Thesis (Ph. D.)--West Virginia University, 1999. / Title from document title page. Document formatted into pages; contains vi, 119 p. : ill. Vita. Includes abstract. Includes bibliographical references.

Thesis (Ph. D.)--West Virginia University, 2004. / Title from document title page. Document formatted into pages; contains ix, 174 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 166-170).

Thesis (Ph. D.)--School of Pharmacy and Dept. of Chemistry. University of Missouri--Kansas City, 2005. / "A dissertation in pharmaceutical sciences and chemistry." Advisor: Simon H. Friedman. Typescript. Vita. Description based on contents viewed June 23, 2006; title from "catalog record" of the print edition. Includes bibliographical references (leaves 327-353). Online version of the print edition.

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Since its discovery in the 1980’s, HIV has affected the lives of millions of individuals around the globe. Despite obvious need and an enormous amount of research a cure has remained elusive due to the rapid onset of mutated forms of the virus. However, there has been considerable success in reducing viral levels of infected individuals through the use of highly active antiretroviral therapy (HAART). The first-line regimen HAART mainly targets reverse transcriptase (RT) through the employment of two nucleoside RT inhibitors (NRTIs) and a nonnucleoside RT inhibitor (NNRTI). NNRTIs target an allosteric pocket situated about 10 Å from the catalytic site and cause a conformational change in the enzyme upon binding, leading to the inhibition of viral replication. There are currently 5 FDA approved NNRTIs on the market which successfully inhibit viral replication, but the use of these drugs is becoming limited due to the onset of drug resistant strains of the virus. In light of this need for the development of novel NNRTIs, we set out to explore new territory in NNRTI drug design with a goal of maintaining efficacy in the presence of both wild-type and mutated forms of HIV-1. To this end we designed three different NNRTI scaffolds along three different research thrusts. The first of these focused on the synthesis of 15 novel flexible triazole containing compounds. With these compounds we sought to achieve π-π stacking interactions with conserved amino acid residue Trp229 in the hope that we would be able to maintain efficacy in the presence of mutated forms of the virus. An additional feature included hydrogen bonding interactions to the backbone of Lys103. However, despite having thoroughly explored the triazole ring with multiple substitution arrangements, these compounds had very poor to no activity against whole cell HIV-1. Secondly we focused on the synthesis of a 4-hydroxyindole scaffold as a potential NNRTI. The focus here was to achieve interactions to Trp229 and simultaneously achieve hydrogen bonding interactions to the backbone of Lys101 at the entrance of the pocket. This was a novel concept in this class of compounds. We were able to successfully synthesize the indole core as a proofof-concept using the Knoevenagel-Hemetsberger method however; this compound had no activity against HIV-1. Lastly, in our quest to synthesize a novel NNRTI that could maintain efficacy against HIV-1 we decided to attempt to improve upon the stability of a lead indole-based compound synthesized previously within our research group. The lead compound was found to be potent with an IC50 of 1 nM but was unstable in acidic media due to the presence of a methoxy functionality situated at the 3-position on the indole. We sought to overcome this issue by introducing a substituted aryl amine functionality at this position. We were successful in synthesizing our desired compound but unfortunately it was significantly less active against whole cell HIV-1 than the lead compound. However, we were not completely deterred as there are a number of unexplored bioiososteres as possibilities to improve upon the stability of the lead compound while maintaining its excellent activity profile. / AFRIKAANSE OPSOMMING: Sedert die ontdekking van die menslike immuniteitsvirus (MIV) in die 1980’s, het die virus al die lewens van miljoene mense wêreldwyd geaffekteer. Ten spyte van die ooglopende behoefte aan ‘n geneesmiddel sowel as meer navorsing, bly ‘n keermiddel sover onbekombaar as gevolg van die verskillende mutasies wat binne die virus gebeur. Ten spyte hiervan, was daar al heelwat sukses in terme van ‘n verlaging van die virale vlakke in besmette individue deur die gebruik van hoogsaktiewe antiretrovirale terapie (HAART). As ‘n eerste behandeling, teiken HAART meestal trutranskriptase (RT) deur die inspanning van twee nukleosied trutranskriptase inhibeerders (NRTIs) en ‘n nie-nukleosied trutranskriptase inhibeerder (NNRTI). NNRTIs teiken ‘n allosteriese leemte wat ongeveer 10 Å weg van die katalitiese posisie is en veroorsaak dan ‘n konformasie verandering in die ensiem tydens die bindingsproses, wat dan lei tot die inhibisie van die virus se replikasie. Daar is tans 5 FDA goedgekeurde NNRTIs op die mark wat virale replikasie inhibeer, maar die gebruik van hierdie middels word alhoemeer belemmer as gevolg van die onwikkeling van weerstandige stamme van die virus. Met die oog op hierdie nood aan die ontwikkeling van nuwe NNRTIs, het ons gepoog om new gebiede te ondersoek in terme van die ontwerp van NNRTIs, met die doel om die effektiwiteit teen beide die wilde-tipe sowel as die gemuteerde vorme van HIV-1 te behou. Vir hierdie doeleindes het ons drie verskillende NNRTI steiers ontwerp, wat drie navorsingsdoeleindes na streef. Die eerste van hierdie doeleindes was die sintese van 15 nuwe buigsame triasool-bevattende middels. Met hierdie middels het on gepoog om π-π pakkingsinteraksies te behaal met aminosuur residu, Trp229, en sodoende die effektiwiteit van die NNRTIs in die gemuteerde vorm van die virus te behou. ‘n Additionele eienskap wat bygevoeg is, is ‘n waterstofbindingsinteraksie met die ruggraat van Lys103. Ten spyte van pogings om verskeie substitusie patrone om die triasool-ring te ondersoek, het hierdie middels baie swak tot geen aktiwiteit teen heel sel HIV-1 getoon nie. Tweedens, was die fokus op die sintese van ‘n 4-hidroksieindool steier as ‘n potensiele NNRTI. Die fokus hier was om ‘n interaksie met Trp229 te kry terselfdetyd as ‘n waterstofbindingsinteraksie met die ruggraat van Lys101, wat by die opening van die bindingssak is. Hierdie was ‘n nuwe konsep vir hierdie klas van middele. Ons het die indool-kern van hierdie molekules suksesvol gesintetiseer deur middel van ‘n Knoevenagel-Hemetsberger metode, maar ongelukkig het hulle geen aktiwiteit teen HIV-1 getoon nie. Laastens het ons gepoog om ‘n nuwe NNRTI te sintetiseer wat effiktiwiteit teen HIV-1 behou, deur te probeer om vorderings te maak op die stabiliteit van ‘n indool-gebaseerde hoof-middel wat al voorheen deur ons navorsingsgroep geraporteer is. Hierdie hoof-middel het ‘n IC50 waarde van 1 nM gelewer, maar was onstabiel in suur medium as gevolg van die teenwoordigheid van ‘n metoksie-groep in die 3-posisie van die indool. Ons het gepoog om hierdie probleem te oorkom deur ‘n gesubtitueerde arielamien in hierdie posisie te plaas. Ons was suksesvol hierin, maar ongelukkig was die middel heelwat minder aktief teen die heel sel HIV-1 as die metoksie-weergawe. Ten spyte hiervan, is ons optimisties dat ons hierdie probleem kan oorkom, aangesien daar verskeie bioisostere is wat die stabilitiet van middel kan verbeter terwyl dit moontlik die effektiwiteit kan behou.

Group II introns are a class of mobile ribozymes found in bacteria and eukaryotic organelles that self-splice from precursor RNAs. The resulting lariat intron RNA can then insert into new genomic DNA sites through a reverse splicing reaction. Collectively, this process of intron mobility is termed “retrohoming.” Mobile group II introns encode a reverse transcriptase (RT) that stabilizes the catalytically active form of the intron RNA for both the forward and reverse splicing reactions and also converts the integrated intron RNA into DNA. This work aims to elucidate the structure of bacterial group II intron-encoded RTs and ultimately determine how they function in intron mobility. Although efforts to crystallize group II introns RTs have been unsuccessful, small angle X-ray scattering studies in conjunction with homology modeling have provided new insights into the structure and function of these enzymes. / text

The Lactococcus lactis Ll.LtrB group II intron encodes a reverse transcriptase (LtrA protein), which binds the intron RNA to promote RNA splicing and intron mobility. Mobility occurs by intron RNA reverse splicing directly into a DNA strand and reverse transcription by LtrA. I used LtrA-GFP fusions and immunofluorescence microscopy to show that LtrA localizes to the cellular poles in both Escherichia coli and L. lactis. This polar localization occurs with or without co-expression of the intron RNA, is observed over a wide range of cellular growth rates and expression levels, and is independent of replication origin function. The same localization pattern was found for three non-overlapping LtrA subsegments, reflecting dependence on common redundant signals and/or protein physiochemical properties. When coexpressed in E. coli, LtrA interferes with the polar localization of the Shigella IcsA protein, which mediates polarized actin tail assembly, suggesting competition for a common localization determinant. In E. coli, the Ll.LtrB intron inserts preferentially into the chromosomal ori and ter regions, which are pole localized during much of the cell cycle. Thus, the polar localization of LtrA could account for the preferential insertion of the Ll.LtrB intron in these regions. I established a high throughput method using cellular array and automated fluorescence microscopy for screening transposon-induced mutants, and identified five E. coli genes (gppA, uhpT, wcaK, ynbC, and zntR) in which disruptions result in increased proportion of cells having diffuse LtrA distribution. This altered localization is correlated with a more uniform distribution of Ll.LtrB insertion sites throughout the E. coli genome. Finally, I find that altered LtrA localization in all five disruptants is correlated with accumulation and more diffuse intracellular distribution of polyphosphate, and that a ppx disruptant, which also results in polyphosphate accumulation, shows similar LtrA mislocalization. These findings may reflect interaction between LtrA and intracellular polyphosphate. My findings support the hypothesis that the intracellular localization of LtrA is a major determinant of Ll.LtrB insertion site preference in the E. coli genome. Further, they show that alterations in polyphosphate metabolism can lead to protein mislocalization, and suggest that polyphosphate is an important factor affecting intracellular protein localization.

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Diss. (sammanfattning) Stockholm : Karol. inst. / Härtill 6 uppsatser.

Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisor: Andrew D. Ellington. Vita. Includes bibliographical references.