Affibody molecules have lately shown great potential as tools for in vivo molecular imaging. These small, 3-helical bundles, with their highly stable protein scaffold, are well suited for the often harsh conditions of radiolabeling. Their small size allows for rapid clearance from the blood circulation which permits the collection of images already within hours after injection. This thesis includes four papers aimed at engineering different variants of a HER2-binding Affibody molecule to enable effective  and  flexible  radiolabeling  and  enhancing  the  molecular  imaging  in  terms  of  imaging contrast and resolution. In paper I an Affibody molecule was engineered to function as a multifunctional platform for site-specific labeling with different nuclides for radionuclide imaging. This was done using only natural amino  acids,  thereby  allowing  for  both  synthetic  and  recombinant  production.  By  grafting  the amino acid sequence -GSECG to the C-terminal of our model-protein, a HER2-binding Affibody molecule, we enabled site specific labeling with both trivalent radiometals and with  99m Tc. Maleim-ide-DOTA was conjugated to the cysteine residue for labeling with  111 In, while the peptide sequence was able to chelate  99m Tc directly. This approach can also be used for site-specific labeling with other probes available for thiol-chemistry, and is applicable also to other protein scaffolds. In paper II we investigated the impact of size and affinity of radiolabeled Affibody molecules on tumor targeting and image contrast. Two HER2-targeting Affibody molecules, a two-helix (~5 kDa) and a three-helix (~7 kDa) counterpart, were synthetically produced, labeled with  111 In via chelation by  DOTA  and  directly  compared  in  terms  of  biodistribution  and  targeting  properties.  Results showed  that  the  smaller  variant  can  provide  higher  contrast  images,  at  the  cost  of  lower  tumor uptake,  in  high-expressing  HER2-tumors.  However,  neither  the  tumor  uptake  nor  the  contrast of the two-helix variant is sufficient to compete with the three-helix molecule in tumors with low expression of HER2. In paper III and IV we were aiming to find methods to improve the labeling of Affibody molecules with  18 F for PET imaging. Current methods are either complex, time-consuming or generate heavily lipophilic conjugates. This results in low yields of radiolabeled tracer, low specific activity left for imaging, undesirable biodistribution or a combination thereof. In paper III we demonstrate a swift and efficient 2-step, 1-pot method for labeling HER2-binding Affibody molecules by the formation of aluminum  18 F-fluoride (Al 18 F) and its chelation by NOTA, all in 30 min. The results show that the  18 F-NOTA-approach is a very promising method of labeling Affibody molecules with  18 F and further investigation of this scheme is highly motivated. In the last paper we pursued the possibility of decreasing the high kidney retention that is common among small radiotracers with residual-izing radiometabolites. In this work  18 F-4-fluorobenzaldehyde (FBA) was conjugated to a synthetic HER2-targeting Affibody molecule via oxime ligation. However, to avoid elevated liver retention, as seen in previous studies with this kind of label, a hydrophilic triglutamyl spacer between the aminooxy moiety and the N-terminal was introduced. A comparison of the two constructs (with and without the triglutamyl spacer) showed a clear reduction of retention in both kidney and liver in NMRI mice at 2 h p.i. when the spacer was included. In the light of these promising results, further studies including tumor-bearing mice, are in preparation. / <p>QC 20130203</p>

A CLCA protein (CL for chloride channel and CA for calcium) cloned from porcine ileum was expressed and characterized. The regulatory behavior, inhibitor sensitivity, and functional properties of chloride conductance associated with the expression of pCLCA1 cDNA were investigated in non-epithelial NIH/3T3 fibroblasts and in an epithelial Caco-2 cell line. These properties were also investigated in freshly isolated retinal pigment epithelial (RPE) cells and in primary cultures of these cells which express an endogenous cCLCA1. In NIH/3T3 fibroblasts, the chloride efflux induced by pCLCA1 was directly activated by calcium. A and C kinase agonists were without effect. The electrogenic nature of chloride efflux was confirmed by detection of outwardly rectified chloride currents. Selected anion channel blockers inhibited both the pCLCA1 agonist-induced current and chloride efflux. The inhibitors also reduced Ussing chamber short circuit current and chloride efflux from primary RPE cultures. However, these same agents did not inhibit chloride efflux in fibroblasts expressing the cystic fibrosis transmembrane regulator (CFTR) conductive chloride channel. The expression of pCLCA1 increased cAMP/A kinase-dependent chloride ion release from fibroblasts and Caco-2 cells expressing CFTR. These pleiotropic effects of CLCA protein expression suggested that the protein may regulate the activity of chloride conductance, rather than functioning as a primary ion transporter. This putative regulatory behavior was further investigated in Caco-2 cells. The rate of 36Cl efflux and the amplitude of currents in patch clamp studies after activation of A kinase or intracellular Ca2+ mobilization was significantly increased in freshly passaged Caco-2 cells expressing pCLCA1. However, 36Cl efflux and short circuit Ussing chamber studies in polarized Caco-2 cells provided evidence that both endogenous and pCLCA1-dependent Ca2+-sensitive chloride conductance were lost from 14 day post-passage cells. cAMP-dependent chloride conductance continued to be modulated by pCLCA1 expression in differentiated 14 day post-passage Caco-2 cells, demonstrating the retention of pCLCA1 effects in these mature cells. We conclude that pCLCA1 expression enhances the sensitivity of endogenous chloride channels to both natural agonists, Ca2+and cAMP, but that it lacks inherent Ca2+-dependent chloride channel activity.

Three classes of bifunctional compounds related to frustrated Lewis pair chemistry were studied. The first class, alkynyl-linked phosphonium borates, was strategically synthesized and the corresponding neutral alkynyl-linked phosphine boranes generated in solution. They were reacted with THF, alkenes and alkynes to undergo either ring-opening or multiple bond addition reactions, giving rise to zwitterionic macrocycles. In two select alkynyl-linked phosphonium borates, thermolysis resulted in unique rearrangements transforming the phosphino- and boryl-substituted alkynyl moieties into C4 chains. The alkynyl-linked phosphine boranes were further demonstrated to coordinate as η3-BCC ligands in Ni(0) complexes. The rigid nature of the coordination was confirmed by dimerization without cleavage of the Ni–B interaction upon the addition of acetonitrile or carbon monoxide. Moreover, reactions with Al-, Zn- and B-based Lewis acids prompted hydride transfer within the alkynyl-linked phosphonium borate and interesting functional group transfer reactions. The second class of the bifunctional systems, a series of gem-substituted bis-boranes, was subjected to reactions with tBu3P and CO2. The O-linked bis-borane was shown to coordinate the phosphino-carboxylate moiety with one B, while the methylene-linked bis-boranes were demonstrated to chelate the carboxyl group. The third bifunctional system class, vinyl-group tethered boranes, was examined to elucidate the mechanism of the frustrated Lewis pair addition reaction to olefins. Using a bis(pentafluorophenyl)alkylborane, the close proximity of the olefinic protons and the ortho-fluorine nuclei were evident by both NOE measurements and DFT calculations. Moreover, its reactions with phosphine bases suggested that an initial interaction between the highly electrophilic borane and the olefinic fragment precedes such frustrated Lewis pair addition reaction. Furthermore, a bis(pentafluorophenyl)alkoxyborane was synthesized and reacted with P-, N-, C- and H-based nucleophiles, demonstrating the wide range of Lewis bases that can be applied in olefin addition reactions with complementary regioselectivity.

Gold(I) and copper(I) imidazolium complexes were synthesized and probed for use as bulky Lewis acids in frustrated Lewis pairs (FLPs) with bulky phosphines and amines. Their reactivity with small molecules was investigated and the compounds were fully characterized by multinuclear NMR spectroscopy, elemental analysis and X-ray crystallography. Secondly, a new methylene-linked boron-sulfur Lewis acid was synthesized. Its thermodynamic properties were determined and its reactivity with terminal and internal alkynes was demonstrated. Adducts and heterocycles of this boron-sulfur system were fully characterized by multinuclear NMR spectroscopy, elemental analysis and X-ray crystallography. The application of these new systems for the activation of small molecules is described in this thesis.

Gold(I) and copper(I) imidazolium complexes were synthesized and probed for use as bulky Lewis acids in frustrated Lewis pairs (FLPs) with bulky phosphines and amines. Their reactivity with small molecules was investigated and the compounds were fully characterized by multinuclear NMR spectroscopy, elemental analysis and X-ray crystallography. Secondly, a new methylene-linked boron-sulfur Lewis acid was synthesized. Its thermodynamic properties were determined and its reactivity with terminal and internal alkynes was demonstrated. Adducts and heterocycles of this boron-sulfur system were fully characterized by multinuclear NMR spectroscopy, elemental analysis and X-ray crystallography. The application of these new systems for the activation of small molecules is described in this thesis.

SHAPE-DEPENDENT MOLECULAR RECOGNITION OF SPECIFIC SEQUENCES OF DNA BY HETEROCYCLIC CATIONS by YI MIAO Under the Direction of Dr. W. David Wilson ABSTRACT DB921 and DB911 are biphenyl-benzimidazole-diamidine isomers with a central para- and meta-substituted phenyl group, respectively. Unexpectedly, linear DB921 has much stronger binding affinity with DNA than its curved isomer, DB911. This is quite surprising and intriguing since DB911 has the classical curved shape generally required for strong minor groove binding while DB921 clearly does not match the groove shape. Several biophysical techniques including thermal melting (Tm), circular dichroism (CD), biosensor-surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC) have been utilized to investigate the interactions between these compounds and DNA. The structure of the DB921-DNA complex reveals that DB921 binds to DNA with a reduced twist of the biphenyl for better fit of DB921 into the minor groove. A bound water molecule complements the curvature of DB921 and contributes for tight binding by forming H-bonds with both DNA and DB921. Structure-affinity relationship studies of a series of DB921 analogs show that the benzimidazole group is one of the key groups of DB921 for its strong binding to the minor groove. Thermodynamic studies show that the stronger binding of DB921 is due to a more favorable binding enthalpy compared to DB911 even though the complex formation with DNA for these compounds are all predominantly entropically driven. DB921 also has more negative heat capacity change than DB911. The initial studies of inhibition of the interaction between an AT hook peptide of HMGA proteins and its target DNA by a set of diamidine AT-minor groove binders using biosensor-SPR technique show that the inhibitory ranking order is consistent with that of binding affinity and linear-shaped DB921 still has excellent inhibitory effects. These heterocyclic cations rapidly inhibit the binding of DBD2 peptide to the DNA and may only block the specific AT binding of the peptide without hindering the non-specific binding interaction. The results of this project have shown that DB921 represents a new novel effective minor groove binder that does not fit the traditional model and is a potential inhibitor for DNA/protein complexes. INDEX WORDS: Molecular recognition, DNA binding, Minor groove binding, Linear shape, Compound curvature, Binding affinity, Binding kinetics, Thermodynamics, Surface plasmon resonance, Isothermal titration calorimetry, Inhibition

A CLCA protein (CL for chloride channel and CA for calcium) cloned from porcine ileum was expressed and characterized. The regulatory behavior, inhibitor sensitivity, and functional properties of chloride conductance associated with the expression of pCLCA1 cDNA were investigated in non-epithelial NIH/3T3 fibroblasts and in an epithelial Caco-2 cell line. These properties were also investigated in freshly isolated retinal pigment epithelial (RPE) cells and in primary cultures of these cells which express an endogenous cCLCA1. In NIH/3T3 fibroblasts, the chloride efflux induced by pCLCA1 was directly activated by calcium. A and C kinase agonists were without effect. The electrogenic nature of chloride efflux was confirmed by detection of outwardly rectified chloride currents. Selected anion channel blockers inhibited both the pCLCA1 agonist-induced current and chloride efflux. The inhibitors also reduced Ussing chamber short circuit current and chloride efflux from primary RPE cultures. However, these same agents did not inhibit chloride efflux in fibroblasts expressing the cystic fibrosis transmembrane regulator (CFTR) conductive chloride channel. The expression of pCLCA1 increased cAMP/A kinase-dependent chloride ion release from fibroblasts and Caco-2 cells expressing CFTR. These pleiotropic effects of CLCA protein expression suggested that the protein may regulate the activity of chloride conductance, rather than functioning as a primary ion transporter. This putative regulatory behavior was further investigated in Caco-2 cells. The rate of 36Cl efflux and the amplitude of currents in patch clamp studies after activation of A kinase or intracellular Ca2+ mobilization was significantly increased in freshly passaged Caco-2 cells expressing pCLCA1. However, 36Cl efflux and short circuit Ussing chamber studies in polarized Caco-2 cells provided evidence that both endogenous and pCLCA1-dependent Ca2+-sensitive chloride conductance were lost from 14 day post-passage cells. cAMP-dependent chloride conductance continued to be modulated by pCLCA1 expression in differentiated 14 day post-passage Caco-2 cells, demonstrating the retention of pCLCA1 effects in these mature cells. We conclude that pCLCA1 expression enhances the sensitivity of endogenous chloride channels to both natural agonists, Ca2+and cAMP, but that it lacks inherent Ca2+-dependent chloride channel activity.

The synthesis of monodentate biphenyl-amido proligands is reported as well as a series of complexes of lithium with these ligand systems. The solid-state molecular structure of these lithium amides are described as well as their use as synthons in the preparation of amido-arene aluminum complexes. Structural and spectroscopic data suggest that these species exhibit weak arene to metal donation. Attempts to generate aluminum cations from these species are detailed. A new synthetic route to titanium “constrained geometry” precatalysts was utilized to prepare a series of titanium complexes with similar pendant arene groups. The homopolymerization activity of these catalyst systems with ethylene and styrene is detailed. Combination of a sterically encumbered phosphine and large, electrophilic borane was used to effect heterolytic cleavage of disulfides to afford novel thiophosphoniumthioborate salts. A series of exchange reactions demonstrated the facile reversal of this reaction. Similar phosphine-borane systems are found to exhibit divergent reactivity with terminal alkynes, affording either phosphonium-alkynylborate salts from deprotonation or phosphonium-vinyl-borate zwitterions from addition. The scope of Lewis acid, Lewis base and alkyne combinations used to effect similar reactivity is detailed. It was found that the reaction of pyrroles, boranes, and alkynes formed similar addition products that were found to undergo further reactivity to afford C-vinyl pyrroles and nitrogen-boron bicyclic compounds. The synthesis of N-alkyl-bis(pentafluorophenyl)boryl amidinates is presented. The reactivity of these compounds with a variety of small molecules is reported. Reaction with CO2, CO, di-iso-propylcarbodiimide, tert-butyl isocyanide, and benzaldehyde as well as thermally-induced intramolecular rearrangement of these compounds affords a variety of novel nitrogen-boron heterocycles.

The synthesis of monodentate biphenyl-amido proligands is reported as well as a series of complexes of lithium with these ligand systems. The solid-state molecular structure of these lithium amides are described as well as their use as synthons in the preparation of amido-arene aluminum complexes. Structural and spectroscopic data suggest that these species exhibit weak arene to metal donation. Attempts to generate aluminum cations from these species are detailed. A new synthetic route to titanium “constrained geometry” precatalysts was utilized to prepare a series of titanium complexes with similar pendant arene groups. The homopolymerization activity of these catalyst systems with ethylene and styrene is detailed. Combination of a sterically encumbered phosphine and large, electrophilic borane was used to effect heterolytic cleavage of disulfides to afford novel thiophosphoniumthioborate salts. A series of exchange reactions demonstrated the facile reversal of this reaction. Similar phosphine-borane systems are found to exhibit divergent reactivity with terminal alkynes, affording either phosphonium-alkynylborate salts from deprotonation or phosphonium-vinyl-borate zwitterions from addition. The scope of Lewis acid, Lewis base and alkyne combinations used to effect similar reactivity is detailed. It was found that the reaction of pyrroles, boranes, and alkynes formed similar addition products that were found to undergo further reactivity to afford C-vinyl pyrroles and nitrogen-boron bicyclic compounds. The synthesis of N-alkyl-bis(pentafluorophenyl)boryl amidinates is presented. The reactivity of these compounds with a variety of small molecules is reported. Reaction with CO2, CO, di-iso-propylcarbodiimide, tert-butyl isocyanide, and benzaldehyde as well as thermally-induced intramolecular rearrangement of these compounds affords a variety of novel nitrogen-boron heterocycles.

This project considers the diffusion of water molecules through a cellular medium in which the cells are modeled by square compartments placed symmetrically in a square domain. We assume the diffusion process is governed by the 2D diffusion equations and the solution is provided by implementing the Crank-Nicolson scheme. These results are verified and illustrated to agree well with the finite element method using the Comsol Multiphysics package. The model is used to compute the values of the apparent diffusion coefficient, (ADC) which is a measure that is derived from diffusion weighted MRI data and can be used to identify, e.g., regions of ischemia in the brain. With our model, it is possible to examine how the value of the apparent diffusion coefficient is affected whenever the extracellular space is varied. We observe that the average distance that the water molecules travel in a definite time is highly dependent on the geometrical properties of the cellular media. / UOIT