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.

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.

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）.

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.

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.

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.

Inhibitors of HIV-1 Integrase-Human LEDGF/p75 Interaction Identified from Natural Products via Virtual Screening

HIV-1 integrase （IN）-mediated integration of viral DNA into the host chromosome is an essential step in the virus life cycle. Human lens epithelium-derived growth factor （LEDGF/p75） has been found to function as a cellu- lar cofactor in this process. The LEDGF/p75-1N interaction hence represents an attractive target for anti-HIV ther- apy. In this study, natural products were virtually screened against the LEDGF/p75 binding pocket of HIV-1 IN. 24 compounds were selected and obtained from the National Compound Resource Center of China. AlphaScreen as- says characterized 8 of these 24 natural products as potent LEDGF/p75-IN interaction inhibitors. The active com- pounds whose ICs0 values ranged from 0.56 to 14.55 ~mol/L could be used as lead compounds for further investi- gation. This work confirmed that natural products are valuable resources for antiviral drug discovery.

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.

Development of a high-throughput assay for the HIV-1 integrase disintegration reaction

Both HIV-1 integrase (IN) and the central catalytic domain of IN (IN-CCD) catalyze the disintegration reaction in vitro.In this study,IN and IN-CCD proteins were expressed and purified,and a high-throughput format enzyme-linked immunosorbent assay (ELISA) was developed for the disintegration reaction.IN exhibited a marked preference for Mn2+ over Mg2+ as the divalent cation cofactor in disintegration.Baicalein,a known IN inhibitor,was found to be an IN-CCD inhibitor.The assay is sensitive and specific for the study of disintegration reaction as well as for the in vitro identification of antiviral drugs targeting IN,especially targeting IN-CCD.

Study on the drug resistance and the binding mode of HIV-1 integrase with LCA inhibitor

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. The binding mode of the wild type IN core domain and its G140S mutant with L-Chicoric acid (LCA) inhibitor were investigated by using multiple conformation molecular docking and molecular dynamics (MD) simulation. Based on the binding modes, the drug resistance mechanism was explored for the G140S mutant of IN with LCA. The results indicate that the binding site of the G140S mutant of IN core domain with LCA is different from that of the core domain of the wild type IN, which leads to the partial loss of inhibition potency of LCA. The flexibility of the IN functional loop region and the interactions between Mg2+ ion and the three key residues (i.e., D64, D116, E152) stimulate the biological operation of IN. The drug resistance also lies in several other important effects, such as the repulsion between LCA and E152 in the G140S mutant core domain, the weakening of K159 binding with LCA and Y143 pointing to the pocket of the G140S mutant. All of the above simulation results agree well with experimental data, which provide us with some helpful information for designing the drug of anti-HIV based on the structure of IN.

In vitro selection of G-rich RNA aptamers that target HIV-1 integrase

Aptamers that interact with various HIV-1 proteins,such as reverse transcriptase,Rev,Tat protein,and nuclear capsule protein,have been prepared through SELEX (systematic evolution of ligands by ex-ponential enrichment) technique. However,there are few reports about the DNA or RNA aptamers that target HIV-1 integrase. In this investigation,we selected alternative RNA aptamers specific for the HIV-1 integrase by using a different binding buffer containing 10 mmol·L-1 MgCl2 and 100 mmol·L-1 KCl. Aptamer IN1,IN2,IN3 had similar and the highest Kd values from 145 to 239 nmol·L-1. Structural studies showed that they formed similar stem-loop structure. Deletion of any stem structure resulted in diminished affinity. In addition,structure probing study with antisense DNA indicated that the stem-loop structure in the random region was critical for integrase binding. Although aptamer IN1 failed to form G-quartet structure,it might directly interact with the DDE motif of integrase,which is the virus DNA-binding site,because G-quadruplex T40214 competitively inhibited the interaction between IN1 and integrase. Together,this study generated a novel RNA aptamer IN1,which could be useful in basic research and anti-HIV drug screening.

Suppression of HIV-1 Integration by Targeting HIV-1 Integrase for Degradation with A Chimeric Ubiquitin Ligase

Human immunodeficiency virus(HIV) attacks human immune system and causes life-threatening acquired immune deficiency syndrome(AIDS). Treatment with combination antiretroviral therapy(cART) could inhibit virus growth and slow progression of the disease, however, at the same time posing various adverse effects. Host ubiquitin-proteasome pathway(UPP) plays important roles in host immunity against pathogens including viruses by inducing degradation of viral proteins. Previously a series of methods for retargeting substrates for ubiquitin-proteasome degradation have been successfully established. In this study, we attempted to design and construct artificial chimeric ubiquitin ligases(E3 s) based on known human E3 s in order to manually target HIV-1 integrase for ubiquitin proteasome pathway-mediated degradation.Herein, a series of prototypical chimeric E3 s have been designed and constructed, and original substrate-binding domains of these E3 s were replaced with host protein domains which interacted with viral proteins. After functional assessment screening, 146 LI was identified as a functional chimeric E3 for HIV-1 NL4-3 integrase. 146 LI was then further optimized to generate 146 LIS(146 LI short) which has been shown to induce Lys48-specific polyubiquitination and reduce protein level of HIV-1 NL4-3 integrase more effectively in cells. Lymphocyte cells with 146 LIS knock-in generated by CRISPR/Cas-mediated homology-directed repair(HDR) showed remarkably decreased integration of HIV-1 NL4-3 viral DNAs and reduced viral replication without obvious cell cytotoxicity. Our study successfully obtained an artificial chimeric E3 which can induce Lys48-specific polyubiquitination and proteasome-mediated degradation of HIV-1 NL4-3 integrase, thus effectively inhibiting viral DNA integration and viral replication upon virus infection.

姜黄素调控转录因子FOXP3影响HIV-1感染辅助受体CCR5的作用机制研究

目的:探讨姜黄素通过调控转录因子FOXP3影响HIV-1感染辅助受体CCR5的作用机制。方法:利用生物信息学方法预测并分析转录因子FOXP3与CCR5启动子的结合位点;采用AutoDock 4.2软件对姜黄素与FOXP3进行柔性对接;MTT法检测姜黄素对Jurkat细胞活性的影响;qRT-PCR和Western blot检测不同浓度姜黄素作用于Jurkat细胞后CCR5和FOXP3 mRNA和蛋白表达水平;构建pcDNA3.1-FOXP3真核表达载体;结合转录因子预测结果,运用Overlap PCR法扩增突变型CCR5基因片段,构建突变型CCR5启动子报告载体pFireRluc-Mt-CCR5;利用双荧光素酶报告基因技术验证转录因子FOXP3与CCR5的启动子结合位点。结果:JASPAR转录因子预测结果显示,CCR5启动子区与转录因子FOXP3存在结合位点;分子对接结果显示,姜黄素能够与FOXP3的酶活区域结合;MTT结果显示,姜黄素作用24 h后对Jurkat细胞活性产生抑制作用,IC50为34.48μmol/L;qRT-PCR和Western bot结果显示,不同浓度姜黄素作用于Jurkat细胞后,CCR5和FOXP3 mRNA和蛋白表达水平均降低,且存在剂量依赖性;双荧光素酶报告基因技术证实FOXP3能够与CCR5启动子结合,且转录因子FOXP3可调控CCR5启动子活性;过表达FOXP3后,姜黄素对CCR5的作用结果显示:当姜黄素浓度为60μmol/L时,作用于共转染pcDNA3.1-FOXP3和pFireRluc-Wt-CCR5的HEK293T细胞CCR5启动子荧光素酶活性相对值明显高于pFireRluc-Wt-CCR5+curcumin-60组(P<0.01)。结论:FOXP3能够调控CCR5启动子活性,其作用机制可能是姜黄素通过作用于FOXP3与CCR5启动子结合位点影响CCR5启动子活性。

HIV-1整合酶基因序列分析方法验证

目的 验证实验室自建人类免疫缺陷病毒1型(HIV-1)整合酶基因序列分析方法。该方法可用于评估HIV-1整合酶区段基因型耐药水平。方法 根据世界卫生组织自建基因序列分析方法验证的建议,从20份HIV-1阳性样本中提取RNA,扩增HIV-1整合酶区基因片段,并测序。通过与病毒质量保证(VQA)共识进行比对,评估实验室自建的HIV-1整合酶基因序列分析方案的准确性,通过扩增成功率评估其灵敏度,通过同一样本的重复检测结果评估其精密度和重现性。结果 20份样本与VQA共识的核苷酸一致率均>98%;10个高病毒载量(>10 000拷贝·mL^(-1))样本和5个低病毒载量(1 000~5 000拷贝·mL^(-1))样本的扩增成功率均为100%;4个样本的同批次5复孔和5个样本5次检测的结果均符合90%的样本配对比较核苷酸一致率>98%的要求。结论 该HIV-1整合酶基因序列分析方法的准确性、灵敏度、精密度和重现性均符合要求,适用于HIV-1整合酶基因序列分析。

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.

黄芩、猫眼草、连翘单味中药体外抗HIV-1病毒活性的研究

目的:构建抗人类免疫缺陷病毒(human immunodeficiency virus,HIV)-1假病毒药物筛选平台,在此基础上观察黄芩、猫眼草、连翘单味中药对HIV假病毒感染MAGI-CCR5细胞系的影响,评价其抗病毒作用。方法:选用重组质粒PLAI(含HIV包膜蛋白基因)和重组质粒JRFC(含HIV骨架基因)共转染293T细胞制备假病毒,建立假病毒筛选平台;采用MTT法检测药物对MAGI-CCR5细胞增殖的影响,筛选出对细胞无毒性的最合适浓度。通过药物体外对假病毒感染MAGI-CCR5的抑制实验,观察3种单味中药水煎液体外抗HIV-1病毒的活性。结果:3种单味中药均有体外抗HIV假病毒作用,且抗病毒作用与药物质量分数呈明显的剂量效应关系,2.17 mg/L黄芩、3.45 mg/L猫眼草、2.50 mg/L连翘表现出最高抑制率,依次是41.87%、37.38%、14.12%。结论:单味中药黄芩、猫眼草具有较好的体外抗HIV病毒的作用,连翘的抗HIV病毒作用相对较弱。

2021—2023年贵港市HIV-1感染者的流行特征和检测结果分析

目的分析2021—2023年贵港市人类免疫缺陷病毒1型(HIV-1)抗体阳性者的免疫蛋白印迹试验(WB)带型特征,探讨免疫状况及相关指标在获得性免疫缺陷综合征(AIDS)发展中的作用。方法对2021—2023年1719份经贵港市AIDS确证实验室确证为HIV-1抗体阳性且在治疗前开展了CD4^(+)T淋巴细胞检测的样本,用SPSS 25.0分析人口学特征和实验室相关检测结果。结果1719例HIV-1抗体阳性以男性、40岁以上、已婚、农民、文化程度较低、医疗机构临床筛查为主;CD4^(+)T淋巴细胞计数与年龄呈负相关,与WB条带数呈正相关(P<0.05)。带型p55、p39、p17检出阳性率在不同免疫程度和病程间差异有统计学意义(P<0.05)。结论农民仍然是贵港市AIDS宣教、检测工作的重点人群,p55、p39和p17可作为疾病发展和免疫情况的一个潜在判别依据。

HIV-1耐药检测技术进展

艾滋病病毒已在全球肆虐40多年,对全球公共卫生造成极大压力,时至今日艾滋病仍然是全球公共卫生面临的一道医学难题。高效联合抗病毒疗法(HAART)是艾滋病治疗的首选方案,已为众多艾滋病患者/人类免疫缺陷病毒(HIV)感染者带来巨大福祉,并为减缓艾滋病病毒的进一步传播发挥了很大作用。但随着这一方案的全面推广与应用,HIV-1耐药性也日益突出。HIV-1耐药性是影响临床抗病毒治疗效果的主要原因之一,因此进行HIV-1耐药性检测,对抗病毒药物的优化与选择、降低传播性耐药发生与防控十分重要。HIV-1耐药检测方法众多,因应用场景不同而方法各异,本文汇总国内外众多文献资料,就HIV-1耐药检测方法进行综述。

2016-2022年湖州市无偿献血人群HIV-1新发感染特征研究

目的探讨2016-2022年湖州市无偿献血人群人类免疫缺陷病毒(HIV)-1新发感染特征情况。方法回顾性纳入2016年1月-2022年12月湖州市无偿献血人群血液标本233552份。经健康检查合格的献血者,献血时通过旁路留取EDTA-K2抗凝血液标本,采用酶联免疫吸附实验(ELISA法)分别进行HIV抗原/抗体的初检和复检,严格按照《全国艾滋病检测技术规范》(2015年修订版)中标准判定结果,将HIV-1抗体阳性的标本使用HIV-1新发感染酶免疫检测试剂盒,采用限制性抗原亲和力法检测标本是否为新发感染,若标本CD4细胞>200个/L且病毒载量>1000拷贝/mL则定义为新发感染。比较各年度的HIV-1抗体阳性情况,以HIV-1抗体阳性作为基数,采用卡方检验,比较HIV-1抗体阳性患者不同类型(性别、年龄、职业等)亚组HIV-1新发感染率。结果2016-2022年湖州市无偿献血人群血液标本233552份,其中HIV-1抗体阳性标本共15份,感染率为6.42/10万,其中新发感染和既往感染占比分别为40.00%和60.00%。2016-2022年,HIV-1感染率逐年下降(1.62%、1.24%、0.63%、0.31%、0.30%、0.28%和0.27%)。比较HIV-1抗体阳性15名患者不同类型(性别、年龄、职业等)亚组HIV-1新发感染率发现:重复献血亚组HIV-1新发感染率高于初次献血亚组,但组间比较统计学无差异(P>0.05);男性HIV-1新发感染率高于女性,但组间比较统计学无差异(P>0.05);在不同学历HIV-1抗体阳性献血者中,初中及以下新发感染占比较高,但与其他学历亚组人群比较无差异(P>0.05);不同职业亚组的HIV-1新发感染率比较也无统计学差异(P>0.05)。结论湖州地区近年来HIV-1新发感染率逐年下降,且新发感染的发生在初次献血与重复献血亚组及不同性别、学历、职业等亚组中无明显分布特征。

Evolution of Mother-to-Child HIV-1 Transmission Rate in Mali from 2009 to 2018

Despite enormous efforts to achieve the goal of eliminating mother-to-child transmission of HIV-1, it remains a major challenge for many countries in sub-Saharan Africa, particularly Mali. Our objective is to assess changes in the rate of mother-to-child transmission of HIV-1. We conducted a cross-sectional study between January 1, 2009 to December 31, 2018 (10 years) of early diagnosis activity in newborns and children born to HIV-1-positive mothers at the National Institute for Public Health (INSP). The samples came from health and referral centers in mali. All samples were received at the Laboratory of Molecular Biology at the INSP. Proviral DNA extraction was performed from a blood spot sample with a Roche DNA kit, Cobas AmpliPrep/Cobas TaqMan HIV-1 qualitative Test, V2.0 (Roche Molecular System, Inc, USA) following the company procedures. Molecular diagnosis was performed using the same kits using an algorithm of three identical PCRs. The Epi Info version 7 software was used for data analysis with a significance threshold of 5%. A total of 10,714 samples of infants and children born to HIV-positive mothers were analyzed by PCR. Ninety-six percent of mothers were on ARV prophylaxis (AZT 3TC NVP and AZT NVP) and 60% of newborns received the same ARV prophylaxis. Of these children, 956 tested positive with an overall transmission rate of 8.92%, varying between 7.27% in 2009 and 08.01% in 2018. This rate was relatively low among children receiving prophylaxis at 2.04% and remained high for children who received breastfeeding at 5.62%. However, the transmission rate remains low for those who have benefited from mixed and artificial breastfeeding at 1.58% and 1.27% respectively. A significant proportion of children remained infected by their mothers during pregnancy, childbirth or breastfeeding. This study shows the importance of early diagnosis of HIV in children using molecular technology.