Weak Affinity Chromatography (WAC) is a technology that was developed to analyse weak (KD > 10-5 M) although selective interactions between biomolecules. The focus of this thesis was to develop this method for various applications in the drug development process.   Fragment Based Drug Discovery is a new approach in finding new small molecular drugs. Here, relatively small libraries (a few hundreds to a few thousands of compounds) of fragments (150 – 300 Da) are screened against the target. Fragment hits are then developed into lead molecules by linking, growing or merging fragments binding to different locations of the protein’s active site. However, due to the weakly binding nature of fragments, methods that are able to detect very weak binding events are needed. In this thesis, WAC is presented as a new robust and highly reproducible technology for fragment screening. The technology is demonstrated against a number of different protein targets – proteases, kinases, chaperones and protein-protein interaction (PPI) targets. Comparison of data from fragment screening of 111 fragments by WAC and other more established technologies for fragment screening, such as surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR), validates WAC as a screening technology. It also points at the importance of performing fragment screening by multiple methods as they complement each other.   Other applications of WAC in drug development are also presented. The method can be used for chiral separations of racemic mixtures during fragment screening, which enables affinity measurements of individual enantiomers binding to the target of interest. Further, analysis of crude reaction mixtures is shown. By these procedures, the affinity of the product can be assessed directly after synthesis without any time-consuming purification steps. In addition, a high performance liquid chromatography (HPLC) system for highly efficient drug partition studies was developed by stable immobilization of lipid bilayer disks – lipodisks – on a high performance silica support material. These lipodisks are recognized model membranes for drug partition studies. A WAC system with incorporated membrane proteins into immobilized lipodisks has also been produced and evaluated with the ultimate objective to study affinity interactions between ligands and membrane proteins. / Ett läkemedel utövar sin funktion genom att påverka aktiviteten hos ett protein i kroppen då det binder till dess aktiva säte. Förändringen i aktivitet leder till fysiologiska förändringar i kroppen beroende på vilken funktion proteinet har. Med läkemedelsmolekyl avses här en liten organisk molekyl. Fragment-baserad läkemedelsutveckling är en ny metod for att ta fram nya läkemedel. Metoden fungerar genom att man bygger läkemedelsmolekyler utifrån mindre fragment som binder till målproteinet. Fragmenten hittar man genom att screena hela bibliotek av olika fragment mot samma målprotein för att urskilja de som binder till proteinets aktiva säte. Fördelen med den här metoden är bl. a. att med mindre molekyler som utgångspunkt kan en större del av antalet möjliga kombinationer av atomer representeras med ett mindre antal fragment än för större molekyler. Normalt utgörs ett fragmentbibliotek enbart av några hundra till några tusen substanser. Eftersom fragmenten är små har de få interaktionspunker och binder relativt svagt. De svaga bindningarna är svåra att se och mycket känsliga metoder behövs.   Svagaffinitetskromatografi är en vätskekromatografisk metod som utvecklades för att studera svaga men mycket selektiva bindningar mellan biomolekyler. Den här avhandlingen syftar till att utveckla metoden för olika användningsområden inom läkemedelsutveckling, främst som en ny metod för fragment-screening. Här mäter man interaktionen mellan ett protein och ett fragment. Proteinet kopplas till ett material som sedan packas i en kolonn i formen av en cylinder. När provet pumpas igenom kolonnen kommer de analyter med affinitet till proteinets aktiva säte att fördröjas på kolonnen i relation till hur starkt de interagerar med målproteinet.   I den här avhandlingen presenteras fragment-screening med svagaffinitetskromatografi gentemot ett antal olika typer av målproteiner. Resultatet överensstämmer väl med andra metoder för fragment-screening. Analys av reaktionsblandningar med svagaffinitetskromatografi demonstreras också. Därmed kan bindningen mellan en produkt i en reaktionsblandning och ett målprotein mätas direkt utan föregående uppreningssteg av reaktionsblandningen. Lipodiskar är små diskformade modellmembran som kan användas för att bl. a. mäta hur effektivt läkemedlet tas upp i kroppen vid behandling. Ett system med immobiliserade lipodiskar i en kolonn utvecklades med det framtida målet att kunna arbeta med membranproteiner med svagaffinitetskromatografi.   Detta arbete utgör en del i att utveckla svagaffinitetskromatografi som en lättillgänglig och relativt billig metod för användning inom industrin och akademin för läkemedelsutveckling.

No description available.

Matrix metalloproteinases (MMPs) network with other biological molecules to maintain the extracellular matrix (ECM) in normal physiology and perform different roles. Understanding and assigning specific role to each of 24 members of these endoproteinases is impeded because of lack of specific and efficient detection methods in biological samples. Moreover, MMP-based anti-cancer drug development has also been challenged because, currently, there is no robust methodology to distinguish the inactive pro-enzymes, active enzymes or those complexed with endogenous inhibitors in biological specimens. The objective of this project is to develop a chemical proteomics strategy based on Matrix assisted laser desorption ionization tandem mass spectrometry (MALDI-MS/MS) to help identify and discriminate the various MMP forms. Firstly, a triazine dye-based ligand immobilized on chromatography beads was utilized to assess whether it binds to recombinant human MMPs (rhMMPs). The results highlighted that the ligand interacts with latent forms of MMPs in agreement with the literature. Secondly, the potential of the ligand was assessed using MALDI-MS/MS based methodology in in vitro cancer models. Cell line culture supernatants were used in amounts to emulate the availability of tumour biopsies in clinical settings. The MS/MS spectral peaks specific to MMPs (MMP-2 and MMP- 14), and two endogenous inhibitors TIMP-1 and TIMP-2 were found in affinity chromatography eluates of cell culture supernatants with higher Mascot scores for the latter. While western blot detected MMP-2 in cell extracts, MALDI-MS/MS did not detect MMPs because of amounts below the limit of detection (LOD) of the instrument. Although the ligand was found to be interacting with MMPs and detergent-free salt elution buffers improved MALDI analysis, recovery of MMPs from biological samples was sub-optimal. The dye ligand was observed to bind other enzymes and despite various strategies to reduce non-specific binding of proteins or enable selective elution did not improve MMP enrichment. Further work using methodology described in this study is required after scaling up the MMP amounts in biological specimen and to resolve the issue of non-specific binding of proteins to the ligand by understanding its structure.

No description available.

<p>On the surface heat shock protein 90 (Hsp90) is an unlikely drug target for the treatment of any disease, let alone cancer. Hsp90 is highly conserved and ubiquitously expressed in all cells. There are four major isoforms encoded by distinct genes and together they may constitute 1-3% of the cellular protein. Genetic deletion results in nonviable phenotypes in some organisms, and there are no recognized polymorphisms suggesting an association or causal relationship with any human disease. With respect to cancer, the proteins absence from some recent high profile articles underlines the perception that it is an unlikely bona fide target to treat this disease. Yet, to date, there are 17 distinct Hsp90 inhibitors in clinical trials for multiple indications in cancer. The protein has been championed for over 20 years by the National Cancer Institute as a cancer target since the discovery of the antitumor activity of geldanamycin. Rather than focus on the intracellular inhibition of Hsp90, we have shifted our aim to the differences of Hsp90 between cancer and normal tissue, namely its extracellular expression.</p><p>My graduate thesis work has focused on the characterization of a series of novel small molecule imaging agents (fluor-tethered Hsp90 inhibitors) that enable the specific detection of ectopically expressed Hsp90 on tumor cells. We believe that these molecules will have a large impact in the near future on the diagnosis and treatment of metastatic breast cancer as well as other cancers. This hypothesis is based on recent findings in the clinical literature that have linked upregulation of Hsp90 with poor outcomes in multiple subtypes of breast cancer. Additionally, several papers have also reported an association of the expression of extracellular Hsp90 and metastatic progression in several human cancers. Hsp90 is currently considered by some as a cutting edge cancer drug target. The Haystead lab synthesized a series of tethered Hsp90 inhibitors that were modified with fluorophores and other imaging moieties in such a way as to preserve the binding to Hsp90 and enable detection through non-invasive imaging techniques. In a series of cell-based, live animal and biochemical studies we demonstrated that these molecules are highly selective for Hsp90 and can be used to specifically recognize intact tumor cells expressing ectopic Hsp90. Furthermore, we also observed that once bound to ectopic Hsp90, our tethered-inhibitors are actively internalized and this process can be blocked with Hsp90 antibodies. These findings have two implications; first, Hsp90 is undergoing active cycling at the plasma membrane; second, the finding that once bound to surface Hsp90 our fluor-tethered inhibitors can be internalized despite their polar nature. These results suggest a new therapeutic strategy that will enable specific delivery of tumor killing agents (e.g. 131I or metabolic poisons) to metastatic cells. This is unique because the use of small molecule inhibitors and not antibody- or nanoparticle-based payload delivery strategies offers advantages in formulation, cost and reproducibility.</p><p> In addition to payload delivery possibilities, we also show the utility of the tethered-inhibitors diagnostically by demonstrating their use in the detection of tumors in mouse models of human breast cancer. As a result of our animal studies, we believe our molecules in their present form could be used to address a currently unmet need in the early diagnosis of aggressive breast cancer and discriminating this from more indolent forms. </p><p>Furthermore, the tethered Hsp90 inhibitors have been used to make ligand affinity chromatography resins that have facilitated the discovery of other unique Hsp90 expressions and functions associated with cancer. We have found a pool of Hsp90 that is misfolded as determined by affinity chromatography depletion and a leftward thermal stability shift in the population of Hsp90 that flows through the ligand affinity resins. Differential trypsin digest patterns detected by mass spectrometry reveal also that the native protein has sites that are more accessible to trypsinization. This could have further implications in treating and detecting differences between cancerous tissues and normal tissues by designing an antibody that recognizes the exposed portions of the misfolded Hsp90. Together this body of work illustrates that not only is Hsp90 different in total expression levels in cancers, but is ectopically expressed and misfolded so as to provide other opportunities for therapeutic intervention that improve the safety for more clinical applications.</p> / Dissertation

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 137-143).

Cette thèse de doctorat a été réalisée au Centre de Recherche sur les Macromolécules Végétales (CERMAV) sous la direction du Dr Sébastien Fort, responsable de l'équipe Chimie et Biotechnologie des Oligosaccharides (CBO) et du Dr Sami Halila de l'équipe PhysicoChimie des Glycopolymères (PCG). Cette thèse intitulée « Synthèse par chimie click non metallo-catalysée de glycoconjugués macromoléculaires pour des applications médicales» est financée par le ministère de l'enseignement supérieur et de la recherche (bourse MESR). L'objectif de ce travail était de développer de nouvelles méthodes de modification et de couplage regiosélectif d'oligosaccharides pour la préparation de glycoconjugués par une chimie « click » sans catalyse métallique. Ces travaux s'appuient sur l'expertise de l'équipe CBO pour la synthèse chimio-enzymatique d'oligosaccharides complexes ainsi que sur les méthodes de modification sélective de la position réductrice des oses.Un premier aspect concerne l'utilisation des propriétés physico-chimiques des oligosaccharides pour l'obtention de nanoparticules de taille contrôlée. Ces particules sont constituées de copolymères à blocs hybrides obtenus par couplage entre un polymère de synthèse et un oligosaccharide. La structure des nano-objets préparés sera analysée au sein de l'équipe PCG.Le deuxième aspect concerne l'utilisation des propriétés de reconnaissance biochimique des oligosaccharides. Cette partie sera focalisée sur le couplage efficace d'oligosaccharides d'intérêt biologiques sur support solide pour la purification de protéines. / The aim of the project is to develop new anomeric modification of oligosaccharides for the synthesis of glycoconjugates by metal-free click chemistry. Synthetic glycans have shown a great potential in medical and nanotechnology related fields. The current use of metallic catalyst during synthesis and the risk of contamination of the final product represent a drawback which could restrain their applications. Therefore an efficient metal free synthesis of glycoconjugates could be of great interest to circumvent this obstacle.Two distinct synthetic strategies have been explored for the metal free coupling of complex oligosaccharides on polymers to yield block-copolymers and glycoadsorbants. The glycopolymers were synthetized by a Michael addition between a thiol functionalized oligosaccharide and a maleimide or bromo-maleimide functionalized polymer. The nanoparticles obtained from the self-assembly of theses amphiphilic copolymers in water were characterized. The polycaprolactone-b-xylooligosaccharides copolymers presenting a reducible linkage were self-assembled into nanoparticles and assessed as model for the delivery of hydrophobic drugs. This system showed a selective release of the entrapped molecules in reducing environment making it an interesting system for the intra-tumoral delivery of anti-cancer drugs. Glycoadsorbents were prepared by a Diels Alder reaction between a solid matrix displaying a maleimide moiety and furyl functionalized oligosaccharides. The affinity matrixes obtained allowed the selective purification of lectins. The blood group antigen (A;B) grafted matrixes displayed good properties for the trapping of corresponding anti-A or anti-B antibodies. These types of immunoadsorbants have great potential for the treatment of immune diseases like the Guillain-Barré syndrome.To conclude, two efficient anomeric modification and coupling strategies of oligosaccharides have been developed, opening the way to the metal free synthesis of various glycoconjugates.

The aim of this work was to characterize a member of the Drosophila Idgf family. IDGF2 was expresed in Drosophila S2 cells and purified by affinity chromatography. Function of wild-type and mutant IDGF2 was compared.

O uso de DNA plasmidial (pDNA) visando a aplicações terapêuticas tem aumentado nos últimos anos. A cromatografia aparece como a técnica de purificação mais comum para obtenção de amostras de pDNA com o elevado grau de pureza exigido. Porém, as resinas cromatográficas disponíveis apresentam ainda uma série de desafios, nomeadamente no desenvolvimento de ligantes específicos e matrizes capazes de acomodar este tipo de molécula. Relativamente à apuração de novos ligantes, alguns estudos têm mostrado o potencial do aminoácido arginina para estabelecer interações específicas e preferenciais com o pDNA. Por outro lado, resinas monolíticas surgem como suportes interessantes devido às suas excelentes propriedades de transferência de massa e altas capacidades de adsorção. Neste estudo, diferentes ligantes baseados em arginina (arginina, di-arginina e tri-arginina) foram imobilizados em resinas de agarose previamente ativadas. Um primeiro estudo de adsorção em batelada foi realizado a fim de avaliar e compreender os mecanismos envolvidos no processo de adsorção dos ácidos nucleicos pDNA e RNA em resina com o aminoácido arginina. Na sequência, apresentamos uma proposta inovadora para o uso de ligantes de arginina em resinas de agarose, em um único passo de purificação em modo negativo a seguir ao passo de concentração por isopropanol. A capacidade da resina para o pDNA foi substancialmente maior do que a obtida para o mesmo tipo de resina no modo positivo, com notória vantagem de capacidade no uso de di-arginina face a arginina com rendimentos próximos de 100% do plasmídeo carregado. Os ligantes di-arginina e tri-arginina foram também imobilizados em resinas monolíticas. Em comparação com o aminoácido arginina, a imobilização dos homopeptídeos nas resinas monolíticas levou ao aumento da capacidade de adsorção (cerca de 2,5 vezes superior) e especicificidade de interações, mostrando-se como uma estratégia promissora para processos de purificação de pDNA. / The use of plasmid DNA (pDNA) for therapeutic applications has increased in recent years. Chromatography appears as the most common purification technique to obtain samples of pDNA with the high degree of purity required. However, the available chromatographic resins still present a series of challenges, namely in the development of specific ligands and matrices capable of accommodating this type of molecule. Regarding the determination of new ligands, several studies have shown the potential of the arginine amino acid to establish specific and preferential interactions with the pDNA. On the other hand, monolithic resins appear as interesting approaches due to their excellent mass transfer properties and high adsorption capacities. In this study, different arginine based ligands (arginine and di-arginine) were firstly immobilized on activated agarose resins. The first part of the work describes the adsorption equilibrium of plasmid DNA adsorption process, as well as the interaction with its main impurity (RNA) on arginine supports in a batch format, in order to compare and gather crucial information about adsorption mechanisms involved in this type of affinity system. Then, a new use for chromatographic bead matrixes based on arginine ligands was proposed, working as an adsorption matrix pDNA purification in negative mode after isopropanol concentration of the sample. The arginine based supports capacity for pDNA under negative mode for pDNA was substantially higher than that obtained with the same type of resin in the conventional positive mode, with a notable advantage of using di-arginine with recovery yields near 100%. The homopeptides (di-arginine and tri-arginine) were also immobilized on functionalized monolithic resins (BIA Separations, Slovenia). Effectively, the immobilization of the arginine homopeptides made the monolithic resins more functional compared to the (mono)arginine based resin, exhibiting greater binding capacities (around 2,5 times higher) and interaction intensities, proving to be a promising strategy for purification processes of pDNA.

Orientador: Prof. Dr. Rodrigo L. O. R. Cunha. / Dissertação (mestrado) - Universidade Federal do ABC. Programa de Pós-Graduação em Ciência e Tecnologia/Química, 2017. / Nos últimos anos o rol de propriedades biológicas de compostos de selênio e de telúrio tem aumentado e outras atividades, além das bem descritas propriedades antioxidantes, também vêm sendo demonstradas. Neste contexto, a inibição enzimática promovida por espécies hipervalentes de selênio e telúrio (organocalcogenanas) foi relatada para cisteína proteases, tirosina fosfatases e o proteasoma, por exemplo. Esta inibição é resultado da particular reatividade que compostos hipervalentes de telúrio e selênio apresentam com tióis. Como a quantidade de biotióis reativos em sistemas celulares é vasta e nem todos estão disponíveis para ensaios in vitro com as organocalcogenanas, é possível vislumbrar a aplicação desses compostos como ligantes em cromatografia de afinidade para a identificação de proteínas reativas a esses compostos. Para atingir este objetivo foram utilizados organocalcogenetos derivados de benzaldeído. A estrutura dos ligantes é constituída por um grupo fenilcalcogenila ligado a um derivado de poliéter funcionalizado com um grupo amina que é ancorado à uma matriz de agarose. Foram preparadas duas classes de ligantes para a modificação de agarose que diferem na estrutura do espaçador, a primeira contém uma unidade de ácido succínico entre o organocalcogeneto e o derivado de poliéter (ligantes de Classe I) e a outra, isenta dessa unidade de ácido succínico, possui um grupo amino ionizável (ligantes catiônicos de Classe II). A rota de preparação dos ligantes de classe I envolveu uma sequencia sintética de seis etapas com rendimentos globais de 26% e 19% e os ligantes de Classe II foram preparados em uma sequencia de duas etapas com rendimentos globais de 43% e 22%, para os selenetos e teluretos, respectivamente. A oxido-redução do ligante de telúrio da classe II se mostrou rápido e satisfatório nos estudos preliminares, dando bons indícios para aplicação como ligante na cromatografia de afinidade. Por fim, os ligantes foram imobilizados na agarose funcionalizada com brometo de cianogênio e avaliados com papaína, utilizada como modelo de biotiol nesse trabalho. Notadamente os ligantes de telúrio apresentaram um comportamento distinto do que os de selênio quanto à eluição da papaína da matriz sólida, requerendo maior volume de solução com agente redutor para a eluição da proteína. Coletivamente os resultados apresentados nesse trabalho demonstram que matrizes sólidas funcionalizadas com organocalcogenetos são funcionais para a retenção e liberação de biomoléculas tioladas (funcionalidade "catch & release"), abrindo perspectivas para o estudo mais aprofundado da interação entre calcogenetos com tióis e, ainda para produção, caracterização e estudo de aplicações de diversas matrizes funcionalizadas com organocalcogenetos. / In recent years the role of biological properties of selenium compounds and tellurium compounds has increased, and other activities besides the well-described antioxidant properties have also been demonstrated. In this context, enzymatic inhibition promoted by hypervalent species of selenium and tellurium have been reported for cysteine proteases and tyrosine phosphatases. This activity is due to the particular reactivity of thiols with the chalcogenides atom in their hypervalent state. Apart from these enzymes, one can envisage a plenty of other potential reactive thiols in cellular systems that are prone to react with organocalcogenuranes which are still unknown. As the identification of these unknown targets would be helpful to understand therapeutical and toxicological aspects of these compounds, efforts in this direction are required. One strategy for this purpose consists in using the affinity purification technique using organochalcogenides as ligands, this is proposed in the present work. To achieve this goal, the use of organochalcogenides derived from benzylamines as ligands in affinity chromatography. The structure of this ligands contains a phenylchalcogenide moiety, a polyether spacer group functionalized with an amino group to attach it to an agarose substrate. Two different spacer classes were prepared, the first has a succinic acid spacer between the organochalcogenide and the polyether (Class I ligand); the second class has the polyether moiety directly linked to the phenylchalcogenide group and has an ionizable secondary amine (Class II cationic ligand). The preparation route of the class I ligands involved a six-step synthetic sequence in overall yields of 26% and 19%, and the Class II ligands were prepared in a two-step sequence in global yields of 43% and 22% of the selenides and tellurides, respectively. The studied oxidation and reduction reactions of Class II tellurium ligands revealed fast processes, suitable for a practical application of these novel organochalcogenides in affinity chromatography. Finally, ligands were immobilized in cyanogen bromide activated agarose and the modified matrices evaluated with papain as a model biothiol. Noteworthy, the selenide ligands released papain promptly by washing the matrix with dithiothreitol solution whereas telluride ligands showed the opposite behavior. Collectively, the results presented in this work demonstrate that organochalcogenide-modified agarose is a new class of functional materials for the retention and release of biothiols presenting a "catch & release" functionality. This work brings new perspectives for a more detailed study of the interaction between chalcogenides with thiols and also to the production, characterization and the study of novel applications of organochalcogenide-modified solid matrices.