VEGFR-2 与抑制剂Sunitinib 的分子对接及分子动力学研究

用分子对接方法研究了VEGFR-2 和抑制剂Sunitinib 的相互作用模式, 并对其复合物进行了10 ns 的分子动力学(Molecular Dynamics, MD)模拟. 结果表明, 抑制剂Sunitinib 能与VEGFR-2 中位于活性空腔的Glu885, Ile888, His1026,Asp1028, Asp1046 五个氨基酸残基形成疏水作用; 另外, VEGFR-2 中His1026, Cys1024, Asp1046 三个氨基酸残基能与Sunitinib 形成三个作用强度不同的氢键. 这些基团之间的相互作用是Sunitinib 抑制VEGFR-2 活性的关键因素. 研究结果可为VEGFR-2 抑制剂的结构改良、分子设计、合成提供理论参考, 并有助于寻找活性更高、效果更好的抗肿瘤药物.     

血管紧张素转换酶与抑制肽结合模式的分子动力学研究

应用分子模拟方法研究了血管紧张素转换酶(Angiotensin-converting enzyme,ACE)C端结构域(C-domain)与两种抑制肽(RIGLF/AHEPVK)的结合机制,预测了两个体系的结合模式,提出在C-domain-RIGLF中His353,Asp377,Asp453,Phe457,His513,Tyr523和Phe527为RIGLF主要结合残基,而在C-domainAHEPVK中Gln281,His353,Ser355,Glu384,Lys511,His513和Tyr523等残基起关键作用.应用结合自由能计算比较了两个体系的结合能力,结果表明,RIGLF和AHEPVK均与C-domain活性位点残基存在较强作用,且AHEPVK对C-domain的结合能力较强,与实验结果一致.     

漆酶与酚类模式底物的结合及反应活性的理论研究

通过生物信息学分析、分子动力学模拟及量子化学计算,对21种邻对位取代酚类模式底物与漆酶的结合能力以及反应活性进行了探讨.生物信息学结构比对分析发现漆酶的活性口袋含有Asp/Glu206,Asn/His208,Asn264,Gly392和His458等保守的氨基酸残基(氨基酸残基编号以Trametes versicolor漆酶为例,PDB:1KYA);采用MM-GBSA方法计算了21种酚类模式底物与T.versicolor漆酶的结合自由能.分子力学计算结果表明,漆酶与底物的结合力主要来自Asp206和Asn264等残基与底物分子形成的分子间氢键,并且Phe265残基和酚类底物的芳香环形成π-π相互作用.量子化学计算表明,芳环上取代基的推拉电子效应显著影响协同电子转移的底物去质子化过程,其中推电子能力较强的—NH2,—OH,—OCH3和—CH CHCH3等基团能够明显增强酚羟基反应活性,而吸电子的—CONH2和—Cl则具有相反的效应.     

稀土天冬氨酸邻菲咯啉三元配合物的合成、表征及其生物活性研究

以稀土氯化物、L-天冬氨酸和邻菲咯啉为原料,制备了5种新型稀土三元配合物.通过元素分析、摩尔电导、红外光谱、拉曼光谱,确定了该类配合物的化学组成为： RE（Asp）3PhenCl3·3H2O（RE： La^3＋,Eu^3＋,Tb^3＋,Dy^3＋,Y^3＋; Asp=L-天冬氨酸; Phen=邻菲咯啉）.通过抗菌实验表明,稀土三元配合物对大肠杆菌、金黄色葡萄球菌和白色念珠菌有较强的抑制作用,属于广谱抗菌剂; 通过MTT比色法对配合物使癌细胞凋亡能力做了初步研究,结果表明,对癌细胞具有较强的抑制杀伤作用; 用紫外吸收光谱法研究了稀土配合物与小牛胸腺DNA（CTDNA）的作用.结果表明,稀土配合物以插入的方式和CTDNA间发生了强烈的相互作用.     

硫化氢信号分子与L-乳酸脱氢酶蛋白相互作用机制的研究

硫化氢(H_2S)作为信号分子与目标蛋白相互作用而实现信号传导机制的研究一直是研究热点。本研究以L-乳酸脱氢酶为目标蛋白,选用3种H_2S供体试剂(NaHS、Na_2S、PS),采用分子荧光实时监测L-乳酸脱氢酶活性变化,研究H_2S与目标蛋白的相互作用。SDS-PAGE电泳结果显示,H_2S不是通过形成二硫键/三硫键的方式与L-乳酸脱氢酶蛋白相互作用;圆二色谱结果表明,L-乳酸脱氢酶的二级结构发生变化,提示H_2S可能存在半胱氨酸巯基衍生能力,以硫烷硫存在的PS具有最强的巯基作用力;MALDI-TOF-MS/MS分析结果表明,L-乳酸脱氢酶蛋白中部分半胱氨酸巯基位点发生了硫烷化,进一步揭示了H_2S是通过与活性半胱氨酸巯基位点硫烷化的方式与L-乳酸脱氢酶发生作用。     

酶法转化液中L-瓜氨酸的分光光度法测定

根据L-瓜氨酸在强酸性溶液中与二乙酰一肟的专一性显色反应及反应复合物在490nm处吸光度与L-瓜氨酸浓度呈线性关系的特点,通过考察酶转化液中转化底物L-精氨酸、副产物L-鸟氨酸、增效剂、磷酸盐缓冲溶液、细胞自溶释放物以及显色剂用量、显色反应时间等条件对L-瓜氨酸测定的影响,建立了一种准确、简便、灵敏的L-精氨酸酶法转化液中L-瓜氨酸的光度分析方法。该方法的相关系数r=0．999,样品回收率达99．58％。     

掺铜(Ⅱ)聚合物的制备及其在免疫亲和色谱中的应用

过渡金属离子Cu(Ⅱ)、Ni(Ⅱ)、Zn(Ⅱ)等与氨基酸残基如组氨酸、半胱氨酸、色氨酸等的咪唑基、硫醇基和吲哚基具有配位作用,因此对蛋白质具有较强的亲和力.     

环糊精包结谷胱甘肽的机理

使用分子动力学模拟结合自由能计算的方法在原子水平上研究了谷胱甘肽与α-,β-和γ-环糊精的包结模式,计算了谷胱甘肽与3种环糊精之间6种可能包结过程的自由能变化.结果表明,谷胱甘肽的谷氨酸残基从α-环糊精大口端进入空腔最终形成的包结复合物最稳定;在该复合物中,谷氨酸残基的亚甲基链部分被完全包结在疏水空腔中,其氨基与羧基位于与α-环糊精的小口端,并与环糊精的伯羟基形成了氢键,同时半胱氨酸中的巯基位于环糊精的大口端,得到了有效的保护.因此,疏水相互作用和氢键相互作用构成了包结的主要驱动力.β-环糊精的优势包结模式与α-环糊精类似,但形成复合物的稳定性次之,而γ-环糊精由于空腔较大,优势的包结模式是谷氨酸残基从γ-环糊精小口端进入空腔,但所形成的复合物结构的稳定性最弱.     

酶法测定人尿中L-瓜氨酸含量

L-瓜氨酸是人体多种疾病的重要检测指标。利用鸟氨酸甲氨酰转移酶和氨甲酰激酶对L-瓜氨酸的专一性作用,建立了一种准确、简便、灵敏的L-瓜氨酸含量酶法测定方法。较为适宜的酶转化条件是:30℃~35℃,pH6~7。固定化酶有较高的稳定性,4℃保存60d后酶活回收率仍高达95%。该方法测定L-瓜氨酸的线性范围为2~10mg/L;工作曲线回归系数r=0.9987;样品回收率达99%以上。     

多种精氨酸衍生物与ＡＴＰ作用及其催化ＡＴＰ水解的影响研究

分别使用荧光光谱法、 ~1H和~(31)P核磁方法对腺苷-5′-三磷酸(ATP)和多种L-精氨酸衍生物(L)的相互作用做了系统的研究, 得到了一些有意义的结果.在荧光滴定实验中, L对ATP有很强的荧光猝灭作用, 说明两者有较强的相互作用. ~1H和~(31)P核磁结果进一步证实了L与ATP的识别位点在ATP的嘌呤环和磷酸链上, 结合力为氢键和静电作用. 另外, 用~(31)P 核磁滴定的方法考察了L对ATP水解的影响, 发现不同的精氨酸衍生物对ATP水解的催化影响有很大的差异, 说明L对ATP的识别和催化其水解作用有较强的选择性. 此识别及催化作用的研究对深入理解精氨酸残基在ATP合酶中起到"触点"作用有一定的参考价值.     

Searching for DDAH inhibitors: S-nitroso-L-homocysteine is a chemical lead

The cysteine-hydrolase dimethylargininase-1 (DDAH-1) is an important regulator of NO production in mammalian tissue for which the availability of an inhibitor for clinics and research would be most appreciated. While studying the effect of the endogenously occurring S-nitroso-l-homocysteine on DDAH-1, an unusual N-thiosulfoximide modification was identified in the active site of the enzyme. Thus, S-nitroso-l-homocysteine in combination with the mechanism proposed herein offers a basis for the rational design of DDAH inhibitors.     

Exploring the redox reactions between heme and tetrahydrobiopterin in the nitric oxide synthases

The NO synthases (NOSs) catalyze a two-step oxidation of L-arginine (Arg) to generate nitric oxide (NO) plus L-citrulline. Because NOSs are the only hemeproteins known to contain tetrahydrobiopterin (H4B) as a bound cofactor, the function and role of H4B in their heme-based oxygen activation and catalysis is of current interest. Distinct oxidative and reductive transitions of bound H4B cofactor occur during catalysis and are associated with distinct redox transitions of the NOS heme and flavin prosthetic groups. In this perspective, we discuss the redox transitions of H4B and heme with regard to their kinetics, regulation, role in the catalytic mechanism, and how and why they may be linked.     

二甲基精氨酸二甲胺水解酶-1的理论研究

运用分子对接和分子动力学方法研究二甲基精氨酸二甲胺水解酶-1(DDAH-1)与其抑制剂亚胺基烯丁基-L-鸟氨酸(L-VNIO)和亚胺基丙基-L-鸟氨酸(Me-L-NIO)的相互作用和结合模式,并根据实验得到的结论设计了亚胺基苯乙基-L-鸟氨酸(Ph-L-NIO)抑制剂.结果表明:L-VNIO比Me-L-NIO对DDAH-1的抑制效果更强,这个结果与实验测得L-VNIO和Me-L-NIO对DDAH-1的半抑制浓度IC50值大小一致.Phe75、Asp78、His172、Ser175和Asp268这五个氨基酸残基在三种抑制剂形成的复合物中起到非常重要的作用,从计算结果推断在这三个抑制剂中我们设计得到的Ph-L-NIO对DDAH-1的抑制效果最好.     

Discovery of halopyridines as quiescent affinity labels: inactivation of dimethylarginine dimethylaminohydrolase

In an effort to develop novel covalent modifiers of dimethylarginine dimethylaminohydrolase (DDAH) that are useful for biological applications, a set of "fragment"-sized inhibitors that were identified using a high-throughput screen are tested for time-dependent inhibition. One structural class of inactivators, 4-halopyridines, show time- and concentration-dependent inactivation of DDAH, and the inactivation mechanism of one example, 4-bromo-2-methylpyridine (1), is characterized in detail. The neutral form of halopyridines is not very reactive with excess glutathione. However, 1 readily reacts, with loss of its halide, in a selective, covalent, and irreversible manner with the active-site Cys249 of DDAH. This active-site Cys is not particularly reactive (pK(a) ca. 8.8), and 1 does not inactivate papain (Cys pK(a) ca. ≤4), suggesting that, unlike many reagents, Cys nucleophilicity is not a predominating factor in selectivity. Rather, binding and stabilization of the more reactive pyridinium form of the inactivator by a second moiety, Asp66, is required for facile reaction. This constraint imparts a unique selectivity profile to these inactivators. To our knowledge, halopyridines have not previously been reported as protein modifiers, and therefore they represent a first-in-class example of a novel type of quiescent affinity label.     

Structure-activity relationships of 2-aminothiazole derivatives as inducible nitric oxide synthase inhibitor

Nitric oxide synthase (NOS) has been divided into two major sub-enzymes, i.e. inducible NOS (iNOS) and constitutive NOS (cNOS). Although nitric oxide (NO) plays an important role as host defense mediator, excessive production of NO by iNOS has been involved in the pathology of many inflammatory diseases. Recently, we reported that the 2-imino-1,3-oxazolidine (1a) weakly inhibits iNOS and that introduction of an alkyl moiety on the oxazolidine ring of 1a enhances the inhibitory activity and selectivity for iNOS. In our search for better iNOS inhibitors, we focused our efforts on the 2-aminothiazole scaffold 3 as it possesses a ring similar to that of 1a. In this study, we evaluated the inhibitory activity of a series of 2-aminothiazole derivatives against both iNOS and neuronal NOS (nNOS). Our results show that introduction of appropriately-sized substituents at the 4- and 5-position of the 2-aminothiazole ring improves the inhibitory activity and selectivity for iNOS. We also found that the selectivity of 5a [5-(1-methyl)ethyl-4-methylthiazol-2-ylamine] and 5b [5-(1,1-dimethyl)ethyl-4-methylthiazol-2-ylamine] for iNOS was similar to that of oxazolidine derivative 1b (4-methyl-5-propyl-2-imino-1,3-oxazolidine) and much higher than that of L-NAME. However, we could not enhance the inhibitory activity against iNOS by introducing an alkyl substituent into the 2-aminothiazole ring as we could in the case of oxazolidine one. On the other hand, introduction of bulky or hydrophilic substituent at any position of the 2-aminothiazole ring remarkably decreased or even abolished the inhibitory activity against NOS.     

Synthetic approaches to N(delta)-methylated L-arginine, N(omega)-hydroxy-L-arginine, L-citrulline, and N(delta)-cyano-L-ornithine

Nomega-Methylated arginines such as asymmetric dimethyl-L-arginine (ADMA) and monomethyl-l-arginine (NMMA) are known as potent physiological inhibitors of nitric oxide synthases (NOSs). To explore a possible physiological and pharmaceutical relevance of N(delta)-methylated analogues, a synthetic scheme had to be developed that would not lead to N(delta)-methyl-L-arginine only but also to its presumed metabolites of NOS catalysis. Two basic synthetic approaches have been pursued to obtain N(delta)-methylated derivatives of L-ornithine, L-citrulline, L-arginine, and N(omega)-hydroxy-L-arginine. A first attempt utilized conventionally protected L-ornithine, i.e., the tert-butyl ester and Boc-amine, and led to three end compounds in excellent yields. Simultaneous protection of the alpha-amino acid moiety by formation of boroxazolidinones, particularly by employing 9-borabicyclo[3.3.1]nonane (9-BBN-H), proved to be a convenient option to perform side chain modifications and led to all of the desired end compounds. Additionally, enantiomeric excess (ee, %) of crucial synthetic intermediates and end compounds was determined by chiral HPLC.     

Mechanism of Nitric Oxide Synthase Regulation: Electron Transfer and Interdomain Interactions

Nitric oxide synthase (NOS), a flavo-hemoprotein, tightly regulates nitric oxide (NO) synthesis and thereby its dual biological activities as a key signaling molecule for vasodilatation and neurotransmission at low concentrations, and also as a defensive cytotoxin at higher concentrations. Three NOS isoforms, iNOS, eNOS and nNOS (inducible, endothelial, and neuronal NOS), achieve their key biological functions by tight regulation of interdomain electron transfer (IET) process via interdomain interactions. In particular, the FMN-heme IET is essential in coupling electron transfer in the reductase domain with NO synthesis in the heme domain by delivery of electrons required for O(2) activation at the catalytic heme site. Compelling evidence indicates that calmodulin (CaM) activates NO synthesis in eNOS and nNOS through a conformational change of the FMN domain from its shielded electron-accepting (input) state to a new electron-donating (output) state, and that CaM is also required for proper alignment of the domains. Another exciting recent development in NOS enzymology is the discovery of importance of the the FMN domain motions in modulating reactivity and structure of the catalytic heme active site (in addition to the primary role of controlling the IET processes). In the absence of a structure of full-length NOS, an integrated approach of spectroscopic (e.g. pulsed EPR, MCD, resonance Raman), rapid kinetics (laser flash photolysis and stopped flow) and mutagenesis methods is critical to unravel the molecular details of the interdomain FMN/heme interactions. This is to investigate the roles of dynamic conformational changes of the FMN domain and the docking between the primary functional FMN and heme domains in regulating NOS activity. The recent developments in understanding of mechanisms of the NOS regulation that are driven by the combined approach are the focuses of this review. An improved understanding of the role of interdomain FMN/heme interaction and CaM binding may serve as the basis for the design of new selective inhibitors of NOS isoforms.     

2‐[(4‐Hydroxyphenyl)iminomethyl]­thiophene

The molecular structure of the title compound, C₁₁H₉NOS, has three planar moieties, two of which are rings, namely the hydroxy­phenyl and the thio­phene, with an angle of 20.76 (10)° between them. The crystal structure is stabilized by an O—H?N hydrogen bond and by C—H?O intermolecular interactions. The C?O intermolecular contact distance is 3.443 (2) Å.     

化学-生物法制备D-精氨酸和L-瓜氨酸

在水溶液中以水杨醛为催化剂,L-精氨酸可以快速消旋为DL-精氨酸．后以DL-精氨酸为底物,利用粪链球菌（Streptococcus faecalis）精氨酸脱亚胺酶对L-精氨酸的专一脱亚胺作用,同时制备D精氨酸和L-瓜氨酸,分别以92．3％,94．2％的产率获得光学纯的D-精氨酸和L-瓜氨酸．     

Bis[1-hydroxypyridine-2(1H)-thion­ato-S,O]copper(II)

The crystal structure of the widely used title fungicidal material, [Cu(C₅H₄NOS)₂], has been determined at 150 (2) K from a microcrystalline fragment using synchrotron radiation. The mol­ecule adopts a trans-square-planar configuration, with the Cu atom sited at a crystallographic centre of inversion.