芳香噻嗪类衍生物作为选择性醛糖还原酶抑制剂的分子对接和基于受体的三维定量构效关系研究

芳香噻嗪类衍生物被证明是一类选择性较好的高活性醛糖还原酶抑制剂(ARIs).本文对44个芳香噻嗪类化合物进行了分子对接(docking)和三维定量构效关系(3D-QSAR)研究,并探索了此类化合物与醛糖还原酶(ALr²)的作用机理.醛糖还原酶与醛还原酶(ALR1)活性位点的叠加结果显示, ALr²中残基Leu 300和Cys298的存在是化合物1m具有高选择性的原因.分别建立了比较分子场分析方法(CoMFA, q² = 0.649, r² =0.934; q²:交叉验证相关系数, r²:非交叉验证相关系数)和比较分子相似性指数分析方法(CoMSIA, q² = 0.746, r² = 0.971)模型,并对影响此类化合物生物活性的结构进行了鉴定.结果显示,两个模型均具有较高预测能力,并通过测试集中的7个化合物进行了验证,其中CoMFA模型和CoMSIA模型的预测相关系数(r_Pred²)分别为0.748和0.828. 3D-QSAR模型中的三维等值线图表明,在化合物1m的苄基环上C3和C4位置以及苯并噻嗪母核上C5和C7位置进行改进可能对生物活性的提高有利,此预测与我们前期报道的苯并噻嗪母核C7位改进结果一致.本文所建3D-QSAR模型能够在理性设计具有更高生物活性的新型ARIs中发挥重要作用.     

3C-like蛋白酶抑制剂的构效关系、分子对接和分子动力学

3C-like蛋白酶是中东呼吸综合征冠状病毒（MERS-CoV）等其它冠状病毒的繁殖过程中极为重要的蛋白酶。它已成为人类在抗冠状病毒领域中的研究热点。本文基于计算生物学方法对与MERS-CoV同属的蝙蝠冠状病毒HKU4（HKU4-CoV）的43个肽类3C-like蛋白酶抑制剂分子,建立三维定量构效关系（3D-QSAR）模型。在基于配体叠合的基础上,发现比较分子相似性指数分析法（CoMSIA）中的四个场组合（位阻场、静电场、氢键供体场与氢键受体场）为最优的模型（Q²=0.522,R_ncv²=0.996,R_pre²=0.904;Q²：交叉验证相关系数,R_ncv²：非交叉验证相关系数,R_pre²：验证集分子的预测值相关系数）,并借助该模型通过分子对接（docking）与分子动力学（MD）方法阐明了配受体结合作用。实验结果表明：（1）基于最优的CoMSIA模型基础上的三维等势图形象地说明了分子基团的位阻作用、静电作用、氢键供体与氢键受体作用对分子生物活性的影响;（2）分子对接研究结果显示了疏水性以及结晶水、氨基酸His166和Glu169在配体和受体结合过程中产生重要作用;（3）分子动力学模拟进一步验证了分子对接模型的可靠性,并发现了两个新的关键氨基酸Ser24与Gln192,它们与配体产生了两个较强的氢键。此外,根据这些结果,一些新的具有潜在抑制活性的肽类化合物作为3C-like蛋白酶抑制剂被获得。以上结果能够帮助深入了解3C-like蛋白酶与肽类抑制剂的作用机理,并且能够为今后的抗MERS-CoV药物设计提供有价值的参考。     

脒类KARI酶抑制剂的分子对接和3D-QSAR研究

对设计合成的20个单脒类化合物的水稻KARI酶体外抑制活性和体内除草活性进行了分子对接和三维定量构效关系研究. 前者采用AutoDock3.0方法, 研究发现化合物活性变化趋势与分子对接计算结果基本一致, 通过分析化合物9与KARI酶活性氨基酸残基结合模式发现, 残基Glu319, Asp315, Glu496, Gly253, Met254, Cys517等对氢键和静电相互作用以及疏水作用都有重要贡献; 后者研究采用比较分子力场分析(CoMFA)方法, 结果表明立体场和静电场对活性的贡献分别为67.8%和32.2%, 交叉验证系数r_cv²＝0.774, 非交叉验证r²＝0.999, F＝1593.134, 标准偏差s＝0.036, 所建立的3D-QSAR模型对化合物除草活性具有较好的预测能力. 两种方法研究结果为进一步设计合成更高活性的KARI酶抑制剂提供了指导.     

乙酰羟酸合成酶突变体对除草剂阔草清抗性的预测研究

本工作测定了商品化除草剂阔草清对大肠杆菌乙酰羟酸合成酶II及其突变体的抑制常数. 利用生物大分子的定量构效关系方法(MB-QSAR)建立了定量、可视的突变体性质与结构关系模型. 实验数据与计算数据之间显示了良好的相关性: MB-QSAR/CoMFA (comparative molecular field analysis)模型的交叉验证系数q²=0.691, 非交叉验证相关性系数r²=0.947, 外部预测能力r²_pred=0.759; MB-QSAR/CoMSIA (comparative molecular similarity indices analysis)模型的相应值分别为0.625, 0.960和0.619. 模型的三维结构-性质关系图为突变体抗性提供了直观阐释, 为抗性规避性农药的设计提供了有价值的信息. 同时, 该模型也在一定程度上显示了除草剂种属选择性的预测能力.     

1,2-萘醌类化合物抑制PTP1B的三维定量构效关系研究

蛋白酪氨酸磷酸酶1B (protein tyrosine phosphatase 1B, PTP-1B)是近年来发现的治疗II型糖尿病的新靶点, 1,2-萘醌类化合物对PTP-1B有较好的抑制活性, 具有良好的药用前景. 为了设计出本类化合物抑制效果更好的分子构型, 用比较分子力场分析(CoMFA)和比较分子相似性指数分析(CoMSIA)对该类化合物进行了三维定量构效关系(3D-QSAR)的研究, 并建立了相关的预测模型. 其中, CoMFA模型的交叉验证相关系数(q²)为0.555, 非交叉验证相关系数(r²)为0.991, 标准偏差(SEE)为0.049, F值为564.910. CoMSIA模型的q²为0.558, r²为0.991, SEE为0.050, F值为542.773. 计算结果表明, 获得的CoMFA和CoMSIA模型具有良好的预测能力, 可以应用于指导该类化合物的设计.     

二肽肽酶IV抑制剂的三维定量构效关系研究

二肽肽酶IV是一类用于治疗II型糖尿病具有潜在价值的关键酶, 很多此类酶的抑制剂用于处理此病具有相当好的有效性. 一系列N-取代的甘氨酰氰基吡咯烷衍生物对于二肽肽酶具有高的活性和选择性. 我们使用比较分子力场分析方法建立DPP-IV抑制剂——N-取代的甘氨酰氰基吡咯衍生物的三维定量构效关系, 该模型为设计用于治疗II型糖尿病的高效DPP-IV抑制剂提供结构信息. CoMFA模型的交叉验证相关系数q²＝0.575, 非交叉验证相关系数r²＝0.981, 绝对误差S＝0.184, F_9.68＝388.5. 使用七个预测集检验了模型的预测能力. 所得的模型解释了已有的构效关系, 并对同类化合物有较好的预测能力, 该模型可用于指导新型的DPP-IV抑制剂的设计与优化.     

酪氨酸蛋白磷酸酯酶1B抑制剂的分子对接和三维定量构效关系研究

用一种柔性分子对接方法(FlexX)将12个2-草酰胺苯甲酸类抑制剂和酪氨酸蛋白磷酸酯酶(PTP1B)活性口袋进行分子对接,对接程序预测的抑制剂和酶之间的相互作用能与抑制活性之间有很好的相关性(非线性相关系数R²达0.859),这说明对接结果可以比较准确地预测抑制剂和PTP1B之间的结合模式.然后,将33个同类抑制剂的骨架叠合在分子对接预测的结合构象上,用比较分子力场分析方法(CoMFA)对其进行三维定量活性构效关系研究,得到的CoMFA模型具有很好的统计相关性(交互验证回归系数q²为0.650),并可以准确地预测测试集6个化合物的活性(平均标准偏差为0.177).同时,由CoMFA模型得出的抑制剂改造信息与用FlexX预测的结合模式是一致的,进一步证明我们预测的结合模式是正确的.为研究这类抑制剂和PTP1B的结合模式及对抑制剂进行结构改造提供了信息.     

紫杉醇衍生物的三维定量构效关系研究

利用比较分子力场分析(CoMFA)方法对98个紫杉醇衍生物的三维定量构效关系(3D-QSAR)进行了分析,发现影响其活性的立体能与静电能之比为61.6/38.4.进一步分析表明,C-13侧链基团的改变对其活性影响较大,尤其是2'-OH对保持活性是至关重要的;而母环其它位置取代基的改变对活性影响较小.该模型交叉验证r_cv²=0.714,非交叉验证r₂=0.901;以此模型对验证组10个化合物活性进行预测,r_pred²=0.812,表明模型具有很好的预测能力,对紫杉醇的改性或新类似物的合成具有指导意义.     

计算机方法确定Darunavir衍生物作为HIV-1蛋白酶抑制剂的结构决定因素与结合机制

HIV-1是地球上最可怕以及最致命的病毒之一,它是导致艾滋病的主要原因．HIV-1蛋白酶在HIV-1病毒的复制过程中承担重要角色,因此通过抑制HIV-1蛋白酶的活性从而将其作为治疗方案被认为是一种十分有效的策略．为此探究HIV-1蛋白酶抑制剂的结构决定因素而进行设计与改进成为急需解决的问题．本文建立了一个包含193个Darunavir衍生物抑制剂的数据库,在此基础上,通过使用基于配体的三维定量结构-活性关系(3D-QSAR)研究,确定了一系列关键的结构特征．此外,我们还利用分子对接进一步阐明了配体与受体之间的复杂相互作用．结果显示最优的CoMSIA模型在有效性和可预测性方面都表现出了适当的性能(Q²=0.500,R_ncv²=0.882,R_pred²=0.797)．另外,数据集中活性最高的化合物171与Asp25,Gly27,Gly48,Asp124,Asp128和Asp129形成了若干个氢键,以交叉构象稳定结合在活性空腔中．根据从最佳CoMSIA模型和分子对接中获得的信息,我们...     

MMPs抑制剂咖啡酸苯乙酯衍生物的3D-QSAR及分子对接研究

MMP-2是基底膜降解的关键酶,参与宫颈癌病发的整个过程,被认为是治疗宫颈癌的潜在新靶点。本文采用三维定量构效关系(3D-QSAR)研究32个咖啡酸苯乙酯类化合物与抗宫颈癌肿瘤细胞增殖活性的构效关系,通过比较分子场分析(CoMFA)模型(Q~2=0.638,R~2=0.972)及分子相似性指数分析(CoMSIA)模型(Q~2=0.665,R~2=0.975),表明所建立的QSAR模型具有稳定的预测能力。基于上述两种模型设计了18种新型咖啡酸苯乙酯类抑制剂,其中5种化合物具有较好的抗癌活性,抑制活性最强的为WS-1。将WS-1与MMP-2蛋白结合,结合模式显示WS-1主要通过氢键作用及疏水作用与MMP-2蛋白紧密结合,并能有效地占据MMP-2蛋白的结合位点。本研究构建的3D-QSAR模型也为进一步设计治疗宫颈癌其他抑制剂提供了理论参考。     

The pure rotational Raman spectra of cyanogen, C2N2 and C2N2

The pure rotational Raman spectra of C₂¹⁴N₂ and C₂¹⁵N₂ have been recorded photographically using a 3-metre spectrograph with a reciprocal linear dispersion of 1.4 cm⁻¹ mm⁻¹ at 488.0 nm and analysed to give the rotational and centrifugal distortion constants for both species. Corrections were applied to compensate for the effect of molecules in excited vibrational states on the pure rotational spectra. Comparisons are made with previous infrared vibration—rotational studies on these species and with previous Raman studies on C₂¹⁴N₂. The following bond lengths were calculated: r₀(C---N) = 116 ± 1 pm; r₀(C---C) = 138 ± 2 pm.     

An efficient closed-shell singles and doubles coupled-cluster method

A reformulated set of equations for the closed-shell singles and doubles coupled-cluster (CCSD) method is presented. A computational cost of n_v⁴n₀²+7n_v³n₀³+1n_v²n₀⁴ for the n⁶ steps is obtained, where n_v is the number of virtual molecular orbitals included in the CCSD procedure, n₀ is the number of doubly occupied molecular orbitals and n=n₀+n_v. Test calculations for the cis and trans isomers of FNNF and planar and pyramidal CH₃⁻ are presented. Equilibrium structures determined with large Gaussian basis sets at the second-order Møller-Plesset (MP2) perturbation level of theory are reported and used for the other electron correlation methods. With the largest one-particle basis set (144 contracted Gaussian functions), the equilibrium geometries of cis- and trans-FNNF agree with experiment. Based on analyses of planar and pyramidal CH₃⁻ wavefunctions and the calculated inversion barrier, it is suggested that the molecular anion may not exist in a planar configuration but that autodetachment of an electron occurs before the transition state is reached. Comparisons of our new CCSD procedure demonstrate that coupled-cluster methods are not significantly more expensive than similar electron correlation techniques.     

Atomic and molecular absorption spectra of indium in air-acetylene flame

Absorption spectra of both atomic and molecular species in the air-acetylene flame, which are produced when the aqueous solutions of indium dissolved in HNO₃, HF, HCl, HBr and HI were aspirated into the flame, have been investigated in the u.v. region. Numerous atomic absorption lines of indium have been observed in the absorption spectra. Most of these lines were previously listed only as emission lines. Those atomic lines have been ascribed to the electronic transitions from the ground states of 5p ²P_1/2⁰ and 5p ²P_3/2⁰ to the excited states such as ls ²S_1/2, md ²D_3/2, nd ²D_5/2, 4p^{2 4}P_1/2, 4p^{2 4}P_3/2 and 4p^{2 4}P_5/2, respectively, where 13 l 6 and 14 m,n 5. The molecular absorption bands for InF, InCl and InBr in the airacetylene flame have been also observed near 234 nm, 267 nm and 282 nm, respectively, as the electronic transition of ¹Σ⁺ → ¹Π₁ Those absorption bands show fine structures due to the molecular vibrations. The spectral parameters for the molecular vibrations have been obtained from the simulations of the observed spectra. The molecular absorption band for InI was not observed because of the decomposition of the molecule in the flame. In addition, the molecular absorption band for InO has been observed near 273 nm and those for NO near 205 and 215 nm.     

Transport phenomenon as a function of counter and co-ions in solution: chronopotentiometric behavior of anion exchange membrane in different aqueous electrolyte solutions

Anion exchange membrane has been investigated in different electrolyte solutions by chronopotentiometry to explore the influence of co-ion and counterion of the exchange group of the membrane, on the transport phenomena. Chloride, nitrate, sulfate and acetate in sodium salts were used as counterions and sodium, potassium, calcium and ammonium in chloride salts were used as co-ions. The membrane showed a potential drop (E₀) in all these electrolytes when a constant current was applied across it, which remained constant for a period less than τ, called the transition time and rose gradually to a maximum (E_max) value. The parameters such as τ, E₀ and E_max and the potential jump (ΔE) and τ and the inflection zone (Δt) along the time axis have been measured and compared at an applied current density (I) of 10 mA cm⁻² in 10 mM solutions. The values of τ^1/2/z_A[A₀] or τ^1/2/z_C[C₀], with or , E₀ and ΔE with or (where r_A and r_C are the ionic radii of counter and co-ions, respectively) have been correlated. Permselectivity (P) and transference number of the membrane with respect to each one of the above electrolytes have been evaluated and discussed.     

Oxygen abstraction from tetrahydrofuran by molybdenum-iodide complexes. X-ray molecular structure of [Mo2(μ-O)(μ-I)(μ-O2CCH3)I2(THF)4][MoOI4(THF)] (THF = tetrahydrofuran)

The interaction between Mo₂(O₂CCH₃)₄, Me₃SiI and I₂ in THF resulted in oxygen abstraction from the solvent and formation of [Mo₂(μ-O)(μ-I)(μ-O₂CCH₃) I₂(THF)₄]⁺[MoOI₄(THF)]⁻ and I---(CH₂)₄---I. The molybdenum complex has been characterized by X-ray diffractometry. Crystal data: triclinic, space group P , a = 13.827(3) Å; b = 15.803(7) Å; c = 9.950(3) Å; = 93.34(4)°; β = 102.40(2)°; γ = 90.09(2)°; V = 2120(2) Å₃; Z = 2; d_calc = 2.559 g cm⁻³; R = 0.0476 (R_w = 0.0613) for 370 parameters and 3938 data with F₀²> 3σ(F₀²). The metal-metal distance in the cation is 2.527(2) Å and indicates a strong interaction. The magnetic behavior is consistent with the assignment of one unpaired electron to the Mo₂⁷⁺ core of the cation and one to the d¹ Mo(V) center of the anion. The interaction between Mo(CO)₆ and I₂ in THF also results in the formation of 1,4-diiodobutane.     

Multiresolution analysis for quantification of optical properties in scattering media using pulsed photon time-of-flight measurements

A simplified photon time-of-flight (TOF) instrument based on a nanosecond rise-time diode laser at 635 nm was used for the quantification of optical properties of samples. A series of transmittance photon time-of-flight measurements were acquired from absorbing/scattering Intralipid™ samples of known composition (0<μ_a<0.0014 mm⁻¹; 13<μ_s<24 mm⁻¹). Time-of-flight distributions were analyzed using Haar transform with selection of the most parsimonious set of wavelets by genetic algorithm optimization. Results showed that the scattering coefficient could be estimated with a coefficient of variation (CV) of 4.4% and r²=0.95 using wavelets of frequency up to 400 MHz. Absorption coefficients were estimated with a CV of 6.9% and r²=0.99 using steady-state intensity of blank- and scatter-corrected data. Furthermore, it was shown that quantification using simplified electronics can estimate scattering to within 7.2% (r²=0.88) and absorption with an error of 8.3% (r²=0.99). The above findings suggest that a simplified instrument based on a pulsed laser diode and low frequency switches could be developed to quantify absorption in highly scattering media.