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.

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.

Pharmacophore and Docking-based 3D-QSAR Studies on HIV-1 Integrase Inhibitors

Integrase（IN） plays an essential role in the process of HIV-1 replication.IN inhibitors of diketo acid derivatives（DKAs） were analysed by the Comparative Molecular Field Analysis（CoMFA） and Comparative Molecular Similarity Induces Analysis（CoMSIA） methods.A set of 42 compounds were randomly selected as the training set（35） and test set（7）.Firstly,a good pharmacophore（goodness of hit=0.787） was obtained and used to align ligands.Then,predictive models were constructed with the CoMFA and CoMSIA methods based on the pharmacophore alignment.As a result,the CoMS1A method yielded the best model with an r2 of 0.955 and a q2 of 0.665,which can predict the activities of the tested DKAs very well（r2=0.559）.Finally,DKAs were docked into IN,and the predicit modes were superimposed on the contour maps obtained from the best CoMSIA model.The superimposed maps gave a visualized and meaningful insight into the inhibitory behaviors,providing significantly useful information for the rational drug design of anti-IN agents.

A Simple and Highly Efficient Preparation of Structurally Diverse Aryl β-diketoacids as HIV-1 Integrase Inhibitors

In order to provide a facile and practical access to structurally diverse aryl -diketoacids, An improved and highly efficient oxalylation method was developed which employed commercially available and cheap reagents. The oxalylation of aryl methyl ketones, the key step to construct the pharmacophore of aryl -diketoacids, was con-siderably facilitated by a new combination of dimethyl oxalate as an oxalic source and sodium tert-butoxide as a base. A wide variety of aryl -diketoacids bearing different functional groups can be prepared rapidly in high yields at room temperature with this method, which has significant advantages over the previously reported procedures in a wider application range, much less amount of reagents, pretty higher yields and quite shorter reaction time. The bis-aryldiketoacids 3k and 3l, readily prepared by this method, displayed interesting and promising inhibitory ac-tivities against HIV-1 integrase and HIV-1 replication in cells.

Investigation of formation of dimeric G-quadruplex of HIV-1 integrase inhibitor by nuclear magnetic resonance

In this research, an unusually dimeric G-quadruplex of d（GGGTGGGTGGGTGGGT） （SI）, the potent nanomolar HIV-1 integrase inhibitor, was detected by nuclear magnetic resonance （NMR）. This result has been confirmed by electrospray ionization mass spectrometry （ESI-MS） and circular dichroism （CD）.

Synthesis and HIV-1 Integrase Inhibitory Activity of Furanone Derivatives

Twenty novel furanone derivatives, based on the structure of raltegravir which was the first HIV-1 inte- grase（IN） inhibitor approved by the United States Food and Drug Administration（US FDA）, were designed, synthesized and characterized by ^1H NMR, IR and MS. The biological activities of these compounds against HIV-1 IN in vitro were evaluated. The assay results indicate that the replacement of pyrimidinone with furanone decreased the inhibitory activity of the compounds to HIV-1 IN. Compounds 3i, 3j and 3t show moderate inhibitory activity against HIV-1 IN and selectively inhibit the strand transfer reaction.

Peptide Inhibitors of HIV-1 Virus Infection Based on Cullin-5

Virion infectivity factor（Vif） is one of the six accessory proteins of HIV-1 and is necessary for viral infectivity. Human Apolipoprotein B editing complex protein 3G（h-APOBEC3G） is a cytidine deaminase only expressed in ＂nonpermissive＂ cells and exhibits virus suppressive activity. With the aid of a Cullin-5 E3 ligase, Vif induces h-APOBEC3G degradation and with the destruction of this ligase, Vif is functionally inactive. Therefore, it is expected that blocking this E3 pathway would be a new therapeutic strategy against HIV-1 infection. In this article, the authors＇ took sequence alignment of the N-termini of Cullin-5 and three other members of the Cullin protein family, respectively. A set of small peptides has been synthesized based on the sequence comparison results and possible Vif-Cullin-5 interaction domains. Moreover, it has been demonstrated that several peptides can reduce virus infectivity in ＂nonpermissive＂ cells with a dose-responsive manner, but not in ＂permissive＂ cells. The results also indicate that the loss of viral infectivity may be because of the increase of APOBEC3G amount in the peptide-treated cells. It is concluded that peptides derived from Cullin-5 can block the APOBEC3G degradation induced by Vif and suppress HIV-1 infectivity. Therefore this study starts a novel strategy for the development of a new HIV-1 inhibitor.

Synthesis of aromatic-linked polyamine macrocyclic derivatives as HIV-1 entry inhibitors

A series of novel aromatic-linked polyamine macrocyclic derivatives have been synthesized. Their structures were confirmed by MS and ^1H NMR. These compounds exhibited potent anti-HIV-1 activities.

Estimated Binding Energies of Drug-Like and Nondrug-Like Molecules in the Active Site of HIV-1 Integrase, 1BIS.pdb, and Two Mutant Models: Y143R and N155H

Lipinski’s “Rule of Five” was introduced for predicting oral bioavailability to describe drug-like molecules. For the purpose of this research the rules were used to separate potential inhibitors of HIV-1 integrase (1BIS.pdb) into two groups: drug-like and nondrug-like. If one of Lipinski’s “Rule of Five” was not followed the potential inhibitor was classified as nondrug-like. Thirty molecules were identified from the literature, twenty-four drug-like and six nondrug-like, that were docked into the active site of 1BIS.pdb (considered the non-mutated protein) and two mutant models, Y143R and N155H. These are two of the mutations that have led to increased resistance to HIV-1 integrase drugs such as raltegravir and elvitegravir. The computational software, ICM-Pro (Molsoft L.L.C.), was used to determine the estimated binding energy (EBE) of the drug/protein complex. It was found that the nondrug-like molecules generally had a more negative EBE, that is, tighter binding with 1BIS. pdb, though there were several exceptions in the drug-like group. With the protein mutant model Y143R, the majority of drug-like (58%) and nondrug-like molecules (67%) had tighter binding. However, for the mutant model N155H, there was the same percent (46%) of drug-like molecules with tighter binding with the mutant model as with 1BIS.pdb. The drug-like molecules were used when there was a ≥1 kcal/mole difference between 1BIS.pdb and either of the two mutant models to suggest a pharmacophore with structural characteristics for an HIV-1 integrase inhibitor.

Structure-Based Pharmacophore Modeling to Discover Novel CCR5 Inhibitors for HIV-1/Cancers Therapy

CC chemokine receptor 5 (CCR5), a member of G protein-coupled receptors (GPCRs), not only plays a significant role in inflammatory responses, but also correlates with HIV-1 infection and cancer progression. Recently, blocking of CCR5 has been considered as an effective strategy in HIV-1/cancers therapy. So far, only Maraviroc has been approved by FDA in 2007, while the other CCR5 inhibitors have failed in their clinical trials. In this study, a highly selective structure-based pharmacophore model was constructed, validated, and applied for virtual screening to retrieve novel CCR5 inhibitors from NCI database. Finally, one potential CCR5 inhibitor candidate, NSC13165, was identified after molecular docking, molecular dynamics (MD) simulations, binding free energy analyses and ADMET prediction. Docking and MD simulation results not only suggested that NSC13165 reserves the common binding mode of the most known CCR5 inhibitors, but also provided important insights toward the allosteric inhibition mechanism of CCR5. The results of binding free energy analyses indicated that the binding affinity of NSC13165 is much better than that of Maraviroc and that van der Waals interaction is the key driving force during the binding process. ADMET prediction suggested that NSC13165 exhibits very low risk of causing lethal side effects. Altogether, our results strongly suggest that NSC13165 has great potential to serve as a novel CCR5 inhibitor, which may be further tested in vitro/in vivo as a drug target for HIV-1/cancers therapy or be used as a lead compound for improving its efficacy through chemical modifications.

Mechanism of inhibitor ADS-J1 and ADS-J2 binding to HIV-1 gp41

In order to analyze and explain the mechanism of the two small inhibitors （ADS-JI and ADS-J2） binding to HIV-1 gp41, a computational study is carried out to help identifying possible binding modes by docking these compounds onto the hydrophobic pocket on gp41 and characterize structures of binding complexes. The binding interactions of gp41-molecule and free energies of binding are obtained through molecular dynamics simulation and molecular mechanic/Poisson- Boitzmann surface area （ MM/PBSA ） calculation. Specific molecular interactions in the gp41-inhibitor complexes are identified. The present computational study complements the corresponding experimental investigation and helps establish a good starting point tbr further refinement of small molecular gp41 inhibitors.

Synthesis, Crystal Structure and Anti-integrase Activity of 25,27-Bis[(Z)-4-(p-methoxyphenyl)-4-hydroxybut-3-en-2-one-1-methyl]-26,28-dihydroxycalix[4]arene

The title compound （C50H.44010） was synthesized and structurally determined by single-crystal X-ray diffraction method. It crystallizes in monoclinic, space group P21/c with a = 16.713（4）, b --- 13.189（3）, c = 19.434（5） A, β = 104.411（4）°, Mr = 804.85, Dc = 1.288 g/cm3, V = 4149.2（17） A3, Z = 4, F（000） = 1696, #（MoKa） = 0.089 mm-1T = 296（2） K, 7279 independent reflections with 3172 observed ones （I 〉 2δ（/））, R = 0.0520 and wR = 0.1203 with GOF = 0.928 （R = 0.1464 and wR = 0.1657 for all data）. The calixarene moiety maintains the symmetric cone conformation through intramolecular O-H…O hydrogen bonds. Preliminary bioassays indicated that the title compound has a potent inhibitory activity against the strand transfer process of HIV-1 integrase.

HIV-1 fusion inhibitor VIR576 interferes with T-cell activation by targeting TCR

Aim To determine the effect of VIR576, a dimeric 20-mer peptide potently inhibits HIV-1 entry, on antigen-specific T cell and non-antigen-specific T cell activation. Methods In vitro T-cell proliferation assays were estalished to investigate the potential effect of FP16, VIR576 on the proliferation of A2b cells in response to MOG35-55. A fluorescence-based binding assay using Rhodamine （Rho）-conjugated VIR576 was estalished to e- valuate the potential interaction between VIR576 and TCR-TMD. Fluorescence confocal microscopy was used to to study whether VIR576 could colocalize with CD4 molecule in the CD4 ＋ T cell membrane to interact with TCR. Re- suits The effects of VIR576 on the proliferation of MOG-specific A2b T cells in response to the stimulation of MOG 35 -55 peptide wasevaluated. VIR576 itself could directly inhibit antigen-specific T-cell activation. Further studies confirmed that VIR576 also inhibited the proliferation of splenocytes and primary CD4 ＋ CD25- T cells iso- lated from the spleens of DOll. 10 OVA Tg mice in response to OVA stimulation in vitro. However, VIR576 had no effect on the proliferation of normal mouse splenocytes and T lymphocytes stimulated with Con A or anti-CD3 anti- body. The FRET assay confirmed that VIR576 effectively binds to the core peptide （CP） , corresponding to the N- terminal 9-residue region of TCR-TMD. Confocal microscopy revealed that VIR576 colocalizes with CD4 on the ac- tivated CD4 ＋ T-cell membrane, particularly within the activation cluster including re-assembled CD4 and TCR mol- ecules. Conclusion These results suggest that VIR576 is effective in suppressing antigen-specific T-cell activa- tion, but it has no effect on non-specific T-cell proliferation, and VIR576 has the ability to down-regulate antigen- specific T-cell activation by interaction with TCR transmembrane domain.

HIV-1整合酶抑制剂的研究进展

HIV-1整合酶(integrase)是逆转录病毒复制所必需的酶,因而成为抗艾滋病(AIDS)药物设计的一个合理的靶点。本文综述了近几年的HIV-1整合酶及其抑制剂的发展现状,就如何将作用于整合酶靶点的先导化合物转变成有效的抗艾滋病药物进行了讨论。

多羟基芳香族化合物对HIV-1整合酶的抑制作用

目的 研究HIV 1整合酶抑制剂 ,为艾滋病的治疗提供新作用靶位的抗HIV药物。方法 用HIV 1整合酶ELISA法检测 3种萘醌类化合物 ,10种白藜芦醇及其衍生物和 7种吡喃香豆素类化合物对整合酶的抑制作用。结果 双羟基 1,4 萘醌 (NQ 2 )对HIV 1整合酶有抑制活性 ,IC50 为 78 5 μmol·L- 1 ,发现萘醌类新化合物NQ 3对HIV 1整合酶的抑制作用优于NQ 2 ,IC50 为 3 7 2 μmol·L- 1 。用分步测定法发现NQ 2主要抑制HIV 1整合酶的链转移活性 ,而NQ 3则对装配和链转移都有较强的抑制。结论 萘醌类化合物 (NQ 2 ,3 )对HIV 1整合酶有抑制作用 ,NQ

HIV-1整合酶3′端加工抑制剂筛选方法的建立与优化

目的建立与优化HIV-1整合酶3'端加工抑制剂筛选方法。方法利用荧光共振能量转移原理建立筛选方法,用DNaseⅠ切割底物DNA确定底物检测波长,在该检测波长下,对缓冲液成分、底物浓度、酶浓度、金属离子浓度等影响整合酶活性的条件进行优化,并用阳性药物雷特格韦和杨梅黄素进行方法验证。结果检测波长为495 nm/525 nm,使用缓冲液1、底物浓度500 nmol·L-1,整合酶浓度1μmol·L-1,镁离子浓度20 mmol·L-1时整合酶3'端加工活性最强。在此反应条件下雷特格韦和杨梅黄素能有效地抑制整合酶3'端加工活性。用所建立的方法筛选到2个有较强抑制整合酶3'端加工活性的抑制剂。结论该文成功建立并优化了HIV-1整合酶3'端加工抑制剂筛选方法。

HIV-1整合酶链转移抑制剂的QSAR研究与分子设计

为了研究人类免疫缺陷病毒1型(HIV-1)整合酶链转移抑制剂(INSTIs)抑制活性的定量构效关系(QSAR),从而获得活性更好的抑制剂,基于拓扑理论,计算了32种INSTIs分子的电拓扑状态指数(Ei)和电性距离矢量(Mj)。通过最佳变量子集回归(LBR)方法建立了化合物抑制活性的六元(M57,M14,E7,E13,E21,M36)QSAR模型。以模型中的6个参数为人工神经网络输入层构建反向传播(BP)算法模型,设定6∶2∶1的网络结构,相关系数R2由多元线性回归的0.946提升到0.992。分析模型的6个变量可知,影响INSTIs抑制活性的主要结构片段是>N—、—N—、—C—、—X、—C<、—CH和—OH。通过结构修饰提出3种具有较高抑制活性的新化合物。

基于结构的HIV-1整合酶抑制剂设计:计算机模拟方法

HIV整合酶是一种病毒编码蛋白质 ,它催化病毒DNA整合进入宿主基因组 ,这为开发新的抗HIV和抗艾滋病疗法提供了一个重要的靶标。综述通过计算机模拟方法进行基于结构的HIV 1整合酶抑制剂设计 ,内容包括基于配体 (如药效团 )和基于靶向 (如对接 )的设计方法以及三维定量构效关系研究。

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1.39kJ·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.

二酮酸类HIV-1整合酶抑制剂的定量构效关系

应用遗传函数分析法（GFA）和分子场分析法（MFA）对一系列二酮酸类整合酶抑制剂分别进行了二维和三维定量构效关系研究,并对随机选择的5个化合物组成的测试集进行了预测,外在预测的rpred^2值分别达到0.987和0.759,表明模型具有良好的预测能力,同时利用药效团分析的方法,验证了QSAR（quantitave structure- activity relationship）模型,并概括了疏水作用对抑制剂活性的重要影响.研究结果表明,电性描述符（Apol）对活性有重要影响,意味着抑制剂与金属离子的螯合作用,同时空间和结构因素特别是疏水作用也对活性有重要作用.利用这些规律进行了分子设计,在理论上获得了一些具有较高抑制剂活性的新的二酮酸类衍生物,并期待实验证实.