Exhaustive computational search of ionic-charge clusters that mediate interactions between mammalian cytochrome P450 (CYP) and P450-oxidoreductase (POR) proteins

In this work, a model for the interaction between CYP2B4 and the FMN domain of rat P450-oxidoreductase is built using as template the structure of a bacterial redox complex. Amino acid residues identified in the literature as cytochrome P450 (CYP)–redox partner interfacial residues map to the interface in our model. Our model supports the view that the bacterial template represents a specific electron transfer complex and moreover provides a structural framework for explaining previous experimental data.We have used our model in an exhaustive search for complementary pairs of mammalian CYP and P450-oxidoreductase (POR) charge clusters. We quantitatively show that among the previously defined basic clusters, the 433K–434R cluster is the most dominant (32.3% of interactions) and among the acidic clusters, the 207D–208D–209D cluster is the most dominant (29%). Our analysis also reveals the previously not described basic cluster 343R–345K (16.1% of interactions) and 373K (3.2%) and the acidic clusters 113D–115E–116E (25.8%), 92E–93E (12.9%), 101D (3.2%) and 179E (3.2%).Cluster pairings among the previously defined charge clusters include the pairing of cluster 421K–422R to cluster 207D–208D–209D. Moreover, 433K–434R and 207D–208D–209D, respectively the dominant positively and negatively charged clusters, are uncorrelated. Instead our analysis suggests that the newly identified cluster 113D–115E–116E is the main partner of the 433K–434R cluster while the newly described cluster 343R–345K is correlated to the cluster 207D–208D–209D.     

Determination of molindone enantiomers in human plasma by high-performance liquid chromatography-tandem mass spectrometry using macrocyclic antibiotic chiral stationary phases

A sensitive and selective bioanalytical assay was developed and validated for the determination of enantiomeric molindone in human plasma using high-performance liquid chromatography-tandem mass spectrometry along with supported liquid extraction procedures. The chiral separation was evaluated and optimized on macrocyclic antibiotic type chiral stationary phases (CSPs) based on teicoplanin aglycone (Chirobiotic TAG) in polar organic, polar ionic, and reversed-phase mode chromatography, respectively. Complete baseline separation was achieved on a Chirobiotic TAG column under isocratic condition in reversed-phase chromatography. The method validation was conducted using a Chirobiotic TAG column (100 mm x 2.1 mm) over the curve range 0.100-100 ng/ml for each molindone enantiomer using 0.0500 ml of plasma sample. The flow rate was 0.8 ml/min and the total run time was 9 min. Supported liquid extraction in a 96-well plate format was used for sample preparation. Parameters including recovery, matrix effect, linearity, sensitivity, specificity, carryover, precision, accuracy, dilution integrity, and stability were evaluated. The intra- and inter-day precision and accuracy of the quality control samples at low, medium, and high concentration levels were RSD 相似文献   

First-principles prediction of the pK(a)s of anti-inflammatory oxicams

The gas- and aqueous-phase acidities of a series of oxicams have been computed by combining M05-2X/6-311+G(3df,2p) gas-phase free energies with solvation free energies from the CPCM-UAKS, COSMO-RS, and SMD solvent models. To facilitate accurate gas-phase calculations, a benchmarking study was further carried out to assess the performance of various density functional theory methods against the high-level composite method G3MP2(+). Oxicams are typically diprotic acids, and several tautomers are possible in each protonation state. The direct thermodynamic cycle and the proton exchange scheme have been employed to compute the microscopic pK(a)s on both solution- and gas-phase equilibrium conformers, and these were combined to yield the macroscopic pK(a) values. Using the direct cycle of pK(a) calculation, the CPCM-UAKS model delivered reasonably accurate results with MAD ~ 1, whereas the SMD and COSMO-RS models' performance was less satisfactory with MAD ~ 3. Comparison with experiment also indicates that direct cycle calculations based on solution conformers generally deliver better accuracy. The proton exchange cycle affords further improvement for all solvent models through systematic error cancellation and therefore provides better reliability for the pK(a) prediction of compounds of these types. The latter approach has been applied to predict the pK(a)s of several recently synthesized oxicam derivatives.     

Amine-directed intramolecular hydroacylation of alkenes and alkynes

Medium-ring heterocycles are prepared via an amine-directed, rhodium(I)-catalyzed intramolecular hydroacylation. The presence of an allyl substituent on the amine accelerates the reaction and increases product yields.     

Synthesis,alkali metal picrate extraction,and alkali metal cation binding selectivities of some new cage‐annulated polyoxamacrocyclic crown ethers

Five new cage‐annulated crown ethers, i.e., 4a, 4b, 6b, 11a, and 11b, have been synthesized and their respective alkali metal picrate extraction profiles along with that of a previously synthesized host molecule, 6a, have been obtained. These results are compared with the corresponding results obtained for electrospray ionization mass spectrometric (ESI‐MS) measurements of relative binding selectivities displayed by the same hosts toward a series of alkali metal chlorides. Among the crown‐5 hosts studied, 6a displays enhanced avidity toward complexation with K⁺ picrate in liquid‐liquid extraction experiments. Among the three crown‐6 hosts, 4b proved to be the best alkali metal picrate extractant and displayed significant levels of avidity toward complexation with the larger alkali metal cations (i.e., K⁺, Rb⁺, and Cs⁺). The trends in the picrate extraction and the ESI‐MS results obtained herein show several notable similarities and some differences. The similarities generally stem from size‐selective binding properties that are intrinsic to the different cavity sizes of the cage‐annulated macrocycles, whereas the differences reflect the important influence of solvation effects on the binding properties of the macrocycles.     

Efficient tetrahydropyranyl and tetrahydrofuranyl protection/deprotection of alcohols and phenols with Al(OTf)3 as catalyst

A simple and efficient method for the conversion of alcohols and phenols into their corresponding THP and THF ethers at room temperature has been developed using 1 mol % aluminium triflate as catalyst. The deprotection reaction in the presence of methanol using Al(OTf)₃ was equally successful and could be performed at ambient temperature in high yields.     

Targeted lipidomics using electron capture atmospheric pressure chemical ionization mass spectrometry

There is an increasing need to be able to conduct quantitative lipidomics analyses as a complement to proteomics studies. The highest specificity for proteomics analysis can be obtained using methodology based on electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) coupled with liquid chromatography/tandem mass spectrometry (LC/MS/MS). For lipidomics analysis it is often necessary to be able to separate enantiomers and regioisomers. This can be very challenging when using methodology based on conventional reversed-phase chromatography. Normal-phase chromatography using chiral columns can provide dramatic improvements in the resolution of enantiomers and regioisomers. However, conventional ESI- and APCI-MS/MS has limited sensitivity, which makes it difficult to conduct studies in cell culture systems where only trace amounts of non-esterified bioactive lipids are present. The use of electron capture APCI-MS/MS overcomes this problem. Enantiomers and regioisomers of diverse bioactive lipids can be quantified using stable isotope dilution methodology coupled with normal-phase chiral chromatography and electron capture APCI-MS/MS. This methodology has allowed a lipidomics profile from rat epithelial cells maintained in culture to be delineated and allowed the effect of a non-selective lipoxygenase inhibitor to be assessed.     

Nucleophilic additions to fused bicyclic five-membered ring oxocarbenium ions: evidence for preferential attack on the inside face

Evidence is provided that nucleophilic attack on five-membered ring oxocarbenium ions occurs from the inside face of the envelope. An eight-five fused-bicyclic system in which two substituents are constrained to pseudoequatorial positions underwent nucleophilic addition with selectivity that was comparable to an unconstrained monocyclic system. On the other hand, a bicyclic six-five analogue underwent reaction with low selectivity. This observation indicates that minimization of eclipsing interactions by attacking inside the envelope is not enough to control selectivity, but that the changes in the overall three-dimensional structure of the ring must be favorable as well. In the bicyclic six-five series, the six-membered ring is accommodated in the cation, but it destabilizes the transition state structure leading to the first-formed product of inside attack.     

Infrared spectra of aluminum hydrides in solid hydrogen: Al2H4 and Al2H6

The reaction of laser-ablated Al atoms and normal-H(2) during co-deposition at 3.5 K produces AlH, AlH(2), and AlH(3) based on infrared spectra and the results of isotopic substitution (D(2), H(2) + D(2) mixtures, HD). Four new bands are assigned to Al(2)H(4) from annealing, photochemistry, and agreement with frequencies calculated using density functional theory. Ultraviolet photolysis markedly increases the yield of AlH(3) and seven new absorptions for Al(2)H(6) in the infrared spectrum of the solid hydrogen sample. These frequencies include terminal Al-H(2) and bridge Al-H-Al stretching and AlH(2) bending modes, which are accurately predicted by quantum chemical calculations for dibridged Al(2)H(6), a molecule isostructural with diborane. Annealing these samples to remove the H(2) matrix decreases the sharp AlH(3) and Al(2)H(6) absorptions and forms broad 1720 +/- 20 and 720 +/- 20 cm(-1) bands, which are due to solid (AlH(3))(n). Complementary experiments with thermal Al atoms and para-H(2) at 2.4 K give similar spectra and most product frequencies within 2 cm(-1). Although many volatile binary boron hydride compounds are known, binary aluminum hydride chemistry is limited to the polymeric (AlH(3))( solid. Our experimental characterization of the dibridged Al(2)H(6) molecule provides an important link between the chemistries of boron and aluminum.