Diss. (sammanfattning) Stockholm : Karol. inst., 2002. / Härtill 6 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 4 uppsatser.

Thesis (Ph.D.). / Written for the Institute of parasitology. Title from title page of PDF (viewed 2009/06/10). Includes bibliographical references.

Thesis (Ph. D.)--University of California, Riverside, 2009. / Includes abstract. Includes bibliographical references. Issued in print and online. Available via ProQuest Digital Dissertations.

Thesis (M.S.)--Mississippi State University. Department of Basic Sciences. / Title from title screen. Includes bibliographical references.

Thesis (Ph. D.)--Ohio State University, 2007. / Title from first page of PDF file. Includes bibliographical references (p. 201-220).

Thesis (Ph. D.)--University of Oregon, 2006. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 88-100). Also available for download via the World Wide Web; free to University of Oregon users.

Thesis (MSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Efavirenz is an antiretroviral drug used in the treatment of HIV-positive patients as part of first line triple-highly active antiretroviral therapy. Treatment response varies among individuals and adverse drug reactions tend to occur, as a result of the variation in the rate of efavirenz metabolism among individuals. This is partly caused by genetic variation; therefore the study of genes involved in the metabolism of efavirenz, such as CYP2B6, could potentially enhance treatment success. The effect of CYP2B6 SNP 516G>T (part of the CYP2B6*6 allele) is particularly important, as individuals homozygous for the minor allele of this SNP have significantly increased efavirenz levels. Furthermore, nuclear receptors, specifically constitutive androstane receptor, encoded by NR1I3, and pregnane X receptor, encoded by NR1I2, are involved in the regulation of the genes responsible for efavirenz metabolism and could therefore indirectly influence the pharmacokinetics of efavirenz. The current study identified variants in the NR1I3 and NR1I2 genes through in silico analysis, bi-directional sequencing and literature searches. A total of nine NR1I3 and ten NR1I2 target variants were subsequently genotyped in 132 HIV-positive female patients from the Xhosa and Cape Mixed Ancestry populations. The resulting genotype and allele frequencies were statistically analysed to search for correlations between genetic variations and available efavirenz levels in hair samples, treatment outcome as measured by viral load, and the occurrence of adverse drug reactions. The minor allele of a NR1I2 5’-upstream SNP, rs1523128 (6334A>G), was significantly associated with decreased efavirenz levels. From analysis of the effect of composite SNPs, NR1I3 5’-upstream SNP rs55802895 (258G>A) in conjunction with CYP2B6*6, was significantly associated with efavirenz-levels. It was found that the minor allele of rs55802895 inhibited the effect of CYP2B6*6, resulting in normal efavirenz levels for individuals homozygous for the minor allele of both SNPs. Additionally, when the target NR1I3 and NR1I2 variants were analysed in conjunction with six SNPs from CYP1A2, CYP2A6, CYP3A4 and CYP3A5, 11 compound genotypes were shown to be statistically associated with mean EFV plasma levels. The study emphasises the complexity of efavirenz metabolism, and the importance of transcriptional regulation in xenobiotic metabolism. / AFRIKAANSE OPSOMMING: Efavirenz is ‘n antiretrovirale middel wat gebruik word in die behandeling van HIV-positiewe pasiënte as deel van drievoudige hoogs-aktiewe antiretrovirale terapie. Reaksie op behandeling verskil tussen individue en nadelige newe-effekte, wat veroorsaak word deur die verskil in tempo waarteen efavirenz gemetaboliseer word, neig om voor te kom. Hierdie verskille word gedeeltelik veroorsaak deur genetiese variasie; dus kan die studie van gene betrokke by die metabolisme van efavirenz, soos CYP2B6, moontlik die sukses van behandeling verhoog. Die effek van CYP2B6 SNP 516G>T (deel van die CYP2B6*6-alleel) is veral belangrik, want individue wat homosigoties is vir die minderheids-alleel het betekenisvol hoë efavirenz-vlakke. Nukleêre reseptore, spesifiek konstitutiewe androstane reseptor, deur NR1I3 gekodeer, en pregnane X reseptor, deur NR1I2 gekodeer, is betrokke by die regulering van die gene verantwoordelik vir efavirenz-metabolisme en kan dus die farmakokinetika van efavirenz beïnvloed. Die huidige studie het variante in NR1I3 en NR1I2 identifiseer deur in silico-analise, bi-direksionele volgordebepaling en ’n literatuurstudie. Nege NR1I3 en tien NR1I2-variante in totaal is vervolglik gegenotipeer in 132 HIV-positiewe vroulike pasiënte van Xhosa en Kaapse Gemengde Afkoms populasies. Die gevolglike genotipe- en alleelfrekwensies is statisties geanaliseer om vir korrelasies tussen genetiese variasies en beskikbare efavirenz-vlakke in haarmonsters, uitkoms van behandeling gemeet in virale lading en die voorkoms van nadelige newe-effekte te soek. Daar is gevind dat die minderheids-alleel van ’n NR1I2 5’-stroomop SNP, rs1523128 (6334A>G), betekenisvol geassosieer is met ’n daling in efavirenz-vlakke. Vanuit die saamgestelde SNPs, is die NR1I3 5’-stroomop SNP rs55802895 (258G>A), tesame met CYP2B6*6, betekenisvol geassosieer met efavirenz-vlakke. Daar is gevind dat die minderheids-alleel van rs55802895 die effek van CYP2B6*6 demp, en gevolglik normale efavirenz-vlakke in individue homosigoties vir die minderheids-allele van albei SNPs veroorsaak. Addisioneel is die teiken NR1I3 en NR1I2 variante gemeenskaplik met ses SNPs van CYP1A2, CYP2A6, CYP3A4 en CYP3A5 geanaliseer en 11 gekombineerde genotipes is statisties geassosieer met gemiddelde EFV plasma vlakke. Hierdie studie beklemtoon die kompleksiteit van efavirenz-metabolisme en die belangrikheid van transkripsionele regulering in xenobiotiese metabolisme. / National Research Foundation (NRF)

Os receptores nucleares constituem uma superfamília de fatores de transcrição regulados pela interação com hormônios. Esta superfamília inclui, por exemplo, os receptores de hormônio tireoidiano, estrogênio, androgênio, glicocorticóide e mineralocorticóide. Neste trabalho, empregamos técnicas de biologia estrutura e bioinformática para estudar as interações entre alguns dos membros da família de receptores nucleares e seus respectivos ligantes. Para o receptor de hormônio tireoidiano, foi demonstrado, através da análise das estruturas cristalográficas das duas isoformas do receptor ligados aos tiromimético Triac, que os componentes entálpicos visíveis nas estruturas não explicam a seletividade do ligante. Dados de dinâmica molecular confirmaram que a seletividade do hormônio tem um importante componente entrópico. Empregando a técnica de dinâmica molecular, estudamos a ligação do receptor de mineralocorticóide humano à aldosterona, ao cortisol, à espironolactona e à cortisona e simulamos ainda o efeito da mutação S810L, conhecida por converter a atividade antagonista da cortisona e da espironolactona em agonista. A análise das simulações revelou um perfil de ligações de hidrogênio similar na ligação do receptor selvagem ao cortisol e à aldosterona. A cortisona perde, por conta da inserção de uma hidroxila na posição 11, uma ligação de hidrogênio importante com a Asn770 e, por isso, tem menor energia potencial de ligação. A espironolactona perde a mesma ligação de hidrogênio ao mesmo tempo em que aumenta o número de contatos de van der Waals pela inserção do grupo tioacetil na posição 7. A mutação S810L simulada no complexo com cortisona, cortisol e espironolactona não interfere no padrão de ligações de hidrogênio estabelecidas entre o receptor e os ligantes, mas altera a mobilidade de uma das regiões propostas como rota de dissociação. Propomos, portanto, que a mutação interfere na cinética de dissociação dos ligantes e não no padrão de interações estabelecidas no equilíbrio. Simulações de dissociação induzida do ligante confirmam esta proposição. Na última etapa, utilizamos os modelos experimentalmente determinados para o receptor ativado por proliferadores peroxissomais gama para a busca de novos ligantes através da técnica de docking molecular. Neste trabalho, utilizamos uma base de dados com aproximadamente um milhão de compostos. Destes, quatro foram selecionados após o docking molecular e testados experimentalmente. Um dos compostos testados se mostrou ativo neste receptor, apresentando uma atividade de 60-70% da atividade da rosiglitazona, conhecido agonista total do PPARg. / Nuclear receptors are a superfamily of hormone-regulated transcriptional factors. This superfamily includes, for example, the receptor for thyroid hormone, estrogen, androgen, gluco and mineralocorticoid. In this work, we used structural biology and bioinformatic tools to study the interactions between some members of the nuclear receptor superfamily and its respective ligands. We showed by the analysis of the crystal structures of both thyroid hormone receptor isoforms bound to the thyromimetic Triac that the enthalpic components visible in the structures do not explain the ligand selectivity. Molecular dynamics simulation data confirmed later that the hormone selectivity has an important entropic component. Using the molecular dynamics simulation, we studied, in a second stage, the interaction between the human mineralocorticoid receptor bound to aldosterone, cortisol, spironolactone and cortisone and also simulated the effects of the mutations S810L, known to convert the antagonist properties of spironolactone and cortisone in an agonist activity. The analysis of the simulations showed a similar profile in hydrogen bonds established between the wild type receptor bound to cortisol and aldosterone. Cortisone looses an important hydrogen bond with Asn770 because of the insertion of a carbonyl group in the 11 position and shows a decreased binding potential energy. Spironolactone loses the same interaction but has an increased number of van der Waals contacts because of the insertion of a tioacetyl group in the 7 position. The mutant S810L simulated in complex with cortisol, cortisone and spironolactone showed that the mutation do not interfere with the hydrogen bond profile established between the receptor and the ligands but changes the mobility of a region in the receptor previously proposed as a ligand dissociation route. Ligand unbinding simulations through steered molecular dynamics (SMD) confirm that aldosterone and cortisol unbind differentially and the mutation S810L alters the unbinding profile. We then propose that the mutation changes the kinetics of ligand association/dissociation without changing the profile of the interactions established in the equilibrium. In the last stage, we used the experimentally determined structural model of the peroxissome proliferator-activated receptor gamma to search for novel ligands using the molecular docking technique. For this work, we used a database containing about 1 million compounds. Among those, four compounds were selected after the docking computation and experimentally tested. One of these compounds was found to be active in the receptor, showing about 60-70% of the agonistic activity of rosiglitzone, a known PPARg total agonist.