Doctor of Philosophy / Department of Chemistry / Duy H. Hua / Three research projects are described in this dissertation and they consist of the discovery of norovirus protease inhibitors, modification of graphene oxides (GO) for the detection of norovirus, and design and fabrication of nanoelectronic device based on nanocarbon fibers for the detection of breast cancer proteases, legumain and cathepsin B. A novel class of tripeptidyl anti-noroviral compounds which strongly inhibit NV3CL[superscript]pro in enzyme and cell based assays was discovered. An example of one of the most active compounds is (1-{3-methyl-1-[2-oxo-1-(2-oxo-pyrrolidin-3-ylmethyl)-ethylcarbamoyl]-butylcarbamoyl}-2-naphthalen-1-yl-ethyl)-carbamic acid benzyl ester, which showed an IC₅₀ value of 0.14 ± 0.2 μM (enzyme assay) and EC₅₀ value of 0.04 ± 0.02 μM (cell based assay). This compound has an aldehyde warhead, a P1 glutamine surrogate, a P2 leucine, a P3 L-1-napthylalanine and an N-terminal carboxybenzyl cap. The corresponding bisulfite adduct, 2-[2-(2-benzyloxycarbonylamino-3-naphthalen-1-yl-propionylamino)-4-methyl-pentanoylamino]-1-hydroxy-3-(2-oxo-pyrrolidin-3-yl)-propane-1-sulfonic acid monosodium salt, has a comparable activity in enzyme and cell based assays (IC₅₀ 0.24 ± 0.1 μM; EC₅₀ 0.04 ± 0.03 μM). (1-{3-methyl-1-[2-oxo-1-(2-oxo-pyrrolidin-3-ylmethyl)-ethylcarbamoyl]-butylcarbamoyl}-2-naphthalen-1-yl-ethyl)-carbamic acid benzyl ester and its ketoamide derivative, (1-{1-[2-isopropylcarbamoyl-2-oxo-1-(2-oxo-pyrrolidin-3-ylmethyl)-ethylcarbamoyl]-3-methyl-butylcarbamoyl}-2-naphthalen-1-yl-ethyl)-carbamic acid benzyl ester, exhibited very good broad spectrum anti-viral activity, especially in human rhino virus and severe acute respiratory syndrome bioassays. We demonstrated that the surface of graphene oxide can be chemically modified with t-butylester and carboxylic acid functionalities. Fourier transform infrared spectroscopy, Raman spectroscopy and solid state nuclear magnetic resonance spectroscopy confirmed the presence of t-butylester and carboxylic acid functional groups. One sided oligonucleotide functionalized graphene oxide was synthesized using a solid state technique. A carboxylic acid functionalized graphene oxide was deposited onto the surface of electronic chips to bridge two gold electrodes, using a direct deposition technique. The carboxylic acid functionalized graphene oxide displayed semi-conductive properties and its use in an electronic biosensor device to detect noroviral RNA was investigated. Novel redox-active protease substrate peptides H₂N-(CH₂)₄CO-Ala-Ala-Asn-Leu-NHCH₂-ferrocene and H₂N-(CH₂)₄CO-Leu-Arg-Phe-Gly-NHCH₂-ferrocene were synthesized successfully and used in an alternating current voltammetry technique to facilitate the detection of the cancer related protease enzymes legumain and cathepsin B. After attachment of these peptides to the tips of carbon nanofiber nanoelectrode arrays, the presence of active protease enzymes could be detected as manifest by an exponential decay in current signal detect when monitored by alternating current voltammetry, at initial enzyme concentrations of 80.1 nM (legumain) and 30.7 nM (cathepsin B). The peptide cleavage sites were confirmed by analyses of the cleaved fragments using high performance liquid chromatography and mass spectrometry. Results showed that the cleavage of H₂N-(CH₂)₄CO-Ala-Ala-Asn-Leu-NHCH₂-ferrocene at the C-terminal side of asparagine residues by legumain and cleavage of H₂N-(CH₂)₄CO-Leu-Arg-Phe-Gly-NHCH₂-ferrocene at the C-terminal side of arginine residues by cathepsin B. Legumain exhibited a specificity constant (k[subscript]cat/K[subscript]m) of 11.3 x 10ᶟ M⁻¹S⁻¹ while cathepsin B exhibited a higher value of specificity constant (4.3 x 10⁴ M⁻¹S⁻¹) which agreed with the values obtained from fluorescence enzyme assay.

ABSTRACT PURIFICATION AND CHARACTERIZATION OF CYTOPLASMIC AND PROTEASOME ASSOCIATED CHYMOTRYPSIN-LIKE PROTEASES FROM THERMOPLASMA VOLCANIUM &Ouml / zdemir, F.inci Ph.D., Department of Biology Supervisor: Prof. Dr. Semra Kocabiyik September, 147 pages In this study, two novel cytoplasmic serine proteases were isolated and characterized from thermophilic archaea Thermoplasma volcanium. The first protease was purified by ion exchange and affinity chromatographies and identified as a chymotrypsin-like serine protease mainly based on its substrate profile and inhibition pattern. The presence of protease activity was analyzed by gelatin zymography which was detected as a single band (35 kDa). Optimum temperature was found to be 60oC for azocasein hydrolysis and 50oC for N-Suc-Phe-pNA hydrolysis. Optimum activity was observed in the pH range of 6.0-8.0 with a maximum value at pH 7.0. The Km and Vmax values for the purified protease were calculated to be 2.2 mM and 40 &micro / moles of p-nitroanilide released min-1.ml-1, respectively, for N-Suc-Phe-PNA as substrate. Ca2+ and Mg2+ at 4 mM concentrations were the most effective divalent cations in activating the enzyme. In the second stage of this study, 20S proteasome of Tp. volcanium with substantial chymotrypsin-like activity was purified and characterized. This enzyme complex was purified with 19.1 U/mg specific activities from cell free extract by a four-step procedure. SDS-PAGE analysis revealed two strong bands with relative molecular masses of 26 kDa (&amp / #945 / -subunit) and 21.9 kDa (&amp / #946 / -subunit). Tp. volcanium 20S proteasome predominantly catalyzed cleavage of peptide bonds carboxyl to the acidic residue Glu (postglutamyl activity) and the hydrophobic residue Phe (chymotrypsin-like activity) in short chromogenic peptides. Low-level hydrolyzing activity was also detected carboxyl to basic residue Arg (trypsin-like activity). Chymotrypsin-like activity of Tp. volcanium 20S proteasome was significantly inhibited by chymotrypsin specific serine protease inhibitor chymostatin. When N-CBZ-Arg was used which is a substrate for trypsin, 20S proteasome was strongly inhibited by TLCK. The optimum temperature for Ala-Ala-Phe-pNA hydrolysis by the Tp. volcanium 20S proteasome was 55oC and the optimum pH was 7.5. The chymotryptic activity was significantly enhanced by divalent cations such as Ca+2 and Mg2+ at high concentrations, i.e. 125-250 mM. Keywords:Serine protease, 20S proteasome, archaea, thermophilic protease, Thermoplasma volcanium, chymotrypsin-like serine protease.

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Human tissue kallikrein-related peptidases (KLK) are fifteen genes located on chromosome 19q13.4, encoding hormonally regulated, secreted serine proteases with trypsin/chymotrypsin-like activity. I identified expression of many KLKs in tissues throughout the female reproductive system and in cervico-vaginal fluid (CVF). The female reproductive system is hormonally regulated during the menstrual cycle, suggesting KLKs may also be regulated by these hormones. Measurement of KLKs levels in CVF and saliva samples throughout the menstrual cycle revealed a peak in expression following ovulation in both fluids. Progesterone levels rise during this period suggesting KLK regulation by progesterone during the menstrual cycle. Using proteomic techniques, I resolved the CVF proteome to identify potential KLK substrates. Among 685 proteins identified, several cell-cell adhesion molecules, cervical mucins and defense-related proteins were found. KLKs play a role in the desquamation of skin corneocytes through cleavage of cell-cell adhesion proteins. The vaginal epithelium undergoes cyclical changes during the menstrual cycle involving desquamation of cells upon rising progesterone levels. The post-ovulatory peak in KLK expression suggests that KLKs may contribute to cell desquamation during the menstrual cycle. Cervical mucus acts to block the uterus from vaginal microorganisms. Around ovulation, cervical mucus loses viscosity to facilitate sperm passage through the cervix. Proteolytic enzymes are thought to aid in this mucus remodelling. Our immunohistochemical studies localized KLK expression to the mucus secreting cervical epithelium and I investigated KLK processing of cervical mucin proteins in vitro. KLKs 5 and 12 were found to cleave mucins, suggesting their potential involvement in cervical mucus remodelling. CVF plays a role in host defense. KLKs are known to process the antimicrobial cathelicidin protein in skin and I investigated whether KLKs may also process antimicrobial proteins found in CVF. KLK5 was found to cleave defensin-1 alpha, in vitro, suggesting KLKs may aid in defense of the female reproductive system. Here I provide evidence of potential physiological roles for KLKs in the female reproductive system: in desquamation of vaginal epithelial cells, remodelling of cervical mucus and processing of antimicrobial proteins. These findings suggest KLKs may function in female fertility, in pathological conditions such as vaginitis and in host defense.