For survival and successful propagation, every organism has to maintain the genomic integrity of the cell. The information content, in the form of nucleotide bases, is constantly threatened by endogenous agents and environmental pollutants. In particular, pathogenic mycobacteria are constantly exposed to DNA-damaging assaults such as reactive oxygen species (ROS) and reactive nitrogen intermediate (RNI), in their habitat which is inside host macrophage. In addition, the genome of Mycobacterium tuberculosis makes it more susceptible for guanine oxidation and cytosine deamination as it is G-C rich. Therefore DNA repair mechanisms are extremely important for the mycobacterium. An important enzyme involved in DNA repair is uracil-DNA glycosylase (Ung). To access the genomic information, during repair as well as DNA replication and recombination, dsDNA must unwind to form single stranded (ss) intermediates. ssDNA is more prone to chemical and nuclease attacks that can produce breaks or lesions and can also inappropriately self associate. In order to preserve ssDNA intermediates, cells have evolved a specialized class of ssDNA-binding proteins (SSB) that associate with ssDNA with high affinity. As part of a major programme on mycobacterial proteins in this laboratory, structural studies on mycobacterial uracil-DNA glycosylase (Ung) and single-stranded DNA binding protein (SSB) have been carried out. The structures were solved using the well-established techniques of protein X-ray crystallography. The hanging drop vapour diffusion and microbatch methods were used for crystallization in all cases. X-ray intensity data were collected on a MAR Research imaging plate mounted on a Rigaku RU200 X-ray generator. The data were processed using the HKL program suite. The structures were solved by the molecular replacement method using the program PHASER and AMoRe. Structure refinements were carried out using the programs CNS and REFMAC. Model building was carried out using COOT. PROCHECK, ALIGN, INSIGHT and NACCESS were used for structure validation and analysis of the refined structures. MD simulations were performed using the software package GROMACS v 3.3.1. Uracil-DNA glycosylase (UNG), a repair enzyme involved in the excision of uracil from DNA, from mycobacteria differs from UNGs from other sources, particularly in the sequence in the catalytically important loops. The structure of the enzyme from Mycobacterium tuberculosis (MtUng) in complex with a proteinaceous inhibitor (Ugi) has been determined by X-ray analysis of a crystal containing seven crystallographically independent copies of the complex. This structure provides the first geometric characterization of a mycobacterial UNG. A comparison of the structure with those of other UNG proteins of known structure shows that a central core region of the molecule is relatively invariant in structure and sequence, while the N- and C-terminal tails exhibit high variability. The tails are probably important in folding and stability. The mycobacterial enzyme exhibits differences in UNG-Ugi interactions compared with those involving UNG from other sources. The MtUng-DNA complex modelled on the basis of the known structure of the complex involving the human enzyme indicates a domain closure in the enzyme when binding to DNA. The binding involves a larger burial of surface area than is observed in binding by human UNG. The DNA-binding site of MtUng is characterized by the presence of a higher proportion of arginyl residues than is found in the binding site of any other UNG of known structure. In addition to the electrostatic effects produced by the arginyl residues, the hydrogen bonds in which they are involved compensate for the loss of some interactions arising from changes in amino-acid residues, particularly in the catalytic loops. The results arising from the present investigation represent unique features of the structure and interaction of mycobacterial Ungs. To gain further insights, the structure of Mycobacterium tuberculosis Ung (MtUng) in its free form was also determined. Comparison with appropriate structures indicate that the two domain enzyme slightly closes up when binding to DNA while it slightly opens up when binding to its proteinaceous inhibitor Ugi. The structural changes on complexation in the catalytic loops reflect the special features of their structure in the mycobacterial protein. A comparative analysis of available sequences of the enzyme from different sources indicates high conservation of amino acid residues in the catalytic loops. The uracil binding pocket in the structure is occupied by a citrate ion. The interactions of the citrate ion with the protein mimic those of uracil in addition to providing insights into other possible interactions that inhibitors could be involved in. SSB is an essential accessory protein required during DNA replication, repair and recombination, and various other DNA transactions. Eubacteral single stranded DNA binding (SSB) proteins constitute an extensively studied family of proteins. The variability in the quaternary association in these tetrameric proteins was first demonstrated through the X-ray analysis of the crystal structure of Mycobacterium tuberculosis SSB (MtSSB) and Mycobacterium smegmatis (MsSSB) in this laboratory. Subsequent studies on these proteins elsewhere have further explored this variability, but attention was solely concentrated on the variability in the relative orientation of the two dimers that constitute the tetramer. Furthermore, the effect of this variability on the properties of the tetrameric molecule was not adequately addressed. In order to further explore this variability and strengthen structural information on mycobacterial SSBs in particular, and on SSB proteins in general, the crystal structures of two forms of Mycobacterium leprae single stranded DNA-binding protein (MlSSB) has been determined. Comparison of the structures with other eubacterial SSB structures indicates considerable variation in their quaternary association although the DNA binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but it appears to correlate well with variation in protein stability. Molecular dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype E. coli SSB and the individual subunits of both the proteins. The X-ray studies and molecular dynamics simulations together yield information on the relatively rigid and flexible regions of the molecule and the effect of oligomerization on flexibility. The simulations provide insights into the changes in the subunit structure on oligomerization. They also provide insights into the stability and time evolution of the hydrogen bonds/water-bridges that connect two pairs of monomers in the tetramer. In continuation of our effort to understand structure-function relationships of mycobacterial SSBs, the structure of MsSSB complexed with a 31-mer polydeoxy-cytidine single stranded DNA (ssDNA) was determined. The mode of ssDNA binding in the MsSSB is different from the modes in the known structures of similar complexes of the proteins from E. coli (EcSSB) and Helicobacter pylori (HpSSB). The modes in the EcSSB and HpSSB also exhibit considerable differences between them. A comparison of the three structures reveals the promiscuity of DNA-binding to SSBs from different species in terms of symmetry and the path followed by the bound DNA chain. It also reveals commonalities within the diversity. The regions of the protein molecule involved in DNA-binding and the nature of the residues which interact with the DNA, exhibit substantial similarities. The regions which exhibit similarities are on the central core of the subunit which is unaffected by tetramerisation. The variable features of DNA binding are associated with the periphery of the subunit, which is involved in oligomerization. Thus, there is some correlation between variability in DNA-binding and the known variability in tetrameric association in SSBs. In addition to the work on Ung and SSB, the author was involved in X-ray studies on crystals of horse methemoglobin at different levels of hydration, which is described in the Appendix of the thesis. The crystal structure of high-salt horse methaemoglobin has been determined at environmental relative humidities (r.h.) of 88, 79, 75 and 66%. The molecule is in the R state in the native and the r.h. 88% crystals. At r.h.79% the molecule appears to move towards the R2 state. The crystal structure at r.h.66% is similar, but not identical, to that at r.h.75%. Thus variation in hydration leads to variation in the quaternary structure. Furthermore, partial dehydration appears to shift the structure from the R state to the R2 state. This observation is in agreement with the earlier conclusion that the changes in protein structure that accompany partial dehydration are similar to those that occur during protein action. A part of the work presented in the thesis has been reported in the following publications. 1. Singh, P., Talawar, R.K., Krishna, P.D., Varshney, U. & Vijayan, M. (2006). Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor. Acta Crystallogr. F62, 1231-1234. 2. Kaushal, P.S., Talawar, R.K., Krishna, P.D., Varshney, U. & Vijayan, M. (2008). Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources. Acta Crystallogr. D64, 551-560. 3. Kaushal, P.S., Sankaranarayanan, R. & Vijayan, M. (2008). Water-mediated variability in the structure of relaxed-state haemoglobin. Acta Crystallogr. F64, 463-469.

No description available.

Base teórica: As fluoropirimidinas possuem significativa variabilidade na resposta terapêutica e na ocorrência de toxicidade, o que tem sido relacionado à deficiência na depuração metabólica mediada pela enzima diidropirimidina desidrogenase (DPD). Mutações nos genes codificadores da enzima, bem como fatores ambientais podem levar à baixa ou nula expressão enzimática, provocando efeitos adversos graves devido ao acúmulo destes fármacos. Até o presente, nenhum teste reconhecidamente valido para a identificação de indivíduos em risco de toxicidade severa está estabelecido na prática oncológica. A genotipagem para o gene DPYD apresenta poder preditivo limitado, pois é capaz de rastrear somente as mutações já conhecidas, que apresentam baixa frequência populacional. Por esta razão, ensaios funcionais baseados na avaliação da redução fisiológica do uracil (U) para diidrouracil (UH2), igualmente medidada pela DPD, têm sido propostos na identificação de pacientes predispostos à toxicidade. Nesta abordagem são estimadas as razões plasmáticas [UH2]/[U] em níveis basais ou após uma dose oral do U. Recentemente, foi sugerida a realização do teste funcional em saliva como amostra alternativa ao plasma, com maior estabilidade dos analitos. Entretanto, a associação entre as razões metabólicas nesta matriz e a toxicidade não foi validada em amostras clínicas. Objetivos: Avaliar a efetividade dos métodos de determinação da razão metabólica [UH2]/[U] em plasma e saliva e a genotipagem para o gene DPYD como preditores de toxicidade por fluoropirimidinas em pacientes com neoplasias gastrointestinais. Adicionalmente, o trabalho propôs o desenvolvimento de um método bioanalítico para a determinação de U e UH2 por cromatografia líquida de alta eficiência. Métodos: Foram obtidas amostras pareadas de plasma e saliva de 60 pacientes diagnosticados com neoplasia gastrointestinal e com indicação de tratamento com fluoropirimidinas. As concentrações de U e UH2 foram determinadas nas duas matrizes através de LC-MS/MS. Os efeitos adversos do primeiro ciclo de quimioterapia foram classificados de acordo com o NCI-CTCAE versão 4. A genotipagem da DYDP foi realizada por PCR tempo real e incluiu os alelos *2A; *13, Y186C; I560S, *7 Y186C. Resultados: 35% dos pacientes apresentaram toxicidade severa (graus 3/4), sendo a neutropenia a mais frequente (n=11). A genotipagem da DYDP não foi capaz de identificar pacientes em risco de toxicidade, uma vez que não foram encontrados portadores de alelos variáveis. As razões [UH2]/[U] variaram amplamente entre os pacientes, de 0,09 a 26,73 no plasma e de 0,08 a 24 na saliva. As razões [UH2]/[U] no plasma e na saliva demonstraram correlação elevada (rs=-0,575; P<0,01), porém, a saliva demonstrou maior correlação com o grau de toxicidade quando comparada ao plasma (rs=-0,515; P<0,01 vs rs=-0,282 P<0,05). Pacientes com grau de toxicidade 3/4 (n=21) apresentaram menor razão metabólica em comparação a pacientes com grau 1/2 (n=26) ou com ausência de toxicidade (n=13) (média 0.59 vs 2.22 e 2.83 no plasma e 1.62 vs 6.88 e 6.75 na saliva, P<0.01). A partir de curva ROC foi determinado o valor de corte de 1,16 para a razão em saliva com 86% de sensibilidade e 77% de especificidade para a identificação de pacientes com toxicidade severa. Nas amostras de plasma o valor de corte foi 4.0 com 71% de sensibilidade e 76% de especificidade. Adicionalmente, foi desenvolvido e validado um método bioanalítico para a dosagem de U e UH2 com exatidão (98.4–105.3%) e precisão precisão intra-ensaio (5.1–12.1%) e inter-ensaios (5.3–10.1%) satisfatórios. Conclusão: Neste grupo de pacientes a genotipagem dos alelos *2A; Y186C; I560S, Y186C e *7 da DPYD não mostrou-se útil na identificação de indivíduos com deficiência severa da DPD. Entretanto, as razões metabólicas [UH2]/[U] demonstraram ser um promissor teste para avaliar a funcionalidade da enzima e identificar a maioria dos casos de pacientes com sujeitos a toxicidade grave à fluoropirimidinas, com sensibilidade superior da saliva. / Background: Variation on therapeutic response to fluoropirimidines and toxicity have been related to impaired dihydropyrimidine dehydrogenase (DPD) mediated metabolism. Mutations in genes encoding the enzyme as well as environmental factors can lead to reduced or absent enzyme expression, causing serious adverse effects due to the accumulation of these drugs. To date, there is no clinically recognized valid assay, for the identification of individuals at risk of severe toxicity in oncological practice. DPYD genotyping has a limited prediction power, since it is able to identify only the already known mutations, which have low frequency in population. Therefore, functional DPD assays based on the assessment of uracil (U) to dihydrouracil (UH2) metabolism, which is also dependent on DPD, have been proposed to identify patients prone to toxicity. Thus, endogenous metabolic ratios of [UH2]/[U] or after an oral dose of U are determined in plasma. Recently, the use of saliva has been suggested as alternative matrix to plasma, with higher stability of analytes. However, the association between salivary metabolic ratios and toxicity has not been validated in clinical samples. Objective: To evaluate the use of plasma and saliva uracil (U) to dihydrouracil (UH2) metabolic ratios and DPYD genotyping, as a means to identify patients with dihydropyrimidine dehydrogenase (DPD) deficiency and fluoropyrimidine toxicity. Additionally, the work proposed the development of a bioanalytical method for the determination of U and UH2 by high-performance liquid chromatography. Methods: Paired plasma and saliva samples were obtained from 60 patients with gastrointestinal cancer before fluoropyrimidine treatment. U and UH2 concentrations were measured by LC-MS/MS. DPYD was genotyped for alleles *2A; Y186C; I560S, Y186C and *7. Results: 35% of the patients had severe toxicity. There was no variant allele carrier for DPYD. The [UH2]/[U] metabolic ratios were 0.09-26.73 in plasma and 0.08-24.0 in saliva, with higher correlation with toxicity grade in saliva compared to plasma (rs=-0.515 vs rs=-0.282). Median metabolic ratios were lower in patients with severe toxicity as compared to those with absence of toxicity (0.59 vs 2.83 plasma; 1.62 vs 6.75 saliva, P<0.01). A cut-off of 1.16 for salivary ratio was set with 86% sensitivity and 77% specificity for the identification of patients with severe toxicity. Similarly, a plasma cut-off of 4.0 revealed a 71% sensitivity and 76% specificity. Additionally, a bioanalytical method for the quantification of U and UH2, with adequate accuracy (98.4–105.3%) and precision (intra-assay CV 5.1–12.1% and inter-assay CV 5.3–10.1%) was develop and validated. Conclusions: DPYD genotyping for alleles *2A; Y186C; I560S, Y186C and *7 was not helpful in the identification of patients with severe DPD deficiency in this series of patients. The [UH2]/[U] metabolic ratios, however, proved to be a promising functional test to identify the majority of cases of severe DPD activity, with saliva performing better than plasma.

The genomes of the hemiascomycetes Saccharomyces cerevisiae and Ashbya gossypii have been completely sequenced, allowing a comparative analysis of these two genomes, which reveals that a small number of genes appear to have entered these genomes as a result of horizontal gene transfer from bacterial sources. One potential case of horizontal gene transfer in A. gossypii and 10 potential cases in S. cerevisiae were identified, of which two were investigated further. One gene, encoding the enzyme dihydroorotate dehydrogenase (DHOD), is potentially a case of horizontal gene transfer, as shown by sequencing of this gene from additional bacterial and fungal species to generate sufficient data to construct a well-supported phylogeny. The DHOD-encoding gene found in S. cerevisiae, URA1 (YKL216W), appears to have entered the Saccharomycetaceae after the divergence of the S. cerevisiae lineage from the Candida albicans lineage and possibly since the divergence from the A. gossypii lineage. This gene appears to have come from the Lactobacillales, and following its acquisition the endogenous eukaryotic DHOD gene was lost. It was also shown that the bacterially derived horizontally transferred DHOD is required for anaerobic synthesis of uracil in S. cerevisiae. The other gene discussed in detail is BDS1, an aryl- and alkyl-sulfatase gene of bacterial origin that we have shown allows utilization of sulfate from several organic sources. Among the eukaryotes, this gene is found in S. cerevisiae and Saccharomyces bayanus and appears to derive from the alpha-proteobacteria. / Dissertation

Le virus d'Epstein-Barr (EBV) est un γ -herpesvirus humain. Il est responsable de maladies telles que la mononucléose-infectieuse et il est associé à de nombreux<br />carcinomes et syndromes immunoprolifératifs. A la différence d'autres herpesvirus tel que herpes-simplex, il n'existe actuellement aucun médicament efficace contre EBV. Le génome d'EBV contient 86 cadres de lecture soit autant de cibles potentielles pour une approche de génomique structurale, permettant le développement rationnel de nouvelles thérapies. La première série de cibles sur laquelle nous avons travaillé code pour 23 protéines. De façon inattendue, le principal problème rencontré lors de ce projet fut la faible expression ainsi que l'insolubilité d'une grande partie des cibles.<br />Parmi les 8 protéines solubles, 5 furent cristallisées à l'issue de quoi, 4 structures furent résolues. La clef de la réussite de ce projet fut un traitement individuel de chaque cible plutôt que l'utilisation de protocoles standards. La partie centrale de ce travail porte sur l'Uracile-ADN Glycosylase (UNG). C'est une enzyme de réparation de l'ADN. Il nous fut impossible d'obtenir des cristaux de la protéine seule, mais, grâce à la formation d'un complexe avec une protéine inhibitrice produite par le phage PBS-2, nous obtînmes des cristaux diffractant à 2.3 Å. La structure de ce complexe nous permis l'expliquer l'organisation de la « boucle leucine », un domaine du site actif, qui comporte une insertion de 7 résidus chez tous les γ-herpesvirus. Malgré cette différence, les constantes catalytiques de l'UNG d'EBV sont proches de celles des autres UNGs ce qui suggère un mécanisme similaire d'interaction avec l'ADN. Le travail sur d'autres cibles et les difficultés qui leur sont <br />inhérentes est également abordé (notamment l'Alkaline Exonucléase).

Using computational methods, the formation pathways and structures of four experimentally-observed DNA intrastrand cross-links are determined. These lesions originate from the uracil radical and are of particular importance due to their potential role in the activity of the 5-halouracils as radiosensitizing agents in anti-tumour treatments. The formation pathways are studied with density functional theory under conditions relevant to both UV and ionizing radiation. Results reveal these intrastrand cross-links are likely to form under therapeutic conditions and provide an explanation for their observed formation preferences. The structures of the cross-links in DNA are determined with molecular dynamics simulations to reveal the distortions these lesions induce to the helix. This has provided information about the potential biological implications of these lesions, where results indicate intrastrand cross-links are likely both mutagenic and cytotoxic. Therefore, these lesions may contribute to tumour cell death in the therapeutic use of halouracils. / xvi, 147 leaves : ill. (chiefly col.) ; 29 cm + 1 CD-ROM

Thesis (Ph. D.)--University of Alabama at Birmingham, 2007. / Title from first page of PDF file (viewed Oct. 13, 2008). Includes bibliographical references.

Base teórica: As fluoropirimidinas possuem significativa variabilidade na resposta terapêutica e na ocorrência de toxicidade, o que tem sido relacionado à deficiência na depuração metabólica mediada pela enzima diidropirimidina desidrogenase (DPD). Mutações nos genes codificadores da enzima, bem como fatores ambientais podem levar à baixa ou nula expressão enzimática, provocando efeitos adversos graves devido ao acúmulo destes fármacos. Até o presente, nenhum teste reconhecidamente valido para a identificação de indivíduos em risco de toxicidade severa está estabelecido na prática oncológica. A genotipagem para o gene DPYD apresenta poder preditivo limitado, pois é capaz de rastrear somente as mutações já conhecidas, que apresentam baixa frequência populacional. Por esta razão, ensaios funcionais baseados na avaliação da redução fisiológica do uracil (U) para diidrouracil (UH2), igualmente medidada pela DPD, têm sido propostos na identificação de pacientes predispostos à toxicidade. Nesta abordagem são estimadas as razões plasmáticas [UH2]/[U] em níveis basais ou após uma dose oral do U. Recentemente, foi sugerida a realização do teste funcional em saliva como amostra alternativa ao plasma, com maior estabilidade dos analitos. Entretanto, a associação entre as razões metabólicas nesta matriz e a toxicidade não foi validada em amostras clínicas. Objetivos: Avaliar a efetividade dos métodos de determinação da razão metabólica [UH2]/[U] em plasma e saliva e a genotipagem para o gene DPYD como preditores de toxicidade por fluoropirimidinas em pacientes com neoplasias gastrointestinais. Adicionalmente, o trabalho propôs o desenvolvimento de um método bioanalítico para a determinação de U e UH2 por cromatografia líquida de alta eficiência. Métodos: Foram obtidas amostras pareadas de plasma e saliva de 60 pacientes diagnosticados com neoplasia gastrointestinal e com indicação de tratamento com fluoropirimidinas. As concentrações de U e UH2 foram determinadas nas duas matrizes através de LC-MS/MS. Os efeitos adversos do primeiro ciclo de quimioterapia foram classificados de acordo com o NCI-CTCAE versão 4. A genotipagem da DYDP foi realizada por PCR tempo real e incluiu os alelos *2A; *13, Y186C; I560S, *7 Y186C. Resultados: 35% dos pacientes apresentaram toxicidade severa (graus 3/4), sendo a neutropenia a mais frequente (n=11). A genotipagem da DYDP não foi capaz de identificar pacientes em risco de toxicidade, uma vez que não foram encontrados portadores de alelos variáveis. As razões [UH2]/[U] variaram amplamente entre os pacientes, de 0,09 a 26,73 no plasma e de 0,08 a 24 na saliva. As razões [UH2]/[U] no plasma e na saliva demonstraram correlação elevada (rs=-0,575; P<0,01), porém, a saliva demonstrou maior correlação com o grau de toxicidade quando comparada ao plasma (rs=-0,515; P<0,01 vs rs=-0,282 P<0,05). Pacientes com grau de toxicidade 3/4 (n=21) apresentaram menor razão metabólica em comparação a pacientes com grau 1/2 (n=26) ou com ausência de toxicidade (n=13) (média 0.59 vs 2.22 e 2.83 no plasma e 1.62 vs 6.88 e 6.75 na saliva, P<0.01). A partir de curva ROC foi determinado o valor de corte de 1,16 para a razão em saliva com 86% de sensibilidade e 77% de especificidade para a identificação de pacientes com toxicidade severa. Nas amostras de plasma o valor de corte foi 4.0 com 71% de sensibilidade e 76% de especificidade. Adicionalmente, foi desenvolvido e validado um método bioanalítico para a dosagem de U e UH2 com exatidão (98.4–105.3%) e precisão precisão intra-ensaio (5.1–12.1%) e inter-ensaios (5.3–10.1%) satisfatórios. Conclusão: Neste grupo de pacientes a genotipagem dos alelos *2A; Y186C; I560S, Y186C e *7 da DPYD não mostrou-se útil na identificação de indivíduos com deficiência severa da DPD. Entretanto, as razões metabólicas [UH2]/[U] demonstraram ser um promissor teste para avaliar a funcionalidade da enzima e identificar a maioria dos casos de pacientes com sujeitos a toxicidade grave à fluoropirimidinas, com sensibilidade superior da saliva. / Background: Variation on therapeutic response to fluoropirimidines and toxicity have been related to impaired dihydropyrimidine dehydrogenase (DPD) mediated metabolism. Mutations in genes encoding the enzyme as well as environmental factors can lead to reduced or absent enzyme expression, causing serious adverse effects due to the accumulation of these drugs. To date, there is no clinically recognized valid assay, for the identification of individuals at risk of severe toxicity in oncological practice. DPYD genotyping has a limited prediction power, since it is able to identify only the already known mutations, which have low frequency in population. Therefore, functional DPD assays based on the assessment of uracil (U) to dihydrouracil (UH2) metabolism, which is also dependent on DPD, have been proposed to identify patients prone to toxicity. Thus, endogenous metabolic ratios of [UH2]/[U] or after an oral dose of U are determined in plasma. Recently, the use of saliva has been suggested as alternative matrix to plasma, with higher stability of analytes. However, the association between salivary metabolic ratios and toxicity has not been validated in clinical samples. Objective: To evaluate the use of plasma and saliva uracil (U) to dihydrouracil (UH2) metabolic ratios and DPYD genotyping, as a means to identify patients with dihydropyrimidine dehydrogenase (DPD) deficiency and fluoropyrimidine toxicity. Additionally, the work proposed the development of a bioanalytical method for the determination of U and UH2 by high-performance liquid chromatography. Methods: Paired plasma and saliva samples were obtained from 60 patients with gastrointestinal cancer before fluoropyrimidine treatment. U and UH2 concentrations were measured by LC-MS/MS. DPYD was genotyped for alleles *2A; Y186C; I560S, Y186C and *7. Results: 35% of the patients had severe toxicity. There was no variant allele carrier for DPYD. The [UH2]/[U] metabolic ratios were 0.09-26.73 in plasma and 0.08-24.0 in saliva, with higher correlation with toxicity grade in saliva compared to plasma (rs=-0.515 vs rs=-0.282). Median metabolic ratios were lower in patients with severe toxicity as compared to those with absence of toxicity (0.59 vs 2.83 plasma; 1.62 vs 6.75 saliva, P<0.01). A cut-off of 1.16 for salivary ratio was set with 86% sensitivity and 77% specificity for the identification of patients with severe toxicity. Similarly, a plasma cut-off of 4.0 revealed a 71% sensitivity and 76% specificity. Additionally, a bioanalytical method for the quantification of U and UH2, with adequate accuracy (98.4–105.3%) and precision (intra-assay CV 5.1–12.1% and inter-assay CV 5.3–10.1%) was develop and validated. Conclusions: DPYD genotyping for alleles *2A; Y186C; I560S, Y186C and *7 was not helpful in the identification of patients with severe DPD deficiency in this series of patients. The [UH2]/[U] metabolic ratios, however, proved to be a promising functional test to identify the majority of cases of severe DPD activity, with saliva performing better than plasma.

Made available in DSpace on 2016-06-02T20:36:54Z (GMT). No. of bitstreams: 1 6474.pdf: 7823491 bytes, checksum: cbbaea4fa6954870c877181c315c0a3d (MD5) Previous issue date: 2014-07-28 / Universidade Federal de Minas Gerais / In this work the synthesis of new porphyrin derivatives were proposed. The preparations of new compounds containing uracil groups at &#946;-pirrolic position were studied based on their interest in organics synthesis. We also have performed reactions with metals salt in order to evaluate the different photophysical properties of the porphyrin complex. In the first step was performed the synthesis of precursors 2, 3 and 4 in order to prepare porphyrins 5 and 6 (SCHEME 1). The pyrrole 3 was obtained from the protected uracil 2. For the synthesis of the pyrrole 4, a deprotection was performed before, to yield the compound 3. After the synthesis both 3 and 4, tetramerization reactions were tested under acid conditions, to yield porphyrins 5 and 6 after aromatization. Classic conditions for the porphyrin synthesis were tested aiming at the obtainment of porphyrinoids in good yields, thus a systematic study was performed. Until this part, only the porphyrin 5a was obtained. And the synthesis of the compound 5a, we have observed a regioisomer mixture through the 1H NMR. It was expected since pyrrole 3 was not symmetric. (CONTINUE.......) / Neste trabalho foram propostas as sínteses de novos heterociclos do tipo porfirinas, com grupos uracila fundidos nas posições &#946;-pirrólicas. Também foram realizadas reações de complexação com metais, tendo como objetivo avaliar diferenças nas características fotofísicas. Na primeira abordagem sintética foi feita a síntese dos precursores 2, 3 e 4, visando a preparação das porfirinas 5 e 6 (ESQUEMA 1). O pirrol 3 foi obtido a partir da uracila protegida 2. Para a síntese do pirrol 4, foi feita a desproteção dos nitrogênios da pirimidina do composto 3. Depois da síntese destes dois precursores 3 e 4 foram feitos testes de tetramerização em condições ácidas, seguido de aromatização do heterociclo para a obtenção das porfirinas 5 e 6. Foram testadas condições clássicas de síntese de porfirinas e uma vez sintetizada a molécula desejada, foi feito um estudo sistemático objetivando melhores rendimentos. Nesta primeira etapa somente foi obtido o composto 5a. Através do espectro de RMN de 1H deste, foi observado a formação de uma mistura de regioisômeros, devido à não simetria do pirrol 3. (CONTINUA.......)

Base teórica: As fluoropirimidinas possuem significativa variabilidade na resposta terapêutica e na ocorrência de toxicidade, o que tem sido relacionado à deficiência na depuração metabólica mediada pela enzima diidropirimidina desidrogenase (DPD). Mutações nos genes codificadores da enzima, bem como fatores ambientais podem levar à baixa ou nula expressão enzimática, provocando efeitos adversos graves devido ao acúmulo destes fármacos. Até o presente, nenhum teste reconhecidamente valido para a identificação de indivíduos em risco de toxicidade severa está estabelecido na prática oncológica. A genotipagem para o gene DPYD apresenta poder preditivo limitado, pois é capaz de rastrear somente as mutações já conhecidas, que apresentam baixa frequência populacional. Por esta razão, ensaios funcionais baseados na avaliação da redução fisiológica do uracil (U) para diidrouracil (UH2), igualmente medidada pela DPD, têm sido propostos na identificação de pacientes predispostos à toxicidade. Nesta abordagem são estimadas as razões plasmáticas [UH2]/[U] em níveis basais ou após uma dose oral do U. Recentemente, foi sugerida a realização do teste funcional em saliva como amostra alternativa ao plasma, com maior estabilidade dos analitos. Entretanto, a associação entre as razões metabólicas nesta matriz e a toxicidade não foi validada em amostras clínicas. Objetivos: Avaliar a efetividade dos métodos de determinação da razão metabólica [UH2]/[U] em plasma e saliva e a genotipagem para o gene DPYD como preditores de toxicidade por fluoropirimidinas em pacientes com neoplasias gastrointestinais. Adicionalmente, o trabalho propôs o desenvolvimento de um método bioanalítico para a determinação de U e UH2 por cromatografia líquida de alta eficiência. Métodos: Foram obtidas amostras pareadas de plasma e saliva de 60 pacientes diagnosticados com neoplasia gastrointestinal e com indicação de tratamento com fluoropirimidinas. As concentrações de U e UH2 foram determinadas nas duas matrizes através de LC-MS/MS. Os efeitos adversos do primeiro ciclo de quimioterapia foram classificados de acordo com o NCI-CTCAE versão 4. A genotipagem da DYDP foi realizada por PCR tempo real e incluiu os alelos *2A; *13, Y186C; I560S, *7 Y186C. Resultados: 35% dos pacientes apresentaram toxicidade severa (graus 3/4), sendo a neutropenia a mais frequente (n=11). A genotipagem da DYDP não foi capaz de identificar pacientes em risco de toxicidade, uma vez que não foram encontrados portadores de alelos variáveis. As razões [UH2]/[U] variaram amplamente entre os pacientes, de 0,09 a 26,73 no plasma e de 0,08 a 24 na saliva. As razões [UH2]/[U] no plasma e na saliva demonstraram correlação elevada (rs=-0,575; P<0,01), porém, a saliva demonstrou maior correlação com o grau de toxicidade quando comparada ao plasma (rs=-0,515; P<0,01 vs rs=-0,282 P<0,05). Pacientes com grau de toxicidade 3/4 (n=21) apresentaram menor razão metabólica em comparação a pacientes com grau 1/2 (n=26) ou com ausência de toxicidade (n=13) (média 0.59 vs 2.22 e 2.83 no plasma e 1.62 vs 6.88 e 6.75 na saliva, P<0.01). A partir de curva ROC foi determinado o valor de corte de 1,16 para a razão em saliva com 86% de sensibilidade e 77% de especificidade para a identificação de pacientes com toxicidade severa. Nas amostras de plasma o valor de corte foi 4.0 com 71% de sensibilidade e 76% de especificidade. Adicionalmente, foi desenvolvido e validado um método bioanalítico para a dosagem de U e UH2 com exatidão (98.4–105.3%) e precisão precisão intra-ensaio (5.1–12.1%) e inter-ensaios (5.3–10.1%) satisfatórios. Conclusão: Neste grupo de pacientes a genotipagem dos alelos *2A; Y186C; I560S, Y186C e *7 da DPYD não mostrou-se útil na identificação de indivíduos com deficiência severa da DPD. Entretanto, as razões metabólicas [UH2]/[U] demonstraram ser um promissor teste para avaliar a funcionalidade da enzima e identificar a maioria dos casos de pacientes com sujeitos a toxicidade grave à fluoropirimidinas, com sensibilidade superior da saliva. / Background: Variation on therapeutic response to fluoropirimidines and toxicity have been related to impaired dihydropyrimidine dehydrogenase (DPD) mediated metabolism. Mutations in genes encoding the enzyme as well as environmental factors can lead to reduced or absent enzyme expression, causing serious adverse effects due to the accumulation of these drugs. To date, there is no clinically recognized valid assay, for the identification of individuals at risk of severe toxicity in oncological practice. DPYD genotyping has a limited prediction power, since it is able to identify only the already known mutations, which have low frequency in population. Therefore, functional DPD assays based on the assessment of uracil (U) to dihydrouracil (UH2) metabolism, which is also dependent on DPD, have been proposed to identify patients prone to toxicity. Thus, endogenous metabolic ratios of [UH2]/[U] or after an oral dose of U are determined in plasma. Recently, the use of saliva has been suggested as alternative matrix to plasma, with higher stability of analytes. However, the association between salivary metabolic ratios and toxicity has not been validated in clinical samples. Objective: To evaluate the use of plasma and saliva uracil (U) to dihydrouracil (UH2) metabolic ratios and DPYD genotyping, as a means to identify patients with dihydropyrimidine dehydrogenase (DPD) deficiency and fluoropyrimidine toxicity. Additionally, the work proposed the development of a bioanalytical method for the determination of U and UH2 by high-performance liquid chromatography. Methods: Paired plasma and saliva samples were obtained from 60 patients with gastrointestinal cancer before fluoropyrimidine treatment. U and UH2 concentrations were measured by LC-MS/MS. DPYD was genotyped for alleles *2A; Y186C; I560S, Y186C and *7. Results: 35% of the patients had severe toxicity. There was no variant allele carrier for DPYD. The [UH2]/[U] metabolic ratios were 0.09-26.73 in plasma and 0.08-24.0 in saliva, with higher correlation with toxicity grade in saliva compared to plasma (rs=-0.515 vs rs=-0.282). Median metabolic ratios were lower in patients with severe toxicity as compared to those with absence of toxicity (0.59 vs 2.83 plasma; 1.62 vs 6.75 saliva, P<0.01). A cut-off of 1.16 for salivary ratio was set with 86% sensitivity and 77% specificity for the identification of patients with severe toxicity. Similarly, a plasma cut-off of 4.0 revealed a 71% sensitivity and 76% specificity. Additionally, a bioanalytical method for the quantification of U and UH2, with adequate accuracy (98.4–105.3%) and precision (intra-assay CV 5.1–12.1% and inter-assay CV 5.3–10.1%) was develop and validated. Conclusions: DPYD genotyping for alleles *2A; Y186C; I560S, Y186C and *7 was not helpful in the identification of patients with severe DPD deficiency in this series of patients. The [UH2]/[U] metabolic ratios, however, proved to be a promising functional test to identify the majority of cases of severe DPD activity, with saliva performing better than plasma.