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.     

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.     

HIV-1整合酶与抑制剂金精三羧酸复合物的分子动力学模拟

用分子对接程序(Autodock)将含有一个Mg²⁺的HIV-1整合酶核心区(以下简称IN-A)与抑制剂小分子金精三羧酸(简称Aurin)进行对接,预测其未知的复合物结构,然后用分子动力学(MD)方法对IN-A与Aurin的对接结果进行了950 ps的模拟.MD模拟结果发现,IN-A与Aurin形成了两个稳定的氢键,Mg²⁺也与Aurin上的氧原子形成了稳定的配键,IN-A与Aurin之间的静电相互作用能和范德华相互作用能的平均值分别为-205.8和-162.7 kJ/mol.根据MD模拟得到的IN-A与Aurin相互作用后的构象变化信息,我们对对接复合物结构进行了修正,给出了更加合理和稳定的复合物预测结构.本工作得到的HIV-1整合酶与抑制剂Aurin的结合模式信息将有助于设计和改造出效果更好的抗HIV-1整合酶的先导化合物.     

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.     

双金属存在下整合酶和抑制剂5CITEP的分子对接研究

在HIV-1整合酶(IN)和5CITEP复合物晶体结构的基础上, 用分子对接程序(Affinity)将含有单Mg2+和双Mg2+ 的HIV-1 IN核心区与抑制剂5CITEP进行对接, 获得了能形成复合物结构的理论模型. 通过配体与受体之间的相互作用能和结构分析给出此种抑制剂的结合模式, 并与晶体结构进行比较, 揭示出引入的第二个Mg2+原子在整合过程中所起的重要作用. 前后相互作用能的变化趋势很明显, 配体和受体的作用模式比单Mg2+体系更加清晰. 由单Mg2+体系的4种作用方式改变到双Mg2+体系的两种作用方式, 相互作用能提高了将近40 kJ/mol. 为基于整合酶结构的药物设计提供了参考信息.     

HIV-1整合酶与抑制剂LCA的结合模式及抗药性研究

Ⅰ型人体免疫缺陷病毒(HIV-1)整合酶(integrase, IN)是病毒生命周期中一个重要的酶, 也是研究抗HIV新药的一个重要靶点. 运用多构象分子对接和分子动力学(molecular dynamics, MD)模拟, 研究了野生型整合酶核心区及G140S点突变的突变态整合酶核心区与抑制剂L-菊苣酸(L-chicoric acid, LCA)的结合模式, 并基于该结合模式探讨了G140S突变态整合酶对抑制剂LCA的抗药性. 结果表明: LCA结合到G140S突变态整合酶核心区中的位置与结合到野生型整合酶核心区的位置不同, 结合位置的差异导致LCA抑制作用的部分丧失; IN功能Loop区的柔性以及Mg²⁺离子与三个关键残基D64, D116和E152之间的相互作用有助于IN发挥生物学功能; G140S突变态整合酶核心区中的E152与LCA的排斥作用、K159与LCA结合能力的变弱以及Y143指向IN的口袋区是产生抗药性的重要原因. 这些模拟结果与实验结果吻合, 可为基于IN的抗HIV药物分子设计提供一些有用信息.     

结构多样的HIV-1整合酶抑制剂:过去、现在和未来

HIV-1整合酶是逆转录病毒复制的必需酶,它催化病毒DNA与宿主染色体DNA的整合,而且在人类细胞中没有类似物,因此成为治疗艾滋病的富有吸引力和合理的靶标.最近十年,一大批HIV-1整合酶抑制剂被鉴定出来,其中一些化合物显示选择性的抑制HIV-1整合酶和阻断病毒复制的活性,而最有影响的两类抑制剂是含邻苯二酚的多羟基芳环化合物和最近报道的芳基β-二酮酸类化合物.全面综述了用于HIV-1整合酶抑制剂研究以发展抗HIV新药的不同种类的化合物,包括苯并咪唑类衍生物、核苷类、多肽、羟基取代的芳环化合物及二酮酸类化合物等,并阐述了这些化合物中对抑制活性重要的结构特征.同时也介绍了HIV-1整合酶的结构、功能以及HIV-1整合酶抑制剂的设计原理和作用机制.     

用分子对接方法预测HIV-1整合酶与金精三羧酸抑制剂的相互作用

用分子对接方法(Docking)研究了HIV-1整合酶与其抑制剂金精三羧酸的结合过程.为弄清金属离子在结合中所起的作用,选择含有一个Mg+2或不含Mg+2的两种不同的整合酶受体分别与金精三羧酸对接.结果表明, Mg+2对稳定配体与受体的结合起了重要作用. 金精三羧酸配体与含有一个金属Mg+2的整合酶受体对接,最优结合自由能为-45.19 kJ/mol. 当Mg+2失去后,整合酶的活性中心构象将发生变化,使金精三羧酸抑制剂与整合酶的结合自由能(-24.35 kJ/mol)明显增加. 预测了未知的HIV-1整合酶与其抑制剂金精三羧酸的复合物结构, 并可对基于结构的抗HIV-1整合酶的药物设计提供重要信息.     

新型二氟甲基磷酸类酪氨酸蛋白磷酸酯酶1B抑制剂的分子动力学模拟和结合自由能计算

通过分子对接建立了一系列含二氟甲基磷酸基团(DFMP)或二氟甲基硫酸基团(DFMS)的抑制剂与酪氨酸蛋白磷酸酯酶1B(PTP1B)的相互作用模式, 并通过1 ns的分子动力学模拟和molecular mechanics/generalized Born surface area (MM/GBSA)方法计算了其结合自由能. 计算获得的结合自由能排序和抑制剂与靶酶间结合能力排序一致; 通过基于主方程的自由能计算方法, 获得了抑制剂与靶酶残基间相互作用的信息, 这些信息显示DFMP/DFMS基团的负电荷中心与PTP1B的221位精氨酸正电荷中心之间的静电相互作用强弱决定了此类抑制剂的活性, 进一步的分析还显示位于DFMP/DFMS基团中的氟原子或其他具有适当原子半径的氢键供体原子会增进此类抑制剂与PTP1B活性位点的结合能力.     

表皮生长因子受体和抑制剂之间分子对接的研究

研究了表皮生长因子受体(EGFR)和4-苯胺喹唑啉类抑制剂之间的相互作用模式，表皮生长因子受体的三维结构通过同源蛋白模建的方法得到，而抑制剂和靶酶结合复合物结构则通过分子力学和分子动力学结合的方法计算得到。从模拟结果得到的抑制剂和靶酶之间的相互作用模式表明范德华相互作用、疏水相互作用以及氢键相互作用对抑制剂的活性都有重要的影响，抑制剂的苯胺部分位于活性口袋的底部，能够与受体残基的非极性侧链产生很强的范德华和疏水相互作用，抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏水性相互作用，而抑制剂喹唑啉环上的氮原子能和周围的残基形成较强的氢键相互作用，对抑制剂的活性有较大的影响，计算得到抑制剂和靶酶之间的非键相互作用能以及抑制剂和靶酶之间的相互作用信息能够很好地解释抑制剂活性和结构的关系，为全新抑制剂的设计提供了重要的结构信息。     

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.     

Homology model-guided 3D-QSAR studies of HIV-1 integrase inhibitors

In the present study, we report the exploration of binding modes of potent HIV-1 integrase (IN) inhibitors MK-0518 (raltegravir) and GS-9137 (elvitegravir) as well as chalcone and related amide IN inhibitors we recently synthesized and the development of 3D-QSAR models for integrase inhibition. Homology models of DNA-bound HIV-1 IN were constructed on the basis of the X-ray crystal structure of the foamy virus IN-DNA complex (PDB ID: 3L2T ) and used for docking. The binding modes of raltegravir and elvitegravir in our homology models are in accordance with those in the foamy virus structure revealing interactions important for inhibitor-IN binding. To gain further insights into the structural requirements for IN inhibition, three-dimensional quantitative structure activity relationship (3D-QSAR) studies were conducted using raltegravir, elvitegravir, and their analogs; our synthesized 3-keto salicylic acid IN inhibitor series; as well as other structurally related HIV-1 IN inhibitors. In the first part of the study with 103 compounds, atom-fit alignments, I and II, and docking-based alignment, III, were used to develop 3D-QSAR models 1, 2, and 3, respectively, each comprising comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) 3D-QSARs. This initial analysis indicated that the docking-based (structure-based) model 3 performed better than the atom-fit (ligand-based) models 1 and 2, in terms of statistical significance and robustness. Thus, the docking-based alignment was then subsequently used with an expanded data set of 296 compounds for building a more comprehensive 3D-QSAR, model 4. Model 4 afforded good q2 values of 0.70 and 0.75 for CoMFA and CoMSIA 3D-QSARs, respectively, and showed good predictive performance on an external validation test set of 59 compounds with predictive r2 values up to 0.71. The HIV IN-DNA homology model of biological relevance and the comprehensive 3D-QSAR models developed in the present study provide insights and new predictive tools for structure-based design and optimization of IN inhibitors.     

3D-QSAR and molecular modeling of HIV-1 integrase inhibitors

Three-dimensional quantitative structure-activity relationship (3D QSAR) methods were applied on a series of inhibitors of HIV-1 integrase with respect to their inhibition of 3-processing and 3-end joining steps in vitro.The training set consisted of 27 compounds belonging to the class of thiazolothiazepines. The predictive ability of each model was evaluated using test set I consisting of four thiazolothiazepines and test set II comprised of seven compounds belonging to an entirely different structural class of coumarins. Maximum Common Substructure (MCS) based method was used to align the molecules and this was compared with other known methods of alignment. Two methods of 3D QSAR: comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were analyzed in terms of their predictive abilities. CoMSIA produced significantly better results for all correlations. The results indicate a strong correlation between the inhibitory activity of these compounds and the steric and electrostatic fields around them. CoMSIA models with considerable internal as well as external predictive ability were obtained. A poor correlation obtained with hydrophobic field indicates that the binding of thiazolothiazepines to HIV-1 integrase is mainly enthalpic in nature. Further the most active compound of the series was docked into the active site using the crystal structure of integrase. The binding site was formed by the amino acid residues 64-67, 116, 148, 151-152, 155-156, and 159. The comparison of coefficient contour maps with the steric and electrostatic properties of the receptor shows high level of compatibility.     

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.     

Investigation of formation,recognition, stabilization,and conversion of dimeric G-quadruplexes of HIV-1 integrase inhibitors by electrospray ionization mass spectrometry

The dimeric G-quadruplex structures of d(GGGTGGGTGGGTGGGT) (S1) and d(GTGGTGGGTGGGTGGGT) (S2), the potent nanomolar HIV-1 integrase inhibitors, were detected by electrospray ionization mass spectrometry (ESI-MS) for the first time. The formation and conversion of the dimers were induced by NH(4)(+), DNA concentration, pH, and the binding molecules. We directly observed the specific binding of a perylene derivative (Tel03) and ImImImbetaDp in one system consisting of the intramolecular and the dimeric G-quadruplexes of the HIV-1 integrase inhibitor, which suggested that Tel03 could shift the equilibrium to the dimeric G-quadruplex formation, while ImImImbetaDp induces preferentially a structural change from the dimer to the intramolecular G-quadruplex. The results of this study indicated that Tel03 and ImImImbetaDp favor the stabilization of the dimeric G-quadruplex structures.     

Three-dimensional Quantitative Structure-activity Relationship Models of HIV-1 Integrase Inhibitors of DKAs

As one of the three viral encoded enzymes of HIV-1 infection, HIV-1 integrase has become an attractive drug target for the treatment. Diketoacid compounds (DKAs) are one kind of potent and selective inhibitors of HIV-1 IN. In the present work, two three-dimensional QSAR techniques (CoMFA and CoMSIA) were employed to correlate the molecular structure with the activity of inhibiting the strand transfer for 147 DKAs. The all-oritation search (AOS) and all-placement search (APS) were used to optimize the CoMFA model. The diketo and keto-enol tautomers of DKAs were also used to establish the CoMFA models. The results indicated that the enol was the dominant conformation in the HIV-1 IN and DKAs complexes. It can provide a new method and reference to identify the bioactive conformation of drugs by using QSAR analysis. The best CoMSIA model, with five fields combined, implied that the hydrophobic field is very important as well as the steric and electrostatic fields. All models indicated favorable internal validation. A comparative analysis with the three models demonstrated that the CoMFA model seems to be more predictive. The contour maps could afford steric, electrostatic, hydrophobic and H-bond information about the interaction of ligand-receptor complex visually. The models would give some useful guidelines for designing novel and potent HIV-1 integrase inhibitors.     

Hyperbranched molecular structures with potential antiviral activity: derivatives of 5,6-dihydroxyindole-2-carboxylic Acid

In the search of new HIV-1 integrase (IN) inhibitors, we synthesized a series of multimeric 5,6-dihydroxyindole-2-carboxylic acid (DHICA) derivatives. Preliminary results indicate that hyperbranched architectures could represent a peculiar molecular requisite for the development of new antiviral lead compounds.