Ligand- and protein-based modeling studies of the inhibitors of human cytochrome P450 2D6 and a virtual screening for potential inhibitors from the Chinese herbal medicine, Scutellaria baicalensis (Huangqin,Baikal Skullcap)

We have previously examined the binding patterns of various substrates to human cytochrome P450 2D6 (CYP2D6) using a series of molecular modeling methods. In this study, we further explored the binding modes of various types of inhibitors to CYP2D6 using a combination of ligand- and protein-based modeling approaches. Firstly, we developed and validated a pharmacophore model for CYP2D6 inhibitors, which consisted of two hydrophobic features and one hydrogen bond acceptor feature. Secondly, we constructed and validated a quantitative structure-activity relationship (QSAR) model for CYP2D6 inhibitors which gave a poor to moderate prediction accuracy. Thirdly, a panel of CYP2D6 inhibitors were subject to molecular docking into the active site of wild-type and mutated CYP2D6 enzyme. We demonstrated that 8 residues in the active site (Leu213, Glu216, Ser217, Gln244, Asp301, Ser304, Ala305, and Phe483) played an important role in the binding to the inhibitors via hydrogen bond formation and/or π-π stacking interaction. Apparent changes in the binding modes of the inhibitors have been observed with Phe120Ile, Glu216Asp, Asp301Glu mutations in CYP2D6. Finally, we screened for potential binders/inhibitors from the Chinese herbal medicine Scutellaria baicalensis (Huangqin, Baikal Skullcap) using the established pharmacophore model for CYP2D6 inhibitors and molecular docking approach. Overall, 18 out of 40 compounds from S. baicalensis were mapped to the pharmacophore model of CYP2D6 inhibitors and most herbal compounds from S. baicalensis could be docked into the active site of CYP2D6. Our study has provided insights into the molecular mechanisms of interaction of synthetic and herbal compounds with human CYP2D6 and further benchmarking studies are needed to validate our modeling and virtual screening results.     

Quantitative selenium speciation in human urine by using liquid chromatography–electrospray tandem mass spectrometry

A liquid chromatography–electrospray-tandem mass spectrometry (ES-MS/MS) method was developed for the speciation analysis of four organic selenium species of relevance to human urinary metabolism, namely trimethylselenomium ion (TMSe⁺), selenomethionine (SeMet) and the two selenosugars, methyl 2-acetamido-2-deoxy-1-seleno-β-d-galactos/-glucos-amine (SeGalNAc and SeGluNAc, respectively). Their chromatographic separation was achieved by using a cation exchange pre-column coupled in-series with a reversed-phase high-performance liquid chromatography column, along with an isocratic mobile phase. Online detection was performed using ES-MS/MS in selective reaction monitoring mode. SeGalNAc was detected as the major human urinary metabolite of selenium in the samples analysed, whereas TMSe⁺ was detected in the urine of one volunteer before and after receiving a selenium supplement. SeMet was not detected as a urine excretory metabolite in this study. Spiking experiments performed with the urine samples revealed significant signal suppression caused by coeluting matrix constituents. To overcome such interferences, isotopically labelled ¹³CD₃⁸²SeGalNAc was used as an internal standard, whereas in the absence of an isotopically labelled internal standard for TMSe⁺, the standard addition method was applied. Quality control for the accurate quantitation of TMSe⁺ and SeGalNAc was carried out by analysing spiked human urine samples with appropriate selenium standards over a concentration range of 10–50 μg Se L⁻¹. The method has achieved a limit of detection in the presence of urine matrix comparable to that of HPLC-inductively coupled plasma-mass spectrometry for the four selenium species: 1.0 μg Se L⁻¹ for TMSe⁺, 5.6 μg Se L⁻¹ for SeMet, and 0.1 μg Se L⁻¹ for both SeGalNAc and SeGluNAc.     

Low rank Runge–Kutta methods,symplecticity and stochastic Hamiltonian problems with additive noise

In this paper we extend the ideas of Brugnano, Iavernaro and Trigiante in their development of HBVM (s,r$s,r$) methods to construct symplectic Runge–Kutta methods for all values of s$s$ and r$r$ with s≥r$s\ge r$. However, these methods do not see the dramatic performance improvement that HBVMs can attain. Nevertheless, in the case of additive stochastic Hamiltonian problems an extension of these ideas, which requires the simulation of an independent Wiener process at each stage of a Runge–Kutta method, leads to methods that have very favourable properties. These ideas are illustrated by some simple numerical tests for the modified midpoint rule.     

Formation of phosphino-substituted isocyanate by reaction of CO2 with group 2 complexes based on the (Me3Si)(i-Pr2P)NH ligand

The group 2 complexes [(Me(3)Si)(i-Pr(2)P)N](2)M(THF)(x) (M = Mg, x = 1; M = Ca/Sr, x = 2) as well as an unusual dimagnesium complex {[(Me(3)Si)(i-Pr(2)P)N](3)Mg}Mg(n-C(4)H(9)) have been prepared and characterized by multinuclear NMR spectroscopy and single crystal X-ray diffraction. Each complex was shown to react with CO(2) under extremely mild conditions (15 min, 1 atm, room temperature) to give the isocyanate (i-Pr)(2)P-N═C═O. The independent syntheses of (i-Pr)(2)P-N═C═O and the carbodiimide dimer [(i-Pr)(2)PNCNP(i-Pr)(2)](2) are also reported.     

Reactivity of Cr(III) μ-oxo compounds: catalyst regeneration and atom transfer processes

Oxidation of CpCr[(XylNCMe)(2)CH] (Xyl = 2,6-Me(2)C(6)H(3)) with pyridine N-oxide or air generated the μ-oxo dimer, {CpCr[(XylNCMe)(2)CH]}(2)(μ-O). The μ-oxo dimer was converted to paramagnetic Cr(III) CpCr[(XylNCMe)(2)CH](X) complexes (X = OH, O(2)CPh, Cl, OTs) via protonolysis reactions. The related Cr(III) alkoxide complexes (X = OCMe(3), OCMe(2)Ph) were prepared by salt metathesis and characterized by single crystal X-ray diffraction. The interconversion of the Cr(III) complexes and their reduction back to Cr(II) with Mn powder were monitored using UV-vis spectroscopy. The related CpCr[(DepNCMe)(2)CH] (Dep = 2,6-Et(2)C(6)H(3)) Cr(II) complex was studied for catalytic oxygen atom transfer reactions with PPh(3) using O(2) or air. Both Cr(II) complexes reacted with pyridine N-oxide and γ-terpinene to give the corresponding Cr(III) hydroxide complexes. When CpCr[(DepNCMe)(2)CH] was treated with pyridine N-oxide in benzene in the absence of hydrogen atom donors, a dimeric Cr(III) hydroxide product was isolated and structurally characterized, apparently resulting from intramolecular hydrogen atom abstraction of a secondary benzylic ligand C-H bond followed by intermolecular C-C bond formation. The use of very bulky hexaisopropylterphenyl ligand substituents did not preclude the formation of the analogous μ-oxo dimer, which was characterized by X-ray diffraction. Attempts to develop a chromium-catalyzed intermolecular hydrogen atom transfer process based on these reactions were unsuccessful. The protonolysis and reduction reactions of the μ-oxo dimer were used to improve the previously reported Cr-catalyzed radical cyclization of a bromoacetal.     

Photoelectron spectra and structures of three cyclic dipeptides: PhePhe, TyrPro, and HisGly

We have investigated the electronic structure of three cyclic dipeptides: cyclo(Histidyl-Glycyl) (cHisGly), cyclo(Tyrosyl-Prolyl) (cTyrPro), and cyclo(Phenylalanyl-Phenylalanyl) (cPhePhe) in the vapor phase, by means of photoemission spectroscopy and theoretical modeling. The last compound was evaporated from the solid linear dipeptide, but cyclised, losing water to form cPhePhe in the gas phase. The results are compared with our previous studies of three other cyclopeptides. Experimental valence and core level spectra have been interpreted in the light of calculations to identify the basic chemical properties associated with the central diketopiperazine ring, and with the additional functional groups. The valence spectra are generally characterized by a restricted set of outer valence orbitals separated by a gap from most other valence orbitals. The theoretically simulated core and valence spectra of all three cyclic dipeptides agree reasonably well with the experimental spectra. The central ring and the side chains act as independent chromophores whose spectra do not influence one another, except for prolyl dipeptides, where the pyrrole ring is fused with the central ring. In this case, significant changes in the valence and core level spectra were observed, and explained by stronger hybridization of the valence orbitals.     

Synthesis of α-hydroxyacetophenones

A general method for the preparation of α-hydroxyacetophenones is presented. Functionalized arylmagnesium species are transmetalated to the corresponding arylzinc intermediates, which undergo Cu(I)-catalyzed reaction with acetoxyacetyl chloride. Acidic hydrolysis of the acetate group releases the target α-hydroxyacetophenones with minimal production of undesired polymeric degradates that are often observed under alternative conditions.     

Statistical properties of the electrophoretic collision of a long DNA molecule with a small obstacle

We present experimental results for the collision of a single λ-DNA molecule with isolated cylindrical nanoposts whose radii range from 350 nm to 1.37 μm. The experimental apparatus was fabricated in oxidized silicon using a plasma-thinning method. The probability density for the dimensionless holdup time is described by a gamma distribution, which accurately represents the behavior of the probability density for X collisions and U/J collisions for short-lived and long-lived collisions, respectively. The shape parameter of the gamma distribution reflects the nature of the short-lived collisions, whereas the scaling parameter captures the role of the finite size of the post on the U/J collisions. When rendered in an appropriate dimensionless form, the existing models for the role of electric field gradients extend to all post sizes, indicating that 350 nm is still well above the point-sized limit. Our experiments provide insights into a regime that is very challenging for numerical simulations but highly relevant for separation processes.     

The Chromatographic Role in High Resolution Mass Spectrometry for Non-Targeted Analysis

Resolution improvements in time-of-flight instrumentation and the emergence of the Orbitrap mass spectrometer have researchers using high resolution mass spectrometry to determine elemental compositions and performing screening methods based on the full-scan data from these instruments. This work is focused on examining instrument performance of both a QTOF and a bench-top Orbitrap. In this study, the impact of chromatographic resolution on mass measurement accuracy, mass measurement precision, and ion suppression is examined at a fundamental level. This work was extended to a mixture of over 200 pesticides to determine how well two different software algorithms componentized and correctly identified these compounds under different sets of chromatographic conditions, where co-elution was expected to vary markedly.