全氟丙酸与人血清白蛋白结合作用机制的计算模拟与光谱法研究

通过分子对接和动力学模拟的计算方法模拟人血清白蛋白(HSA)的三维空间结构,建立了HSA与全氟丙酸(IPC-PFFA-3)相互作用的模型,研究了HSA与全氟丙酸复合物在水溶液中的稳定性以及在结合位点中的动力学性质。在模拟人体生理的实验条件下,采用荧光光谱法和同步荧光光谱法研究了HSA与IPCPFFA-3的相互作用。实验结果表明,IPC-PFFA-3与HSA形成的复合物HSA-IPC-PFFA-3对HSA产生荧光猝灭作用,其猝灭机理是静态猝灭;热力学参数计算得出两者结合的主要作用力为氢键作用力;竞争实验的结果表明IPC-PFFA-3与HSA的结合位点位于HSA的SiteⅡ,与分子对接的模拟结果相吻合。同步荧光光谱实验与动力学模拟的结果证明IPC-PFFA-3与HSA能够稳定结合,并使HSA的构象发生变化。     

2'-羟基-2,4-二溴二苯醚与人血清白蛋白作用机制的光谱研究与计算模拟

采用分子对接、分子动力学模拟和光谱法研究了2'-羟基-2,4-二溴二苯醚(2'-OH-BDE-7)与人血清白蛋白(HSA)的相互作用.同步荧光光谱研究表明,2'-OH-BDE-7诱导HSA的构象产生变化,并与分子动力学模拟的结果相吻合.荧光光谱表明,2'-OH-BDE-7能引起HSA荧光猝灭,且其作用机制为静态猝灭和非辐射能量转移.热力学分析得出ΔG0,ΔH0和ΔS0,表明氢键和范德华力在HSA-2'-OH-BDE-7的体系中起着重要作用.竞争实验和分子对接结果表明2'-OH-BDE-7主要结合在HSA的位点Ⅰ.将计算模拟和光谱实验研究相结合,为研究小分子和蛋白质相互作用机制提供更多的信息.     

分子荧光光谱法结合分子动力学模拟研究2′-OH-BDE-68与HSA的相互作用

结合分子荧光光谱法、分子对接和分子动力学模拟等方法研究了在生理条件(pH 7.40)下2′-羟基-2,3′,4,5-四溴二苯醚(2′-OH-BDE-68)与人血清白蛋白(HSA)的相互作用及其对HSA构象的影响。结果表明:1 2′-OH-BDE-68对HSA内源性荧光的猝灭属静态猝灭和非辐射能量转移过程;2两者之间的反应是以疏水作用力为主辅以微弱的静电作用的自发反应过程;3 2′-OH-BDE-68与HSA的结合在10ns内趋于平衡,结合位点在SiteⅠ;4复合物的形成使HSA分子中的色氨酸的疏水性增加,从而HSA的二级结构发生改变。     

光谱法及分子对接研究邻苯二甲酸单乙基己基酯与人血清白蛋白的相互作用

通过荧光光谱法、紫外分光光度法以及分子对接技术探究邻苯二甲酸单乙基己基酯(MEHP)与人血清白蛋白(HSA)之间的相互作用及其作用机制。光谱学数据显示,MEHP诱导HSA内源荧光猝灭是因为两者间发生非辐射能量转移并形成稳定的复合物;不同温度下的热力学常数表明范德华力或氢键为MEHP与HSA结合的主要驱动力;三维荧光光谱结果证实MEHP改变了HSA的构象;同步荧光光谱和位点实验表明,MEHP在位点Ⅰ与HSA结合。根据光谱学的研究结果,采用分子对接技术模拟MEHP与HSA在分子水平上的相互作用机制,结果与光谱学研究结果一致。     

光谱-分子模拟法分析杨梅素与人血清白蛋白的分子作用机制

在模拟生理条件下,用多种光谱法结合分子对接法测定了杨梅素(MY)与人血清白蛋白(HSA)的相互作用。研究结果表明,MY能够明显猝灭HSA的荧光,MY与HSA的相互作用为复合式静态结合过程,结合强度较强。热力学和分子对接结果表明,MY与HSA是自发结合的,维持MY与HSA的相互作用力主要是氢键和范德华力。能量转移结果表明,MY与HSA的结合距离小于7 nm,说明MY与HSA间可以发生能量转移。MY对HSA的结构域微区构象产生了影响,使结合位域的疏水性发生了改变。本研究阐述了MY与HSA的相互作用分子机制,为天然小分子在体内转运等提供了有用信息。     

水溶性阳离子型吡啶基咔咯镓配合物与人血清蛋白的相互作用

利用紫外吸收光谱、荧光光谱、圆二色(CD)光谱和分子对接计算探究了5,10,15-三[4-(N-甲基-吡啶)]咔咯镓配合物(1-Ga)与人血清蛋白(HSA)的相互作用.结果表明,HSA的荧光能被1-Ga静态猝灭,两者的结合常数为2.82×104L/mol,作用距离为3.342 nm.热力学参数显示1-Ga主要通过氢键和疏水作用与HSA结合,位点标记竞争实验表明1-Ga优先结合HSA的布洛芬位点Ⅱ.此外,紫外吸收光谱和CD光谱显示二者的相互作用会导致HSAα-螺旋结构的减少.分子对接计算结果表明1-Ga优先结合在HSA亚结构域ⅢA的位点Ⅱ疏水袋中.     

噻螨酮与人血清白蛋白的作用机制

用分子对接方法及紫外-可见吸收光谱、同步荧光光谱、三维荧光光谱等实验手段研究了噻螨酮(HEX)与人血清白蛋白(HSA)的相互作用及对HSA构象的影响.预测结果表明,HEX能与HSA发生相互作用,且作用位点site II比site I的打分小约4.5.实验结果表明,HEX猝灭HSA的内源荧光且作用机制为静态猝灭;HEX使HSA周围的微环境发生变化,导致蛋白质的肽链结构改变;298和291 K时HEX与HSA相互作用的结合常数(KA)和结合位点数分别为7.35×103 mol/L、0.82和1.02×104 mol/L、0.86,证实HEX仅在site II存在作用位点;HEX与Trp214的结合距离为3.01 nm,作用力主要为氢键、范德华力和疏水作用力.这些研究所获得的多种信息有助于在分子水平上理解农药对人体造成的毒性及可能的生物累积性.     

高效亲和色谱法测定丹皮酚与固定化人血清白蛋白结合域

利用亲和色谱,在模拟人体生理环境下(37 ℃、pH 7.4),采用竞争置换法研究了丹皮酚(PAE)与固定化人血清白蛋白(HSA)的相互作用。通过对PAE的自我竞争分析及PAE与HSA上结合位点的标记物间的竞争置换分析,得到了PAE和HSA间的结合常数、结合位点数和结合域。结果表明: PAE在HSA分子中仅存在一类结合位点,结合常数为4.84×103 L/mol,该结合位点为HSA上的Sudlow siteII;通过对PAE与HSA相互作用的热力学研究,推断出二者间的作用力类型为氢键或范德华力。     

光谱法结合原子力显微镜和分子对接技术研究金丝桃苷与人血清白蛋白的相互作用

在模拟生理条件下,采用荧光、共振散射、圆二色谱(CD)等光谱法和原子力显微镜及分子对接技术,研究了金丝桃苷与人血清白蛋白(HSA)的相互作用。应用分子对接技术预测金丝桃苷结合在HSA的SiteⅠ位,预测结果与位点探针竞争实验结果吻合。原子力显微镜(AFM)图像和共振散射光谱表明,与金丝桃苷结合后HSA的分子直径变大,产生相互聚集。金丝桃苷对HSA内源荧光的猝灭机制属于形成基态复合物所引起的静态猝灭。测得的热力学参数表明,金丝桃苷与HSA作用主要由疏水作用和氢键驱动。根据Frster非辐射能量转移理论求得两者间的结合距离为3.52nm。CD谱显示金丝桃苷诱导HSA的二级结构产生稍许的变化。     

考拉维酸对人血清白蛋白结构的影响

利用多种荧光光谱法、紫外光谱法并结合分子模拟等方法, 表征了模拟生理条件下一种植物药活性组分考拉维酸(KA)影响人血清白蛋白(HSA)的结构信息. 同步荧光及紫外光谱证实考拉维酸的存在影响了HSA的微环境; 二维及三维荧光光谱表明考拉维酸可以猝灭HSA的内源荧光, 使其构象发生变化. 荧光偏振的测定提供了考拉维酸与HSA作用后生成的配合物弛豫时间与聚集特性的信息, 揭示KA的存在使HSA的流动性和微粘度发生变化. 定量求得不同温度下(298、308 和318 K)考拉维酸与HSA作用的键合参数和热力学参数. 分子模拟表明考拉维酸键合位点于HSA分子的疏水腔内, 并与赖氨酸Lys195 和天冬氨酸Asp451 形成三个氢键, 与HSA的键合模式主要是疏水作用; 位点竞争实验证明考拉维酸在HSA亚结构域的位点Ⅱ位发生作用. 另外, 获得的相关物理化学参数从分子水平上揭示了考拉维酸与HSA相互作用的机制. 结果表明, HSA对考拉维酸有较强的结合能力, 提示人血清白蛋白对考拉维酸可起到储存和转运的作用.     

Combined QSAR/QSPR,Molecular Docking,and Molecular Dynamics Study of Environmentally Friendly PBDEs with Improved Insulating Properties

To improve the insulating properties of polybrominated diphenyl ethers(PBDEs), we studied the molecular structures and energy gap(Eg) values of 209 PBDEs using a three-dimensional quantitative structure-activity relationship(3D-QSAR) model, molecular docking, and molecular dynamics. We also analyzed the interaction mechanisms of PBDEs using a 2D-QSAR model, molecular substitution characteristics, and molecular docking. The 3D-QSAR model showed that the 2-, 4-, 5-, and 6-positions significantly influenced the PBDE insulating properties. Using BDE-34 as a template molecule, we designed six derivatives with 0.47%-28.44% higher insulation tlian BDE-34. Compared with BDE-34, the stability and flame retardancy of the above six derivatives were not adversely affected. These derivatives, except for 2,6-cyanomethyl-BDE, 2-cyanomethyl-BDE, and 2-aniinomethyl-BDE, were more toxic and biodegradable than BDE-34, but showed weaker bioaccumulation and migration abilities than BDE-34. Mechanism analysis showed that the highest occupied orbital energy, the most negative charge, and the dipole moment were the main quantitative parameters that aflected the PBDE insulating properties. PBDE insulation gradually decreased as the number of Br atoms increased. The level of similarity between the substitution patterns on the two benzene rings was significantly correlated with PBDE insulation, with hydrophobic groups having a more significant efiect on PBDE insulation.     

Molecular Modifications and Control of Processes to Facilitate the Synergistic Degradation of Polybrominated Diphenyl Ethers in Soil by Plants and Microorganisms Based on Queuing Scoring Method

In this paper, a combination of modification of the source and regulation of the process was used to control the degradation of PBDEs by plants and microorganisms. First, the key proteins that can degrade PBDEs in plants and microorganisms were searched in the PDB (Protein Data Bank), and a molecular docking method was used to characterize the binding ability of PBDEs to two key proteins. Next, the synergistic binding ability of PBDEs to the two key proteins was evaluated based on the queuing integral method. Based on this, three groups of three-dimensional quantitative structure-activity relationship (3D-QSAR) models of plant-microbial synergistic degradation were constructed. A total of 30 PBDE derivatives were designed using BDE-3 as the template molecule. Among them, the effect on the synergistic degradation of six PBDE derivatives, including BDE-3-4, was significantly improved (increased by more than 20%) and the environment-friendly and functional evaluation parameters were improved. Subsequently, studies on the synergistic degradation of PBDEs and their derivatives by plants and microorganisms, based on the molecular docking method, found that the addition of lipophilic groups by modification is beneficial to enhance the efficiency of synergistic degradation of PBDEs by plants and microorganisms. Further, while docking PBDEs, the number of amino acids was increased and the binding bond length was decreased compared to the template molecules, i.e., PBDE derivatives could be naturally degraded more efficiently. Finally, molecular dynamics simulation by the Taguchi orthogonal experiment and a full factorial experimental design were used to simulate the effects of various regulatory schemes on the synergistic degradation of PBDEs by plants and microorganisms. It was found that optimal regulation occurred when the appropriate amount of carbon dioxide was supplied to the plant and microbial systems. This paper aims to provide theoretical support for enhancing the synergistic degradation of PBDEs by plants and microorganisms in e-waste dismantling sites and their surrounding polluted areas, as well as, realize the research and development of green alternatives to PBDE flame retardants.     

Analysis of Ah receptor binding affinities of polybrominated diphenyl ethers via in silico molecular docking and 3D-QSAR

Polybrominated diphenyl ethers (PBDEs) have become ubiquitous contaminations due to their use as flame retardants. The structural similarity of PBDE to some dioxin-like compounds suggested that they may share similar toxicological effects: they might activate the aryl hydrocarbon receptor (AhR) signal transduction pathway and thus might have adverse effects on wildlife and humans. In this study, in silico computational workflow combining molecular docking and three-dimensional quantitative structure–activity relationship (3D-QSAR) was performed to investigate the binding interactions between PBDEs and AhR and the structural features affecting the AhR binding affinity of PBDE. The molecular docking showed that hydrogen-bond and hydrophobic interactions were the major driving forces for the binding of ligands to AhR, and several key amino acid residues were also identified. The CoMSIA model was developed from the conformations obtained from molecular docking and exhibited satisfactory results as q ² of 0.605 and r ² of 0.996. Furthermore, the derived model had good robustness and statistical significance in both internal and external validations. The 3D contour maps generated from CoMSIA provided important structural features influence the binding affinity. The obtained results were beneficial to better understand the toxicological mechanism of PBDEs.     

两种组氨酸酰胺衍生物的合成及其与人血清白蛋白的结合

L-组氨酸对生物有机体有着良好的亲和能力,通过修饰其化学结构以期寻找药理活性和生物利用度高的衍生物。本文将L-组氨酸分别与反式肉桂酸和对甲氧基肉桂酸反应,合成了两种组氨酸酰胺类衍生物,利用傅里叶变换红外光谱、质谱、氢谱/碳谱核磁共振谱进行了结构表征。采用分子操作环境(MOE)软件分子对接技术、荧光光谱法、同步荧光光谱法(SFS)、紫外-可见光谱法(UV-Vis),共同研究了两种衍生物分别和人血清白蛋白(HSA)相结合的机理。MOE对接结果显示,这两种衍生物与HSA的模拟结合能分别为-13.82和-16.25 kcal/mol,主要是通过范德华力和疏水作用结合在HSA亚结构域ⅡA(即siteⅠ)的疏水腔内。荧光猝灭数据表明,衍生物与HSA相互作用并形成了新的基态配合物,荧光猝灭过程为静态猝灭;不同温度(300、305和310 K)下衍生物与HSA相互作用的结合常数分别为1.773×104、6.354×10~3、1.260×10~3和5.314×10~4、4.614×10~3、1.420×10~3;由热力学参数得到衍生物与HSA的结合过程是由范德华力驱动;SFS表明,衍生物使得HSA的二级结构发生了变化。结合UV-Vis的结果可以确定,在体外生理条件下,组氨酸酰胺类衍生物均可以通过范德华力与HSA结合,并对HSA内源荧光产生静态猝灭及构象影响,这与分子对接结果一致,从而为组氨酸酰胺类衍生物药物的进一步开发提供了参考。     

Studies on the binding of nevadensin to human serum albumin by molecular spectroscopy and modeling

The binding of nevadensin to human serum albumin (HSA) in aqueous solution was investigated for the first time by molecular spectroscopy and modeling at pH 7.4. Spectrophotometric observations are rationalized in terms of a static quenching process and binding constant (K_a, K_b) and the number of binding sites (n ≈ 1) were evaluated by fluorescence quenching methods. Thermodynamic data showed that nevadensin was included in the hydrophobic cavity of HSA mainly via hydrophobic interactions. The value of 3.09 nm for the distance r between the donor (HSA) and acceptor (nevadensin) was derived from the fluorescence resonance energy transfer. Spectrophotometric techniques were also applied to investigate the structural information of HSA molecules on the binding of nevadensin and the results showed that the binding of nevadensin to HSA did not change significantly molecular conformation of HSA in our experimental conditions. Furthermore, the study of molecular modeling also indicated that nevadensin could strongly bind to the site I (subdomain IIA) of HSA mainly by a hydrophobic interaction and there are hydrogen bond interactions between nevadensin and the residues Arg-218, Arg-222, Lys-195, and Asp-451. As compared to the other flavonoids, the flavonoids containing methoxy groups which are in aromatic rings can bind to HSA with higher affinity.     

嘧啶衍生物与人血清白蛋白的相互作用

在模拟生理条件下,运用荧光光谱、激光闪光光解(LFP)和分子对接等技术研究了8种具有抗肿瘤活性的嘧啶衍生物(PDs,其中PDs A 5-FU为成药,PDs B-H为实验室自制)与人血清白蛋白(HSA)的相互作用.利用Stern-Volmer方程和激光闪光光解技术分析了PDs对HSA的荧光猝灭机制,PDs A和B为静态猝灭,PDs G和H为动态猝灭.用双倒数曲线法得出5种PDs与HSA的结合常数Ka和结合位点数n,在测定条件下5种PDs与载体结合位点数均为1,且均以弱结合力结合,通过热力学参数ΔH,ΔS和ΔG推测出PDs B,C和E与HSA之间的作用力为静电作用力和疏水作用力,PDs A和D与HSA之间的作用力是氢键和范德华力,分子对接结果与其一致.根据F9rster非辐射能量转移理论(FRET)分析了HSA和PDs之间的结合距离(r),其结果均小于4 nm,符合能量转移理论.进一步利用同步荧光、三维荧光和圆二色光谱考察了PDs与HSA结合过程中HSA空间构象的变化,结果显示,仅PDs A和C对HSA的芳香族氨基酸周围的疏水性略有增强作用.体外实验结果表明,HSA可以作为优良的载体来运输和储存PDs A~E,这为嘧啶衍生物的后续研究提供了可参考的实验数据.     

Investigating the interaction of juglone (5-hydroxy-1, 4-naphthoquinone) with serum albumins using spectroscopic and in silico methods

The interaction between juglone at the concentration range of 10–110 µM and bovine serum albumin (BSA) or human serum albumin (HSA) at the constant concentration of 11 µM was investigated by fluorescence and UV absorption spectroscopy under physiological-like condition. Performing the experiments at different temperatures showed that the fluorescence intensity of BSA/HSA was decreased in the presence of juglone by a static quenching mechanism due to the formation of the juglone–protein complex. The binding constant for the interaction was in the order of 10³ M^?1, and the number of binding sites for juglone on serum albumins was determined to be equal to one. The thermodynamic parameters including enthalpy (ΔH), entropy (ΔS) and Gibb’s free energy (ΔG) changes were obtained by using the van’t Hoff equation. These results indicated that van der Waals force and hydrogen bonding were the main intermolecular forces stabilizing the complex in a spontaneous association reaction. Moreover, the interaction of BSA/HSA with juglone was verified by UV absorption spectra and molecular docking. The results of synchronous fluorescence, UV–visible and CD spectra demonstrated that the binding of juglone with BSA/HSA induces minimum conformational changes in the structure of albumins. The increased binding affinity of juglone to albumin observed in the presence of site markers (digoxin and ibuprofen) excludes IIA and IIIA sites as the binding site of juglone. This is partially in agreement with the results of molecular docking studies which suggests sub-domain IA of albumin as the binding site.     

Spectroscopic and Molecular Docking Approaches for Investigation of Interaction of Phellopterin with Human Serum Albumin

The mechanism of interaction between human serum albumin (HSA) and natural product phellopterin (PL) from Angelica dahurica was investigated by spectroscopic techniques with molecular docking under simulated physiological conditions. The experimental results showed that the fluorescence of HSA was regularly quenched by PL, and the quenching constants (K_SV) decreased with increasing temperature, which indicated that the quenching mechanism was a static quenching procedure. The binding constants (K_A) were larger than 10^?5 M^?1 and the number of binding sites (n) was approximate to 1 at different temperatures, which indicated that the binding affinity was hige and there was just one main binding site in HSA for PL. According to thermodynamic parameters from Van't Hoff equation, the binding process of PL with HSA was spontaneous and exothermic process due to ΔG < 0, and the electrostatic force played major role in the binding between PL and HSA according to ΔH < 0 and ΔS > 0. The binding distance (r) was calculated to be about 3.35 nm, which implied that the energy transfer from HSA to PL occurred with high possibility according to the theory of Förster's non-radiation energy transfer. The microenvironment and conformation of HSA changed with the addition of PL based on the results of synchronous and three-dimensional fluorescence methods. The molecular docking analysis revealed the binding locus of PL to HSA in subdomain IIIA (Sudlow's site II).