applied to this project. A combination between specific ligands, known by their efficiency to activate strong C−O bonds, and literature-based conditions has been designed for the chosen transformations. Using this strategy, two promising hits have been obtained using the same NHC ligand: a decarbonylative Suzuki-Miyaura and a decarbonylative borylation reaction.

Ao contrário da percepção da sociedade em geral, a tuberculose ainda é uma das mais graves doenças infecciosas da atualidade, estando à frente da HIV/AIDS como uma das maiores causas de morte por infecção. Apesar de todos os avanços recentes, o aparecimento de cepas multirresistentes não permitiu sua erradicação. Em 2016, a OMS lançou novos alvos rumo à erradicação global da enfermidade (End TB), alvos estes que, no Brasil, foram divulgados no Plano Nacional pelo Fim da TB, do Ministério da Saúde. Para que estas metas possam ser atingidas, a pesquisa em busca de novos fármacos, que possam diminuir o tempo de tratamento e seus efeitos adversos, tem papel fundamental. Modelagem molecular e planejamento racional otimizam a busca das novas drogas potenciais. Assim, modelos de QSAR aliados a metodologias de planejamento de fármacos auxiliados por computador (CADD) foram usados para a proposição das moléculas que se tornaram o alvo da síntese deste trabalho. Dois procedimentos distintos foram utilizados para sintetizar 1-H-2-aminoindol a partir de orto-cloronitrobenzeno. Paralelamente, quatro ácidos succinâmicos foram preparados pela reação de anidrido succínico com diferentes aminas. Posteriormente, cada ácido succinâmico deveria ser acoplado ao 1-H-2-aminoindol por meio de agentes de acoplamento como as carbodiimidas. Os resultados obtidos indicam que DCC em diclorometano pode ser eficiente para a síntese dos potenciais novos fármacos. / Contrary to popular belief, tuberculosis TB is still one of the most serious of infectious diseases today, surpassing AIDSHIV as one of the major causes of death by infection. ln spite of recent advances, the appearance of multi-resistant strains prevents its eradication. ln 2016, the OMS launched new geais for global eradication of the disease (End TB), geais that, in Brazil, were disclosed through the \"National Planto End TB,\" from the Ministry of Health. ln arder to reach these geais, studies in search of new anti-mycobacterials that could lessen the treatment time and its adverse effects have a fundamental role. Molecular modeling and rational planning optimize the search for new potential drugs. Thus, QSAR models in line with computer-aided drug design (CADD) were used for the molecule proposition that became the synthesis target of this work. Two distinct proceedings were utilized to synthesize 1-H-2-aminoindole from the ortho-chloronitrobenzene. Simultaneously, four succinamic acids were prepared by the reaction of succinic anhydride with different amines. Posteriorly, each succinamic acid should be coupled with 1-H-2-aminoindole by way of coupling agents such as carbodiimides. The results obtained indicate that DCC in dichloromethane can be efficient for the synthesis of potential new drugs.

Ao contrário da percepção da sociedade em geral, a tuberculose ainda é uma das mais graves doenças infecciosas da atualidade, estando à frente da HIV/AIDS como uma das maiores causas de morte por infecção. Apesar de todos os avanços recentes, o aparecimento de cepas multirresistentes não permitiu sua erradicação. Em 2016, a OMS lançou novos alvos rumo à erradicação global da enfermidade (End TB), alvos estes que, no Brasil, foram divulgados no Plano Nacional pelo Fim da TB, do Ministério da Saúde. Para que estas metas possam ser atingidas, a pesquisa em busca de novos fármacos, que possam diminuir o tempo de tratamento e seus efeitos adversos, tem papel fundamental. Modelagem molecular e planejamento racional otimizam a busca das novas drogas potenciais. Assim, modelos de QSAR aliados a metodologias de planejamento de fármacos auxiliados por computador (CADD) foram usados para a proposição das moléculas que se tornaram o alvo da síntese deste trabalho. Dois procedimentos distintos foram utilizados para sintetizar 1-H-2-aminoindol a partir de orto-cloronitrobenzeno. Paralelamente, quatro ácidos succinâmicos foram preparados pela reação de anidrido succínico com diferentes aminas. Posteriormente, cada ácido succinâmico deveria ser acoplado ao 1-H-2-aminoindol por meio de agentes de acoplamento como as carbodiimidas. Os resultados obtidos indicam que DCC em diclorometano pode ser eficiente para a síntese dos potenciais novos fármacos. / Contrary to popular belief, tuberculosis TB is still one of the most serious of infectious diseases today, surpassing AIDSHIV as one of the major causes of death by infection. ln spite of recent advances, the appearance of multi-resistant strains prevents its eradication. ln 2016, the OMS launched new geais for global eradication of the disease (End TB), geais that, in Brazil, were disclosed through the \"National Planto End TB,\" from the Ministry of Health. ln arder to reach these geais, studies in search of new anti-mycobacterials that could lessen the treatment time and its adverse effects have a fundamental role. Molecular modeling and rational planning optimize the search for new potential drugs. Thus, QSAR models in line with computer-aided drug design (CADD) were used for the molecule proposition that became the synthesis target of this work. Two distinct proceedings were utilized to synthesize 1-H-2-aminoindole from the ortho-chloronitrobenzene. Simultaneously, four succinamic acids were prepared by the reaction of succinic anhydride with different amines. Posteriorly, each succinamic acid should be coupled with 1-H-2-aminoindole by way of coupling agents such as carbodiimides. The results obtained indicate that DCC in dichloromethane can be efficient for the synthesis of potential new drugs.

La transglutaminase microbienne (Microbial transglutaminase : MTG) est fortement exploitée dans l’industrie textile et alimentaire afin de modifier l’apparence et la texture de divers produits. Elle catalyse la formation de liaisons iso-peptidiques entre des protéines par l’entremise d’une réaction de transfert d’acyle entre le groupement γ-carboxamide d’une glutamine provenant d’un substrat donneur d’acyle, et le groupement ε-amino d’une lysine provenant d’un substrat accepteur d’acyle. La MTG est tolérante à un large éventail de conditions réactionnelles, ce qui rend propice le développement de cette enzyme en tant que biocatalyseur. Ayant pour but le développement de la MTG en tant qu’alternative plus soutenable à la synthèse d’amides, nous avons étudié la réactivité d’une gamme de substrats donneurs et accepteurs non-naturels. Des composés chimiquement diversifiés, de faible masse moléculaire, ont été testés en tant que substrats accepteurs alternatifs. Il fut démontré que la MTG accepte une large gamme de composés à cet effet. Nous avons démontré, pour la première fois, que des acides aminés non-ramifiés et courts, tels la glycine, peuvent servir de substrat accepteur. Les α-acides aminés estérifiés Thr, Ser, Cys et Trp, mais pas Ile, sont également réactifs. En étendant la recherche à des composés non-naturels, il fut observé qu’un cycle aromatique est bénéfique pour la réactivité, bien que les substituants réduisent l’activité. Fait notable, des amines de faible masse moléculaire, portant les groupements de forte densité électronique azidure ou alcyne, sont très réactives. La MTG catalyse donc efficacement la modification de peptides qui pourront ensuite être modifiés ou marqués par la chimie ‘click’. Ainsi, la MTG accepte une variété de substrats accepteurs naturels et non-naturels, élargissant la portée de modification des peptides contenant la glutamine. Afin de sonder le potentiel biocatalytique de la MTG par rapport aux substrats donneurs, des analogues plus petits du peptide modèle Z-Gln-Gly furent testés; aucun n’a réagi. Nous avons toutefois démontré, pour la première fois, la faible réactivité d’esters en tant que substrats donneurs de la MTG. L’éventuelle amélioration de cette réactivité permettrait de faire de la MTG un biocatalyseur plus général pour la synthèse d’amides. Mots clés: Lien amide, biocatalyse, biotransformation, transglutaminase, arrimage moléculaire, criblage de substrats, ingénierie de substrats. / Microbial transglutaminase (MTG) is used extensively in the food and textile industry to alter the appearance and texture of products. MTG catalyses the formation of isopeptide linkages between proteins by an acyl transfer reaction between the γ-carboxamide group of a glutamine ‘acyl-donor’ substrate, and the ε-amino group of a lysine ‘acyl-acceptor’ substrate. MTG is tolerant to a broad range of reaction conditions and is therefore suitable for further development as a biocatalyst. Toward developing MTG as a “green” alternative for amide synthesis, we have investigated a range of non-native donor and acceptor substrates to probe the scope of MTG reactivity. Small, chemically varied compounds were tested as alternative acyl-acceptor substrates. We observed a broad acceptor specificity. We show, for the first time, that very short-chain alkyl-based amino acids such as glycine can serve as acceptor substrates. The esterified α-amino acids Thr, Ser, Cys and Trp – but not Ile – also show reactivity. Extending the search to non-natural compounds, an aromatic ring was observed to be beneficial for reactivity, although ring substituents reduced reactivity. Overall, bonding of the amine to a less hindered carbon increases reactivity. Importantly, very small amines carrying either the electron-rich azide or the alkyne groups required for click chemistry were highly reactive as acceptor substrates, providing a ready route to minimally modified, ‘clickable’ peptides. These results demonstrate that MTG is tolerant to a variety of chemically varied natural and non-natural acceptor substrates, which broadens the scope for modification of glutamine-containing peptides. To further probe the biocatalytic potential of MTG in terms of the donor substrate, smaller analogues of the model substrate Z-Gln-Gly were tested. We did not find product formation with substrates smaller than the model substrate. We observed, for the first time, trace esterase activity with MTG. Future improvement of this activity would render MTG a more attractive, general biocatalyst for amide bond formation.

La transglutaminase microbienne (Microbial transglutaminase : MTG) est fortement exploitée dans l’industrie textile et alimentaire afin de modifier l’apparence et la texture de divers produits. Elle catalyse la formation de liaisons iso-peptidiques entre des protéines par l’entremise d’une réaction de transfert d’acyle entre le groupement γ-carboxamide d’une glutamine provenant d’un substrat donneur d’acyle, et le groupement ε-amino d’une lysine provenant d’un substrat accepteur d’acyle. La MTG est tolérante à un large éventail de conditions réactionnelles, ce qui rend propice le développement de cette enzyme en tant que biocatalyseur. Ayant pour but le développement de la MTG en tant qu’alternative plus soutenable à la synthèse d’amides, nous avons étudié la réactivité d’une gamme de substrats donneurs et accepteurs non-naturels. Des composés chimiquement diversifiés, de faible masse moléculaire, ont été testés en tant que substrats accepteurs alternatifs. Il fut démontré que la MTG accepte une large gamme de composés à cet effet. Nous avons démontré, pour la première fois, que des acides aminés non-ramifiés et courts, tels la glycine, peuvent servir de substrat accepteur. Les α-acides aminés estérifiés Thr, Ser, Cys et Trp, mais pas Ile, sont également réactifs. En étendant la recherche à des composés non-naturels, il fut observé qu’un cycle aromatique est bénéfique pour la réactivité, bien que les substituants réduisent l’activité. Fait notable, des amines de faible masse moléculaire, portant les groupements de forte densité électronique azidure ou alcyne, sont très réactives. La MTG catalyse donc efficacement la modification de peptides qui pourront ensuite être modifiés ou marqués par la chimie ‘click’. Ainsi, la MTG accepte une variété de substrats accepteurs naturels et non-naturels, élargissant la portée de modification des peptides contenant la glutamine. Afin de sonder le potentiel biocatalytique de la MTG par rapport aux substrats donneurs, des analogues plus petits du peptide modèle Z-Gln-Gly furent testés; aucun n’a réagi. Nous avons toutefois démontré, pour la première fois, la faible réactivité d’esters en tant que substrats donneurs de la MTG. L’éventuelle amélioration de cette réactivité permettrait de faire de la MTG un biocatalyseur plus général pour la synthèse d’amides. Mots clés: Lien amide, biocatalyse, biotransformation, transglutaminase, arrimage moléculaire, criblage de substrats, ingénierie de substrats. / Microbial transglutaminase (MTG) is used extensively in the food and textile industry to alter the appearance and texture of products. MTG catalyses the formation of isopeptide linkages between proteins by an acyl transfer reaction between the γ-carboxamide group of a glutamine ‘acyl-donor’ substrate, and the ε-amino group of a lysine ‘acyl-acceptor’ substrate. MTG is tolerant to a broad range of reaction conditions and is therefore suitable for further development as a biocatalyst. Toward developing MTG as a “green” alternative for amide synthesis, we have investigated a range of non-native donor and acceptor substrates to probe the scope of MTG reactivity. Small, chemically varied compounds were tested as alternative acyl-acceptor substrates. We observed a broad acceptor specificity. We show, for the first time, that very short-chain alkyl-based amino acids such as glycine can serve as acceptor substrates. The esterified α-amino acids Thr, Ser, Cys and Trp – but not Ile – also show reactivity. Extending the search to non-natural compounds, an aromatic ring was observed to be beneficial for reactivity, although ring substituents reduced reactivity. Overall, bonding of the amine to a less hindered carbon increases reactivity. Importantly, very small amines carrying either the electron-rich azide or the alkyne groups required for click chemistry were highly reactive as acceptor substrates, providing a ready route to minimally modified, ‘clickable’ peptides. These results demonstrate that MTG is tolerant to a variety of chemically varied natural and non-natural acceptor substrates, which broadens the scope for modification of glutamine-containing peptides. To further probe the biocatalytic potential of MTG in terms of the donor substrate, smaller analogues of the model substrate Z-Gln-Gly were tested. We did not find product formation with substrates smaller than the model substrate. We observed, for the first time, trace esterase activity with MTG. Future improvement of this activity would render MTG a more attractive, general biocatalyst for amide bond formation.

Rheumatoid arthritis (RA) is an autoimmune inflammatory disease that leads to degradation of cartilage and bone mainly in peripheral joints. In collagen-induced arthritis (CIA), a mouse model for RA, activation of autoimmune CD4+ T cells depends on a molecular recognition system where T-cell receptors (TCRs) recognize a complex between the class II MHC Aq protein and CII259-273, a glycopeptide epitope from type II collagen (CII). Interestingly, vaccination with the Aq/CII259-273 complex can relieve symptoms and cause disease regression in mice. This thesis describes the use of modified glycopeptides to explore interactions important for binding to the Aq protein and recognition by autoimmune T-cell hybridomas obtained from mice with CIA. The CII259-273 glycopeptide was modified by replacement of backbone amides with different amide bond isosteres, as well as substitution of two residues that anchor the glycopeptide in prominent pockets in the Aq binding site. A three-dimensional structure of the Aq/glycopeptide complex was modeled to provide a structural basis for interpretation of the modified glycopeptide’s immunological activities. Overall, it was found that the amide bond isosteres affected Aq binding more than could be explained by the static model of the Aq/glycopeptide complex. Molecular dynamics (MD) simulations, however, revealed that the introduced amide bond isosteres substantially altered the hydrogen-bonding network formed between the N-terminal 259-265 backbone sequence of CII259-273 and Aq. These results indicated that the N-terminal hydrogen-bonding interactions follow a cooperative model, where the strength and presence of individual hydrogen bonds depended on the neighboring interactions. The two important anchor residues Ile260 and Phe263 were investigated using a designed library of CII259-273 based glycopeptides with substitutions by different (non-)natural amino acids at positions 260 and 263. Evaluation of binding to the Aq protein showed that there was scope for improvement in position 263 while Ile was preferred in position 260. The obtained SAR understanding provided a valuable basis for future development of modified glycopeptides with improved Aq binding. Furthermore, the modified glycopeptides elicited varying T-cell responses that generally could be correlated to their ability to bind to Aq. However, in several cases, there was a lack of correlation between Aq binding and T-cell recognition, which indicated that the interactions with the TCRs were determined by other factors, such as presentation of altered epitopes and changes in the kinetics of the TCR’s interaction with the Aq/glycopeptide complex. Several of the modified glycopeptides were also found to bind well to the human RA-associated DR4 protein and elicit strong responses with T-cell hybridomas obtained from transgenic mice expressing DR4 and the human CD4 co-receptor. This encourages future investigations of modified glycopeptides that can be used to further probe the MHC/glycopeptide/TCR recognition system and that also constitute potential therapeutic vaccines for treatment of RA. As a step towards this goal, three modified glycopeptides presented in this thesis have been identified as candidates for vaccination studies using the CIA mouse model.