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.     

Photoelectron spectra of some antibiotic building blocks: 2-azetidinone and thiazolidine-carboxylic Acid

X-ray photoelectron spectra of the core and valence levels of the fundamental building blocks of β-lactam antibiotics have been investigated and compared with theoretical calculations. The spectra of the compounds 2-azetidinone and the 2- and 4-isomers of thiazolidine-carboxylic acid are interpreted in the light of theoretical calculations. The spectra of the two isomers of thiazolidine-carboxylic acid are rather similar, as expected, but show clear effects due to isomerization. Both isomers are analogues of proline, which is well-known to populate several low energy conformers in the gas phase. We have investigated the low energy conformers of thiazolidine-4-carboxylic acid theoretically in more detail and find some spectroscopic evidence that multiple conformers may be present. The measured valence levels are assigned for all three compounds, and the character of the frontier orbitals is identified and analyzed.     

UPTAKE KINETICS AND INTRACELLULAR LOCALIZATION OF HYPOCRELLIN PHOTOSENSITIZERS FOR PHOTODYNAMIC THERAPY: A CONFOCAL MICROSCOPY STUDY

Hypocrellins are naturally occurring compounds with photosensitizing properties in biological systems. We have prepared synthetic derivatives of hypocrellin B, which have promise as photosensitizers in the clinical application of photodynamic therapy. The intracellular localization and uptake kinetics of hypocrellin B and several selected hypocrellin congeners were determined semiquantitatively by fluorescence confocal microscopy in monolayer cultures of EMT6/Ed murine tumor cells. Each compound had unique uptake kinetics. Although no compound tested to date has demonstrated nuclear labeling, most could be detected in lysosomes, Golgi, endoplasmic reticulum and, to a minor extent, in cellular membranes. No two compounds gave identical labeling distributions. The differences are assumed to originate in physicochemical properties characteristic of each compound, which may ultimately impact upon the primary modality of phototoxicity.     

Modified horner–emmons reaction of polymeric phosphonates: Versatile synthesis of pendant stilbene-containing polymers

Poly[styrene-co-(diethyl vinylbenzylphosphonate)] and poly[methylmethacrylate-co-(diethyl vinylbenzylphosphonate)] were prepared and used in modified Horner-Emmons reactions to synthesize polymers with covalently attached stilbene groups. This versatile new method allowed for the preparation of polymers with either electron-donor (OCH₃, CH₃) or electron acceptor (Br, NO₂) substituents on the stilbene aromatic ring. The resulting polymers were characterized by ¹H NMR, FT-IR, UV-visible, DSC, and size exclusion chromatography. Efficient transformation of polymeric phosphonates to the polymeric stilbene derivatives was realized. Size exclusion chromatographic analyses demonstrated that the reaction conditions have no deleterious effect on the molecular weight distribution of the various polymers that were prepared. Photochromic behavior was demonstrated for one of the derivatives. © 1995 John Wiley & Sons, Inc.     

Ring-Closing Metathesis Strategies to P -heterocycles

A general approach to the synthesis of P -heterocycles using the ring-closing metathesis reaction is described. We have developed a new method utilizing phosphorus nuclei as suitable temporary tethers for the coupling of non-racemic allylic amines. This approach allows for the generation of symmetric and unsymmetric 1,4-diamines. Subsequent coupling of these 1,4-diamines with various nuclei produces an array of 7-membered heterocycles.     

Flexible ligand docking without parameter adjustment across four ligand–receptor complexes

Understanding molecular recognition is one of the fundamental problems in molecular biology. Computationally, molecular recognition is formulated as a docking problem. Ideally, a molecular docking algorithm should be computationally efficient, provide reasonably thorough search of conformational space, obtain solutions with reasonable consistency, and not require parameter adjustments. With these goals in mind, we developed DIVALI (Docking wIth eVolutionary AlgorIthms), a program which efficiently and reliably searches for the possible binding modes of a ligand within a fixed receptor. We use an AMBER-type potential function and search for good ligand conformations using a genetic algorithm (GA). We apply our system to study the docking of both rigid and flexible ligands in four different complexes. Our results indicate that it is possible to find diverse binding modes, including structures like the crystal structure, all with comparable potential function values. To achieve this, certain modifications to the standard GA recipe are essential. © 1995 John Wiley & Sons, Inc.     

A combined solid-state NMR and X-ray crystallography study of the bromide ion environments in triphenylphosphonium bromides

Multinuclear ((31)P and (79/81)Br), multifield (9.4, 11.75, and 21.1 T) solid-state nuclear magnetic resonance experiments are performed for seven phosphonium bromides bearing the triphenylphosphonium cation, a molecular scaffold found in many applications in chemistry. This is undertaken to fully characterise their bromine electric field gradient (EFG) tensors, as well as the chemical shift (CS) tensors of both the halogen and the phosphorus nuclei, providing a rare and novel insight into the local electronic environments surrounding them. New crystal structures, obtained from single-crystal X-ray diffraction, are reported for six compounds to aid in the interpretation of the NMR data. Among them is a new structure of BrPPh(4), because the previously reported one was inconsistent with our magnetic resonance data, thereby demonstrating how NMR data of non-standard nuclei can correct or improve X-ray diffraction data. Our results indicate that, despite sizable quadrupolar interactions, (79/81)Br magnetic resonance spectroscopy is a powerful characterisation tool that allows for the differentiation between chemically similar bromine sites, as shown through the range in the characteristic NMR parameters. (35/37)Cl solid-state NMR data, obtained for an analogous phosphonium chloride sample, provide insight into the relationship between unit cell volume, nuclear quadrupolar coupling constants, and Sternheimer antishielding factors. The experimental findings are complemented by gauge-including projector-augmented wave (GIPAW) DFT calculations, which substantiate our experimentally determined strong dependence of the largest component of the bromine CS tensor, δ(11), on the shortest Br-P distance in the crystal structure, a finding that has possible application in the field of NMR crystallography. This trend is explained in terms of Ramsey's theory on paramagnetic shielding. Overall, this work demonstrates how careful NMR studies of underexploited exotic nuclides, such as (79/81)Br, can afford insights into structure and bonding environments in the solid state.     

A unified route to the welwitindolinone alkaloids: total syntheses of (-)-N-methylwelwitindolinone C isothiocyanate, (-)-N-methylwelwitindolinone C isonitrile, and (-)-3-hydroxy-N-methylwelwitindolinone C isothiocyanate

As part of a comprehensive strategy to the welwitindolinone alkaloids possessing a bicyclo[4.3.1]decane core, we report herein concise asymmetric total syntheses of (-)-N-methylwelwitindolinone C isothiocyanate (2a), (-)-N-methylwelwitindolinone C isonitrile (2b), and (-)-3-hydroxy-N-methylwelwitindolinone C isothiocyanate (3a) from a common tetracyclic intermediate. The crucial vinyl chloride moiety was installed through electrophilic chlorination of a hydrazone, but only after adjustment of reactivity to circumvent a facile skeletal rearrangement. Selective desulfurization and oxidation of 2a provided access to 2b and 3a, respectively. Notably, this work provides corrected (1)H and (13)C NMR spectral data for 3a.     

A Luminescent and Sublimable Dy(III) -Based Single-Molecule Magnet

The reaction of [Ln(hfac)(3) ]?2?H(2) O and pyridine-N-oxide (PyNO) leads to isostructural dimers of the formula [Ln(hfac)(3) (PyNO)](2) (Ln=Eu, Gd, Tb, Dy). The Dy derivative shows a remarkable single-molecule magnet behavior with complex hysteresis at 1.4?K. The dynamics of the magnetization features are two relaxation regimes: a thermally activated one at high temperature (τ(0) =(5.62±0.4)×10(-11) s and Δ=(167±1)?K) and a quantum tunneling regime at low temperature with a tunneling frequency of 0.42?Hz. The analysis of the Gd derivative evidences intradimer antiferromagnetic interactions (J=(-0.034±0.001)?cm(-1) ). Moreover, the Eu, Tb, and Dy derivatives are luminescent with quantum yield of 51, 53, and 0.1?%, respectively. The thermal investigation of [Dy(hfac)(3) (PyNO)](2) shows that the dimers can be sublimated intact, suggesting their possible exploit as active materials for surface-confined nanostructures to be investigated by fluorimetry methods.