The work in this thesis reports studies directed to developing a calpain cysteine protease inhibitor that could be of value in slowing cataract development in humans. The work focuses on the development of macrocyclic compounds which can have advantages over acyclic compounds due to their resistance to proteolytic hydrolysis, improved selectivity, bioavailability and membrane permeability. A review of X-ray crystal structures of natural and synthetic calpain inhibitors complexed with the cysteine protease calpain show the inhibitors generally bind in the enzyme active site in an extended β-strand conformation. The calpain inhibitor SJA-6017 has been identified as a suitable lead compound. The importance of the para-fluoro group in SJA-6017 has been investigated. Modifications have been made to constrain this basic structure within a macrocycle and restrict the peptide chain as a β-strand conformation. Macrocycle CAT811 is a potent calpain 1 and 2 inhibitor and shows promise in slowing the progression of cortical cataract in trials with sheep having a hereditary propensity towards the development of cataract. In this thesis I report studies directed to improve the yield of the key RCM macrocyclisation step in the synthesis of aldehyde CAT811 and of three ester analogues (2.1, 2.3 and 2.4). I also report the development of a more commercial route to CAT811 not involving RCM but using intramolecular nucleophilic cyclisation. This intramolecular nucleophilic cyclisation strategy was attempted for the preparation of a histidine containing macrocyclic ester (4.1a) but was unsuccessful. An alternate strategy involving intramolecular lactamization proved successful for the synthesis of histidine-based macrocyclic esters (4.1a-4.3a). Reduction to the corresponding alcohols (4.1b-4.3b) was successful and oxidation of (4.1b and 4.3b) afforded the corresponding aldehydes (4.1c and 4.3c) for biological assay against ovine calpain 2. Aldehyde 4.3c has an IC50 of 1 μM and the corresponding alcohol 4.3b shows no activity (IC50 > 50 μM) consistent with the modelling which indicated that these two compounds did not adopt a β-strand conformation in the docking studies. Aldehyde 4.1c, on the other hand, shows significant inhibitory activity with an IC50 of 238 nM but as expected the corresponding alcohol 4.1b shows little activity (IC50 = 29 μM). Modelling studies showed that both the aldehyde 4.1c and the alcohol 4.1b on docking can form a β-strand with appropriate H-bonding interactions. The aldehyde is more active than the alcohol due to the reactivity of the aldehyde warhead allowing for the reversible formation of a hemiacetal. A similar difference in reactivity is observed for CAT811 (30 nM) and its alcohol analogue (700 nM). These results demonstrate the value of molecular modelling as a screening mechanism before unproductive synthetic work is considered.

This thesis summarises the progress made in the design and synthesis of conformationally constrained β-strand peptidomimetic compounds using ring closing metathesis methodology under microwave irridation conditions. The best macrocycle were elaborated into an inhibitor for a specific protease target. Calpain was used as an example of protease targeting cataract disease. Chapter One introduces proteases in general centring on the general context of protease inhibitor design. The significant of the β-strand 'bioactive' conformation is discussed in details in particular the exploitation of conformationally constrained to potential lock the 'bioactive' conformation. Chapter Two illustrates in silico methods used to design a series of β-strand macrocycle 2.1-2.7. The analysis of these is performed using molecular modelling software Schrodinger suite (2005). A brief discussion of ring closing metathesis methodology is also included. Chapter Three describes the synthesis of the precursor required for RCM reactions (tripeptides dienes). Various types of allylated amino acid side chains were synthesised. The tripeptides were obtained using standard peptide coupling methodology utilising reagents such as HATU, EDC and HOAT. Chapter Four describes the application of ring closing metathesis for the synthesis of β-strand macrocycles. The development of a new reaction conditions to optimise the ring closing metathesis reaction is discussed. In particular the effect of the use of a Lewis acid (chlorodicyclohexylborane) additive in RCM reactions is investigated. Chapter Five discusses the mechanism of cataract formation, cataract treatment and the potential development of calpain inhibitors. One of the macrocycles synthesised in chapter 4 is elaborated into a calpain inhibitor. The in-vitro assay result of this is presented and this compound is currently undergoing in vivo evaluation.

Thesis (M. Sc.)--University of Canterbury, 2008. / Typescript (photocopy). Includes bibliographical references (leaves 124-131). Also available via the World Wide Web.

Thesis (Ph. D.)--Colorado State University, 2004. / Includes bibliographical references.

Thesis (M.S.)--State University of New York at Binghamton, Biological Sciences Department, 2005. / Includes bibliographical references.

Duchenne Muscular Dystrophy (DMD) is a severe X-linked progressive muscle wasting disease resulting from the absence of the membrane-associated protein dystrophin and the secondary components of the dystrophin-glycoprotein complex. Although the genetic basis of the disease has been known for over 15 years, the onset mechanism of the disease is not yet known and no treatment is yet available to significantly increase the lifespan of DMD patients. Increased levels of intracellular calcium have been noted in dystrophic muscle (Turner et al., 1991) and increased intracellular levels of calcium in skeletal muscle lead to increased levels of calcium-dependent proteolysis (Zeman et al., 1985). Increased levels of calpain, a calcium-dependent protease have been reported as early as age 4 weeks in mdx (dystrophin-deficient) mice (Spencer et al., 1995). Increased calpain activity has been demonstrated in mdx myotubes (Alderton et al., 2000a). There is also evidence of a role for calpain in DMD, but the contribution of calpain activity to the onset of DMD has not yet been determined. The purpose of this study was to test the hypothesis that increased calpain activity contributes to the onset of DMD in maturing (birth to weaning) dystrophic skeletal muscles and to determine if increased calpain activity was due to the relative distribution of calpain and calpastatin, calpain's endogenous inhibitor. Calpain activity was assessed in quadriceps and diaphragm muscle homogenate supernatant and pellet fractions from C57BL/6 control and mdx mice at ages 7, 14, and 21 days. Total calpain and calpastatin content were determined by Western analysis. In both the quadriceps and diaphragm samples, calpain activity in the supernatant increased with age. There was a significant increase (47.7%; p<0.05) in calciumdependent calpain activity in mdx quadriceps pellet compared to control at age 7 days. In the quadriceps at age 7 days, calpain activity in the pellet in the presence of calcium was significantly greater than at age 14 (61.2%) and 21 days (52.6%; p<0.05). In the diaphragm, there were no significant differences in pellet activity in either the presence or absence of calcium at any age between control and mdx samples. In both control and mdx diaphragms, pellet calpain activity in the absence compared with the presence of calcium was significantly greater at both age 7 (control, 46.4%; mdx, 45.4%) and 14 days (control, 42.4%; mdx, 43.6%; p<0.05). At age 21 days, both control and mdx calpain activities in the diaphragm supernatants in the presence of calcium were significantly greater than those at ages 7 (control, 66.7%; mdx, 72.1%) and 14 days (control, 39.9%; mdx 49.5%; p<0.05). In general, there were no differences in total calpain and calpastatin content that would account for the differences in calpain activity. There were similar patterns of calpain activity and total calpain and calpastatin content in both control and mdx samples, suggesting a similar pattern of development in control and mdx muscle from ages 7-21 days. The increase in calcium-dependent calpain activity in mdx quadriceps pellet compared to control at age 7 days may be due to differences in regulation and/or distribution of the calpain system early in mdx maturation compared to control. From the present study, the role of calpain in the onset of DMD appears to be minor if global calcium-dependent activity is evaluated. / Master of Science

Increased calcium-activated calpain proteolysis in the sarcolemma membrane is thought to be a primary mechanism in the pathophysiology of Duchenne Muscular Dystrophy (DMD). However, few studies have tested this possibility prior to the overt signs of the dystrophy. The purpose of this study was to test the hypothesis that there is greater calpain content and total relative calpain activity in membranes obtained from dystrophic (mdx; mdx:utrophin-deficient (mdx:utrn-/-)) compared to wildtype (wt) mouse skeletal muscles during maturation at ages 7- and 21-d,and at a post-maturation age of 35-d. Calpain activity was determined as the calcium-dependent cleavage of the flurogenic substrate SLY-AMC, and content was determined by Western analysis with an anti-calpain antibody. There were several intriguing findings: 1. There was an inverse relationship between calpain content and relative activity in the whole muscle in both wt and mdx mice from age 7- to 35-d: calpain content decreased, and relative calpain activity increased as the mice aged. This suggests a similar role for calpain in both genotypes, which might relate to specific maturation processes, possibly up to age 21-d. Although the inverse relation was evident at 35-d, the targets for calpain in mdx compared to wt likely differed. 2. The increased relative calpain activity in the membrane fraction of mdx mice at age 35-d (26.73 Arbitrary Units, (AU)) compared to that of age 7- (4.9AU; p<0.05) and 21-d (8.74AU; p<0.05) is temporally related to degeneration and regeneration processes, and may also indicate activation of apoptosis, in mdx muscles at this age. 3. At age 7-d, there were no significant differences in either calpain content or relative calpain activity in all subcellular fractions for wt and mdx mice. This result might suggest similar calpain distribution and activities that are related to the regulation of muscle maturation and differentiation in both genotypes. (Note:data were not obtained for the mdx:utrn-/- mice at age 7-d because of insufficient animals). 4. At age 21-d, there was greater relative calpain activity in the myofibrillar supernatant fraction in mdx (15.13AU) than wt mice (1.18AU; p<0.05). This could indicate calpain's role in the initiation of myofibrillar protein turnover and the proteolysis of submembranous networks in the mdx muscles. 5. At age 21-d, greater calpain content in the mdx (1.40ìg) compared to wt (0.23 ìg; p<0.05) membrane fraction might suggest a broader distribution of calpain along membranes that contributes to the onset of dystrophy in the mdx muscles. 6. At age 35-d, there was greater calpain content in the mdx:utrn-/- compared to the wt membrane (0.48ìg vs 0.13 ìg), cytosolic (0.88ìg vs 0.30ìg), and myofibrillar supernatant (0.49ìg vs 0.17ìg; p<0.05 ) fractions This increased content and broad distribution across several subcellular fractions may reflect degeneration and regeneration processes, and potentially activation of apoptosis, in the mdx:utrn-/- muscles. These data suggest that calpain activity contributes to dystrophic pathophysiology mainly in the membrane fraction of mdx skeletal muscles at age ~21-d, but appears to contribute later at 35-d and in more subcellular fractions in mdx:utrn-/- skeletal muscles. / Master of Science

Thesis (Ph. D.)--Medical College of Ohio, 2003. / "In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Medical Sciences." Major advisor: Ronald Mellgren. Includes abstract. Document formatted into pages: iv, 126 p. Title from title page of PDF document. Includes bibliographical references (p. 92-124).

Glioblastoma is the most malignant primary brain tumor with the average patients surviving only one year after diagnosis, even with aggressive therapy. The formation of numerous micro-tumors dispersed into the brain due to rapid invasion of tumor cells, presents the primary challenge to the surgical removal of tumors and limits the effectiveness of current treatments. This dissertation presents studies aimed at understanding the molecular mechanisms regulating invasion of human glioblastoma cells. Transplantation of human glioblastoma cells in the zebrafish brain showed that the knockdown of calpain 2, a calcium-activated protease, resulted in a three fold decrease in the tumor cell invasion. The result was further verified in the organotypic mouse brain slices where the knockdown cells demonstrated 2-fold decrease in the area of dispersal compared to control cells. Our data show that calpain 2 plays a role in the process of tumor cell angiogenesis. Glioblastoma cells were transplanted into the brain of zebrafish expressing GFP in the blood vessels and we observed that 23% of animals injected with control tumor cells demonstrated angiogenesis. In contrast, only 9% of fish that received calpain 2 knockdown cells showed the formation of new vessels. Consistent to the reports from human glioblastoma patients and rodent models, we did not observe metastasis of transplanted cells outside of the brain in the zebrafish, supporting for the use of zebrafish as an important model for glioblastoma cell invasion studies. These results provide evidence that calpain 2 protease activity is required for the dispersal of glioblastoma cells in the brain microenvironment. To determine the mechanism of calpain 2 regulation of tumor cell invasion, proteolysis of filamin by calpain 2 was studied. Filamin is an important actin cross-linking protein which develops orthogonal actin networks in the periphery of the cell. In this study, we show that the expression of filamin inhibits glioblastoma cell invasion. Hence, knocking down filamin expression by 80% resulted in 220% increase in the invasion of glioblastoma cells through Matrigel extracellular matrix. The regulated proteolysis of filamin is a potential mechanism to facilitate the cyclic turnover of actin orthogonal networks which is required for glioblastoma cell invasion. In this study, we identified a novel mechanism that the PI3 kinase activity regulates the cleavage of filamin by calpain 2 in glioblastoma cells. Binding of a membrane phospholipid phosphatidylinositol (3,4,5) triphosphate [PtdIns (3,4,5)-P₃] to filamin induces its proteolysis by calpain 2 after the amino acid lysine 268, removing the actin binding domain which in-turn abolishes the actin binding ability of filamin. / Graduation date: 2011 / Access restricted to the OSU Community at author's request from Jan. 31, 2011 - Jan. 31, 2012

This thesis reports the development of potent and selective inhibitors of m-calpain for the treatment of cataract. SJA6017 has been proven to prevent lens opacity in rat and has been our lead compound. A series of Val-Leu peptidyl aldehyde inhibitors (33a-e, 33g, 33i and 35) have been designed, synthesized, and tested for therapeutic potential as cataract inhibitors. Chapter 1 is an introduction to calpain and the diseases associated with it's over activation. A review of the literature on calpain inhibition is given. Structure activity relationship (SAR) theory is presented. The techniques that have been applied in our research group to drug design include molecular modeling, synthesis, assay and animal studies which are all briefly discussed. The importance of a -strand conformation for an inhibitor to bind to calpain is discussed. Chapter 2 describes the synthesis of m-calpain inhibitors. This comprises the preparation of the Val-Leu dipeptide core 29, Val-Leu dipeptidyl alcohols 31a-g and 31i, and the synthesis of dipeptidyl aldehydes 33a-e, 33g, 33i and 35. The choice of coupling regents and conditions in the coupling reactions is investigated. Sulfur trioxide pyridine oxidation for the conversion of Val-Leu dipeptidyl alcohols to aldehydes is discussed. The molecular modeling and biological assay results are presented.