基于虚拟现实的分子对接教学软件*

由于其强大的沉浸性和交互性等特征,虚拟现实技术在教育教学方面有着独特的优势。基于分子建模工具和虚拟现实技术构建了一种关于分子对接的教学软件,该软件将语音讲解、动画演示、分子可视化、交互操作等内容有机整合在虚拟现实环境中,从理论知识讲解和VR实验操作2个方面展开,深入浅出地讲解了分子对接的知识点,达到辅助教学的目的。     

A comparative study of CE-SDS,SDS-PAGE,and Simple Western: Influences of sample preparation on molecular weight determination of proteins

The development of capillary electrophoresis, especially CE-SDS devices, has led CE-SDS to become an established tool in a wide range of applications in the analysis of biopharmaceuticals and is increasingly replacing its method of origin, SDS-PAGE. The goal of this study was to evaluate the comparability of molecular weight (MW) determination especially by CE-SDS and SDS-PAGE. For ensuring comparability, model proteins that have little or no posttranslational modifications and an IgG antibody were used. Only a minor influence of sample preparation conditions, including sample buffer, temperature conditions, and different reducing agents on the MW determination were found. In contrast, the selection of the MW marker plays a decisive role in determining the accurate apparent MW of a protein. When using different MW markers, the deviation in MW determination can exceed 10%. Interestingly, CE-SDS and 10% SDS-PAGE hardly differ in their trueness of MW determination. The trueness in relation to the reference MW for each protein was calculated. Although the trueness values for the model proteins considered range between 1.00 and 1.11 using CE-SDS, they range between 0.93 and 1.03 on SDS-PAGE, depending on the experimental conditions chosen.     

Synthesis,anti‐inflammatory activity,and molecular docking study of novel azo bis antipyrine derivatives against cyclooxygenase‐2 enzyme

We have synthesized a new series of azo‐bis antipyrine derivatives from a one‐pot multicomponent Knoevenagel/Michael addition reaction of antipyrine, with a diversity of azo aldehydes in ethanol and L‐Proline as a catalyst under reflux condition. The anti‐inflammatory activity of the final products was assessed using the inhibition of albumin denaturation technique. Compound 3f showed an inhibitory effect with IC₅₀ values of 3.6 μM with respect to the standard anti‐inflammatory drug Aspirin, with IC₅₀ values of 2 μM. In addition, molecular docking was performed to confirm the in vitro results against the enzymatic inhibition activity of COX‐2 enzymes in which compound 3f showed good binding affinity with an inhibition constant (Ki) of 1.79 nM.     

电子束敏感材料的原子尺度结构研究

分子筛和金属有机骨架(MOF)材料以其独特的孔道和骨架结构在催化、 储能、 干燥及净化和吸附分离等领域有着广泛应用, 对其结构的原子尺度表征对于深入理解其构效关系具有重要意义. 但其大孔道结构和有机骨架使得它们对电子束辐照极为敏感, 在常规透射电镜成像模式下结构会很快被破坏变为非晶, 从而无法获得孔道和骨架的原子排列信息. 最近发展起来的基于积分差分相位衬度扫描透射电子显微(iDPC-STEM)技术在电子敏感材料和轻元素组分成像方面展现出明显优势, 使得对多孔骨架材料及烃池物种的表征成为了可能. 本文综述了本课题组近期利用该技术对分子筛和MOF材料原子尺度结构方面的研究. 将iDPC-STEM技术应用到ZSM-5分子筛催化剂中, 实现了对该分子筛的原子级骨架结构的成像分析. 在MOF体系中, 利用该技术观察到MIL-101骨架内部有机连接体与金属节点的配位方式, 在此基础上解析了MIL-101结构中有机配体的连接和金属节点的苯环结构, 并观察了MOF的原子级表面、 界面和缺陷等局域结构特征. 最后对iDPC-STEM技术在原子尺度成像方面的应用潜力进行了总结与展望.     

Synthesis,spectral and quantum mechanical studies and molecular docking studies of Schiff base (E)2-hydroxy-5-(((4-(N-pyrimidin-2-yl)sulfamoyl)phenyl)imino)methyl benzoic acid from 5-formyl salicylic acid and sulfadiazine

A new Schiff base (E)2-hydroxy-5-(((4-(N-pyrimidin-2-yl)sulfamoyl)phenyl)imino)methyl benzoic acid (5FSADA) compound was synthesized by condensation of 5-formyl salicylic acid and sulfadiazine, and the product formed was characterized using FTIR and UV–Visible spectroscopy. The geometry was optimized using DFT. The FTIR were computed from DFT and is compared with experimental spectra, followed by detailed vibrational assignment, which shows that the experimental and simulated data is in close agreement. The UV–Vis spectrum calculated using TD-DFT, IEFPCM solvation model with DMSO as solvent. Wave function based properties like localized orbital locator, electron localization function and non-covalent interactions has been studied extensively. The physical properties (ADMET) of the compound 5FSADA indicated that the compound has excellent drug likeness and PASS studies showed that it has anti-infective properties, which is confirmed by a docking score of −9.0 ​kcal/mol.     

质子水合结构的振动态密度分析

使用基于多态经验价键模型的分子动力学模拟, 对水溶液中质子的水合结构及其在质子传递过程中的动力学过程进行了研究. 在价键模型的方法下, 质子的水合结构主要以H₉O₄⁺(Eigen)以及过渡态的H₅O₂⁺(Zundel)结构形态存在, 且在这两种结构中以Eigen的形态表现明显. 通过对质子传递过程中不同水合结构的态密度频谱分析, 发现一个在2000~3000 cm^-1范围内的明显连续的宽吸收谱带, 主要归因于Eigen结构的贡献, 这些特征峰的出现与水合氢离子第一溶剂化层内的强氢键作用密切相关. 对于Zundel的结构, 在1760 cm^-1处出现一个较为明显的肩峰, 归属为质子传递模式的特征振动. 通过对质子水合结构态密度频谱的分析, 可望增强对于稀酸溶液红外光谱中的连续宽吸收带以及质子传递的微观动力学过程的理解.     

高通量虚拟筛选CDK2/Cyclin A2靶点抑制剂

CDK2/Cyclin A2复合蛋白的异常表达与乳腺癌、 口腔癌、 食管鳞状细胞癌的发生密切相关. CDK2/ Cyclin A2复合蛋白的活性位点不同于CDK2单体. 至今临床上尚无靶向此复合蛋白的药物分子. 针对CDK2/Cyclin A2复合蛋白, 以实验报道的10个抑制剂分子构建药效团模型, 通过药物体外药代动力学（ADME）、 Docking、 聚类分析、 毒性预测, 从DrugBank, ChEMBL和TCM@Taiwan 3个数据库约90万组数据中进行高通量虚拟筛选, 进一步进行MD模拟、 MM/PBSA结合自由能计算、 能量分解和平均非共价作用(aNCI)分析, 筛选出3个抑制效果优于阳性实验药Roscovitine的先导分子: DrugBank-2004, DrugBank-583和ChEMBL-7122. 与CDK2蛋白相比, CDK2/Cyclin A2复合蛋白结合位点空间变大, 先导分子与Lys33, Asp86, Lys129和Asp145残基之间的排斥作用有所降低, 导致结合自由能更大.     

A molecular docking study of potential inhibitors and repurposed drugs against SARS-CoV-2 main protease enzyme

COVID-19 has affected millions of people. Although many drugs are in use to combat disease, there is not any sufficient treatment yet. Having critical role in propagation of the novel coronavirus (SARS-CoV-2) works Main Protease up into a significant drug target. We have performed a molecular docking study to define possible inhibitor candidates against SARS-CoV-2 Main Protease enzyme. Besides docking Remdesivir, Ribavirin, Chloroquine and 28 other antiviral inhibitors (totally 31 inhibitors) to Main Protease enzyme, we have also performed a molecular docking study of 2177 ligands, which are used against Main Protease for the first time by using molecular docking program Autodock4. All ligands were successfully docked into Main Protease enzyme binding site. Among all ligands, EY16 coded ligand which previously used as EBNA1-DNA binding blocker candidate showed the best score for Main Protease with a binding free energy of −10.83 ​kcal/mol which was also lower than re-docking score of N3 ligand (−10.72 ​kcal/mol) contained in crystal structure of Main Protease. After analyzing the docking modes and docking scores we have found that our ligands have better binding free energy values than the inhibitors in use of treatment. We believe that further studies such as molecular dynamics or Molecular Mechanic Poisson Boltzmann Surface Area studies can make contribution that is more exhaustive to the docking results.     

Multiple QSAR and molecular modelling for identification of potent human adenovirus inhibitors

This study has investigated docking-based 2D- and 3D-quantitative structure-activity relationships (QSARs) for a range of 53 hydroxybenzamide analogues as anti- Human adenoviruses (HAdVs). The best 3D-QSAR (Schrodinger, LLC, NY, 2020) and 2D-QSAR models were obtained for the training set and were found to be statistically significant, with cross-validated coefficients (q²) of 0.6775 and 0.7875, and coefficients of determination (r²) of 0.8106 and 0.8122, respectively. Our in-silico docking and virtual screening studies revealed significant higher binding affinity of dataset molecule 34 (-141.444 ​kcal/mol) and hit ZINC01088642 (-114.357 ​kcal/mol) with 4PIE protein than the standard drugs. In in-silico ADME/toxicity studies, molecule 34 and proposed hit ZINC01088642 were found safe with good intestinal absorption, aqueous solubility, medium blood–brain barrier (BBB), no eye corrosion, no skin irritancy, and non-mutagenic profiles. Molecular dynamics analysis showed good stability of complex, hit ZINC01088642 with protein, 4PIE over the simulation period of 20 ns. We believe that further experimental, as well as in-vitro investigation, will shed more lights on the identification of ZINC01088642 as a potential human adenovirus agent.     

新型嘧啶单环类非经典叶酸拮抗剂的合成及抗肿瘤活性研究

以课题组前期设计合成的非经典叶酸拮抗剂6-(4'-甲基苯乙基)-N5-氯乙酰基-2,4-二氨基哌啶并[3,2-d]嘧啶(wm-8.2)为先导化合物,将wm-8.2中的哌啶并嘧啶双环结构简化为嘧啶单环结构,以提高分子柔韧性并简化分子结构,根据6-位空间占位设计6-H和6-甲基两个系列,考察了不同桥链长度和不同芳香杂环侧链对抗肿瘤活性的影响.同时对具有叶酸抑制剂分子结构特征的关键中间体进行活性对比测定,研究了N(5)位氯乙酰基对活性的影响.两个系列目标化合物和关键中间体共36个化合物的结构均经1H NMR,13C NMR和MS确证.生物活性测定表明,6位为甲基的化合物中,具有三碳桥链及对甲基苯环侧链的6-甲基-2,4-二氨基-5-(N-(4-甲基苯基)丙基-N-(2-氯乙酰基))氨基嘧啶(6b-3)具有最好的HL-60、A549和HCT116细胞增殖抑制活性,IC50分别为0.25,0.83和0.63μmol?L^-1.化合物6b-3在N(5)位氯乙酰基取代之前的关键中间体6-甲基-2,4-二氨基-5-(N-(4-甲基苯基)丙基)氨基嘧啶(5b-3)具有最优的二氢叶酸还原酶抑制活性.总结了化合物的构效关系,并用计算机模拟进行了阐释.