抑制性谷氨酸门控氯离子通道的研究进展

作为半胱氨酸环配体门控离子通道中的一员,抑制性谷氨酸门控氯离子通道（IGIucl）的亚基及其装配具有多样性,从而导致其药理性质的不同。通道对某种化合物的选择性结合与通道中存在的一些关键位点的氨基酸残基有关。通道mRNA的转录后修饰作用是通道亚型及其功能多样化的原因。有关通道门控及离子选择机制的研究为新药及杀虫剂的开发和筛选奠定了基础。从药理性质、通道中影响药物结合特性的残基位点、通道基因的转录后修饰作用以及配体门控离子通道的门控机制等方面综述了IGluCl通道的研究情况。     

风疹病毒E1蛋白与受体结合特定结合域的预测

目的同源模建E1蛋白及其受体髓鞘少突胶质细胞糖蛋白(myelin oligodendrocyte glycoprotein,MOG)的三维结构,应用分子对接的方法预测E1蛋白与其受体MOG的候选结合氨基酸残基。方法采用MODELLER程序预测E1蛋白及其受体MOG的三维结构,并应用CASTp server进行活性口袋的预测;采用ProtScale进行疏水性分析,应用基于隐马尔可夫模型(HMM)算法的SMART程序搜索蛋白序列的motif;采用PyMOL-APBS软件设计E1蛋白及其受体MOG分子的腔介质结构,分析其表观静电势,应用PLATINUM程序进行分子对接,寻找其结合位点。结果 E1蛋白由3个结构域组成,其中D1、D3处于结构的底部,形成一个大的口袋,C-末端与D2的一侧形成另一个大的口袋,其余口袋主要集中在D2上半部的融合面中;MOG的结构模型为8个反平行的β折叠组成的一个β折叠桶,预测结构的主链构象的所有氨基酸均处于允许区。在MOG N-末端1~17位的氨基酸残基形成一个motif(low complexity region),46~127位的氨基酸残基形成了一个motif V型免疫球蛋白样结构域(Immunoglobulin V-Type,IGv);low complexity region段氨基酸残基表现为强疏水性。MOG N-末端的5个残基基序及ARG101~GLU107构成的β转角共同形成一个突起的结构,插入到E1蛋白的活性口袋中,与口袋中的ALA86、TYR90、TYR101、PHE102、ASN103、GLY105、SER107、TYR109、ALA122、PHE123、HIS125、SER126相互结合。结论应用计算机模拟技术预测了E1蛋白与其受体MOG结合的特定结合域,为今后进一步研究其相互作用奠定了基础。     

GABA受体小分子调节剂合成

γ-氨基丁酸(γ-aminobutyric acid,GABA)是哺乳动物和昆虫中枢神经系统中重要的抑制性神经递质。20世纪70年代末发现GABAA受体是重要医药作用靶标,也是农药杀虫剂的作用靶标。GABAA受体上至少存在4种互相变构体的结合位点,与这些结合位点结合的不同化合物,对氯离子通道的作用机制不同,表现出不同的生物活性。具有杀虫活性的化合物有氟虫腈、林丹、狄氏剂和阿维菌素等,具有医用生物活性的化合物有用于治疗抑郁症的巴比妥、氟硝西泮和氟马西尼以及安定类镇静剂和印防己毒素等抗痉挛剂。分类概述了部分GABA受体小分子调节剂的制备方法与生物活性及其合成路线的研究进展,并对未来开发GABA受体调节剂进行了展望。     

基于化学修饰法探讨脂肪酶对手性伯醇的识别机理

洋葱假单胞菌脂肪酶（PcL）催化多种手性伯醇酯的不对称水解反应显示其对结构中含有额外的非酯键氧原子的手性伯醇酯的对映体选择性较高,而对不含额外氧原子的选择性差。分别用多种氨基酸残基特异性的修饰剂修饰 PcL,结果发现经 N-乙酰咪唑（NAI）修饰酪氨酸残基（Tyr）后 PcL 对含额外非酯键氧原子的手性伯醇酯对映体选择性显著降低,而对不含额外氧的伯醇酯选择性几乎不受影响。蛋白质谱证实产生主要影响的是位于 PcL 活性口袋内的 Tyr29 残基,手性伯醇酯能否与 Tyr29 形成额外氢键决定了 PcL对其选择性。分子动力学模拟表明,Tyr29被修饰的 PcL 不能与底物形成氢键,因此选择性明显下降。这一发现成功揭示了脂肪酶对手性伯醇对映体选择性的分子识别机理。     

新烟碱类杀虫剂选择作用的分子机理

新烟碱类杀虫剂的选择作用可以从昆虫和脊椎动物烟碱型乙酰胆碱受体（nAChR）的特点、新烟碱类杀虫剂同nAChR天然激动剂乙酰胆碱（acetylcholine，ACh）的分子特点以及激动剂和受体之间互作的分子机制等方面加以说明。激动剂的分子特点研究表明，新烟碱类杀虫剂和ACh药效基团在静电性上分别显示负电性和正电性。用昆虫α亚基和脊椎动物β亚基组成的杂合受体同激动剂相互作用的研究，主要集中在受体亚基上不同氨基酸残基与不同激动剂结合电生理效应的特点上。研究结果发现，ACh结合部位D环上的碱性氨基酸对新烟碱类杀虫剂选择性的作用尤其明显，同时C环上YXCC模序也引起了大家的注意，而吡虫啉结合部位的芳香氨基酸残基有可能在稳定激动剂四氢咪唑环部分上起作用。乙酰胆碱结合蛋白的晶体结构帮助人们进一步认识了D环上碱性氨基酸残基在新烟碱类选择机制上的作用。     

鲫鱼GABAARβ_3亚基生物信息学分析与同源建模

A型γ-氨基丁酸(aminobutyric acid,GABA)是一类配体门控离子通道型受体,亦为脊椎动物和非脊椎动物的中枢神经系统内最主要的抑制性神经递质GABA的受体,其离子通道上存在氟虫腈等杀虫剂的作用靶点,是医药和农药工作者研究的重点。通过RACE-PCR技术成功获取新基因鲫鱼GABAARβ_3的全长(GenBank登录号:KC964110)。序列分析显示该基因核苷酸序列共2 767 bp,含有1个由502个氨基酸残基组成的开放阅读框,编码蛋白分子量约为56 KD。报道了该基因的生物信息学分析和三维结构模拟及其与氟虫腈作用情况,BLAST结果表明,氨基酸序列与其他已知GABAARβ_3基因家族成员间序列相似性介于76%~89%之间,并与其他亚族蛋白基因存在很高的同源性。以线虫体内对阿维菌素敏感的谷氨酸门控氯离子通道受体蛋白的α亚基(PDB ID:3RHW)作为模板,用DS(Discovery Studio)模拟鲫鱼GABAAβ_3亚基的同源五聚体结构,优化结构模型,与农药配体分子做分子对接,计算作用模式和结合能力。研究鱼类GABAAR亚基与农药分子的作用。     

作用于烟碱乙酰胆碱受体的新颖杀虫剂Flupyrimin

<正>烟碱乙酰胆碱受体(nAChR)是配体门控氯离子通道,快速地传递神经的兴奋性,是杀虫剂的一个重要作用靶标。烟碱型杀虫剂和相关相似配体能够与软体动物烟碱乙酰胆碱结合蛋白(AChBP)结合,此蛋白是烟碱乙酰胆碱受体胞外配体结合域的适合替代物,可用于用高分辨率的化学/结构生物学方法来弄明白药物结合域的识别特性。随后用与烟碱配体结合的位点的三维结构成功设计出具有独特药效团的新颖杀虫化合物。     

人白细胞介素-29的生物信息学分析

目的利用生物信息学技术对人白细胞介素-29(Human nterleukin-29,IL-29)进行分析,为定点突变hIL-29,以提高其生物学活性奠定理论基础。方法利用生物信息学技术分析克隆得到的hIL-29基因,预测hIL-29基因编码蛋白的理化性质、结构、功能及可能影响其生物学活性的关键氨基酸位点;预测其三维结构,并与IFNλ3的晶体结构进行比对;对检索到的9个物种的IL-29基因同源序列进行比对,并构建系统进化树。结果 hIL-29基因编码蛋白含200个氨基酸残基,其N-末端19个氨基酸为信号肽,成熟肽的相对分子质量为20 018,理论等电点为9.08,肽链中含一个由胞内向胞外的跨膜结构域;hIL-29的空间构象由6个α螺旋(A～F)和无规则卷曲组成,螺旋A、B和F可能是hIL-29与特异性受体结合而发挥生物学效应的活性部位,A、F螺旋中有4个氨基酸残基可能是影响其生物学活性的关键氨基酸位点;系统进化分析显示,hIL-29与狗、猫、大熊猫、马、野猪、黑猩猩、长臂猿的IL-29具有较高的同源性,处于同一个大分枝,而人、黑猩猩、长臂猿的IL-29处于同一个小分枝,在系统进化树中的距离最近。结论关键位点氨基酸的差异可能对hIL-29的生物学活性影响较大,可作为对hIL-29进行分子改造的突变位点。本研究为后续进行hIL-29的定向改构及其构效关系等的深入研究奠定了理论基础。     

分子模拟和光谱法研究华法林与人血清白蛋白的结合机制

华法林(WF)是临床常用口服抗凝药物,有关它与人血清白蛋白(HSA)结合位点处的热点残基、作用力类型以及对HSA构象影响报道较少。通过在模拟人体生理条件下,利用分子模拟、内源荧光光谱、三维荧光光谱和同步荧光光谱,研究了WF与HSA之间作用机理。WF能使HSA构象发生改变,导致Tyr残基微环境极性降低、Trp残基周围亲水性增强。WF能有效猝灭HSA内源荧光,猝灭机制属静态猝灭,通过Lineweaver-Burk方程求得两者间结合常数(K_A)为3.55×10⁵L/mol(310 K)、结合位点数(n)约为1。Van′t Hoff定律计算得到的热力学参数(ΔH=169.56 kJ/mol和ΔS=653.23 J/(mol·K)),说明WF与HSA之间的主要作用力为疏水作用力。根据F9rster′s能量转移定律确定,WF与HSA结合距离为2.87 nm。WF通过氢键和疏水作用力与HSA的亚域ⅡA中氨基酸残基进行作用,WF周围4.0?区域还存在ⅠB、ⅡB、ⅢA亚结构域的30个氨基酸残基。     

基于奥司他韦衍生物的抗流感病毒H7N9的分子对接

研究奥司他韦类衍生物对新型禽流感病毒H7N9的抑制作用,本人选取32个奥司他韦类的合成化合物为配体,从PDB(Protein Data Bank)数据库中下载了H7N9的受体蛋白,因H7N9具有R292K-N9和R294K-N9两个突变型病毒,所以下载了包括4MWQ(N9-R294)、2QWE(R292K-N9)和4MWW(R294K-N9)三个神经氨酸酶的受体蛋白,将32个配体分子与3个受体蛋白分别进行分子对接,分子对接软件采用SYBYL-2.0中Surflex-Dock软件。结果发现,这32个奥司他韦类衍生物通过与4MWQ、2QWE、4MWW受体蛋白活性位点主要氨基酸残基主要产生氢键结合力、疏水作用和静电作用力而产生抑制作用,为新的神经氨酸酶抑制剂的研发设计提供了有用的结构信息,对流感病毒的新药研发具有积极的意义。     

Identifying a putative common binding site shared by substance P receptor and an anti-substance P monoclonal antibody

Substance P G-protein coupled receptor and the antigen recognitionsite of a monoclonal antibody raised against substance P sharea stretch of five contiguous identical amino acids. This observationprompted us to build an atomic model of both the receptor andthe antibody and to analyse their common features. In particular,we report here that a pocket of similar size and compositionis present in both proteins, strongly suggesting a similarityin the mode of binding of both macromolecules to substance P.From the analysis of our models, the available data on the modeof binding of the antibody to substance P and recent data onsubstance P receptor mutants, we concluded that the pocket isvery likely to be involved in binding of the C-terminal 'messagesequence' of the tachykinin. This allowed us to suggest specificsite-directed mutants of the receptor which should shed somelight on the mechanism of peptide recognition by G-protein coupledreceptors.     

Decoupled Roles for the Atypical,Bifurcated Binding Pocket of the ybfF Hydrolase

Serine hydrolases have diverse intracellular substrates, biological functions, and structural plasticity, and are thus important for biocatalyst design. Amongst serine hydrolases, the recently described ybfF enzyme family are promising novel biocatalysts with an unusual bifurcated substrate‐binding cleft and the ability to recognize commercially relevant substrates. We characterized in detail the substrate selectivity of a novel ybfF enzyme from Vibrio cholerae (Vc‐ybfF) by using a 21‐member library of fluorogenic ester substrates. We assigned the roles of the two substrate‐binding clefts in controlling the substrate selectivity and folded stability of Vc‐ybfF by comprehensive substitution analysis. The overall substrate preference of Vc‐ybfF was for short polar chains, but it retained significant activity with a range of cyclic and extended esters. This broad substrate specificity combined with the substitutional analysis demonstrates that the larger binding cleft controls the substrate specificity of Vc‐ybfF. Key selectivity residues (Tyr116, Arg120, Tyr209) are also located at the larger binding pocket and control the substrate specificity profile. In the structure of ybfF the narrower binding cleft contains water molecules prepositioned for hydrolysis, but based on substitution this cleft showed only minimal contribution to catalysis. Instead, the residues surrounding the narrow binding cleft and at the entrance to the binding pocket contributed significantly to the folded stability of Vc‐ybfF. The relative contributions of each cleft of the binding pocket to the catalytic activity and folded stability of Vc‐ybfF provide a valuable map for designing future biocatalysts based on the ybfF scaffold.     

Inhibition of Bacterial Dihydrofolate Reductase by 6‐Alkyl‐2,4‐diaminopyrimidines

(±)‐6‐Alkyl‐2,4‐diaminopyrimidine‐based inhibitors of bacterial dihydrofolate reductase (DHFR) have been prepared and evaluated for biological potency against Bacillus anthracis and Staphylococcus aureus. Biological studies revealed attenuated activity relative to earlier structures lacking substitution at C6 of the diaminopyrimidine moiety, though minimum inhibitory concentration (MIC) values are in the 0.125–8 μg mL^?1 range for both organisms. This effect was rationalized from three‐ dimensional X‐ray structure studies that indicate the presence of a side pocket containing two water molecules adjacent to the main binding pocket. Because of the hydrophobic nature of the substitutions at C6, the main interactions are with protein residues Leu 20 and Leu 28. These interactions lead to a minor conformational change in the protein, which opens the pocket containing these water molecules such that it becomes continuous with the main binding pocket. These water molecules are reported to play a critical role in the catalytic reaction, highlighting a new area for inhibitor expansion within the limited architectural variation at the catalytic site of bacterial DHFR.     

Structure-based design of novel pyrimido[4,5-c]pyridazine derivatives as dihydropteroate synthase inhibitors with increased affinity

Dihydropteroate synthase (DHPS) is the validated drug target for sulfonamide antimicrobial therapy. However, due to widespread drug resistance and poor tolerance, the use of sulfonamide antibiotics is now limited. The pterin binding pocket in DHPS is highly conserved and is distinct from the sulfonamide binding site. It therefore represents an attractive alternative target for the design of novel antibacterial agents. We previously carried out the structural characterization of a known pyridazine inhibitor in the Bacillus anthracis DHPS pterin site and identified a number of unfavorable interactions that appear to compromise binding. With this structural information, a series of 4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazines were designed to improve binding affinity. Most importantly, the N-methyl ring substitution was removed to improve binding within the pterin pocket, and the length of the side chain carboxylic acid was optimized to fully engage the pyrophosphate binding site. These inhibitors were synthesized and evaluated by an enzyme activity assay, X-ray crystallography, isothermal calorimetry, and surface plasmon resonance to obtain a comprehensive understanding of the binding interactions from structural, kinetic, and thermodynamic perspectives. This study clearly demonstrates that compounds lacking the N-methyl substitution exhibit increased inhibition of DHPS, but the beneficial effects of optimizing the side chain length are less apparent.     

Glycine 85 of the trp-repressor of E.coli is important in forming the hydrophobic tryptophan binding pocket: experimental and computational approaches

Experimental and computational analyses were performed on thecorepressor (L-tryptophan) binding site of the trp-repressorof Escherichia coli to investigate the ligandprotein interactions.Gly 85, one of the residues forming the hydrophobic pocket ofthe binding site, was systematically replaced with Ala, Val,Leu and Trp by cassette mutagenesis. Biochemical characterizationshowed that all these mutations caused significant decreasesin tryptophan binding activity. Free energy perturbation calculationswere performed for the mutants and were consistent with theexperimental results. The lack of a side chain at position 85was concluded to be essential for binding the corepressor; thestructure of the binding pocket was suggested to be tight inthe vicinity of Gly85.     

Architectural Repertoire of Ligand‐Binding Pockets on Protein Surfaces

Knowledge of the three‐dimensional structure of ligand binding sites in proteins provides valuable information for computer‐assisted drug design. We present a method for the automated extraction and classification of ligand binding site topologies, in which protein surface cavities are represented as branched frameworks. The procedure employs a growing neural gas approach for pocket topology assignment and pocket framework generation. We assessed the structural diversity of 623 known ligand binding site topologies based on framework cluster analysis. At a resolution of 5 Å only 23 structurally distinct topology groups were formed; this suggests an overall limited structural diversity of ligand‐accommodating protein cavities. Higher resolution allowed for identification of protein‐family specific pocket features. Pocket frameworks highlight potentially preferred modes of ligand–receptor interactions and will help facilitate the identification of druggable subpockets suitable for ligand affinity and selectivity optimization.     

Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions

A congeneric series of four bis-benzamidine inhibitors sharing a dianhydrosugar isosorbide scaffold in common has been studied by crystal structure analysis and enzyme kinetics with respect to their binding to trypsin and factor Xa. Within the series, aromatic interactions are an important determinant for selectivity discrimination among both serine proteases. To study the selectivity-determining features in detail, we used trypsin mutants in which the original binding site is gradually substituted to finally resemble the factor Xa binding pocket. The influence of these mutations has been analyzed on the binding of the closely related inhibitors. We present the crystal structures of the inhibitor complexes obtained by co-crystallizing an "intermediate" trypsin mutant. They could be determined to a resolution of up to 1.2 A, and we measured the inhibitory activity (K(i)) of each ligand against factor Xa, trypsin, and the various mutants. From these data we were able to derive a detailed structure-activity relationship which demonstrates the importance of aromatic interactions in protein-ligand recognition and their role in modulating enzyme selectivity. Pronounced preference is experienced to accommodate the benzamidine anchor with meta topology in the S(1) specificity pocket. One ligand possessing only para topology deviates strongly from the other members of the series and adopts a distinct binding mode addressing the S(1)' site instead of the distal S(3)/S(4) binding pocket.     

Synthesis and characterization of cytidine derivatives that inhibit the kinase IspE of the non-mevalonate pathway for isoprenoid biosynthesis

The enzymes of the non-mevalonate pathway for isoprenoid biosynthesis are attractive targets for the development of novel drugs against malaria and tuberculosis. This pathway is used exclusively by the corresponding pathogens, but not by humans. A series of water-soluble, cytidine-based inhibitors that were originally designed for the fourth enzyme in the pathway, IspD, were shown to inhibit the subsequent enzyme, the kinase IspE (from Escherichia coli). The binding mode of the inhibitors was verified by co-crystal structure analysis, using Aquifex aeolicus IspE. The crystal structures represent the first reported example of a co-crystal structure of IspE with a synthetic ligand and confirmed that ligand binding affinity originates mainly from the interactions of the nucleobase moiety in the cytidine binding pocket of the enzyme. In contrast, the appended benzimidazole moieties of the ligands adopt various orientations in the active site and establish only poor intermolecular contacts with the protein. Defined binding sites for sulfate ions and glycerol molecules, components in the crystallization buffer, near the well-conserved ATP-binding Gly-rich loop of IspE were observed. The crystal structures of A. aeolicus IspE nicely complement the one from E. coli IspE for use in structure-based design, namely by providing invaluable structural information for the design of inhibitors targeting IspE from Mycobacterium tuberculosis and Plasmodium falciparum. Similar to the enzymes from these pathogens, A. aeolicus IspE directs the OH group of a tyrosine residue into a pocket in the active site. In the E. coli enzyme, on the other hand, this pocket is lined by phenylalanine and has a more pronounced hydrophobic character.     

Fragment Screening of RORγt Using Cocktail Crystallography: Identification of Simultaneous Binding of Multiple Fragments

The retinoic‐acid‐related orphan receptor γ t (RORγt), as a master regulator of Th17 cell pathology, has become an attractive target for small‐molecule drug discovery for the treatment of Th17‐cell‐related autoimmune diseases. A crystallographic fragment screening was carried out for RORγt using the ligand binding domain. An overall hit rate of 5.5 % was obtained by screening 384 compounds in 96 cocktails. Five distinct hotspots were identified, and four regions of anchoring polar interactions were observed. In addition, significant induced fit was found for the binding of several fragments. Strikingly, a simultaneous binding of three fragments was revealed which presents interesting features including π–π stacking, multiple hydrogen bonds to the protein, and significant induced fit. Overall, the results offer a complete mapping of the ligand binding pocket and provide valuable inspiration in structure‐based design for RORγt lead generation and optimization. The crystallographic screening also resulted in fragment hits that bind at the surface away from the ligand binding pocket. This surface site is near the plausible dimer interface by analogy with other nuclear receptor systems, which can provide initial hints to explore alternative ways to modulate RORγt through protein–protein interactions.