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    40 results match your criteria BMC Chemical Biology [Journal]

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    Anti-cancer activity of novel dibenzo[b,f]azepine tethered isoxazoline derivatives.
    BMC Chem Biol 2012 Oct 3;12. Epub 2012 Oct 3.
    Department of Studies in Chemistry, University of Mysore, Mysore, 570006, India.
    Background: Dibenzoazepine (DB) derivatives are important and valuable compounds in medicinal chemistry. The synthesis and chemotherapeutic properties of naturally occurring DBs and different heterocyclic moiety tethered DBs are reported. Herein, we report the DB-fused hybrid structure that containing isoxazolines (DBIs) and their anti-cancer activity, which could throw light on the structural and functional features of new molecules. Read More

    Identification Of Small Molecule TRABID Deubiquitinase Inhibitors By Computation-Based Virtual Screen.
    BMC Chem Biol 2012 May 14;12. Epub 2012 May 14.
    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA.
    Background: Wnt/β-catenin-mediated gene transcription plays important roles in a wide range of biological and pathophysiological processes including tumorigenesis where β-catenin-mediated transcription activity frequently elevates. TRABID, a deubiquitinase, was shown to have a positive Wnt/β-catenin-mediated gene transcription and hence holds a promise as a putative anti-cancer target.

    Results: In this study, we used a combination of structure based virtual screening and an in vitro deubiquitinase (DUB) assay to identify several small molecules that inhibit TRABID DUB activity. Read More

    High toxicity and specificity of the saponin 3-GlcA-28-AraRhaxyl-medicagenate, from Medicago truncatula seeds, for Sitophilus oryzae.
    BMC Chem Biol 2012 Jul 2;12. Epub 2012 Jul 2.
    Université de Lyon, INRA, INSA-Lyon, IFR-41, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, 20 ave A, Einstein, Villeurbanne, F-69621, France.
    Background: Because of the increasingly concern of consumers and public policy about problems for environment and for public health due to chemical pesticides, the search for molecules more safe is currently of great importance. Particularly, plants are able to fight the pathogens as insects, bacteria or fungi; so that plants could represent a valuable source of new molecules.

    Results: It was observed that Medicago truncatula seed flour displayed a strong toxic activity towards the adults of the rice weevil Sitophilus oryzae (Coleoptera), a major pest of stored cereals. Read More

    Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications.
    BMC Chem Biol 2012 Apr 5;12. Epub 2012 Apr 5.
    Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan.
    Background: Identification of the target proteins of bioactive compounds is critical for elucidating the mode of action; however, target identification has been difficult in general, mostly due to the low sensitivity of detection using affinity chromatography followed by CBB staining and MS/MS analysis.

    Results: We applied our protocol of predicting target proteins combining in silico screening and experimental verification for incednine, which inhibits the anti-apoptotic function of Bcl-xL by an unknown mechanism. One hundred eighty-two target protein candidates were computationally predicted to bind to incednine by the statistical prediction method, and the predictions were verified by in vitro binding of incednine to seven proteins, whose expression can be confirmed in our cell system. Read More

    HIV-1 Nef interaction influences the ATP-binding site of the Src-family kinase, Hck.
    BMC Chem Biol 2012 Mar 15;12. Epub 2012 Mar 15.
    Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
    Background: Nef is an HIV-1 accessory protein essential for viral replication and AIDS progression. Nef interacts with a multitude of host cell signaling partners, including members of the Src kinase family. Nef preferentially activates Hck, a Src-family kinase (SFK) strongly expressed in macrophages and other HIV target cells, by binding to its regulatory SH3 domain. Read More

    Development of an HPLC method for determination of pentachloronitrobenzene, hexachlorobenzene and their possible metabolites.
    BMC Chem Biol 2011 Nov 23;11. Epub 2011 Nov 23.
    Institute of Microbial Technology (CSIR), Sector 39-A, Chandigarh-160036, India.
    Background: Pentachloronitrobenzene (PCNB) and hexachlorobenzene (HCB) are highly toxic and widespread in every environmental compartment. Some of metabolic products such as amino/nitro containing chlorinated aromatic compounds can be determined by gas chromatography coupled with electron capture detector (GC-ECD). However, it is difficult to identify some of chlorophenolic and chloroquinolic intermediates produced from PCNB and HCB by the above mentioned technique. Read More

    Chemical modification of L-glutamine to alpha-amino glutarimide on autoclaving facilitates Agrobacterium infection of host and non-host plants: A new use of a known compound.
    BMC Chem Biol 2011 May 31;11. Epub 2011 May 31.
    CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur-176061, H. P. India.
    Background: Accidental autoclaving of L-glutamine was found to facilitate the Agrobacterium infection of a non host plant like tea in an earlier study. In the present communication, we elucidate the structural changes in L-glutamine due to autoclaving and also confirm the role of heat transformed L-glutamine in Agrobacterium mediated genetic transformation of host/non host plants.

    Results: When autoclaved at 121°C and 15 psi for 20 or 40 min, L-glutamine was structurally modified into 5-oxo proline and 3-amino glutarimide (α-amino glutarimide), respectively. Read More

    The Terebridae and teretoxins: Combining phylogeny and anatomy for concerted discovery of bioactive compounds.
    BMC Chem Biol 2010 Sep 17;10. Epub 2010 Sep 17.
    The City University of New York-York College and The Graduate Center, The American Museum of Natural History NYC, USA.
    The Conoidea superfamily, comprised of cone snails, terebrids, and turrids, is an exceptionally promising group for the discovery of natural peptide toxins. The potential of conoidean toxins has been realized with the distribution of the first Conus (cone snail) drug, Prialt (ziconotide), an analgesic used to alleviate chronic pain in HIV and cancer patients. Cone snail toxins (conotoxins) are highly variable, a consequence of a high mutation rate associated to duplication events and positive selection. Read More

    Chemical-genetic profile analysis of five inhibitory compounds in yeast.
    BMC Chem Biol 2010 Aug 6;10. Epub 2010 Aug 6.
    Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1 S 5B6, ON, Canada.
    Background: Chemical-genetic profiling of inhibitory compounds can lead to identification of their modes of action. These profiles can help elucidate the complex interactions between small bioactive compounds and the cell machinery, and explain putative gene function(s).

    Results: Colony size reduction was used to investigate the chemical-genetic profile of cycloheximide, 3-amino-1,2,4-triazole, paromomycin, streptomycin and neomycin in the yeast Saccharomyces cerevisiae. Read More

    Novel protein kinase D inhibitors cause potent arrest in prostate cancer cell growth and motility.
    BMC Chem Biol 2010 May 5;10. Epub 2010 May 5.
    Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
    Background: Protein kinase D (PKD) has been implicated in a wide range of cellular processes and pathological conditions including cancer. However, targeting PKD therapeutically and dissecting PKD-mediated cellular responses remains difficult due to lack of a potent and selective inhibitor. Previously, we identified a novel pan-PKD inhibitor, CID755673, with potency in the upper nanomolar range and high selectivity for PKD. Read More

    Dietary phenethylisothiocyanate attenuates bowel inflammation in mice.
    BMC Chem Biol 2010 Apr 27;10. Epub 2010 Apr 27.
    Department of Nutrition, Food Science and Hospitality, South Dakota State University, Box 2275A, Brookings, SD 57007, USA.
    Background: Phenethylisothiocyanate (PEITC) is produced by Brassica food plants. PEO is a PEITC Essential Oil containing >95% natural PEITC. PEITC is known to produce various health benefits but its effect in alleviation of ulcerative colitis signs is unknown. Read More

    MyD88-dependent and independent pathways of Toll-Like Receptors are engaged in biological activity of Triptolide in ligand-stimulated macrophages.
    BMC Chem Biol 2010 Apr 12;10. Epub 2010 Apr 12.
    Biotech Center, Rutgers University, 59 Dudley Rd, New Brunswick, NJ 08901, USA.
    Background: Triptolide is a diterpene triepoxide from the Chinese medicinal plant Tripterygium wilfordii Hook F., with known anti-inflammatory, immunosuppressive and anti-cancer properties.

    Results: Here we report the expression profile of immune signaling genes modulated by triptolide in LPS induced mouse macrophages. Read More

    Mitotic slippage in non-cancer cells induced by a microtubule disruptor, disorazole C1.
    BMC Chem Biol 2010 Feb 11;10. Epub 2010 Feb 11.
    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
    Background: Disorazoles are polyene macrodiolides isolated from a myxobacterium fermentation broth. Disorazole C1 was newly synthesized and found to depolymerize microtubules and cause mitotic arrest. Here we examined the cellular responses to disorazole C1 in both non-cancer and cancer cells and compared our results to vinblastine and taxol. Read More

    NAD+ metabolite levels as a function of vitamins and calorie restriction: evidence for different mechanisms of longevity.
    BMC Chem Biol 2010 Feb 22;10. Epub 2010 Feb 22.
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
    Background: NAD+ is a coenzyme for hydride transfer enzymes and a substrate for sirtuins and other NAD+-dependent ADPribose transfer enzymes. In wild-type Saccharomyces cerevisiae, calorie restriction accomplished by glucose limitation extends replicative lifespan in a manner that depends on Sir2 and the NAD+ salvage enzymes, nicotinic acid phosphoribosyl transferase and nicotinamidase. Though alterations in the NAD+ to nicotinamide ratio and the NAD+ to NADH ratio are anticipated by models to account for the effects of calorie restriction, the nature of a putative change in NAD+ metabolism requires analytical definition and quantification of the key metabolites. Read More

    Glycosylated VCAM-1 isoforms revealed in 2D western blots of HUVECs treated with tumoral soluble factors of breast cancer cells.
    BMC Chem Biol 2009 Nov 22;9. Epub 2009 Nov 22.
    Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, Ciudad Universitaria, Circuito Interior apartado postal 70228, CP04510, México DF.
    Background: Several common aspects of endothelial phenotype, such as the expression of cell adhesion molecules, are shared between metastasis and inflammation. Here, we analyzed VCAM-1 variants as biological markers of these two types of endothelial cell activation. With the combination of 2-DE and western blot techniques and the aid of tunicamycin, we analyzed N-glycosylation variants of VCAM-1 in primary human endothelial cells stimulated with either TNF or tumoral soluble factors (TSF's) derived from the human breast cancer cell line ZR75. Read More

    DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening.
    BMC Chem Biol 2009 Nov 13;9. Epub 2009 Nov 13.
    MTI, INSERM U973 - University Paris Diderot, 5 rue Marie-Andrée Lagroua, 75205 Paris Cedex 13, France.
    Background: Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Read More

    Bioinformatic analysis of xenobiotic reactive metabolite target proteins and their interacting partners.
    BMC Chem Biol 2009 Jun 12;9. Epub 2009 Jun 12.
    Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA.
    Background: Protein covalent binding by reactive metabolites of drugs, chemicals and natural products can lead to acute cytotoxicity. Recent rapid progress in reactive metabolite target protein identification has shown that adduction is surprisingly selective and inspired the hope that analysis of target proteins might reveal protein factors that differentiate target- vs. non-target proteins and illuminate mechanisms connecting covalent binding to cytotoxicity. Read More

    Local and global modes of drug action in biochemical networks.
    BMC Chem Biol 2009 Apr 7;9. Epub 2009 Apr 7.
    Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.
    Background: It is becoming increasingly accepted that a shift is needed from the traditional target-based approach of drug development towards an integrated perspective of drug action in biochemical systems. To make this change possible, the interaction networks connecting drug targets to all components of biological systems must be identified and characterized.

    Results: We here present an integrative analysis of the interactions between drugs and metabolism by introducing the concept of metabolic drug scope. Read More

    Chemical tools selectively target components of the PKA system.
    BMC Chem Biol 2009 Feb 12;9. Epub 2009 Feb 12.
    Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany.
    Background: In the eukaryotic cell the cAMP-dependent protein kinase (PKA) is a key enzyme in signal transduction and represents the main target of the second messenger cAMP. Here we describe the design, synthesis and characterisation of specifically tailored cAMP analogs which can be utilised as a tool for affinity enrichment and purification as well as for proteomics based analyses of cAMP binding proteins.

    Results: Two sets of chemical binders were developed based on the phosphorothioate derivatives of cAMP, Sp-cAMPS and Rp-cAMPS acting as cAMP-agonists and -antagonists, respectively. Read More

    Transcriptional profiling of the effects of 25-hydroxycholesterol on human hepatocyte metabolism and the antiviral state it conveys against the hepatitis C virus.
    BMC Chem Biol 2009 Jan 16;9. Epub 2009 Jan 16.
    Steacie Institute for Molecular Sciences, The National Research Council of Canada, Ottawa, K1A 0R6 Canada .
    Background: Hepatitis C virus (HCV) infection is a global health problem. A number of studies have implicated a direct role of cellular lipid metabolism in the HCV life cycle and inhibitors of the mevalonate pathway have been demonstrated to result in an antiviral state within the host cell. Transcriptome profiling was conducted on Huh-7 human hepatoma cells bearing subgenomic HCV replicons with and without treatment with 25-hydroxycholesterol (25-HC), an inhibitor of the mevalonate pathway that alters lipid metabolism, to assess metabolic determinants of pro- and antiviral states within the host cell. Read More

    Catalytic inhibition of topoisomerase II by a novel rationally designed ATP-competitive purine analogue.
    BMC Chem Biol 2009 Jan 7;9. Epub 2009 Jan 7.
    Department of Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland.
    Background: Topoisomerase II poisons are in clinical use as anti-cancer therapy for decades and work by stabilizing the enzyme-induced DNA breaks. In contrast, catalytic inhibitors block the enzyme before DNA scission. Although several catalytic inhibitors of topoisomerase II have been described, preclinical concepts for exploiting their anti-proliferative activity based on molecular characteristics of the tumor cell have only recently started to emerge. Read More

    Chemogenetic fingerprinting by analysis of cellular growth dynamics.
    BMC Chem Biol 2008 Aug 22;8. Epub 2008 Aug 22.
    Department of Cell and Molecular biology, University of Gothenburg, Gothenburg, Sweden.
    Background: A fundamental goal in chemical biology is the elucidation of on- and off-target effects of drugs and biocides. To this aim chemogenetic screens that quantify drug induced changes in cellular fitness, typically taken as changes in composite growth, is commonly applied.

    Results: Using the model organism Saccharomyces cerevisiae we here report that resolving cellular growth dynamics into its individual components, growth lag, growth rate and growth efficiency, increases the predictive power of chemogenetic screens. Read More

    Charting calcium-regulated apoptosis pathways using chemical biology: role of calmodulin kinase II.
    BMC Chem Biol 2008 Aug 1;8. Epub 2008 Aug 1.
    Cancer Center Karolinska, Department of Oncology-Pathology, Karolinska Institute, S-171 76 Stockholm, Sweden.
    Background: Intracellular free calcium ([Ca2+]i) is a key element in apoptotic signaling and a number of calcium-dependent apoptosis pathways have been described. We here used a chemical biology strategy to elucidate the relative importance of such different pathways.

    Results: A set of 40 agents ("bioprobes") that induce apoptosis was first identified by screening of a chemical library. Read More

    Identification of cellular pathways affected by Sortin2, a synthetic compound that affects protein targeting to the vacuole in Saccharomyces cerevisiae.
    BMC Chem Biol 2008 Jan 7;8. Epub 2008 Jan 7.
    Center for Plant Cell Biology and Department of Botany and Plant Sciences at University of California. 2109 Batchelor Hall, University of California Riverside, CA 92521 USA.
    Background: Sortin2 is a low mass compound that interferes with vacuolar delivery of proteins in plants and yeast. The Sortin2 phenotype was tested in Arabidopsis thaliana and found to be reversible upon drug removal, demonstrating the ability of chemical genomics to induce reversible phenotypes that would be difficult to achieve using conventional genetics 1. However, standard genetic methods can be used to identify drug target pathways in a high-throughput manner. Read More

    Enhancement of intracellular gamma-tocopherol levels in cytokine-stimulated C3H 10T1/2 fibroblasts: relation to NO synthesis, isoprostane formation, and tocopherol oxidation.
    BMC Chem Biol 2007 Jul 3;7. Epub 2007 Jul 3.
    University of Hawaii Cancer Research Center, Natural Products and Cancer Biology Program, 1236 Lauhala Street, Honolulu, Hawaii 96813, USA.
    Background: Stimulation of C3H 10T1/2 murine fibroblasts with interferon-gamma(IFN) and bacterial lipopolysaccharide (LPS) generates reactive oxygen and nitrogen species leading to DNA damage, lipid oxidation, and tocopherol oxidation. The tocopherols possess unique chemical and biological properties that suggest they have important roles related to intracellular defense against radical-mediated damage.

    Results: Despite increased levels of reactive oxidants and decreased media tocopherol, cellular levels of gamma-tocopherol, but not alpha-tocopherol, were observed to increase significantly when cells were treated with IFN/LPS. Read More

    The effect of amino acid deletions and substitutions in the longest loop of GFP.
    BMC Chem Biol 2007 Jun 26;7. Epub 2007 Jun 26.
    Departamento de Ingeniería Celular y Biocatálisis. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México.
    Background: The effect of single and multiple amino acid substitutions in the green fluorescent protein (GFP) from Aequorea victoria has been extensively explored, yielding several proteins of diverse spectral properties. However, the role of amino acid deletions in this protein -as with most proteins- is still unknown, due to the technical difficulties involved in generating combinatorial in-phase amino acid deletions on a target region.

    Results: In this study, the region I129-L142 of superglo GFP (sgGFP), corresponding to the longest loop of the protein and located far away from the central chromophore, was subjected to a random amino acid deletion approach, employing an in-house recently developed mutagenesis method termed Codon-Based Random Deletion (COBARDE). Read More

    Studies on the synthesis, characterization, binding with DNA and activities of two cis-planaramineplatinum(II) complexes of the form: cis-PtL(NH3)Cl2 where L = 3-hydroxypyridine and 2,3-diaminopyridine.
    BMC Chem Biol 2006 Mar 13;6. Epub 2006 Mar 13.
    School of Biomedical Sciences, Cumberland Campus, C42, The University of Sydney, East Street, PO Box 170, Lidcombe, NSW 1825, Australia.
    Background: Cis-planaramineplatinum(II) complexes like their trans isomers are often found to be active against cancer cell lines. The present study deals with the synthesis, characterization and determination of activity of new cis-planaramineplatinum(II) complexes.

    Results: Two cis-planaramineplatinum(II) complexes: cis-(3-hydroxypyridine)(ammine)dichloroplatinum(II) (code named AH3) and cis-(2,3-diaminopyridine)(ammine)dichloroplatinum(II) (code named AH7) have been prepared and characterised based on elemental analyses, IR, Raman, mass and 1H NMR spectral measurements. Read More

    Small-molecule and mutational analysis of allosteric Eg5 inhibition by monastrol.
    BMC Chem Biol 2006 Feb 27;6. Epub 2006 Feb 27.
    MPI-CBG, Pfotenhauer Strasse 108, 01307 Dresden, Germany.
    Background: A recent crystal structure of monastrol in a ternary complex with the kinesin Eg5 motor domain highlights a novel, induced-fit drug binding site at atomic resolution. Mutational obliteration of the monastrol binding site results in a monastrol-resistant, but otherwise catalytically active Eg5 motor domain. However, considering the conformational changes at this site, it is unclear what specific interactions stabilize the interaction between monastrol and the Eg5 motor domain. Read More

    Uncharged isocoumarin-based inhibitors of urokinase-type plasminogen activator.
    BMC Chem Biol 2006 Feb 8;6. Epub 2006 Feb 8.
    Department of Chemistry, University of New Mexico, Albuquerque, NM, USA.
    Background: Urokinase-type plasminogen activator (uPA) plays a major role in extracellular proteolytic events associated with tumor cell growth, migration and angiogenesis. Consequently, uPA is an attractive target for the development of small molecule active site inhibitors. Most of the recent drug development programs aimed at nonpeptidic inhibitors targeted at uPA have focused on arginino mimetics containing amidine or guanidine functional groups attached to aromatic or heterocyclic scaffolds. Read More

    Covalent attachment of the plant natural product naringenin to small glass and ceramic beads.
    BMC Chem Biol 2005 Oct 10;5. Epub 2005 Oct 10.
    Department of Plant Cellular and Molecular Biology, Plant Biotechnology Center, The Ohio State University, Columbus, OH 43210, USA.
    Background: Natural products have numerous medicinal applications and play important roles in the biology of the organisms that accumulate them. Few methods are currently available for identifying proteins that bind to small molecules, therefore the discovery of cellular targets for natural products with pharmacological activity continues to pose a significant challenge in drug validation. Similarly, the identification of enzymes that participate in the biosynthesis or modification of natural products remains a formidable bottleneck for metabolic engineering. Read More

    Electronic properties of amino acid side chains: quantum mechanics calculation of substituent effects.
    BMC Chem Biol 2005 Aug 3;5. Epub 2005 Aug 3.
    LSU Health Sciences Center, School of Medicine, Shreveport, LA 71130, USA.
    Background: Electronic properties of amino acid side chains such as inductive and field effects have not been characterized in any detail. Quantum mechanics (QM) calculations and fundamental equations that account for substituent effects may provide insight into these important properties. PM3 analysis of electron distribution and polarizability was used to derive quantitative scales that describe steric factors, inductive effects, resonance effects, and field effects of amino acid side chains. Read More

    Development of ERK Activity Sensor, an in vitro, FRET-based sensor of Extracellular Regulated Kinase activity.
    BMC Chem Biol 2005 Jul 5;5. Epub 2005 Jul 5.
    Division of Biology, California Institute of Technology, M/C 147-75, 1200 E, California Blvd, Pasadena, CA 91125, USA.
    Background: Study of ERK activation has thus far relied on biochemical assays that are limited to the use of phospho-specific antibodies and radioactivity in vitro, and analysis of whole cell populations in vivo. As with many systems, fluorescence resonance energy transfer (FRET) can be utilized to make highly sensitive detectors of molecular activity. Here we introduce FRET-based ERK Activity Sensors, which utilize variants of Enhanced Green Fluorescent Protein fused by an ERK-specific peptide linker to detect ERK2 activity. Read More

    An informatics search for the low-molecular weight chromium-binding peptide.
    BMC Chem Biol 2004 Dec 16;4(1). Epub 2004 Dec 16.
    Department of Chemistry, University of Missouri-Kansas City, 5110 Rockhill Road, Kansas City, MO 64110, USA.
    BACKGROUND: The amino acid composition of a low molecular weight chromium binding peptide (LMWCr), isolated from bovine liver, is reportedly E:G:C:D::4:2:2:2, though its sequence has not been discovered. There is some controversy surrounding the exact biochemical forms and the action of Cr(III) in biological systems; the topic has been the subject of many experimental reports and continues to be investigated. Clarification of Cr-protein interactions will further understanding Cr(III) biochemistry and provide a basis for novel therapies based on metallocomplexes or small molecules. Read More

    Redesigned and chemically-modified hammerhead ribozymes with improved activity and serum stability.
    BMC Chem Biol 2004 Dec 9;4(1). Epub 2004 Dec 9.
    CSIRO Molecular Science, PO Box 184 North Ryde NSW 1670, Australia.
    BACKGROUND: Hammerhead ribozymes are RNA-based molecules which bind and cleave other RNAs specifically. As such they have potential as laboratory reagents, diagnostics and therapeutics. Despite having been extensively studied for 15 years or so, their wide application is hampered by their instability in biological media, and by the poor translation of cleavage studies on short substrates to long RNA molecules. Read More

    Chemical cleavage reactions of DNA on solid support: application in mutation detection.
    BMC Chem Biol 2003 May 13;3(1). Epub 2003 May 13.
    Genomic Disorders Research Centre (the University of Melbourne) 7th Floor, Daly Wing, St, Vincent's Hospital, 35 Victoria parade, Fitzroy, Vic, 3065, Australia.
    BACKGROUND: The conventional solution-phase Chemical Cleavage of Mismatch (CCM) method is time-consuming, as the protocol requires purification of DNA after each reaction step. This paper describes a new version of CCM to overcome this problem by immobilizing DNA on silica solid supports. RESULTS: DNA test samples were loaded on to silica beads and the DNA bound to the solid supports underwent chemical modification reactions with KMnO4 (potassium permanganate) and hydroxylamine in 3M TEAC (tetraethylammonium chloride) solution. Read More

    Synthesis and cytotoxicity of a biotinylated CC-1065 analogue.
    BMC Chem Biol 2002 ;2(1)
    Panorama Research, Inc, 2462 Wyandotte Stree, Mountain View, California, 94043, USA.
    BACKGROUND: The use of pretargeting technology for cancer imaging and treatment has made significant progress in the last few years. This approach takes advantage of the fact that biotin binds strongly to proteins avidin and streptavidin. Thus, a non-toxic tumor cell specific antibody is conjugated with avidin/streptavidin, and is administered to patients. Read More

    Synthesis and preliminary cytotoxicity study of a cephalosporin-CC-1065 analogue prodrug.
    BMC Chem Biol 2001 ;1(1)
    Panorama Research, Inc, 2462 Wyandotte Stree, Mountain View, California, 94043, USA.
    BACKGROUND: Antibody-directed enzyme prodrug therapy (ADEPT) is a promising new approach to deliver anticancer drugs selectively to tumor cells. In this approach, an enzyme is conjugated to a tumor-specific antibody. The antibody selectively localizes the enzyme to the tumor cell surface. Read More

    Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study).
    BMC Chem Biol 2001 ;1(1)
    Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
    BACKGROUND: Molecular mechanics (MM) and quantum chemical (QM) calculations are widely applied and powerful tools for the stereochemical and conformational investigations of molecules. The same methods have been extensively used to probe the conformational profile of Taxol (Figure 1) both in solution and at the beta-tubulin protein binding site. RESULTS: In the present work, the relative energies of seven conformations of Taxol derived from NMR and X-ray analyses were compared with a set of widely used force fields and semiempirical MO methods coupled to a continuum solvent treatment. Read More

    Di-, tri- and tetra-5'-O-phosphorothioadenosyl substituted polyols as inhibitors of Fhit: Importance of the alpha-beta bridging oxygen and beta phosphorus replacement.
    BMC Chem Biol 2001 ;1(1)
    Structural Biology & Bioinformatics Program, Kimmel Cancer Center, Philadelphia, USA.
    BACKGROUND: The human FHIT gene is inactivated early in the development of many human cancers and loss of Fhit in mouse predisposes to cancer while reintroduction of FHIT suppresses tumor formation via induction of apoptosis. Fhit protein, a diadenosine polyphosphate hydrolase, does not require hydrolase activity to function in tumor suppression and may signal for apoptosis as an enzyme-substrate complex. Thus, high affinity nonhydrolyzable substrate analogs may either promote or antagonize Fhit function, depending on their features, in Fhit + cells. Read More

    Analysis of fluorescently labeled substance P analogs: binding, imaging and receptor activation.
    BMC Chem Biol 2001 ;1(1)
    Department of Neurobiology and Pharmacology, Northeastern Ohio Universities College of Medicine, Rootstown, OH 44272 and The Neuropharmacology Lab, Department of Neurobiology and Pharmacology, Marshall University School of Medicine, Huntington, WV 25704, USA.
    BACKGROUND: Substance P (SP) is a peptide neurotransmitter found in central and peripheral nerves. SP is involved in the control of smooth muscle, inflammation and nociception. The amino acid sequence of SP is Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-NH2. Read More

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