Target-guided synthesis is an approach to drug discovery that uses the biological target as a template to direct synthesis of its own best inhibitors from small molecule fragments. The process bridges the gap between chemical synthesis of drug candidates and their biological binding assay, merging the two operations into a single process whereby the active site or a binding pocket within the structure of the biological target directly controls the assembly of the best inhibitor in situ. Two different approaches to target-guided synthesis, the thermodynamic approach, making use of reversible reactions, and the kinetic approach, which uses an irreversible reaction, have been employed to discover novel, isoform selective inhibitors of the glutathione transferase (GST) enzyme family – possible drug targets in cancer and parasitic disease treatments. The thermodynamic approach described in this thesis uses the aniline-catalysed reversible acyl hydrazone formation reaction to create a dynamic covalent library of bivalent ligands designed to bind the dimeric structure of GST. In the presence of GST one of the bivalent ligands was selectively amplified at the expense of the other library members. This ligand was shown, via biological assays, to be a specific inhibitor for one isoform of GST, the mu isoform mGSTM1-1. A kinetic approach has also been investigated as a way to identify novel bivalent GST inhibitors utilising the Huisgen 1, 3 dipolar cycloaddition reaction. An azide and alkyne fragment library was designed to bind across the dimeric GST structure. The inhibitor structures are therefore bivalent, containing two anchoring fragments known to bind to the GST active site, linked by a triazolopeptide spacer. The triazole provides the click chemistry disconnection, enabling rapid in situ screening of candidate alkyne and azide fragments for inhibitor discovery. Whilst the in situ reaction with GST yielded inconclusive results, a number of the triazole products were found to have low nanomolar inhibitory activity towards GST.

The glutathione-S-transferases (GSTs) (EC.2.5.1.18) are enzymes that participate in cellular detoxification of endogenous as well as foreign electrophilic compounds, function in the cellular detoxification systems and are evolved to protect cells against reactive oxygen metabolites by conjugating the reactive molecules to the nucleophile scavenging tripeptide glutathione (GSH, &amp / #61543 / -glu-cys-gly). The GSTs are found in all eukaryotes and prokaryotic systems, in the cytoplasm, on the microsomes, and in the mitochondria. Cytosolic GSTs have been grouped into seven distinct classes as: alpha (&amp / #61537 / ), mu (&amp / #61549 / ), pi (&amp / #61552 / ), sigma (&amp / #61555 / ), omega, theta (&amp / #61553 / ) and zeta (&amp / #61540 / ). In comparison with other GSTs, class theta enzymes have proven difficult to isolate and characterize. Two distinct theta GSTs have been identified in man, GSTT1-1 and GSTT2-2 three in the rat rGST1-1, rGSTT2-2 and 13-13 and one in the mouse. this study, a class theta GST (GSTT2-2), with high activity towards 1-MS was isolated and purified from bovine liver in 3% yield with a purification factor of 3-fold. The purification protocol included a sequential DEAE cellulose anion exchanger liquid chromatography column, S-hexylglutathione agarose affinity column, dye binding orange A and chromatofocusing columns. The enzyme activity and protein content decreased rapidly after the last step of purification. The purified GSTT2-2 showed significant activity only towards 1-MS as 77 nmole/min/mg. The GSTT2-2 purified from bovine liver had a molecular weigth (Mr) value of about 28,200 which was also confirmed by Western Blott Analysis. The purified farctions of GSTT2-2 with other kolon farctions were tested with anti GSTT2-2, antiGST alfa, antiGST mu and antiGST pi antibodies. The enzyme activities towards CDNB, 4-nitrobenzylchloride (NBC) and 1-menapthyl sulfate were measured as described by Habig and Jacoby.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2007. / Härtill 4 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2007. / Härtill 4 uppsatser.

Hydroxycinnamoyl conjugates (HCC)s are an extremely diverse class of natural products that serve a wide variety of key functions in plant physiology, for example during wood formation, and in defence. They have diverse biological properties and act as antioxidants, antimicrobials, and antivirals. The biochemical basis of HCC diversity, however, has not yet been fully elucidated. Plants in the Populus genus are known to produce a particularly diverse range of HCCs and they constitute up to 5% of the leaf dry mass in some Populus species. HCCs can be formed by hydroxycinnamoyl transferases (HCTs) and distinct HCT isoforms in Populus may have distinct biological functions related to the synthesis of specific classes of HCCs. These can be identified on the basis of their evolutionary history and I show that many of the biochemically characterised HCTs belong to the BAHD superfamily of acyltransferases. My phylogenetic reconstruction of the BAHD superfamily has also defined a subclass containing most of the already-characterised HCTs, including nine potential HCT candidates in Populus. Caffeoyl-shikimate is a central precursor in the formation of lignin, a biopolymer (along with cellulose) that imparts mechanical stability to wood. Based on the transcript abundance of two candidate genes PtHCTA1 (Potri.001G042900)) and PtHCTA2 (Potri.003G183900) were hypothesised to be responsible for caffeoyl-shikimate formation in secondary xylem (i.e., wood). As part of this project, RNAi whole-plant knock-downs were generated for the xylem-associated PtHCTA1/2. The PtHCTA1/2 RNAi knock-downs have stunted growth, reminiscent of other mutants with impaired lignin biosynthesis. Based on thioacidolysis GC-MS, I found that the mutants produced a lignin with enriched hydroxyphenyl (H) subunits, which were derived from precursors upstream of the HCT-catalysed reaction and normally do not occur in Populus lignin. Interestingly, in one of the RNAi lines, the lignin phenotype was uncoupled from the developmental dwarfing phenotype. This is of high interest from a bioethanol perspective, since wood rich in H-lignin is more easily fermented than wood that is rich in guaiacyl (G) and syringyl (S) lignin. Another candidate gene (Potri.018G109900, HCT-E2) was linked to the formation of caffeoyl-spermidine in male catkins (which function in pollen coat formation), and one candidate gene (Potri.018G104700, HCT-C2) was associated with the formation of bioactive, soluble HCCs in leaves and roots. Since RNAi-mediated down-regulation proved ineffective, CRISPR-based gene knock-out methodology was developed and utilised for the Populus hairy root system. Targeted knock-out mutants for the leaf-associated HCT-C2 were generated. HCC identity was determined by metabolite purification and subsequent MS/MS/MS from leaf extracts, and the metabolite concentrations were determined by LC-MS. A decrease in chlorogenic acid concentration was apparent in CRISPR hairy-root knockouts of HCT-C2 indicating that HCTC2 is involved in HCC biosynthesis and can directly produce chlorogenic acid. Candidates for the HCTs involved in lignin biosynthesis, soluble ester biosynthesis, and pollen coat formation were identified and plant genetics confirmed the role of the lignin and soluble ester HCT candidates. / Graduate

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, Division of Biochemistry, 1966 / In title on t.p., "[epsilon]" appears as the lower-case Greek letter. "September, 1966." / Includes bibliographical references (leaves 157-165). / by John Mahlon Keller. / Ph. D. / Ph. D. Massachusetts Institute of Technology, Department of Biology, Division of Biochemistry

In acetone/butanol-producing clostridia, the metabolic intermediate acetoacetyl-CoA can be directed toward butyrate or butanol formation by the reaction catalyzed by 3-hydroxybutyryl-CoA dehydrogenase, or toward acetone formation by the reaction catalyzed by acetoacetate:acetate/butyrate CoA-transferase. 3-Hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.35 or 1.1.1.157) has been purified 45-fold to apparent homogeneity from the solvent-producing anaerobe Clostridium beijerinckii strain NRRL B593. The identities of 34 of the 35 N-terminal amino acid residues have been determined. The enzyme exhibited a native M_r of 213,000 and a subunit M_r of 30,800. It is specific for the (S)-enantiomer of 3-hydroxybutyryl-CoA. Michaelis constants for NADH and acetoacetyl-CoA were 8.6 and 14 µM, respectively. The maximum velocity of the enzyme was 540 µmol/(min mg) for the reduction of acetoacetyl-CoA with NADH. The enzyme could use either NAD(H) or NADP(H) as cosubstrate; however, NAD(H) appeared to be the physiological substrate. In the presence of 9.5 µM NADH, the enzyme was inhibited by acetoacetyl-CoA at concentrations as low as 20 µM, but the inhibition was relieved as the concentration of NADH was increased, suggesting a possible mechanism for modulating the energy efficiency during growth. Acetoacetate:acetate/butyrate CoA-transferase (EC 2.8.3.9) has been purified 308-fold to apparent homogeneity from the same organism. The enzyme exhibited a native M_r of 89,100. The subunits of the enzyme were separated by preparative SDS-PAGE, and exhibited M, values of 28,400 and 25,200. The identities of the 34 N-terminal amino acids of the large subunit and 38 of the 39 N-terminal amino acids of the small subunit were determined. The N-terminal region of the two subunits showed significant similarity with several other CoA transferase enzymes. Michaelis constants for butyrate and acetoacetyl-CoA were 11.7 mM and 107 µM, respectively, while those for acetate and acetoacetyl-CoA were 424 mM and 118 µM, respectively. The value of k_cat/K_m was approximately 100 times higher with butyrate than with acetate. Implications of the properties of these two enzymes for the acetone-butanol fermentation are discussed, and a model for the induction of the enzymes responsible for solvent production is suggested. / Ph. D.

Phanerochaete chrysosporium est un champignon ligninolytique largement étudié pour ses capacités à dégrader la lignine et certains xénobiotiques grâce à un important système d'enzymes extracellulaires. Son génome est entièrement séquencé et constitue un inventaire de séquences protéiques prédites qui a permis la description de nombreuses superfamilles de protéines. Parmi elles, les Glutathion S-transférases sont essentiellement impliquées dans le métabolisme secondaire du champignon. Cependant, malgré les nombreux travaux montrant l'implication de ces enzymes dans la réponse aux stress, le développement cellulaire et plus globalement dans certaines fonctions métaboliques, leurs réelles fonctions restent inconnues à cause de leur grande diversité et le manque de données concernant leurs spécificités catalytiques. P. chrysosporium possède 27 isoformes de GSTs qui se regroupent en 7 classes. Parmi elles, 3 sont étendues chez les champignons saprophytes : les classes Omega, Ure2p et ethérase. Deux membres de la classe Omega ont été caractérisés au niveau biochimique et montrent desspécificités de substrat. En effet, PcGTO1 fait partie d'une nouvelle classe appelée S-glutathionyl-phydroquinone reductase, alors que PcGTO3 est plutôt active avec le phenylacetophenone. La structure tridimensionnelle de PcGTO1 suggère que l'enzyme appartient également à une nouvelle classe structurale que nous avons appelée xi. La deuxième classe majoritaire que nous avons étudiée est la classe des Ure2p qui est composée de 9 isoformes et se regroupent en 2 sous-classes. Trois isoformes ont été étudiées au niveau transcriptionnel, biochimique et physiologique. PcUre2p4 et PcUre2p6 appartenant à la première sous-classe sont spécifiquement exprimés dans des cultures fongiques en présence d'hydrocarbures aromatiques polycycliques et l'activité des protéines recombinantes correspondantes est classique des GSTs à savoir le transfert de glutathion sur un substrat hydrophobe. A l'inverse, PcUre2p1 qui appartient à la deuxième sous-classe est exprimé de manière constitutive au niveau transcriptionnel et la protéine présente une activité thiol transférase comparable aux protéines de la classe Omega. Les analyses physiologiques menées grâce à la complémentation de souche déficience de Saccharomyces cerevisiae ont montré que PcUre2p1, PcUre2p4 et PcUre2p6 n'avaient pas la même fonction que l'isoforme de la levure puisqu'aucune complémentation n'a été détectée en ce qui concerne la résistance au stress ou la régulation du métabolisme azoté. Ces résultats suggèrent que leschampignons, en particulier ceux qui présentent des propriétés saprophytes ont développé des spécificités de fonction de leur GSTs probablement en réponse à des contraintes environnementales. / Phanerochaete chrysosporium is a ligninolytic fungus widely studied because of its capacities to degrade wood and xenobiotics through an extracellular enzymatic system. Its genome has been sequenced and has provided researchers with a complete inventory of the predicted proteins produced by this organism. This has allowed the description of many protein superfamilies. Among them, Glutathione S-transferases (GSTs) constitute a complex and widespread superfamily classified as enzymes of secondary metabolism. However, despite the numerous associations of GSTs with stress responses, cell development and metabolism in various organisms, the functions of these enzymes remain usually evasive mainly due to their high diversity and also to the lack of knowledge about their catalytic specificities. In P. chrysosporium 27 GST isoforms have been highlighted and clustered into seven classes. Among them three are extended in saprophytic fungi: the Omega, the Ure2p and the etherase classes. Two members of the Omega class have been characterized at the biochemical level showing difference in substrate specificities. Indeed, PcGTO1 is member of a new class of Sglutathionyl- p-hydroquinone reductase, while PcGTO3 is rather active with phenylacetophenone. The three-dimensional structure of PcGTO1 confirms the hypothesis not only of a new biological class, but also of a new structural class that we propose to name GST xi. The second extended class we have studied is the Ure2p one. It is composed of nine isoforms in P. chrysosporium and clusters into two subclasses. Three Ure2p class members have been studied in more details at transcriptional, biochemical and physiological levels. PcUre2p4 and PcUre2p6 of the first subclass are specifically expressed in cultures treated with polycyclic aromatic hydrocarbons and the recombinant proteins are active as typical glutathione transferases. By contrast, PcUre2p1, which belongs to the second subclass is constitutively expressed whatever the condition tested and is active with small molecules as substrate, such as proteins from the Omega class. Physiological studies have revealed that these proteins do not have the same function than the Saccharomyce cerevisiae isoform, concerning both the response to oxidative stress and its involvement in the nitrogen catabolite repression. These results suggest that fungi, especially those with saprophytic capabilities, have developed specificities of GST function as an adaptation to environmental constraints

Xenobiotic biotransformation process and its capacity is crucial for xenobiotic chemicals elimination that may cause damage toward cell structures. The effectiveness of the enzymes included in this process depends on the gene variants that encodes them. The aim of this work was to compare certain polymorphisms of selected genes between cases and control groups. Studied polymorphisms were null genotypes of the glutathione S-transferase gene M1 and T1 and the insertion of TA dinucleotide in the promotor region of UDP-glucuronosyl transferase 1A1. The number of cases group was six included patients with colorectal, lung, prostate, breast, pancreatic and head and neck cancer. Total number of analysed individuals was 1 118 for cancer cases and 470 for healthy controls. The control group was divided into two groups, the first one was called general and the second one was called special included healthy individuals with no cancer history in their closest family members. Gilbert syndrome (GS) is caused by homozygous insertion of the TA dinucleotide in the TATA box of the gene UGT1A1 and it causes elevated bilirubin levels. Bilirubin is a potent antioxidant in human body, so the aim was to attest its protective effect toward cancer. We expected lower frequency of GS as a protective factor in the cases groups compared with controls. This hypothesis was confirmed in the breast cancer group (GS frequency 10,0 %) and pancreatic cancer group (GS frequency 11,1 %). In the general and special control groups the frequency of GS was 16,0 % and 15,4 % respectively. Although the other case groups show lower frequency of GS, the results weren´t statistically significant. Null GSTM1 genotype was observed with 50,4 % frequency in the general control groups and with 55,3 % frequency in the special control group. Neither the one of the cases groups hasn´t showed significantly lower percentage of null genotype. Despite expectation we observed statistically significant lower frequency of null genotype in the group of lung and pancreatic cancer group (37,4 % and 39,3 % respectively). According to this study, we can say that the lack of glutathione S-transferase M1 activity is not a risk factor for cancer development. Null genotype of GSTT1 wasn´t identified in both control groups at all. In case groups of breast and prostate cancer, there was only one individual carrying the null GSTT1 genotype. Statistically significant higher frequency of this polymorphism was observed in patients with colorectal cancer (9,7 %), lung cancer (17,2 %), pancreatic cancer (3,0 %) and head and neck cancer (15,9 %). In these groups the lack of glutathion S-transferase T1 activity might be considered as risk factor for cancer development. Nevertheless, for further verification it needs to take more investigation in this field, especially enlarge the number of patient in the case groups of head and neck, lung and pancreatic cancer.

Glutathione transferases (GSTs, EC.2.5.1.18) are multifunctional enzymes that are universally distributed in all cellular life forms. They play important roles in metabolism and detoxication of endogenously produced toxic compounds and xenobiotics. GSTs have gained considerable interest over the years for biomedical and biotechnological applications due to their involvement in the conjugation of glutathione (GSH) to a vast array of chemical species. Additionally, the emergence of non-detoxifying functions of GSTs has further increased their biological significance. The present work encompasses four scientific studies aimed at investigating human as well as fruit fly Drosophila melanogaster GSTs. Paper I presents the immobilization of GSTs on nanoporous alumina membranes. Kinetic analyses with 1-chloro-2,4-dinitrobenzene followed by specificity screening with alternative substrates showed a good correlation between the data obtained from immobilized enzymes and the enzymes in solution. Furthermore, immobilization showed no adverse effects on the stability of the enzymes. Paper II presents inhibition studies of human hematopoietic prostaglandin D2 synthase (HPGDS), a promising therapeutic target for anti-allergic and anti-inflammatory drugs. Our screening results with an FDA-approved drug library revealed a number of effective inhibitors of HPGDS with IC50 values in the low micromolar range. Paper III concerns the toxicity of organic isothiocyanates (ITCs) that showed high catalytic activities with GSTE7 in vitro. The in vivo results showed that phenethyl isothiocyanate (PEITC) and allyl isothiocyanate in millimolar dietary concentrations conferred toxicity to the adult fruit flies leading to death or shortened life-span. The transgenic female flies overexpressing GSTE7 showed increased tolerance against PEITC toxicity compared to the wild-type. However, the effect was opposite in male flies overexpressing GSTE7 after one week exposure. Notably, the transgene enhanced the oviposition activity of flies with and without ITCs exposure. Paper IV highlights Drosophila GSTs as efficient catalysts of the environmental pollutant and explosive 2,4,6-trinitrotoluene and the related 2,4-dinitrotoluene degradation. This result suggests the potential of GST transgenes in plants for biotransformation and phytoremediation of these persistent environmental pollutants.