A total synthesis of spiruchostatin A

We achieved the total synthesis of the histone deacetylase inhibitor spiruchostatin A, as the prelude to the preparation of a combinatorial library of its analogues. Two key reactions were an asymmetric acetate aldol reaction using a Zr-enolate and macrolactonization using the Shiina method.     

Total synthesis of spiruchostatin B, a potent histone deacetylase inhibitor, from a microorganism

The first total synthesis of spiruchostatin B, a potent histone deacetylase inhibitor, was achieved in a convergent manner; the synthesis established stereochemistry at the C5' position.     

Total synthesis of spiruchostatin B aided by an automated synthesizer

The total synthesis of a natural product HDAC inhibitor, spiruchostatin B, was successfully achieved. A 5-step synthesis that included an asymmetric aldol reaction was carried out in an automated synthesizer to provide an (E)-(S)-3-hydroxy-7-thio-4-heptenoic acid segment that is the crucial structure of cysteine-containing, depsipeptidic natural products such as spiruchostatins, FK228, FR901375, and largazole for their inhibitory activity against HDACs.     

Total Synthesis of the Bicyclic Depsipeptide HDAC Inhibitors Spiruchostatins A and B, 5′′‐epi‐Spiruchostatin B,FK228 (FR901228) and Preliminary Evaluation of Their Biological Activity

The bicyclic depsipeptide histone deacetylase (HDAC) inhibitors spiruchostatins A and B, 5′′‐epi‐spiruchostatin B and FK228 were efficiently synthesized in a convergent and unified manner. The synthetic method involved the following crucial steps: i) a Julia–Kocienski olefination of a 1,3‐propanediol‐derived sulfone and a L ‐ or D ‐malic acid‐derived aldehyde to access the most synthetically challenging unit, (3S or 3R,4E)‐3‐hydroxy‐7‐mercaptohept‐4‐enoic acid, present in a D ‐alanine‐ or D ‐valine‐containing segment; ii) a condensation of a D ‐valine‐D ‐cysteine‐ or D ‐allo‐isoleucine‐D ‐cysteine‐containing segment with a D ‐alanine‐ or D ‐valine‐containing segment to directly assemble the corresponding seco‐acids; and iii) a macrocyclization of a seco‐acid using the Shiina method or the Mitsunobu method to construct the requisite 15‐ or 16‐membered macrolactone. The present synthesis has established the C5′′ stereochemistry of spiruchostatin B. In addition, HDAC inhibitory assay and the cell‐growth inhibition analysis of the synthesized depsipeptides determined the order of their potency and revealed some novel aspects of structure–activity relationships. It was also found that unnatural 5′′‐epi‐spiruchostatin B shows extremely high selectivity (ca. 1600‐fold) for class I HDAC1 (IC₅₀=2.4 nM ) over class II HDAC6 (IC₅₀=3900 nM ) with potent cell‐growth‐inhibitory activity at nanomolar levels of IC₅₀ values.     

Intercalation and photophysical characterization of 1-pyrenemethylamine in zirconium phosphate layered materials

The ion exchange of the luminescent probe 1-pyrenemethylamine (PYMA) into zirconium phosphate (ZrP) layered materials has been accomplished. The matrices used were the hexahydrated 10.3 A phase of ZrP (10.3 A ZrP, where 10.3 A represents the interlayer distance) and butylammonium-exchanged ZrP (BAZrP) with an expanded 18.6 A interlayer distance. The XRPD patterns for the 10.3 A ZrP after PYMA exchange (PYMA-exchanged ZrP), at high PYMA concentrations, show an increase in the interlayer distance from 10.3 A in unexchanged 10.3 A ZrP to 23.5 A in PYMA-exchanged ZrP, indicating PYMA intercalation. The luminescence spectrum for the PYMA-exchanged ZrP exhibits an excimer band at 458 nm that is absent in the luminescence spectrum of PYMA in aqueous solution at low concentrations. The intensity of the excimer emission increased at low PYMA concentrations. These results are in contrast to experiments using the BAZrP matrix. The XRPD patterns for PYMA-exchanged BAZrP do not show changes in the interlayer distance, which suggests that PYMA is not being intercalated and is only surface bound. The luminescence spectrum for PYMA-exchanged BAZrP exhibits a lower emission intensity in its excimer band, at different PYMA concentrations, compared with the PYMA-exchanged ZrP excimer band. For PYMA-exchanged ZrP, we propose a process in which exchange at low PYMA concentrations occurs at external surface sites with clustering promoting excimer formation followed by exchange at high PYMA concentrations occurring at interior sites reducing excimer formation.     

The mobile proton in polyalanine peptides

Ion mobility measurements have been performed for protonated polyalanine peptides (A10 + H+, A15 + H+, A20 + H+, A25 + H+, and A15NH2 + H+) as a function of temperature using a new high-temperature drift tube. Peaks due to helices and globules were found at room temperature for all peptides, except for A10 + H+ (where only the globule is present). As the temperature is increased, the helix and globule peaks broaden and merge to give a single narrow peak. This indicates that the two conformations interconvert rapidly at elevated temperatures. The positions of the merged peaks show that A15 + H+ and A15NH2 + H+ spend most of their time as globules when heated, while A20 + H+ and A25 + H+ spend most of their time as helices. The helix/globule transitions are almost certainly accompanied by intramolecular proton transfer, and so, these results suggest that the proton becomes mobile (able to migrate freely along the backbone) at around 450 K. The peptides dissociate as the temperature is increased further to give predominantly the bn(+), b(n-1)(+), b(n-2)(+), ... series of fragment ions. There is a correlation between the ease of fragmentation and the time spent in the helical conformation for the An + H+ peptides. Helix formation promotes dissociation because it pools the proton at the C-terminus where it is required for dissociation to give the observed products. In addition to the helix and globule, an antiparallel helical dimer is observed for the larger peptides. The dimer can be collisionally dissociated by injection into the drift tube at elevated kinetic energies.     

Adsorption-desorption isotherm hysteresis of beta-lactoglobulin A with a weakly hydrophobic surface.

Adsorption-desorption isotherms of bovine beta-lactoglobulin A (beta-lact A) on a weakly hydrophobic stationary phase (C1-ether) were measured by frontal analysis. The adsorption isotherms obtained at different pH were found to be dramatically different in shape, column capacity and desorption reversibility. At pH 4.5, an S-shaped adsorption isotherm was observed whereas at pH 6.0 a Langmuir isotherm was found. In addition, the desorption isotherm at pH 6.0 was found to overlap with the adsorption isotherm, and the adsorption-desorption process of beta-lact A under this condition could be characterized by a fully reversible Langmuir model. The desorption isotherm at pH 4.5, however, did not retrace the adsorption isotherm, resulting in hysteresis loops. A higher aggregate (tetramer) of beta-lact A is shown to be in an equilibrium with the beta-lact A protomer (dimer) at pH 4.5 whereas the dimer alone is predominant at pH 6.0. It is further shown that changes in the absorption coefficient between the adsorption and the desorption cycles for the tetramer at pH 4.5 can account for the hysteresis. The results demonstrate that pH can be a sensitive parameter in protein adsorption isotherm behavior and ultimately the behavior of species in preparative-scale chromatography.     

Isomerization of alkenes during drying over zeolites

We observed that zeolite 5A, a zeolite commonly used for drying, isomerized 1-butene and 1-hexene at room temperature. The activity for 1-butene isomerization on 3A, 4A, 5A and 13X zeolites at temperatures of 300 to 565 K is reported.     

The HLA-A2-supermotif: a QSAR definition

Identification of epitopes capable of binding multiple HLA types will significantly rationalise the development of epitope-based vaccines. A quantitative method assessing the contribution of each amino acid at each position was applied to over 500 nonamer peptides binding to 5 MHC alleles--A*0201, A*0202, A*0203, A*0206 and A*6802--which together define the HLA-A2-like supertype. FXIGXI (L)IFV was identified as a supermotif for the A2-supertype based on the contributions of the common preferred amino acids at each of the nine positions. The results indicate that HLA-A*6802 is an intermediate allele standing between A2 and A3 supertypes: at anchor position 2 it is closer to A3 and at anchor position 9 it is nearer to A2. Models are available free on-line at http://www.jenner.ac.uk/MHCPred and can be used for binding affinity prediction.     

Crystal structure of a genomically encoded fosfomycin resistance protein (FosA) at 1.19 A resolution by MAD phasing off the L-III edge of Tl(+)

The fosfomycin resistance protein (FosA) catalyzes the Mn(II)- and K+-dependent addition of glutathione to the oxirane of the antibiotic fosfomycin. The crystal structure of FosA from Pseudomonas aeruginosa was solved at a resolution of 1.19 A by multiwavelength anomalous diffraction at the L-III edge of a Tl+ derivative. The structure solution took advantage of the ability of Tl+ to substitute for K+. The existence of multiple Tl sites in the asymmetric unit suggests that this may be a generally useful technique for phasing protein crystal structures. A 1.35 A resolution structure with phosphate bound in the active site shows that the Mn(II) center has a rare four-coordinate geometry. The structure of the fosfomycin complex at 1.19 A resolution indicates that the Mn(II) center is close to five-coordinate with trigonal bipyramidal geometry and a ligand set consisting of two histidines (H7 and H64) and one phosphonate oxygen occupying the equatorial sites and the carboxylate of E110 at one of the apical sites. The oxirane oxygen of the substrate is located at the other apical site but is 0.2 A beyond the average Mn-O distance for five-coordinate Mn(II). The Mn(II) center is proposed to stabilize the alkoxide in the transition state, while the nearby hydroxyl group of T9 acts as a proton donor in the reaction. The K+ ion located 6.5 A from the Mn(II) appears to help orient the substrate for nucleophilic attack.     

n-Decyl-glucopyranoside and n-decyl-maltopyranoside gibbs monolayers. Phase changes in the dilute liquid-expanded range

Surface tension isotherms were recorded for n-decyl-beta-d-glucopyranoside (Glu) and n-decyl-beta-D-maltopyranoside (Mal) solutions at temperatures of 8, 22, and 29 degrees C. Comparison was made with isotherms of n-decyl-beta-D-thiomaltopyranoside (S-Mal) at 22 degrees C. In addition to the transition from the gaseous to the liquid-expanded (LE) state, a second transition was observed in the early stages of the LE regime for Glu, Mal, and S-Mal at room temperature. The adsorption isotherm of Mal and Glu obtained at 22 degrees C shows the presence of an adsorption step at an average area/molecule of about 79 A2 between, approximately, 0.02 and 0.1 mM (the critical micelle concentration (cmc) is 2 mM) and 0.015 and 0.03 mM (the cmc is 2 mM), respectively. Similarly, for S-Mal an adsorption plateau is observed at 70 A2 between 0.01 and 0.03 mM (the cmc is 0.7 mM). From the temperature dependence of the surface tension, we have seen that there are considerable differences in the adsorption of Glu and Mal. For Mal, the adsorption plateau is also observed at 29 degrees C at around 79 A2, whereas Glu exhibits no adsorption plateau at this temperature. At 8 degrees C, both Mal and Glu exhibit saturation behavior in the dilute part of the liquid-expanded range, but at this temperature the average molecular areas are lower than at 22 degrees C: around 66 A2 for Glu and 75 A2 for Mal. Thus, the temperature sensitivity of Glu is considerably greater than for Mal in this range. The saturation regime coincides with a pronounced surface entropy minimum for Mal. The transition in the dilute liquid-expanded range supposedly occurs from a state with deformed surface micelles arranged in a hexagonal pattern, referred to as the granular range, to a true LE monolayer with a fluid hydrocarbon tail layer covering the entire surface.     

A novel method for monolayer deposition: water seepage method

A method has been developed to deposit monolayers of a supramolecular assembly of amphiphiles onto solid substrates. A stable monolayer in a solid state is allowed to form at the air-water interface. The subphase is then allowed to seep out at a controlled rate and the monolayer descends and ultimately is deposited on the solid substrate. The quality of the films thus formed is comparable to that of the film deposited by the Langmuir-Blodgett technique. The method is simple, cost-effective and adaptable for scaling up for industrial application or scaling down for specialized use.     

The Emission in the Acetone Photochemical System

The emission in the acetone photochemical system has been measured as a function of irradiating time and pressure. The emission yield generally increases with increase in irradiating time at both 3130 and 2654A. The increase of emission yields is due to the sensitized phosphorescence of the product biacetyl. The higher emission yield and lower biacetyl quantum yields at 3130A than that at 2654A support for that most of the excited acetone molecules are in the triplet state at 3130A.     

Detection of DNA fragments separated by capillary electrophoresis based on their native fluorescence inside a sheath flow

A scheme for the separation and detection of native DNA fragments in capillary electrophoresis is presented. A UV laser at 275 nm excites the intrinsic fluorescence of the fragments, which is greatly enhanced at pH 2.8. To provide a compatible system, methylcellulose-based size separation is performed at the identical pH. A sheath-flow arrangement isolates the detection region from the linear polymer for a reduced background level. The performance is an order-of-magnitude enhancement in detectability over absorption detection. We also uncovered a selective degradation/ligation process at these pH conditions that may be useful as additional selectivity for DNA characterization.     

Absolute cross sections for electronic excitations of cytosine by low energy electron impact

The absolute cross sections (CSs) for electronic excitations of cytosine by electron impact between 5 and 18 eV were measured by electron-energy-loss (EEL) spectroscopy of the molecule deposited at low coverage on an inert Ar substrate. The lowest EEL features found at 3.55 and 4.02 eV are ascribed to transitions from the ground state to the two lowest triplet 1?(3)A(')(π→π(?)) and 2?(3)A(')(π→π(?)) valence states of the molecule. Their energy dependent CSs exhibit essentially a common maximum at about 6 eV with a value of 1.84×10(-17)?cm(2) for the former and 4.94×10(-17)?cm(2) for the latter. In contrast, the CS for the next EEL feature at 4.65 eV, which is ascribed to the optically allowed transition to the 2?(1)A(')(π→π(?)) valence state, shows only a steep rise to about 1.04×10(-16)?cm(2) followed by a monotonous decrease with the incident electron energy. The higher EEL features at 5.39, 6.18, 6.83, and 7.55 eV are assigned to the excitations of the 3?(3,1)A(')(π→π(?)), 4?(1)A(')(π→π(?)), 5?(1)A(')(π→π(?)), and 6?(1)A(')(π→π(?)) valence states, respectively. The CSs for the 3?(3,1)A(') and 4?(1)A(') states exhibit a common enhancement at about 10 eV superimposed on a more or less a steep rise, reaching, respectively, a maximum of 1.27 and 1.79×10(-16)?cm(2), followed by a monotonous decrease. This latter enhancement and the maximum seen at about 6 eV in the lowest triplet states correspond to the core-excited electron resonances that have been found by dissociative electron attachment experiments with cytosine in the gas phase. The weak EEL feature found at 5.01 eV with a maximum CS of 3.8×10(-18)?cm(2) near its excitation threshold is attributed to transitions from the ground state to the 1?(3,1)A(")(n→π(?)) states. The monotonous rise of the EEL signal above 8 eV is attributed to the ionization of the molecule. It is partitioned into four excitation energy regions at about 8.55, 9.21, 9.83, and 11.53 eV, which correspond closely to the ionization energies of the four highest occupied molecular orbitals of cytosine. The sum of the ionization CS for these four excitation regions reaches a maximum of 8.1×10(-16)?cm(2) at the incident energy of 13 eV.     

High-performance liquid chromatographic assay for pilocarpine in aqueous humor

A high-performance liquid chromatographic assay for pilocarpine has been developed for the determination of pilocarpine in aqueous humor. A structurally similar internal standard is used, and pilocarpine is separated from isopilocarpine under the chromatographic conditions used. A 100-microliter sample is mixed with an aliquot of internal standard at pH 8.3 and extracted with methylene chloride. The extract is evaporated to dryness and the alkaloids are quaternized with p-nitrobenzyl bromide. Following the quaternization, the sample is evaporated to dryness, washed and diluted with a mobile phase--triethylamine mixture and analyzed by high-performance liquid chromatography using a reversed-phase octadecylsilane column with detection at a wavelength of 254 nm. This is a highly sensitive, reproducible and selective assay for measuring pilocarpine at physiological levels in individual aqueous humor samples.     

Simultaneous quantitation of the highly lipophilic atovaquone and hydrophilic strong basic proguanil and its metabolites using a new mixed-mode SPE approach and steep-gradient LC

A bioanalytical method is described for the simultaneous quantitative analysis of the highly lipophilic atovaquone and the strong basic proguanil with metabolites in plasma. The drugs are extracted from protein precipitated plasma samples on a novel mixed-mode solid-phase extraction (SPE) column containing carboxypropyl and octyl silica as functional groups. The analytes are further separated and quantitated using a steep-gradient liquid chromatographic method on a Zorbax SB-CN column with UV detection at 245 nm. Two different internal standards (IS) are used in the method to compensate for both types of analytes. A structurally similar IS to atovaquone is added with acetonitrile to precipitate proteins from plasma. A structurally similar IS to proguanil and its metabolites is added with phosphate buffer before samples are loaded onto the SPE columns. A single elution step is sufficient to elute all analytes. The method is validated according to published guidelines and shows excellent performance. The within-day precisions, expressed as relative standard deviation, are lower than 5% for all analytes at three tested concentrations within the calibration range. The between-day precisions are lower than 13% for all analytes at the same tested concentrations. The limit of quantitation is 25 nM for the basic substances and 50 nM for atovaquone. Several considerations regarding development and optimization of a method for determination of analytes with such a difference in physiochemical properties are discussed.     

Terthiophene radical cations end-capped by bicyclo[2.2.2]octene units: formation of bent pi-dimers mutually attracted at the central position

A terthiophene fused with bicyclo[2.2.2]octene units only at both ends was newly synthesized. Since there is no steric hindrance at the central position, this terthiophene has a possibility to interact only at the central position. One-electron oxidation of this terthiophene afforded a highly stable radical-cation salt as deep blue crystals. The result of X-ray crystal structural analysis demonstrated a characteristically bent pi-dimereric structure, which is formed by mutual attraction of single radical-cation species at the central position to minimize the steric repulsion. Remarkably short intermolecular distances between the central thiophene rings of each unit of the dimeric pair, that is, 2.976(10) A for Cbeta-Cbeta, 3.091(10) A for Calpha-Calpha, and 3.779(3) A for S-S, are good indication of the existence of attracting interaction, which was confirmed by theoretical calculations. This interaction was experimentally demonstrated by the reversible formation of the pi-dimer in CH2Cl2 solution using ESR and UV-vis-NIR spectroscopy. The crystal of the pi-dimer is in its singlet state and ESR silent in the solid state at 300 K, but the signal of a triplet state of the pi-dimer was observed by heating the solid at 400 K. This indicates that this pi-dimer has a quite small triplet-singlet enegy gap and the triplet state is thermally accessible.     

The radiation-induced copolymerization of tetrafluoroethylene and styrene at high pressure

The radiation-induced copolymerization of tetrafluoroethylene (A) and styrene (B) was studied in bulk and in perfluorotoluene at 22°C at autogenous pressure and 260 and 510 MPa. The reactivity ratio for addition to A-ended radicals, r_A, is effectively zero at the two lower pressures and is in the range 0.002–0.008 at 510 MPa. The other reactivity ratio, r_B, is 6 at autogenous pressure and also at 260 and 510 MPa if the A content of the charge is less than 50%. If the A content is greater than 95%, r_B appears to be 100 at pressures of 260 and 510 MPa. The apparent variation in r_B cannot be explained by invoking a penultimate unit effect for B-ended radicals. Polymerization rates scatter somewhat, but all rates are quite small when the A content of the charge is in the range 95–99.8%. Polymers containing as much as 66% A appear to be inherently benzene soluble but frequently contain some gel because of radiation-induced crosslinking after their formation. No very high polymers were formed that contained more than a few percent A, even at high pressure. Features that complicated the study were immiscibility of the liquid monomers, extreme variation of the monomer—copolymer compatibility with charge composition, and freezing of B at high pressure.     

X-ray absorption spectroscopic characterization of the molybdenum site of Escherichia coli dimethyl sulfoxide reductase

Structural studies of dimethyl sulfoxide (DMSO) reductases were hampered by modification of the active site during purification. We report an X-ray absorption spectroscopic analysis of the molybdenum active site of Escherichia coli DMSO reductase contained within its native membranes. The enzyme in these preparations is expected to be very close to the form found in vivo. The oxidized active site was found to have four Mo-S ligands at 2.43 A, one Mo=O at 1.71 A, and a longer Mo-O at 1.90 A. We conclude that the oxidized enzyme is a monooxomolybdenum(VI) species coordinated by two molybdopterin dithiolenes and a serine. The bond lengths determined for E. coli DMSO reductase are very similar to those determined for the well-characterized Rhodobacter sphaeroides DMSO reductase, suggesting similar active site structures for the two enzymes. Furthermore, our results suggest that the form found in vivo is the monooxobis(molybdopterin) species.