No / Discovery of new catalysts for demanding aqueous reactions is challenging. Here, we describe methodology for selection of catalytic phages by taking advantage of localized assembly of the product of the catalytic reaction that is screened for. A phage display library covering 109 unique dodecapeptide sequences is incubated with nonassembling precursors. Phages which are able to catalyze formation of the self-assembling reaction product (via amide condensation) acquire an aggregate of reaction product, enabling separation by centrifugation. The thus selected phages can be amplified by infection of Escherichia coli. These phages are shown to catalyze amide condensation and hydrolysis. Kinetic analysis shows a minor role for substrate binding. The approach enables discovery and mass-production of biocatalytic phages.

Interferon regulatory factor 1 (IRF-1) is a tumour suppressor protein and transcription factor. It has been shown to modulate target gene expression in response to stimuli, which include viral infection and DNA damage, and to be down-regulated in several forms of cancer. This thesis details the development of an intrabody, an intracellular antibody, that binds specifically to endogenous IRF-1. The binding of the intrabody to IRF-1 enhanced transcription from IRF-1-responsive reporter gene constructs and endogenous promoters, thus it was shown to activate IRF-1. Intrabody binding also increased the rate at which IRF-1 was degraded, suggesting that the intrabody epitope may be regulating both IRF-1 activity and turnover. These results were supported point mutation within the intrabody epitope (P325 to A) as the resultant mutant also displayed both a higher transcriptional activity and increased rate of degradation. In an effort to understand the mechanisms which regulate IRF-1 activity a search for novel IRF-1-interacting proteins was carried out using phage peptide display. This in vitro technique enables the identification of peptides able to bind a specific target protein. The sequence of these peptides can then be used to search protein databases for homologous, full-length proteins that could also bind the target protein. This led to the identification of an IRF-1-binding peptide that held sequence similar to a region of Zinc Finger 350 (ZNF350), a transcription factor involved in regulating the DNA damage response. Subsequently, endogenous ZNF350 and IRF-1 were co-immunoprecipitated from a human cancer cell line. The extreme C-terminus of IRF-1 was shown to be sufficient for an interaction with ZNF350, although a second, more N-terminal site was also shown to be essential for a stable intracellular interaction. This data sheds new light on the role of the extreme C-terminus of IRF-1 in modulating the protein‟s activity. This study also provides new and IRF-1-specific molecular tools, in the form of intrabodies and IRF-1-binding peptides, which could be used in the future to further characterise the activity and regulation of this tumour suppressor protein.

<p>In affinity protein biotechnology the selective bindingbetween a chosen protein and an interacting biomolecule isutilized for a variety of applications including bioseparation,detection and therapy. Traditionally, affinity proteinsrecruited for such applications have been derived from naturalproteins or immunoglobulins generated via immunization routes.More recently, advances in the construction and handling oflarge collections of proteins(denoted libraries) generated invitro have opened up for new routes for the development ofaffinity proteins with desired properties.</p><p>In this study, phage display selection technology was usedfor the isolation of novel human CD28 (hCD28)-specific affinityproteins from a protein library constructed by combinatorialprotein engineering of a 58 aa protein domain (Z) derived fromstaphylococcal protein A (SPA). From selections using hCD28 asa target molecule, several hCD28-specific affinity proteins(denoted affibodies) could be identified and analysis of theisolated affibody variants revealed a high degree of sequencehomology between the different clones. The biosensor analysisshowed that all variants bound to hCD28 with micromolardissociation constants (KD) and no significant cross-reactivitytowards the structurally related T-cell receptor hCTLA-4 couldbe observed. The apparent binding affinity for hCD28 of one ofthe isolated affibodies was further improved through fusion toa human Fc fragment fusion partner, resulting in a homodimericversion of the affibody ligand showing avidity effects uponhCD28 binding. Further, a co-culture experiment involvingJurkat T-cells and CHO cell lines tranfected to express eitherhuman CD80 or LFA-3 on the cell surface showed that apreincubation of Jurkat cells with one of the affibody variantsresulted in a specific concentration-dependent inhibition ofthe CD80 induced IL-2 production. This indicates that thisaffibody binds to hCD28 and specifically interferes with theco-stimulation signal mediated via hCD28 and hCD80. ACD28-specific binding protein could have potential as an agentfor various immunotherapy applications. In a second study, anaffinity protein-based strategy was investigated forsite-specific anchoring of proteins onto cellulose for woodfiber engineering purposes. Here, affinity proteins derivedfrom different sources were used for the assembly of acellulosome-like complex for specific and reversible anchoringof affinity domain-tagged reporter proteins to acellulose-anchored fusion protein. A fusion protein between acellulose binding module (Cel6A CBM1) derived from the fungalTrichoderma reesei and a five-domain staphylococcal protein A(SPA) moiety was constructed to serve as a platform for thedocking of reporter proteins produced as fusion to two copiesof a SPA-binding affibody affinity protein (denoted ZSPA-1),selected by phage display technology from a Z domain basedprotein library. In a series of experiments, involving repeatedwashing and low pH elutions, affinity tagged Enhanced GreenFluorescent Protein (EGFP) and Fusarium solani pisi lipasecutinase reporter proteins were both found to be specificallydirected from solution to a region of a cellulose-based filterpaper where the SPA-CBM fusion protein previously had beenpositioned. This showed that the cellulose-anchored SPA-Cel6ACBM1 fusion protein had been stably anchored to the surfacewith retained binding activity and that the interaction betweenSPA and the ZSPA-1 affibody domain was selective.</p><p>phage display, combinatorial, selection, CD28, cellulosome,cellulose, affibody</p>

Protein kinases function as key regulators in a variety of signaling pathways by executing the phosphorylation of a variety of protein substrates. Perturbation in the activity of numerous proteins kinases has been implicated in a large number of diseases including cancer, diabetes, inflammation and neurological disorders. Therefore, selective modulation of kinase activity is highly desirable for the dissection of complex signaling pathways and substantiating therapeutic targets. To develop potent and selective inhibitors for an array of kinases, our group has developed a fragment based bivalent methodology utilizing phage display. The strategy involves an ATP active site targeted small molecule which directs the selection of cyclic peptides, from a phage displayed library, on the target kinase surface through coiled coil interactions. The selected cyclic peptides can be conjugated to the ATP mimetic to generate bivalent inhibitors. In this thesis, I have expanded the scope of the bivalent phage-display selection approach. To interrogate the generality of this approach, we targeted several kinases from different groups within the human kinome using the staurosporine warhead. Fyn and PDGFRβ represented the tyrosine kinase group and CLK2 and Pim-1 kinases represented the CMGC and CaMK groups respectively. The selections against these four kinases did not result in potent inhibitors though they provided an avenue for the refinement of the bivalent phage-display approach as well as method development. Application of this methodology to AKT2 in the AGC family resulted in bivalent inhibitors which were interrogated for their selectivity and mode of action. The bivalent strategy was further explored for its utility to target inactive kinases, and success was achieved against AKT1. Finally, we demonstrated the modularity of ATP site targeted ligand by carrying out a selection against STK33 kinase using a new small molecule warhead, sunitinib. This resulted in potent and selective bivalent inhibitors for STK33. The use of different ATP site targeting molecules potentially increases the number of targetable kinases with our strategy. In all the selections, the identified cyclic peptides inhibited the kinase and showed a non-competitive mode of inhibition with respect to the kinase substrate. This suggests that the selected peptides do not target the substrate site and possibly bind to unidentified pockets on the kinase surface, which potentially provides new methods to target kinases outside the traditional ATP binding cleft. The strategy may prove to be a robust method to discover new allosteric sites on kinases as well as other proteins. The potent and selective bivalent inhibitors obtained by our strategy have the potential to provide insight towards the design of new non-ATP targeted approaches for inhibiting protein kinases and elucidating their specific functions.

Despite intense research efforts, a safe and effective HIV-1/AIDS vaccine still remains far away. HIV-1 escapes the humoral immune response through various mechanisms and until now, only a few nAbs have been identified. A promising strategy to identify new epitopes that may elicit such nAbs is to dissect and analyze the humoral immune response of sera with broadly reactive nAbs. The identified epitopes recognized by these antibodies might then be incorporated into a vaccine to elicit similar nAbs and thus provide protection from HIV-1 infection. Using random peptide phage display libraries, the Ruprecht laboratory has identified the epitopes recognized by polyclonal antibodies of a rhesus monkey with high-titer, broadly reactive nAbs that had been induced after infection with a SHIV encoding env of a recently transmitted HIV-1 clade C. The laboratory analyzed phage peptide inserts for conformational and linear homology with computational assistance. Several of the identified peptides mimicked domains of the original HIV-1 clade Env, such as conformational V3 loop epitopes and the conserved linear region of the gp120 C-terminus. As part of this work, these mimotopes were analyzed for cross-reactivity with other sera obtained from rhesus monkeys with nAbs and antibody recognition was shown for several mimotopes, particularly those representing the V3 loop. In addition, these mimotopes were incorporated into a novel DNA prime/phage boost strategy to analyze the immunogenicity of such phage-displayed peptides. Mice were primed only once with HIV-1 clade C gp160 DNA and subsequently boosted with mixtures of recombinant phages. This strategy was designed to focus the humoral immune response on a few, selected Env epitopes (immunofocusing) and induced HIV-1 clade C gp160 binding antibodies and cross-clade nAbs. Furthermore, the C-terminus of gp120, a conserved HIV Env region, was linked to the induction of nAbs for the first time. The identification of such conserved antigens may lead to the development of a vaccine that is capable of inducing broadly reactive nAbs that might confer protection form HIV-1 infection. / Trotz enormer Forschungsleistungen liegt ein sicherer und effektiver Impfstoff gegen HIV-1/AIDS immer noch in weiter Ferne. HIV-1 entkommt der humoralen Immunantwort aufgrund mehrerer Mechanismen und daher wurden bis zu diesem Zeitpunkt nur wenige neutralisierende Antikörper identifiziert. Eine vielversprechende Strategie zur Identifizierung neuer Epitope, die neutralisierende Antikörper induzieren könnten, ist die Analyse von Seren mit solchen Antikörper. Die dabei identifizierten Epitope könnten dann zur Herstellung eines Impfstoffes verwendet werden, der ähnliche neutralisierende Antikörper induziert und damit vor einer Infektion mit HIV-1 schützt. Mittels Phage-Display hat das Labor von Ruth Ruprecht mehrere solcher Epitope von polyklonalen Antikörpern aus Rhesus Affen mit hochtitrigen, breit-neutralisierenden Antikörpern identifiziert. Diese Antikörper wurden nach einer Infektion mit einem SHIV induziert, das das virale Hüllprotein eines kürzlich übertragenen HIV-1 clade C Virus enthielt. Die Phagenpeptide wurden auf konformelle und lineare Homologie mittels einer Computer Software untersucht. Mehrere dieser Peptide entsprachen Domänen des viralen Hüllproteins, wie z.B. konformelle V3 loop Epitope and Epitope des linearen C-Terminus von gp120. Im Rahmen dieser Arbeit wurden diese Mimotope auf Kreuzreaktivität mit anderen Seren von Rhesus Affen mit neutralisierenden Antikörpern untersucht. Dabei wurden insbesondere die Mimotope des V3 loops von anderen Seren erkannt. Des Weiteren wurden diese Phagen-Mimotope im Rahmen einer neuen DNA prime/phage boost Strategie zur Immunisierung verwendet. Mäuse wurden einmalig mit HIV-1 clade C gp160 DNA immunisiert und anschließend mehrfach mit rekombinanten Phagen geboostet. Mittels dieser Strategie sollte das Immunsystem auf einige, spezielle Epitope des viralen Hüllproteins fokusiert werden (Immunofocusing). Hierbei wurden HIV-1 clade gp160-bindende Antikörper und breit-neutralisierende Antikörper induziert. Des Weiteren konnten zum ersten Mal neutralisierende Antikörper gegen den C-terminus von gp120, einer konservierten Region des viralen Hüllproteins, induziert werden. Die Identifikation solcher konservierter Mimotope kann zur Entwicklung von einem HIV-1 Impfstoff beitragen, der breit neutralisierende Antikörper induziert, die vor einer Infektion schützen können.

La détection de l'apoptose revêt un intérêt considérable en raison de son implication dans de nombreuses pathologies d'incidence élevée, comme le cancer ou la maladie d'Alzheimer pour n'en citer que deux. Des méthodes de mise en évidence de ce phénomène se multiplient et se développent sans cesse visant à détecter in vitro voire même in vivo, cette forme de mort cellulaire programmée. Grâce à son pouvoir de résolution élevé et à des agents de contraste spécifiques, l'Imagerie par Résonance Magnétique (IRM) offre la possibilité de détecter, de manière non invasive, les cellules apoptotiques. Cette approche trouvera son utilité pour la mise au point de traitements anti-tumoraux et pour leur suivi en clinique. Aujourd'hui, il existe des agents de contraste magnétiques capables de reconnaître les cellules apoptotiques, mais leurs molécules vectrices sont constituées de protéines, d'anticorps ou de leurs domaines dont on ne peut ignorer l'important pouvoir immunogène. Des molécules mimétiques ou des oligomères de petite taille comme des peptides seraient plus adaptés et plus simples à synthétiser chimiquement. Notre travail porte sur la sélection, de peptides capables de reconnaître spécifiquement les cellules apoptotiques, en se fixant à la phosphatidylsérine (molécule marqueur des cellules apoptotiques). Ces peptides ont été sélectionnés par la méthode du phage display. Le phage display est une technique de biologie moléculaire permettant de sélectionner, entre autre, des peptides de longueur déterminée, en fonction de leur affinité pour une cible donnée. Plusieurs milliards de séquences peptidiques exposées par les phages constituant la bibliothèque, peuvent être testés simultanément. Les meilleures séquences sont ensuite synthétisées chimiquement et testées indépendamment du phage. Dans la première partie de ce travail, plusieurs protocoles de phage display basés sur différentes méthodes d'immobilisation de la cible, et différents types de bibliothèques de phages ont été testés et comparés. A l'issue de ces sélections, plusieurs phages présentant une affinité élevée pour la phosphatidylsérine ont été sélectionnés. Un des peptides exposés par un de ces phages, nommé E3, a été synthétisé et étudié dans la seconde partie de ce travail. Le peptide E3 a été d'abord greffé à un contrastophore magnétique de type superparamagnétique (Ultra Small Particle Iron Oxide) pour être testé in vitro sur des systèmes biologiques (apoptose induite chez des cellules Hep G2 par la camptothécine). Après avoir été testé avec succès sur culture cellulaire, ce nouvel agent de contraste magnétique a été utilisé, in vivo dans le modèle murin d'apoptose hépatique induite par injection i.v. d'anticorps anti-Fas. Comme tout agent de contraste de type particulaire, le GG-E3-USPIO (peptide E3 greffé aux USPIOs par un pont diglycyle) serait capté de manière non spécifique par le foie. Il doit donc être rendu "furtif" pour permettre l'exploitation de sa spécificité. Afin de contourner le problème de capture non spécifique par le foie, le GG-E3-Gd-DTPA (peptide E3 greffé au Gd-DTPA par un pont diglycyle), un autre agent de contraste, cette fois de type paramagnétique, a été synthétisé. Les agents de contraste GG-E3-USPIO-PEG (peptide E3 greffé aux USPIO recouvertes de polyéthylèneglycol par un pont diglycyle) et GG-E3-Gd-DTPA se sont avérés efficaces, provoquant respectivement une diminution et un rehaussement du signal des foies apoptotiques de souris en IRM.

Antibody phage display technology mimics the natural immune system, and has been widely used for rapid isolation of single-domain antibodies (sdAbs) with various binding specificities and affinities in the micromolar to low nanomolar range. SdAbs are the variable regions of immunoglobulins (e.g., VH, VL, VHH) and serve as potential probes with therapeutic value. The small size, high solubility, high expression and stability, and high specificity and affinity for the cognate antigen, make sdAbs ideal in improving drug delivery and the overall therapeutic value of antibodies. The main objective of this thesis was to construct a large VL phage display library (~1010 diversity); analyze it via sequence analysis, and to subtractively pan the library for isolation of Neuropilin-1 (NRP1)-specific VLs. Neuropilin-1 (NRP1), a cell-surface receptor for both vascular endothelial growth factor (VEGF) and class 3 Semaphorins (Sema3A), contributes to neuron cell death through its interaction with Sema3A in stroke patients. Disruption of this NRP1-Sema3A interaction would allow for axonal outgrowth and neuron regeneration in the area of the brain affected by stroke. Construction of the synthetic phage antibody library utilized a single VL framework with selected positions in the complementarity-determining regions (CDRs) targeted for randomization in vitro using synthetic oligonucleotides that introduced sequence degeneracy. Specific VLs were then selected from the repertoire through subtractive panning against a cell line endogenously expressing NRP1 (PC12) as well as a negative cell line that does not express NRP1 (HEK293) with competitive elution carried out using a synthetic Sema3A-derived peptide. Fifteen VL clones were isolated, cloned in E. coli, expressed and purified, and of these, nine were determined to be non-aggregating by size exclusion chromatography. Further studies will determine the potential therapeutic use of these VL sdAbs as agents in recovery from stroke and neuron degeneration.

Antibody phage display technology mimics the natural immune system, and has been widely used for rapid isolation of single-domain antibodies (sdAbs) with various binding specificities and affinities in the micromolar to low nanomolar range. SdAbs are the variable regions of immunoglobulins (e.g., VH, VL, VHH) and serve as potential probes with therapeutic value. The small size, high solubility, high expression and stability, and high specificity and affinity for the cognate antigen, make sdAbs ideal in improving drug delivery and the overall therapeutic value of antibodies. The main objective of this thesis was to construct a large VL phage display library (~1010 diversity); analyze it via sequence analysis, and to subtractively pan the library for isolation of Neuropilin-1 (NRP1)-specific VLs. Neuropilin-1 (NRP1), a cell-surface receptor for both vascular endothelial growth factor (VEGF) and class 3 Semaphorins (Sema3A), contributes to neuron cell death through its interaction with Sema3A in stroke patients. Disruption of this NRP1-Sema3A interaction would allow for axonal outgrowth and neuron regeneration in the area of the brain affected by stroke. Construction of the synthetic phage antibody library utilized a single VL framework with selected positions in the complementarity-determining regions (CDRs) targeted for randomization in vitro using synthetic oligonucleotides that introduced sequence degeneracy. Specific VLs were then selected from the repertoire through subtractive panning against a cell line endogenously expressing NRP1 (PC12) as well as a negative cell line that does not express NRP1 (HEK293) with competitive elution carried out using a synthetic Sema3A-derived peptide. Fifteen VL clones were isolated, cloned in E. coli, expressed and purified, and of these, nine were determined to be non-aggregating by size exclusion chromatography. Further studies will determine the potential therapeutic use of these VL sdAbs as agents in recovery from stroke and neuron degeneration.

Phage display is a molecular technique accomplished by incorporation of the nucleotide sequence encoding the protein to be displayed into a phage or phagemid genome as a fusion to a gene encoding a phage coat protein. After several rounds of selection and amplification, high affinity phage clones, and thus high affinity ¡§homing peptides¡¨ can be obtained. Cell-binding homing peptides selected in this manner could be linked by physical or genetic manipulation to gene therapy vectors that mediate their own entry (viral or non-viral vectors) to facilitate targeting. Homing peptides that target specific cellular receptors can also be used as a treatment modality to induce various signal transduction pathways or even apoptotic signals of cancer cells. Oral squamous cell carcinoma (OSCC) is one of the most common cancers in the world. It has become the fourth cancer death reason of males in Taiwan. Radical surgery combined with postoperative chemotherapy and/or radiotherapy is still the major modality for treatment of OSCC. The 5-year survival rate of OSCC is still discouraged in recent years. Patients with OSCC present numerous challenges to treating physicians. In this study, we aimed to isolate and identify homing phage clones specific to oral cancer cells by panning with a random phage peptide library. The homing phage clones will be used as a basis to improve targeting specificity of gene therapy vectors. A NCBI BLAST search was performed and close similarities were found to several important molecules biologically with the homing peptides carried by phage clones. Characterization of the selected phage-29 was then studied by immunohistochemical methods. Internalization of this phage-29 is sequence-specific and mediated by integrin £\v£]6 in HSC-3 cells rapidly. We also confirmed that the integrin £\v£]6-targeting homing peptide is universally useful in all major kinds of head and neck cancer. We will further study the possible biological functions of the other homing peptides to see whether these peptides could have potential applications for oral cancer treatment.

The glycine receptor (GlyR) is a ligand-gated ion channel and a member of the cys-loop receptor family. Like other members of this family, the GlyR is a target for many drugs of abuse, including alcohol. While the effects of alcohol on these receptors have been well-characterized, the contribution of each receptor subtype to the overall physiological and behavioral effects of alcohol use are unclear. This is partially due to the limited pharmacology of the GlyR, which limits the ability to isolate GlyR function within a complex system. One method for identifying compounds that bind to and modulate a given target is phage display. This approach uses bacteriophage to screen a large number of peptide sequences for affinity at a given target. We developed a phage selection protocol to identify peptides that bind to the GlyR. These peptides were then tested for functional effects at the GlyR using two-electrode voltage clamp physiology. We identified several peptides that were able to modulate GlyR function. Peptide D12-116 showed specificity for the GlyR over two closely related γ-aminobutyric acid (GABA) channels. In addition, this method is easily adapted for the selection of peptides that bind to any cell-expressed target, increasing the utility of phage display in the neurobiology field. Another shortcoming in GlyR pharmacology is the lack of modulators with specificity for a single GlyR subtype. We next adjusted our selection protocol to search for peptides that can distinguish between the different Gly R α subtypes. We identified several promising lead peptides that show subtype preference. Finally, we found that trifluoroacetic acid (TFA), a common peptide contaminant, also modulates GlyR function. This finding has important implications for both previously reported peptide modulators and the pharmacology of several volatile anesthetics, for which TFA is the major metabolite / text