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.     

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.     

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.     

贯叶连翘有效成分金丝桃素与HIV逆转录酶相互作用的研究

采用理论计算化学分子动力学模拟方法研究金丝桃素的分子结构,并从分子水平上研究金丝桃素与HIV逆转录酶的相互作用,建立了酶-抑制剂复合物模型,分析可能的相互作用关系和作用机理．研究结果表明,金丝桃素分子结构具有刚性特征．金丝桃素与HIV逆转录酶以氢键相互作用和Ⅱ-Ⅱ相互作用结合．     

Use of 3D QSAR to investigate the mode of binding of pyrazinones to HIV-1 RT

Abstract  Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) based on the docked conformation were performed for 24 pyrazinone derivatives. All compounds were docked into the wild-type HIV-1 RT binding pocket and the lowest-energy docked configurations were used to construct the 3D QSAR models. The CoMFA and CoMSIA models enable good prediction of inhibition by the pyrazinones, with  = 0.703 and 0.735. Results obtained from CoMFA and CoMSIA based on the docking conformation of the pyrazinones are, therefore, powerful means of elucidating the mode of binding of pyrazinones and suggesting the design of new potent NNRTIs. Graphical Abstract        

金属离子对HIV-1整合酶与硫氮硫扎平抑制剂作用模式影响的分子模拟研究

HIV-1整合酶（IN）通过依赖金属离子的两步反应将病毒DNA整合入宿主细胞过程中。结合于HIV-1上的金属离子个数的变化直接影响整合酶与抑制剂之间的结合。本工作用同源模建方法搭建了每条单链核心区具有两个Mg2+ 的（2Mg-IN-Core）和具有一个Mg2+ 的HIV-1 IN二聚体核心区模型（1Mg-IN-Core）。分子对接分别得到它们与硫氮硫扎平类化合物能量较低的复合物结构,把对接结果进行了比较。研究发现：当整合酶中结合的Mg2+个数改变时,它与抑制剂的结合模式也会发生很大的变化;抑制剂能够特异的且稳定的与2Mg-IN-Core模型的活性位点结合;同时与ASP64和GLU152螯合的那个Mg2+离子对于硫氮硫扎平抑制剂与整合酶上的结合有很大的影响。2Mg-IN-Core模型与抑制剂的复合物平均结构进行了2000 ps的 分子动力学模拟,分析发现同时与ASP64及ASP116螯合的Mg2+与IN蛋白形成了四个稳定的螯合键;同时与ASP64及GLU152螯合的Mg2+可与IN结合、也可与抑制剂形成稳定的配位键,这个Mg2+对IN与硫氮硫扎平抑制剂之间的结合有较大影响。     

Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design

Summary We report structural models of the full-length integrase enzyme (IN) of the human immunodeficiency virus type 1 (HIV-1) and its complex with viral and human DNA. These were developed by means of molecular modeling techniques using all available experimental evidence, including X-ray crystallographic and NMR structures of portions of the full-length protein. Special emphasis was placed on obtaining a model of the enzyme’s active site with the viral DNA apposed to it, based on the hypothesis that such a model would allow structure-based design of inhibitors that retain activity in vivo. This was because bound DNA might be present in vivo after 3’-processing but before strand transfer. These structural models were used to study the potential binding modes of various diketo-acid HIV-1 IN inhibitors (many of them preferentially inhibiting strand transfer) for which no experimentally derived complexed structures are available. The results indicate that the diketo-acid IN inhibitors probably chelate the metal ion in the catalytic site and also prevent the exposure of the 3’-processed end of the viral DNA to human DNA.     

In silico virtual screening of potent inhibitor to hamper the interaction between HIV-1 integrase and LEDGF/p75 interaction using E-pharmacophore modeling,molecular docking,and dynamics simulations

The rapid increase of HIV-1 infection throughout the globe has a high demand for a superior drug with lesser side effects. LEDGF/p75, the human Lens Epithelium-Derived Growth Factor is identified as a promising cellular cofactor with integrase in facilitating the viral replication in an early stage by acting as a tethering factor in the pre-integration to the chromatin. Therefore, the present study was designed to identify a potent inhibitor by applying an E-pharmacophore based virtual screening, molecular docking, and dynamics simulation approaches. Finally, ZINC22077550 and ZINC32124441 were best identified potent molecules with the efficient binding affinity, strong hydrogen bonding, and acceptable pharmacological properties to hamper the interaction between integrase and LEDGF/p75. Further, the DFT and MDS studies were also analyzed, and shown a favorable energetic state and dynamic stability then reference compound. In conclusion, we suggest that these findings could be novel therapeutics in the future and may increase the lifespan of individuals suffering from viral infection.     

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.     

金丝桃素分子结构及其与HIV病毒蛋白酶作用的分子动力学研究

采用用计算化学方法研究金丝桃素分子结构特征, 并用分子动力学方法研究其与HIV蛋白酶的相互作用, 探讨其可能的抗HIV病毒作用机理. 结果表明, 金丝桃素分子结构具有刚性特征, 与HIV蛋白酶在酶的催化活性位点与ASP-A25 and ASP-B25以氢键作用相结合.     

Molecular electrostatic potentials as input for the alignment of HIV-1 integrase inhibitors in 3D QSAR

Comparative molecular similarity indices analysis (CoMSIA), a three-dimensional quantitative structure activity relationship (3D QSAR) paradigm, was used to examine the correlations between the calculated physicochemical properties and the in vitro activities (3'-processing and 3'-strand transfer inhibition) of a series of human immunodeficiency virus type 1 (HIV-1) integrase inhibitors. The training set consisted of 34 molecules from five structurally diverse classes: salicylpyrazolinones, dioxepinones, coumarins, quinones, and benzoic hydrazides. The data set was aligned using extrema of molecular electrostatic potentials (MEPs). The predictive ability of the resultant model was evaluated using a test set comprised of 7 molecules belonging to a different structural class of thiazepinediones. A CoMSIA model using an MEP-based alignment showed considerable internal as well external predictive ability (r2(cv) = 0.821, r2(pred) = 0.608 for 3'-processing; and r2(cv) = 0.759, r2(pred.) = 0.660 for 3'-strand transfer).     

基于“底物包膜”假说筛选新型HIV-1蛋白酶抑制剂

基于“底物包膜”假说, 以现有HIV-1蛋白酶抑制剂Darunavir为模板构建药效团模型并对中药化学数据库进行搜索; 采用分子对接方法进一步考察化合物与HIV-1蛋白酶结合情况及其与“底物包膜”符合程度, 优先选出两个化合物Annomonicin和去乙酰蟾蜍它灵; 应用分子动力学方法对这两个化合物进行动力学模拟, 观察它们与蛋白酶结合的复合物在动力学过程中的稳定性并计算其结合自由能, 综合评价筛选结果, 最终确定化合物Annomonicin具有更潜在的深入研究价值.     

Docking-based CoMFA and CoMSIA study of azaindole carboxylic acid derivatives as promising HIV-1 integrase inhibitors

Three-dimensional quantitative structure–activity relationship (3D-QSAR) studies were performed based on a series of azaindole carboxylic acid derivatives that had previously been reported as promising HIV-1 integrase inhibitors. Docking studies to explore the binding mode were performed based on the highly active molecule 36. The best docked conformation of molecule 36 was used as template for alignment. The comparative molecular field analysis (CoMFA) model (including steric and electrostatic fields) yielded the cross validation q ² = 0.655, non-cross validation r ² = 0.989 and predictive r ² _pred = 0.979. The best comparative molecular similarity indices analysis (CoMSIA) model (including steric, electrostatic, hydrophobic and hydrogen-bond acceptor fields) yielded the cross validation q ² = 0.719, non-cross validation r ² = 0.992 and predictive r ² _pred = 0.953. A series of new azaindole carboxylic acid derivatives were designed and the HIV-1 integrase inhibitory activities of these designed compounds were predicted based on the CoMFA and CoMSIA models.     

Structural Basis of 2-Phenylamino-4-phenoxyquinoline Derivatives as Potent HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors

New target molecules, namely, 2-phenylamino-4-phenoxyquinoline derivatives, were designed using a molecular hybridization approach, which was accomplished by fusing the pharmacophore structures of three currently available drugs: nevirapine, efavirenz, and rilpivirine. The discovery of disubstituted quinoline indicated that the pyridinylamino substituent at the 2-position of quinoline plays an important role in its inhibitory activity against HIV-1 RT. The highly potent HIV-1 RT inhibitors, namely, 4-(2′,6′-dimethyl-4′-formylphenoxy)-2-(5″-cyanopyridin-2″ylamino)quinoline (6b) and 4-(2′,6′-dimethyl-4′-cyanophenoxy)-2-(5″-cyanopyridin-2″ylamino)quinoline (6d) exhibited half-maximal inhibitory concentrations (IC50) of 1.93 and 1.22 µM, respectively, which are similar to that of nevirapine (IC50 = 1.05 µM). The molecular docking results for these two compounds showed that both compounds interacted with Lys101, His235, and Pro236 residues through hydrogen bonding and interacted with Tyr188, Trp229, and Tyr318 residues through π–π stacking in HIV-1 RT. Interestingly, 6b was highly cytotoxic against MOLT-3 (acute lymphoblastic leukemia), HeLA (cervical carcinoma), and HL-60 (promyeloblast) cells with IC50 values of 12.7 ± 1.1, 25.7 ± 0.8, and 20.5 ± 2.1 µM, respectively. However, 6b and 6d had very low and no cytotoxicity, respectively, to-ward normal embryonic lung (MRC-5) cells. Therefore, the synthesis and biological evaluation of 2-phenylamino-4-phenoxyquinoline derivatives can serve as an excellent basis for the development of highly effective anti-HIV-1 and anticancer agents in the near future.     

用分子对接方法研究HIV-1整合酶与病毒DNA的结合模式

用分子对接方法研究了HIV-1整合酶(Integrase, IN)二聚体与3’ 端加工(3’ Processing, 3’-P)前的8 bp及27 bp病毒DNA的相互作用, 并获得IN与27 bp病毒DNA的特异性结合模式. 模拟结果表明, IN有特异性DNA结合区和非特异性DNA结合区; IN二聚体B链的K14, R20, K156, K159, K160, K186, K188, R199和A链的K219, W243, K244, R262, R263是IN结合病毒DNA的关键残基; 并从结构上解释了能使IN发挥活性的病毒DNA的最小长度是15 bp. 通过分析结合能发现, IN与DNA稳定结合的主要因素是非极性相互作用, 而关键残基与病毒DNA相互识别主要依赖于极性相互作用. 模拟结果与实验数据较吻合.     

Computational design of novel cyclic urea as HIV-1 protease inhibitor

A series of novel cyclic urea molecules 5,6-dihydroxy-1,3-diazepane-2,4,7-trione as HIV-1 protease inhibitors were designed using computational techniques. The designed molecules were compared with the known cyclic urea molecules by performing docking studies, calculating their ADME (Absorption, Distribution, Metabolism, and Excretion) properties and protein ligand interaction energy. These novel molecules were designed by substituting the P ₁/P′ ₁ positions (4 ^th and 7 ^th position of 1, 3-diazepan-2-one) with double bonded oxygens. This reduces the molecular weight and increases the bioavailability, indicating better ADME properties. The docking studies showed good binding affinity towards HIV-1 protease. The biological activity of these inhibitors were predicted by a model equation generated by the regression analysis between biological activity (log 1/K ⁱ ) of known inhibitors and their protein ligand interaction energy. The synthetic studies are in progress.      

Surface plasmon resonance study on HIV-1 integrase strand transfer activity

Understanding the molecular mechanism of HIV-1 integrase (IN) activity is critical to find functional inhibitors for an effective AIDS therapy. A robust, fast, and sensitive method for studying IN activity is required. In this work, an assay for real-time label-free monitoring of the IN activity based on surface plasmon resonance was developed. This assay enabled direct monitoring of the integration of a viral doubled-stranded (ds) DNA into the host genome. The strand transfer reaction was detected by using two different DNA targets: supercoiled plasmid (pUC 19) and short palindrome oligonucleotide. The effect of the length of the DNA target on the possibility to monitor the actual process of the strand transfer reaction is discussed. The surface density of integrated ds-DNA was determined. IN binding to the oligonucleotide complexes and model DNA triplexes in the presence of various divalent ions as metal cofactors was investigated as well. The assay developed can serve as an important analytical tool to search for potential strand transfer reaction inhibitors as well as for the study of compounds interfering with the binding of ds long terminal repeats–IN complexes with the host DNA. HIV-1 integrase strand transfer activity was monitored in real time using a multichannel surface plasmon resonance biosensor. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.