Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics,thrombin and thermolysin inhibitors

Summary A relative comparison of the binding properties of different drug molecules requires their mutual superposition with respect to various alignment criteria. In order to validate the results of different alignment methods, the crystallographically observed binding geometries of ligands in the pocket of a common protein receptor have been used. The alignment function in the program SEAL that calculates the mutual superposition of molecules has been optimized with respect to these references. Across the reference data set, alignments could be produced that show mean rms deviations of approximately 1 Å compared to the experimental situation. For structures with obvious skeletal similarities a multiple-flexible fit, linking common pharmacophoric groups by virtual springs, has been incorporated into the molecular mechanics program MOMO. In order to combine conformational searching with comparative alignments, the optimized SEAL approach has been applied to sets of conformers generated by MIMUMBA, a program for conformational analysis. Multiple-flexible fits have been calculated for inhibitors of ergosterol biosynthesis. Sets of different thrombin and thermolysin inhibitors have been conformationally analyzed and subsequently aligned by a combined MIMUMBA/SEAL approach. Since for these examples crystallographic data on their mutual alignment are available, an objective assessment of the computed results could be performed. Among the generated conformers, one geometry could be selected for the thrombin and thermolysin inhibitors that approached reasonably well the experimentally observed alignment.     

THE EFFECTS OF THROMBOXANE INHIBITORS ON THE MICROVASCULAR AND TUMOR RESPONSE TO PHOTODYNAMIC THERAPY

Abstract— Vascular stasis and tissue ischemia are known to cause tumor cell death in several experimental models after photodynamic therapy (PDT); however, the mechanisms leading to this damage remain unclear. Because previous studies indicated that thromboxane release is implicated in vessel damage, we further examined the role of throm-boxane in PDT. Rats bearing chondrosarcoma were injected with 25 mg/kg Photofrin® (intravenously) 24 h before treatment. Light (135 J/cm ² , 630 nm) was delivered to thc tumor area after injection of one of the following inhibitors: (1) R68070: a thromboxane synthetase inhibitor; (2) SQ-29548: a thromboxane receptor antagonist; and (3) Flunarizine: an inhibitor of platelet shape change. Systemic thromboxane levels were determined. Vessel constriction and leakage were evaluated by intravital microscopy. Tumor response was assessed after treatment. Thromboxane levels were decreased more than 50% with SQ-29548 as compared to controls. Thromboxane levels in animals given R68070 and Flunarizine remained at baseline levels. SQ-29548 and R68070 reduced vessel constriction compared to controls, while Flunarizine totally prevented vessel constriction. R68070 and SQ-29548 inhibited vessel permeability compared to PDT controls; Flunarizine did not. Animals given these inhibitors showed markedly reduced tumor cure. These results indicate that the release of thromboxane is linked to the vascular response in PDT.     

Synthese und Molekülstrukturen von N‐substituierten Diethylgallium‐2‐pyridylmethylamiden

Synthesis and Molekular Structures of N‐substituted Diethylgallium‐2‐pyridylmethylamides (2‐Pyridylmethyl)(tert‐butyldimethylsilyl)amine ( 1a ) and (2‐pyridylmethyl)‐di(tert‐butyl)silylamine ( 1b ) form with triethylgallane the corresponding red adducts 2a and 2b via an additional nitrogen‐gallium bond. These oily compounds decompose during distillation. Heating under reflux in toluene leads to the elimination of ethane and the formation of the red oils of [(2‐pyridylmethyl)(tert‐butyldimethylsilyl)amido]diethylgallane ( 3a ) and [(2‐pyridylmethyl)‐di(tert‐butyl)silylamido]diethylgallane ( 3b ). In order to investigate the thermal stability solvent‐free 3a is heated up to 400 °C. The elimination of ethane is observed again and the C‐C coupling product N, N′‐Bis(diethylgallyl)‐1, 2‐dipyridyl‐1, 2‐bis(tert‐butyldimethylsilyl)amido]ethan ( 4 ) is found in the residue. Substitution of the silyl substituents by another 2‐pyridylmethyl group and the reaction of this bis(2‐pyridylmethyl)amine with GaEt₃ yield triethylgallane‐diethylgallium‐bis(2‐pyridylmethyl)amide ( 5 ). The metalation product adds immediately another equivalent of triethylgallane regardless of the stoichiometry. The reaction of GaEt₃ with 2‐pyridylmethanol gives quantitatively colorless 2‐pyridylmethanolato diethylgallane ( 6 ).     

A Novel Environmentally Benign Method for the Selective Oxidation of Alcohols to Aldehydes and Ketones

In the presence of [Ru(terpyridine)(2,6‐pyridinedicarboxylate)], aliphatic and benzylic alcohols are oxidized to the corresponding aldehydes or ketones with high selectivity by using hydrogen peroxide as the oxidant. There is no need for the addition of co‐catalysts or organic solvents. By applying an optimized reaction protocol, high catalyst productivity (turnover number>10 000) and activity (turnover frequency up to 14 800 h^?1) has been achieved.     

Structure elucidation of β-carotene isomers by HPLC-NMR coupling using a C30 bonded phase

The separation of cis/trans isomers of β-carotene has been performed with a C₃₀ stationary phase employing ¹H NMR spectroscopy as an on-line detection technique. 1D as well as 2D NMR spectra have been recorded in the stopped-flow mode for the predominant chromatographic peaks. Structural assignment of the five identified isomers was performed via comparison of simulated 1D ¹H NMR spectra on the basis of the structures of β-carotene cis/trans isomers with the experimental data, and also by the analysis of the proton-proton connectivities in the 2D NMR spectra of three isomers with the highest concentration. The chromatographic retention behaviour of the isomers agreed well with previously reported data. The advantage of the applied hyphenated coupling technique compared to conventional off-line techniques lies in the fact that chromatographic separation and NMR detection are performed in a closed system, so that reisomerization of the separated compounds is inhibited. Received: 29 May 1996 / Revised: 1 July 1996 / Accepted: 4 July 1996     

Reactions of bis(hexamethylbenzene)iron(0) with carbon monoxide and with unsaturated hydrocarbons

Thermal decomposition of bis(hexamethylbenzene)iron(0) in the presence of carbon monoxide yields a novel carbonyl iron complex, [C₆(CH₃)₆]Fe(CO)₂. The cyclohexadiene complex [C₆(CH₃)₆]Fe(C₆H₈) is obtained from reaction of bis(hexamethylbenzene)iron(0) with either 1,3-cyclohexadiene or benzene, and the yield is much greater in the presence of hydrogen gas. Interaction of bis-(hexamethylbenzene)iron(0) with 2-butyne induces a catalytic cyclotrimerization to give more hexamethylbenzene. Kinetic and isotope distribution studies indicate that the primary step in these reactions is not a direct loss of one ring ligand, but rather an insertion of the iron center into one of the ligand methyl CH bonds, leading to a benzyl hydride complex species. Mechanisms for the subsequent reactions of this iron hydride species are proposed.     

Screening, library-assisted identification and validated quantification of 23 benzodiazepines, flumazenil, zaleplone, zolpidem and zopiclone in plasma by liquid chromatography/mass spectrometry with atmospheric pressure chemical ionization

A liquid chromatographic/mass spectrometric assay with atmospheric pressure chemical ionization (LC/APCI-MS) is presented for fast and reliable screening and identification and also for precise and sensitive quantification in plasma of the 23 benzodiazepines alprazolam, bromazepam, brotizolam, camazepam, chlordiazepoxide, clobazam, clonazepam, diazepam, flunitrazepam, flurazepam, desalkylflurazepam, lorazepam, lormetazepam, medazepam, metaclazepam, midazolam, nitrazepam, nordazepam, oxazepam, prazepam, temazepam and tetrazepam, triazolam, their antagonist flumazenil and the benzodiazepine BZ1 (omega 1) receptor agonists zaleplone, zolpidem and zopiclone. It allows confirmation of the diagnosis of an overdose situation and monitoring of psychiatric patients' compliance. The analytes were isolated from plasma using liquid-liquid extraction and were separated on a Merck LiChroCART column with Superspher 60 RP Select B as the stationary phase. Gradient elution was performed using aqueous ammonium formate and acetonitrile. After screening and identification in the scan mode using the authors' LC/MS library, the analytes were quantified in the selected-ion monitoring mode. The quantification assay was fully validated. It was found to be selective proved to be linear from sub-therapeutic to over therapeutic concentrations for all analytes, except bromazepam. The corresponding reference levels the assay's accuracy and precision data for all studied substances are listed. The accuracy and precision data were within the required limits with the exception of those for bromazepam. The analytes were stable in frozen plasma for at least 1 month. The validated assay was successfully applied to several authentic plasma samples from patients treated or intoxicated with various benzodiazepines or with zaleplone, zolpidem or zopiclone. It has proven to be appropriate for the isolation, separation, screening, identification and quantification of the drugs mentioned above in plasma for clinical toxicology, e.g. in cases of poisoning, and forensic toxicology, e.g. in cases of driving under the influence of drugs.     

The surface and materials science of tin oxide

The study of tin oxide is motivated by its applications as a solid state gas sensor material, oxidation catalyst, and transparent conductor. This review describes the physical and chemical properties that make tin oxide a suitable material for these purposes. The emphasis is on surface science studies of single crystal surfaces, but selected studies on powder and polycrystalline films are also incorporated in order to provide connecting points between surface science studies with the broader field of materials science of tin oxide. The key for understanding many aspects of SnO₂ surface properties is the dual valency of Sn. The dual valency facilitates a reversible transformation of the surface composition from stoichiometric surfaces with Sn⁴⁺ surface cations into a reduced surface with Sn²⁺ surface cations depending on the oxygen chemical potential of the system. Reduction of the surface modifies the surface electronic structure by formation of Sn 5s derived surface states that lie deep within the band gap and also cause a lowering of the work function. The gas sensing mechanism appears, however, only to be indirectly influenced by the surface composition of SnO₂. Critical for triggering a gas response are not the lattice oxygen concentration but chemisorbed (or ionosorbed) oxygen and other molecules with a net electric charge. Band bending induced by charged molecules cause the increase or decrease in surface conductivity responsible for the gas response signal. In most applications tin oxide is modified by additives to either increase the charge carrier concentration by donor atoms, or to increase the gas sensitivity or the catalytic activity by metal additives. Some of the basic concepts by which additives modify the gas sensing and catalytic properties of SnO₂ are discussed and the few surface science studies of doped SnO₂ are reviewed. Epitaxial SnO₂ films may facilitate the surface science studies of doped films in the future. To this end film growth on titania, alumina, and Pt(1 1 1) is reviewed. Thin films on alumina also make promising test systems for probing gas sensing behavior. Molecular adsorption and reaction studies on SnO₂ surfaces have been hampered by the challenges of preparing well-characterized surfaces. Nevertheless some experimental and theoretical studies have been performed and are reviewed. Of particular interest in these studies was the influence of the surface composition on its chemical properties. Finally, the variety of recently synthesized tin oxide nanoscopic materials is summarized.     

Stille Cross‐Coupling of a Racemic Planar‐Chiral Ferrocene and Crystallographic Trace Analysis of Catalysis Intermediates and By‐products

A pressure‐controlled procedure for the S_N1 reaction of rac‐1‐[(dimethylamino)methyl]‐2‐(tributylstannyl)ferrocene ( 1 ) to rac‐1‐(phthalimidomethyl)‐2‐(tributylstannyl)ferrocene ( 2 ) was developed. Pd⁰‐Catalyzed Stille coupling of 2 with iodobenzene afforded rac‐1‐phenyl‐2‐(N‐phthalimidomethyl)ferrocene ( 5 ) in 74% yield; after trace enrichment by crystallization of the combined mother liquors, one single crystal of each, 5 , catalysis intermediate trans‐iodo(σ‐phenyl)bis(triphenylarsino)palladium(II) ( 7 ), trans‐diiodobis(triphenylarsino)palladium(II) ( 8 ), and rac‐2,2′‐bis(phthalimidomethyl)‐1,1′‐biferrocene ( 9 ) could be isolated by crystal sorting under a microscope and characterized by X‐ray crystal structure analysis. Furthermore, 5 was deprotected to amine ( 11 ), which does even survive the Birch reduction to rac‐1‐(aminomethyl)‐2‐(cyclohexa‐2,5‐dienyl)ferrocene ( 12 ).     

Übergangsmetall—methylen-komplexe: LXI. Übergangsmetall—vinyliden-komplexe: Neuartige synthese aus diazoalken-vorstufen

The diazoolefines of composition N₂CCR₂ (R/R = CH₃/CH₃ and(-CH₂-)₅) are suitable precursors of the corresponding vinylidene ligands CCR₂. Thus, treatment of the RhRh complex [(η⁵-C₅Me₅)Rh(μ-CO)]₂ (1) with the N-nitrosourethanes 2a and 2b, resp., in the presence of lithium t-butoxide yields the otherwise inaccessible μ-vinylidene complexes (μ-CCR₂)[(η⁵-C₅Me₅)Rh(CO)]₂ (R = CH₃ (3a), R,R = (-CH₂-)₅ (3b)). The analogous cobalt compound (μ-CCMe₂)[(η⁵-C₅Me₅)Co(CO)]₂ (5a) is obtained similarly. This procedure extends the well-documented diazoalkane method for the synthesis of μ-alkylidene complexes to the less stable diazoalkenes. A single-crystal X-ray diffraction study of the dimethylvinylidene derivative 3a shows the CMe₂ ligand to adopt an almost symmetrically metal-bridging position (d(RhC) 197.8(1) and 204.3(1) pm), with a rhodium-rhodium single bond completing a three-membered Rh₂C-metallacycle (d(RhRh) 268.4(0) pm) analogous with cyclopropane.