UMD Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/3
New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a given thesis/dissertation in DRUM.
More information is available at Theses and Dissertations at University of Maryland Libraries.
Browse
3 results
Search Results
Item DISCOVERY OF A POTENT AND SELECTIVE RIOK1 INHIBITOR ACTIVE IN CRC CELL LINES USING STRUCTURE-BASED DRUG DESIGN(2021) Kim, Minkyung; LaRonde, Nicole; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Colorectal cancer (CRC) is the second leading cause of cancer-related death in the United State. CRC has aggressive malignancy characterized by poor prognosis and its metastasis and recurrence is the cancer stem cell driven. Homo sapiens RIOK1 (hsRIOK1 also known as RIOK1) is an atypical protein kinase which is an essential ribosome biogenesis factor, and it supports cancer cellular proliferation via its critical role in ribosome biogenesis and through stimulation of RAS signaling. The Inhibition of RIOK1 activity represents an opportunity to target CRC. So far, several RIOK1 inhibitors have been reported but none of them are active in any cancer cell line. Toyocamycin, 7-cyano-7-deazaadenosine, is the first RIOK1 inhibitor reported with high binding affinity of 40nM. The lead molecule toyocamycin had to be optimized because of its high toxicity to normal cells and low selectivity from targeting three other kinases. Based on two X-ray crystal structures of afRio1-toyocamycin complex and RIOK1(143-494)-ADP-Mg2+ complex having pAsp, toyocamycin analogs with different alkyl groups on C5’ position were designed and virtually screened in the RIOK1 crystal structure. Considering their physicochemical property calculations, a series of toyocamycin and adenosine analogs were synthesized and tested to see their binding affinities to the drug target. In the virtual screening, two major interactions were observed in the hit molecules: pi-pi interaction with PHE328 and hydrogen bond interaction with ASP341. TSA binding assay demonstrated the hydrogen bond might be a critical interaction to increase the RIOK1-drug binding. These small molecule inhibitors were tested in CRC cell/stem cell lines to study their inhibition efficacy and showed their potency with nano molar to single digit micro molar IC50 values in the cancer cell inhibition, reporting the first cell-active RIOK1 inhibitors. These compounds were tested alone or in the presence of MTA to see the effect of a combinatory inhibition against RIOK1 and its binding partner PRMT5 activities on CRC tumorigenesis. As a result, the co-targeting two oncogenic enzymes sensitized CRC cell/stem cell responses to the inhibitors and in the treatment of the compounds, RIOK1 and PRMT5 binding was promoted in their pull-down assay.Item Intercepting Cyclic Dinucleotide Signaling with Small Molecules(2016) Zheng, Yue; Sintim, Herman O; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Bacterial infections, especially the ones that are caused by multidrug-resistant strains, are becoming increasingly difficult to treat and put enormous stress on healthcare systems. Recently President Obama announced a new initiative to combat the growing problem of antibiotic resistance. New types of antibiotic drugs are always in need to catch up with the rapid speed of bacterial drug-resistance acquisition. Bacterial second messengers, cyclic dinucleotides, play important roles in signal transduction and therefore are currently generating great buzz in the microbiology community because it is believed that small molecules that inhibit cyclic dinucleotide signaling could become next-generation antibacterial agents. The first identified cyclic dinucleotide, c-di-GMP, has now been shown to regulate a large number of processes, such as virulence, biofilm formation, cell cycle, quorum sensing, etc. Recently, another cyclic dinucleotide, c-di-AMP, has emerged as a regulator of key processes in Gram-positive and mycobacteria. C-di-AMP is now known to regulate DNA damage sensing, fatty acid synthesis, potassium ion transport, cell wall homeostasis and host type I interferon response induction. Due to the central roles that cyclic dinucleotides play in bacteria, we are interested in small molecules that intercept cyclic dinucleotide signaling with the hope that these molecules would help us learn more details about cyclic dinucleotide signaling or could be used to inhibit bacterial viability or virulence. This dissertation documents the development of several small molecule inhibitors of a cyclic dinucleotide synthase (DisA from B. subtilis) and phosphodiesterases (RocR from P. aeruginosa and CdnP from M. tuberculosis). We also demonstrate that an inhibitor of RocR PDE can inhibit bacterial swarming motility, which is a virulence factor.Item Mitochondrial outer membrane permeability to metabolites influences the onset of apoptosis(2007-05-08) Tan, Wenzhi; Colombini, Marco; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Apoptosis is a process in multicellular organisms to signal and induce death of specific cells, while avoiding inflammatory reactions. It is an important way to recycle the materials of unwanted cells and maintain cell balance. The execution phase of apoptosis can be initiated by proteins released from mitochondria (such as cytochrome c). Results reported here are consistent with this release being influenced by changes in the mitochondrial outer membrane permeability to metabolites. Phosphorothioate oligonucleotides induce cell death and block VDAC, a protein in the mitochondrial outer membrane that facilitates metabolite flow. These properties seem to be linked in that both require the phosphorothioate modification, both are enhanced by an increase in oligonucleotide length, and both are insensitive to nucleotide sequence. VDAC reconstituted into planar phospholipid membranes is blocked by phosphorothioate oligonucleotides with a 1:1 stoichiometry. They block the pore of the channel through interacting with the inner wall of the pore. The rate of binding occurs at a 100 μs scale but the binding is usually unstable. However, some conformational change stabilizes the complex resulting in long-term complete blockage of VDAC. In mitochondria, this blockage interferes with metabolite flow and inhibits the respiration of mitochondria. It is very specific for VDAC at sub-micromolar concentrations of phosphorothioate oligonucleotide and under these conditions there is minimal effect on enzymatic processes in the mitochondrial inner membrane. The ability of PorB from Neisseria meningitidis to inhibit apoptosis by moving to the mitochondrial outer membrane, was investigated in light of VDAC's role in apoptosis. PorB is unable to alter VDAC's gating properties but does allow ATP to cross membranes. Thus it may restore metabolite flux when VDAC channels close early in apoptosis. Attempts to test this in yeast were not successful. VDAC gating influences transmembrane Ca2+ flux. The closed states favor calcium permeation and the open state limits calcium flux. In mitochondria this gating could influence the rate of Ca2+-dependent mitochondrial swelling and subsequent cytochrome c release. Thus, the mitochondrial outer membrane permeability regulated by VDAC gating may play an important role in mitochondrial function and control of apoptosis.