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。     

甲基丙烯酸三丁基锡酯与甲基丙烯酸甲酯共聚物的分子量测定和K、α值的订定

甲基丙烯酸三丁基锡酯与甲基丙烯酸甲酯共聚物的分子量测定和K、α值的订定     

Triindolo-Truxene Derivatives: Design,Synthesis, and Fine-Tuning of Electronic Properties and Molecular Assembly through Molecular Engineering

Triindolo-truxene, a C₃-symmetric molecule with a large π-conjugated plane, has six methylene carbon atoms and three aromatic carbon atoms that can be facilely functionalized. Herein, butyl, carbonyl, cyano, and/or malononitrile groups were introduced at six methylene carbon atoms (6-, 14-, 22- or 8-, 16-, 24-positions) and/or three aromatic carbon atoms (2-, 10-, and 18-positions) of triindolo-truxene to produce eight derivatives. Their photophysical properties, electrochemical properties, and molecular assembly can be effectively modulated by substituents and substitution patterns. Incorporation of electron-deficient groups led to redshifts in both the absorption and emission of these derivatives and also lowered their HOMO and LUMO levels. Different substitution patterns resulted in the different intramolecular donor–acceptor interactions. Electron-deficient substituents at the methylene carbon atoms in the 6-, 14-, and 22-positions led to intramolecular charge transfer from the fluorene arms to the truxene core, whereas the corresponding substitutions at the methylene carbon atoms in the 8-, 16-, and 24-positions resulted in intramolecular charge transfer from the truxene core to the fluorene arms. The molecular packing in single crystals and molecular aggregation in solution are also influenced by the substituents and substitution patterns. This work provides a straightforward strategy to alter the properties of triindolo-truxene.     

Molecular Volume of Phosphates, Arsenates and Vanadates

The present paper discusses some characteristics of the molecular volumes of phosphates, arsenates and vanadates. In the salts, the volumes of per acid radical ((?)) quantitatively depend on the radii, charges, numbers of cations and anions. The functional relations between the (?) values of phosphates, arsenates, vanadates and the factors mentioned above are obtained. The molecular volumes of these salts are equal to the sum of the topological volumes of cations and anions. The authors have got a series of universally united topological volume values of cations and anions. It confirms that the topological molecular volume of the crystal water (H_2O) in the hydrates of the salts approximates to a constant, 244 (?)~3 with σ_(n-1)= 2.1. The topological volume of the hydroxide ion (OH~-) approximates to a constant too. The average value is 16.89 (?)~3 with σ_(n-1)=1.68.     

Synthesis,Biological Evaluation,and Molecular Modeling of Aza-Crown Ethers

Synthetic and natural ionophores have been developed to catalyze ion transport and have been shown to exhibit a variety of biological effects. We synthesized 24 aza- and diaza-crown ethers containing adamantyl, adamantylalkyl, aminomethylbenzoyl, and ε-aminocaproyl substituents and analyzed their biological effects in vitro. Ten of the compounds (8, 10–17, and 21) increased intracellular calcium ([Ca²⁺]_i) in human neutrophils, with the most potent being compound 15 (N,N’-bis[2-(1-adamantyl)acetyl]-4,10-diaza-15-crown-5), suggesting that these compounds could alter normal neutrophil [Ca²⁺]_i flux. Indeed, a number of these compounds (i.e., 8, 10–17, and 21) inhibited [Ca²⁺]_i flux in human neutrophils activated by N-formyl peptide (fMLF). Some of these compounds also inhibited chemotactic peptide-induced [Ca²⁺]_i flux in HL60 cells transfected with N-formyl peptide receptor 1 or 2 (FPR1 or FPR2). In addition, several of the active compounds inhibited neutrophil reactive oxygen species production induced by phorbol 12-myristate 13-acetate (PMA) and neutrophil chemotaxis toward fMLF, as both of these processes are highly dependent on regulated [Ca²⁺]_i flux. Quantum chemical calculations were performed on five structure-related diaza-crown ethers and their complexes with Ca²⁺, Na⁺, and K⁺ to obtain a set of molecular electronic properties and to correlate these properties with biological activity. According to density-functional theory (DFT) modeling, Ca²⁺ ions were more effectively bound by these compounds versus Na⁺ and K⁺. The DFT-optimized structures of the ligand-Ca²⁺ complexes and quantitative structure-activity relationship (QSAR) analysis showed that the carbonyl oxygen atoms of the N,N’-diacylated diaza-crown ethers participated in cation binding and could play an important role in Ca²⁺ transfer. Thus, our modeling experiments provide a molecular basis to explain at least part of the ionophore mechanism of biological action of aza-crown ethers.     

Combined QSAR/QSPR,Molecular Docking,and Molecular Dynamics Study of Environmentally Friendly PBDEs with Improved Insulating Properties

To improve the insulating properties of polybrominated diphenyl ethers(PBDEs), we studied the molecular structures and energy gap(Eg) values of 209 PBDEs using a three-dimensional quantitative structure-activity relationship(3D-QSAR) model, molecular docking, and molecular dynamics. We also analyzed the interaction mechanisms of PBDEs using a 2D-QSAR model, molecular substitution characteristics, and molecular docking. The 3D-QSAR model showed that the 2-, 4-, 5-, and 6-positions significantly influenced the PBDE insulating properties. Using BDE-34 as a template molecule, we designed six derivatives with 0.47%-28.44% higher insulation tlian BDE-34. Compared with BDE-34, the stability and flame retardancy of the above six derivatives were not adversely affected. These derivatives, except for 2,6-cyanomethyl-BDE, 2-cyanomethyl-BDE, and 2-aniinomethyl-BDE, were more toxic and biodegradable than BDE-34, but showed weaker bioaccumulation and migration abilities than BDE-34. Mechanism analysis showed that the highest occupied orbital energy, the most negative charge, and the dipole moment were the main quantitative parameters that aflected the PBDE insulating properties. PBDE insulation gradually decreased as the number of Br atoms increased. The level of similarity between the substitution patterns on the two benzene rings was significantly correlated with PBDE insulation, with hydrophobic groups having a more significant efiect on PBDE insulation.     

Molecular and Crystal Structure of 2, 3, 5, 6-dipropylene-r-pyrone

11NTRODUCT1ONWeattemptedtosynthesizeanextractant(1)bythereactionofadipylchloridewithcyclopentanonepiperidineenamineaccordingtoHunig'sprocedure"',however,wemainlyobtainedthetitlecompound,whichmaybepossiblyapotentialmedicinet2'3i.Itsmolecularstructurewasfinallyconfirmedbythesingle-crystalstructuredeterminationafterconventionalUV,IR,lHNMR,MSandelementana-lyticalworks.2EXPER1MENTALSECT1ON2.1SynthesisToastirredsolutioncontaining8Omlofchloroform,2.8mloftri-ethylamineand1.51g(O-Olmol)…     

螺环吲哚类MDM2抑制剂的分子对接、定量构效关系和分子动力学模拟

采用分子对接、三维定量构效关系(3D-QSAR)和分子动力学方法研究了21个螺环吲哚类化合物与MDM2蛋白的相互作用, 并建立了相关预测模型. 比较分子场分析法(CoMFA)和比较分子相似性指数分析法(CoMSIA)模型的交互验证相关系数q²分别为0.573 和0.651, 非交互验证相关系数r²分别为0.948和0.980. 分子对接得到的结合模式与分子动力学模拟得到的结果一致, 结合模式表明该类螺环吲哚化合物主要通过疏水相互作用和氢键与MDM2结合. 基于上述相互作用模型设计并合成了6个新结构螺环吲哚化合物, 并在MDM2高表达的前列腺癌LNCaP细胞株上测定其活性, 结果表明化合物5, 6的半数抑制浓度均低于1μg·mL^-1, 可作为新的抗肿瘤药物先导化合物进一步深入研究. 本研究对以MDM2为靶点的新结构螺环吲哚类抑制剂的开发提供了理论和实验依据.     

Homology Modeling,Molecular Docking,and Molecular Dynamic Simulation of the Binding Mode of PA-1 and Botrytis cinerea PDHc-El

To reveal the potential fungicidal mechanism of 5-((4-((4-chlorophenoxy)methyl)-5-iodo-1 H-1,2,3-triazole-1-yl)methyl)-2-methylpyrimidin-4-amine(PA-1) against Botrytis cinerea(B. cinerea), the three-dimensional structure of B. cinerea pyruvate dehydrogenase complex E1 component(PDHc-E1) is homology modeled, as the PA-1 shows potent E. coli PDHc-E1 and B. cinerea inhibition. Subsequent molecular docking indicates the PA-1 can tightly bind to B. cinerea PDHc-E1. Molecular dynamic simulation and MM...     

HIV-1整合酶链转移抑制剂的3D-QSAR、分子对接和分子动力学模拟研究

为了获得高活性、结构新颖的整合酶链转移(INST)抑制剂,本文采用Co MFA和Co MSIA两种方法对32个萘啶类INST抑制剂进行了三维定量构效关系研究,并建立了相关模型,其交叉验证系数分别为q~2=0. 809和q~2=0. 816,拟合验证系数分别为r~2=0. 998和r~2=0. 981,表明所建立的模型是可靠的且具有一定的预测能力。利用分子对接探讨小分子化合物与INST蛋白的相互作用模式,结果表明,萘啶类化合物主要通过疏水作用和氢键作用与INSTIs蛋白结合。最后通过分子动力学模拟进一步验证对接结果发现,对接的结合模式与分子动力学模拟得到的结果是一致的。本研究获得的综合模型和推论可以为开发有效的HIV INSTIs提供重要的理论信息。     

Molecular Orbital Calculations on 2, 4, 6-Trinitrotoluene

Three ab initio calculations (HF/6-3IG, HF/6-3IG*, and HF/6-3IG**) on 2,4,6-trinitrotoluene were made, The results compare well with xray data, except dihedral angles of NO₂ relative to the plane of the benzene ring. The deviations are attributed to packing forces and steric effects in the crystal. The most stable structure was a torsional angle 10° of the methyl top with the benzene ring, unlike toluene. The rotational barriers of the methyl top and the 4-nitro group are small. Hydrogen bonding, dipole moments and total atomic charges arc calculated.     

吡唑啉-β-二酮类分子设计合成和抑菌活性

利用系统搜索和模拟退火程序对1－苯基－3－甲基－4－（4－氯苯甲酰基）－吡唑啉－5－酮和1－苯基－3－甲基－4－（4－硝基苯甲酰基）－吡唑啉－5－酮两个吡唑啉β－二酮分子进行分子力学计算和分子动力学研究。采用纸碟法测定它们的广谱抗菌活性。利用Gaussian94程序进行量子化学从头算，计算结果与抑菌活性测定结果相吻合。     

低分子量含氟聚合物的制备、官能化及特性

低分子量含氟聚合物是重要的新型功能材料,在国防工业中占有特殊地位。同时,作为高科技战略物资,近年来逐渐成为研究热点。本文对低分子量含氟聚合物的制备方法、官能化及特性进行了综述,重点介绍了低分子量含氟聚合物的制备和官能化方法的研究进展,并总结和详细介绍了低分子量含氟聚合物的特性,最后对该领域的前景和发展方向进行了展望。     

过碳酰胺分子合成条件优化、晶体结构及其热稳定性

采用四因素、三水平的方法研究了过碳酰胺分子合成中物料比、反应温度、反应时间、稳定剂的种类对合成收率的影响,获得了合成的最佳工艺条件。 在最佳合成条件下,测得过碳酰胺的产率可达到99%,活性氧含量最高可达到17.5%。 通过热分析方法研究了过碳酰胺分子热稳定性。 研究表明,温度超过65 ℃过碳酰胺含量和含氧量均迅速下降。 利用X射线单晶衍射仪测定了其晶体结构,使用Diamond软件解析出过碳酰胺分子的三维空间超分子结构及其氢键的连接方式。     

Molecular valence calculations on cyclohexasulfur,cycloheptasulfur, and cyclooctasulfur

A theoretical study of homocyclic sulfur species S₆, S₇, and S₈ was carried out using a molecular valence method involving stepwise approximations for orthogonality and core-valence interactions. The valence shell orbitals are described at the minimal basis level. The geometries of the molecules are predicted well as compared with other theoretical studies and the experimental values. The slight overestimation of the SS bond length is typical to the nonpolarized basis sets. The energies of the valence orbitals are well in accord with the conventional all-electron ab initio results. The trend in the stabilities of the three molecules is discussed. The present method provides an attractive possibility to study homocyclic and heterocyclic systems involving heavier chalcogens with no increase of the computing time.     

Molecular Modeling,Synthesis, and Biological Evaluation of Macrocyclic Calpain Inhibitors

The design and elaboration of a series of macrocyclic templates that exhibit a propensity to adopt a β‐strand‐like peptide‐backbone conformation led to potent and selective inhibitors of calpain 2. Macrocycle 1 retarded calcium‐induced opacification in an ovine‐lens culture assay and is a lead compound for the development of a drug for cataract treatment. Cbz=carbobenzyloxy.