HIV-1 蛋白酶异位抑制剂体系的长时间分子动力学模拟

采用新开发的ff12SB力场在NVIDIA CUDA GPU上对HIV-1蛋白酶的活性位抑制剂体系和异位抑制剂体系分别进行了100 ns的长时间分子动力学模拟,并用MM-PB/GBSA方法计算了活性位点抑制剂TL-3与HIV-1蛋白酶的结合自由能。异位抑制剂体系中分子片段2-甲基环己醇结合在Exo位,有利于抑制剂被束缚在活性位点附近。异位抑制剂体系中抑制剂TL-3与蛋白酶的结合自由能为-85.78 kcal/mol,活性位抑制剂体系中为-79.45 kcal/mol。这些结果有助于深入了解HIV-1 PR的动力学过程,为设计新型强效抑制剂提供了新见解。     

两种雌激素受体与抑制剂作用的机制

对雌激素受体ERα和ERβ与抑制剂244结合的体系进行了12 ns的分子动力学模拟,用MM PBSA方法计算了体系的结合自由能,抑制剂与ERα的结合自由能是-30.11 kJ/mol,与ERβ的是-33.32 kJ/mol。ERα中Met421侧链原子与抑制剂间的静电排斥作用使活性口袋周围的残基构象发生变化,导致活性区域中结合空穴变大,从而使ERα与抑制剂的亲和性降低。自由能分解计算进一步说明了各个残基对自由能的贡献。     

HIV-1蛋白酶与抑制剂结合中桥接水分子作用的QM/MM研究

对HIV-1蛋白酶与抑制剂2AH和4AH结合的两个复合物体系进行了水溶液环境下量子力学分子力学混合方法(hybrid QM/MM)的1ns分子动力学模拟,用MM-GBSA方法得到桥接水分子W301与HIV-1蛋白酶和抑制剂结合体的结合自由能分别为-24.93 kJ/mol和-20.29 kJ/mol,表明W301在抑制剂和HIV-1蛋白酶结合的过程中起到了不能被忽略的作用。     

羟基取代脂肪族一元酸的电子结构与化学反应性的讨论

为引导和构建结构决定性质教学,通过含羟基取代的直链型脂肪族羧酸化合物羟基代十一酸的空间构象和电子结构分析,获得α-羟基十一酸的α-C-COOH单键旋转能垒为9.0337 kcal/mol和α-C-OH键单键自由旋转能垒为28.1556 kcal/mol,表明α-C-OH键单键旋转受阻;羟基酸化合物的碳原子电荷受羟基氧原子和羧基影响,随链长度n取代羟基,α-C、β-C、γ-C、δ-C、ε-C、ζ-C等碳原子负电荷减少;羟基取代酸体系能E随n位羟基取代关系E=-614.651 0.059/n(2≤n≤11).     

尼古丁生物降解产物中烟碱型乙酰胆碱受体α7亚型靶向化合物的虚拟筛选

在以微生物降解尼古丁的代谢途径中,已被分离出多种与尼古丁结构类似的中间产物.烟碱型乙酰胆碱受体α7亚型(α7-n AChR)是阿尔茨海默病和多种炎症药物研发的重要靶点,而尼古丁是与其特异性结合的天然配体.计算机虚拟筛选技术是现代新药研发的一种重要方法.采用尼古丁降解产物及其结构相似物与α7-n AChR进行活性位点对接及分子计算,探寻是否可以从尼古丁的降解产物中寻找出新型以α7-n AChR为靶点的小分子治疗药物.选用9个尼古丁代谢的中间产物和与其结构相似的78个化合物为筛选对象.计算结果显示:9个尼古丁代谢中间产物与α7-n AChR的结合能量在-5.7 kcal/mol~-6.7 kcal/mol之间,3个结构相似化合物与α7-n AChR的结合能量约为-8.0 kcal/mol.这些化合物均可以与α7-n AChR的活性区域进行结合,其结合能与其天然配体接近或更好.筛选的结果为此类化合物的下一步的药理学研究提供了参考.     

新型冠状病毒主蛋白酶天然产物抑制剂的筛选

为寻找新型冠状病毒主蛋白酶天然产物抑制剂,本文以SARS-CoV-2主蛋白酶为研究对象,通过计算机辅助药物筛选方法初步筛选出16个潜在抑制剂并进行体外酶活测试.其中,野黄岑素对SARS-CoV-2主蛋白酶的IC50为（10.79 ± 2.116 ） μmol/L,没食子儿茶素没食子酸酯抑制SARS-CoV-2主蛋白酶的IC50为（2.104 ± 0.346） μmol/L.最后,将两种天然产物与主蛋白酶进行分子动力学模拟发现没食子儿茶素没食子酸酯和野黄岑素与新型冠状病毒主蛋白酶结合时的复合物RMSD都在0.22 ?附近,说明两个天然产物与新型冠状病毒主蛋白酶结合较为稳定,可以作为新型冠状病毒主蛋白酶的抑制剂或先导化合物.     

HIV-1 Tat与P-TEFb复合物的分子动力学模拟及结合自由能计算

P-TEFb结构中与Tat蛋白的结合位点是新型抗HIV-1药物设计和虚拟筛选的重要靶标.对含有两个锌指结构的Tat.P-TEFb复合物体系进行了14ns的分子动力学模拟,应用MM-PBSA/GBSA方法计算体系的结合自由能,以及通过基于氨基酸残基的能量分解来探究体系中蛋白质之间的相互作用.结果表明范德华作用能是复合物形成的主要驱动力,Cys261与ZN88之间的配位作用是结合自由能的最大贡献者.根据Tat.P-TEFb体系的动力学结构信息和残基能量分解结果预测了P-TEFb结构中可能的活性位点.位点Ⅰ和位点Ⅱ应可作为基于受体三维结构的抗HIV-1药物分子设计的起始位点.模拟计算的结果可以为进一步指导药物设计奠定基础.     

二聚体水分子的10种稳定结构的MP2方法研究

二聚体水体系是液态水分子体系中氢键存在的原型,目前对它的研究大多是关于其最稳定构型, 而忽略了势能面上的其它稳定结构. 本文在MP2/aug-cc-pVDZ理论水平下对二聚体水分子进行均衡(CP)校正梯度优化, 计算得到二聚体水分子势能面上的10种稳定构型, 并进一步计算得到了它们的相互作用能和偶极矩等重要性质. 结果表明, 具有Cs对称性的构型1最稳定, 其相互作用能ΔE为-4.47 kcal/mol;而具有C2h对称性的构型8最不稳定,其相互作用能ΔE仅为-1.15 kcal/mol.     

以柯萨奇B3病毒3C蛋白酶为靶点的体外药物筛选模型的建立及应用

建立以柯萨奇B组3型病毒3C蛋白酶(CVB3-3C)为靶点的药物筛选模型,并筛选新型抑制剂。使用原核表达模型实现CVB3-3C蛋白酶体外重组表达。经Ni-NTA亲和层析、阴离子交换层析纯化获得高纯度CVB3-3C蛋白。应用荧光共振能量转移法检测蛋白酶活性,建立药物筛选模型。对768种化合物进行筛选,获得了2种对CVB3-3C蛋白酶有较强抑制作用的化合物(MDCE-A008和MDCE-A043),IC50值分别为(60.61±6.26)μmol/L、(105.7±14.88)μmol/L。建立的CVB3-3C蛋白酶药物筛选模型为获得有效抑制剂提供了技术保证。     

新型1,5-二芳基咪唑类制剂的分子对接研究

采用PM5半经验量子化学方法对29个新型1,5-二芳基咪唑类选择性环氧合酶(COX-2)抑制剂的结构进行了全优化,将这些优化结构与COX-2的活性位点进行了分子对接。对接研究表明：活性1,5－二芳基咪唑类COX-2抑制剂具有类似塞来昔布等三环类环氧合酶-2选择性抑制剂的立体结构,对接自由能与抑制剂活性有较好的相关性。     

植物miRNAs前体的生物信息分析

miRNAs前体（pre-miRNAs）是产生成熟miRNAs的基因表达产物，能形成较为稳定的发卡环结构，具有较低的最小折叠自由能（minimal folding free cnergy，MFE）。在对植物pre-miRNAs长度、不同碱基含量、MFE、熵分析基础上，重点比较不同RNAs序列之间MFE与其长度的比值（MFEL）。结果表明MFEL是区分植物pre-miRNAs的一个很有效的参数：pre-miRNAs的MFEL值平均为-45．98kcal／mol，明显低于mRNAs（-23．08kcal／mol），tRNAs（-22．13kcal／mol）和rRNAs（-16．83kcal／mol）。使用MFEL参数可提高预测植物miRNAs基因的效率。     

Conversion of allosteric inhibition to activation in phosphofructokinase by protein engineering

Many enzymes are subject to allosteric control, often with inhibitors and activators binding to the same effector site. Phosphofructokinase in Escherichia coli is such an enzyme, being inhibited by phosphoenolpyruvate (PEP) and activated by ADP and GDP. How do individual interactions with effectors affect the balance between activation and inhibition, especially when both ligands share aspects of the same binding site? We find that mutation of a single residue in the effector site, Glu----Ala 187, leads to PEP being an activator rather than an inhibitor. With low concentrations of the substrate fructose-6-phosphate, the mutant enzyme is more than one hundred times more active than wild-type enzyme at millimolar concentrations of PEP. The classical Monod-Wyman-Changeux two-state model is too simple to account for the properties of the mutant enzyme.     

Searching for more effective HCV NS3 protease inhibitors via modification of corilagin

Corilagin was seperated from extract of Phyllanthus urinaria L. and used as the precursor of inhibitors of hepatitis C virus (HCV) NS3 serine protease. Six derivatives were obtained through the chemical modification of corilagin and their structures were elucidated by the spectra analysis. Bioassay of these compounds showed that two of them had improved inhibitory efficiency than the precursor, with IC₅₀ values of 2.28 μmol/L and 1.52 μmol/L, respectively. The binding mode of two active compounds with substrate binding site of HCV NS3 protease was also investigated by molecular docking method.     

Structure of mammalian AMPK and its regulation by ADP

The heterotrimeric AMP-activated protein kinase (AMPK) has a key role in regulating cellular energy metabolism; in response to a fall in intracellular ATP levels it activates energy-producing pathways and inhibits energy-consuming processes. AMPK has been implicated in a number of diseases related to energy metabolism including type 2 diabetes, obesity and, most recently, cancer. AMPK is converted from an inactive form to a catalytically competent form by phosphorylation of the activation loop within the kinase domain: AMP binding to the γ-regulatory domain promotes phosphorylation by the upstream kinase, protects the enzyme against dephosphorylation, as well as causing allosteric activation. Here we show that ADP binding to just one of the two exchangeable AXP (AMP/ADP/ATP) binding sites on the regulatory domain protects the enzyme from dephosphorylation, although it does not lead to allosteric activation. Our studies show that active mammalian AMPK displays significantly tighter binding to ADP than to Mg-ATP, explaining how the enzyme is regulated under physiological conditions where the concentration of Mg-ATP is higher than that of ADP and much higher than that of AMP. We have determined the crystal structure of an active AMPK complex. The structure shows how the activation loop of the kinase domain is stabilized by the regulatory domain and how the kinase linker region interacts with the regulatory nucleotide-binding site that mediates protection against dephosphorylation. From our biochemical and structural data we develop a model for how the energy status of a cell regulates AMPK activity.     

甲烷水合物(H_2O)_(20)…CH_4稳定性的量子化学研究

采用密度泛函理论PBE方法和二级微扰(MP2)理论,对甲烷水合物(H2O)20…CH4两种不同构型512(H2O)20…CH4和435663(H2O)20…CH4进行了理论研究。在PBE/6-31++G(d,p)水平下进行结构优化,得到了它们的平衡稳定结构;在MP2/aug-cc-pVTZ水平下,结合基函数重叠误差(BSSE)完全均衡校正法,对其复合物进行能量计算。通过计算得出:512(H2O)20…CH4和435663(H2O)20…CH4的结合能分别为-4.75 kcal/mol和-4.44 kcal/mol,大约是相同水平下单一H2O…CH4结合能的8~9倍;512(H2O)20…CH4构型较435663(H2O)20…CH4稳定。     

Structure and control of phosphofructokinase from Bacillus stearothermophilus.

The allosteric enzyme phosphofructokinase binds its substrate fructose-6-phosphate between two subunits of the tetramer, and allosteric effectors between another pair of subunits. The effector binding site accommodates both the activator and the inhibitor. The substrate cooperativity and allosteric control are mediated by these ligand bridges between subunits.     

Thermodynamics of the B-Z transition in superhelical DNA

One of the most exciting events in recent years in molecular biology was the discovery of the left-handed Z form of the DNA double helix. Originally found in linear self-complementary d(GC)x . d(GC)x polymers and oligomers in non-physiological conditions (a rather high salt concentration), it was recently shown to be easily enough adopted in physiological conditions when purine-pyrimidine sequences are inserted into superhelical DNA. From such a system, superhelical DNA carrying an artificial purine-pyrimidine insert, we can obtain data allowing the determination of the energy of the junction between the B and Z stretches, Fj, and the free energy change delta FBZ per base pair (bp). We present here a simple thermodynamic consideration of the B-Z transition in such a system. By applying the results to experimental data we have shown that the thermodynamic parameters for both sequences studied so far (d(GC)x . d(GC)x and d(GT)x . d(AC)x) are similar and equal to Fj = 4-5 kcal per mol per junction and delta FBZ = 0.5 divided by 0.7 kcal per mol per bp.