Electronic effects steer the mechanism of asymmetric hydrogenations of unfunctionalized aryl-substituted alkenes

Density functional theory (PBE and B3LYP) was used to study asymmetric hydrogenations of alkenes catalyzed by an iridium imidazolylidine oxazoline complex. The calculation predicts that the alkene preferentially coordinates to the site trans to the carbene. The coordinated alkene then reacts first with the H2 ligand, then with the hydride to form alkane. Finally, the alkane is released by equilibrating with extrinsic H2 and alkene. Enantioface selectivities for hydrogenations of trisubstituted alkenes seem to be driven primarily by steric interactions with the adamantyl part of the ligand; only the smallest substituents can adopt a site close to it. Application of this theoretical model leads to correct predictions regarding the experimentally observed sense and magnitude of the enantioselectivities.     

Spectrofluorimetric determination of cysteine by 5-maleimidyl-2-(m-methylphenyl)benzoxazole

A new thiol weak-fluorescence probe, 5-maleimidyl-2-(m-methylphenyl)benzoxazole (MMPB), gives a highly fluorescence product in the presence of Cys. In this paper, MMPB has been developed for the fluorimetric determination of cysteine (Cys). At lambda(ex)/lambda(em) = 305.6/425.6 nm, the linear range is from 0 to 3.3 x 10(-7) mol l(-1) and the detection limit (sigma = 3) of 6.2 x 10(-10) mol l(-1). The main advantage of this method lies in the relative high selectivity compared with the methods using other N-substituted maleimide type of thiol reagents, in which 0.15-fold (molar ratio) of GSH is allowed and most of other amino acids at 100-fold (molar ratio) level had no obvious effect on the results. The proposed method has been applied to the determination of Cys in real samples.     

Diels-Alder reactions of quinol lactones: a change of regioselectivity with stannic chloride catalysis

Lewis acid-mediated Diels-Alder reactions of quinol lactone 2 gave regioselectivity opposite to that of the uncatalyzed reaction. Compound 12 is proposed as the reactive intermediate generated by the reaction of 2 with stannic chloride.     

PA.FPNS: its synthesis and use in spectrophotometric determination of magnesium

A new polymeric chromogenic reagent PA.FPNS has been synthesized by condensing polyallylamine (PA) with 3-(4-formylphenylazo)-4,5-dihydroxynaphthalene-2,7-disulfonic acid (FPNS) and its properties studied. In alkaline media, PA.FPNS reacts with magnesium to form a water-soluble blue complex, whose absorption maximum is at 604 nm. The molar absorptivity (varepsilon) of the complex is 5.2 x 10(4)l mol(-1) cm(-1), which is four times that of the FPNS-Mg complex, and Beer's law is obeyed over the range 0-0.35 mug ml(-1) magnesium. Compared to the corresponding low-molecular-weight FPNS and other chromogenic reagents, PA.FPNS offers considerably improved sensitivity and selectivity for magnesium, which may be attributed to incorporating FPNS into a water-soluble polymer and the effect of the polymeric chain on the reaction microenvironment. Also, a simple and sensitive spectrophotometric method for the determination of magnesium has been developed and applied to water and human fluid samples with satisfactory results.     

Use of the tubulin bound paclitaxel conformation for structure-based rational drug design

A new computational docking protocol has been developed and used in combination with conformational information inferred from REDOR-NMR experiments on microtubule bound 2-(p-fluorobenzoyl)paclitaxel to delineate a unique tubulin binding structure of paclitaxel. A conformationally constrained macrocyclic taxoid bearing a linker between the C-14 and C-3'N positions has been designed and synthesized to enforce this "REDOR-taxol" conformation. The novel taxoid SB-T-2053 inhibits the growth of MCF-7 and LCC-6 human breast cancer cells (wild-type and drug resistant) on the same order of magnitude as paclitaxel. Moreover, SB-T-2053 induces in vitro tubulin polymerization at least as well as paclitaxel, which directly validates our drug design process. These results open a new avenue for drug design of next generation taxoids and other microtubule-stabilizing agents based on the refined structural information of drug-tubulin complexes, in accordance with typical enzyme-inhibitor medicinal chemistry precepts.     

Synthesis of 2‐Dihydrooxadiazolinyl Chromones

Reactions of the substituted 2‐formyl chromones with aroylhydrazines gave corresponding 2‐(aroylhydrazonomethylidyne) chromones. Then 2‐(3′‐acetyl‐5′‐aryl‐2′,3′‐dihydro‐1′,3′,4′‐oxadiazol‐2′‐yl) chromones were prepared by these 2‐(aroylhydrazonomethylidyne) chromones under refluxing with Ac₂O. All target compounds were characterized through elemental analysis and IR, ¹H NMR, MS.     

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols

The accuracy of biological simulations depends, in large part, on the treatment of electrostatics. Due to the availability of accurate experimental values, calculation of pKa provides stringent evaluation of computational methods. The generalized solvent boundary potential (GSBP) and Ewald summation electrostatic treatments were recently implemented for combined quantum mechanical and molecular mechanics (QM/MM) simulations by our group. These approaches were tested by calculating pKa shifts due to differences in electronic structure and electrostatic environment; the shifts were determined for a series of small molecules in solution, using various electrostatic treatments, and two residues (His 31, Lys 102) in the M102K T4-lysozyme mutant with large pKa shifts, using the GSBP approach. The calculations utilized a free energy perturbation scheme with the QM/MM potential function involving the self-consistent charge density functional tight binding (SCC-DFTB) and CHARMM as the QM and MM methods, respectively. The study of small molecules demonstrated that inconsistent electrostatic models produced results that were difficult to correct in a robust manner; by contrast, extended electrostatics, GSBP, and Ewald simulations produced consistent results once a bulk solvation contribution was carefully chosen. In addition to the electrostatic treatment, the pKa shifts were also sensitive to the level of the QM method and the scheme of treating QM/MM Coulombic interactions; however, simple perturbative corrections based on SCC-DFTB/CHARMM trajectories and higher level single point energy calculations were found to give satisfactory results. Combining all factors gave a root-mean-square difference of 0.7 pKa units for the relative pKa values of the small molecules compared to experiment. For the residues in the lysozyme, an accurate pKa shift was obtained for His 31 with multiple nanosecond simulations. For Lys 102, however, the pKa shift was estimated to be too large, even after more than 10 nanosecond simulations for each lambda window; the difficulty was due to the significant, but slow, reorganization of the protein and water structure when Lys 102 was protonated. The simulations support that Lys 102 is deprotonated in the X-ray structure and the protein is highly destabilized when this residue is protonated.     

Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine

Precision medicine has been strongly promoted in recent years. It is used in clinical management for classifying diseases at the molecular level and for selecting the most appropriate drugs or treatments to maximize efficacy and minimize adverse effects. In precision medicine, an in-depth molecular understanding of diseases is of great importance. Therefore, in the last few years, much attention has been given to translating data generated at the molecular level into clinically relevant information. However, current developments in this field lack orderly implementation. For example, high-quality chemical research is not well integrated into clinical practice, especially in the early phase, leading to a lack of understanding in the clinic of the chemistry underlying diseases. In recent years, mass spectrometry (MS) has enabled significant innovations and advances in chemical research. As reported, this technique has shown promise in chemical mapping and profiling for answering “what”, “where”, “how many” and “whose” chemicals underlie the clinical phenotypes, which are assessed by biochemical profiling, MS imaging, molecular targeting and probing, biomarker grading disease classification, etc. These features can potentially enhance the precision of disease diagnosis, monitoring and treatment and thus further transform medicine. For instance, comprehensive MS-based biochemical profiling of ovarian tumors was performed, and the results revealed a number of molecular insights into the pathways and processes that drive ovarian cancer biology and the ways that these pathways are altered in correspondence with clinical phenotypes. Another study demonstrated that quantitative biomarker mapping can be predictive of responses to immunotherapy and of survival in the supposedly homogeneous group of breast cancer patients, allowing for stratification of patients. In this context, our article attempts to provide an overview of MS-based chemical mapping and profiling, and a perspective on their clinical utility to improve the molecular understanding of diseases for advancing precision medicine.

An overview of MS-based chemical mapping and profiling, indicating its contributions to the molecular understanding of diseases in precision medicine by answering "what", "where", "how many" and "whose” chemicals underlying clinical phenotypes.     

The biosynthesis of quadrone and terrecyclic acid

Feedings of [1-¹³C]- and [1,2-¹³C₂]acetate Aspergillus terreus gave quadrone and terrecyclic acid which were analyzed by ¹³C NMR. The pattern of ¹³C-enrichments and couplings is consistent with the formation of 1 and 2 by cyclization of farnesyl pyrophosphate.     

LC-ESI-MS Determination of Bilobalide and Ginkgolides in Canine Plasma

A sensitive and selective method using liquid chromatography with electrospray ionization mass spectrometric detection was developed for the quantification of bilobalide and ginkgolides in canine plasma. The analytes were extracted with diethyl ether-dichloromethane-isopropanol (6:3:1, v/v) after spiking the samples with daidzein (internal standard). The lower limit of quantification (LLOQ) of the method was 2.5 μg L⁻¹ for ginkgolide B and 10.0 μg L⁻¹ for bilabolide, ginkgolide A and ginkgolide C. The accuracy of the method was within 15% of the actual values over a wide range of plasma concentrations. The intra-day and inter-day precision was better than 15% (R.S.D.). Finally, the LC-ESI-MS method was successfully applied to study the pharmacokinetics of ginkgolides and bilabolide after administration of Ginkgo biloba extracts to dogs.