Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields

Summary A methodology aimed at improving the accuracy of current docking–scoring procedures is proposed, and validated through detailed tests of its performance in predicting the activity of HIV-1 protease inhibitors. This methodology is based on molecular dynamics simulations using a force field whose effective charges are refined by means of a novel procedure that relies on quantum-mechanical calculations and preserves the internal consistency of the parameterization scheme.     

Identification and assay of wild-type and modified nucleoside mixtures by turbo ionspray ionization tandem mass spectrometry

A method is presented which allows the identification and assay of a nucleoside in the presence of other analogues and homologues. The method is based on the conventional multiple reaction monitoring approach performed on the [M + H]+ ions of wild-type and modified nucleosides produced by the turbo ionspray ionization method on a triple-quadrupole mass spectrometer. The accuracy of the quantitative determination relies on the evaluation of a response factor rho, which takes into account the kinetics of dissociation of the parent ions into the protonated [B + 2H]+ nucleobase ions. The evaluation of the absolute concentration of each analyte in the examined mixture does not require any previous chromatographic separation.     

IR Reflection Spectra of Ferroelectric Ceramics Based on Solid Solutions of Lead Zirconate-Titanate

We have investigated the IR reflection spectra of ferroelectric ceramics based on solid solutions of lead zirconate-titanate with a rhombohedral structure obtained by high-pressure cold precompaction. In the 55–65-cm^–1 frequency range, we have revealed by experiment that the soft ferroelectric-active mode for the ceramics compacted by a higher pressure under the conditions of cold compaction is shifted into the region of lower frequencies. For the ceramics precompacted at various pressures, we have determined the frequencies of longitudinal and transverse phonons and calculated the frequency dependences of the imaginary and real parts of the dielectric constant.     

Exciton spectra of layered PbI<Subscript>2</Subscript> and PbI<Subscript>2</Subscript>:Zr crystals

We have analyzed the surface morphology of single crystal samples of lead diiodide and studied the absorption edge and the temperature variation of their photoluminescence spectra. We have established that the zirconium impurity is uniformly incorporated into the crystal lattice of the samples and promotes appreciable quenching of photoluminescence due to formation of electron traps. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 74, No. 2, pp. 252–257, March–April, 2007.     

Contamination of therapeutic human immunoglobulin preparations with apolipoprotein H (β2‐glycoprotein I)

Polyclonal immunoglobulin (Ig) concentrates are important biological medicinal products and the assurance of their quality and safety is crucial. In our present approach we used proteomic methods to check the purity of commercial Ig products of different origin. The experimental setup included nonreducing 2DE or DIGE combined with MALDI‐TOF and the thrombin generation assay, a routine safety test for pharmaceutical Ig preparations, and was complemented by a specific immunoassay. 2DE patterns displayed contaminations with trace amounts of human apolipoprotein H (Apo‐H), transferrin, albumin, and its fragments. In contrast to the latter, Apo‐H is a protein that is active in the coagulation cascade, and thus a potential involvement in thromboembolic events in vivo cannot be excluded. It was found by 2DE and MALDI‐TOF to be a contaminant of several Ig preparations. Spiking experiments of Ig preparations with pure Apo‐H demonstrated an Apo‐H concentration dependent increase in thrombin generation assay values. Traces of Apo‐H are possibly also contributing to unwanted side effects, as already known for factor XIa. The significance of Apo‐H contaminations for these side effects might be verified by detailed analyses of pharmacovigilance data.     

Determination of Human Alpha-Fetoprotein (AFP) by Solid Substrate Room Temperature Phosphorescence Enzyme-Linked Immune Response Using Luminescent Nanoparticles

Luminescent nanoparticles of silicon dioxide (SiO₂) containing fluorescein isothiocyanate (FITC) with a particle size of 20 nm were synthesized using the Sol–Gel method (abbreviated FITC–SiO₂). FITC–SiO₂ nanoparticles whose surfaces are modified (FITC–SiO₂–S–CH₂COOH) can emit strong and stable solid substrate room temperature phosphorescence (SS-RTP) on acetyl cellulose membranes. When the original color-producing agent (R) in the enzyme-linked immunosorbent assay (ELISA) kits for determination of alpha-fetoprotein (AFP) was substituted with (FITC–SiO₂–S–CH₂COOH), the system maintained good FITC–SiO₂ phosphorescence properties. Furthermore, the phosphorescence intensity enhanced markedly after the ELISA reaction. The relationship between the phosphorescence intensity and the content of AFP obeyed Beer’s law. Based on the facts stated above, a new method for the determination of human AFP by SS-RTP-ELISA (using the luminescent nanoparticle as marker) was established. The linear range of this method is 0.040–16.0 pg of human AFP per spot (sample volume: 0.40 μL spot⁻¹, corresponding concentration: 0.10–40.0 ng mL⁻¹). The regression equation of the working curve is ΔIp = −6.289+18.075 m_AFP (pg spot⁻¹) (r = 0.9960, n = 6). The detection limit (LD) of this method calculated by 3 S_b/k is 6.7 fg spot⁻¹ (corresponding concentration: 17 ng L⁻¹). Compared to the ELISA method using a traditional color-producing agent, the new method exhibited a 34.8 times higher sensitivity and a wider linear range. The method has been successfully applied to the determination of human AFP in serum.     

NMR study of the stoichiometry,stability and exchange kinetics of complexation reaction between Pb2+ ion and 18-crown-6 in binary acetonitrile-water mixtures

Proton NMR was used to study the complexation reaction between lead ion and 18-crown-6 in a number of binary acetonitrile-water mixtures. Formation constant for the resulting 11 complexes in different solvent mixtures was determined by computer fitting of the chemical shift-mole ratio data. There is an inverse relationship between the complex stability and amount of water in the mixed solvent. The dissociative kinetics of the complex was studied by proton line-shape analysis. The Arrhenius plots showed a distinct isokinetic temperature at about 25°C at which the decomplexation rate is more or less independent of the solvent composition. the complexation rate and the activation parameters E _a , H and S, for the exchange have been determined and found to be strongly solvent dependent. There is actually a linear relationship between the mole fraction of acetonitrile in the mixed solvent and logarithm of the stability constant as well as activation parameters.     

Coordination polymers of CdII and PbII derived from bipyridine–glycoluril: influence of metal‐ion size and counter‐ions

Two new one‐dimensional (1D) coordination polymers (CPs), namely catena‐poly[[[aquacadmium(II)]‐bis(μ‐4b,5,7,7a‐tetrahydro‐4b,7a‐epiminomethanoimino‐6H‐imidazo[4,5‐f][1,10]phenanthroline‐6,13‐dione)] bis(perchlorate) dihydrate], {[Cd(C₁₄H₁₀N₆O₂)₂(H₂O)](ClO₄)₂·2H₂O}_n or {[Cd(BPG)₂(H₂O)](ClO₄)₂·2H₂O}_n, 1 , and catena‐poly[[lead(II)‐bis(μ‐4b,5,7,7a‐tetrahydro‐4b,7a‐epiminomethanoimino‐6H‐imidazo[4,5‐f][1,10]phenanthroline‐6,13‐dione)] bis(perchlorate) dihydrate], {[Pb(C₁₄H₁₀N₆O₂)₂](ClO₄)₂·2H₂O}_n or {[Pb(BPG)₂](ClO₄)₂·2H₂O}_n, 2 , have been synthesized using bipyridine–glycoluril (BPG; systematic name: 4b,5,7,7a‐tetrahydro‐4b,7a‐epiminomethanoimino‐6H‐imidazo[4,5‐f][1,10]phenanthroline‐6,13‐dione), a urea‐fused tecton, in a mixed‐solvent system. The Cd^II ion in 1 is heptacoordinated and the Pb^II ion in 2 is hexacoordinated, with the Cd^II ion adopting a pentagonal bipyramidal geometry and the Pb^II ion adopting a distorted octahedral geometry. Both CPs form infinite linear chain structures which are hydrogen bonded to each other leading to the formation of three‐dimensional supramolecular network structures. Topological analysis of CPs 1 and 2 reveals that the structures exhibit 1D chain‐like arrangements in an AB–AB sequence and shows platonic uniform 2‐connected uninodal topologies. Furthermore, a comparative analysis of a series of structures based on the BPG ligand indicates that the size of the metal ion and the types of counter‐ions used have a great influence on the resulting frameworks and properties.     

Oxidation of 1-methylcyclobutanol by Pb(IV) and Mn(III) compounds

The main product of the reaction of 1-methylcyclobutanol with Pb(OAc)₄ in benzene is 1-phenyl-4-pentanone; the use of Mn(OAc)₃ in acetic acid gives a mixture of 2,9-decanedione and methyl propyl ketone; 1-(chloro-, bromo-, thiocyano-, or cyano)-4-pentanone is formed in the presence of the systems Pb(OAc)₄-metal halide or Mn(OAc)₃-metal halide.N. D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences, 117913 Moscow. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 12, pp. 2760–2763, December, 1992.