Ionic-liquid-supported peptide synthesis demonstrated by the synthesis of Leu(5)-enkephalin

A new strategy for the synthesis of oligopeptides was developed using an ionic liquid as a soluble support. The efficiency of this ionic liquid-phase approach was demonstrated by the synthesis of a bioactive pentapeptide, Leu(5)-enkephalin, in good yield and reasonable purity. The structures and purities of the reaction intermediates in each step were verified easily by routine spectroscopic analysis, and no chromatographic procedures were needed during the synthesis.     

Structure and dynamics of the hydrogen-bond network around (R,R)-pterocarpans with biological activity in aqueous solution

Molecular dynamics simulations were carried out in the presence of 2380 water molecules (TIP3P) to explore the conformational preferences of 3,9-dimethoxy-4-prenylpterocarpan (bitucarpin A) and 3,9-dihydroxy-4,8-diprenylpterocarpan (erybraedin C) and the H-bond network around them, using the empirical general AMBER force field (GAFF). Specific angle and torsional parameters have been improved in order to match the geometries of the minimum energy structures obtained from an earlier DFT/ab initio study in vacuo, taking into account a few configurations [Alagona, G.; Ghio, C.; Monti, S. Phys. Chem. Chem. Phys. 2004, 6, 2849-2857]. RESP partial charges were assigned to reproduce the electrostatic potential determined at the HF/6-31G level of theory. The analysis of trajectories allowed the conformations of bitucarpin and erybraedin as well as the distribution of water molecules around them to be elucidated. During one of the simulations only, the scaffold of erybraedin undergoes interconversion from its most stable Ht conformation to the Ot one and vice versa. Radial distribution functions, coordination numbers, and angular distributions put forward the extent of solvent structure and the hydrogen bonding behavior of their various (methoxy, hydroxyl, or ethereal) oxygen atoms. The distribution of solvent molecules in the first and second solvation shells as well as the residence times for the different solute-solvent interacting sites have been considered.     

Biomimetic dyes as affinity chromatography tools in enzyme purification

Affinity adsorbents based on immobilized triazine dyes offer important advantages circumventing many of the problems associated with biological ligands. The main drawback of dyes is their moderate selectivity for proteins. Rational attempts to tackle this problem are realized through the biomimetic dye concept according to which new dyes, the biomimetic dyes, are designed to mimic natural ligands. Biomimetic dyes are expected to exhibit increased affinity and purifying ability for the targeted proteins. Biocomputing offers a powerful approach to biomimetic ligand design. The successful exploitation of contemporary computational techniques in molecular design requires the knowledge of the three-dimensional structure of the target protein, or at least, the amino acid sequence of the target protein and the three-dimensional structure of a highly homologous protein. From such information one can then design, on a graphics workstation, the model of the protein and also a number of suitable synthetic ligands which mimic natural biological ligands of the protein. There are several examples of enzyme purifications (trypsin, urokinase, kallikrein, alkaline phosphatase, malate dehydrogenase, formate dehydrogenase, oxaloacetate decarboxylase and lactate dehydrogenase) where synthetic biomimetic dyes have been used successfully as affinity chromatography tools.     

Optical CO(2) sensor of the combination of colorimetric change of alpha-naphtholphthalein in poly(isobutyl methacrylate) and fluorescent porphyrin in polystyrene

An optical CO₂ sensor based on the overlay of the CO₂ induced absorbance change of pH indicator dye α-naphtholphthalein in poly(isobutyl methacrylate) (polyIBM) layer with the fluorescence of tetraphenylporphyrin (TPP) in polystyrene layer is developed. The observed luminescence intensity from TPP at 655 nm increased with increasing the CO₂ concentration. The ratio I₁₀₀/I₀ value of the sensing film consisting of α-naphtholphthalein in polyIBM and TPP in polystyrene layer, where I₀ and I₁₀₀ represent the detected luminescence intensities from a layer exposed to argon and CO₂ saturated conditions, respectively, that the sensitivity of the sensor, is estimated to be 192. The response and recovery times of the sensing film are less than 6.0 s for switching from argon to CO₂, and for switching from CO₂ to argon. The signal changes are fully reversible and no hysterisis is observed during the measurements. The highly sensitive optical CO₂ sensor based on fluorescence intensity changes of TPP due to the absorption change of α-naphtholphthalein in polyIBM layer with CO₂ is achieved.     

Electron-transfer reaction of cinnamic acids and their methyl esters with the DPPH(*) radical in alcoholic solutions

The kinetic behavior of cinnamic acids, their methyl esters, and two catechols 1-10 (ArOH) in the reaction with DPPH(*) in methanol and ethanol is not compatible with a reaction mechanism that involves hydrogen atom abstraction from the hydroxyl group of 1-10 by DPPH(*). The rate of this reaction at 25 degrees C is, in fact, comparatively fast despite that the phenolic OH group of ArOH is hydrogen bonded to solvent molecules. The observed rate constants (k(1)) relative to DPPH(*) + ArOH are 3-5 times larger for the methyl esters than for the corresponding free acids and, for the latter, decrease as their concentration is increased according to the relation k(1) = B/[ArOH](0)(m), where k(1) is given in units of M(-1) s(-1), m is ca. 0.5, and B ranges from 0.02 (p-coumaric acid) to ca. 3.48 (caffeic acid) in methanol and from 0.04 (p-coumaric acid) to ca. 13 (sinapic acid) in ethanol. Apparently, the reaction mechanism of DPPH(*) + ArOH involves a fast electron-transfer process from the phenoxide anion of 1-10 to DPPH(*). Kinetic analysis of the reaction sequence for the free acids leads to an expression for the observed rate constant, k(1), proportional to [ArOH](0)(-1/2) in excellent agreement with the experimental behavior of these phenols. The experimental results are also interpreted in terms of the influence that adventitious acids or bases present in the solvent may have. These impurities dramatically influence the ionization equilibrium of phenols and cause a reduction or an enhancement, respectively, of the measured rate constants.     

A rapid and sensitive method for simultaneous determination of lamivudine and zidovudine in human serum by on-line solid-phase extraction coupled to liquid chromatography/tandem mass spectrometry detection

A method based on solid-phase extraction (SPE) coupled to high-performance liquid chromatography (HPLC) with positive ion electrospray ionization tandem mass spectrometry (ESI-MS/MS) detection was developed for the simultaneous determination of lamivudine (3TC) and zidovudine (AZT) in human serum, using didanosine (ddI) as internal standard. The acquisition was performed in multiple reaction monitoring (MRM) mode, monitoring the transitions m/z 230.0 --> 111.8 for 3TC, m/z 268.1 --> 126.8 for AZT, and m/z 237.2 --> 136.8 for ddI. The limits of detection and quantitation were 3 and 10 ng/mL for 3TC, and 5 and 15 ng/mL for AZT. The method was linear in the studied ranges (10-1500 ng/mL for 3TC and 15-3000 ng/mL for AZT), with r(2) > 0.99 for each drug, and the run time was 4 min. The intra-assay precisions (%) were in the ranges 1.9-8.7 (3TC) and 2.2-8.9 (AZT), the inter-assay precisions were in the ranges 2.6-9.0 (3TC) and 4.2-8.1 (AZT), and the intra- and inter-assay accuracies were >97% for both drugs. The absolute recoveries were 95-99% for 3TC (45, 600 and 1200 ng/mL) and 104-112% for AZT (45, 1000 and 2400 ng/mL). The analytical method was applied to a bioequivalence study in which 24 healthy adult volunteers received single oral doses of the reference formulation and two test combined AZT/3TC tablets, in an open, three-period, balanced, randomized, crossover protocol. Based on the 90% confidence interval of the individual ratios (test formulation/reference formulation) for C(max) (peak serum concentration) and AUC(0-inf) (extrapolated area under the serum concentration vs. time curve from time zero to infinity), it was concluded that the two test formulations are bioequivalent to the reference formulation with respect to the rate and extent of absorption of both 3TC and AZT.     

Fully quantum mechanical energy optimization for protein-ligand structure

We present a quantum mechanical approach to study protein-ligand binding structure with application to a Adipocyte lipid-binding protein complexed with Propanoic Acid. The present approach employs a recently develop molecular fractionation with a conjugate caps (MFCC) method to compute protein-ligand interaction energy and performs energy optimization using the quasi-Newton method. The MFCC method enables us to compute fully quantum mechanical ab initio protein-ligand interaction energy and its gradients that are used in energy minimization. This quantum optimization approach is applied to study the Adipocyte lipid-binding protein complexed with Propanoic Acid system, a complex system consisting of a 2057-atom protein and a 10-atom ligand. The MFCC calculation is carried out at the Hartree-Fock level with a 3-21G basis set. The quantum optimized structure of this complex is in good agreement with the experimental crystal structure. The quantum energy calculation is implemented in a parallel program that dramatically speeds up the MFCC calculation for the protein-ligand system. Similarly good agreement between MFCC optimized structure and the experimental structure is also obtained for the streptavidin-biotin complex. Due to heavy computational cost, the quantum energy minimization is carried out in a six-dimensional space that corresponds to the rigid-body protein-ligand interaction.     

Optically active 1,2-bis(1-arylhydroxymethyl) ferrocene: a new, efficient chiral ligand for scandium-catalyzed asymmetric Diels-Alder reaction

[reaction: see text] The Sc(OTf)3/FERRODIOL (2) complex was prepared at -78 degrees C in CH2Cl2 in the presence of 2,6-lutidine and MS 4A. The chiral scandium Lewis acid-catalyzed asymmetric Diels-Alder reaction of cyclopentadiene (3) with 3-acyloxazolidin-2-ones (4) effectively produced the adduct (5) in a high yield with good selectivity, i.e., endo/exo = 90:10 up to 91% ee (endo).     

Chemical ionization mass spectrometry of nitrosamines

The mass spectra of eight nitrosamines have been recorded, with excitation by chemical ionization (CI) and electron impact (EI). Comparison of the intensities of the base peaks under CI and El conditions gives intensity ratios in the range 1.4-1.9 for low resolution measurements and up to 10 for high resolution measurements, confirming the enhanced sensitivity available in the CI mode.     

Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives

The structural, dynamical, and recognition properties of antiparallel DNA triplexes formed by the antiparallel d(G#G.C), d(A#A.T), and d(T#A.T) motifs (the pound sign and dot mean reverse-Hoogsteen and Watson-Crick hydrogen bonds, respectively) are studied by means of "state of the art" molecular dynamics simulations. Once the characteristics of the helix are defined, molecular dynamics and thermodynamic integration calculations are used to determine the expected stabilization of the antiparallel triplex caused by the introduction of 8-aminopurines. Finally, oligonucleotides containing 8-aminopurine derivatives are synthesized and tested experimentally using several approaches in a variety of systems. A very large stabilization of the triplex is found experimentally, as predicted by simulations. These results open the possibility for the use of oligonucleotides carrying 8-aminopurines to bind single-stranded nucleic acids by formation of antiparallel triplexes.