Pharmacophore Modeling for Anti-Chagas Drug Design Using the Fragment Molecular Orbital Method

BackgroundChagas disease, caused by the parasite Trypanosoma cruzi, is a neglected tropical disease that causes severe human health problems. To develop a new chemotherapeutic agent for the treatment of Chagas disease, we predicted a pharmacophore model for T. cruzi dihydroorotate dehydrogenase (TcDHODH) by fragment molecular orbital (FMO) calculation for orotate, oxonate, and 43 orotate derivatives.Conclusions/SignificanceFMO-based interaction energy analyses revealed a pharmacophore model for TcDHODH inhibitor. Hydrogen bond acceptor pharmacophores correspond to Lys43 and Lys214, hydrogen bond donor and acceptor pharmacophores correspond to Asn67 and Asn194, and the aromatic ring pharmacophore corresponds to FMN, which shows important characteristics of compounds that inhibit TcDHODH. In addition, the Lys214 residue is not conserved between TcDHODH and human DHODH. Our analysis suggests that these orotate derivatives should preferentially bind to TcDHODH, increasing their selectivity. Our results obtained by pharmacophore modeling provides insight into the structural requirements for the design of TcDHODH inhibitors and their development as new anti-Chagas drugs.     

Development of microsatellite markers for Quercus miyagii Koidz. (Fagaceae), an endemic species in the Ryukyu Islands, Japan

Quercus miyagii is an endemic tree species in the Ryukyu Islands, Japan. We isolated and characterized 15 microsatellite loci in this species. The number of alleles ranged from 2 to 16 and expected heterozygosities from 0.07 to 0.92. This set of markers is potentially useful to investigate the genetic structure, gene flow, and the biogeographic history of Q. miyagii in the Ryukyu Islands, Japan.     

Involvement of Galectin-3 with Vascular Cell Adhesion Molecule-1 in Growth Regulation of Mouse BALB/3T3 Cells

β-Galactose residues on N-glycans have been implicated to be involved in growth regulation of cells. In the present study we compared the galactosylation of cell surface N-glycans of mouse Balb/3T3 cells between 30 and 100% densities and found the β-1,4-galactosylation of N-glycans increases predominantly in a 100-kDa protein band on lectin blot analysis in combination with digestions by diplococcal β-galactosidase and N-glycanase. When cells at 100% density were treated with jack bean β-galactosidase, the incorporation of 5-bromodeoxyuridine into the cells was stimulated in a dose-dependent manner, suggesting the involvement of the galactose residues in growth regulation of cells. A galactose-binding protein was isolated from the plasma membranes of cells at 100% density by affinity chromatography using an asialo-transferrin-Sepharose column and found to be galectin-3 as revealed by mass spectrometric analysis. The addition of recombinant galectin-3 into cells at 50% density inhibited the incorporation of 5-bromodeoxyuridine in a dose-dependent manner, but the inhibition was prevented with haptenic sugar. An immunocytochemical study showed that galectin-3 is present at the surface of cells at 100% density but not at 30% density where it locates inside the cells. Several glycoproteins bind to a galectin-3-immobilized column, a major of which was identified as vascular cell adhesion molecule (VCAM)-1. Immunocytochemical studies showed that some galectin-3 and VCAM-1 co-localize at the surface of cells at 100% density, indicating that the binding of galectin-3 secreted from cells to VCAM-1 is one of the pathways involved in the growth regulation of Balb/3T3 cells.     

Cholesterol transport between red blood cells and lipoproteins contributes to cholesterol metabolism in blood

Lipoproteins play a key role in transport of cholesterol to and from tissues. Recent studies have also demonstrated that red blood cells (RBCs), which carry large quantities of free cholesterol in their membrane, play an important role in reverse cholesterol transport. However, the exact role of RBCs in systemic cholesterol metabolism is poorly understood. RBCs were incubated with autologous plasma or isolated lipoproteins resulting in a significant net amount of cholesterol moved from RBCs to HDL, while cholesterol from LDL moved in the opposite direction. Furthermore, the bi-directional cholesterol transport between RBCs and plasma lipoproteins was saturable and temperature-, energy-, and time-dependent, consistent with an active process. We did not find LDLR, ABCG1, or scavenger receptor class B type 1 in RBCs but found a substantial amount of ABCA1 mRNA and protein. However, specific cholesterol efflux from RBCs to isolated apoA-I was negligible, and ABCA1 silencing with siRNA or inhibition with vanadate and Probucol did not inhibit the efflux to apoA-I, HDL, or plasma. Cholesterol efflux from and cholesterol uptake by RBCs from Abca1^+/+ and Abca1^−/− mice were similar, arguing against the role of ABCA1 in cholesterol flux between RBCs and lipoproteins. Bioinformatics analysis identified ABCA7, ABCG5, lipoprotein lipase, and mitochondrial translocator protein as possible candidates that may mediate the cholesterol flux. Together, these results suggest that RBCs actively participate in cholesterol transport in the blood, but the role of cholesterol transporters in RBCs remains uncertain.     

Inorganic nitrogen source utilization byFagus crenata on different soil types

The nitrogen source utilization by Fagus crenata distributed on soils with different forms of inorganic nitrogen in a cool-temperate deciduous forest in central Japan was determined by measuring foliar ¹⁵N. Two soil habitat types along a slope were delineated based on nitrogen transformation patterns, i.e., soils with high net nitrification rates and with no or low net nitrification, respectively. Despite differences in soil types, the study species, F. crenata, was distributed along the entire slope. The foliar ¹⁵N value of F. crenata from the lower slope area was significantly lower than that from the upper slope. Given the finding of a previous study that the ¹⁵N of NO₃^– was lower than that of NH₄⁺, our results indicate that reliance on NO₃^– as a nitrogen source was greater in the lower slope area than in the upper slope area. Differences in the values of foliar ¹⁵N were about 1, which is far less than the 10 ¹⁵N value of soil inorganic N reported in the previous study. This discrepancy might suggest that the study species utilized NO₃^– even in the upper site where net nitrification had not been detected. Measurements of nitrate reductase activity, an index of NO₃^– uptake, also supported this interpretation. Nitrate reduction occurred in leaves and roots at both the lower and the upper sites. Thus, the study species may be able to use NO₃^– even in soils with no net nitrification, a factor that could allow the distribution of F. crenata along the entire length of the slope.     

Lipids of Leaves and Seeds

The lipids in rice bran lipoprotein were separated and their qualitative and quantitative analyses were carried out by column, thin-layer, gas-liquid, and paper chromatographic methods. More than twenty lipid components were detected, of which triglycerides and glycolipids were found to be the major components. Considerable amounts of free fatty acids were also found. The glycolipids were composed of mono- and digalactosyl glycerides, sterol glycosides and their esters, probably phytocerebrosides, and other unknown glycolipids. Phospholipids were present as the minor components of rice bran lipoprotein. The presence of oryzanols in the lipoprotein was observed.     

Genetic and reproductive consequences of forest fragmentation for populations of <Emphasis Type="Italic">Magnolia obovata</Emphasis>

In order to evaluate the consequences of forest fragmentation on populations of Magnolia obovata, we compared genetic diversity and reproductive characteristics at two nearby sites, one conserved and one fragmented. The genetic diversity between adults trees of the different sites was not significantly different. However, saplings in the conserved site showed a significantly higher genetic diversity than both adult trees in the conserved site and saplings in the fragmented sites; this was found to be the result of the larger gene flow into the conserved site. The density of the adult trees was significantly related to all of the reproductive traits analyzed (fertilization of ovules, insect attack to seeds, ovules that developed into seeds and outcrossing at the stage of seeds) at both sites. At both sites, fertilization of ovules and insect attack on seeds were positively correlated to adult tree density while outcrossing rate was negatively correlated to adult tree density. The fertilization of ovules and outcrossing were more dependent on adult tree density in the fragmented site than in the conserved site. The probability of ovules developing into outcrossed seeds showed a negative correlation with adult tree density at both sites, indicating the advantage of low density for this species and possibly implying a resilience to habitat fragmentation. A two-generation-analysis did not identify significant differences between sites in terms of the structure of the pollen pool and the number of pollen donors. Although fragmentation affected reproductive characteristics, the effect on seedling establishment and subsequent survival remains to be determined. Proposals for future studies that will assist in the development of management strategies for forests suffering fragmentation are made.     

Regulation of the MDM2-P53 pathway and tumor growth by PICT1 via nucleolar RPL11

PICT1 (also known as GLTSCR2) is considered a tumor suppressor because it stabilizes phosphatase and tensin homolog (PTEN), but individuals with oligodendrogliomas lacking chromosome 19q13, where PICT1 is located, have better prognoses than other oligodendroglioma patients. To clarify the function of PICT1, we generated Pict1-deficient mice and embryonic stem (ES) cells. Pict1 is a nucleolar protein essential for embryogenesis and ES cell survival. Even without DNA damage, Pict1 loss led to p53-dependent arrest of cell cycle phase G(1) and apoptosis. Pict1-deficient cells accumulated p53, owing to impaired Mdm2 function. Pict1 binds Rpl11, and Rpl11 is released from nucleoli in the absence of Pict1. In Pict1-deficient cells, increased binding of Rpl11 to Mdm2 blocks Mdm2-mediated ubiquitination of p53. In human cancer, individuals whose tumors express less PICT1 have better prognoses. When PICT1 is depleted in tumor cells with intact P53 signaling, the cells grow more slowly and accumulate P53. Thus, PICT1 is a potent regulator of the MDM2-P53 pathway and promotes tumor progression by retaining RPL11 in the nucleolus.     

Autotaxin stabilizes blood vessels and is required for embryonic vasculature by producing lysophosphatidic acid

Autotaxin (ATX) is a cancer-associated motogen that has multiple biological activities in vitro through the production of bioactive small lipids, lysophosphatidic acid (LPA). ATX and LPA are abundantly present in circulating blood. However, their roles in circulation remain to be solved. To uncover the physiological role of ATX we analyzed ATX knock-out mice. In ATX-null embryos, early blood vessels appeared to form properly, but they failed to develop into mature vessels. As a result ATX-null mice are lethal around embryonic day 10.5. The phenotype is much more severe than those of LPA receptor knock-out mice reported so far. In cultured allantois explants, neither ATX nor LPA was angiogenic. However, both of them helped to maintain preformed vessels by preventing disassembly of the vessels that was not antagonized by Ki16425, an LPA receptor antagonist. In serum from heterozygous mice both lysophospholipase D activity and LPA level were about half of those from wild-type mice, showing that ATX is responsible for the bulk of LPA production in serum. The present study revealed a previously unassigned role of ATX in stabilizing vessels through novel LPA signaling pathways.