Modified AutoDock for accurate docking of protein kinase inhibitors

Protein kinases are an important class of enzymes controlling virtually all cellular signaling pathways. Consequently, selective inhibitors of protein kinases have attracted significant interest as potential new drugs for many diseases. Computational methods, including molecular docking, have increasingly been used in the inhibitor design process [1]. We have considered several docking packages in order to strengthen our kinase inhibitor work with computational capabilities. In our experience, AutoDock offered a reasonable combination of accuracy and speed, as opposed to methods that specialize either in fast database searches or detailed and computationally intensive calculations.However, AutoDock did not perform well in cases where extensive hydrophobic contacts were involved, such as docking of SB203580 to its target protein kinase p38. Another shortcoming was a hydrogen bonding energy function, which underestimated the attraction component and, thus, did not allow for sufficiently accurate modeling of the key hydrogen bonds in the kinase-inhibitor complexes.We have modified the parameter set used to model hydrogen bonds, which increased the accuracy of AutoDock and appeared to be generally applicable to many kinase-inhibitor pairs without customization. Binding to largely hydrophobic sites, such as the active site of p38, was significantly improved by introducing a correction factor selectively affecting only carbon and hydrogen energy grids, thus, providing an effective, although approximate, treatment of solvation.     

Dipole,quadrupole, octupole,and dipole–octupole polarizabilities at real and imaginary frequencies for H,HE, and H2 and the dispersion-energy coefficients for interactions between them

We have calculated certain dynamic polarizabilities (for both real and imaginary frequencies) for H, He, and H₂ and the dispersion-energy coefficients for long-range interactions between them. We have done so in a sum-over-states formalism with explicitly electron-correlated wave functions to describe the states. To be precise, we have determined the dipole (α₁), quadrupole (α₂), and octupole (α₃) polarizabilities of H and He for real frequencies (ω) in a range between zero and the first electronic-transition frequency and for imaginary frequencies (iω) on a 32-point Gauss-Legendre grid running from zero to ?ω = 20 E_h, and for H₂, we have found the dipole (α), quadrupole (C), and dipole–octupole (E) polarizability tensors for the same real and imaginary frequencies. The dispersion-energy coefficients, obtained by combining the sum-over-states for-malism for the polarizabilities with analytic integration over ω, gave values of C₆, C₈, and C₁₀ for the atom–atom systems; C, C, C, C, and C for the atom–diatom systems; and C₆, C and C for the H₂? H₂ system. Nearly all the results are considered to be more reliable than those hitherto published and some have been obtained for the first time, e.g., C(iω), E(ω), and E(iω) for H₂ and C, C, and C for the H? H₂ system. © 1993 John Wiley & Sons, Inc.     

Gravitational redshift and the equivalence principle

Two problems have long been confused with each other: the gravitational redshift as discussed by the equivalence principle; and the Doppler shift observed by a detector which moves with constant proper acceleration away from a stationary source. We here distinguish these two problems and give for the first time a solution of the former which is exact within the context of the equivalence principle in a sense discussed in the paper. The equivalence principle leads to transformations between flat spacetimes. These are analyzed, and a generalized Lorentz transformation is proposed which covers transformations from inertial to uniformly accelerated frames of reference.     

Synthesis and characterization of novel elastomeric poly(D,L-lactide urethane) maleate composites for bone tissue engineering

Here, we report the synthesis and characterization of a novel 4-arm poly(lactic acid urethane)-maleate (4PLAUMA) elastomer and its composites with nano-hydroxyapatite (nHA) as potential weight-bearing composite. The 4PLAUMA/nHA ratios of the composites were 1:3, 2:5, 1:2 and 1:1. FTIR and NMR characterization showed urethane and maleate units integrated into the PLA matrix. Energy dispersion and Auger electron spectroscopy confirmed homogeneous distribution of nHA in the polymer matrix. Maximum moduli and strength of the composites of 4PLAUMA/nHA, respectively, are 1973.31 ± 298.53 MPa and 78.10 ± 3.82 MPa for compression, 3630.46 ± 528.32 MPa and 6.23 ± 1.44 MPa for tension, 1810.42 ± 86.10 MPa and 13.00 ± 0.72 for bending, and 282.46 ± 24.91 MPa and 5.20 ± 0.85 MPa for torsion. The maximum tensile strains of the polymer and composites are in the range of 5–93%, and their maximum torsional strains vary from 0.26 to 0.90. The composites exhibited very slow degradation rates in aqueous solution, from approximately 50% mass remaining for the pure polymer to 75% mass remaining for composites with high nHA contents, after a period of 8 weeks. Increase in ceramic content increased mechanical properties, but decreased maximum strain, degradation rate, and swelling of the composites. Human bone marrow stem cells and human endothelial cells adhered and proliferated on 4PLAUMA films and degradation products of the composites showed little-to-no toxicity. These results demonstrate that novel 4-arm poly(lactic acid urethane)-maleate (4PLAUMA) elastomer and its nHA composites may have potential applications in regenerative medicine.     

Controlling domain orientation of liquid crystalline block copolymer in thin films through tuning mesogenic chemical structures

Controlling the macroscopic orientation of nanoscale periodic structures of amphiphilic liquid crystalline block copolymers (LC BCPs) is important to a variety of technical applications (e.g., lithium conducting polymer electrolytes). To study LC BCP domain orientation, a series of LC BCPs containing a poly(ethylene oxide) (PEO) block as a conventional hydrophilic coil block and LC blocks containing azobenzene mesogens is designed and synthesized. LC ordering in thin films of the BCP leads to the formation of highly ordered, microphase‐separated nanostructures, with hexagonally arranged PEO cylinders. Substitution on the tail of the azobenzene mesogen is shown to control the orientation of the PEO cylinders. When the substitution on the mesogenic tails is an alkyl chain, the PEO cylinders have a perpendicular orientation to the substrate surface, provided the thin film is above a critical thickness value. In contrast, when the substitution on the mesogenic tails has an ether group the PEO cylinders assemble parallel to the substrate surface regardless of the film thickness value. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 532–541     

人教版高中化学必修教科书的内容呈现方式及特点分析*

高中化学教科书是发展学生化学学科核心素养的重要载体和资源平台。依据《普通高中化学课程标准(2017年版)》编写的人教版普通高中化学必修教科书作为分析文本,着重从栏目系统、图像系统、习题系统角度对其呈现方式进行分析,具体特点表现为:栏目系统强化功能性,图像系统凸显直观性,习题系统体现针对性、情境性、开放性,以期为高中化学教师有效使用教科书、落实化学学科核心素养的培养发挥积极作用。     

三维还原氧化石墨烯/β-环糊精复合物的合成及其电化学检测水中左氧氟沙星北大核心CSCD

成功构筑了β-环糊精修饰的三维还原氧化石墨烯复合材料(3D-rGO/β-CD),并对该复合材料进行扫描电子显微镜、傅里叶红外光谱、热重分析和拉曼光谱分析等一系列的表征,分析了其形貌和结构的特征。进一步将其修饰到玻碳电极(GCE)表面,构建了一种新型电化学传感器(3D-rGO/β-CD/GCE)。利用3D-rGO/β-CD/GCE电化学传感器,通过微分脉冲伏安法(DPV)对左氧氟沙星(LEV)进行了检测。其中,具有多孔结构的三维还原氧化石墨烯具有优异的导电性能、比表面积大、化学稳定性好等优良的性质,而修饰的β-环糊精能在其环形腔内与客体分子结合形成超分子包合物,进而可以对LEV进行有效识别。研究结果显示,在最优实验条件下,3D-rGO/β-CD/GCE对左氧氟沙星的检测具有较宽的线性范围(1~150μmol/L),且检测限可达0.33μmol/L,同时该修饰电极还表现出良好的选择性和稳定性。此外,成功将其应用于实际水样中LEV的检测,表明该传感器具有一定的应用潜力。