Showing papers by "Emil F. Pai published in 2008"

Mammalian xanthine oxidoreductase - mechanism of transition from xanthine dehydrogenase to xanthine oxidase.

Abstract: Reactive oxygen species are generated by various biological systems, including NADPH oxidases, xanthine oxidoreductase, and mitochondrial respiratory enzymes, and contribute to many physiological and pathological phenomena. Mammalian xanthine dehydrogenase (XDH) can be converted to xanthine oxidase (XO), which produces both superoxide anion and hydrogen peroxide. Recent X-ray crystallographic and site-directed mutagenesis studies have revealed a highly sophisticated mechanism of conversion from XDH to XO, suggesting that the conversion is not a simple artefact, but rather has a function in mammalian organisms. Furthermore, this transition seems to involve a thermodynamic equilibrium between XDH and XO; disulfide bond formation or proteolysis can then lock the enzyme in the XO form. In this review, we focus on recent advances in our understanding of the mechanism of conversion from XDH to XO.

Mechanism of inhibition of xanthine oxidoreductase by allopurinol: crystal structure of reduced bovine milk xanthine oxidoreductase bound with oxipurinol.

Abstract: Inhibitors of xanthine oxidoreductase block conversion of xanthine to uric acid and are therefore potentially useful for treatment of hyperuricemia or gout. We determined the crystal structure of reduced bovine milk xanthine oxidoreductase complexed with oxipurinol at 2.0 A resolution. Clear electron density was observed between the N2 nitrogen of oxipurinol and the molybdenum atom of the molybdopterin cofactor, indicating that oxipurinol coordinated directly to molybdenum. Oxipurinol forms hydrogen bonds with glutamate 802, arginine 880, and glutamate 1261, which have previously been shown to be essential for the enzyme reaction. We discuss possible differences in the hypouricemic effect of inhibitors, including allopurinol and newly developed inhibitors, based on their mode of binding in the crystal structures.

Germline V‐genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus

Abstract: Immunoglobulin genes are generated somatically through specialized mechanisms resulting in a vast repertoire of antigen-binding sites. Despite the stochastic nature of these processes, the V-genes that encode most of the antigen-combining site are under positive evolutionary selection, raising the possibility that V-genes have been selected to encode key structural features of binding sites of protective antibodies against certain pathogens. Human, neutralizing antibodies to human cytomegalovirus that bind the AD-2S1 epitope on its gB envelope protein repeatedly use a pair of well-conserved, germline V-genes IGHV3-30 and IGKV3-11. Here, we present crystallographic, kinetic and thermodynamic analyses of the binding site of such an antibody and that of its primary immunoglobulin ancestor. These show that these germline V-genes encode key side chain contacts with the viral antigen and thereby dictate key structural features of the hypermutated, high-affinity neutralizing antibody. V-genes may thus encode an innate, protective immunological memory that targets vulnerable, invariant sites on multiple pathogens.

Structure–Activity Relationships of C6-Uridine Derivatives Targeting Plasmodia Orotidine Monophosphate Decarboxylase†

Abstract: Malaria, caused by Plasmodia parasites, has re-emerged as a major problem, imposing its fatal effects on human health, especially due to multidrug resistance. In Plasmodia, orotidine 5'-monophosphate decarboxylase (ODCase) is an essential enzyme for the de novo synthesis of uridine 5'-monophosphate. Impairing ODCase in these pathogens is a promising strategy to develop novel classes of therapeutics. Encouraged by our recent discovery that 6-iodo uridine is a potent inhibitor of P. falciparum, we investigated the structure-activity relationships of various C6 derivatives of UMP. 6-Cyano, 6-azido, 6-amino, 6-methyl, 6- N-methylamino, and 6- N, N-dimethylamino derivatives of uridine were evaluated against P. falciparum. The mononucleotides of 6-cyano, 6-azido, 6-amino, and 6-methyl uridine derivatives were studied as inhibitors of plasmodial ODCase. 6-Azidouridine 5'-monophosphate is a potent covalent inhibitor of P. falciparum ODCase. 6-Methyluridine exhibited weak antimalarial activity against P. falciparum 3D7 isolate. 6- N-Methylamino and 6- N, N-dimethylamino uridine derivatives exhibited moderate antimalarial activities.

Pyrimidine Derivatives As Anticancer Agents

Abstract: The present invention includes methods of treating or preventing cancer by administering an effective amount of 6-substituted pyrimidine derivatives of the Formula I to a subject need thereof:

Inhibition of Orotidine 5-Monophosphate Decarboxylase and Its Therapeutic Potential

Abstract: Orotidine 5'-monophosphate decarboxylase (ODCase) is among the most proficient enzymes, and catalyzes the decarboxylation of OMP to UMP. An overview of ODCase and various proposals for its catalytic mechanism of decarboxylation are briefly presented here. A number of inhibitors of ODCase and new developments in the X-ray structures of ODCases from different species are discussed in the context of their therapeutic potential against cancer and infectious diseases. Latest discoveries in the inhibition of ODCase, for example using the novel C6 substitutions on the uridine, open new doors for drug discovery targeting parasitic diseases such as malaria.

Structural diversity and plasticity associated with nucleotides targeting orotidine monophosphate decarboxylase.

Abstract: Orotidine monophosphate decarboxylase (ODCase) generally accepts pyrimidine-based mononucleotides as ligands, but other nucleotides are also known to bind to this enzyme. We investigated the kinetic properties of eight common and endogenous nucleotides with ODCases from three species: Methanobacterium thermoautotrophicum, Plasmodium falciparum, and Homo sapiens. UMP and XMP exhibited higher affinities as compared to the other nucleotides tested. The product of ODCase catalyzed decarboxylation, UMP, displayed inhibition constants (Ki) of 330 µM against the Mt enzyme and of 210 and 220 µM against the Pf and Hs ODCases, respectively. The Ki values for XMP were 130 µM and 43 µM, respectively, for Mt and Pf ODCases. Interestingly, XMP’s affinity for human ODCase (Ki = 0.71 µM) is comparable and even slightly better than that of the substrate OMP. Binding of various nucleotides and their structural features in the context of ODCase inhibition and inhibitor design are discussed.

Crystallization and preliminary X-ray analysis of the inducible lysine decarboxylase from Escherichia coli.

Abstract: The decameric inducible lysine decarboxylase (LdcI) from Escherichia coli has been crystallized in space groups C2 and C222(1); the Ta6Br12(2+) cluster was used to derivatize the C2 crystals. The method of single isomorphous replacement with anomalous scattering (SIRAS) as implemented in SHELXD was used to solve the Ta6Br12(2+)-derivatized structure to 5 A resolution. Many of the Ta6Br12(2+)-binding sites had twofold and fivefold noncrystallographic symmetry. Taking advantage of this feature, phase modification was performed in DM. The electron-density map of LdcI displays many features in agreement with the low-resolution negative-stain electron-density map [Snider et al. (2006), J. Biol. Chem. 281, 1532-1546].

Inhibition of orotidine-5'-monophosphate decarboxylase--discoveries and lessons.

Abstract: Orotidine-5'-monophosphate decarboxylase (ODCase) is one of most proficient enzymes, and this enzyme catalyzes the decarboxylation of orotidine-5'- monophosphate (OMP) to uridine-5'-monophosphate (UMP). A number of C6-substituted uridine derivatives are designed to investigate the mechanism of decarboxylation by this enzyme. In this process, novel reactions and mechanisms were uncovered for this decarboxylase. This led to the discovery of novel ODCase inhibitors and their biological activities. Medicinal chemistry of these novel inhibitors of ODCase in the context of its catalytic mechanism, and therapeutics development will be discussed.

Dérivés de pyrimidine comme agents anti-cancer

Abstract: La presente invention comprend des procedes de traitement ou de prevention du cancer par administration d'une quantite efficace de derives de pyrimidine substitues en position 6, representes par la Formule I, chez un sujet en ayant besoin.

Identification of novel fragment-based hits for P. berghei orotidine 5′-monophosphate decarboxylase

Abstract: For a quarter of a century the isolation of polymorph from III of paracetamol has been a problem due to its instability. In 1997 P. Di Martino et al [1] published the first route to prepare form III of paracetamol but they were not able to observe an x-ray diffractogram from form III. Recently J.B. Burley et al [2] isolated the polymorphic form III, but they could not draw conclusions from the powder diffractogram due to the large noncrystalline fraction. In this paper we present x-ray powder diffraction data from paracetamol form III as well as data from forms II and I. Also data collected at non-ambient temperatures will be discussed. Lattice parameters and a structure for form III will be proposed on the basis of the collected x-ray powder diffraction data. [1] P. Di Martino et al, Journal of thermal analysis vol.48 (1997) 447-458 [2] J. C. Burley et al, European journal of pharmaceutical sciences 31 (2007) 271-276