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We have initiated the development of a screening platform to design a library of small molecules on the same solid support surface. This solid support surface, and the chemistry involved, can be utilized as a means of developing lead target molecules, namely ligands and catalysts. Evidence shows the successful assembly of both simple amino acids, as well as successful employment of our synthetic compounds. We support our efforts by showing compatibility for binding studies with larger macromolecules. Thus, intrigue remains by the prospects of this project. Challenges within our efforts are highlighted and emphasis is placed on presenting solutions to current issues, in order to attain further development. Notwithstanding difficulty, the desire to establish efficient processes for the discovery of lead target molecules and to ascertain the utility of our synthesized compounds, can be captured within this body of work. Lastly, the framework for continued efforts has been set to enable future progression. / Chemistry

Effective detection and treatment of tumor malignancies depends upon identifying targets – molecular markers that differentiate cancer cells from healthy cells. Current cancer therapies involve targeting overexpressed specific gene products. An alternative approach is proposed here: to specifically target combinations of cell-surface receptors using heteromultivalent ligands (htMVLs). There are about 2500 genes encoding for cellsurface proteins in the human genome that can potentially be targeted. Taken as sets, there can be ~ 10⁶ two-receptor combinations and ~ 10⁹ three-receptor combinations available. Our group envisions that using cell-surface protein combinations that are expressed on a cancer cell but not on a normal cell, multivalent constructs displaying complementary ligands of weak affinities can be assembled. These multivalent ligands should bind with high avidity to cancer populations in vivo, and provide a degree of specificity not seen with current approaches. As a proof-of-concept, a series of multivalent ligands were designed and synthesized for a model system consisting of the human Melanocortin subtype 4 receptor (hMC4R) and the Cholecystokinin subtype 2 receptor (CCK-2R). Modeling studies on GPCR dimers predicted that a minimum linker span of 20 - 50 Å would be required to non-covalently crosslink these two receptors. The multivalent ligands were assembled using a modular parallel synthesis approach and using solidphase chemistries. A variety of linkers were explored ranging from highly rigid to highly flexible, and using natural and/or synthetic building blocks. Ligand binding affinities were evaluated using a lanthanide based competitive binding assay in cells that expressed both receptors (bivalent binding) vs those that expressed only one of the receptors (monovalent binding), and were demonstrated to have enhanced binding affinities of up to nearly two orders of magnitude. The promising ligands were further explored by synthesizing fluorescently labeled and/or lanthanide chelate labeled monovalent and heterobivalent ligands designed for in vitro and in vivo studies. More explorative work using these labeled constructs is in progress. To the best of our knowledge, the author believes this is the first such demonstration of a 'synthetic htMVL' directed recruitment and crosslinking of two heterologous cell-surface receptors. This receptor combination approach opens up new possibilities for single cell imaging, cancer detection and therapeutic intervention, and can provide a revolutionary new platform technology with which to direct therapeutics to defined cell populations.

Small robust affinity proteins have shown great potential for use in therapy, in vivo diagnostics, and various biotechnological applications. However, the affinity proteins often need to be modified or functionalized to be successful in many of these applications. The use of chemical synthesis for the production of the proteins can allow for site-directed functionalization not achievable by recombinant routes, including incorporation of unnatural building blocks. This thesis focuses on chemical engineering of Affibody molecules and an albumin binding domain (ABD), which both are three-helix bundle proteins of 58 and 46 amino acids, respectively, possible to synthesize using solid phase peptide synthesis (SPPS). In the first project, an alternative synthetic route for Affibody molecules using a fragment condensation approach was investigated. This was achieved by using native chemical ligation (NCL) for the condensation reaction, yielding a native peptide bond at the site of ligation. The constant third helix of Affibody molecules enables a combinatorial approach for the preparation of a panel of different Affibody molecules, demonstrated by the synthesis of three different Affibody molecules using the same helix 3 (paper I). In the next two projects, an Affibody molecule targeting the amyloid-beta peptide, involved in Alzheimer’s disease, was engineered. Initially the N-terminus of the Affibody molecule was shortened resulting in a considerably higher synthetic yield and higher binding affinity to the target peptide (paper II). This improved variant of the Affibody molecule was then further engineered in the next project, where a fluorescently silent variant was developed and successfully used as a tool to lock the amyloid-beta peptide in a β-hairpin conformation during studies of copper binding using fluorescence spectroscopy (paper III). In the last two projects, synthetic variants of ABD, interesting for use as in vivo half-life extending partners to therapeutic proteins, were engineered. In the first project the possibility to covalently link a bioactive peptide, GLP-1, to the domain was investigated. This was achieved by site-specific thioether bridge-mediated cross-linking of the molecules via a polyethylene glycol (PEG)-based spacer. The conjugate showed retained high binding affinity to human serum albumin (HSA) and a biological activity comparable to a reference GLP-1 peptide (paper IV). In the last project, the possibility to increase the proteolytic stability of ABD through intramolecular cross-linking, to facilitate its use in e.g. oral drug delivery applications, was investigated. A tethered variant of ABD showed increased thermal stability and a considerably higher proteolytic stability towards pepsin, trypsin and chymotrypsin, three important proteases found in the gastrointestinal (GI) tract (paper V). Taken together, the work presented in this thesis illustrates the potential of using chemical synthesis approaches in protein engineering. / <p>QC 20140207</p>

The thesis is focused on site-specific labeling of affinity molecules for different applications where two types of binding proteins, Affibody molecules and antibodies, have been used. For the purpose of improving the properties of Affibody molecules for in vivo imaging, novel bi-functional chelators for radiolabeling using the radionuclide 111In were evaluated. In a first study, two chelators denoted NOTA and DOTA, respectively, were separately conjugated via maleimide chemistry to a C-terminal cysteine residue in a HER2-binding Affibody molecule (ZHER2:2395). In vivo evaluation using mice with prostate carcinoma cell line xenografts showed that the 111In-NOTA-MMA-ZHER2:2395 tracer exhibited faster clearance from blood than the 111In-DOTA-MMA-ZHER2:2395 counterpart,resulting in improved tumor-to-organ ratios. In a second study the in vivo imaging properties of a third tracer, 111In-NODAGA-MMA-ZHER2:2395, was investigated in tumor-bearing mice. While the tumor uptake was lower than seen for the 111In-DOTA-MMA-ZHER2:2395 tracer, a low uptake in non-targeted organs and a fast clearance from blood resulted in higher tumor-to-organ ratios for 111In-NODAGA-MMA-ZHER2:2395 compared to the DOTA variant. In a following study, a synthetically produced HER2-targeting affibody variant, denoted ZHER2:S1, was used where NODAGA, NOTA and DOTA chelators instead were conjugated via an amide bond to the N-terminus. In vivo evaluation in mice showed an unfavorable uptake in liver for 111In-NOTA-ZHER2:S1, resulting in a discontinuation. The study showed faster clearance of 111In-NODAGA-ZHER2:S1 from blood, but also an increased uptake in bone in comparison to 111In-DOTA-ZHER2:S1. As bone is a common metastatic site in prostate cancer, the favorable tumor-to-bone ratio for 111In-DOTA-ZHER2:S1 suggests it as the tracer of choice for prostate cancer. Further, the DOTA chelator was also evaluated as conjugated to either N- or C-terminus or to the back of helix 3 via an amide bond, where the in vivo evaluation showed that that C-terminal conjugation resulted in the highest contrast. Site specificity is also of great importance for labeling antibodies, as conjugation in the antigen-binding regions might influence the affinity. A method for site-specific labeling of antibodies using an IgG-binding domain that becomes covalently attached to the Fc-region of an antibody by photoconjugation was optimized. By investigation of positions most suitable for incorporation of the photoreactive probe, the conjugation efficiencies were increased for antibody subclasses important for both diagnostic and therapeutic applications. In addition, optimized variants were used in combination with an incorporated click-reactive handle for selective labeling of the antibody with a detection molecule. / <p>QC 20140929</p>

Plant signaling involves the transport of information within and between plant cells from receptors to effectors. Plants are affected by biotic and abiotic stress conditions like insect attack and extreme temperatures, respectively, which cause disease, the induction of senescence and the reduction of crop yield. To improve plant traits for feed, fiber, and energy applications, it is critical to understand the short- and long-range signaling mechanisms plants use to control growth, biomass composition, senescence and responses to environmental stresses. It is known that many plant signaling molecules have profound effects on plants, through mechanisms that remain largely obscure. A key gap in knowledge is the understanding of the mechanisms that govern the movement and fate of signaling molecules. This study seeks to synthesize signaling probes based on flagellin 22 (flg22), a 22-amino acid peptide that induces defense gene expression to trigger both local and systemic immune responses in plants. Solid-phase synthesis of fluorescently-tagged derivatives of flg22 was initiated, and studies on the uptake of labeled probes was conducted using a fiber-optic fluorescence microscope that was adapted for use in plants. Fluorescence microscopy showed uptake and internalization of TAMRA-flg22 in cells of Arabidopsis thaliana Columbia (wild-type strain), which was not observed in the fls2 strain in which FLS2, the receptor for flg22, had been knocked out.

<p dir="ltr">A study on the impact of the position of the attachment of the photolabile, backbone amide linker, 4-formyl-3-hydroxy-5-nitrobenzoic acid, on the synthesis of a model cyclic pentapeptide was conducted. The peptide was synthesized on a solid support and cleaved photolytically. The crude product was analyzed for the effect of changing position by LC/MS, 1HNMR, and yield. The target peptide could not be identified convincingly by LC/MS or NMR. It was observed that attachment of the backbone amide linker to the N alpha of tyrosine provided the highest crude product yield.</p>

The next generation of toxic chemicals and hazardous wastes from sophisticated chemical industries will demand the environmental agencies to employ biological methods over the conventional physical and chemical remediation methods. Over the past decade, natural metallo-enzymes have been identified to degrade some of the major chemical contaminants through electron transfer pathways. However, these natural enzymes are less stable in organic solvents and they are not effective for the degradation of toxic compounds such as polychlorinated biphenyls or dioxins. This thesis explores the use of protein design approaches to produce chemically and molecularly modified enzymes, which are highly stable, possess little substrate specificity, and have higher activity than the natural enzymes. The experiments presented in this thesis make use of solid phase synthesis and site-directed mutagenesis for the synthesis and production of these enzymes and popular chromatographic techniques for their purification. The partial characterization of these proteins revealed the essential structural features of these proteins, and their catalytic activity was demonstrated by the use of peroxidase assays. / Master of Science

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