Unraveling complex small-molecule binding mechanisms by using simple NMR spectroscopy

Heteronuclear NMR spectroscopy provides a unique way to obtain site-specific information about protein-ligand interactions. Usually, such studies rely on the availability of isotopically labeled proteins, thereby allowing both editing of the spectra and ligand signals to be filtered out. Herein, we report that the use of the methyl SOFAST correlation experiment enables the determination of site-specific equilibrium binding constants by using unlabeled proteins. By using the binding of L- and D-tryptophan to serum albumin as a test case, we determined very accurate dissociation constants for both the high- and low-affinity sites present at the protein surface. The values of site-specific dissociation constants were closer to those obtained by isothermal titration calorimetry than those obtained from ligand-observed methods, such as saturation transfer difference. The possibility of measuring ligand binding to serum albumin at physiological concentrations with unlabeled proteins may open up new perspectives in the field of drug discovery.     

Tetramethylnorbornadiene, a versatile alkene for cyclopentenone synthesis through intermolecular Pauson-Khand reactions

1,2,3,4-Tetramethyl-bicyclo[2.2.1]hepta-2,5-diene (TMNBD, for tetramethylnorbornadiene) has been prepared and used successfully as an acetylene equivalent in the synthesis of substituted cyclopentenones. TMNBD is easily accessible on a multigram scale and displays excellent reactivity toward the intermolecular Pauson-Khand reaction. Conjugate additions on the resulting tricyclic compounds proceed with exquisite diastereoselectivity. The retro-Diels-Alder reaction of these TMNBD derivatives occurs under much smoother conditions than those required for its norbornadiene homologues.     

Trigocherrin A, the first natural chlorinated daphnane diterpene orthoester from Trigonostemon cherrieri

Trigocherrin A, a chlorinated and highly oxygenated daphnane diterpenoid orthoester (DDO), was isolated from the bark of Trigonostemon cherrieri. Trigocherrin A is the first example of a naturally occurring halogenated DDO. Its structure was elucidated by comprehensive analysis of NMR spectroscopic data, and its absolute configuration was determined by comparison of experimental and theoretically calculated ECD spectra. Trigocherrin A exhibited a potent and selective effect against Chikungunya virus in Vero cells.     

Collaborative study for the detection of toxic compounds in shellfish extracts using cell-based assays. Part I: screening strategy and pre-validation study with lipophilic marine toxins

Human poisoning due to consumption of seafood contaminated with phycotoxins is a worldwide problem, and routine monitoring programs have been implemented in various countries to protect human consumers. Following successive episodes of unexplained shellfish toxicity since 2005 in the Arcachon Bay on the French Atlantic coast, a national research program was set up to investigate these atypical toxic events. Part of this program was devoted to fit-for-purpose cell-based assays (CBA) as complementary tools to collect toxicity data on atypical positive-mouse bioassay shellfish extracts. A collaborative study involving five laboratories was conducted. The responses of human hepatic (HepG2), human intestinal (Caco2), and mouse neuronal (Neuro2a) cell lines exposed to three known lipophilic phycotoxins-okadaic acid (OA), azaspiracid-1 (AZA1), and pectenotoxin-2 (PTX2)-were investigated. A screening strategy composed of standard operating procedures and a decision tree for dose-response modeling and assay validation were designed after a round of "trial-and-error" process. For each toxin, the shape of the concentration-response curves and the IC(50) values were determined on the three cell lines. Whereas OA induced a similar response irrespective of the cell line (complete sigmoid), PTX2 was shown to be less toxic. AZA1 induced cytotoxicity only on HepG2 and Neuro2a, but not on Caco2. Intra- and inter-laboratory coefficients of variation of cell responses were large, with mean values ranging from 35 to 54 % and from 37 to 48 %, respectively. Investigating the responses of the selected cell lines to well-known toxins is the first step supporting the use of CBA among the panel of methods for characterizing atypical shellfish toxicity. Considering these successful results, the CBA strategy will be further applied to extracts of negative, spiked, and naturally contaminated shellfish tissues.     

A novel method for quantification of sulfolane (a metabolite of busulfan) in plasma by gas chromatography–tandem mass spectrometry

The role of busulfan (Bu) metabolites in the adverse events seen during hematopoietic stem cell transplantation and in drug interactions is not explored. Lack of availability of established analytical methods limits our understanding in this area. The present work describes a novel gas chromatography-tandem mass spectrometric assay for the analysis of sulfolane (Su) in plasma of patients receiving high-dose Bu. Su and Bu were extracted from a single 100 μL plasma sample by liquid-liquid extraction. Bu was separately derivatized with 2,3,5,6-tetrafluorothiophenolfluorinated agent. Mass spectrometric detection of the analytes was performed in the selected reaction monitoring mode on a triple quadrupole instrument after electronic impact ionization. Bu and Su were analyzed with separate chromatographic programs, lasting 5?min each. The assay for Su was found to be linear in the concentration range of 20-400?ng/mL. The method has satisfactory sensitivity (lower limit of quantification, 20?ng/mL) and precision (relative standard deviation less than 15?%) for all the concentrations tested with a good trueness (100?±?5?%). This method was applied to measure Su from pediatric patients with samples collected 4?h after dose 1 (n?=?46), before dose 7 (n?=?56), and after dose 9 (n?=?54) infusions of Bu. Su (mean?±?SD) was detectable in plasma of patients 4?h after dose 1, and higher levels were observed after dose 9 (249.9?±?123.4?ng/mL). This method may be used in clinical studies investigating the role of Su on adverse events and drug interactions associated with Bu therapy.     

Hydrogels Incorporating GdDOTA: Towards Highly Efficient Dual T(1) /T(2) MRI Contrast Agents

Do not tumble dry: Gadolinium-DOTA encapsulated into polysaccharide nanoparticles (GdDOTA?NPs) exhibited high relaxivity (r(1) =101.7?s(-1) mM(-1) per Gd(3+) ion at 37?°C and 20?MHz). This high relaxation rate is due to efficient Gd loading, reduced tumbling of the Gd complex, and the hydrogel nature of the nanoparticles. The efficacy of the nanoparticles as a T(1) /T(2) dual-mode contrast agent was studied in C6 cells.     

Detection of peginesatide in equine serum using liquid chromatography-tandem mass spectrometry for doping control purposes

Erythropoietin (EPO) and its recombinant analogues are suspected to be illicitly administered to horses for performance enhancing purposes and, consequently, prohibited in equine sports. Recently, a new erythropoiesis-stimulating agent, peginesatide (Omontys, formerly referred to as Hematide), belonging to the upcoming class of EPO-mimetic peptides, received approval for the treatment of anaemia in humans with chronic kidney disease on dialysis. As the pegylated dimeric peptide of approximately 45 kDa without sequence homology to EPO is not detectable by conventional EPO detection assays, specific methods are bound to be established for horse sports drug testing. Thus, by fortifying equine serum with peginesatide, an approach consisting of a proteolytic digestion with subtilisin after protein precipitation was developed, eventually targeting a proteotypic and xenobiotic pentapeptide which is easily accessible to liquid chromatography- tandem mass spectrometry analysis. The method was validated for qualitative purposes and demonstrated to be specific, precise (relative standard deviations below 14%), sensitive (limit of detection 10 ng mL(-1)) and linear. Being simple, cost-effective and readily transferable to other doping control laboratories, a mass spectrometric assay for the detection of therapeutic concentrations of peginesatide in equine serum is, in terms of preventive doping research, applicable to routine analysis shortly after approval of the drug.     

The smallest stable fullerene, M@C28 (m = Ti, Zr, U): stabilization and growth from carbon vapor

The smallest fullerene to form in condensing carbon vapor has received considerable interest since the discovery of Buckminsterfullerene, C(60). Smaller fullerenes remain a largely unexplored class of all-carbon molecules that are predicted to exhibit fascinating properties due to the large degree of curvature and resulting highly pyramidalized carbon atoms in their structures. However, that curvature also renders the smallest fullerenes highly reactive, making them difficult to detect experimentally. Gas-phase attempts to investigate the smallest fullerene by stabilization through cage encapsulation of a metal have been hindered by the complexity of mass spectra that result from vaporization experiments which include non-fullerene clusters, empty cages, and metallofullerenes. We use high-resolution FT-ICR mass spectrometry to overcome that problem and investigate formation of the smallest fullerene by use of a pulsed laser vaporization cluster source. Here, we report that the C(28) fullerene stabilized by encapsulation with an appropriate metal forms directly from carbon vapor as the smallest fullerene under our conditions. Its stabilization is investigated, and we show that M@C(28) is formed by a bottom-up growth mechanism and is a precursor to larger metallofullerenes. In fact, it appears that the encapsulating metal species may catalyze or nucleate endohedral fullerene formation.     

Histone-catalyzed cleavage of nucleosomal DNA containing 2-deoxyribonolactone

Oxidized abasic sites such as 2-deoxyribonolactone (L) are produced in DNA by a variety of oxidizing agents, including potent cytotoxic antitumor natural products. 2-Deoxyribonolactone is labile under alkaline conditions, but its half-life in free DNA at pH 7.5 is approximately 1 week. Independent generation of L at defined positions within nucleosomes reveals that the histone proteins catalyze strand scission and increase the rate between 11- and ～43-fold. Mechanistic studies indicate that DNA-protein cross-links are not intermediates en route to strand scission and that C2 deprotonation is the rate-determining step. The use of mutant histone H4 proteins demonstrates that the lysine-rich tail that is often post-translationally modified in cells contributes to the cleavage of L but is not the sole source of the enhanced cleavage rates. Consideration of DNA repair in cells suggests that L formation in nucleosomal DNA as part of bistranded lesions by antitumor antibiotics results in de facto double strand breaks, the most deleterious form of DNA damage.