基于框架核酸的细胞表面受体配体相互作用研究进展

细胞表面受体与配体之间的特异性相互作用在细胞生物学过程中起着重要作用。然而,与均相溶液不同,受体分子在细胞膜上的分布是非连续的、动态的,因此细胞表面的受体配体相互作用通常呈现复杂的非线性结合模式。框架核酸作为一类具有确定几何形状的DNA纳米支架,可用于多价配体的偶联,为深入揭示受体配体相互作用机制提供了可靠的工具。利用框架核酸纳米分辨率的可寻址特性,可实现对配体数目、间距及空间构象等参数的精确调控,进而研究细胞表面受体配体的结合特性及影响因素,优化结合条件最终实现高效的分子识别及靶向治疗。本文综述了基于框架核酸的细胞表面受体配体相互作用研究进展,通过探讨细胞表面受体配体相互作用的重要影响因素及生物学应用,对该研究领域的发展前景和未来趋势予以展望。     

Hydroxamate类抑制剂与MMP-3的结合自由能的计算

用自由能微扰方法(FEP)计算了两种hydroxamate类的抑制剂和MMP-3的相对结合自由能。在计算中,对于催化区的锌离子与其共价结合的配体(包括抑制和组氨酸)采用了键合的模型,抑制剂和周围配体的部分电荷的计算采用两步静电势收敛方法。自由能计算采用了慢增长(Slowgrowth)和固定窗口增长(Fixedwidthwindowgrowth)两种方法,并且在每次计算中都采用了双向采样(Double-widesampling)的策略。两种方法计算得到的相对结合自由能都能和实验值很好的符合。同时从动力学模拟的得到的分子轨迹得到了抑制剂和受体之间相互作用模式,抑制剂的P1部分可以和受体的S1'口袋形成很强范德华和疏水相互作用,P1上的苯环可以和Tyr223上的苯环形成较好的π键堆积相互作用。     

计算机化学模拟—分子构象识别的新方法

简介了几种利用计算机图形技术研究化合物分子构象的新方法。重点介绍了分子力学计算方法中的系统搜索、随机搜索方法和分子动力学计算方法中的模拟淬火、模拟退火等新技术 ,为药物分子设计中受体与配体分子构象的识别提供了合理可行的方法。     

有机分子识别和聚集体组装中的非共价键协同作用

综述了近年来不同的非共价键作用力包括分子间氢键、供体-受体相互作用、π-π堆积作用、静电作用、疏溶剂作用和金属-配体配位作用等的协同作用在有机分子识别和有序聚集体组装研究中的应用.     

拉伸分子动力学模拟配体-受体相互作用

配体和受体之间的相互作用研究有助于阐明配体的作用机理, 为合理药物设计提供线索. 新发展的拉伸分子动力学模拟使原来在微秒至秒时间范围内发生的生物化学过程可以在纳秒尺度内进行模拟, 从而动态再现目前实验所无法提供的配体与受体的结合或解离过程. 文中通过详细介绍拉伸分子动力学方法对石杉碱甲与乙酰胆碱酯酶结合和解离过程以及HIV-1逆转录酶和其非核苷酸类似物抑制剂α-APA解离过程的成功模拟, 综述拉伸分子动力学模拟在研究配体和受体相互作用中的应用.     

柔性原子受性模型（FLARM）

柔性原子受体模型(Flexible Atom Receptor Model, FLARM)方法使用了改进 的遗传算法(IGA),比传统的受体模型方法具有更快的计算速度;FLARM受体模型中 的原子空间坐标在遗传演化过程中是可变的,避免了不合适的起始位点对模型的影 响;另外,FLARM用增加空原子权重的方法,可以生成不完全封闭的、允许有大段 空区域的受体模型,这样的模型能更好地模拟实际受体的结构,并且容易和药效团 模型找到对应关系。我们用FLARM方法分别计算了甾类化合物体系的CBG蛋白亲和性 和1,1,3-三氧-2H,4H-噻吩并[3,4-e] [1,2,4]噻二嗪衍生物(TTD)体系的抗HIV-1活 性,计算结果表明FLARM生成的虚拟受体模型对配体分子的活性具有较高的预测能 力,在此虚拟受体模型的基础上还可以进一步分析虚拟受体分子与配体分子的相互 作用机制,对真实受体分子结构的活性位点进行初步预测。     

柔性原子受性模型（FLARM）

柔性原子受体模型(Flexible Atom Receptor Model, FLARM)方法使用了改进 的遗传算法(IGA)，比传统的受体模型方法具有更快的计算速度；FLARM受体模型中 的原子空间坐标在遗传演化过程中是可变的，避免了不合适的起始位点对模型的影 响；另外，FLARM用增加空原子权重的方法，可以生成不完全封闭的、允许有大段 空区域的受体模型，这样的模型能更好地模拟实际受体的结构，并且容易和药效团 模型找到对应关系。我们用FLARM方法分别计算了甾类化合物体系的CBG蛋白亲和性 和1,1,3-三氧-2H,4H-噻吩并[3,4-e] [1,2,4]噻二嗪衍生物(TTD)体系的抗HIV-1活 性，计算结果表明FLARM生成的虚拟受体模型对配体分子的活性具有较高的预测能 力，在此虚拟受体模型的基础上还可以进一步分析虚拟受体分子与配体分子的相互 作用机制，对真实受体分子结构的活性位点进行初步预测。     

γ-氨基丁酸与其突变受体的相互作用

采用同源建模技术构建了大鼠γ-氨基丁酸a型受体(GABAaR)模型及β97Tyr突变受体模型. 采用分子对接技术研究了γ-氨基丁酸(GABA)与突变前后受体的相互作用. 计算结果显示, 突变及未突变受体之间在氢键作用和对接能量方面存在显著差异, 配体与突变受体的结合能力随突变残基中氟原子数目的增加而降低.     

氨基酸突变对GABAa受体结合能力的影响

采用同源建模技术构建了大鼠γ-氨基丁酸a型受体(GABAaR)模型, 并将氨基酸残基β157Tyr和β205Tyr突变为相应的突变受体模型. 使用分子对接方法计算了γ-氨基丁酸(GABA)与突变前后受体的相互作用. 对接计算结果显示, Tyr突变为Phe后, 两种突变受体的对接能量大幅提高, GABA生物活性降低; 当Phe的对位引入氟原子后, 对接能量与未突变受体相比更低. 另外, 与β205Tyr突变相比, 与配体距离较近的β157Tyr突变, 对受体与配体作用的影响更大.     

基于分子对接的苯丙素甙（PPGs）类化合物的虚拟筛选和合理设计

采用虚拟化合物生成法对抗肿瘤的苯丙素甙(PPGs)类化合物进行了配体受体对 接研究。以三种不同的骨架结构为基础分别生成了五十个虚拟苯丙素甙(PPGs)类化 合物，并将它们与端粒DNA受体进行分子对接，分析已知结构的对接结果，通过虚 拟筛选的方法得到了一批与受体相互作用能较高并且复合物能量较低的新的有潜力 的活性化合物。该方法可以弥补分子对接研究中，只能计算药物与受体的相互作用 ，无法有效设计新化合物的不足。这种方法在基于结构的药物分子设计中具有重要 的意义。     

Study of binding constant of toll-like receptor 4 and lipopolysaccharide using capillary zone electrophoresis

This short communication describes the interaction between toll-like receptor 4 (TLR4) and lipopolysaccharide (LPS, its specific ligand) using analytical methods. Their interaction has been evidenced in many reports. Nevertheless, there are few reports focused on their binding constant. In this research, the interaction between TLR4 and LPS is investigated using mobility shift method by CZE. To optimize the electrophoresis conditions, the effecting factors, running buffer, sample concentration, injection duration, and operation voltage of electrophoretic on the mobility shift are studied in detail. Electrophoresis conditions were described as follows: borate buffer (pH 7.4, 20 mM), 5 s for 50 mbar pressure injection duration, and 13 kV of separation voltage in 41.5 cm fused silica capillary with 75 μm id and 375?μm od. The combination constant of TLR4 and LPS is calculated using Scatchard methods. The Scatchard liner correlation is y=-0.0165x+0.1456, binding constant is K=1.65 x 10? (g/mL)?1.     

Structure-activity relationship studies: methods and ligand design for G-protein coupled peptide receptors

The exchange of information between cells represents an important regulatory mechanism for cellular activities. Such regulation processes mainly occur by hydrophilic compounds, unable to penetrate the cell membrane. Accordingly such signals have to be transmitted into the cell that is performed by transmembrane receptors. The widespread group of G-protein coupled receptors plays a decisive role in extracellular signal recognition and transition into cellular response. The importance of this interaction is evidently shown by the severe diseases that correlate with dysfunction of the interaction between ligand and G-protein coupled receptor. The development of drugs against these diseases needs the comprehension of signal recognition and transition as well as the understanding of intracellular signal pathways. In this review, we describe concepts and methods to identify the structure-activity relationships of G-protein coupled peptide receptors and their successful application. Furthermore we provide an insight into peptide based drug design. Examples are taken from the field of CGRP, orexin and growth hormone secretagogue receptor ligands.     

Conformational and MO studies of hydroxy-2-aminotetralins

Attempting to explain the differences in the pharmacological profiles of the isomeric monohydroxy-and dihydroxy-2-aminotetralins (DHAT) which are potent dopaminergic agonists we have calculated the conformational energies of 2-aminotetralin and its N,N-dipropyl derivative using the QCFF/Pi and PCILO methods. Molecular electrostatic potential (MEP) maps based on ab initio (STO-3G) wave functions were computed for both dihydroxytetralins. Root-mean-square (rms) deviations from steric congruence between the enantiomeric 5,6- and 6,7-DHAT based either on atomic centers or on the minima in MEP near the putative points of attachment to the receptor are small, but may nevertheless be sufficient to cause differences in activity on subtypes of the dopamine receptor. N,N-dipropyl substitution influences the conformational energies of the skeleton and the preferences in the orientation of the propyl groups in the isomeric DHAT may be important for the interaction with the receptor. The HOMO energies of the isomeric HAT and DHAT do not correlate with their potencies.     

AIDS病毒与CD^＋4靶细胞检测方法的研究

本文对ＡＩＤＳ病毒原及其靶细胞检测方法的研究进展了较系统的评述。深入分析了ｇｐ１２０，ＣＤ４受体分子与小肽的相互作用。并给出了抗ＡＩＤＳ病毒药物分析 方法的最新研究方向。     

Fluorescence detection of single-nucleotide polymorphisms with two simple and low cost methods: a double-DNA-probe method and a bulge form method

Two 10-mer DNA probes, or one 20-mer DNA probe, respectively, hybridize with a 21-mer target DNA to form a vacancy or bulge opposite the target nucleotide. The former double-DNA-probe method and the latter bulge form method are applicable to the detection of single-nucleotide polymorphisms (SNPs). A small fluorescent dye enters into the vacancy or bulge and binds with a target nucleotide via a hydrogen bonding interaction, which causes fluorescence quenching. The interaction between fluorescent dye and the target nucleotide is confirmed by measuring the melting temperature and fluorescence spectra. The fluorescent dye, ADMND (2-amino-5,7-dimethyl-1,8-naphthyridine), is found to selectively bind with C over A or G. The methods proposed here are economic, convenient, and effective for the fluorescence detection of SNPs. Finally, the double-DNA-probe method and bulge form method are successfully applied to the detection of C/G and C/A mutations in the estrogen receptor 2 gene and progesterone receptor gene using ADMND.     

A Fluorescent 1,3‐Diaminonaphthalimide Conjugate of Calix[4]arene for Sensitive and Selective Detection of Trinitrophenol: Spectroscopy,Microscopy, and Computational Studies,and Its Applicability using Cellulose Strips

A new fluorescent 1,3‐diaminonaphthalimide conjugate of calix[4]arene receptor ( R ) was synthesized and characterized. The receptor displays good selectivity towards trinitrophenol (TNP) over other explosive aromatic‐ and aliphatic‐nitro compounds by exhibiting changes in its fluorescence emission. Receptor‐coated cellulose paper strips are equally effective in terms of their selective detection of TNP over other aromatic‐ and aliphatic‐nitro compounds. When used in solution or on cellulose paper strips, R can detect up to submicromolar concentration of TNP by exhibiting changes in its fluorescence emission and in its supramolecular structure upon interaction. Interestingly, the microscopy features of R , TNP, and { R +TNP} are quite distinct, indicating the interactions present between R and TNP, as studied by using AFM and TEM. Computationally modeled complexes of receptor with TNP and TNT show enormous difference in their interaction energies in the favor of TNP by showing the host–guest interaction of cation ??? anion type in the presence of TNP but not TNT. This is because the receptor adopts an “arms‐open”‐type structure in the case of the TNP complex, whereas it adopts an “arms‐closed”‐type structure in the presence of TNT. Both the experimental and the computational studies reveal that the receptor selectively binds to TNP over TNT. Thus, R ‐coated Whatman No.1 filter paper strips provide easy, rapid, and economical detection of trace amounts of TNP both by visual and spectral measurement.     

Design,Synthesis, and In Vivo and In Silico Evaluation of Coumarin Derivatives with Potential Antidepressant Effects

In this study, a series of coumarin derivatives were designed and synthesized, their structures were characterized using nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS) testing methods. In the pharmacological experiment, two behavior-monitoring methods, the forced swim test (FST) and the tail suspension test (TST), were used to determine the antidepressant activity of coumarin derivatives. Compounds that showed potential activity were analyzed for their effects on 5-hydroxytryptamine (5-HT) levels in the brains of mice. Molecular docking experiments to simulate the possible interaction of these compounds with the 5-HT_1A receptor was also be predicted. The results of the pharmacological experiments showed that most coumarin derivatives exhibited significant antidepressant activity. Among these compounds, 7-(2-(4-(4-fluorobenzyl)piperazin-1-yl)-2-oxoethoxy)-2H-chromen-2-one (6i) showed the highest antidepressant activity. The results of the measurement of 5-HT levels in the brains of mice indicate that the antidepressant activity of coumarin derivatives may be mediated by elevated 5-HT levels. The results of molecular docking demonstrated that compound 6i had a significant interaction with amino acids around the active site of the 5-HT_1A receptor in the homology model. The physicochemical and pharmacokinetic properties of the target compounds were also predicted using Discovery Studio (DS) 2020 and Chemdraw 14.0.     

Time Window Expansion for HDX Analysis of an Intrinsically Disordered Protein

Application of typical HDX methods to examine intrinsically disordered proteins (IDP), proteins that are natively unstructured and highly dynamic at physiological pH, is limited because of the rapid exchange of unprotected amide hydrogens with solvent. The exchange rates of these fast exchanging amides are usually faster than the shortest time scale (10 s) employed in typical automated HDX-MS experiments. Considering the functional importance of IDPs and their association with many diseases, it is valuable to develop methods that allow the study of solution dynamics of these proteins as well as the ability to probe the interaction of IDPs with their wide range of binding partners. Here, we report the application of time window expansion to the millisecond range by altering the on-exchange pH of the HDX experiment to study a well-characterized IDP; the activation domain of the nuclear receptor coactivator, peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α). This method enabled mapping the regions of PGC-1α that are stabilized upon binding the ligand binding domain (LBD) of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ). We further demonstrate the method’s applicability to other binding partners of the IDP PGC-1α and pave the way for characterizing many other biologically important ID proteins.