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.     

分子动力学模拟残基突变对芳香烃受体配体结合区的影响

芳香烃受体(Aryl hydrocarbon receptor,AhR)属于配体依赖性的转录因子蛋白。本文通过对AhR配体结合区域(Ligand binding domain,LBD)的结构功能及物种特异性分析,发现在其结合腔口有一些关键残基可能起到"门控"作用,进一步将野生型(WT)和3个突变模型(Phe289Ala、Tyr316Ala、Ile319Ala)进行分子动力学模拟,从蛋白稳定性、蛋白结构变化、蛋白结合腔变化及蛋白和配体结合能力4个方面分析3个残基的门控作用。研究发现,Phe289、Tyr316、Ile319氨基酸残基通过形成疏水作用为AhR LBD起到"门控"作用;而将这些氨基酸分别突变后,其蛋白稳定性降低,整体运动性增加,配体亲和力减弱,其中Tyr316、Ile319对腔内体积影响较大,Phe289使腔内环境稳定性降低。本研究可为基于芳香烃受体的药物设计提供相关理论指导。     

家蝇与大鼠GABA受体抑制剂的药效团模型及其3D-QSAR研究

采用DISCOtech方法,用7个大鼠γ-氨基丁酸(GABA)A受体抑制剂和11个家蝇GABAA受体抑制剂分别建立了其药效团模型;用CoMFA方法建立了22个大鼠GABAA受体抑制剂和29个家蝇GABAA受体抑制剂的3D-QSAR模型,模型的交叉验证相关系数分别为0.526和0.679,验证了药效团模型的合理性,为设计更高活性和更高选择性的化合物提供了参考     

水杨醛缩乙二胺双席夫碱及其Ni(Ⅱ)配合物的电子结构和非线性光学性质的INDO/CI研究

采用量子化学ab initio HF方法, 在6.31G(d)基组水平上, 对水杨醛缩乙二胺类双席夫碱及其Ni配合物体系进行几何构型优化. 以优化的稳定构型为基础, 利用INDO/CI方法计算体系的电子光谱, 同时用ZINDO.SOS方法给出该系列分子二阶(βijk)和三阶(γijkl)非线性光学系数. 计算结果表明, 共轭性增强有助于增大分子的二阶及三阶非线性光学系数, 双席夫碱化合物1的β和γ值分别为35.54×10-30和-1.20×10-34 esu, 而共轭桥为萘环的化合物4的β和γ值分别为54.22×10-30和2.00×10-34 esu, 端部引入苯并环的化合物5的β和γ值增加幅度更大. 对应的金属Ni(Ⅱ)配合物的β值增加较明显, 为配体的1.7~10.8倍, γ值也有不同程度的增加.     

二维电荷转移型水杨醛缩乙二胺类双席夫碱及其Zn(Ⅱ)配合物的电子光谱及非线性光学性质的DFT理论研究

用密度泛函理论(DFT)B₃LYP方法,在6-31G(d)基组水平上优化水杨醛缩乙二胺类双席夫碱化合物及其Zn()配合物的几何结构.在稳定构型基础上,引入外电场,运用有限场(FF)方法,计算标题化合物体系的非线性光学(NLO)系数,并与其独立的对称分子片结构进行比较.同时用含时密度泛函理论(TD-DFT)计算各体系的电子光谱.结果表明,两个单席夫碱分子片结合为双席夫碱时,二阶及三阶NLO系数明显增大,且γ比β显著.双键桥连Zn配合物1a的β,γ值均小于相应配体,而单键桥连Zn配合物2a的β和γ值大于相应配体,说明金属Zn在完全共轭和局域共轭体系中所起的作用不同.     

荧光标记法研究鱼类GABA受体与Ro7-1986/1和Fipronil的相互作用

以苯二氮卓类化合物Ro7-1986/1和氟虫腈(Fipronil)分别与异硫氰酸荧光素(FITC)反应合成了2种γ-氨基丁酸(GABA)受体的配体荧光复合物,即FITC-Ro7-1986/1(简称FITC-Ro7)和FITC-Fipronil;利用傅里叶变换红外光谱(FTIR)和核磁共振氢谱(1H NMR)等手段对其结构进行了表征.以2种荧光配体为探针,采用荧光标记法研究了Ro7-1986/1和Fipronil与鳙鱼(Hypophthalmichthys nobilis)脑内GABA受体的相互作用,得到了亲和常数Kd和最大结合量[RT].同时考察了GABA对Ro7-1986/1与受体相互作用的影响.研究结果表明,Ro7-1986/1和Fipronil与受体的亲和常数Kd分别为(67±5)nmol/L和(346±6)nmol/L;最大结合量[RT]分别为(13.8±1.8)pmol/mg protein和(40.6±3.5)pmol/mg protein;GABA促进了Ro7-1986/1与受体的结合,进一步的研究结果表明,鱼类与哺乳动物脑中GABA受体结构相似;相对于哺乳动物,苯吡唑类杀虫剂Fipronil对鱼类GABA的亲和力较高.     

4-苄基哌啶类拮抗剂选择性识别hCCR3的分子模拟

以牛视网膜紫质X射线衍射晶体结构为模板, 参考定位突变实验数据, 采用配体支持同源模建(Ligand-supported homology modeling)方法构建了拮抗剂键合(Antagonist-bound)的人类趋化因子受体hCCR3和hCCR1的三维结构模型. 将一系列1,4-二取代哌啶类拮抗剂分别对接进优化后的hCCR3和hCCR1模型中, 以配体在hCCR3中的结合自由能理论值对-lgIC₅₀值进行线性回归, 确定性系数r²为0.94. 分析对接结果发现, 配体主要通过疏水芳香作用与hCCR3结合, 而4-苄基哌啶类拮抗剂对hCCR3产生选择性的主要原因在于配体的哌啶环与hCCR3中Tyr255(TM7)的苯酚侧链产生面对面的范德华作用, 而且hCCR3中处于结合口袋的EL2区的疏水性也为拮抗剂对hCCR3的选择性做出了贡献.     

胰高血糖素样肽-1受体胞外区域突变体复合物的动力学研究

采用分子动力学模拟方法研究了胰高血糖素样肽-1(GLP-1)与GLP-1受体(GLP-1R)胞外区域的相互作用.结果表明,配体的结合导致受体的构象发生改变,Loop2区域的氨基酸Pro90和Trp91以及C末端的Glu128向配体移动.根据保守位点突变受体(P73A,V81L,Y88A,P90A和W91A)后所得多肽模拟数据,发现Loop2区域在突变体中的结构和柔性均发生了明显变化,Trp91和Tyr88的突变将导致配体亲和力丧失.研究结果证明,P73A突变型受体和野生型受体分别与配体相互作用后,二者数值差别不大,因此Pro73不是关键残基;V81L突变体则会导致配体亲和力的丧失.该结果为GLP-1药物设计提供了重要理论依据.     

马来酰胺类糖原合成酶激酶-3β抑制剂的分子对接和三维定量构效关系

通过分子对接和三维定量构效关系(3D-QSAR)两种方法来确定两类马来酰胺类的糖原合成酶激酶-3β(GSK-3β)抑制剂的结合方式. 首先, 用分子对接确定抑制剂与GSK-3β结合模式及其相互作用; 然后用比较分子力场分析法(CoMFA)与比较分子相似性指数分析法(CoMSIA)对48个化合物做三维定量构效关系的分析. 两种方法得出的交互验证回归系数分别为0.669(CoMFA)和0.683(CoMSIA), 证明该模型具有很好的统计相关性, 同时也说明该模型具有较高的预测能力.根据该模型提供的信息, 设计出9个预测活性较好的分子.     

GC-MS方法诊断新生儿苯丙酮尿症

用甲醇提取血样中的苯丙氨酸(Phe)、酪氨酸(Tyr),提取液离心去蛋白质,用正丁醇将其中的苯丙氨酸和酪氨酸丁酯比,再用三氟醋酸酐酰化后进行GC-MS分析,测定Phe,Tyr特征离子峰面积,用外标法计算出Phe和Tyr的摩尔浓度,根据Phe和Tyr摩尔浓度比值来诊断新生儿苯丙酮尿症(PKU)。     

Molecular modeling and mutagenesis reveals a tetradentate binding site for Zn2+ in GABA(A) alphabeta receptors and provides a structural basis for the modulating effect of the gamma subunit

Gamma-aminobutyric acid type A receptors (GABA(A)-R) containing alpha1beta2gamma2 subunits are weakly inhibited by Zn2+, whereas receptors containing only the alpha1beta2 subunits are strongly inhibited. We built homology models of the ion pores of alpha1beta2 and alpha1beta2gamma2 GABA(A)-R using coordinates of the nicotinic acetylcholine receptor as a template. Threading the GABA(A)-R beta2 sequence onto this template placed the 17' histidine and the 20' glutamate residues at adjacent locations in the mouth of the pore, such that a nearly ideal tetradentate site for Zn2+ was formed from two histidine and two glutamate residues between adjacent beta subunits in the alpha1beta2 GABA(A)-R. Following optimization with CHARMM, the distance between the alpha-carbons of the adjacent histidine residues was approximately 9.2 A, close to the ideal distance for a Zn2+ binding site. Loss of inhibition by Zn2+ in alpha1beta2gamma2 GABA(A)-R can be explained by the geometry of these residues in the arrangement alpha1beta2gamma2alpha1beta2, in which the nearest C-alpha-C-alpha distance between the histidine residues is 15.5 A, too far apart for an energetically optimal Zn2+ binding site. We then mutated the gamma subunit at the 17' and/or 20' positions. Zn2+ inhibition was not restored in alpha1beta2gamma2 (I282H) receptors. A novel finding is that the modeling shows the native 20' lysine in gamma2 can compete with Zn2+ for binding to the inserted 17' histidine. Sensitivity to Zn2+ was restored in the double mutant receptor, alpha1beta2gamma2 (I282H; K285E), in which the competition with lysine was removed and a more favorable Zn2+ binding site was formed.     

The Molecular Dynamic Simulation of Zolpidem Interaction with Gamma Aminobutyric Acid Type A Receptor

Our goal was to generate the extracellular domain of gamma‐aminobutyric acid type A receptor (GABA_A receptor) by comparative modeling and to study the interaction of zolpidem with the GABA_A receptor. The modeling strategy was verified to provide reasonable 3‐dimensional coordinates. These coordinates helped to combine all the subunits well. The benzodiazepine (BZ) binding site was located in a binding pocket between the α₁ and γ₂ subunits of the GABA_A receptor. Zolpidem was selected to dock into the binding site. In our study, the residues of the binding pocket were suggested to be αHis129, αTyr187, αGly228, αThr234, αTyr237, γMet96, γPhe116, γSer130, γGly143, and γMet169. By the calculation of the docking module, the conformation of zolpidem docking in the BZ binding site was investigated. A hydrogen bond was found at γArg136 when zolpidem's conformation was in rank 2 of the docking score. The contracted binding pocket showed residues at αHis129, αTyr187, αGly228, αTyr237, γPhe116, and γMet169. Zolpidem docking in a contracted binding pocket might generate a hydrogen bond in α His 129.     

Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models

The resistance to dieldrin (RDL) receptor is an insect pentameric ligand-gated ion channel (pLGIC). It is activated by the neurotransmitter γ-aminobutyric acid (GABA) binding to its extracellular domain; hence elucidating the atomistic details of this interaction is important for understanding how the RDL receptor functions. As no high resolution structures are currently available, we built homology models of the extracellular domain of the RDL receptor using different templates, including the widely used acetylcholine binding protein and two pLGICs, the Erwinia Chrysanthemi ligand-gated ion channel (ELIC) and the more recently resolved GluCl. We then docked GABA into the selected three dimensional structures, which we used as starting points for classical molecular dynamics simulations. This allowed us to analyze in detail the behavior of GABA in the binding sites, including the hydrogen bond and cation-π interaction networks it formed, the conformers it visited and the possible role of water molecules in mediating the interactions; we also estimated the binding free energies. The models were all stable and showed common features, including interactions consistent with experimental data and similar to other pLGICs; differences could be attributed to the quality of the models, which increases with increasing sequence identity, and the use of a pLGIC template. We supplemented the molecular dynamics information with metadynamics, a rare event method, by exploring the free energy landscape of GABA binding to the RDL receptor. Overall, we show that the GluCl template provided the best models. GABA forming direct salt-bridges with Arg211 and Glu204, and cation-π interactions with an aromatic cage including Tyr109, Phe206 and Tyr254, represents a favorable binding arrangement, and the interaction with Glu204 can also be mediated by a water molecule.     

Assessment of programs for ligand binding affinity prediction

The prediction of the binding free energy between a ligand and a protein is an important component in the virtual screening and lead optimization of ligands for drug discovery. To determine the quality of current binding free energy estimation programs, we examined FlexX, X-Score, AutoDock, and BLEEP for their performance in binding free energy prediction in various situations including cocrystallized complex structures, cross docking of ligands to their non-cocrystallized receptors, docking of thermally unfolded receptor decoys to their ligands, and complex structures with "randomized" ligand decoys. In no case was there a satisfactory correlation between the experimental and estimated binding free energies over all the datasets tested. Meanwhile, a strong correlation between ligand molecular weight-binding affinity correlation and experimental predicted binding affinity correlation was found. Sometimes the programs also correctly ranked ligands' binding affinities even though native interactions between the ligands and their receptors were essentially lost because of receptor deformation or ligand randomization, and the programs could not decisively discriminate randomized ligand decoys from their native ligands; this suggested that the tested programs miss important components for the accurate capture of specific ligand binding interactions.     

Computer‐aided design of a novel ligand for retinoic acid receptor in cancer chemotherapy

The isotypes of RAR and RXR are retinoic acid and retinoid X acid receptors, respectively, whose ligand‐binding domain contains the ligand‐dependent activation function, with distinct pharmacological targets for retinoids, involved in the treatment of various cancers and skin diseases. Due to the major challenge which cancer treatment and cure still imposes after many decades to the international scientific community, there is actually considerable interest in new ligands with increased bioactivity. We have focused on the retinoid acid receptor, which is considered an interesting target for drug design. In this work, we carried out density functional geometry optimizations and different docking procedures. We performed screening in a large database (hundreds of thousands of molecules which we optimized at the AM1 level) yielding a set of potential bioactive ligands. A new ligand was selected and optimized at the B3LYP/6‐31G* level. A flexible docking program was used to investigate the interactions between the receptor and the new ligand. The result of this work is compared with several crystallographic ligands of RAR. Our theoretically more bioactive new ligand indicates stronger and more hydrogen bonds as well as hydrophobic interactions with the receptor. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Increasing the Efficacy of Seproxetine as an Antidepressant Using Charge–Transfer Complexes

The charge transfer interactions between the seproxetine (SRX) donor and π-electron acceptors [picric acid (PA), dinitrobenzene (DNB), p-nitrobenzoic acid (p-NBA), 2,6-dichloroquinone-4-chloroimide (DCQ), 2,6-dibromoquinone-4-chloroimide (DBQ), and 7,7′,8,8′-tetracyanoquinodi methane (TCNQ)] were studied in a liquid medium, and the solid form was isolated and characterized. The spectrophotometric analysis confirmed that the charge–transfer interactions between the electrons of the donor and acceptors were 1:1 (SRX: π-acceptor). To study the comparative interactions between SRX and the other π-electron acceptors, molecular docking calculations were performed between SRX and the charge transfer (CT) complexes against three receptors (serotonin, dopamine, and TrkB kinase receptor). According to molecular docking, the CT complex [(SRX)(TCNQ)] binds with all three receptors more efficiently than SRX alone, and [(SRX)(TCNQ)]-dopamine (CTcD) has the highest binding energy value. The results of AutoDock Vina revealed that the molecular dynamics simulation of the 100 ns run revealed that both the SRX-dopamine and CTcD complexes had a stable conformation; however, the CTcD complex was more stable. The optimized structure of the CT complexes was obtained using density functional theory (B-3LYP/6-311G++) and was compared.     

Enzyme-based microtiter plate assay for γ-aminobutyric acid: Application to the screening of γ-aminobutyric acid-producing lactic acid bacteria

An enzyme-based microtiter plate assay for γ-aminobutyric acid (GABA) was developed. GABA was quantified using γ-aminobutyrate glutamate aminotransferase and succinic semialdehyde dehydrogenase in the presence of NADP⁺ and -ketoglutarate. The NADPH produced by the series of enzymatic reactions was measured spectrophotometrically at 340 nm. A linear relationship between absorbance and the concentration of GABA was obtained in the ranges from 5.0 × 10⁻⁴ to 1.0 × 10⁻² M. The relative standard deviation for 10 successive measurements was 0.9% at the 10 mM GABA level. This analytical method was applied to the screening of GABA-producing lactic acid bacteria in de Man–Rogosa–Sharpe (MRS) medium. The proposed method enables one to assay 96 samples for an hour without the pre-treatment of samples. The method is by far superior to the traditional HPLC method from the point of view of rapidity and simplicity.     

Stereodivergent synthesis of cyclic γ-aminobutyric acid – GABA analogues

A novel synthetic route towards two series of enantiomerically pure cyclic analogues of 2,3-cis- and 2,3-trans-γ-aminobutyric acid (GABA) was developed. The route is based on the elongation and stereodivergent manipulation of a readily accessible enantiomerically pure γ-substituted α-aminolactone. The five-step route towards the 2,3-cis-substituted GABA analogues was achieved via straightforward carbon chain extension of the lactone using a non-classical Wittig reaction followed by chemoselective reduction and a protecting group switch. The five-step route towards the 2,3-trans-substituted GABA analogues employed elongation of the same aminolactone using a Horner-Wadsworth-Emmons reaction and highly stereoselective intramolecular oxa-Michael addition as the key synthetic manipulations. Altogether this chemistry has allowed the stereodivergent preparation of a novel class of GABA analogues in two diastereomeric series.     

天然产物法卡林二醇与人类GABAA受体相互作用的机制

通过分子动力学模拟、伞形采样模拟、结合自由能计算和分子对接等方法,研究了法卡林二醇在γ-氨基丁酸A型(GABA_A)受体上结合作用的模式和对GABA_A受体动态属性的影响,确定了3个有效结合位点均对此受体产生拮抗作用,为后续研究聚乙炔醇类化合物对GABA_A受体作用及相应药物开发提供了理论依据.