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Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange.
Burns MC, Sun Q, Daniels RN, Camper D, Kennedy JP, Phan J, Olejniczak ET, Lee T, Waterson AG, Rossanese OW, Fesik SW
(2014) Proc Natl Acad Sci U S A 111: 3401-6
MeSH Terms: Chromatography, Liquid, Chromatography, Thin Layer, Crystallography, X-Ray, Fluorescence Polarization, HeLa Cells, Humans, Indoles, Ligands, Magnetic Resonance Spectroscopy, Mass Spectrometry, Models, Molecular, Molecular Structure, Multiprotein Complexes, Piperidines, Protein Conformation, Proto-Oncogene Proteins p21(ras), SOS1 Protein
Show Abstract · Added March 21, 2014
Aberrant activation of the small GTPase Ras by oncogenic mutation or constitutively active upstream receptor tyrosine kinases results in the deregulation of cellular signals governing growth and survival in ∼30% of all human cancers. However, the discovery of potent inhibitors of Ras has been difficult to achieve. Here, we report the identification of small molecules that bind to a unique pocket on the Ras:Son of Sevenless (SOS):Ras complex, increase the rate of SOS-catalyzed nucleotide exchange in vitro, and modulate Ras signaling pathways in cells. X-ray crystallography of Ras:SOS:Ras in complex with these molecules reveals that the compounds bind in a hydrophobic pocket in the CDC25 domain of SOS adjacent to the Switch II region of Ras. The structure-activity relationships exhibited by these compounds can be rationalized on the basis of multiple X-ray cocrystal structures. Mutational analyses confirmed the functional relevance of this binding site and showed it to be essential for compound activity. These molecules increase Ras-GTP levels and disrupt MAPK and PI3K signaling in cells at low micromolar concentrations. These small molecules represent tools to study the acute activation of Ras and highlight a pocket on SOS that may be exploited to modulate Ras signaling.
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17 MeSH Terms
Influence of dietary fat type on benzo(a)pyrene [B(a)P] biotransformation in a B(a)P-induced mouse model of colon cancer.
Diggs DL, Myers JN, Banks LD, Niaz MS, Hood DB, Roberts LJ, Ramesh A
(2013) J Nutr Biochem 24: 2051-63
MeSH Terms: Animals, Aryl Hydrocarbon Hydroxylases, Benzo(a)pyrene, Biotransformation, Carcinogens, Chromatography, Thin Layer, Colon, Colonic Neoplasms, Cytochrome P-450 CYP1B1, DNA Adducts, Dietary Fats, Disease Models, Animal, Liver, Male, Mice
Show Abstract · Added March 7, 2014
In the US alone, around 60,000 lives/year are lost due to colon cancer. Diet and environment have been implicated in the development of sporadic colon tumors. The objective of this study was to determine how dietary fat potentiates the development of colon tumors through altered B(a)P biotransformation, using the Adenomatous polyposis coli with Multiple intestinal neoplasia mouse model. Benzo(a)pyrene was administered to mice through tricaprylin, and unsaturated (USF; peanut oil) and saturated (SF; coconut oil) fats at doses of 50 and 100 μg/kg via oral gavage over a 60-day period. Blood, colon, and liver were collected at the end of exposure period. The expression of B(a)P biotransformation enzymes [cytochrome P450 (CYP)1A1, CYP1B1 and glutathione-S-transferase] in liver and colon were assayed at the level of protein, mRNA and activities. Plasma and tissue samples were analyzed by reverse phase high-performance liquid chromatography for B(a)P metabolites. Additionally, DNA isolated from colon and liver tissues was analyzed for B(a)P-induced DNA adducts by the (32)P-postlabeling method using a thin-layer chromatography system. Benzo(a)pyrene exposure through dietary fat altered its metabolic fate in a dose-dependent manner, with 100 μg/kg dose group registering an elevated expression of B(a)P biotransformation enzymes, and greater concentration of B(a)P metabolites, compared to the 50 μg/kg dose group (P<.05). This effect was more pronounced for SF group compared to USF group (P<.05). These findings establish that SF causes sustained induction of B(a)P biotransformation enzymes and extensive metabolism of this toxicant. As a consequence, B(a)P metabolites were generated to a greater extent in colon and liver, whose concentrations also registered a dose-dependent increase. These metabolites were found to bind with DNA and form B(a)P-DNA adducts, which may have contributed to colon tumors in a subchronic exposure regimen.
© 2013.
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15 MeSH Terms
Phosphorylation of dopamine transporter serine 7 modulates cocaine analog binding.
Moritz AE, Foster JD, Gorentla BK, Mazei-Robison MS, Yang JW, Sitte HH, Blakely RD, Vaughan RA
(2013) J Biol Chem 288: 20-32
MeSH Terms: Animals, Binding Sites, Chromatography, Thin Layer, Cocaine, Corpus Striatum, Dopamine Plasma Membrane Transport Proteins, Dopamine Uptake Inhibitors, HEK293 Cells, Humans, Kinetics, Male, Mass Spectrometry, Mutagenesis, Site-Directed, Mutation, Phosphorylation, Protein Binding, Protein Conformation, Rats, Rats, Sprague-Dawley, Serine
Show Abstract · Added July 10, 2013
As an approach to elucidating dopamine transporter (DAT) phosphorylation characteristics, we examined in vitro phosphorylation of a recombinant rat DAT N-terminal peptide (NDAT) using purified protein kinases. We found that NDAT becomes phosphorylated at single distinct sites by protein kinase A (Ser-7) and calcium-calmodulin-dependent protein kinase II (Ser-13) and at multiple sites (Ser-4, Ser-7, and Ser-13) by protein kinase C (PKC), implicating these residues as potential sites of DAT phosphorylation by these kinases. Mapping of rat striatal DAT phosphopeptides by two-dimensional thin layer chromatography revealed basal and PKC-stimulated phosphorylation of the same peptide fragments and comigration of PKC-stimulated phosphopeptide fragments with NDAT Ser-7 phosphopeptide markers. We further confirmed by site-directed mutagenesis and mass spectrometry that Ser-7 is a site for PKC-stimulated phosphorylation in heterologously expressed rat and human DATs. Mutation of Ser-7 and nearby residues strongly reduced the affinity of rat DAT for the cocaine analog (-)-2β-carbomethoxy-3β-(4-fluorophenyl) tropane (CFT), whereas in rat striatal tissue, conditions that promote DAT phosphorylation caused increased CFT affinity. Ser-7 mutation also affected zinc modulation of CFT binding, with Ala and Asp substitutions inducing opposing effects. These results identify Ser-7 as a major site for basal and PKC-stimulated phosphorylation of native and expressed DAT and suggest that Ser-7 phosphorylation modulates transporter conformational equilibria, shifting the transporter between high and low affinity cocaine binding states.
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20 MeSH Terms
High-throughput, cell-free, liposome-based approach for assessing in vitro activity of lipid kinases.
Demian DJ, Clugston SL, Foster MM, Rameh L, Sarkes D, Townson SA, Yang L, Zhang M, Charlton ME
(2009) J Biomol Screen 14: 838-44
MeSH Terms: Adenosine Triphosphate, Calorimetry, Cell-Free System, Chromatography, Thin Layer, Crystallography, X-Ray, Densitometry, High-Throughput Screening Assays, Humans, Inhibitory Concentration 50, Kinetics, Lipid Metabolism, Liposomes, Phosphorus Radioisotopes, Phosphotransferases, Protein Kinase Inhibitors, Reproducibility of Results, Substrate Specificity
Show Abstract · Added December 10, 2018
Lipid kinases are central players in lipid signaling pathways involved in inflammation, tumorigenesis, and metabolic syndrome. A number of these kinase targets have proven difficult to investigate in higher throughput cell-free assay systems. This challenge is partially due to specific substrate interaction requirements for several of the lipid kinase family members and the resulting incompatibility of these substrates with most established, homogeneous assay formats. Traditional, cell-free in vitro investigational methods for members of the lipid kinase family typically involve substrate incorporation of [gamma-32P] and resolution of signal by thin-layer chromatography (TLC) and autoradiograph densitometry. This approach, although highly sensitive, does not lend itself to high-throughput testing of large numbers of small molecules (100 s to 1 MM+). The authors present the development and implementation of a fully synthetic, liposome-based assay for assessing in vitro activity of phosphatidylinositol-5-phosphate-4-kinase isoforms (PIP4KIIbeta and alpha) in 2 commonly used homogeneous technologies. They have validated these assays through compound testing in both traditional TLC and radioactive filterplate approaches as well as binding validation using isothermic calorimetry. A directed library representing known kinase pharmacophores was screened against type IIbeta phosphatidylinositol-phosphate kinase (PIPK) to identify small-molecule inhibitors. This assay system can be applied to other types and isoforms of PIPKs as well as a variety of other lipid kinase targets.
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MeSH Terms
Multiple pathways involved in the biosynthesis of anandamide.
Liu J, Wang L, Harvey-White J, Huang BX, Kim HY, Luquet S, Palmiter RD, Krystal G, Rai R, Mahadevan A, Razdan RK, Kunos G
(2008) Neuropharmacology 54: 1-7
MeSH Terms: Animals, Arachidonic Acids, Cell Line, Transformed, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Drug Interactions, Endocannabinoids, Glycerophosphates, Hydrolases, Hydrolysis, Inositol Polyphosphate 5-Phosphatases, Lipopolysaccharides, Macrophages, Metabolic Networks and Pathways, Mice, Mice, Knockout, Neomycin, Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases, Phospholipase D, Phosphoric Monoester Hydrolases, Polyunsaturated Alkamides, Protein Synthesis Inhibitors, Protein Tyrosine Phosphatase, Non-Receptor Type 22, RNA, Small Interfering, Transfection, Type C Phospholipases
Show Abstract · Added April 10, 2014
Endocannabinoids, including anandamide (arachidonoyl ethanolamide) have been implicated in the regulation of a growing number of physiological and pathological processes. Anandamide can be generated from its membrane phospholipid precursor N-arachidonoyl phosphatidylethanolamine (NAPE) through hydrolysis by a phospholipase D (NAPE-PLD). Recent evidence indicates, however, the existence of two additional, parallel pathways. One involves the sequential deacylation of NAPE by alpha,beta-hydrolase 4 (Abhd4) and the subsequent cleavage of glycerophosphate to yield anandamide, and the other one proceeds through phospholipase C-mediated hydrolysis of NAPE to yield phosphoanandamide, which is then dephosphorylated by phosphatases, including the tyrosine phosphatase PTPN22 and the inositol 5' phosphatase SHIP1. Conversion of synthetic NAPE to AEA by brain homogenates from wild-type and NAPE-PLD(-/-) mice can proceed through both the PLC/phosphatase and Abdh4 pathways, with the former being dominant at shorter (<10 min) and the latter at longer (60 min) incubations. In macrophages, the endotoxin-induced synthesis of anandamide proceeds uniquely through the phospholipase C/phosphatase pathway.
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26 MeSH Terms
Characterization of a Thermobifida fusca beta-1,3-glucanase (Lam81A) with a potential role in plant biomass degradation.
McGrath CE, Wilson DB
(2006) Biochemistry 45: 14094-100
MeSH Terms: Actinomycetales, Base Sequence, Biomass, Chromatography, Thin Layer, DNA Primers, Electrophoresis, Polyacrylamide Gel, Glucan Endo-1,3-beta-D-Glucosidase, Nuclear Magnetic Resonance, Biomolecular, Plants, Polymerase Chain Reaction
Show Abstract · Added January 27, 2012
Thermobifida fusca is a filamentous soil bacterium that plays a major role in the breakdown of plant biomass. In this paper, we report the cloning, expression, purification, and characterization of the T. fusca enzyme, Lam81A. The Carbohydrate Active Enzymes Database (http://afmb.cnrs-mrs.fr/CAZY/) indicates that Lam81A belongs to a relatively uncharacterized family of beta-1,3-glucanases, family GH-81 [Coutinho, P. M., and Henrissat, B. (1999) in Recent Advances in Carbohydrate Bioengineering (Gilbert, H. J., Davies, G., Henrissat, B., and Svensson, B., Eds.) pp 3-12, The Royal Society of Chemistry, Cambridge, U.K.]. Microarray analysis suggests that Lam81A plays a role in biomass degradation, where its natural substrate may be the plant cell wall polysaccharide, callose, which is a polymer of beta-1,3-linked glucose. Characterization of Lam81A has shown that the enzyme is specific for beta-1,3-linked glucose polysaccharides, is endohydrolytic, and utilizes an inverting mechanism for substrate hydrolysis. In addition, the enzyme has a broad pH optimum from 5.5 to 10, a temperature optimum of 50 degrees C, and demonstrates substrate inhibition, as well as showing a high basal level of expression.
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10 MeSH Terms
Effects of age and caloric restriction on lipid peroxidation: measurement of oxidative stress by F2-isoprostane levels.
Ward WF, Qi W, Van Remmen H, Zackert WE, Roberts LJ, Richardson A
(2005) J Gerontol A Biol Sci Med Sci 60: 847-51
MeSH Terms: Age Factors, Aging, Animal Nutritional Physiological Phenomena, Animals, Biomarkers, Caloric Restriction, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, DNA, Deoxyguanosine, F2-Isoprostanes, Gas Chromatography-Mass Spectrometry, Kidney, Lipid Peroxidation, Liver, Male, Oxidative Stress, Rats, Rats, Inbred F344
Show Abstract · Added December 10, 2013
The free radical theory of aging proposes that the accumulation of oxidative damage is a key component of the aging process. The discovery of F2-isoprostanes (F2-isoPs) and their establishment as a sensitive and accurate biomarker of lipid peroxidation represents a major advance for measuring the oxidative stress status of an organism. We have shown that plasma free and total (free plus esterified) F2-isoPs increase with age (185% and 66%, respectively), and that these increases are reduced by life-extending caloric restriction (50% and 23%, respectively). In addition, we found that levels of esterified F2-isoPs increase 68% with age in liver, and 76% with age in kidney. Caloric restriction modulated the age-related increase, reducing the esterified F2-isoPs levels 27% in liver and 35% in kidney. These age-related increases in esterified F2-isoPs levels correlate well with DNA oxidation, as measured by 8-oxodeoxyguanosine production demonstrating that F2-isoPs are an excellent biomarker for age-related changes in oxidative damage to membranes.
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19 MeSH Terms
Regiochemistry of neuroprostanes generated from the peroxidation of docosahexaenoic acid in vitro and in vivo.
Yin H, Musiek ES, Gao L, Porter NA, Morrow JD
(2005) J Biol Chem 280: 26600-11
MeSH Terms: Animals, Arachidonic Acid, Brain, Chromatography, Gas, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, DNA, Docosahexaenoic Acids, Electrons, Gas Chromatography-Mass Spectrometry, In Vitro Techniques, Isoprostanes, Lipid Metabolism, Lipids, Mass Spectrometry, Models, Chemical, Oxidative Stress, Oxygen, Rats, Rats, Sprague-Dawley, Spectrometry, Mass, Electrospray Ionization, Stereoisomerism, Time Factors
Show Abstract · Added May 29, 2014
Isoprostanes (IsoPs) are isomers of prostaglandins that are generated from the free radical-initiated peroxidation of arachidonic acid (C20.4 omega-6). IsoPs exert potent bioactivity and are regarded as the "gold standard" to assess oxidative stress in various human diseases. Analogously, autoxidation of docosahexaenoic acid (DHA, C22.6 omega-3) generates an array of IsoP-like compounds that are termed neuroprostanes (NPs). A major class of NPs identified in vitro and in vivo contains F-type prostane rings and are know as F4-NPs. A number of different F4-NP regioisomers are formed from the peroxidation of DHA. Among the eight possible regioisomeric groups, we hypothesize that 4- and 20-series NPs are generated in greater amounts than other classes because the precursors that lead to regioisomers other than those of the 4- and 20-series can be further oxidized to form novel dioxolane-IsoP-like compounds, analogous to those generated from arachidonate. Various mass spectrometric approaches, including electron capture atmospheric pressure chemical ionization mass spectrometry, were utilized to analyze NPs formed in vitro and in vivo based on their characteristic fragmentation in the gas phase. Experimental results were consistent with our hypothesis that 4- and 20-series NP regioisomers are preferentially generated. The discovery of regioselectivity in the formation of NPs will allow studies of the biological activities of NPs to focus on the more abundantly generated compounds to determine their role in modulating the pathophysiological consequences of DHA oxidation and oxidant stress.
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23 MeSH Terms
Studies on the endogenous phospholipids of mammalian kidney and their in vitro hydrolysis by endogenous phospholipases: a thin layer chromatographic and densitometric study.
Helmy FM, Hassanein M, Juracka A
(2004) Cell Biochem Funct 22: 379-87
MeSH Terms: Animals, Cardiolipins, Cats, Chromatography, Thin Layer, Densitometry, Dogs, Guinea Pigs, Hydrolysis, Kidney, Mammals, Mice, Phosphatidylglycerols, Phospholipases, Rats
Show Abstract · Added May 29, 2014
The phosphoglycerides profile of six species of mammalian kidney (guinea pig, pig, cat, dog, mouse and rat) and their in vitro response to the endogenous phospholipases were determined by TLC technology in conjunction with densitometric measurements. Changes in their phospholipids profile subsequent to in vitro incubation of whole tissue homogenate of these kidneys for 60 min, at pH 7.4, 38 degrees C, and prior to phospholipids extraction have shown that the deacylation of the endogenous cardiolipin (CL) is the most prevalent lipolytic event of all mammalian kidneys studied. Concurrent with the deacylation of CL, there was also formation of monolysocardiolipin (MLCL) and a reduction in CL level. To a much lesser extent, lyso alkenyl phosphatidyl ethanolamine (LPE) was also produced concomitant with a decrease of the endogenous alkenyl phosphatidyl ethanolamine (PE) level. The deacylation of PE plasmalogen to its lyso form confirms the action of endogenous PLA(2) releasing sn-2 fatty acids.
Copyright (c) 2004 John Wiley & Sons, Ltd.
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14 MeSH Terms
Identification of a novel class of endoperoxides from arachidonate autoxidation.
Yin H, Morrow JD, Porter NA
(2004) J Biol Chem 279: 3766-76
MeSH Terms: Arachidonic Acid, Arachidonic Acids, Cholesterol Esters, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Free Radicals, Gas Chromatography-Mass Spectrometry, Humans, Hydrogen Peroxide, Isoprostanes, Leukotrienes, Lipid Metabolism, Lipoproteins, Lipoproteins, LDL, Models, Chemical, Oxygen, Peroxidase, Platelet Aggregation Inhibitors, Silver, Spectrometry, Mass, Electrospray Ionization, Time Factors, Ultraviolet Rays
Show Abstract · Added May 29, 2014
Free radical-initiated lipid autoxidation in low density lipoprotein (LDL) has been implicated in the pathogenesis of atherosclerosis. Oxidation of the lipid components of LDL leads to a complex mixture of hydroperoxides, bicyclic endoperoxides, monocyclic peroxides, and serial cyclic peroxides. The oxidation compounds and/or their decomposition products can modify protein components, which may lead to various diseases. A novel class of peroxides (termed dioxolane-isoprostanes) having a bicyclic endoperoxide moiety characteristic of the isoprostanes and a dioxolane peroxide functionality in the same molecule was identified in the product mixture formed from in vitro autoxidation of cholesteryl arachidonate. The same products are also detected in in vitro oxidized LDL. Various mass spectrometric techniques have been applied to characterize these new peroxides. The structure of these compounds has also been confirmed by independent synthesis. We reason, based on the free radical mechanism of the transformation, that only the 12- and 8-peroxyl radicals (those leading to 12-HPETE and 8-HPETE) of arachidonate can form these new peroxides. We also suggest that the formation of these peroxides provides a rationale to explain the fact that 5- and 15-series isoprostanes are formed in preference to 8- and 12-series. Furthermore, series of other isoprostanes, such as dioxolane A(2), D(2), E(2), etc., can be derived from the dioxolane-isoprostane peroxides. These findings offer further insights into the oxidation products of arachidonate and the opportunity to study their potential biological relevance.
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22 MeSH Terms