磷脂酶A2吲哚类抑制剂的结构和活性关系

应用一种新的预测酶-配体复合物亲和性的方法来研究磷脂酶A2蚓哚类抑制剂的结构-活性关系．磷脂酶A2-抑制剂复合物的三维结构是用分子模构的方法搭建的，复合物的亲和性由程序SCORE计算．共分析了12个抑制剂分子．计算所得的亲和性和实验测定值吻合得很好，明显优于用CoMFA方法分析同一系列化合物所给出的结果．通过分析SCORE的输出结果，识别出了蚓哚类抑制剂和磷脂酶A2相互作用的关键位点，为设计新型的磷脂酶A2抑制剂提供了指导．     

Hydroxamate类抑制剂与MMP-2的分子对接研究

通过分子动力学模拟研究了MMP-2和hydroxamate抑制剂之间的作用模式。在分子动力学模拟中,对于催化区的锌离子和其共价结合的配体(包括抑制剂和组氨酸)采用了键合的模型。从模拟的结果可以看到,R^1取代基和MMP-2的S1疏水口袋中的部分残基能形成很好的几何匹配,从而可以产生很强的范德华和疏水相互作用。模拟结果也表明,两个抑制剂和MMP-2之间分别能形成5个和8个氢键,抑制剂B比A活性更高的原因就是能够形成更加有利氢键作用模式。在整个模拟过程中,催化锌都能保持好的五配位形式,配位键的长度也处于稳定的状态,预测得到的MMP-2和其抑制剂的相互作用模式对于全新抑制剂的设计提供了非常重要的结构信息。     

凝血因子Xa的S4口袋部分关键残基对利伐沙班结合的不同作用机制

通过生物信息学对比、 分子动力学模拟和结合自由能计算分析了利伐沙班与凝血因子Xa的S4口袋部分关键残基之间动态相互作用的细节. 结果表明, 利伐沙班与凝血因子Xa结合不稳定是由S4口袋关键残基突变对疏水盒子完整性的破坏所致. 其中Trp215侧链的疏水作用对抑制剂结合的作用较大, 但对整体结构的影响短时间内较小. Tyr99虽然在结合自由能中贡献较小, 但其突变可能导致99 loop所在结构域的整体构象变化, 从而对于抑制剂或底物的结合特异性产生影响. S4口袋关键残基的不同作用在凝血因子Xa直接抑制剂的药物设计及其拮抗剂的开发中应予以充分考虑.     

激酶ABL与肉豆蔻酰位点小分子作用机理的分子动力学模拟及自由能计算

采用分子动力学方法研究激酶ABL 与ATP 位点小分子imatinib、P16 及变构位点小分子STJ、MS7、MS9、3YY、MYR等的结合, 并用GBSA (generalized Born surface area)方法将结合自由能分解到各残基. 自由能计算结果表明, 小分子STJ、MS7、MS9 有利于imatinib 与ABL 结合; 小分子STJ、MS7、MS9 与激酶ABL的结合自由能接近, 绝对值均大于ABL 与3YY、MYR 的结合自由能. 能量分解表明, ABL 残基ILE502、VAL506、LEU510与STJ和MYR的相互作用是αI 螺旋处于弯曲状态的重要原因. 模拟过程中ABL肉豆蔻酰口袋残基均方根偏差(RMSD)变化值表明, STJ等小分子抑制剂与ABL结合后降低了肉豆蔻酰口袋残基的柔性.     

结合分子模拟探讨共聚酯PBSH在不同溶剂中的PC脂肪酶催化降解

采用固定化洋葱假单胞菌(PC)脂肪酶为催化剂,研究了在氯仿和四氢呋喃(THF)中不同摩尔比的聚(丁二酸丁二醇-co-丁二酸己二醇酯)(PBSH)的酶促降解规律及其差异性.通过PBSH降解前后的相对分子质量变化、降解产物的MALDI-TOF-MS分析研究了共聚酯降解规律,并以分子动力学(MD)及分子对接模拟分别研究了PC酶的溶剂效应及酶与底物的结合机制.研究结果表明,PC酶在2种溶剂中均可催化PBSH降解,但在氯仿中酶的活性较大,PBSH降解率大.分子动力学模拟数据表明,在THF中,PC酶整体氨基酸残基的涨落比氯仿中大,且THF会进入酶活性口袋中与催化残基Ser87结合,破坏了催化残基Ser87和His286之间的相互作用.分子对接结果分析发现,含丁二酸己二醇酯(HS)单元底物与PC酶活性位点的对接比含丁二酸丁二醇酯(BS)单元的更为稳定.     

吡咯烷类胞液型磷脂酶A2抑制剂的比较分子力场分析

胞液型磷脂酶A2能引发关节炎，针对胞液型磷脂酶A2的抑制剂有可能成为治疗关节炎的特效药，因此引起了广泛的关注.文章对于吡咯烷类胞液型磷脂酶A2抑制剂进行了三维定量构效关系研究，利用比较分子力场分析构建了该类分子的定量构效关系，得到三维等值线图，为胞液型磷脂酶A2抑制剂的进一步改造提供了有益的启示.     

3MBA类FtsZ蛋白抑制剂的分子动力学模拟及抗菌作用机制

采用分子动力学模拟、蛋白质二级结构测定(DSSP)、口袋体积测量(POVME)以及MM-PBSA(molecular mechanics Poisson-Boltzmann surface area)方法, 系统研究了金黄色葡萄球菌丝状温度敏感性蛋白Z (SaFtsZ)-二磷酸鸟苷(GDP)二元复合物和SaFtsZ-GDP-3MBA (3-甲氧基苯甲酰胺)类衍生物三元复合物体系的稳定性、蛋白质二级结构、蛋白质构象、关键残基质心距、活性口袋体积以及相对结合自由能的变化规律. 研究表明: 当不含抑制剂存在时SaFtsZ-GDP二元复合物体系稳定性较差, 其T7Loop区域残基(203-209)波动较大, 且蛋白二级结构发生明显变化, 活性口袋体积急剧减小, 底物通道显著变窄且不稳定. 而含有抑制剂PC190723、Compound1 的类衍生物三元复合物体系的表现截然不同, 这主要是由于它们均能和活性口袋T7Loop区周围残基形成关键性的氢键以及疏水作用, 与FtsZ 蛋白紧密结合. 在SaFtsZ-GDP-3MBA三元复合物体系中, 3MBA仅能与活性口袋中部分残基形成疏水作用, 与FtsZ 蛋白亲和力较弱, 使其不能稳定地存在于活性口袋中, 进一步导致它的抗菌活性明显低于PC190723、Compound1. 这些发现深入揭示了3MBA类衍生物对FtsZ 蛋白的作用机制和影响规律, 为该类FtsZ 蛋白抑制剂的结构优化和产品开发应用提供了重要的理论依据.     

表皮生长因子受体和抑制剂之间分子对接的研究

研究了表皮生长因子受体(EGFR)和4-苯胺喹唑啉类抑制剂之间的相互作用模式，表皮生长因子受体的三维结构通过同源蛋白模建的方法得到，而抑制剂和靶酶结合复合物结构则通过分子力学和分子动力学结合的方法计算得到。从模拟结果得到的抑制剂和靶酶之间的相互作用模式表明范德华相互作用、疏水相互作用以及氢键相互作用对抑制剂的活性都有重要的影响，抑制剂的苯胺部分位于活性口袋的底部，能够与受体残基的非极性侧链产生很强的范德华和疏水相互作用，抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏水性相互作用，而抑制剂喹唑啉环上的氮原子能和周围的残基形成较强的氢键相互作用，对抑制剂的活性有较大的影响，计算得到抑制剂和靶酶之间的非键相互作用能以及抑制剂和靶酶之间的相互作用信息能够很好地解释抑制剂活性和结构的关系，为全新抑制剂的设计提供了重要的结构信息。     

具有抗炎、抗过敏活性磷脂酶抑制剂的研究进展

磷脂酶参与细胞跨膜信息传递, 磷脂酶A2 还是机体炎症、过敏介质产生的关键酶。因此, 磷脂酶抑制剂的合成研究对研究细胞表达某种功能的信息传递机制及与磷脂酶A2 激活相关的疾病治疗机制和药物研究具有重要意义。本文主要综述了近期有关磷脂酶A2 抑制剂的合成、结构、抑效性能、构效关系及应用前景等, 对磷脂酶C和磷脂酶D的抑制剂作了简要介绍。     

疏水蛋白在云母表面的吸附

采用分子动力学模拟方法研究了疏水蛋白(HFBI)在亲水云母表面的吸附过程.通过6组平行的分子动力学模拟得到了2种不同的稳定吸附结构,即通过N端和通过亲水的α螺旋与表面吸附,得到了5种吸附残基.进一步用自适应偏置力方法计算了所有吸附残基与表面的结合自由能.结果表明,残基Lys是吸附过程的关键残基,即当HFBI通过含有Lys残基的α螺旋与云母表面作用时,其吸附构象最稳定.静电作用是吸附过程的主要驱动力.在该吸附结构中,HFBI的疏水面暴露在溶液中,有效降低了云母表面的润湿性.     

Protein regulators of eicosanoid synthesis: role in inflammation

A variety of factors contribute to the complex course of inflammation. Microbiological, immunological and toxic agents can initiate the inflammatory response by activating a variety of humoral and cellular mediators. In the early phase of inflammation, excessive amounts of cytokines and inflammatory mediators are released. These factors activate, in addition to other signaling pathways, the lipid synthesis pathways, which play a crucial role in the pathogenesis of organ dysfunction. Arachidonic acid (AA), the precursor of pro-inflammatory eicosanoids, is released from membrane phospholipids by the action of phospholipase A(2) (PLA(2)), and is metabolized to prostaglandins (PGs) and leukotrienes (LTs) by the action of cyclooxygenase (COX) and lipoxygenase (LO) enzymes, respectively. Disordered activation of PLA(2), LO and COX enzymes have been implicated in many inflammatory diseases. PLA(2) is activated by phospholipase-A(2)-activating protein (PLAP) and LO by 5-lipoxygenase-activating protein (FLAP). The inducible form of COX-2 enzyme, which is usually not present under basal conditions, is induced in inflammation. In this article the function of these enzymes in eicosanoid synthesis, their regulation, and their implication in inflammatory disorders will be reviewed. The properties, function and regulation of the protein activators PLAP and FLAP will also be discussed.     

Structure-function relationships in the neurotoxin Vipoxin from the venom of Vipera ammodytes meridionalis

The neurotoxic complex Vipoxin is the lethal component of the venom of Vipera ammodytes meridionalis, the most toxic snake in Europe. It is a complex between a toxic phospholipase A2 (PLA2) and a non-toxic and catalytically inactive protein, stabilizing the enzyme and reducing the activity and toxicity. Structure-function relationships in this complex were studied by spectroscopic methods. A good correlation between the ionization behaviour and accessible surface area (ASA) of the tyrosyl residues was observed. In the toxic PLA2 subunit phenolic groups participate in H-bonding network that stabilizes the catalytically and pharmacologically active conformation. The tryptophan fluorescence decay of Vipoxin is well fitted by two exponentials with lifetimes of 0.1 (54%) and 2.5 (46%) ns. W20P, W31P and W31I are located in the interface between the two subunits and participate in hydrophobic interactions stabilizing the complex. Dissociation of the complex leads to a transition of the tryptophans from hydrophobic to hydrophilic environment, which influences mainly tau2. The longer lifetime is more sensitive to the polarity of the environment. Circular dichroism measurements demonstrate that the two components of the neurotoxin preserve their secondary structure after dissociation of the complex. The results of the spectroscopic studies are in accordance with a mechanism of blockade of transmission across the neuromuscular junctions of the breathing muscles by interaction of a dissociated toxic PLA2 with a membrane. The loss of toxicity is connected with slight changes in the secondary structure of PLA2. CD studies also show a substantial contribution of disulfide bonds to the stability of the neurotoxic complex and its components.     

A molecular dynamics study of the inhibition of chicken dihydrofolate reductase by a phenyl triazine

Molecular dynamics simulations have been used to investigate the ternary complex formed between chicken liver dihydrofolate reductase, a phenyl triazine inhibitor, and reduced nicotinamide adenine dinucleotide phosphate (NADPH). The solvent was represented by a sphere of water molecules encompassing the system. We report the results of quantum mechanical calculations of the rotational barrier in the pyrophosphate link and the barrier to inversion of the triazine ring. AMBER parameters for NADPH and the triazine are provided. Over the course of a 300-ps molecular dynamics simulation of the ternary complex in water, the triazine inhibitor maintains the same hydrogen bonding and hydrophobic interactions with the enzyme that are observed in the X-ray crystal structure. Despite the low calculated barrier to inversion of the triazine ring, a single puckered conformation is observed throughout the simulation. It is proposed that this is primarily due to interactions with Phe34, which maintains an approximately parallel orientation to the triazine ring. The nicotinamide portion of NADPH maintains the interactions observed in the crystal structure, but more conformational change is observed at the adenine end together with associated changes in the protein. Two conformations for the sidechain of Tyr31 are present in the X-ray structure. The main simulation reported here corresponds to the conformation characterized by (χ₁ = ? 161°, χ₂ = ? 103°). A separate simulation was also performed in which the sidechain of Tyr31 was initially set to the other conformation present in the crystal structure (χ₁ = 139°, χ₂ = ?99°). During this simulation, χ₁ of this sidechain gradually changed until it occupied the region characterized by χ₁ = ?160°, thereby suggesting that this is the preferred conformation for this residue. The simulation required 200 ps to reach structural equilibrium (as measured by the root mean square, rms, deviation from the initial crystal structure), thus reinforcing the view that simulations of at least several hundreds of picoseconds are desirable when studying such systems. © 1995 John Wiley & Sons, Inc.     

Characterizing polymorphism and crystal transformation of polylactide by terahertz time-domain spectroscopy

Terahertz time-domain spectroscopy (THz-TDS), which has been proved to show promising application in complex polymer systems, was employed to investigate the polymorphism phenomenon and crystal transformation of polylactide (PLA) in this study. The THz-TDS shows sensitive response on the crystal structure. The α'-form, α-form and stereocomplex crystals exhibit absorption peaks of lattice vibration at 1.82, 2.01 and 2.09 THz, respectively. THz-TDS has no direct chirality identification on the difference between poly (d-lactide) (PDLA) and poly(l-lactide) (PLLA). However, the PLA stereocomplex shows an extra and distinctive absorption peak at 1.43 THz compared with homo-PLA, and the peak was proved to be stemmed from the collective vibration of L-lactic unit and D-lactic unit pairs connecting by hydrogen bonds. This is the first time that THz-TDS has been proved to be of great potential in identification of polymer stereocomplex crystal. Also, the α'→α crystal transformation of PLA were intuitively investigated at 120 °C using THz-TDS, while the transformation rate was quite slow.     

A Monte Carlo simulation study of the effect of chain length on the hydrolysis of poly(lactic acid)

Abstract The intrinsic relationship between molecular chain length and the probability of chain reaction during poly(lactic acid)(PLA)hydrolysis was investigated by Monte Carlo simulation.The chain reaction rate was calculated by introducing a power function of different molecular chain lengths.The hydrolysis of both amorphous and extended-chain crystal PLA was selected as the model system.It is found that,the chain reaction probability was proportional to the chain length with a power of 0.4 for amorphous PLA and 0.7 1 for extended-chain crystal PLA,respectively.These results indicate that PLA with longer chain length usually exhibits larger reaction rate than that with shorter length.Comparing the hydrolysis of the two kinds of PLA,the competition between longer and shorter chains in the different condensed structures is different.     

Structure‐Based Development of an Affinity Probe for Sirtuin 2

Sirtuins are NAD⁺‐dependent protein deacylases that cleave off acetyl groups, as well as other acyl groups, from the ?‐amino group of lysines in histones and other substrate proteins. Dysregulation of human Sirt2 activity has been associated with the pathogenesis of cancer, inflammation, and neurodegeneration, thus making Sirt2 a promising target for pharmaceutical intervention. Here, based on a crystal structure of Sirt2 in complex with an optimized sirtuin rearranging ligand (SirReal) that shows improved potency, water solubility, and cellular efficacy, we present the development of the first Sirt2‐selective affinity probe. A slow dissociation of the probe/enzyme complex offers new applications for SirReals, such as biophysical characterization, fragment‐based screening, and affinity pull‐down assays. This possibility makes the SirReal probe an important tool for studying sirtuin biology.     

Design, synthesis and biological characterization of novel inhibitors of CD38

Human CD38 is a novel multi-functional protein that acts not only as an antigen for B-lymphocyte activation, but also as an enzyme catalyzing the synthesis of a Ca(2+) messenger molecule, cyclic ADP-ribose, from NAD(+). It is well established that this novel Ca(2+) signaling enzyme is responsible for regulating a wide range of physiological functions. Based on the crystal structure of the CD38/NAD(+) complex, we synthesized a series of simplified N-substituted nicotinamide derivatives (Compound 1-14). A number of these compounds exhibited moderate inhibition of the NAD(+) utilizing activity of CD38, with Compound 4 showing the highest potency. The crystal structure of CD38/Compound 4 complex and computer simulation of Compound 7 docking to CD38 show a significant role of the nicotinamide moiety and the distal aromatic group of the compounds for substrate recognition by the active site of CD38. Biologically, we showed that both Compounds 4 and 7 effectively relaxed the agonist-induced contraction of muscle preparations from rats and guinea pigs. This study is a rational design of inhibitors for CD38 that exhibit important physiological effects, and can serve as a model for future drug development.     

Molecular dynamics simulations of biotin carboxylase

Biotin carboxylase catalyzes the ATP-dependent carboxylation of biotin and is one component of the multienzyme complex acetyl-CoA carboxylase that catalyzes the first committed step in fatty acid synthesis in all organisms. Biotin carboxylase from Escherichia coli, whose crystal structures with and without ATP bound have been determined, has served as a model system for this component of the acetyl-CoA carboxylase complex. The two crystal structures revealed a large conformational change of one domain relative to the other domains when ATP is bound. Unfortunately, the crystal structure with ATP bound was obtained with an inactive site-directed mutant of the enzyme. As a consequence the structure with ATP bound lacked key structural information such as for the Mg2+ ions and contained altered conformations of key active-site residues. Therefore, nanosecond molecular dynamics studies of the wild-type biotin carboxylase were undertaken to supplant and amend the results of the crystal structures. Specifically, the protein-metal interactions of the two catalytically critical Mg2+ ions bound in the active site are presented along with a reevaluation of the conformations of active-site residues bound to ATP. In addition, the regions of the polypeptide chain that serve as hinges for the large conformational change were identified. The results of the hinge analysis complemented a covariance analysis that identified the individual structural elements of biotin carboxylase that change their conformation in response to ATP binding.     

氨基乙氧基一价铼羰基配合物的合成、晶体结构与表征

详细研究了[Re2(CO)10]在氧化三甲胺(TMNO.2H2O)的作用下与配体H2NCH2CH2OH的反应,反应产物用丙酮-己烷混合溶剂重结晶,得到Re(Ⅰ)双核配合物[Re2(-μOCH2CH2NCMe2)2(CO)6].采用元素分析、红外光谱和1H NMR对配合物的结构进行了表征.用SMART CCD X射线衍射仪测定了晶体结构,结果表明该晶体属三斜晶系,Pī空间群.在此晶体结构中,2个铼离子被2个氧桥联形成二聚单元,每个Re(Ⅰ)是六配位的变形八面体构型.     

基于水杨酰腙配体的二丁基锡配合物的合成、晶体结构、热稳定性及与DNA相互作用

2-羰基丙酸水杨酰腙与二丁基氧化锡反应, 合成了二丁基锡2-羰基丙酸水杨酰腙配合物, 经元素分析、¹H NMR、¹³C NMR、IR、UV-Vis和X射线单晶衍射等技术手段表征分子结构, 结构分析表明, 该配合物晶体属四方晶系, 锡与配位原子形成变形五角双锥构型的双核有机锡配合物, 分子以Sn₂O₂四元环为中心对称。 热分析结果表明, 在空气氛下, 配合物在103 ℃以下可稳定存在; 研究了配合物在近生理条件下与DNA的相互作用, 用紫外光谱、荧光光谱法及粘度法研究了配合物与鲱鱼精DNA的相互作用, 结果表明, 配合物与鲱鱼精DNA作用方式为插入结合。