计算机模拟三氯生对FabI活性口袋及Loop区的调控机制

应用分子动力学模拟、蛋白质二级结构定义(DSSP)和口袋体积测量(POVME)计算方法分别研究了FabI (烯脂酰-ACP还原酶)-NAD⁺(氧化型烟酰胺腺嘌呤二核苷酸)二元复合物和FabI-NAD⁺-TCL(三氯生)三元复合物体系中活性口袋loop 区构象、loop 区二级结构、活性口袋体积以及底物(酰基不饱和链)通道随模拟时间的变化规律. 研究表明,在FabI-NAD⁺-TCL三元复合物中,三氯生限制了活性口袋及底物通道的变化,活性口袋loop 区呈现为规则、闭合的稳定构象,位于活性口袋正前方,常伴有螺旋二级结构的形成,从而使活性口袋体积变化较小、分布比较集中,底物通道较窄或处于关闭状态. 而在FabI-NAD⁺二元复合物中,活性口袋loop 区以无规则、开启的柔性构象存在,活性口袋体积变化较大,分布比较分散,底物通道明显较宽且不稳定. 可见,三氯生能诱导FabI 活性口袋及loop 区的构象变化,使活性口袋构成了紧密的统一体、封闭了底物通道,从而阻碍了酰基不饱和链通过底物通道进入蛋白酶的催化中心,中断了该酶催化的还原反应和细菌脂肪酸合成循环. 上述发现对深入认识三氯生的抗菌作用机制及相关药物的改良与设计具有重要的指导意义.     

3MBA类FtsZ蛋白抑制剂的分子动力学模拟及抗菌作用机制

采用分子动力学模拟、蛋白质二级结构测定(DSSP)、口袋体积测量(POVME)以及MM-PBSA(molecular mechanics Poisson-Boltzmann surface area)方法, 系统研究了金黄色葡萄球菌丝状温度敏感性蛋白Z (SaFtsZ)-二磷酸鸟苷(GDP)二元复合物和SaFtsZ-GDP-3MBA (3-甲氧基苯甲酰胺)类衍生物三元复合物体系的稳定性、蛋白质二级结构、蛋白质构象、关键残基质心距、活性口袋体积以及相对结合自由能的变化规律. 研究表明: 当不含抑制剂存在时SaFtsZ-GDP二元复合物体系稳定性较差, 其T7Loop区域残基(203-209)波动较大, 且蛋白二级结构发生明显变化, 活性口袋体积急剧减小, 底物通道显著变窄且不稳定. 而含有抑制剂PC190723、Compound1 的类衍生物三元复合物体系的表现截然不同, 这主要是由于它们均能和活性口袋T7Loop区周围残基形成关键性的氢键以及疏水作用, 与FtsZ 蛋白紧密结合. 在SaFtsZ-GDP-3MBA三元复合物体系中, 3MBA仅能与活性口袋中部分残基形成疏水作用, 与FtsZ 蛋白亲和力较弱, 使其不能稳定地存在于活性口袋中, 进一步导致它的抗菌活性明显低于PC190723、Compound1. 这些发现深入揭示了3MBA类衍生物对FtsZ 蛋白的作用机制和影响规律, 为该类FtsZ 蛋白抑制剂的结构优化和产品开发应用提供了重要的理论依据.     

α′-苯磺酰基-α,β-不饱和酮与开链二烯烃的不对称催化环加成反应

在手性金属钛催化剂存在下 ,研究了α′ 苯磺酰基 α ,β 不饱和酮与开链二烯的不对称催化环加成反应 ,讨论了α′ 苯磺酰基 α ,β 不饱和酮与开链二烯的反应活性和对映选择性 ,以高的收率和光学纯度合成了环己烯衍生物 ,并对部分产物的构型进行了鉴定     

α’-苯磺酰基-α，β-不饱和酮与开链二烯烃的不对称催化环加成反应

在手性金属钛催化剂存在下，研究了α’—苯磺酰基—α，β-不饱和酮与开 链二烯的不对称催化环加成反应，讨论了α’—苯磺酰基—α，β—不饱和酮与开 链二烯的反应活性和对映选择性，以高的收率和光学纯度合成了环己烯衍生物，并 对部分产物的构型进行了鉴定．     

HT G-四链体对甲基氮杂杯[6]吡啶的构象调控

甲基氮杂杯[n]吡啶(MACPn)是一类柔性、多构象的新型杂杯杂芳烃化合物,溶液状态中对其构象的调控与分离一直是此类化合物研究的难点之一。我们将DNA G-四链体作为功能分子,调控甲基氮杂杯[6]吡啶(MACP6)在溶液态的构象,结果表明,HT序列在K~+条件下所形成的混合结构的G-四链体可以诱导MACP6的手性构象,而在Na~+条件下所形成的反平行结构不具备此功能。一维核磁共振氢谱、分子对接与碱基突变进一步揭示了HT G-四链体与MACP6以边沿loop为位点的构型匹配作用模式,loop区增长,有利于HT G-四链体对MACP6的调控作用。本研究再次拓展了G-四链体作为氮杂杯吡啶构象调控功能分子的应用。     

HPPK与MgATP复合物的构象变化模拟研究

HPPK一种是重要的激酶和潜在的抗生素靶点,它的作用是催化细菌体内重要生命物质叶酸合成的第一步反应。在HPPK的催化反应过程中,HPPK先与MgATP结合,再与HP结合,然后催化反应发生。HPPK中的3个loop结构在结合过程中起着重要作用:MgATP的结合位点位于loop 3下,HP的结合位点位于loop 2下。loop 3与loop 2的开闭分别意味着MgATP与HP结合位点的开闭,本文运用分子动力学模拟研究HPPK与MgATP复合物构象变化。计算结果表明,在整个模拟过程中loop 3一直处于关闭状态,而loop 2则在全开、半开以及关闭等构象间转换;loop 2的开闭意味着HP结合位点的开闭,这些结果揭示了HP进入HPPKMgATP复合物很可能遵循的是构象选择机制。     

Hg^2＋ -牛血清白蛋白复合体系中蛋白质微观结构的研究

研究了Hg2+在生物体内与牛血清白蛋白相互作用的毒性机理以及蛋白质的微观结构变化.测定了Hg2+与牛血清白蛋白(BSA)复合体系的红外光谱(FT-IR)和圆二色谱(CD),并对图谱进行拟合解析处理.红外光谱实验数据表明Hg2+与BSA发生作用的结合位点可能包括-SH、-OH和-NH基团,采用红外拟合技术对BSA二级结构的变化进行了研究,结果表明蛋白质α-螺旋结构含量降低,β-折叠结构含量升高.圆二色谱图也表明由于一定浓度的Hg2+与BSA结合,从而导致蛋白质的二级结构被破坏,这与拟合红外光谱得到的蛋白质二级结构数据相吻合.Hg2+与牛血清蛋白作用致使蛋白质的构象改变,形成金属离子与蛋白质作用的复合物,因而蛋白质失去活性导致生物体发生病变.     

紫杉醚与αβ微管蛋白的分子对接

采用Insight II/Affinity对紫杉醚与αβ微管蛋白进行分子对接, 共得到10个对接构象. 应用密度泛函B3LYP/6-31G 方法计算对接口袋构象的结合能, 筛选出结合能达-190.53 kJ·mol-1的最优对接构象5. 通过构象分析建立紫杉醚与受体结合的作用模型, 结果表明, 在活性口袋的底部紫杉醚与受体间的作用主要是疏水作用, 而在活性口袋的顶部两者间主要是氢键作用. 氢键作用位置可分为A和B两个作用区, 其中A区有3个氢键, 由C13侧链分别与受体的ASP26和ARG369作用形成; B区也有3个氢键, 是由紫杉醚母环上的极性基团分别与受体的THR276、ARG278和GLN282作用产生的. 紫杉醚与αβ微管蛋白间形成的6个氢键可以有效地将紫杉醚固定在活性口袋中.     

磺酰叠氮和炔参与的多组分反应研究进展

磺酰叠氮和炔参与的铜催化多组分反应成为近年来有机化学研究的热点.磺酰叠氮和炔在铜催化下生成的N-磺酰基烯酮亚胺中间体,可以被胺、醇和水等各类亲核试剂捕捉,也可以和各种类型的烯烃发生[2+2]、[3+2]和[4+2]等环加成反应.N-磺酰基烯酮亚胺中间体受到来自双官能团底物的分子内基团进攻以及随后发生的(环)重排和σ键迁移,更是成为构建结构丰富的具有生理和药物活性(杂)环类化合物的重要手段.主要对该领域近年来的最新研究成果进行了综述.     

丙酮氰醇与3,5-二甲基-N-α,β-不饱和酰基吡唑的反应研究

氰基化合物是一类具有重要价值的有机物.研究了以丙酮氰醇为反应试剂,以取代的3,5-二甲基-N-α,β-不饱和酰基吡唑为底物时发生在不同位点的两种反应.研究结果表明,芳香取代的3,5-二甲基-N-α,β-不饱和酰基吡唑为底物时,使用不同的碱性催化剂会发生两种不同类型的反应:MgBu_2存在时体系发生Michael加成反应,产物收率最高可达95%;在四甲基胍(TMG)存在时体系发生酰胺的醇解反应,生成β-取代苯基丙烯酸氰醇酯,收率最高达84%.脂肪取代的3,5-二甲基-N-α,β-不饱和酰基吡唑与丙酮氰醇在Mg Bu_2或TMG存在下均发生Michael加成反应,产率最高为99%.讨论了使用不同碱性催化剂时的反应机理.     

Mouse thymidylate synthase does not show the inactive conformation,observed for the human enzyme

Crystal structures of mouse thymidylate synthase (mTS) in complexes with (1) sulfate anion, (2) 2′-deoxyuridine 5′-monophosphate (dUMP) and (3) 5-fluoro-dUMP (FdUMP) and N ^5,10-methylenetetrahydrofolate (meTHF) have been determined and deposited in Protein Data Bank under the accession codes 3IHI, 4E5O and 5FCT, respectively. The structures show a strong overall similarity to the corresponding structures of rat and human thymidylate synthases (rTS and hTS, respectively). Unlike with hTS, whose unliganded and liganded forms assume different conformations (“inactive” and “active,” respectively) in the loop 181–197, in each of the three mTS structures, the loop 175–191, homologous to hTS loop 181–197, populates the active conformer, with catalytic Cys 189 buried in the active site and directed toward C(6) of the pyrimidine ring of dUMP/FdUMP, pointing to protein’s inability to adopt the inactive conformation. The binary structures of either dUMP- or sulfate-bound mTS, showing the enzyme with open active site and extended C-terminus, differ from the structure of the mTS–5-FdUMP–meTHF ternary complex, with the active site closed and C-terminus folded inward, thus covering the active site cleft. Another difference pertains to the conformation of the Arg44 side chain in the active site-flanking loop 41–47, forming strong hydrogen bonds with the dUMP/FdUMP phosphate moiety in each of the two liganded mTS structures, but turning away from the active site entrance and loosing the possibility of H-bonding with sulfate in the sulfate-bound mTS structure.     

Isothermal vapor–liquid equilibrium at 303.15 K and excess molar volumes at 298.15 K for the ternary system of propyl vinyl ether + 1-propanol + 2,2,4-trimethyl-pentane and its binary sub-systems

Isothermal vapor–liquid equilibrium data determined by the static method at 303.15 K are reported for the binary systems propyl vinyl ether + 1-propanol, 1-propanol + 2,2,4-trimethylpentane and propyl vinyl ether + 2,2,4-trimethylpentane and also for the ternary system propyl vinyl ether + 1-propanol + 2,2,4-trimethyl-pentane. Additionally, new excess volume data are reported for the same systems at 298.15 K. The experimental binary and ternary vapor–liquid equilibrium data were correlated with different G^E models and excess molar volume data were correlated with the Redlich–Kister equation for the binary systems and the Cibulka equation for the ternary system, respectively.     

Isothermal vapor–liquid equilibrium at 333.15 K,excess molar volumes and refractive indices at 298.15 K for mixtures of tert-amyl methyl ether + ethanol + 2,2,4-trimethylpentane

Isothermal vapor–liquid equilibrium data at 333.15 K are measured for the binary system tert-amyl methyl ether + ethanol and tert-amyl methyl ether + 2,2,4-trimethylpentane and for ternary system tert-amyl methyl ether + ethanol + 2,2,4-trimethylpentane by using headspace gas chromatography. The experimental vapor–liquid equilibrium data were correlated with G^E models (Margules, van Laar, Wilson, NRTL, UNIQUAC) equations. The excess volume and deviations in molar refractivity data are also reported for the same binary and ternary systems at 298.15 K. These data were correlated with the Redlich–Kister equation for the binary systems and the Cibulka equation for the ternary system, respectively. The experimental ternary excess volume and deviations in molar refractivity data, were also compared with the estimated values from the binary contribution models of Tsao–Smith, Kohler, Rastogi and Radojkovi?.     

Isothermal vapor–liquid equilibrium at 333.15 K and excess molar volumes and refractive indices at 298.15 K for the mixtures of di-methyl carbonate,ethanol and 2,2,4-trimethylpentane

Isothermal vapor–liquid equilibrium data at 333.15 K are measured for the binary system ethanol + 2,2,4-trimethylpentane and for ternary system di-methyl carbonate (DMC) + ethanol + 2,2,4-trimethylpentane by using headspace gas chromatography. The experimental binary and ternary vapor–liquid equilibrium data were correlated with different activity coefficient models. Excess volume and deviations in molar refractivity data are also reported for the binary systems DMC + ethanol and DMC + 2,2,4-trimethylpentane and the ternary system DMC + ethanol + 2,2,4-trimethylpentane at 298.15 K. These data were correlated with the Redlich-Kister equation for the binary systems and the Cibulka equation for the ternary system, respectively. The ternary excess volume and deviations in molar refractivity data were also compared with estimated values from the binary contribution models of Tsao–Smith, Kohler, Rastogi and Radojkovi?.     

Volumetric properties of ternary (IL + 2-propanol or 1-butanol or 2-butanol + ethyl acetate) systems and binary (IL + 2-propanol or 1-butanol or 2-butanol) and (1-butanol or 2-butanol + ethyl acetate) systems

The experimental densities for the binary or ternary systems were determined at T = (298.15, 303.15, and 313.15) K. The ionic liquid methyl trioctylammonium bis(trifluoromethylsulfonyl)imide ([MOA]⁺[Tf₂N]⁻) was used for three of the five binary systems studied. The binary systems were ([MOA]⁺[Tf₂N]⁻ + 2-propanol or 1-butanol or 2-butanol) and (1-butanol or 2-butanol + ethyl acetate). The ternary systems were {methyl trioctylammonium bis(trifluoromethylsulfonyl)imide + 2-propanol or 1-butanol or 2-butanol + ethyl acetate}. The binary and ternary excess molar volumes for the above systems were calculated from the experimental density values for each temperature. The Redlich–Kister smoothing polynomial was fitted to the binary excess molar volume data. Virial-Based Mixing Rules were used to correlate the binary excess molar volume data. The binary excess molar volume results showed both negative and positive values over the entire composition range for all the temperatures.The ternary excess molar volume data were successfully correlated with the Cibulka equation using the Redlich–Kister binary parameters.     

Excess Molar Volumes,Viscosities and Speeds of Sound of the Ternary Mixture 1-Heptanol (1) + Tetrachloroethylene (2) + Methylcyclohexane (3) at 298.15 K

Densities (ρ), viscosities (η) and speeds of sound (u) of the ternary mixture (1-heptanol + tetrachloroethylene + methylcyclohexane) and the corresponding binary mixtures (1-heptanol + tetrachloroethylene), (1-heptanol + methylcyclohexane) and (tetrachloroethylene + methylcyclohexane) at 298.15 K were measured over the whole composition range. The data obtained are used to calculate the excess molar volumes (V ^E), excess isobaric thermal expansivities (α ^E), viscosity deviations (Δη), excess Gibbs energies of activation of viscous flow (ΔG ^*E) and excess isentropic compressibilities (κ _S ^E) of the binary and ternary mixtures. The data from the binary systems were fitted by the Redlich–Kister equation whereas the best correlation method for the ternary system was found using the Nagata equation. Viscosities, speeds of sound and isentropic compressibilities of the binary and ternary mixtures have been correlated by means of several empirical and semi-empirical equations. The best correlation method for viscosities of binary systems is found using the Iulan et al. equation and for the ternary system using the Heric and McAllister equations. The best correlation method for the speeds of sound and isentropic compressibilities of the binary system (1-heptanol + methylcyclohexane) is found using IMR (Van Deal ideal mixing relation) and for the binary system (tetrachloroethylene + methylcyclohexane) it is found using the NR (Nomoto relation) and for the binary system (1-heptanol + tetrachloroethylene) and the ternary system (1-heptanol + trichloroethylene + methylcyclohexane) it is obtained from the FLT (Jacobson free length theory).     

Isothermal vapor–liquid equilibrium at 333.15 K and excess molar volumes at 298.15 K for the ternary system di-isopropyl ether + n-propyl alcohol + toluene and its binary subsystems

Isothermal vapor–liquid equilibrium data at 333.15 K are reported for the ternary system di-isopropyl ether (DIPE) + n-propyl alcohol + toluene and the binary subsystems DIPE + n-propyl alcohol, DIPE + toluene and n-propyl alcohol + toluene by using headspace gas chromatography. The excess molar volumes at 298.15 K for the same binary and ternary systems were also determined by directly measured densities. The experimental binary and ternary vapor–liquid equilibrium data were correlated with different G^E models and the excess molar volumes were correlated with the Redlich–Kister equation for the binary systems and the Cibulka equation for the ternary system, respectively.     

Excess Gibbs energies and volumes of the ternary system chloroform + tetrahydrofuran + cyclohexane at 298.15 K

Vapour–liquid equilibria and densities for the ternary system chloroform + tetrahydrofuran + cyclohexane and for the binary mixtures containing chloroform have been determined at 298.15 K. Vapour–liquid equilibrium data have been collected by head-space gas-chromatographic analysis of the vapour phase directly withdrawn from an equilibration apparatus. Density measurements have been carried out by means of a vibrating tube densimeter. Molar excess Gibbs energies G^E and volumes V^E, as well as activity coefficients and apparent molar volumes of the components, have been obtained from the measured quantities and discussed. The binary chloroform + tetrahydrofuran displays negative deviations from ideality, while chloroform + cyclohexane positive deviations, for both volume and Gibbs energy. The G^E's and V^E's for the ternary system are positive in the region rich in cyclohexane while negative in the region rich in chloroform + tetrahydrofuran. This indicates that hydrogen bonding between chloroform and tetrahydrofuran molecules produces negative values of G^E and V^E and strongly influences the behaviour of the ternary system.