SARS冠状病毒3CL蛋白酶及其抑制剂的理论研究

应用AutoDock程序将SARS冠状病毒3CL蛋白酶及其抑制剂配体和受体进行了对接,并用InsightⅡ中的Discover 3模块进行了分子动力学模拟,分析了蛋白酶活性口袋的形状,讨论了其亚基的氢键、静电、疏水等相互作用,为进一步设计药物提供了重要的参考信息.     

SARS冠状病毒E蛋白的结构研究及功能预测

结合生物信息学方法及分子模拟手段,选择较高准确度的方法,预测了SARSE蛋白的分子结构并探讨其潜在的生物学活性和功能.研究结果表明,SARSE蛋白跨膜区25个疏水的氨基酸形成α-螺旋结构,包埋于病毒外壳磷脂双分子层中;N端10个氨基酸残基位于膜外;C端41个残基则附着于磷脂双分子膜内侧.同时发现,C端由9个氨基酸组成的劈裂是一个可能的活性部位.对分子进行进一步静电势分析证实,E蛋白C端可能的活性部位具有较大的静电势,可能的活性残基具有最大电荷密度,故有较强的结合受体或与其它蛋白相互作用的能力.     

SARS冠状病毒主要蛋白酶二聚体静电和疏水效应的研究

从三种冠状病毒主要蛋白酶SARS 3CL, HCoV 3CL和TGEC 3CL蛋白酶结构出发,着重研究了三种蛋白酶二聚体单体之间的静电和疏水相互作用.用连续介质模型有限差分方法计算得到三种蛋白二聚体界面处的静电势,发现三种蛋白酶单体和单体之间静电势分布具有明显的互补性,三种蛋白酶二聚体单体之间具有相同的静电相互作用能.用溶剂可及表面积模型分析了分子表面积及疏水性,发现三种蛋白酶具有相同的疏水分布,其中SARS 3CL蛋白酶疏水率为74%,驱动其单体聚合成二聚体.对三种蛋白酶的去溶剂化能疏水项的计算表明,三种蛋白酶二聚体单体之间具有相似的疏水相互作用能.     

积雪草酸衍生物的合成与表征及体外抗癌活性的研究

为了寻找新型高效、低毒、生物活性良好的积雪草酸衍生物,以具有一定生物活性的积雪草酸为先导化合物,通过对其C-2,C-3,C-11,C-23和C-28位进行结构修饰,设计合成了9种未见文献报道的积雪草酸衍生物.目标化合物的结构经1H NMR,13C NMR,IR和HRMS表征确证.采用MTT法观察其对人宫颈癌细胞(Hela)、人乳腺癌细胞(MCF-7)的抑制作用.结果表明,经修饰的积雪草酸衍生物的抗癌活性较母体化合物有不同程度的增强.     

有机锡联苯乙酸酯的合成、结构表征和体外抗癌活性

合成了4个新的有机锡联苯乙酸酯{[(n-C₄H₉)₄Sn(O₂CCH₂C₆H₄C₆H₅-4)]₂O}₂ (1)和R₃SnO₂CCH₂C₆H₄C₆H₅-4(R=C₄H₅，2；c-C₆H₁₁，3；C₆H₅C(CH₃)₂CH₂，4)，利用元素分析、IR、 ¹H和 ¹³C NMR表征了其结构。通过X-射线单晶衍射测定了1和4的晶体结构。化合物1和化合物4均属三斜晶系，空间群P1。化合物1为具有Sn₂O₂四元环的中心对称二聚体结构，4为畸变的四面体结构。生物活性测试结果表明，化合物1和4对3种人癌细胞HeLa、CoLo205和MCF-7具有较好的体外抑制活性。     

非肽类SARS冠状病毒3CL蛋白酶抑制剂的设计与活性表征

SARS冠状病毒3CL蛋白酶是SARS病毒复制过程中的主要蛋白酶, 针对其开展药物设计有望得到有效的抗SARS病毒药物. 本文基于SARS冠状病毒3CL蛋白酶的三维结构, 对现有化学试剂及临床用药数据库进行虚拟筛选, 选出可能对SARS冠状病毒3CL蛋白酶有抑制的非肽化合物进行初步活性测试, 并研究了已知的人鼻病毒3C蛋白酶抑制剂对SARS冠状病毒3CL蛋白酶的活性, 合成了两种母环的衍生物, 得到靛红和哌嗪两类SARS冠状病毒3CL蛋白酶的抑制剂, 其中一个靛红类化合物的IC₅₀为0.76 µmol•L^－1; 而抗组胺药哌嗪类化合物对SARS冠状病毒3CL蛋白酶及细胞培育的SARS病毒的抑制作用, 提示了老药可以开发出新的用途.     

具有实验抗癌活性的二烃基锡衍生物的研究进展

自从Crown报道了一些二烃基锡衍生物具有抗癌活性以来, 这一领域的研究引起了人们极大的兴越。许多二烃基锡衍生物被制备得到, 并且测定了它们在离体及活性情况下的抗癌活性。本文综述了二烃基锡衍生物抗癌活性的研究进展,包括化合物的结构类型, 抗癌作用机制以及利用QSAR方法对有机锡化合物的抗癌活性进行计算预测等。     

新型含缩氨基硫脲结构的喹唑啉衍生物的合成及体外抗癌活性

以4,5-二甲氧基-2-氨基苯甲酸和醋酸甲脒为原料,经环化、氯化、胺化和缩合反应,合成了15个新的喹唑啉哌嗪缩氨基硫脲衍生物,其结构经1H NMR,13C NMR,HRMS及元素分析确认.采用MTT法测试了化合物6a~6o对表皮生长因子受体(EGFR)过度表达的人乳腺癌MCF-7、人肺癌A549和人前列腺癌PC3的体外抗癌活性.结果表明,部分化合物表现出较强的抗癌活性,其中,化合物6a和6o对3种癌细胞的抗癌活性优于对照药拉帕替尼(Lapatinib),略低于对照药阿霉素(ADM).化合物6a和6o对MCF-7的IC50值分别为6.97和6.99μmol/L,对A549的IC50值分别为5.15和3.11μmol/L,而对PC3的IC50值分别为2.30和1.42μmol/L.本文还初步探讨了化合物结构与抗癌活性之间的关系.     

5-氟尿嘧啶-1-烷氧苯基三间氯苯基卟啉的合成及其体外抗癌活性

为提高5-氟尿嘧啶抗癌的靶向性,降低其不良反应,合成了5种新型卟啉-5-氟尿嘧啶衍生物及其Mn3+配合物,优化了合成反应条件,探索了目标化合物的分离方法。 通过IR、UV-Vis、1H NMR和ESI-MS对化合物结构和组成进行了确认。 采用四甲基偶氮唑蓝(MTT)比色法,以5-氟尿嘧啶为阳性对照药,测试了卟啉化合物对5种肿瘤细胞的体外抑制活性。 初筛结果显示,化合物D3对人卵巢癌细胞Sk-ov-3有较强的抑制作用。     

β-榄香烯聚乙二醇衍生物的合成及体外抗癌活性

以中草药有效成分β-榄香烯为起始原料, 在碱性条件下与氨基化的聚乙二醇(PEG)反应合成了一系列β-榄香烯单取代PEG衍生物, 利用IR, ¹H NMR及¹³C NMR对其结构进行了表征. 并采用WST-1法观察其对人宫颈癌细胞(Hela)、人白血病细胞(K562)的抑制作用, 探讨其体外抗肿瘤活性. 细胞实验结果表明经PEG修饰的β-榄香烯的抗癌活性有不同程度的增强.     

SARS病毒E蛋白的计算机模拟的初步研究

以粗粒化的多肽链模型进行了SARS病毒包膜中E蛋白的计算机模拟,描述了该蛋白质空间构象的概貌.首先扩展了多肽链的HP模型,使之能够用于研究在水或脂环境下蛋白质折叠的行为,并且考虑了全部氨基酸残基疏水相互作用能的差异.相关格子链的MonteCarlo模拟显示了很高的计算效率.模拟再现了蛋白质的coil-globule转变,验证了蛋白质序列分布的重要性.结果表明,在水环境中,E蛋白质空间结构由紧致的疏水内核和部分向外延伸的亲水片段组成;在脂环境中,中部疏水片段会成为向外延伸的环,而当两侧紧致的亲水片段分开时,则形成桥.     

新型室温熔盐二(三氟甲基磺酸酰)亚胺锂-乙酰胺体系的谱学研究

从分析二(三氟甲基磺酸酰)亚胺锂(LiTFSI)与乙酰胺形成熔盐的作用机制出发,通过红外和拉曼光谱的谱学分析并应用非局部密度泛函方法进行量化计算来对二者的相互作用进行了讨论.发现乙酰胺通过Li—O键与LiTFSI中Li+配位而破坏了LiTFSI的离子键,形成很大的配位阳离子,且正电荷被屏蔽在乙酰胺分子中;而TFSI-离子中电荷的部分离域导致电荷被终端—CF3基团屏蔽在整个分子中,这样两个大的阴阳离子间的库伦作用很弱;同时Li—O配位也导致乙酰胺分子间的氢键断裂,因而室温下体系以液体状态稳定存在.     

静电和疏水效应对SARS冠状病毒3CL蛋白酶二聚体稳定性的影响

从TGEV3CL蛋白酶二聚体结构出发,研究了TGEV3CL蛋白酶二聚体单体之间的静电和疏水相互作用.蛋白质的静电相互作用通过有限差分方法求解Poisson-Boltzmann方程得到,疏水相互作用通过分析溶剂可及性表面模型得到.考察了不同pH值对SARS3CL蛋白酶二聚体静电和疏水相互作用的影响,在pH=5.5～8.5时,二聚体静电相互作用能、静电去溶剂化能和疏水自由能都具有较小的数值,表明在该条件下静电和疏水相互作用有利于二聚体的稳定存在.由于SARS3CL蛋白酶活性模式为二聚体,因此,在该pH值范围内,有利于蛋白酶保持活性.在pH=7.0条件下,蛋白酶单体之间具有最强的静电和疏水相互作用,从而使蛋白酶具有最强的活性,这与实验结果相一致.pH值对静电去溶剂化能的影响大于疏水自由能,表明静电作用是造成强酸或强碱条件下二聚体不能稳定存在的主要原因.     

The Inhibitory Effects of Plant Derivate Polyphenols on the Main Protease of SARS Coronavirus 2 and Their Structure–Activity Relationship

The main protease (M^pro) is a major protease having an important role in viral replication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus that caused the pandemic of 2020. Here, active M^pro was obtained as a 34.5 kDa protein by overexpression in E. coli BL21 (DE3). The optimal pH and temperature of M^pro were 7.5 and 37 °C, respectively. M^pro displayed a K_m value of 16 μM with Dabcyl-KTSAVLQ↓SGFRKME-Edans. Black garlic extract and 49 polyphenols were studied for their inhibitory effects on purified M^pro. The IC₅₀ values were 137 μg/mL for black garlic extract and 9–197 μM for 15 polyphenols. The mixtures of tannic acid with puerarin, daidzein, and/or myricetin enhanced the inhibitory effects on M^pro. The structure–activity relationship of these polyphenols revealed that the hydroxyl group in C3′, C4′, C5′ in the B-ring, C3 in the C-ring, C7 in A-ring, the double bond between C2 and C3 in the C-ring, and glycosylation at C8 in the A-ring contributed to inhibitory effects of flavonoids on M^pro.     

Novel Small-Molecule Scaffolds as Candidates against the SARS Coronavirus 2 Main Protease: A Fragment-Guided in Silico Approach

The ongoing pandemic caused by the novel coronavirus has been the greatest global health crisis since the Spanish flu pandemic of 1918. Thus far, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in over 1 million deaths, and there is no cure or vaccine to date. The recently solved crystal structure of the SARS-CoV-2 main protease has been a major focus for drug-discovery efforts. Here, we present a fragment-guided approach using ZINCPharmer, where 17 active fragments known to bind to the catalytic centre of the SARS-CoV-2 main protease (SARS-CoV-2 M^pro) were used as pharmacophore queries to search the ZINC databases of natural compounds and natural derivatives. This search yielded 134 hits that were then subjected to multiple rounds of in silico analyses, including blind and focused docking against the 3D structure of the main protease. We scrutinised the poses, scores, and protein–ligand interactions of 15 hits and selected 7. The scaffolds of the seven hits were structurally distinct from known inhibitor scaffolds, thus indicating scaffold novelty. Our work presents several novel scaffolds as potential candidates for experimental validation against SARS-CoV-2 M^pro.     

Establishing an Analogue Based In Silico Pipeline in the Pursuit of Novel Inhibitory Scaffolds against the SARS Coronavirus 2 Papain-Like Protease

The ongoing coronavirus pandemic has been a burden on the worldwide population, with mass fatalities and devastating socioeconomic consequences. It has particularly drawn attention to the lack of approved small-molecule drugs to inhibit SARS coronaviruses. Importantly, lessons learned from the SARS outbreak of 2002–2004, caused by severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), can be applied to current drug discovery ventures. SARS-CoV-1 and SARS-CoV-2 both possess two cysteine proteases, the main protease (M^pro) and the papain-like protease (PL^pro), which play a significant role in facilitating viral replication, and are important drug targets. The non-covalent inhibitor, GRL-0617, which was found to inhibit replication of SARS-CoV-1, and more recently SARS-CoV-2, is the only PL^pro inhibitor co-crystallised with the recently solved SARS-CoV-2 PL^pro crystal structure. Therefore, the GRL-0617 structural template and pharmacophore features are instrumental in the design and development of more potent PL^pro inhibitors. In this work, we conducted scaffold hopping using GRL-0617 as a reference to screen over 339,000 ligands in the chemical space using the ChemDiv, MayBridge, and Enamine screening libraries. Twenty-four distinct scaffolds with structural and electrostatic similarity to GRL-0617 were obtained. These proceeded to molecular docking against PL^pro using the AutoDock tools. Of two compounds that showed the most favourable predicted binding affinities to the target site, as well as comparable protein-ligand interactions to GRL-0617, one was chosen for further analogue-based work. Twenty-seven analogues of this compound were further docked against the PL^pro, which resulted in two additional hits with promising docking profiles. Our in silico pipeline consisted of an integrative four-step approach: (1) ligand-based virtual screening (scaffold-hopping), (2) molecular docking, (3) an analogue search, and, (4) evaluation of scaffold drug-likeness, to identify promising scaffolds and eliminate those with undesirable properties. Overall, we present four novel, and lipophilic, scaffolds obtained from an exhaustive search of diverse and uncharted regions of chemical space, which may be further explored in vitro through structure-activity relationship (SAR) studies in the search for more potent inhibitors. Furthermore, these scaffolds were predicted to have fewer off-target interactions than GRL-0617. Lastly, to our knowledge, this work contains the largest ligand-based virtual screen performed against GRL-0617.     

离子的本性对溶液导电能力的影响

借助电导率传感器探究向硫酸氢钠溶液中滴入氢氧化钡溶液时溶液导电能力的变化,并对实验结果进行理论分析与解释：电解质溶液的导电能力由离子本性决定,受离子浓度等影响。