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PubMed2001

Real experiences of uHTS: a prototypic 1536-well fluorescence anisotropy-based uHTS screen and application of well-level quality control procedures.

This paper describes, for the first time, a true ultra-high throughput screen (uHTS) based upon fluorescence anisotropy and performed entirely in 1536-well assay plates. The assay is based upon binding and displacement of a BODIPY-FL-labeled antibiotic to a specific binding site on 70S ribosomes from Escherichia coli (Kd approximately 15 nM). The screen was performed at uHTS rates (i.e., >100,000 assay wells/24 h) using entirely commercially available equipment. In order to examine the reproducibility of detection of test compound effects, assays were performed in duplicate. Both overall assay statistics and reproducibility for individual compound results were excellent, at least equivalent to conventional HTS assays. Interference artifacts occurred mainly as a result of autofluorescence from test compounds. Well-level quality control procedures were developed to detect, eliminate, or even correct for such effects. Moreover, development of a brighter, longer wavelength probe (based upon Cy3B) markedly reduced such interferences. Overall, the data demonstrate that fluorescence anisotropy-based uHTS is now a practical reality.

Anti-Bacterial Agents↗

PubMed1976

New derivatives for the analysis of sphingosine long-chain bases by gas-liquid chromatography-mass spectrometry.

Cyclic derivatives formed by reaction of sphingosines with methane-, n-butane- and benzeneboronic acid have been examined by gas-liquid chromatography (GLC) and by combined GLC-mass spectrometry (MS). Analogous compounds have also been studied, in which the amino group has been protected, for example as an acetone Schiff base or N,N-dimethylaminomethylene derivative. Phytosphingosine (4D-hydroxysphinganine) yielded bis-alkaneboronates. Most of the derivatives were satisfactory for GLC. Molecular ions were apparent (1-100% relative abundance) in all electron impact mass spectra, and and (as [M+1](+)ions) were the base peaks in isobutane chemical ionisation mass spectra.

Arteries↗

PubMed2005

Structure, function, and inhibition along the reaction coordinate of CTX-M beta-lactamases.

CTX-M enzymes are an emerging group of extended spectrum beta-lactamases (ESBLs) that hydrolyze not only the penicillins but also the first-, second-, and third-generation cephalosporins. Although they have become the most frequently observed ESBLs in certain areas, there are few effective inhibitors and relatively little is known about their detailed mechanism. Here we describe the X-ray crystal structures of CTX-M enzymes in complex with different transition-state analogues and beta-lactam inhibitors, representing the enzyme as it progresses from its acylation transition state to its acyl enzyme complex to the deacylation transition state. As the enzyme moves along this reaction coordinate, two key catalytic residues, Lys73 and Glu166, change conformations, tracking the state of the reaction. Unexpectedly, the acyl enzyme complex with the beta-lactam inhibitor cefoxitin still has the catalytic water bound; this water had been predicted to be displaced by the unusual 7alpha-methoxy of the inhibitor. Instead, the 7alpha-group appears to inhibit by preventing the formation of the deacylation transition state through steric hindrance. From an inhibitor design standpoint, we note that the best of the reversible inhibitors, a ceftazidime-like boronic acid compound, binds to CTX-M-16 with a K(i) value of 4 nM. When used together in cell culture, this inhibitor reversed cefotaxime resistance in CTX-M-producing bacteria. The structure of its complex with CTX-M enzyme and the structural view of the reaction coordinate described here provide templates for inhibitor design and intervention to combat this family of antibiotic resistance enzymes.

Anti-Bacterial Agents↗

PubMed1997

Disruption of the Saccharomyces cerevisiae homologue to the murine fatty acid transport protein impairs uptake and growth on long-chain fatty acids.

The yeast Saccharomyces cerevisiae is able to utilize exogenous fatty acids for a variety of cellular processes including beta-oxidation, phospholipid biosynthesis, and protein modification. The molecular mechanisms that govern the uptake of these compounds in S. cerevisiae have not been described. We report the characterization of FAT1, a gene that encodes a putative membrane-bound long-chain fatty acid transport protein (Fat1p). Fat1p contains 623 amino acid residues that are 33% identical and 54% with similar chemical properties as compared with the fatty acid transport protein FATP described in 3T3-L1 adipocytes (Schaffer and Lodish (1994) Cell 79, 427-436), suggesting a similar function. Disruption of FAT1 results in 1) an impaired growth in YPD medium containing 25 microM cerulenin and 500 microM fatty acid (myristate (C14:0), palmitate (C16:0), or oleate (C18:1)); 2) a marked decrease in the uptake of the fluorescent long-chain fatty acid analogue boron dipyrromethene difluoride dodecanoic acid (BODIPY-3823); 3) a reduced rate of exogenous oleate incorporation into phospholipids; and 4) a 2-3-fold decrease in the rates of oleate uptake. These data support the hypothesis that Fat1p is involved in long-chain fatty acid uptake and may represent a long-chain fatty acid transport protein.

3T3 Cells↗

PubMed2003

Capillary electrochromatography and preconcentration of neutral compounds on poly(dimethylsiloxane) microchips.

Capillary electrochromatography (CEC) and preconcentration of neutral compounds have been realized on poly(dimethylsiloxane) (PDMS) microchips. The channels are coated with polyelectrolyte multilayers to avoid absorption of hydrophobic analytes into PDMS. The structures of a microchip include an injector and a bead chamber with integrated frits, where the particles of the stationary phase are completely retained. Dimensions of the frit structures are 25 micro mx20 micro m, and the space between the structures is 3 micro m. A neutral compound, BODIPY, that is strongly absorbed into native PDMS, is successfully and selectively retained on octadecylsilane-coated silica beads in the bead chamber with a concentration enhancement of up to 100 times and eluted with elution buffer solution containing 70% acetonitrile. Preconcentrations and CEC separations of coumarins have been conducted with the same device and achieved complete separations in less than 50 s.

Acetonitriles↗

PubMed1997

Strategic planning workshop on research needs for neutron capture therapy.

The workshop 'Research Needs for Neutron Capture Therapy', held in Williamsburg, VA, May 9-12. 1995 addressed key issues and questions related to optimization of boron neutron capture therapy (BNCT), in general, and to the possibility of success of the present BNCT trials at the Brookhaven National Laboratory (BNL) and Massachusetts Institute of Technology (MIT), in particular. Both trials use nuclear fission reactors as neutron sources for BNCT of glioblastoma multiforme (BNL) and of deep seated melanoma (MIT). Presentations and discussions focussed on optimal boron-labeled compounds, mainly for brain tumors such as glioblastoma multiforme, and the best mode of compound delivery to the tumor. Also, optimizing neutron irradiation with dose delivery to the tumor cells and the issues of dosimetry of BNCT especially in the brain were discussed. Planning of treatment and of follow-up of patients, coordination of BNCT at various treatment sites, and the potential of delivery BNCT to various types of cancer with an appropriately tailored protocol were additional issues. The need for multicentric interdisciplinary cooperation among the different medical specialties was highlighted.

Boron Neutron Capture Therapy↗

PubMed2001

Remarkably selective iridium catalysts for the elaboration of aromatic C-H bonds.

Arylboron compounds have intriguing properties and are important building blocks for chemical synthesis. A family of Ir catalysts now enables the direct synthesis of arylboron compounds from aromatic hydrocarbons and boranes under "solventless" conditions. The Ir catalysts are highly selective for C-H activation and do not interfere with subsequent in situ transformations, including Pd-mediated cross-couplings with aryl halides. By virtue of their favorable activities and exceptional selectivities, these Ir catalysts impart the synthetic versatility of arylboron reagents to C-H bonds in aromatic and heteroaromatic hydrocarbons.

Boron Compounds↗

PubMedDate not supplied

Substituted carboranes and polyhedral hydroborate salts as anti-neoplastics.

Substituted carboranes and polyhedral hydroborate salts were observed to be potent anti-neoplastic/cytotoxic agents inhibiting the growth of mouse and human leukemias, human uterine, colon adenocarcinoma, lung bronchogenic and gliomas. Amino-o-carborane-hydrochloride 7, one of the more potent compounds, preferentially inhibited Tmolt3 DNA synthesis. The target of the agent appears to be de novo purine synthesis with significant inhibition of the activities of both regulatory enzymes, PRPP-amido transferase and inosine monophosphate dehydrogenase as well as dihydrofolate reductase. The agent also inhibited nucleoside kinase activities leading to reductions in deoxyribonucleotide pools. The DNA molecule itself was not a target of the agent.

Adenocarcinoma↗

PubMed1998

N-borane-N-(trimethylsilyl)morpholine.

The title compound, C7H20BNOSi, features an N,N-disubstituted six-membered morpholine ring in a chair conformation, with the trimethylsilyl group in the equatorial position and the borane group in the axial position. The least-squares plane formed by the four C atoms of the morpholine ring has a mean deviation of 0.013 (2) A. The O and N atoms are 0.672 (2) and 0.650 (2) A above and below the plane, respectively.

Boron Compounds↗

PubMed2005

2-Aminoethoxydiphenyl borate (2-APB) stimulates a conformationally coupled calcium release pathway in the NG115-401L neuronal cell line.

We report in this study a 2-aminoethoxydiphenyl borate (2-APB) activated Ca2+ pathway in NG115-401L (401L) neuronal cells bearing resemblance to hormonal and ryanodine receptor activated pathways. We observed that 2-APB, in contrast to much earlier work, did not inhibit store operated Ca2+ channel (SOC) function, but rather induced potent Ca2+ discharge responses that robustly activated SOC-mediated Ca2+ influx. Further, these studies intriguingly revealed that the 2-APB-induced Ca2+ release pathway likely couples conformationally to targets in the plasma membrane, as membrane permeabilization or actin perturbation abolished the ability of the compound to stimulate Ca2+ signals. These findings suggest that conformationally sensitive complexes form between endoplasmic reticulum and plasma membrane components that not only regulate Ca2+ influx, previously proposed as the conformational coupling hypothesis, but are also required to promote Ca2+ release from intracellular stores. These observations further characterize the 401L neuronal cell line as having unique characteristics that may prove useful in gaining insight into the nature of the coupling mechanism linking Ca2+ release to Ca2+ influx.

Animals↗

PubMedDate not supplied

[Fluorescent-labeled lipophilic analogues of serotonin, dopamine, and acetylcholine: synthesis, mass spectrometry, and biological activity].

4,4-Difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-dodecanoyl derivatives of serotonin, dopamine, choline, and N,N-dimethylaminoethanol, with the fluorescence maximum at 512 nm (lambda(exc) 470 nm), and 4,4-difluoro-5,7-diphenyl-4-bora-3a,4a-diaza-s-indacene-3-dodecanoyl derivatives of choline and N,N-dimethylaminoethanol, with the fluorescence maximum at 554 nm (lambda(exc) 470 nm), were synthesized. These compounds yield protonated molecular ions of 100% intensity upon mass spectrometry with electrospray ionization at atmospheric pressure. The fragmentation of molecular ions under the conditions of secondary mass spectrometry mainly proceeds through the elimination of hydrogen fluoride from the fluorescent core of the molecules. Experiments on sea urchin Lytechinus variegatus embryos and larvae showed that these compounds easily penetrate into the cells and are accumulated in the cytoplasm. They do not differ in their biological activity from similar derivatives of arachidonic acid described previously and are agonists of serotonin or acetylcholine or antagonists of nicotinic acetylcholine receptors. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 5; see also http: // www.maik.ru.

Acetylcholine↗

PubMed2002

Elucidating drug-metalloprotein interactions with tris(pyrazolyl)borate model complexes.

The tetrahedral zinc complex [(Tp(Me,Ph))ZnOH] (Tp(Me,Ph) = hydrotris(5,3-methylphenylpyrazolyl)borate) was combined with acetohydroxamic acid, 3-mercapto-2-butanone, N-(methyl)mercaptoacetamide, beta-mercaptoethanol, 3-mercapto-2-propanol, and 3-mercapto-2-butanol to generate the complexes [(Tp(Me,Ph))Zn(ZBG)] (ZBG = zinc-binding group). These complexes were prepared to determine the mode of binding for three different types of thiol-derived matrix metalloproteinase (MMP) inhibitors. The solid-state structures of all six metal complexes were determined by X-ray crystallography. The structures reveal that while beta-mercaptoketones and beta-mercaptoamides bind the zinc ion in a bidentate fashion, the three beta-mercaptoalcohol compounds only demonstrate monodentate coordination via the sulfur atom. Prior to this work, no experimental data were available for the binding conformation of these types of inhibitors to the zinc active site of MMPs. The results of these model studies reveal different binding modes for these ZBGs and are useful for explaining the results of inhibition assays and in second-generation drug design. This work demonstrates the utility of model complexes as a tool for revealing drug-metalloprotein interactions.

Binding Sites↗

PubMed2004

Novel retinoid X receptor (RXR) antagonists having a dicarba-closo-dodecaborane as a hydrophobic moiety.

We designed and synthesized novel retinoid X receptor (RXR)-selective antagonists bearing a carborane moiety. Compounds 8a-d or 9a-d themselves have no differentiation-inducing activity toward HL-60 cells and no inhibitory activity towards a retinoic acid receptor (RAR) agonist. However, they inhibit the synergistic activity of an RXR agonist, PA024, in the presence of Am80 on the cell differentiation of HL-60. Transactivation assay using RARs and RXRs suggested that the inhibitory activity of 9b resulted from the selective antagonism at the RXR site of RXR-RAR heterodimers.

Boron Compounds↗

PubMed2006

First synthesis of free cholesterol-BODIPY conjugates.

Analogues of cholesterol (compounds 1 and 2) and coprostanol (compound 3) containing the BODIPY fluorophore in the aliphatic tail of the free sterol have been synthesized starting with bisnorcholenic acid, cholenic acid 3beta-acetate, and lithocholic acid, respectively. An ester linkage joining the fluorophore to the sterol nucleus interfered with the ability of the fluorescent sterol to pack with phospholipids in monolayers. However, an analogue in which the linker was devoid of polar atoms exhibited a substantially similar physical behavior to cholesterol in model membranes with respect to localization in raft domains.

Boron Compounds↗

PubMed2002

Solid-phase synthesis and biochemical studies of O-boranophosphopeptides and O-dithiophosphopeptides.

Signal transduction cascades maintain control over important cellular processes such as cell growth and differentiation by orchestrating protein phosphorylation and dephosphorylation. Specific control of these processes in vivo and in vitro can be achieved with peptide analogues that mimic the binding properties of phosphoproteins. We present here the solid-phase synthesis of two novel classes of phosphopeptide mimetics, O-boranophosphopeptides and O-dithiophosphopeptides, derivatized on tyrosine, serine, and threonine. The use of H-phosphonate and H-phosphonothioate monoesters containing the base labile 9-fluorenemethyl protecting group was key to the synthesis of both phosphopeptide mimetics. O-Boranophosphopeptides were synthesized by condensing O-(9-fluorenemethyl)-H-phosphonate to the peptide hydroxylic component (tyr, ser, or thr) followed by oxidation with borane complexes. Similarly, the synthesis of O-dithiophosphopeptides used the O-(9-fluorenemethyl)-H-phosphonothioate synthon and oxidation with elemental sulfur. Base elimination of the Fmol protecting group and cleavage from the solid support with concentrated ammonium hydroxide afforded the boranophosphopeptide and dithiophosphopeptide target compounds. Ac-YIIPLPG-NH2, having either dithiophosphoryl tyrosine or boranophosphoryltyrosine but no sequence specificity for Yersinia protein tyrosine phosphatase (PTP), was found to competitively inhibit this enzyme with KI values of 430 +/- 50 and 670 +/- 50 microM, respectively. In addition, both phosphopeptide analogues were resistant toward Yersinia PTP enzymatic hydrolysis. Under conditions (pH 8.0) where the phosphopeptide was rapidly dephosphorylated, the boranophosphopeptide hydrolyzed slowly (t1/2 = 15 h) and the dithiophosphopeptide was completely stable over 24 h.

Amino Acid Sequence↗

PubMed2000

Structural basis for activation of alpha-boranophosphate nucleotide analogues targeting drug-resistant reverse transcriptase.

AIDS chemotherapy is limited by inadequate intracellular concentrations of the active triphosphate form of nucleoside analogues, leading to incomplete inhibition of viral replication and the appearance of drug-resistant virus. Drug activation by nucleoside diphosphate kinase and inhibition of HIV-1 reverse transcriptase were studied comparatively. We synthesized analogues with a borano (BH(3)(-)) group on the alpha-phosphate, and found that they are substrates for both enzymes. X-ray structures of complexes with nucleotide diphosphate kinase provided a structural basis for their activation. The complex with d4T triphosphate displayed an intramolecular CH.O bond contributing to catalysis, and the R(p) diastereoisomer of thymidine alpha-boranotriphosphate bound like a normal substrate. Using alpha-(R(p))-boranophosphate derivatives of the clinically relevant compounds AZT and d4T, the presence of the alpha-borano group improved both phosphorylation by nucleotide diphosphate kinase and inhibition of reverse transcription. Moreover, repair of blocked DNA chains by pyrophosphorolysis was reduced significantly in variant reverse transcriptases bearing substitutions found in drug-resistant viruses. Thus, the alpha-borano modification of analogues targeting reverse transcriptase may be of generic value in fighting viral drug resistance.

Anti-HIV Agents↗

PubMed2005

An international dosimetry exchange for boron neutron capture therapy. Part I: Absorbed dose measurements.

An international collaboration was organized to undertake a dosimetry exchange to enable the future combination of clinical data from different centers conducting neutron capture therapy trials. As a first step (Part I) the dosimetry group from the Americas, represented by MIT, visited the clinical centers at Studsvik (Sweden), VTT Espoo (Finland), and the Nuclear Research Institute (NRI) at Rez (Czech Republic). A combined VTT/NRI group reciprocated with a visit to MIT. Each participant performed a series of dosimetry measurements under equivalent irradiation conditions using methods appropriate to their clinical protocols. This entailed in-air measurements and dose versus depth measurements in a large water phantom. Thermal neutron flux as well as fast neutron and photon absorbed dose rates were measured. Satisfactory agreement in determining absorbed dose within the experimental uncertainties was obtained between the different groups although the measurement uncertainties are large, ranging between 3% and 30% depending upon the dose component and the depth of measurement. To improve the precision in the specification of absorbed dose amongst the participants, the individually measured dose components were normalized to the results from a single method. Assuming a boron concentration of 15 microg g(-1) that is typical of concentrations realized clinically with the boron delivery compound boronophenylalanine-fructose, systematic discrepancies in the specification of the total biologically weighted dose of up to 10% were apparent between the different groups. The results from these measurements will be used in future to normalize treatment plan calculations between the different clinical dosimetry protocols as Part II of this study.

Biophysical Phenomena↗

PubMed2005

Synthesis of nucleoside boranophosphoramidate prodrugs conjugated with amino acids.

[structure: see text] Nucleoside boranophosphates and nucleoside amino acid phosphoramidates have been shown to be potent antiviral and anticancer agents with the potential to act as nucleoside prodrugs. A combination of these two types of compounds results in a boranophosphoramidate linkage between the nucleoside and amino acid. This new class of potential prodrugs is expected to possess advantages conferred by both types of parent compounds. Two approaches, specifically the H-phosphonate and oxathiaphospholane approaches, are described here to synthesize nucleoside boranophosphoramidate prodrugs conjugated with amino acids. The H-phosphonate approach involves a key intermediate, silylated nucleoside amino acid phosphoramidite 6, prepared from a series of reactions starting from nucleoside H-phosphonate in the presence of condensing reagent DPCP. Due to the lengthy procedure and the difficulties in removing DPCP from the final products, we switched to the oxathiaphospholane approach in which the DBU-assisted oxathiaphospholane ring-opening process constituted a key step for the generation of nucleoside amino acid boranophosphoramidates 24. We demonstrate that this key step did not cause any measurable C-racemization of boranophosphorylated amino acids 22. Diastereomers of compounds 24a-f were separated by RP-HPLC. An "adjacent"-type mechanism is proposed to explain the diastereomer ratio in the final products obtained via the oxathiaphospholane approach. A tentative assignment of configuration for the diastereomers was carried out based on the mechanism, molecular modeling, and (1)H NMR. Conclusively, the oxathiaphospholane methodology proved to be more facile and efficient than H-phosphonate chemistry in the preparation of the nucleoside amino acid boranophosphoramidate analogues that are promising as a new type of antiviral prodrugs.

Amides↗