Regioselective synthesis of asymmetrically substituted 2-quinoxalinol salen ligands

Diamino-2-quinoxalinols are reacted with salicylaldehyde derivatives to produce 2-quinoxalinol imines regioselectively as one isomer in good yield. Regioselectivity has been determined through the use of isotopic 15N labeling experiments. The 2-quinoxalinol imines may then be reacted without further purification with additional salicylaldehyde derivatives to yield asymmetrically substituted 2-quinoxalinol salens.     

Optimal scaling factors for CM1 and CM3 atomic charges in RM1-based aqueous simulations

Scaling factors for atomic charges derived from the RM1 semiempirical quantum mechanical wavefunction in conjunction with CM1 and CM3 charge models have been optimized by minimizing errors in absolute free energies of hydration, ΔG_hyd, for a set of 40 molecules. Monte Carlo statistical mechanics simulations and free energy perturbation theory were used to annihilate the solutes in gas and in a box of TIP4P water molecules. Lennard–Jones parameters from the optimized potentials for liquid simulations‐all atom (OPLS–AA) force field were utilized for the organic compounds. Optimal charge scaling factors have been determined as 1.11 and 1.14 for the CM1R and CM3R methods, respectively, and the corresponding unsigned average errors in ΔG_hyd relative to experiment were 2.05 and 1.89 kcal/mol. Computed errors in aniline and two derivatives were particularly large for RM1 and their removal from the data set lowered the overall errors to 1.61 and 1.75 kcal/mol for CM1R and CM3R. Comparisons are made to the AM1 method which yielded total errors in ΔG_hyd of 1.50 and 1.64 kcal/mol for CM1A*1.14 and CM3A*1.15, respectively. This work is motivated by the need for a highly efficient yet accurate quantum mechanical (QM) method to study condensed‐phase and enzymatic chemical reactions via mixed QM and molecular mechanical (QM/MM) simulations. As an initial test, the Menshutkin reaction between NH₃ and CH₃Cl in water was computed using a RM1/TIP4P‐Ew/CM3R procedure and the resultant ΔG^?, ΔG_rxn, and geometries were in reasonable accord with other computational methods; however, some potentially serious shortcomings in RM1 are discussed. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Improved Cell-Potent and Selective Peptidomimetic Inhibitors of Protein N-Terminal Methyltransferase 1

Protein N-terminal methyltransferase 1 (NTMT1) recognizes a unique N-terminal X-P-K/R motif (X represents any amino acid other than D/E) and transfers 1–3 methyl groups to the N-terminal region of its substrates. Guided by the co-crystal structures of NTMT1 in complex with the previously reported peptidomimetic inhibitor DC113, we designed and synthesized a series of new peptidomimetic inhibitors. Through a focused optimization of DC113, we discovered a new cell-potent peptidomimetic inhibitor GD562 (IC₅₀ = 0.93 ± 0.04 µM). GD562 exhibited improved inhibition of the cellular N-terminal methylation levels of both the regulator of chromosome condensation 1 and the oncoprotein SET with an IC₅₀ value of ~50 µM in human colorectal cancer HCT116 cells. Notably, the inhibitory activity of GD562 for the SET protein increased over 6-fold compared with the previously reported cell-potent inhibitor DC541. Furthermore, GD562 also exhibited over 100-fold selectivity for NTMT1 against several other methyltransferases. Thus, this study provides a valuable probe to investigate the biological functions of NTMT1.     

CDOCKER and $$\lambda$$-dynamics for prospective prediction in D3R Grand Challenge 2

The opportunity to prospectively predict ligand bound poses and free energies of binding to the Farnesoid X Receptor in the D3R Grand Challenge 2 provided a useful exercise to evaluate CHARMM based docking (CDOCKER) and \(\lambda\)-dynamics methodologies for use in “real-world” applications in computer aided drug design. In addition to measuring their current performance, several recent methodological developments have been analyzed retrospectively to highlight best procedural practices in future applications. For pose prediction with CDOCKER, when the protein structure used for rigid receptor docking was close to the crystallographic holo structure, reliable poses were obtained. Benzimidazoles, with a known holo receptor structure, were successfully docked with an average RMSD of 0.97 \(\AA\). Other non-benzimidazole ligands displayed less accuracy largely because the receptor structures we chose for docking were too different from the experimental holo structures. However, retrospective analysis has shown that when these ligands were re-docked into their holo structures, the average RMSD dropped to 1.18 \(\AA\) for all ligands. When sulfonamides and spiros were docked with the apo structure, which agrees more with their holo structure than the structures we chose, five out of six ligands were correctly docked. These docking results emphasize the need for flexible receptor docking approaches. For \(\lambda\)-dynamics techniques, including multisite \(\lambda\)-dynamics (MS\(\lambda\)D), reasonable agreement with experiment was observed for the 33 ligands investigated; root mean square errors of 2.08 and 1.67 kcal/mol were obtained for free energy sets 1 and 2, respectively. Retrospectively, soft-core potentials, adaptive landscape flattening, and biasing potential replica exchange (BP-REX) algorithms were critical to model large substituent perturbations with sufficient precision and within restrictive timeframes, such as was required with participation in Grand Challenge 2. These developments, their associated benefits, and proposed procedures for their use in future applications are discussed.     

奥伯斯佯谬浅析

给出满足宇宙学原理的宇宙模型中计算星体视光度的一般公式，作为特例，导出“稳恒态”和“大爆炸”模型中星体视光度的表达式，结果表明这些模型是可以避免奥伯斯佯谬的。     

苯二酚异构体的电动毛细管色谱-玻碳微电极柱上安培检测分析方法研究

在玻碳纤维微电极上研究了电解液中β－环糊精（ＣＤ）的浓度对邻、间、对苯二酚的循环伏安特性的影响,从实验结果和分子结构水平方面考察了β－ＣＤ与邻、间、对苯二酚的包结作用。研究结果表明,β－ＣＤ与邻、间、对苯二酚的包结作用强弱顺序为间苯二酚、邻苯二酚、对苯二酚。讨论了电泳缓冲液中ΝΗ４Ｃｌ,ＳＤＳ,β－ＣＤ的浓度及ｐＨ值对邻、间、对苯二酚迁移时间的影响。建立了苯二酚异构体胶束电动毛细管色谱－玻碳微电极柱上安培检测分析方法,方法的回收率在９８％～１０３％之间。     

Mass spectra of aminoacyl adenylate pentacoordinated phosphorus compounds

Aminoacyl adenylate pentacoordinated phosphorus compounds were analyzed by field desorption (FD) and fast atom bombardment (FAB) mass spectrometries, together with the B/E linked scan technique, and their mass spectral fragmentation pathways were investigated. For the five bonds (one P-N bond, three P-O bonds and one mixed anhydride bond P-O-CO), the cleavage usually occurred more on the P-N bond, the mixed anhydride bond and the O-C bond adjacent to the P-O bond, and less on the P-O bond. Ion YH(+), corresponding to water loss from protonated 2',3'-O-isopropylidene-adenosine, was the base peak. The results reflect the structural characteristics of aminoacyl adenylate pentacoordinated phosphorus compounds. Copyright 1999 John Wiley & Sons, Ltd.