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Xu W, Yang H, Liu Y, Yang Y, Wang P, Kim SH, Ito S, Yang C, Wang P, Xiao MT, Liu LX, Jiang WQ, Liu J, Zhang JY, Wang B, Frye S, Zhang Y, Xu YH, Lei QY, Guan KL, Zhao SM, Xiong Y. Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases. Cancer Cell 2011; 19:17-30. [PMID: 21251613 PMCID: PMC3229304 DOI: 10.1016/j.ccr.2010.12.014] [Citation(s) in RCA: 2081] [Impact Index Per Article: 160.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 11/19/2010] [Accepted: 12/16/2010] [Indexed: 12/14/2022]
Abstract
IDH1 and IDH2 mutations occur frequently in gliomas and acute myeloid leukemia, leading to simultaneous loss and gain of activities in the production of α-ketoglutarate (α-KG) and 2-hydroxyglutarate (2-HG), respectively. Here we demonstrate that 2-HG is a competitive inhibitor of multiple α-KG-dependent dioxygenases, including histone demethylases and the TET family of 5-methlycytosine (5mC) hydroxylases. 2-HG occupies the same space as α-KG does in the active site of histone demethylases. Ectopic expression of tumor-derived IDH1 and IDH2 mutants inhibits histone demethylation and 5mC hydroxylation. In glioma, IDH1 mutations are associated with increased histone methylation and decreased 5-hydroxylmethylcytosine (5hmC). Hence, tumor-derived IDH1 and IDH2 mutations reduce α-KG and accumulate an α-KG antagonist, 2-HG, leading to genome-wide histone and DNA methylation alterations.
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Riscob B, Shakir M, Sundar JK, Natarajan S, Wahab MA, Bhagavannarayana G. Synthesis, growth, crystal structure and characterization of a new organic material: glycine glutaric acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 78:543-548. [PMID: 21163691 DOI: 10.1016/j.saa.2010.11.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 11/19/2010] [Indexed: 05/30/2023]
Abstract
Glycine glutaric acid, a new organic compound has been synthesized and good quality single crystals were grown by slow evaporation technique. The structure of the grown crystal was elucidated by using single crystal XRD. The presence of the functional groups was confirmed by using FT-IR spectroscopy. The optical transparency was studied by using UV-vis spectrophotometer and it was found that the crystal is having high optical transparency. The thermal stability of the crystal was studied by using thermo-gravimetric and differential thermal analyses and found that it is stable up to 150°C. The room temperature dielectric studies were also carried out over the wide frequency range: 10 mHz to 10 MHz.
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Anderson RC, Huwe JK, Smith DJ, Stanton TB, Krueger NA, Callaway TR, Edrington TS, Harvey RB, Nisbet DJ. Effect of nitroethane, dimethyl-2-nitroglutarate and 2-nitro-methyl-propionate on ruminal methane production and hydrogen balance in vitro. BIORESOURCE TECHNOLOGY 2010; 101:5345-5349. [PMID: 20194018 DOI: 10.1016/j.biortech.2009.11.108] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 11/17/2009] [Accepted: 11/20/2009] [Indexed: 05/28/2023]
Abstract
Ruminal methanogenesis is considered a digestive inefficiency that results in the loss of 2-12% of the host's gross energy intake and contributes nearly 20% to the United States annual CH(4) emissions. Presently, the effects of the known CH(4) inhibitor, nitroethane, and two synthetic nitrocompounds, dimethyl-2-nitroglutarate and 2-nitro-methyl-propionate, on ruminal CH(4) production and fermentation were evaluated in vitro. After 24 h incubation at 39 degrees C under 100% CO(2), ruminal fluid cultures treated with 2.97 or 11.88 mumol ml(-1) of the respective nitrocompounds produced > 92% less CH(4) (P < 0.05) than non-treated controls. Quantification of fermentation end-products produced and H(2) balance estimates indicate that fermentation efficiencies were not compromised by the nitro-treatments.
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Kanawati B, Schmitt-Kopplin P. Exploring rearrangements along the fragmentation of glutaric acid negative ion: a combined experimental and theoretical study. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:1198-1206. [PMID: 20301136 DOI: 10.1002/rcm.4504] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Glutaric acid, a common short-chain aliphatic dicarboxylic acid, was investigated in the negative ion mode by subjecting its [M-H](-) ion to collision-induced dissociation (CID) experiments in an infinity ion cyclotron resonance (ICR) cell coupled to a hexapole-quadrupole-hexapole ion guide. A 12 Tesla magnet was used for high-resolution measurements. Two distinctive main pathways were observed in the MS/MS spectrum. The fragmentation pathways were also thoroughly investigated in a density functional theory (DFT) study involving a B3LYP/6-311+G(2d,p)//B3LYP/6-311+G(d,p) level of theory. Elimination of CO(2) from the [M-H](-) ion of the dicarboxylic acid takes place in a concerted mechanism, by which a 1,5 proton shift occurs from the intact carboxyl group to the methylene moiety located in the alpha position relative to the deprotonated carboxyl group. This concerted mechanism stabilizes the terminal negative charge and deprotonates the second carboxylic acid group. Water elimination from the [M-H](-) ion does not take place by means of a simple proton removal from the alpha methylene group - and OH(-) release from the carboxylate group to abstract an additional alpha proton thus leading to the formation of a deprotonated ketene anion. In the case of this dicarboxylic acid, a new mechanism was found for water elimination, which differs from that known for aliphatic monocarboxylic acids. An intramolecular interaction between the deprotonated and the intact carboxyl groups plays a key role in making a new energetically favourable mechanism. The DFT study also reveals that a combined loss of CO2 and H2O in the form of H2CO3 is possible.
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Benmalti MEA, Krallafa A, Rekik N, Belhakem M. Theoretical study of the nuO-H IR spectra for the hydrogen bond dimers from the polarized spectra of glutaric and 1-naphthoic acid crystals: Fermi resonances effects. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 74:58-66. [PMID: 19524484 DOI: 10.1016/j.saa.2009.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2008] [Revised: 05/02/2009] [Accepted: 05/11/2009] [Indexed: 05/27/2023]
Abstract
A full quantum theoretical model is proposed to study the nu(O-H) experimental IR line shapes of polarized crystalline glutaric and 1-naphthoic acid dimer crystals at room and liquid nitrogen temperatures. This work is an application of a previous model [M. E-A. Benmalti, D. Chamma, P. Blaise, and O. Henri-Rousseau, J. Mol. Struct. 785 (2006) 27-31] by accounting for Fermi resonances. The approach is dealing with the strong anharmonic coupling, Davydov coupling, multiple Fermi resonances between the first harmonics of some bending modes and the first excited state of the symmetric combination of the two nu(O-H) modes and the quantum direct and indirect relaxation. Numerical results show that mixing of all these effects allows to reproduce satisfactorily the main features of the experimental IR line shapes of crystalline hydrogenated and deuterated glutaric and 1-naphthoic acid crystals and are expected to provide efficient of Fermi resonances effects.
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Nessen MA, Kramer G, Back J, Baskin JM, Smeenk LEJ, de Koning LJ, van Maarseveen JH, de Jong L, Bertozzi CR, Hiemstra H, de Koster CG. Selective enrichment of azide-containing peptides from complex mixtures. J Proteome Res 2009; 8:3702-11. [PMID: 19402736 PMCID: PMC2761887 DOI: 10.1021/pr900257z] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A general method is described to sequester peptides containing azides from complex peptide mixtures, aimed at facilitating mass spectrometric analysis to study different aspects of proteome dynamics. The enrichment method is based on covalent capture of azide-containing peptides by the azide-reactive cyclooctyne (ARCO) resin and is demonstrated for two different applications. Enrichment of peptides derived from cytochrome c treated with the azide-containing cross-linker bis(succinimidyl)-3-azidomethyl glutarate (BAMG) shows several cross-link containing peptides. Sequestration of peptides derived from an Escherichia coli proteome, pulse labeled with the bio-orthogonal amino acid azidohomoalanine as substitute for methionine, allows identification of numerous newly synthesized proteins. Furthermore, the method is found to be very specific, as after enrichment over 87% of all peptides contain (modified) azidohomoalanine.
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Kourtchev I, Copolovici L, Claeys M, Maenhaut W. Characterization of atmospheric aerosols at a forested site in central Europe. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2009; 43:4665-4671. [PMID: 19673249 DOI: 10.1021/es803055w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Mass concentrations, mass size distributions, time series, and diel variations for organic tracers and major inorganic ions in aerosols from K-puszta, Hungary, during a 2003 summer period are reported. Emphasis was placed on alpha-beta-pinene secondary organic aerosol (SOA) tracers comprising cis-pinic acid, 3-hydroxyglutaric acid, and 3-methyl-1,2,3-butanetricarboxylic acid. Only cis-pinic acid and the d-limonene SOA tracer 3-carboxyheptanedioic acid exhibited diel variations with highest concentrations at night Malic acid was fairly well correlated with succinic and oxalic acid, pointing to a similar SOA formation process. No day-night variations were observed for the latter acids, suggesting that they are formed over relatively longtime scales. Of the ionic species sulfate, ammonium, and nitrate, only nitrate showed clear diel variations with highest concentrations at night. As to the size-segregated samples, the 2-methyltetrols were present in both the fine and coarse modes, while the C5-alkene triols and the alpha-/beta-pinene SOA tracers were only associated with the fine mode. The ionic species sulfate, ammonium, and nitrate made up for, on average, 24, 10, and 26% of the PM2.5 mass, while organic matter was responsible for 47% of that mass. Isoprene and alpha-pinene secondary organic carbon (SOC) accounted, on average, for, respectively, 6.8 and at least 4.8% of the PM2.5 organic carbon, but the contribution of isoprene SOC was more pronounced during daytime (9.6%), whereas that of alpha-pinene SOC was largest at night (at least 6.0%).
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Iinuma Y, Böge O, Keywood M, Gnauk T, Herrmann H. Diaterebic acid acetate and diaterpenylic acid acetate: atmospheric tracers for secondary organic aerosol formation from 1,8-cineole oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2009; 43:280-5. [PMID: 19238952 DOI: 10.1021/es802141v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Detailed organic speciation of summer time PM10 collected in Melbourne, Australia, indicated the presence of numerous monoterpene oxidation products that have previously been reported in the literature. In addition, two highly oxygenated compounds with molecular formulas C9H14O6 (MW 218) and C10H16O6 (MW 232), previously unreported, were detected during a period associated with high temperatures and bushfire smoke. These two compounds were also present in laboratory-produced secondary organic aerosol (SOA) through the reaction of OH radicals with 1,8-cineole (eucalyptol), which is emitted by Eucalyptus trees. The retention times and mass spectral behavior of the highly oxygenated compounds in high-performance liquid chromatography (LC) coupled to electrospray ionization-time-of-flight mass spectrometry (MS) in parallel to ion trap MS of agree perfectly between the ambient samples and the laboratory-produced SOA samples, suggesting that 1,8-cineole is the precursor of the highly oxygenated compounds. The proposed structure of the compound with molecular formula C10H16O6 was confirmed by synthesis of a reference compound. The two novel compounds were identified as diaterebic acid acetate (2-[1-(acetyloxy)-1-methylethyl]succinic acid, C9H14O6) and diaterpenylic acid acetate (3-[1-(acetyloxy)-1-methylethyl]glutaric acid, C10H16O6) based on the consideration of reaction mechanisms, the structure of a reference compound, and the interpretation of mass spectral data. Depending on the experimental conditions, the SOA yields determined in chamber experiments ranged between 16 and 20% for approximately 25 ppb of hydrocarbon consumed. The concentrations of these compounds were as high as 50 ng m(-3) during the summertime in Melbourne. This study demonstrates the importance and influence of local vegetation patterns on SOA chemical composition.
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Tseng YH, Mou Y, Chen PH, Tsai TWT, Hsieh CI, Mou CY, Chan JCC. Solid-state P-31 NMR study of the formation of hydroxyapatite in the presence of glutaric acid. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:330-334. [PMID: 18306172 DOI: 10.1002/mrc.2096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We demonstrate that glutaric acid can be used to prepare nanorods of hydroxyapatite under hydrothermal condition at 100 degrees C with a Ca(2+):glutaric acid molar ratio of 1:4. Frequency-switched Lee-Goldburg irradiation is employed to obtain high-resolution (31)P{(1)H} correlation spectra of the reaction mixture at two different reaction periods, from which it is shown that octacalcium phosphate is the precursor phase of the final hydroxyapatite product. In addition, the spectra show that a substantial amount of water molecules is trapped between the glutaric acid and the hydroxyapatite surface, indicating that water molecules may play a prominent role in the noncovalent interaction of the glutaric acid and the HAp surface.
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Vallières K, Petitclerc E, Laroche G. Covalent grafting of fibronectin onto plasma-treated PTFE: influence of the conjugation strategy on fibronectin biological activity. Macromol Biosci 2007; 7:738-45. [PMID: 17457945 DOI: 10.1002/mabi.200600267] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Surface coating of synthetic materials is often considered to improve biomedical devices biocompatibility. In this study, we covalently bound fibronectin (FN) onto ammonia plasma-treated PTFE via two crosslinkers, namely glutaric anhydride (GA) and sulfosuccinimidyl-4-(p-maleimidophenyl)butyrate (sulfo-SMPB). With respect to clean PTFE, cell adhesion increased markedly on both FN grafted surfaces, although it was twice higher on PTFE-GA-FN than on PTFE-SMPB-FN. ELISA experiments performed with a polyclonal antibody revealed that the amount of FN is identical on both surfaces while monoclonal antibody specific to the RGD binding site clearly demonstrated a greater availability when FN is surface grafted through GA. These results provide evidence of a variation in protein conformation correlated with the surface conjugation strategy.
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Vallières K, Chevallier P, Sarra-Bournet C, Turgeon S, Laroche G. AFM imaging of immobilized fibronectin: does the surface conjugation scheme affect the protein orientation/conformation? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:9745-51. [PMID: 17705411 DOI: 10.1021/la701323q] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Covalent grafting of biomolecules could potentially improve the biocompatibility of materials. However, these molecules have to be grafted in an active conformation to play their biological roles. The present work aims at verifying if the surface conjugation scheme of fibronectin (FN) affects the protein orientation/conformation and activity. FN was grafted onto plasma-treated fused silica using two different crosslinkers, glutaric anhydride (GA) or sulfosuccinimidyl 4-(p-maleimidophenyl)butyrate (SMPB). Fused silica was chosen as a model surface material because it presents a roughness well below the dimensions of FN, therefore allowing AFM analyses with appropriate depth resolution. Cell adhesion assays were performed to evaluate the bioactivity of grafted FN. Cell adhesion was found to be higher on GA-FN than on SMPB-FN. Since FN-radiolabeling assays allowed us to rule out a surface concentration effect (approximately 80 ng/cm2 of FN on both crosslinkers), it was hypothesized that FN adopted a more active conformation when grafted via GA. In this context, the FN conformation on both crosslinkers was investigated through AFM and contact angle analyses. Before FN grafting, GA- and SMPB-modified surfaces had a similar water contact angle, topography, and roughness. However, water contact angles of GA-FN and SMPB-FN surfaces clearly show differences in surface hydrophilicity, therefore indicating a dependence of protein organization toward the conjugation strategy. Furthermore, AFM results demonstrated that surface topography and roughness of both FN-conjugated surfaces were significantly different. Distribution analysis of FN height and diameter confirmed this observation as the protein dimensions were significantly larger on GA than SMPB. This study confirmed that the covalent immobilization scheme of biomolecules influences their conformation and, hence, their activity. Consequently, selecting the appropriate conjugation strategy is of paramount importance in retaining molecule bioactivity.
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Tsukamoto T, Wozniak KM, Slusher BS. Progress in the discovery and development of glutamate carboxypeptidase II inhibitors. Drug Discov Today 2007; 12:767-76. [PMID: 17826690 DOI: 10.1016/j.drudis.2007.07.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
During the past 10 years, substantial progress has been made in the discovery and development of small molecule glutamate carboxypeptidase II (GCP II) inhibitors. These inhibitors have provided the necessary tools to investigate the physiological role of GCP II as well as the potential therapeutic benefits of its inhibition in neurological disorders of glutamatergic dysregulation. This review article details key GCP II inhibitors discovered in the last decade and important findings from preclinical and clinical studies.
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Cook MJ, Rovis T. Rhodium-catalyzed enantioselective desymmetrization of meso-3,5-dimethyl glutaric anhydride: a general strategy to syn-deoxypolypropionate synthons. J Am Chem Soc 2007; 129:9302-3. [PMID: 17622150 DOI: 10.1021/ja073269s] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Tiraidis C, Alexacou KM, Zographos SE, Leonidas DD, Gimisis T, Oikonomakos NG. FR258900, a potential anti-hyperglycemic drug, binds at the allosteric site of glycogen phosphorylase. Protein Sci 2007; 16:1773-82. [PMID: 17600143 PMCID: PMC2203354 DOI: 10.1110/ps.072925607] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
FR258900 has been discovered as a novel inhibitor of human liver glycogen phosphorylase a and proved to suppress hepatic glycogen breakdown and reduce plasma glucose concentrations in diabetic mice models. To elucidate the mechanism of inhibition, we have determined the crystal structure of the cocrystallized rabbit muscle glycogen phosphorylase b-FR258900 complex and refined it to 2.2 A resolution. The structure demonstrates that the inhibitor binds at the allosteric activator site, where the physiological activator AMP binds. The contacts from FR258900 to glycogen phosphorylase are dominated by nonpolar van der Waals interactions with Gln71, Gln72, Phe196, and Val45' (from the symmetry-related subunit), and also by ionic interactions from the carboxylate groups to the three arginine residues (Arg242, Arg309, and Arg310) that form the allosteric phosphate-recognition subsite. The binding of FR258900 to the protein promotes conformational changes that stabilize an inactive T-state quaternary conformation of the enzyme. The ligand-binding mode is different from those of the potent phenoxy-phthalate and acyl urea inhibitors, previously described, illustrating the broad specificity of the allosteric site.
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Kumar CSSR, Leuschner C, Urbina M, Ozkaya T, Hormes J. Glutaric acid as a spacer facilitates improved intracellular uptake of LHRH-SPION into human breast cancer cells. Int J Nanomedicine 2007; 2:175-9. [PMID: 17722545 PMCID: PMC2673973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) bound directly to luteinizing hormone releasing hormone (LHRH) have shown high efficiency for intracellular uptake to breast cancer cells, MDA-MB-435S.luc. We demonstrate in this communication that inclusion of a small spacer molecule such as glutaric acid (Glu) in between SPION and LHRH increases further receptor mediated intracellular uptake. LHRH-bound SPIONs with and without the spacer molecule were nontoxic.
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Koponen IK, Riipinen I, Hienola A, Kulmala M, Bilde M. Thermodynamic properties of malonic, succinic, and glutaric acids: evaporation rates and saturation vapor pressures. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2007; 41:3926-33. [PMID: 17612170 DOI: 10.1021/es0611240] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
This work provides thermodynamic data, in particular, liquid-state saturation vapor pressures of three common slightly water soluble secondary organic aerosol components, namely, malonic, succinic, and glutaric acids. A modified tandem differential mobility analyzer system was used to measure evaporation rates of nanometer sized aqueous malonic, succinic, and glutaric acid droplets at relative humidities and temperatures relevant in the lower troposphere. Liquid phase saturation vapor pressures and other thermodynamic properties were derived from the measurements using a binary condensation model. The obtained expressions for liquid phase saturation vapor pressures compare well with extrapolated literature data. The importance of the choice of method for calculating activity coefficients is discussed.
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Choudhury R, Punekar NS. Competitive inhibition of glutamate dehydrogenase reaction. FEBS Lett 2007; 581:2733-6. [PMID: 17531979 DOI: 10.1016/j.febslet.2007.05.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 05/14/2007] [Accepted: 05/14/2007] [Indexed: 11/18/2022]
Abstract
Irrespective of their pyridine nucleotide specificity, all glutamate dehydrogenases share a common chemical mechanism that involves an enzyme bound 'iminoglutarate' intermediate. Three compounds, structurally related to this intermediate, were tested for the inhibition of purified NADP-glutamate dehydrogenases from two Aspergilli, as also the bovine liver NAD(P)-glutamate dehydrogenase. 2-Methyleneglutarate, closely resembling iminoglutarate, was a potent competitive inhibitor of the glutamate dehydrogenase reaction. This is the first report of a non-aromatic structure with a better glutamate dehydrogenase inhibitory potency than aryl carboxylic acids such as isophthalate. A suitably located 2-methylene group to mimic the iminium ion could be exploited to design inhibitors of other amino acid dehydrogenases.
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Sandala GM, Smith DM, Marsh ENG, Radom L. Toward an Improved Understanding of the Glutamate Mutase System. J Am Chem Soc 2007; 129:1623-33. [PMID: 17249667 DOI: 10.1021/ja066432c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-level quantum chemistry calculations have been used to examine the catalytic reactions of adenosylcobalamin-dependent glutamate mutase (GM) with the natural substrate (S)-glutamic acid. We have also examined the rearrangement of (S)-2-hydroxyglutaric acid, (S)-2-thiolglutaric acid, and 2-ketoglutaric acid, all of which have previously been shown to react as substrates or inhibitors of the enzyme. Our calculations support the notion that the 100-fold difference in kcat between glutamate and 2-hydroxyglutarate is associated with the relatively high energy of the glycolyl radical intermediate compared with the glycyl radical. More generally, calculations of radical stabilization energies for a variety of substituted glycyl radical analogues indicate that modifications at the radical center can profoundly affect the relative stability of the resulting radical, leading to important mechanistic consequences. We find that the formation of a thioglycolyl radical, derived from (S)-2-thiolglutaric acid, is highly dependent on the protonation state of sulfur. The neutral radical is found to be of stability similar to that of the glycolyl radical, whereas the S- form of the thioglycolyl radical is much more stable, thus providing a rationalization for the inhibition of the enzyme by the substrate analogue 2-thiolglutarate. Two possible rearrangement pathways have been examined for the reaction of GM with 2-ketoglutaric acid, for which previous experiments had suggested no rearrangement took place. The fragmentation-recombination pathway is associated with a fragmentation step that is very endothermic (by 102.2 kJ mol-1). In contrast, the addition-elimination pathway has significantly lower energy requirements. An alternative possibility, namely, that 2-ketoglutaric acid is bound in its hydrated form, 2,2-dihydroxyglutaric acid, also leads to a pathway with relatively low energy requirements, suggesting that some rearrangement might be expected under such circumstances.
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Siriphannon P, Monvisade P, Jinawath S, Hemachandra K. Preparation and characterization of hydroxyapatite/poly(ethylene glutarate) biomaterials. J Biomed Mater Res A 2007; 81:381-91. [PMID: 17542004 DOI: 10.1002/jbm.a.31032] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hydroxyapatite/poly(ethylene glutarate) (HAp/PEG) biomaterial composites were prepared by ring-opening polymerization (ROP) of cyclic oligo(ethylene glutarate) (C-PEG) in porous HAp scaffolds. The HAp/C-PEG precomposites were prepared by immersing the porous HAp scaffolds in the mixture solution of C-PEG and dibutyl tinoxide catalyst overnight and polymerizing at 200 degrees C for 24, 48, and 72 h under vacuum. The successful ROP of C-PEG in the porous HAp scaffolds was corroborated by the signals of hydroxyl end-group of PEG shown in the (1)H NMR spectrum of the ROP-products extracted from the composites. PEG in the composites was present as a thin layer coating on the HAp grains and was evenly distributed throughout the samples. The PEG content was about 13-16 wt % and decreased with increasing polymerization time. Its molecular weight (M(w), weight average) measured by gel permeation chromatography was in the range of 4300-6800 g/mol. Compressive strength of the HAp/PEG composites was significantly increased from 3 MPa of the porous HAp scaffold to 11-15 MPa, depending on the PEG content in the composites. In vitro bioactivity of the HAp/PEG composites was studied by soaking in simulated body fluid (SBF) at 36.5 degrees C for 7-28 days. After prolonged soaking, the HAp nanocrystals precipitated from the SBF solution and formed as a layer of globular aggregates, coated on the composite surfaces. This result suggested that the HAp/PEG composite was a bioactive material.
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Collman JP, Yan YL, Lei J, Dinolfo PH. Efficient synthesis of trisimidazole and glutaric acid bearing porphyrins: ligands for active-site models of bacterial nitric oxide reductase. Org Lett 2006; 8:923-6. [PMID: 16494475 PMCID: PMC2042138 DOI: 10.1021/ol053118z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ligands (1) for active-site models of bacterial nitric oxide reductase (NOR) have been efficiently synthesized. These compounds (1) feature three imidazolyl moieties and one carboxylic acid residue at the FeB site, which represent the closest available synthetic model ligands of NOR active center. The stereo conformations of these ligands are established on the basis of steric effects and 1H NMR chemical shifts under the ring current effect of the porphyrin.
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Amin EA, Welsh WJ. A preliminary in silico lead series of 2-phthalimidinoglutaric acid analogues designed as MMP-3 inhibitors. J Chem Inf Model 2006; 46:2104-9. [PMID: 16995741 DOI: 10.1021/ci0601362] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix metalloproteinases (MMPs) have been the subject of intense research because of their roles in tumor metastasis and in the rise and spread of degenerative diseases such as osteo- and rheumatoid arthritis. A preliminary class of 140 druglike, small-molecule matrix metalloproteinase-3 inhibitors, intended as starting scaffolds for optimization and synthesis, has been designed in silico using a series of highly predictive three-dimensional quantitative structure-activity relationship models, including comparative molecular field analysis and comparative molecular similarity indices analysis, with docking and scoring. Thalidomide was chosen as the skeleton on which to base the new lead series, as it moderately inhibits MMP-3, is antiangiogenic, and lends itself easily to structural modifications. Most of the new compounds demonstrate medium to high predicted biological activity and good bioavailability as estimated by the octanol-water partition coefficient ClogP. Compound 102 in particular exhibits extremely favorable predicted activity against MMP-3; is moderately bioavailable; satisfies Lipinski's Rule of Five; and shows promise for further optimization, synthesis, and experimental evaluation as a potential adjunct anticancer or antirheumatic therapeutic.
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Chan MN, Lee AKY, Chan CK. Responses of ammonium sulfate particles coated with glutaric acid to cyclic changes in relative humidity: hygroscopicity and Raman characterization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2006; 40:6983-9. [PMID: 17154005 DOI: 10.1021/es060928c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Atmospheric particles, which may have an organic coating, exhibit cyclical phase changes of deliquescence and crystallization in response to changes in the ambient relative humidity(RH). Here, we measured the hygroscopicity and Raman spectra of solid ammonium sulfate ((NH4)2SO4) particles initially coated with water-soluble glutaric acid in two consecutive cycles of deliquescence and crystallization utilizing an electrodynamic balance. (NH4)2SO4 particles with glutaric acid coating (49 wt % glutaric acid) had different hygroscopicity and morphology in the two cycles. Once the particles deliquesced, the dissolution of the solid (NH4)2SO4 core and the glutaric acid coating formed mixed (NH4)2SO4-glutaric acid solution droplets, which was confirmed by Raman characterization. Coating studies with either deliquescence or crystallization measurements, or one complete cycle of these two measurements may not fully assess the effects of the organic coatings on aerosol hygroscopicity. We also present an analysis on the kinetic and chemical effects of organic coating on aerosol hygroscopicity. Glutaric acid coating does not impede the evaporation and condensation rates of water molecules compared to the rates of (NH4)2S04 particles in the two cycles. The coating likely affects the hygroscopicity of aerosol particles through dissolution and its chemical interactions with (NH4)2S04.
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Yoon M, Patwardhan A, Qiao C, Mansoorabadi SO, Menefee AL, Reed GH, Marsh ENG. Reaction of adenosylcobalamin-dependent glutamate mutase with 2-thiolglutarate. Biochemistry 2006; 45:11650-7. [PMID: 16981724 PMCID: PMC2517135 DOI: 10.1021/bi061067n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have investigated the reaction of glutamate mutase with the glutamate analogue, 2-thiolglutarate. In the standard assay, 2-thiolglutarate behaves as a competitive inhibitor with a Ki of 0.05 mM. However, rather than simply binding inertly at the active site, 2-thiolglutarate elicits cobalt-carbon bond homolysis and the formation of 5'-deoxyadenosine. The enzyme exhibits a complicated EPR spectrum in the presence of 2-thiolglutarate that is markedly different from any previously observed with the enzyme. The spectrum was simulated well by assuming that it arises from electron-electron spin coupling between a thioglycolyl radical and low-spin Co2+ in cob(II)alamin. Analysis of the zero-field splitting parameters obtained from the simulations places the organic radical approximately 10 A from the cobalt and at a tilt angle of approximately 70 degrees to the normal of the corrin ring. This orientation is in good agreement with that expected from the crystal structure of glutamate mutase complexed with the substrate. 2-Thiolglutarate appears to react in a manner analogous to that of glutamate by first forming a thiolglutaryl radical at C-4 that then undergoes fragmentation to produce acrylate and the sulfur-stabilized thioglycolyl radical. The thioglycolyl radical accumulates on the enzyme, suggesting it is too stable to undergo further steps in the mechanism at a detectable rate.
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Bae YH, Johnson PA, Florek CA, Kohn J, Moghe PV. Minute changes in composition of polymer substrates produce amplified differences in cell adhesion and motility via optimal ligand conditioning. Acta Biomater 2006; 2:473-82. [PMID: 16793356 DOI: 10.1016/j.actbio.2006.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Revised: 03/15/2006] [Accepted: 04/17/2006] [Indexed: 01/12/2023]
Abstract
We explored the interplay between substratum chemistry of polymeric materials and surface-adsorbed ligand concentration (human plasma fibronectin) in the control of cell adhesion and cell motility. We found that small changes in the chemical composition of a polymeric substratum had different effects on cellular motility--depending on the concentration of preadsorbed fibronectin. We used two tyrosine-derived polyarylates, poly(DTD diglycolate) and poly(DTD glutarate), as substrata for the seeding of NIH-3T3 fibroblasts. The only compositional difference between the two test polymers was that one single oxygen atom in the polymer backbone of poly(DTD diglycolate) had been substituted by a methylene group in the backbone of poly(DTD glutarate), The two polymers had closely matched hydrophobicity and physical properties. Flat, spin-coated surfaces of these polymers were pretreated with different concentrations of human plasma fibronectin (0-20 microg/ml). After seeding with NIH-3T3 fibroblasts, we examined the adhesion and motility behavior of these cells. We found that NIH-3T3 fibroblasts migrated significantly faster on poly(DTD diglycolate), but only when the polymer surfaces were pretreated with intermediate concentrations of fibronectin. Only at these intermediate levels of ligand conditioning, did the presence of an extra oxygen atom in the backbone of poly(DTD diglycolate) relative to poly(DTD glutarate) (i) alter the overall organization/concentration of the fibronectin; (ii) weaken cell attachment strength and inhibited excessive cell spreading; and (iii) promote cell motility kinetics. These findings indicate that the biological effect of minute changes in substratum chemistry is critically dependent on the level of surface-adsorbed cell-binding ligands.
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Trask AV, Motherwell WDS, Jones W. Physical stability enhancement of theophylline via cocrystallization. Int J Pharm 2006; 320:114-23. [PMID: 16769188 DOI: 10.1016/j.ijpharm.2006.04.018] [Citation(s) in RCA: 301] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Revised: 03/26/2006] [Accepted: 04/26/2006] [Indexed: 10/24/2022]
Abstract
The crystal form adopted by the respiratory drug theophylline was modified using a crystal engineering strategy in order to search for a solid material with improved physical stability. Cocrystals, also referred to as crystalline molecular complexes, were prepared with theophylline and one of several dicarboxylic acids. Four cocrystals of theophylline are reported, one each with oxalic, malonic, maleic and glutaric acids. Crystal structures were obtained for each cocrystal material, allowing an examination of the hydrogen bonding and crystal packing features. The cocrystal design scheme was partly based upon a series of recently reported cocrystals of the molecular analogue, caffeine, and comparisons in packing features are drawn between the two cocrystal series. The theophylline cocrystals were subjected to relative humidity challenges in order to assess their stability in relation to crystalline theophylline anhydrate and the equivalent caffeine cocrystals. None of the cocrystals in this study converted into a hydrated cocrystal upon storage at high relative humidity. Furthermore, the theophylline:oxalic acid cocrystal demonstrated superior humidity stability to theophylline anhydrate under the conditions examined, while the other cocrystals appeared to offer comparable stability to that of theophylline anhydrate. The results demonstrate the feasibility of pharmaceutical cocrystal design based upon the crystallization preferences of a molecular analogue, and furthermore show that avoidance of hydrate formation and improvement in physical stability is possible via pharmaceutical cocrystallization.
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