神经氨酸酶与三羟基甲氧基黄酮衍生物相互作用的分子模拟

以5,7,4'-三羟基-8-甲氧基黄酮(MF)为先导物, 以现有的神经氨酸酶(NA)抑制剂类药物的结构特征为参考, 设计了一系列的三羟基甲氧基黄酮衍生物, 并运用分子对接与分子动力学相结合的方法进行了筛选及作用机制分析. 分子对接结果表明, 功能团(羧基及胍基/氮-乙酰氨基)的引入并未影响衍生物在酶活性腔中的结合位置, 衍生物的结构与相互作用能之间存在一定的联系. 将羧基和胍基作为替代基团引入到MF的C7及C5位上所得的新化合物(9)在所合成的衍生物中具有最好的结合能力(-1172.52 kJ/mol), 远远优于现有先导药物4-(氮-乙酰氨基)-5-胍基-3-(3-戊氧基)安息香酸(BA)和MF与NA的结合能力(-672.12和-347.44 kJ/mol). 进一步的作用机制分析发现, 在神经氨酸酶活性腔中, 化合物9的羧基和胍基的空间取向与现有药物中这两个基团的空间取向一致, 且化合物9与先导药物MF一样, 能与活性腔内保守残基Asp151和Glu227发生较强的相互作用. 因此可认为化合物9是一种具有应用潜质的新型神经氨酸酶抑制剂. 本研究结果为实验研究和设计抗流感药物提供了可行性思路.     

1,2,4-三唑-3-硫醚衍生物的合成、晶体结构与神经氨酸酶抑制活性

设计并合成了一系列1,2,4-三唑-3-硫醚衍生物,目标化合物的化学结构经¹H NMR、¹³C NMR、质谱和元素分析确证;采用单晶X射线衍射法测定了(E)-4-(4-羟基-3-甲氧基苯基亚甲氨基)-5-乙基-4H-1,2,4-三唑-3-丙硫醚(1c)的晶体结构.目标化合物体外神经氨酸酶(Neuraminidase, NA, H1N1)抑制活性测试结果表明,大部分化合物1具有较好的NA抑制活性,其中(E)-4-(4-羟基-3-甲氧基苯基亚甲氨基)-5-乙基-4H-1,2,4-三唑-3-乙硫醚(1b)和1c的NA抑制活性最佳,其IC50值分别为(6.86±2.08)和(9.1±1.56)μg/m L.     

三维全息原子场作用矢量(3D-HoVAIF)用于神经氨酸酶抑制剂的结构表征与设计及定量构效关系(QSAR)研究

对100个神经氨酸酶抑制剂抗禽流感药物结构并与其活性建立定量构效关系模型。采用本实验室提出的三维全息原子场作用矢量(3D-HoVAIF)对100个神经氨酸酶抑制剂进行结构表征,然后采用逐步回归对变量进行筛选后,运用偏最小二乘建立3D-HoVAIF描述子与神经氨酸酶抑制剂活性之间的QSAR模型。结果表明:复相关系数(R),交互校验的复相关系数(Q2)和模型的标准偏差(SD)分别为R2=0.805、Q2=0.657和SD=0.936,模型具有良好的稳定性和预测能力,并对文献中23个药物和设计的32个化合物进行了预测。表明三维全息原子场作用矢量能较好表征该类分子结构信息值得进一步推广应用。     

中药黄芩中神经氨酸酶抑制剂的超滤质谱筛选研究

采用超滤质谱分析技术, 结合体外酶活性实验方法, 从传统中药黄芩提取物中筛选神经氨酸酶抑制剂. 研究结果表明, 中药黄芩提取物具有较强的神经氨酸酶抑制活性, 利用超滤质谱方法从中筛选并鉴定出了六种具有潜在神经氨酸酶抑制活性的化合物, 为开发神经氨酸酶抑制剂提供了实验依据.     

新型神经氨酸酶抑制剂的设计合成及抗流感病毒活性

对上市药物扎那米韦、 奥司他韦和帕拉米韦进行结构修饰, 对化合物相应的氨基进行磷酰化, 设计合成了10个新化合物. 新化合物在酶水平和细胞水平均具有一定的抗流感病毒活性, 化合物I-8在酶水平、 化合物I-6在细胞水平具有和阳性对照药奥司他韦相当的活性.     

中国毛虾流感病毒神经氨酸酶抑制活性肽的研究

以中国毛虾为原料, 以抑制流感病毒神经氨酸酶(NA)活性为初筛指标, 通过控制酶切位点制备了具有抑制NA活性的酶解液. 利用凝胶层析和高效液相色谱等技术分离纯化出高活性的抑制肽, 其IC₅₀ 值为96.1 μmol/L.经串联质谱测定该抑制肽序列为EISYIHAEAYRRGELK, 紫外光谱分析结果证明该抑制肽能与NA结合.基于反向对接, 应用SYBYL软件模拟抑制肽与NA活性区域结合, 确定了抑制肽与NA的结合位点. 细胞毒性实验测得该抑制肽对细胞的最大无毒浓度(TC₀)为1.26 mg/mL.在红细胞凝集实验中, 随着抑制肽浓度增大, 病毒的凝集价显著降低, 证明抑制肽的抗病毒作用具有多靶点.     

奥司他韦类似物的设计、合成与活性评价（英文）

本文合成了6个芳香族、氨基酸甲酯取代的奥司他韦衍生物,以及分离纯化得到奥司他韦降解杂质4个。它们均进行了神经氨酸酶(H1N1,H3N2和耐药株H5N1-H275Y)的体外活性测试。其中,化合物4c对H1N1亚型和H5N1-H275Y突变具有明显的抑制作用(IC₅₀分别为0.31±0.16和1.40±0.93μg·mL^-1)。分子对接结果显示4c的酯基和氨基在430环入口附近与Arg118、Arg371、Tyr406和Thr439形成额外的氢键。本文所述的药物设计方法将有助于神经氨酸酶抑制剂前药的研究,化合物4c可进一步优化,为临床提供候选药物。     

毛秔子梢中天然高活性的神经氨酸酶抑制成分的研究

从天然产物中筛选高效低毒的神经氨酸酶抑制剂(NAI), 以期发现可抗流感病毒(H1N1)的化合物. 方法: 采用经典的NA活性检测实验(FL-MH-NANA method), 对从豆科植物毛秔子梢中分离得到10个化合物进行筛选, 检测这些化合物对NA的抑制活性. 结论: 化合物1, 2, 3, 5对流感病毒株的神经氨酸酶(NA)均具有抑制作用, 其中化合物1的抑制活性最强, 其IC₅₀值为16.76 μmol/L. 化合物1～4为新化合物, 化合物5～10为该植物中首次分得.     

4-甲氧基-N-(4-(3-吗啉基丙氧基)苯基)-3-(4-(吡啶-3-基)嘧啶-2-基氨基)苯甲酰胺与人血清白蛋白的相互作用研究

应用分子对接模拟技术结合荧光猝灭法、同步荧光法、三维荧光法和紫外-可见光谱法,模拟生理条件(p H 7.4),在298 K和310 K温度下,研究了人血清白蛋白(HSA)与4-甲氧基-N-(4-(3-吗啉基丙氧基)苯基)-3-(4-(吡啶-3-基)嘧啶-2-基氨基)苯甲酰胺(1z)之间的相互作用。发现1z的加入引起了HSA内源荧光的静态猝灭,蛋白构象发生改变。理论研究与实验结果相结合研究了蛋白与药物的作用机理,从而为进一步寻找治疗慢性粒细胞白血病的药物小分子提供了实验依据。     

(±)-N-叔丁氧羰基-3-乙基-戊氨酸的合成

在最优反应条件[海因2 mmol,n(3-戊酮)∶n(海因)=1.5,乙醇胺为碱,p H 4,于55℃反应6 h]下制得5-(1-乙基亚丙基)海因(4);4用5%Pd/C催化加氢制得5-(3-戊基)海因(5);5先在碱性条件下水解,再通过叔丁氧羰基保护氨基合成了(±)-N-叔丁氧羰基-3-乙基-戊氨酸,总收率43%,其结构经~1H NMR,~(13)C NMR和HR-ESI-MS确证。     

Quantum Computational Investigation of (E)-1-(4-methoxyphenyl)-5-methyl-N′-(3-phenoxybenzylidene)-1H-1,2,3-triazole-4-carbohydrazide

The title compound was synthesized and structurally characterized. Theoretical IR, NMR (with the GIAO technique), UV, and nonlinear optical properties (NLO) in four different solvents were calculated for the compound. The calculated HOMO–LUMO energies using time-dependent (TD) DFT revealed that charge transfer occurs within the molecule, and probable transitions in the four solvents were identified. The in silico absorption, distribution, metabolism, and excretion (ADME) analysis was performed in order to determine some physicochemical, lipophilicity, water solubility, pharmacokinetics, drug-likeness, and medicinal properties of the molecule. Finally, molecular docking calculation was performed, and the results were evaluated in detail.     

Multiple field three dimensional quantitative structure-activity relationship (MF-3D-QSAR)

A new drug design method, the multiple field three-dimensional quantitative structure-activity relationship (MF-3D-QSAR), is proposed. It is a combination and development of classical 2D-QSAR and traditional 3D-QSAR. In addition to the electrostatic and van der Waals potentials, more potential fields (such as lipophilic potential, hydrogen bonding potential, and nonthermodynamic factors) are integrated in the MF-3D-QSAR. Meanwhile, a principal component analysis (PCA) and iterative double least square (IDLS) technique is developed for predicting the bioactivity of query drug candidates. As an example, the MF-3D-QSAR is applied to the design of neuraminidase inhibitor and to prove its predictive power, and some useful findings are obtained for developing drugs against influenza virus.     

Synthesis,Antibacterial and Anthelmintic Activity of Novel 3-(3-Pyridyl)-oxazolidinone-5-methyl Ester Derivatives

In this study, a series of 3-(3-pyridyl)-oxazolidone-5-methyl ester derivatives was synthesized and characterized by ¹H NMR, ¹³C NMR, and LC-MS. The conducted screening antibacterial studies of the new 3-(3-pyridyl)-oxazolidone-5-methyl ester derivatives established that the methyl sulfonic acid esters have broad activity spectrum towards Staphylococcus aureus, Streptococcus pneumoniae, Bacillus subtilis and Staphylococcus epidermidis. Among them, compound 12e has the most potent activity, with an MIC of 16 μg/mL against B.subtilis, and could reduce the instantaneous growth rate of bacteria. Furthermore, molecular docking studies were also simulated for compound 12e to predict the specific binding mode of this compound. In addition, anthelmintic activity of these compounds was also evaluated against adult Indian earthworms (Pheretima posthuman). The results showed that compound 11b had the best effect. These results above can provide experimental reference for the development of novel antibacterial and anthelmintic drugs.     

Light-induced Photoswitching of 4-(Phenylazo)benzoic Acid on Au(111)

Photochromic molecules can undergo a reversible conversion between two isomeric forms upon exposure to external stimuli such as electromagnetic radiation. A significant physical transformation accompanying the photoisomerization process defines them as photoswitches, with potential applications in various molecular electronic devices. As such, a detailed understanding of the photoisomerization process on surfaces and the influence of the local chemical environment on switching efficiency is essential. Herein, we use scanning tunneling microscopy to observe the photoisomerization of 4-(phenylazo)benzoic acid (PABA) assembled on Au(111) in kinetically constrained metastable states guided by pulse deposition. Photoswitching is observed at low molecular density and is absent in tight-packed islands. Furthermore, switching events were noted in PABA molecules coadsorbed in a host octanethiol monolayer, suggesting an influence of the surrounding chemical environment on photoswitching efficiency.     

Discovery of Potential Antiviral Compounds against Hendra Virus by Targeting Its Receptor-Binding Protein (G) Using Computational Approaches

Hendra virus (HeV) belongs to the paramyxoviridae family of viruses which is associated with the respiratory distress, neurological illness, and potential fatality of the affected individuals. So far, no competitive approved therapeutic substance is available for HeV. For that reason, the current research work was conducted to propose some novel compounds, by adopting a Computer Aided Drug Discovery approach, which could be used to combat HeV. The G attachment Glycoprotein (Ggp) of HeV was selected to achieve the primary objective of this study, as this protein makes the entry of HeV possible in the host cells. Briefly, a library of 6000 antiviral compounds was screened for potential drug-like properties, followed by the molecular docking of short-listed compounds with the Protein Data Bank (PDB) structure of Ggp. Docked complexes of top two hits, having maximum binding affinities with the active sites of Ggp, were further considered for molecular dynamic simulations of 200 ns to elucidate the results of molecular docking analysis. MD simulations and Molecular Mechanics Energies combined with the Generalized Born and Surface Area (MMGBSA) or Poisson–Boltzmann and Surface Area (MMPBSA) revealed that both docked complexes are stable in nature. Furthermore, the same methodology was used between lead compounds and HeV Ggp in complex with its functional receptor in human, Ephrin-B2. Surprisingly, no major differences were found in the results, which demonstrates that our identified compounds can also perform their action even when the Ggp is attached to the Ephrin-B2 ligand. Therefore, in light of all of these results, we strongly suggest that compounds (S)-5-(benzylcarbamoyl)-1-(2-(4-methyl-2-phenylpiperazin-1-yl)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide and 5-(cyclohexylcarbamoyl)-1-(2-((2-(3-fluorophenyl)-2-methylpropyl)amino)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide could be considered as potential therapeutic agents against HeV; however, further in vitro and in vivo experiments are required to validate this study.     

Structural Investigation of the Interaction Mechanism between Chlorogenic Acid and AMPA Receptor via In Silico Approaches

Chlorogenic acid (CGA), an important metabolite in natural plant medicines such as honeysuckle and eucommia, has been shown to have potent antinociceptive effects. Nevertheless, the mechanism by which CGA relieves chronic pain remains unclear. α-amino-3-hydroxy-5-methyl-4-isooxazolpropionic acid receptor (AMPAR) is a major ionotropic glutamate receptor that mediates rapid excitatory synaptic transmission and its glutamate ionotropic receptor AMPA type subunit 1 (GluA1) plays a key role in nociceptive transmission. In this study, we used Western blot, surface plasmon resonance (SPR) assay, and the molecular simulation technologies to investigate the mechanism of interaction between CGA and AMPAR to relieve chronic pain. Our results indicate that the protein expression level of GluA1 showed a dependent decrease as the concentration of CGA increased (0, 50, 100, and 200 μM). The SPR assay demonstrates that CGA can directly bind to GluA1 (K_D = 496 μM). Furthermore, CGA forms a stable binding interaction with GluA1, which is validated by molecular dynamics (MD) simulation. The binding free energy between CGA and GluA1 is −39.803 ± 14.772 kJ/mol, where van der Waals interaction and electrostatic interaction are the major contributors to the GluA1–CGA binding, and the key residues are identified (Val-32, Glu-33, Ala-36, Glu-37, Leu-48), which play a crucial role in the binding interaction. This study first reveals the structural basis of the stable interaction between CGA and GluA1 to form a binding complex for the relief of chronic pain. The research provides the structural basis to understand the treatment of chronic pain and is valuable to the design of novel drug molecules in the future.     

HIV-1逆转录酶抑制剂的3D-QSAR研究及分子设计

采用Topomer Co MFA方法对24个二芳基苯胺衍生物进行三维定量构效关系研究,建立了3DQSAR模型,所得优化模型的非交叉相关系数、交互验证系数以及外部验证的复相关系数分别为0.928,0.654和0.940,结果表明该模型具有良好的稳定性和预测能力。采用分子对接技术对药物与受体的作用机制进行了研究,结果显示,药物与HIV-1逆转录酶的LYS172,GLU138,LYS101等位点作用明显。运用这些信息进行分子设计,在理论上获得了一些具有较高活性的新的二芳基苯胺类抗艾滋病药物,该QSAR的研究结果可为新药合成提供理论参考。     

Identification of SARS-CoV-2 Papain-like Protease (PLpro) Inhibitors Using Combined Computational Approach**

In the current pandemic, finding an effective drug to prevent or treat the infection is the highest priority. A rapid and safe approach to counteract COVID-19 is in silico drug repurposing. The SARS-CoV-2 PLpro promotes viral replication and modulates the host immune system, resulting in inhibition of the host antiviral innate immune response, and therefore is an attractive drug target. In this study, we used a combined in silico virtual screening for candidates for SARS-CoV-2 PLpro protease inhibitors. We used the Informational spectrum method applied for Small Molecules for searching the Drugbank database followed by molecular docking. After in silico screening of drug space, we identified 44 drugs as potential SARS-CoV-2 PLpro inhibitors that we propose for further experimental testing.