靶向整合过程不同步骤的HIV-1整合酶抑制剂的结构类型和研究进展

HIV-1整合酶是病毒复制所必需的三个基本酶之一, 为病毒所特有, 人体无对应的酶, 因此整合酶是理想的抗HIV药物设计的新靶标. HIV-1整合酶催化病毒DNA插入宿主染色体的过程涉及到整合酶与前病毒DNA形成整合前复合物、病毒DNA的3’末端切断和DNA链转移等步骤, 目前研究得最多的HIV-1整合酶抑制剂是抑制链转移反应的芳基二酮酸化合物, 其中的电子等排体衍生物Raltegravir (MK-0518)于2007年10月被美国食品药品管理局(FDA)批准上市, 而GS-9137处于三期临床试验, 此外还有多个处于临床前研究和临床阶段的药物. 根据抑制剂的不同作用机理, 本综述介绍了近年来所报道的HIV-1整合酶抑制剂的结构类型、药效团模型、研究进展及化学合成, 将整合酶抑制剂分为链转移反应抑制剂、整合酶-DNA结合抑制剂、整合酶3’端切除反应抑制剂、非专一性整合酶抑制剂以及多肽类抑制剂等几大类. 其中链转移反应抑制剂结构类型最丰富、发展最快. 整合酶抑制剂的出现丰富了高效抗逆转录病毒疗法(HAART), 为多重抗药性艾滋病患者提供了新的有效的治疗方案.     

IOPY/ISPY类HIV-1逆转录酶抑制剂的定量构效关系研究

C-5修饰的3-碘-4-芳氧基/芳硫基吡啶酮(IOPY/ISPY)类化合物是一类潜在的HIV-1非核苷类逆转录酶抑制剂, 特别是这类化合物因具有同时抑制野生型和突变型病毒株的特性, 而受到更加广泛的关注. 首先利用两套2D通用描述符同时构建了该类化合物的线性和非线性定量构效关系模型. 结果表明这些模型都具有较好的预测能力, 并且非线性模型较线性模型预测能力更好些. 为了更好、更形象地描述逆转录酶抑制剂的特征, 进一步结合三维定量构效关系(3D-QSAR)模型, 以及SAReport分析对该类化合物同时抑制野生型和突变型病毒株的结构特征进行了分析, 发现在对这类化合物进行结构修饰时, 需要服从如下三条理论指导原则: (1) R基团中的正负电场分布情况对化合物的活性起着关键作用|(2) R基团最好具有芳香环或芳香杂环和(3) R基团的环结构上连接的取代基不宜太多.     

HIV-1逆转录酶抑制剂的三维定量构效关系

采用比较分子力场分析法(CoMFA)和比较分子相似性指数分析法(CoMSIA)对一系列非核苷类HIV-1逆转录酶抑制剂(苯磺酰基亚胺噻唑类化合物)进行了三维定量构效关系的研究,获得了高可靠性的CoMFA和CoMSIA模型,其交叉验证相关系数q2值分别为0.748和0.607.通过对CoMFA和CoMSIA模型三维等势图的分析,确定了该类化合物抗HIV-1活性的结构要求.研究结果表明,对苯磺酰基亚胺噻唑类化合物而言,在苯环的C-5位引入体积大和电负性强的基团能增加其抑制活性;苯环的C-2位的氢键给体基团对活性有利;噻唑环的R2取代基疏水性增大会降低生物活性.研究结果表明,可以指导新HIV-1逆转录酶抑制剂的设计和合成.     

HIV-1整合酶与芳香二酮酸类抑制剂相互作用的分子模拟研究

用分子对接方法研究了一系列芳香二酮酸类抑制剂与HIV-1整合酶的识别及相互作用. 结果表明, 抑制剂结合到整合酶Asp64～Leu68, Thr115～Phe121, Gln148～Lys159和Mg2＋所构成的口袋区, 抑制机理与5CITEP相似. 采用分子动力学模拟和MM/PBSA方法计算了芳香二酮酸类抑制剂与整合酶之间的结合自由能, 计算结果与实验值相吻合, 平均绝对偏差为3.6 kJ/mol, 体系范德华相互作用和溶剂化效应的非极性项是利于形成复合物的主要因素. 相关性分析结果表明, 结合自由能值与疏水相互作用有较强的线性相关(R＝0.61), 基于此, 用多元线性回归方法给出了一个能较强预测芳香二酮酸类抑制剂与HIV-1整合酶的结合自由能预测模型, 为后续基于抑制剂结构的抗HIV-1药物分子设计提供指导.     

6,7-二氧代-4-芳胺香豆素的设计、合成及分子对接研究

茶酚-氧位-甲基转移(COMT)酶抑制剂在治疗帕金森病中起到重要作用.通过对现有COMT酶抑制剂托卡朋和恩托卡朋结构与活性关系分析,推断含有儿茶酚结构的香豆素类化合物可能具有潜在的COMT酶抑制活性,因此设计合成了一类新型的6,7-二氧代-4-芳胺香豆素,通过理论计算,研究了此类化合物对COMT酶抑制活性.结果表明,设计的10种6,7-二氧代-4-芳胺香豆素与COMT酶的对接效果均较好,其中具有甲氧基乙基保护的儿茶酚结构化合物6,7-二[2-(甲氧基)乙氧]-4-(苯胺)香豆素(6b4)和6,7-二[2-(甲氧基)乙氧]-4-[(3-乙炔基)苯胺]香豆素(6b5)与COMT酶的对接效果尤为显著.     

新多环特特拉姆酸大环内酰胺3-Hydroxycombamide Ⅰ的发现

从链霉菌S001的重组菌株S001-cbm-OX4-ikaD中分离获得1个新多环特特拉姆酸大环内酰胺(Po TeMs)类化合物3-hydroxycombamide Ⅰ (2),通过一维、二维核磁共振波谱(NMR)和高分辨质谱(HRMS)数据分析确定其化学结构.化合物2的C-3位羟基推测为宿主链霉菌S001所含羟基化酶催化形成.分别采用滤纸片法和噻唑蓝(MTT)比色法测定了化合物2的抗菌和细胞毒活性,结果显示化合物2无明显活性.此外,化合物2在100μmol/L时对鼠伤寒沙门菌Ⅲ型分泌系统(T3SS)无抑制活性.结果显示Po TeMs的C-3位羟基化修饰可能发生在多环体系氧化修饰之后.     

HIV整合酶抑制剂的研究进展

HIV整合酶是病毒DNA复制所必需的3个基本酶之一,是新批准上市的抗艾滋病药物Raltegravir(MK-0518,Isentress)的分子靶标.HIV整合酶抑制剂已经成为新一类治疗获得性免疫缺陷综合症的药物.对HIV整合酶抑制剂的研究进展进行了综述,为研究新型人类免疫缺陷病毒整合酶抑制剂提供参考.     

DAPY类化合物抑制野生型HIV-1活性的QSAR研究

应用分子力学、半经验量子化学RM1方法优化了32个抗野生型HIV-1病毒毒株的二芳基嘧啶类(DAPYs)化合物分子结构,从分子构象模型中提取了多种参数并结合疏水性参数与指示性参数建立QSAR多元线性回归方程.回归方程显示:分子体积V的增大会降低其抑制活性,而左苯环与嘧啶环间二面角θ增大可以提高抑制活性.同时指示性参数I表明左苯环CN基团加入可以明显增加抑制活性,嘧啶环上R1位置苯基与硝基的加入可以极大降低抑制活性.     

3-芳氧基-1-丙胺类HIV-1 Tat/PCAF BRD抑制剂的合成及生物活性

为了研究HIV-1 Tat/PCAF BRD抑制剂的构效关系, 合成了6个3-芳氧基-1-丙胺类化合物. 以取代的2-硝基苯酚为起始原料, 在常规加热和微波辐射加热下与1,3-二溴丙烷反应合成3-(2-硝基芳氧基)-1-溴丙烷(3), 结果显示, 微波辐射加热比常规加热下的反应速度明显加快, 收率有所提高. 3和邻苯二甲酰亚胺钾进行N-烷基化反应合成了2-[3-(芳氧基)-丙基]二氢异吲哚-1,3-二酮, 再经肼解得到了目标化合物, 所有化合物的结构均经FTIR, ¹H NMR, ¹³C NMR及HRMS确证. ELISA检测法测定了它们体外抑制HIV-1 Tat/PCAF BRD的活性, 并对影响活性的因素进行了讨论.     

γ-和δ-酮酸衍生物均相催化氢化研究进展

γ-和δ-酮酸衍生物是最重要的双官能团生物质平台化合物之一,如何高效地催化这些酮酸类化合物转化成相应的单一精细化学品是当今研究的难点.我们综述了金属有机配合物均相催化氢化γ-和δ-酮酸的最新进展,重点介绍了用于催化生产γ-和δ-羟基酸、酯、内酯、环醚等的均相催化剂的结构、活性、选择性和反应机理.     

Building the Pharmacophore Model of HIV-1 Integrase Strand Transfer Inhibitors and Studying Their Inhibition Mechanism

The replication of HIV-1 requires the integration of its cyclic DNA into host DNA by HIV-1 integrase (IN), which includes two important reactions, 3'-processing and strand transfer, both catalyzed by HIV-1 IN. Disrupting either of the reactions will fulfill the purpose of inhibiting the replication of HIV-1. In this paper, pharmacophore modeling and molecular docking are employed to investigate the inhibition mechanism of the HIV-1 IN strand transfer inhibitors (INSTIs). Based on the results, we suggest that the inhibition mechanism of INSTIs involves the inhibitor chelating the cofactors Mg2+ and its forming hydrogen bonds with some crucial residues adjacent to the DDE active center.     

Novel virtual screening protocol based on the combined use of molecular modeling and electron-ion interaction potential techniques to design HIV-1 integrase inhibitors

HIV-1 integrase (IN) is an essential enzyme for viral replication and represents an intriguing target for the development of new drugs. Although a large number of compounds have been reported to inhibit IN in biochemical assays, no drug active against this enzyme has been approved by the FDA so far. In this study, we report, for the first time, the use of the electron-ion interaction potential (EIIP) technique in combination with molecular modeling approaches for the identification of new IN inhibitors. An innovative virtual screening approach, based on the determination of both short- and long-range interactions between interacting molecules, was employed with the aim of identifying molecules able to inhibit the binding of IN to viral DNA. Moreover, results from a database screening on the commercial Asinex Gold Collection led to the selection of several compounds. One of them showed a significant inhibitory potency toward IN in the overall integration assay. Biological investigations also showed, in agreement with modeling studies, that these compounds prevent recognition of DNA by IN in a fluorescence fluctuation assay, probably by interacting with the DNA binding domain of IN.     

Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: a molecular modeling perspective

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme for splicing a viral DNA (vDNA) replica of its genome into host cell chromosomal DNA (hDNA) and has been recently recognized as a promising therapeutic target for developing anti-AIDS agents. The interaction between HIV-1 IN and vDNA plays an important role in the integration process of the virus. However, a detailed understanding about the mechanism of this interactions as well as the action of the anti-HIV drug raltegravir (RAL, approved by FDA in 2007) targeting HIV-1 IN in the inhibition of the vDNA strand transfer is still absent. In the present work, a molecular modeling study by combining homology modeling, molecular dynamics (MD) simulations with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and molecular mechanics Generalized-Born surface area (MM-GBSA) calculations was performed to investigate the molecular mechanism of HIV-1 IN-vDNA interactions and the inhibition action of vDNA strand transfer inhibitor (INSTI) RAL. The structural analysis showed that RAL did not influence the interaction between vDNA and HIV-1 IN, but rather targeted a special conformation of HIV-1 IN to compete with host DNA and block the function of HIV-1 IN by forcing the 3'-OH of the terminal A17 nucleotide away from the three catalytic residues (Asp64, Asp116, and Glu152) and two Mg(2+) ions. Thus, the obtained results could be helpful for understanding of the integration process of the HIV-1 virus and provide some new clues for the rational design and discovery of potential compounds that would specifically block HIV-1 virus replication.     

Structure, stereochemistry, and biological activity of integramycin, a novel hexacyclic natural product produced by Actinoplanes sp. that inhibits HIV-1 integrase

[structure: see text] HIV-1 integrase is a critical enzyme for viral replication, and its inhibition is an emerging target for potential antiviral chemotherapy. We have discovered a novel inhibitor, integramycin, from screening of fermentation extracts using an in vitro assay. Integramycin possesses a hexacyclic ring system and exhibited an IC50 value of 4 microM against HIV-1 integrase (strand transfer). The isolation, structure elucidation, stereochemistry, conformation, and biological activity has been described.     

De novo design based identification of potential HIV-1 integrase inhibitors: A pharmacoinformatics study

In the present study, pharmacoinformatics paradigms include receptor-based de novo design, virtual screening through molecular docking and molecular dynamics (MD) simulation are implemented to identify novel and promising HIV-1 integrase inhibitors. The de novodrug/ligand/molecule design is a powerful and effective approach to design a large number of novel and structurally diverse compounds with the required pharmacological profiles. A crystal structure of HIV-1 integrase bound with standard inhibitor BI-224436 is used and a set of 80,000 compounds through the de novo approach in LigBuilder is designed. Initially, a number of criteria including molecular docking, in-silico toxicity and pharmacokinetics profile assessments are implied to reduce the chemical space. Finally, four de novo designed molecules are proposed as potential HIV-1 integrase inhibitors based on comparative analyses. Notably, strong binding interactions have been identified between a few newly identified catalytic amino acid residues and proposed HIV-1 integrase inhibitors. For evaluation of the dynamic stability of the protein-ligand complexes, a number of parameters are explored from the 100 ns MD simulation study. The MD simulation study suggested that proposed molecules efficiently retained their molecular interaction and structural integrity inside the HIV-1 integrase. The binding free energy is calculated through the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) approach for all complexes and it also explains their thermodynamic stability. Hence, proposed molecules through de novo design might be critical to inhibiting the HIV-1 integrase.     

用分子模拟方法研究HIV-1整合酶与咖啡酰基类抑制剂的相互作用

用分子对接和分子动力学(MD)模拟方法研究了一类咖啡酰基和没食子酰基类HIV-1整合酶抑制剂与整合酶之间的相互作用模式, 结果表明该类抑制剂分子上的两个侧链基团(咖啡酰基或没食子酰基)与整合酶的DDE基序之间的相互作用对抑制整合酶活性起到关键作用. 当侧链基团为没食子酰基时, 可以提高该类抑制剂与整合酶的结合能力. 采用线性相互作用能方法(LIE)计算了该类抑制剂与整合酶之间的结合自由能, 预测值与实验值相吻合, 均方根偏差RMSD为1.39 kJ•mol^-1, 以上结果可为基于结构的HIV-1整合酶抑制剂设计提供有用的信息.     

Identification of potential HIV-1 integrase strand transfer inhibitors: In silico virtual screening and QM/MM docking studies

HIV-1 integrase (IN) is a retroviral enzyme that catalyses integration of the reverse-transcribed viral DNA into the host genome, which is necessary for efficient viral replication. In this study, we have performed an in silico virtual screening for the identification of potential HIV-1 IN strand transfer (ST) inhibitors. Pharmacophore modelling and atom-based 3D-QSAR studies were carried out for a series of compounds belonging to 3-Hydroxypyrimidine-2,4-diones. Based on the ligand-based pharmacophore model, we obtained a five-point pharmacophore with two hydrogen bond acceptors (A), one hydrogen bond donor (D), one hydrophobic group (H) and one aromatic ring (R) as pharmacophoric features. The pharmacophore hypothesis AADHR was used as a 3D query in a sequential virtual screening study to filter small molecule databases Maybridge, ChemBridge and Asinex. Hits matching with pharmacophore hypothesis AADHR were retrieved and passed progressively through Lipinski’s rule of five filtering, molecular docking and hierarchical clustering. The five compounds with best hits with novel and diverse chemotypes were subjected to QM/MM docking, which showed improved docking accuracy. We further performed molecular dynamics simulation and found three compounds that form stable interactions with key residues. These compounds could be used as a leads for further drug development and rational design of HIV-1 IN inhibitors.     

A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase

Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Diketo acids such as L-731,988 and S-1360 are potent and selective inhibitors of HIV-1 IN. In this study, we used molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy between HIV-1 IN and L-731,988 and 10 of its derivatives and analogues. This hybrid methodology has the advantage that it includes quantum effects such as ligand polarisation upon binding, which can be very important when highly polarisable groups are embedded in anisotropic environments, as for example in metal-containing active sites. Furthermore, an energy decomposition analysis was performed to determine the contributions of individual residues to the enzyme-inhibitor interactions on averaged structures obtained from rather extensive conformational sampling. Analysis of the results reveals first that there is a correlation between protein-ligand interaction energy and experimental strand transfer into human chromosomes and secondly that the Asn-155, Lys-156 and Lys-159 residues and the Mg(2+) ion are crucial to anti-HIV IN activity. These results may explain the available experimental data.     

Design and synthesis of bis-amide and hydrazide-containing derivatives of malonic acid as potential HIV-1 integrase inhibitors

HIV-1 integrase (IN) is an attractive and validated target for the development of novel therapeutics against AIDS. In the search for new IN inhibitors, we designed and synthesized three series of bis-amide and hydrazide-containing derivatives of malonic acid. We performed a docking study to investigate the potential interactions of the title compounds with essential amino acids on the IN active site.