HIV-1跨膜蛋白gp41螺旋结构的原核表达及功能研究

HIV-1跨膜蛋白gp41是HIV-1包膜与靶细胞膜的融合过程中的关键蛋白,是理想的HIV-1融合抑制剂靶点。为开展以gp41为靶点的抑制剂筛选,以HIV-1 B亚型病毒基因为模板,通过PCR、酶切、连接等方法构建得到gp41 5-helix与6-helix重组质粒,转入大肠杆菌BL21（DE3）进行表达,经变性和复性后亲和层析纯化蛋白。经SDS-PAGE鉴定,纯化后蛋白纯度较高。本研究还通过非变性凝胶电泳证明gp41 5-helix与C-多肽衍生物T-20存在相互作用,为下一步药物筛选模型的建立奠定了基础。     

HIV-1 gp41 NC六螺旋的结构与功能研究

AIDS是严重危害人类健康的疾病,而HIV是导致这种疾病的病毒。gp41六螺旋在介导HIV-1病毒与靶细胞间的膜融合过程中起着重要作用。因此,对于gp41结合蛋白的研究有助于深入了解gp41在HIV-1感染整个过程中扮演的角色,解释gp41对靶细胞的调控机制,为寻找新的抗艾滋病药物靶点以及艾滋病抑制剂的设计提供有益的思路。作者的实验室相继发现了一批与gp41六螺旋结构相互作用的蛋白质,进而对HIV-1 gp41六螺旋介导的膜融合过程和HIV-1感染机理有了更深入的了解。     

基于gp41近膜端外部区域中和表位天然构象的人类免疫缺陷病毒1型疫苗的设计

疫苗一直被视为终结人类免疫缺陷病毒1型和2 型(human immunodeficiency virus type 1/2,HIV-1/2)最有力的武器。位于HIV-1 gp41胞外域C末端的近膜端外部区域(membrane-proximal external region, MPER)是一个重要的抗原位点,但糖蛋白41(glycoprotein 41,gp41)在野生型HIV-1的包膜蛋白中并未充分暴露,单独的gp41或MPER多肽无法模拟gp120/gp41包膜蛋白在病毒包膜上的天然状态。本研究以HIV-1 gp41 MPER为抗原进行疫苗设计,以期能诱导产生具有强效中和作用的MPER特异性抗体。通过在gp41的N末端七肽重复域(N-terminal heptad repeat, CHR)和C末端七肽重复域(C-terminal heptad repeat, NHR)引入突变,阻断二者相互作用形成6螺旋(6-helix bundle, 6-HB)构象;使用不同来源的流感病毒HA1亚基替代gp120,以防止机体产生大量针对HA1的抗体,并构建一系列包含不同HA1亚基的HA/gp41-1605嵌合DNA。结果发现,在细胞上表达的嵌合疫苗抗原能更好地展示MPER上的中和表位,但不显示gp41上免疫优势抗原表位。使用构建的HA/gp41嵌合DNA疫苗对新西兰大耳兔进行肌肉内序贯免疫,提示该疫苗策略的确不可诱生高滴度的HA抗体或gp41的loop及6-HB特异性抗体,而能诱生MPER特异性抗体。然而,该抗体对HIV-1不具有中和作用,说明该疫苗策略还有待进一步优化。     

结合分子相似性、药效团和分子对接筛选新的HIV-1蛋白酶抑制剂

结合分子相似性、药效团和分子对接建立兼顾计算效率和预测准确度的HIV-1蛋白酶抑制剂筛选方法。首先通过对现有HIV-1蛋白酶抑制剂分子进行相似性分析,选取代表性的HIV-1蛋白酶抑制剂作为模板分子,构建和优化药效团模型,并从1万个化合物中优先筛选出500个化合物。而后采用分子对接方法进一步考察化合物与HIV-1蛋白酶结合情况,得到4个新的活性候选化合物,并进行其结合自由能计算和抗突变性分析。结果表明新候选化合物ST025723和HIV-1蛋白酶表现出较好的相互作用和抗突变性,具有深入研究的价值,同时也证明分子相似性、药效团和分子对接相结合能够快速有效地发现新颖活性候选化合物。     

蛋白质-蛋白质分子对接方法研究进展

蛋白质分子间相互作用与识别是21世纪生命科学研究的前沿和热点.分子对接方法是研究这一课题有效的计算机模拟手段.通常,蛋白质-蛋白质分子对接包括四个阶段:搜索受体与配体分子间的结合模式,过滤对接结构以排除不合理的结合模式,优化结构,用精细的打分函数评价、排序对接模式并挑选近天然构象.结合国内外研究蛋白质-蛋白质分子对接方法进展和本研究小组的工作,对以上四个环节做了详细的综述.另外,还分析了目前存在的主要问题,并提出对未来工作的展望.     

分子对接在基于结构药物设计中的应用

分子对接是研究分子间（如配体如受体）相互作用,并预测其结合模式和亲合力的一种理论模拟方法。近年来,分子对接方法已成为计算机辅助药物研究领域的一项重要技术,在数据库搜寻,组合库设计及蛋白作用研究方面得到了广泛发展。     

计算方法研究HIV-1蛋白酶及其变异与小分子GRL-0519的相互作用

艾滋病病毒在世界范围内的传播,严重地威胁到人们的身心健康.HIV-1蛋白酶的残基变异严重地削弱了药物的治疗效果.为了研究残基变异D30N、I54M和V82A对蛋白酶结合抑制剂GRL-0519的影响,本研究进行了4个30 ns的分子动力学(MD)模拟,并采用溶解相互自由能(SIE)方法计算了蛋白酶和抑制剂的结合能.计算结果表明,极性相互作用不利于变异的蛋白酶结合抑制剂,而对于野生型的蛋白酶(WT),极性相互作用有微弱的贡献,极性相互作用是残基变异抗药性的主要原因,计算得到的总结合能与实验的数据一致.为了说明每个残基在抗药性中的贡献,采用分子力场的方法计算了每一个残基与小分子作用的范德华作用能,并分析了抑制剂与蛋白酶形成的氢键.范德华作用分析表明,V82A残基变异对结合模式的影响较小,相对于WT,D30N有5个残基的范德华贡献差异大于0.4 kcal/mol,I54M残基变异的蛋白酶有6个残基.氢键的分析说明,D30N和I54M变异丢失了几个氢键;范德华作用和氢键的分析结果与SIE的计算结果一致.研究结果为设计新的更有效的抗HIV-1蛋白酶变异的抑制剂提供了理论指导.     

共同受体CCR5与HIV gp120的相互作用及相关肽类抑制剂

存在于巨嗜细胞、树突状细胞等胞膜上的G蛋白偶联受体CCR5作为R5嗜性的HIV-1病毒的主要共同受体,可以和病毒的表面糖蛋白gp120相互作用,并由此决定了病毒的另一表面糖蛋白gp41融合构象的形成以及随后的病毒与细胞的膜融合。CCR5在细胞膜上迅速移动,并与其他分子(如CD4和胆固醇)存在相互作用,加速了与gp120的作用。CCR5的这种中心作用已经使其成为抗HIV-1药物研究的很有吸引力的靶点。目前已发现一系列衍生于CCR5的胞外区的多肽、天然存在的蛋白质以及设计的多肽,可干扰CCR5与gp120之间的相互作用,从而抑制病毒复制。     

HIV-1 CRF07 B/C亚型gp41的表达、纯化和初步结构分析

HIV-1跨膜蛋白gp41是HIV-1包膜与靶细胞膜融合过程中的关键蛋白,而且序列保守,是理想的HIV-1作用靶点。为获得HIV-1中国流行株CRF07 B/C gp41蛋白的晶体结构来指导疫苗设计及药物开发,采用CRF07 B/C gp160基因序列为模板,经PCR、酶切、连接,将gp41 helix-bundle区域克隆到pET30-his表达载体中,经表达、纯化和结晶筛选,获得了gp41 helix-bundle的晶体并解析了结构,为针对中国艾滋病病毒流行株疫苗的设计及药物开发提供了结构参考。     

蛋白质与极性配体复合物的绝对结合自由能计算

介绍了用分子动力学模拟与热力学积分法相结合,模拟蛋白质与配体的绝对结合自由能的方法.通过分子转换法,使蛋白质分子（包括水分子）与配体小分子之间的相互作用逐渐减弱 （或增强）至完全消失（或完全出现）. 运用体约束方法,计算了配体与受体结合后平动、转动自由度的丧失即熵效应所引起的自由能变化.以胰蛋白酶双突变体（D189G/G226D）与极性配体苯甲脒为例,研究了蛋白质活性部位与极性配体的相互作用对结合自由能的影响,该复合物绝对结合自由能的模拟结果(－15.5 kJ/mol)与实验值(－10.5 kJ/mol)相近.     

Insights into the functional role of protonation states in the HIV-1 protease-BEA369 complex: molecular dynamics simulations and free energy calculations

The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method combined with molecular dynamics (MD) simulations were used to investigate the functional role of protonation in human immunodeficiency virus type 1 (HIV-1) protease complexed with the inhibitor BEA369. Our results demonstrate that protonation of two aspartic acids (Asp25/Asp25′) has a strong influence on the dynamics behavior of the complex, the binding free energy of BEA369, and inhibitor–residue interactions. Relative binding free energies calculated using the MM-PBSA method show that protonation of Asp25 results in the strongest binding of BEA369 to HIV-1 protease. Inhibitor–residue interactions computed by the theory of free energy decomposition also indicate that protonation of Asp25 has the most favorable effect on binding of BEA369. In addition, hydrogen-bond analysis based on the trajectories of the MD simulations shows that protonation of Asp25 strongly influences the water-mediated link of a conserved water molecule, Wat301. We expect that the results of this study will contribute significantly to binding calculations for BEA369, and to the design of high affinity inhibitors.     

Designing of benzothiazole derivatives as promising EGFR tyrosine kinase inhibitors: a pharmacoinformatics study

Abstract

Benzothiazole derivatives represent an important class of therapeutic chemical agents and are widely used for interesting biological activities and therapeutic functions including anticancer, antitumor and antimicrobial. In this study, we have performed similarity/substructure-based search of eMolecule database to find out promising benzothiazole derivatives as EGFR tyrosine kinase inhibitors. Several screening criteria that included molecular docking, pharmacokinetics and synthetic accessibility were used on initially derived about 7000 molecules consisting of benzothiazole as major component. Finally, four molecules were found to be promising EGFR tyrosine kinase inhibitors. The best docked pose of each molecule was considered for binding interactions followed by molecular dynamics (MD) and binding energy calculation. Molecular docking clearly showed the final proposed derivatives potential to form a number of binding interactions. MD simulation trajectories undoubtedly indicated that the EGFR protein becomes stable when proposed derivatives bind to the receptor cavity. Strong binding affinity was found for all molecules toward the EGFR which was substantiated by the binding energy calculation using the MM-PBSA approach. Therefore, proposed benzothiazole derivatives may be promising EGFR tyrosine kinase inhibitors for potential application as cancer therapy.

Communicated by Ramaswamy H. Sarma     

Intermolecular insights into allosteric inhibition of histone lysine-specific demethylase 1

BackgroundHistone lysine-specific demethylase 1 (LSD1) has become a potential anticancer target for the novel drug discovery. Recent reports have shown that SP2509 and its derivatives strongly inhibit LSD1 as allosteric inhibitors. However, the binding mechanism of these allosteric inhibitors in the allosteric site of LSD1 is not known yet.MethodsThe stability and binding mechanism of allosteric inhibitors in the binding site of LSD1 were evaluated by molecular docking, ligand-based pharmacophore, molecular dynamics (MD) simulations, molecular mechanics generalized born surface area (MM/GBSA) analysis, quantum mechanics/molecular mechanics (QM/MM) calculation and Hirshfeld surface analysis.ResultsThe conformational geometry and the intermolecular interactions of allosteric inhibitors showed high binding affinity towards allosteric site of LSD1 with the neighboring amino acids (Gly358, Cys360, Leu362, Asp375 and Glu379). Meanwhile, MD simulations and MM/GBSA analysis were performed on selected allosteric inhibitors in complex with LSD1 protein, which confirmed the high stability and binding affinity of these inhibitors in the allosteric site of LSD1.ConclusionThe simulation results revealed the crucial factors accounting for allosteric inhibitors of LSD1, including different protein–ligand interactions, the positions and conformations of key residues, and the ligands flexibilities. Meanwhile, a halogen bond interaction between chlorine atom of ligand and key residues Trp531 and His532 was recurrent in our analysis confirming its importance.General significanceOverall, our research analyzed in depth the binding modes of allosteric inhibitors with LSD1 and could provide useful information for the design of novel allosteric inhibitors.     

Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors

Among the available methods for predicting free energies of binding of ligands to a protein, the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA) approaches have been validated for a relatively limited number of targets and compounds in the training set. Here, we report the results of an extensive study on a series of 28 inhibitors of aldose reductase with experimentally determined crystal structures and inhibitory activities, in which we evaluate the ability of MM-PBSA and MM-GBSA methods in predicting binding free energies using a number of different simulation conditions. While none of the methods proved able to predict absolute free energies of binding in quantitative agreement with the experimental values, calculated and experimental free energies of binding were significantly correlated. Comparing the predicted and experimental ΔG of binding, MM-PBSA proved to perform better than MM-GBSA, and within the MM-PBSA methods, the PBSA of Amber performed similarly to Delphi. In particular, significant relationships between experimental and computed free energies of binding were obtained using Amber PBSA and structures minimized with a distance-dependent dielectric function. Importantly, while free energy predictions are usually made on large collections of equilibrated structures sampled during molecular dynamics in water, we have found that a single minimized structure is a reasonable approximation if relative free energies of binding are to be calculated. This finding is particularly relevant, considering that the generation of equilibrated MD ensembles and the subsequent free energy analysis on multiple snapshots is computationally intensive, while the generation and analysis of a single minimized structure of a protein–ligand complex is relatively fast, and therefore suited for high-throughput virtual screening studies. At this aim, we have developed an automated workflow that integrates all the necessary steps required to generate structures and calculate free energies of binding. The procedure is relatively fast and able to screen automatically and iteratively molecules contained in databases and libraries of compounds. Taken altogether, our results suggest that the workflow can be a valuable tool for ligand identification and optimization, being able to automatically and efficiently refine docking poses, which sometimes may not be accurate, and rank the compounds based on more accurate scoring functions.     

A computational insight into binding modes of inhibitors XD29, XD35, and XD28 to bromodomain-containing protein 4 based on molecular dynamics simulations

In the current work, conformational changes of bromodomain-containing protein 4 (1) (BRD4-1) induced by bindings of inhibitors XD29 (57G), XD35 (57F), and XD28 (L28) were investigated using molecular dynamics (MD) simulations and principal component analysis. The results demonstrate that inhibitor bindings produce significant effect on the motion of ZA loop in BRD4-1. Moreover, to further study binding modes of three inhibitors to BRD4-1, binding free energies of inhibitors to BRD4-1 were also calculated using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The results indicate that van der Waals interactions are main factors to modulate inhibitor bindings. Energy decomposition and hydrogen bond analysis demonstrate that residues Pro82, Leu92, Asn140, and Ile146 play important roles in binding processes of inhibitors to BRD4-1. This study is not only helpful for better understanding function and internal dynamics of BRD4-1, but also can provide a theoretical basis for rational designs of effective anticancer drugs targeting BRD4-1.     

Insight into binding mechanisms of inhibitors MKP56, MKP73, MKP86, and MKP97 to HIV-1 protease by using molecular dynamics simulation

HIV-1 protease (PR) has been a significant target for design of potent inhibitors curing acquired immunodeficiency syndrome. Molecular dynamics simulations coupled with molecular mechanics Poisson–Boltzmann surface area method were performed to study interaction modes of four inhibitors MKP56, MKP73, MKP86, and MKP97 with PR. The results suggest that the main force controlling interactions of inhibitors with PR should be contributed by van der Waals interactions between inhibitors and PR. The cross-correlation analyses based on MD trajectories show that inhibitor binding produces significant effect on the flap dynamics of PR. Hydrogen bond analyses indicate that inhibitors can form stable hydrogen bonding interactions with the residues from the catalytic strands of PR. The contributions of separate residues to inhibitor bindings are evaluated by using residue-based free energy decomposition method and the results demonstrate that the CH–π and CH–CH interactions between the hydrophobic groups of inhibitors with residues drive the associations of inhibitors with PR. We expect that this study can provide a significant theoretical aid for design of potent inhibitors targeting PR.     

Some insights into the binding mechanism of Aurora B kinase gained by molecular dynamics simulation

Aurora B kinase is essential in the process of mitosis, and its overexpression has been reported to be associated with a number of solid tumors. We therefore carried out molecular docking, molecular dynamics, and molecular mechanics Poisson-Boltzmann/surface area (MM-PBSA) calculations on several structurally diverse inhibitors (pentacyclic, pyrimidine, quinazoline, and pyrrolopyridine derivatives) and Aurora B kinase to explore the structural and chemical features responsible for the binding recognition mechanism. Molecular simulations reveal that the binding site mainly consists of six binding regions (sites A-F). We have identified that sites B and C are required for optimum binding in Aurora B-inhibitor complexes, sites A and F are needed to improve pharmacokinetic properties, while sites D and E lead to enhanced stability. We verified that hydrogen bonding to the hinge region and hydrophobic contact with the conserved hydrophobic pocket are of critical importance in the systems studied. Specifically, the amino acids Glu171, Phe172, and Ala173 in the hinge region and Leu99, Val107, and Leu223 in the conserved hydrophobic pocket probably account for the high binding affinities of these systems, as shown by hydrogen-bonding analysis and energy decomposition analysis. Hydrophobic contact with Phe172 is also in agreement with experimental data. In addition, the MM-PBSA calculations reveal that the binding of these inhibitors to Aurora B kinase is mainly driven by van der Waals/nonpolar interactions. The findings of this study should help to elucidate the binding pattern of Aurora B inhibitors and aid in the design of novel active ligands.     

Rational design of novel diketoacid-containing ferrocene inhibitors of HIV-1 integrase

Molecular interaction field, density functional, and docking studies of novel potential ferrocene inhibitors of HIV-1 integrase (IN) are reported. The high docking scores, analysis of the ligand-receptor interactions in the active site as well as the molecular interaction potential calculations at the binding site of the receptor indicate important features for novel HIV-1 IN inhibitors. We also confirm in this work a novel binding trench in HIV-1 integrase, recently reported in a theoretical work by other authors. This observation may be interesting since the lack of detailed structural information about IN-ligand interactions has hampered the design of IN inhibitors. Our proposed ligands are open to experimental synthesis and testing.     

Probing the electronic structures and properties of neutral and anionic ScSi n (0,−1) (n = 1–6) clusters using ccCA-TM and G4 theory

We apply molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation to investigate and reveal the binding mechanism between five xanthine inhibitors and DPP-4. The electrostatic and van der Waals interactions of the five inhibitors with DPP-4 are analyzed and discussed. The computed binding free energies using MM-PBSA method are in qualitatively agreement with experimental inhibitory potency of five inhibitors. The hydrogen bonds of inhibitors with Ser630 and Asp663 can stabilize the inhibitors in binding sites. The van der Waals interactions, especially the key contacts with His740, Asn710, Trp629, and Tyr666 have larger contributions to the binding free energy and play important roles in distinguishing the variant bioactivity of five inhibitors.