ABD-Derived Affinity Proteins (ADAPTs) is a novel class of small engineered scaffold proteins based on albumin-binding domain (ABD) of streptococcal protein G. High affinity ADAPT  binders against various therapeutic targets can be selected.  In this thesis, we report a development of ADAPT-based radionuclide imaging agents providing high sensitivity and specificity of molecular imaging of HER2 expression in disseminated cancers. We investigated the feasibility of the use of ADAPTs as imaging agents and influence of molecular design and radiolabeling chemistry on in vivo targeting and biodistribution properties of the tracers. In Paper I we demonstrated the feasibility of the use of anti-HER2 ADAPT6 molecule as a high contrast imaging agent; In Paper II we evaluated the influence of composition of histidine-containing tag on in vivo biodistribution of ADAPT-based tracers labeled with 99mTc using 99mTc(CO)3 binding to histidine-containing tags and 111In using DOTA chelator at N-terminus; In Paper III we evaluated the influence of different aspects of N-terminus leading sequence on targeting including effect of sequence size on clearance rate and effect of the composition of the sequence on biodistribution profile; In Paper IV, we evaluated the influence of residualizing properties and positioning of the label on biodistribution and targeting; and In Paper V, we compared tumor-targeting properties of the ADAPT6 labeled at C-terminus with 99mTc using N3S chelator and 111In using DOTA chelator. In conclusion, ADAPTs constitute a very promising class of targeting probes for molecular imaging providing high contrast. Molecular design of the ADAPT proteins and chelators/linkers for labeling has an appreciable effect on their imaging properties.

The rapid development of the gene engineering techniques, especially methods for in vitro directed evolution and combinatorial mutagenesis, has triggered the generation of new binding agents to almost any antigen of interest as an alternative to broadly used antibodies. These so-called non-Ig scaffolds are often derived from proteins with useful biophysical properties. While the therapeutic market is still dominated by monoclonal antibodies, the easy option of desired customization of non-Ig binders by conventional methods of gene engineering predestine them largely for the use in the diagnostic area. The ABD scaffold, derived from a three-helix bundle of albumin-binding domain of streptococcal protein G, represents one of the small non-Ig scaffolds. In our laboratory, we have established a highly complex combinatorial library developed on the ABD scaffold. This ABD scaffold-derived library was used to generate unique binders of human prostate cancer (PCa) biomarkers PSP94, KLK2, KLK11 for the more precise diagnosis of PCa. The second part of the thesis describes the generation of ABD-derived binders selectively recognizing different phenotypes of circulating tumor cells as a binding component of the cell capture zone of microfluidic chip for lung adenocarcinoma diagnosis. Beside this already...

There has been tremendous amount of effort focused on the development and improvement of genome editing applications over the decades. Particularly, the development of programmable nucleases has revolutionized genome editing with regards to their improvements in mutagenesis efficacy and targeting feasibility. Programmable nucleases are competent for a variety of genome editing applications. There is growing interest in employing the programmable nucleases in therapeutic genome editing applications, such as correcting mutations in genetic disorders. Type II CRISPR-Cas9 bacterial adaptive immunity systems have recently been engineered as RNA-guided programmable nucleases. Native CRISPR-Cas9 nucleases have two stages of sequence-specific target DNA recognition prior to cleavage: the intrinsic binding of the Cas9 nuclease to a short DNA element (the PAM) followed by testing target site complementarity with the programmable guide RNA. The ease of reprogramming CRISPR-Cas9 nucleases for new target sequences makes them favorable genome editing platform for many applications including gene therapy. However, wild-type Cas9 nucleases have limitations: (i) The PAM element requirement restricts the targeting range of Cas9; (ii) despite the presence of two stages of target recognition, wild-type Cas9 can cleave DNA at unintended sites, which is not desired for therapeutic purposes; and (iii) there is a lack of control over the mutagenic editing product that is procuded. In this study, we developed and characterized chimeric Cas9 platforms to provide solutions to these limitations. In these platforms, the DNA-binding affinity of Cas9 protein from S. pyogenes is attenuated such that the target site binding is dependent on a fused programmable DNA-targeting-unit that recognizes a neighboring DNA-sequence. This modification extends the range of usable PAM elements and substantially improves the targeting specify of wild type Cas9. Furthermore, one of the featured chimeric Cas9 variants developed in this study has both robust nuclease activity and ability to generate predictable uniform editing products. These superior properties of the chimeric Cas9 platforms make them favorable for various genome editing applications and bring programmable nucleases one step closer to therapeutic applications.

No description available.

Targeted radionuclide therapy is becoming a widely used cancer treatment strategy. By radiolabeling receptor-specific peptides, cancer cells overexpressing the receptor can be selectively targeted, and the cytotoxic radionuclide can be delivered to the target cell or tissue for therapeutic or diagnostic purposes. Bombesin analogues have been previously developed and utilized to target the gastrin-releasing peptide receptor (GRPR), a receptor commonly overexpressed in prostate cancer cells. The RM26 analogue derived from the native bombesin is an antagonistic ligand of GRPR and a possible candidate for targeted radiotherapy. Prolonging the half-life of the molecule is an important aspect of developing a new protein therapeutic. Using albumin binding domain (ABD) for this purpose is an emerging strategy in recent years. ABD is able to bind to serum albumin and thus remains in the blood circulation for a long period of time. It is also a scaffold for protein engineering efforts and by coupling receptor-specific ligands to ABD, the target-specific binding along with extended in vivo halflife can be achieved. In this project, an RM26 analogue with a PEG linker and ABD with a DOTA chelator for future radiolabeling were synthesized with solid phase peptide synthesis (SPPS), conjugated, purified by RP-HPLC and analyzed by mass spectrometry. The binding properties of the conjugate were evaluated by SPR-based biosensory studies, and further experiments are planned for the testing the product and its potential application in radionuclide therapy. / Riktad radioterapi är en allt vanligare metod för behandling av cancer. Genom att radioinmärka receptor-specifika peptider kan dessa selektivt levereras till tumörceller som uttrycker receptorn. Radioterapi kan användas för diagnostik eller terapi, beroende på kopplad radionuklid. Bombesinanaloger har utvecklats och använts för att selektivt binda gastrinfrisättande peptidreceptor (gastrin-releasing peptide receptor, GRPR), en receptor som ofta är överuttryckt i prostatacancer. Bombesinanalogen RM26, som har sitt ursprung från nativt bombesin, är en antagonist till GRPR och kan möjligen användas för riktad radioterapi av prostatacancer. Vid utvecklingen av nya proteinläkemedel är halveringstiden i serum en viktig aspekt. En nyligen utvecklad strategi för att förlänga halveringstiden i serum är fusion av det  tumörspecifika proteinet till en albumin-bindande domän (ABD). ABD binder till albumin, ochsåledes kan fusionsproteinet bevaras i blodcirkulationen under en längre tid. I detta projekt, har både RM26 med en PEG-linker, och ABD med en DOTA kelator syntetiserats med fastfaspeptidsyntes (solid phase peptide synthesis, SPPS). RM26-PEG och DOTA-ABD har därefter konjugerats, renats med RP-HPLC och analyserats med massspektrometri. Bindning till albumin har utvärderats med ytplasmonresonans (surface plasmon resonance, SPR). Vidare studier planeras för att utvärdera peptid-proteinkonjugatet och dess potential för riktad radioterapi.

Les dinoflagellés jouent un rôle très important dans l’écologie des océans en y réalisant une grande partie de la production primaire, en formant une association symbiotique avec les coraux et en ayant la capacité de produire des fleurs d’algues potentiellement toxiques pour les communautés côtières humaines et animales. Malgré tout, la biologie moléculaire des dinoflagellés n’a que très peu été étudiée dans les dernières années, les connaissances de processus de base comme la régulation de la transcription y étant fortement limitées. Une tentative pour élucider ce mécanisme a été réalisée chez les dinoflagellés photosynthétiques Lingulodinium polyedrum et Amphidinium carterae. Une expérience d’induction de la transcription du gène de la Peridinin chlorophyll-a binding protein, le complexe majeur de collecte de lumière, a été réalisée par une baisse de l’intensité lumineuse et a montré une faible augmentation (moins de 2 fois) du transcrit à court et long terme. Des expériences de simple-hybride et de retard sur gel (EMSA) ont été faits pour identifier de potentielles interactions protéine-ADN dans la région intergénique du gène PCP organisé en tandem. Ces essais ont été infructueux pour identifier de telles protéines. Une analyse du transcriptome de L. polyedrum a été effectuée, montrant une importante sous-représentation de domaines de liaison à l’ADN classique (comme Heat-shock factor, bZIP ou Myb) et une surreprésentation du domaine d’origine bactérienne Cold shock en comparaison avec d’autres eucaryotes unicellulaires. Ce travail suggère que les mécanismes de régulation transcriptionnelle des dinoflagellés pourraient différer substantiellement de ceux des autres eucaryotes. / Dinoflagellates are an important part of the ocean’s ecology due to their large contribution to global carbon fixation, the symbiotic association they can make with corals and by their ability to form algal blooms potentially toxic for humans and animals in coastal communities. However, the molecular biology of dinoflagellates has been poorly studied in the past. Basic knowledge, such as regulation of gene expression, is severely limited. An attempt at deciphering basic gene regulation has been undertaken in the photosynthetic dinoflagellate Lingulodinium polyedrum and Amphidinium carterae using a reduction in available light intensity to induce the expression of the peridinin chlorophyll-a binding gene encoding the major light harvesting complex protein. A small increase in transcript abundance (less than 2 fold) was found in both short and long term experiments, yet neither yeast one-hybrid assays nor electrophoretic mobility shift assays (EMSA) showed any potential protein interactions with sequence derived from the intergenic spacer of the PCP tandem gene array. Interestingly, an analysis of the recently sequenced L. polyedrum transcriptome revealed an important under-representation of classic DNA-binding domains (such has Heat-shock factor, bZIP and Myb) and an over-representation of the bacterial cold-shock DNA-binding domain. This suggested that components of the transcription regulation machinery may be at least partially different in dinoflagellates.

As society draws closer to the post-antibiotic era and the pipeline for alternatives dries, there is an urgent need for the development of novel antimicrobial therapies that do not promote bacterial resistance, particularly for immunocompromised chronic wound patients. Antimicrobial peptides (AMPs), including human-derived LL37, show considerable promise as broad spectrum alternatives that also have wound healing properties; however, few have been clinically implemented as novel antimicrobials due to their cytotoxicity stemming from a poor understanding of their mechanisms and low stability in vivo. It has been suggested that tethering, or attaching AMPs onto surfaces, is a viable strategy of delivering bioactive AMPs to surfaces while reducing cytotoxicity and improving stability. Thus, we designed new chimeric versions of LL37 with collagen-binding domains (CBD), derived from collagenase (cCBD-LL37) and fibronectin (fCBD-LL37) for non-covalent tethering onto collagen, a prevalent biopolymer in commercially available wound dressings and scaffolds. Our overall hypothesis was that CBDs would mediate stable tethering of broadly active, non-cytotoxic CBD-LL37 onto collagen-based scaffolds. We first studied the loading, release and bioactivities (e.g. antimicrobial activity and cytotoxicity) of each CBD-LL37 on commercially available 100% collagen type I PURACOL® wound scaffolds. We found that both cCBD-LL37 and fCBD-LL37 bound highly to collagen, were active against relevant wound pathogens, demonstrated stable activity after 14 days of release, and were not cytotoxic to human fibroblasts. The addition of different CBDs onto LL37 also markedly altered their soluble bioactivities. Using similar methods, we then studied the loading, release and bioactivity of each CBD-LL37 on a commercially available FIBRACOL® wound scaffolds, comprised of 90% collagen type I and 10% calcium alginate biopolymers. We found that both cCBD-LL37 and fCBD-LL37 also bound highly to and retained on collagen for 14 days, but were only active against Gram-negative P. aeruginosa. This suggested that the presence other biopolymers in addition to collagen, which is common among commercial wound dressings, could cause significant differences in binding, retention and bioactivities of CBD-LL37. To better understand how CBD modification affected CBD-LL37 structure leading to different bioactivities, we studied the CBD sequence-, peptide structure-, concentration-, time-, and bilayer composition-dependent interactions of soluble CBD-LL37 and compared these findings with the properties of unmodified LL37. Using Molecular Dynamics (MD) simulations, circular dichroism (CD) spectroscopy, quartz crystal microbalance with dissipation (QCM-D), and fluorescent bilayer imaging we determined the structural basis behind CBD alterations in bioactivities. MD and CD, in addition to other intrinsic CBD properties (helicity, amphiphilicity, charge) we hypothesized that cCBD-LL37 utilized similar mechanisms as unmodified LL37 while fCBD-LL37 demonstrated based primarily on surface adsorption. We used QCM-D and Voigt-Kelvin viscoelastic modeling to determine the time- and concentration-dependent interactions of unmodified LL37 with model mammalian lipid bilayers, the mechanisms of which are still controversial in literature despite being widely studied. These results were used to propose a model for the interaction mechanism of LL37 with zwitterionic bilayers that aligned with its bioactive concentrations. LL37 adsorbed at concentrations where it is immunomodulatory until reaching a threshold which corresponded with its antimicrobial concentrations. The threshold was correlated to lipid bilayer saturation, after which LL37 formed transmembrane pores. We observed collapse of the bilayer into a rigid proteolipid film at concentrations higher than the reported cytotoxic threshold of LL37. The mechanistic and structural information for each CBD-LL37 and unmodified LL37 provided a baseline for QCM-D and Voigt-Kelvin viscoelastic modeling to further elucidate the time-, concentration-, lipid composition- and CBD sequence-dependent basis behind the observed bioactivities of cCBD-LL37 and fCBD-LL37. We found that similar to LL37, cCBD-LL37 demonstrated pore formation mechanisms likely due to their similar charges, structural content and amphiphilicity. fCBD-LL37 demonstrated time-dependent, adsorption-based mechanism likely due to its anchoring aromatic residues, low charge, and low amphiphilicity. Knowledge gained from this study allowed mechanistic predictions of two newly designed hypothetical CBD-LL37 peptides. Results from this study contribute to a better understanding of a new class of antimicrobial, non-cytotoxic therapies based on collagen-tethered CBD-LL37, bringing it closer to clinical implementation in chronic wound applications and demonstrate the viability of biopolymer tethering as a platform toward using AMPs to quench the resistance crisis.

Les glucane-saccharases (GS) de la famille GH70 sont des enzymes produites par certaines bactéries lactiques. A partir de saccharose, substrat renouvelable et peu coûteux, elles sont capables de catalyser la synthèse d’α-glucanes, homopolysaccharides dont les propriétés diffèrent suivant la spécificité de l’enzyme (taille, type de liaisons α-osidiques, degrés de branchement). Les glucanes contenant une très grande majorité de liaisons α-(1,6), appelés dextranes, présentent de nombreuses applications industrielles qui dépendent principalement de leur taille. Cependant, la synthèse directe de dextranes de taille contrôlée (de 1 à plusieurs millions de kg/mol) avec une faible polydispersité et en utilisant une seule enzyme n’est encore pas envisageable. En effet, les mécanismes moléculaires mis en jeu pour le contrôle de la taille des polymères produits n’ont encore été que peu explorés. Dans ce contexte, deux GSs ont été sélectionnées. La première, DSR-M synthétise uniquement des dextranes de faible masse molaire (MM) (28 kg/mol) exclusivement composés de liaisons α-(1,6). A contrario, le second modèle, DSR-OK produit le plus long dextrane décrit à ce jour (>109 g/mol). La caractérisation biochimique et structurale ainsi que la construction de mutants ont permis l’exploration du mode d’action de ces deux candidats. Plusieurs structures 3D de DSR-M2 (forme tronquée de DSR-M) - sans ou en complexe avec son substrat ou ses produits (isomaltotetraose) - ont été résolues. C’est la première fois que de tels complexes sont décrits et l’une de ces structures présente le domaine V le plus complet décrit à ce jour. L’analyse de ces structures couplée au suivi cinétique de la synthèse du polymère ont montré que la spécificité de DSR-M pour la synthèse de dextranes courts s’explique par un mode d’élongation distributif dû à la faible affinité de deux poches à sucre de son domaine V envers la chaîne en cours de synthèse. Des analyses RMN (15N1H – HSQC) – jamais réalisées auparavant sur une protéine si grosse – ont également étayé l’importance de la présence de résidus aromatiques dans le domaine catalytique pour la synthèse de dextranes supérieurs à 2 kg/mol. En comparaison, la synthèse de dextranes de haute MM par DSR-OK est principalement due au plus grand nombre de poches à sucre de son domaine V, permettant d’assurer une meilleure interaction avec la chaîne en cours d’élongation. L’implication de ces poches dans la détermination de la taille du dextrane a été montrée pour les deux candidats. Leur fonctionnalité est fortement liée à la présence d’un résidu aromatique de stacking, et leur répartition le long du domaine V a aussi une influence. L’ensemble de ces résultats démontre la coopération du domaine V avec le domaine catalytique pour l’élongation des dextranes, tout en offrant de nouvelles perspectives pour approfondir la compréhension de ce mécanisme. Ils offrent également des stratégies prometteuses pour l’ingénierie d’enzyme de la famille des GH70 pour la modulation de la taille des glucanes. / Glucansucrases (GS) from glycoside hydrolase family 70 (GH70) are -transglucosylases produced by lactic acid bacteria. From sucrose, an economical and abundant agro resource, they catalyze the polymerization of glucosyl residues. Depending on the enzyme specificity, α-glucans vary in terms of size, types of glucosidic bonds and degree of branching and have found multiple industrial applications mainly related to their molar mass (MM). However synthesizing polymers of controlled size with average MM ranging from 1 kg/mol to several millions g/mol and low polydispersity using one single enzyme remains challenging. Indeed, the molecular mechanisms underpinning the control of polymer size have been scarcely explored. To tackle this question, two GSs producing dextran (glucan composed of a majority of α-(1,6) linkages) were selected, and their mode of action explored via biochemical and structural analyses coupled to mutagenesis. The first enzyme selected, called DSR-M synthesizes only low molar mass (LMM) dextran (28 kg/mol) exclusively composed of -(1→6) linkages without any trace of HMM dextran (105 to 108 g/mol). In contrast, DSR-OK (second model), produces the highest MM dextran (>109 g/mol) described to date. Several 3D crystallographic structures of a truncated form of DSR-M (DSR-M2), either free or in complex with its substrate or product (isomaltotetraose) in the domain V or in the active site were solved. Such complexes were never obtained before. Noteworthy, one structure encompassed the most complete domain V reported to date. Analyses of these structures coupled to dextran synthesis monitoring, showed that the LMM dextran specificity of DSR-M2 is explained by a distributive elongation mode due to the weak affinity of its two sugar binding pockets in the domain V which interact with the growing dextran chains and allow the synthesis of dextran longer than 16 kg/mol. 15N1H NMR analyses (HSQC), for the first time performed with such a big protein, further revealed the crucial role of aromatic residues in the catalytic domain for the production of dextran from 2 to 16 kg/mol. In comparison, synthesis of HMM dextran by DSR-OK was shown to be mainly due to the sugar binding pockets of its domain V, ensuring much stronger interactions with growing dextran chains. The role of these pockets was evidenced for both enzymes, their functionality proposed to be linked to the presence of one aromatic stacking residue. Their positioning along domain V relatively to the active site is also important to promote efficient binding. All these findings highlight the cooperation between domain V and the catalytic domain for dextran elongation, offer new perspectives to acquire a deeper knowledge on this interplay and open promising strategies for GH70 enzyme engineering aiming at modulating glucan size.

No description available.

In order to produce predictable and robust systems forprotein purification and detection, well characterized, small,folded domains descending from bacterial receptors have beenused. These bacterial receptors, staphylococcal protein A (SPA)and streptococcal protein G (SPG), possess high affinity to IgGand / or HSA. They are composed of repetitive units in whicheach one binds the ligand independently. The domains foldindependently and are very stable. Since the domains also havewellknown three-dimensional structures and do not containcysteine residues, they are very suitable as frameworks forfurther protein engineering. Streptococcal protein G (SPG) is a multidomain proteinpresent on the cell surface ofStreptococcus. X-ray crystallography has been used todetermine the binding site of the Ig-binding domain. In thisthesis the region responsible for the HSA affinity of ABD3 hasbeen determined by directed mutagenesis followed by functionaland structural analysis. The analysis shows that the HSAbindinginvolves residues mainly in the second α-helix. Most protein-based affinity chromatography media are verysensitive towards alkaline treatment, which is the preferredmethod for regeneration and removal of contaminants from thepurification devices in industrial applications. Here, aprotein engineering strategy has been used to improve thetolerance to alkaline conditions of different domains fromprotein G, ABD3 and C2. Amino acids known to be susceptibletowards high pH were substituted for less alkali susceptibleresidues. The new, engineered variants of C2 and ABD shownhigher stability towards alkaline pH. Also, very important forthe potential use as affinity ligands, these mutated variantsretained the secondary structure and the affinity to HSA andIgG, respectively. Moreover, dimerization was performed toinvestigate whether a higher binding capacity could be obtainedby multivalency. For ABD, binding studies showed that divalentligands coupled using non-directed chemistry demonstrated anincreased molar binding capacity compared to monovalentligands. In contrast, equal molar binding capacities wereobserved for both types of ligands when using a directed ligandcoupling chemistry involving the introduction and recruitmentof a unique C-terminal cysteine residue. The staphylococcal protein A-derived domain Z is also a wellknown and thoroughly characterized fusion partner widely usedin affinity chromatography systems. This domain is consideredto be relatively tolerant towards alkaline conditions.Nevertheless, it is desirable to further improve the stabilityin order to enable an SPA-based affinity medium to withstandeven longer exposure to the harsh conditions associated withcleaning in place (CIP) procedures. For this purpose adifferent protein engineering strategy was employed. Smallchanges in stability due to the mutations would be difficult toassess. Hence, in order to enable detection of improvementsregarding the alkaline resistance of the Z domain, a by-passmutagenesis strategy was utilized, where a mutated structurallydestabilized variant, Z(F30A) was used as a surrogateframework. All eight asparagines in the domain were exchangedone-by-one. The residues were all shown to have differentimpact on the alkaline tolerance of the domain. By exchangingasparagine 23 for a threonine we were able to remarkablyincrease the stability of the Z(F30A)-domain towards alkalineconditions. Also, when grafting the N23T mutation to the Zscaffold we were able to detect an increased tolerance towardsalkaline treatment compared to the native Z molecule. In allcases, the most sensitive asparagines were found to be locatedin the loops region. In summary, the work presented in this thesis shows theusefulness of protein engineering strategies, both to explorethe importance of different amino acids regarding stability andfunctionality and to improve the characteristics of aprotein. <b>Keywords:</b>binding, affinity, human serum albumin (HSA),albumin-binding domain (ABD), affinity chromatography,deamidation, protein A, stabilization, Z-domain, capacity,protein G, cleaning-in-place (CIP), protein engineering, C2receptor.