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.     

微波消解ICP-MS法测定广西北部湾海鸭蛋中硒和锗的含量

以硝酸-过氧化氢（体积比为5：3）混合溶液为消解剂,微波消解法处理海鸭蛋样品,采用电感耦合等离子体质谱法测定样品溶液中的硒和锗的含量。选择适合的同位素元素,运用碰撞室技术（CCT）降低多原子离子对元素硒、锗的干扰,用钇作为在线内标。硒、锗工作曲线的线性范围均为0．0-100．0ng／mL,相关系数r=0．9996;硒、锗的检出限分别为1．1,0．15ng／mL,测定结果的相对标准偏差分别为4．78％,5．70％（n=6）,加标回收率为92．2％-104．0％。用该法测定国家标准物质黄鱼（GBW08573）中硒的含量,测定值在标称值范围内。     

Molecular Dynamic Study for Chiral Discrimination of α-Phenylethylamine by Modified Cyclodextrin in Gas Chromatography

IntroductionAfter the introduction of modified cyclodextrins (CDs) as a new type ofchiral stationaryphases, great progress has been made in enantioselective gas chromatography, which hasraised many questions about the mechanism of chiral recognition and intermolecularinteractionsl. Theoretical computational methods in conjunction with modellingprocedures have been extensively used to investigate the nature of binding processesresponsible for inclusion complex formation2'3. It is of interest t…     

Water vapor permeability of shape memory polyurethane with amorphous reversible phase

Shape memory thermoplastic polyurethanes (TPUs), based on amorphous soft segment from the reaction of hexamethylene diisocyanate and 1,2‐butane diol, and the crystalline hard segment from 4,4′‐methylenediphenyl diisocyanate and 1,6‐hexanediol, were modified by hydrophilic segments, diol‐terminated poly(ethylene oxide) or dimethylol propionic acid (DMPA). Differential scanning calorimetry, dynamic mechanical testing, tensile testing, and the measurement of shape memory effect, water swell, and water vapor permeability were carried out to examine these TPUs. The hydrophilic segment increased the hysterisis in shape memory effect by reducing the crystallinity of the hard segment. The neutralized DMPA unit enhanced the sensitivity of the thermoresponsive water vapor permeability (WVP) by amplifying the increase of WVP at the temperature range above the glass transition temperature. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 3009–3017, 2000     

Solvent‐Controlled Bifurcated Cascade Process for the Selective Preparation of Dihydrocarbazoles or Dihydropyridoindoles

A solvent‐controlled cascade process has been identified for the dual purpose of the preparation of either dihydrocarbazoles or dihydropyridoindoles from identical N‐aryl‐α,β‐unsaturated nitrones and electron‐deficient allene starting materials. These reactions proceed smoothly under mild metal‐free conditions affording a range of two types of skeletally distinct indole‐based heterocycles in high yield and diastereoselectivity. These transformations demonstrate the use of a bifurcated cascade process that hinges on the ring‐opening event of a benzazepine intermediate for the synthesis of skeletally diverse heterocyclic products and rapid access to biologically‐significant, indole‐based structures.     

Cross‐Conjugated Hexaphyrins and Their Bis‐Rhodium Complexes

A cross‐conjugated hexaphyrin that carries two meso‐oxacyclohexadienylidenyl (OCH) groups 9 was synthesized from the condensation of 5,10‐bis(pentafluorophenyl)tripyrrane with 3,5‐di‐tert‐butyl‐4‐hydroxybenzaldehyde. The reduction of 9 with NaBH₄ afforded the Möbius aromatic [28]hexaphyrin 10 . Bis‐rhodium complex 11 , prepared from the reaction of 10 with [{RhCl(CO)₂}₂], displays strong Hückel antiaromatic character because of the 28 π electrons that occupy the conjugated circuit on the enforced planar structure. The oxidation of 11 with 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone (DDQ) yielded complexes 12 and 13 depending upon the reaction conditions. Both 12 and 13 are planar owing to bis‐rhodium metalation. Although complex 12 bears two meso‐OCH groups at the long sides and is quinonoidal and nonaromatic in nature, complex 13 bears 3,5‐di‐tert‐butyl‐4‐hydroxyphenyl and OCH groups and exhibits a moderate diatropic ring current despite its cross‐conjugated electronic circuit. The diatropic ring current increases upon increasing the solvent polarity, most likely due to an increased contribution of an aromatic zwitterionic resonance hybrid.     

Fast Photochemical Oxidation of Proteins (FPOP) Maps the Epitope of EGFR Binding to Adnectin

Epitope mapping is an important tool for the development of monoclonal antibodies, mAbs, as therapeutic drugs. Recently, a class of therapeutic mAb alternatives, adnectins, has been developed as targeted biologics. They are derived from the 10th type III domain of human fibronectin (¹⁰Fn3). A common approach to map the epitope binding of these therapeutic proteins to their binding partners is X-ray crystallography. Although the crystal structure is known for Adnectin 1 binding to human epidermal growth factor receptor (EGFR), we seek to determine complementary binding in solution and to test the efficacy of footprinting for this purpose. As a relatively new tool in structural biology and complementary to X-ray crystallography, protein footprinting coupled with mass spectrometry is promising for protein–protein interaction studies. We report here the use of fast photochemical oxidation of proteins (FPOP) coupled with MS to map the epitope of EGFR-Adnectin 1 at both the peptide and amino-acid residue levels. The data correlate well with the previously determined epitopes from the crystal structure and are consistent with HDX MS data, which are presented in an accompanying paper. The FPOP-determined binding interface involves various amino-acid and peptide regions near the N terminus of EGFR. The outcome adds credibility to oxidative labeling by FPOP for epitope mapping and motivates more applications in the therapeutic protein area as a stand-alone method or in conjunction with X-ray crystallography, NMR, site-directed mutagenesis, and other orthogonal methods. Figure

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The Jahn-Teller effect in CH3Cl+(X̃2E): a combined high-resolution experimental measurement and ab initio theoretical study

The energy levels of CH(3)Cl(+)X?(2)E showing strong spin-vibronic coupling effect (Jahn-Teller effect) have been measured up to 3500 cm(-1) above the ground vibrational state using one-photon zero-kinetic energy photoelectron and mass-analyzed threshold ionization spectroscopic method. Theoretical calculations have been also performed to calculate the spin-vibronic energy levels using a diabatic model and ab initio adiabatic potential energy surfaces (PESs). In the theoretical calculations the diabatic potential energy surfaces are expanded by the Taylor expansions up to the fourth-order including the multimode vibronic interactions. The calculated spin-orbit energy splitting (224.6 cm(-1)) for the ground vibrational state is in good agreement with the experimental data (219 ± 3 cm(-1)), which indicates that the Jahn-Teller and the spin-orbit coupling have been properly described in the theoretical model near the zero-point energy level. Based on the assignments predicted by the theoretical calculations, the experimentally measured energy levels were fitted to those from the diabatic model by optimizing the main spectroscopic parameters. The PESs from the ab initio calculations at the level of CASPT2/vq(t)z were thus compared with those calculated from the experimentally determined spectroscopic parameters. The theoretical diagonal elements in the diabatic potential matrix are in good agreement with those determined using the experimental data, however, the theoretical off-diagonal elements appreciably deviate from those determined using the experimental data for geometric points far away from the conical intersections. It is also concluded that the JT effect in CH(3)Cl(+) mainly arises from the linear coupling and the mode coupling between the CH(3) deform (υ(5)) and CH(3) rock (υ(6)) vibrations. The mode couplings between the symmetric C-Cl stretching vibration υ(3) with υ(5) and υ(6) are also important to understand the spin-vibronic structure of the molecule.     

Molecular engineering and solvent dependence of excitation energy hopping in self-assembled porphyrin boxes

It has been demonstrated that the direction and magnitude of transition dipole moments, and hence rates in the excitation energy hopping in the self-assembled porphyrin boxes can be tuned by insertion of ethynyl groups as well as the dielectric constant of solvent.     

Stereoselective assembly of complex oligosaccharides using anomeric sulfonium ions as glycosyl donors

The development of selectively protected monosaccharide building blocks that can reliably be glycosylated with a wide variety of acceptors is expected to make oligosaccharide synthesis a more routine operation. In particular, there is an urgent need for the development of modular building blocks that can readily be converted into glycosyl donors for glycosylations that give reliably high 1,2-cis-anomeric selectivity. We report here that 1,2-oxathiane ethers are stable under acidic, basic, and reductive conditions making it possible to conduct a wide range of protecting group manipulations and install selectively removable protecting groups such as levulinoyl (Lev) ester, fluorenylmethyloxy (Fmoc)- and allyloxy (Alloc)-carbonates, and 2-methyl naphthyl ethers (Nap). The 1,2-oxathiane ethers could easily be converted into bicyclic anomeric sulfonium ions by oxidization to sulfoxides and arylated with 1,3,5-trimethoxybenzene. The resulting sulfonium ions gave high 1,2-cis-anomeric selectivity when glycosylated with a wide variety of glycosyl acceptors including properly protected amino acids, primary and secondary sugar alcohols and partially protected thioglycosides. The selective protected 1,2-oxathianes were successfully employed in the preparation of a branched glucoside derived from a glycogen-like polysaccharide isolated form the fungus Pseudallescheria boydii , which is involved in fungal phagocytosis and activation of innate immune responses. The compound was assembled by a latent-active glycosylation strategy in which an oxathiane was employed as an acceptor in a glycosylation with a sulfoxide donor. The product of such a glycosylation was oxidized to a sulfoxide for a subsequent glycosylation. The use of Nap and Fmoc as temporary protecting groups made it possible to install branching points.