Chemical Biology of HIV-1 Nef

HIV-1 Nef 的化学生物学

• 批准号: 10684695
• 负责人: Thomas E. Smithgall
• 金额: $ 62.75万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10684695
• 关键词: 3-Dimensional; Acquired Immunodeficiency Syndrome; Affect; Anti-Retroviral Agents; Autologous; Binding; Binding Sites; Biological Assay; Biology; CD4 Positive T Lymphocytes; CD8-Positive T-Lymphocytes; Cell Surface Receptors; Cell surface; Cells; Chemicals; Coculture Techniques; Codon Nucleotides; Complement; Complex; Crystallography; Cytoplasmic Tail; Cytotoxic T-Lymphocytes; Data; Development; Down-Regulation; Drug Targeting; Effector Cell; Exclusion; Fluorescence; HIV; HIV Infections; HIV-1; HIV/AIDS; Immune; Immune system; In Vitro; Infection; Laboratories; Libraries; Life Cycle Stages; Ligand Binding; Link; Maps; Mediating; Methods; Molecular; Molecular Conformation; Mutagenesis; Mutation; Nucleotides; Patients; Peripheral Blood Mononuclear Cell; Pharmaceutical Chemistry; Pharmaceutical Preparations; Phosphotransferases; Protein Tyrosine Kinase; Proteins; Proteomics; Publishing; Receptor Down-Regulation; Reporter; Reporting; Role; SH3 Domains; Structure; Surface; System; Tail; Testing; Therapeutic; Transcription Factor AP-1; Triplet Multiple Birth; Viral; Viral reservoir; Virion; Virus; Virus Replication; Work; X-Ray Crystallography; antiretroviral therapy; clinical translation; cytotoxicity; deep sequencing; drug candidate; drug development; experimental study; ezrin; in vivo; inhibitor; innovation; insight; latent HIV reservoir; mutant; nef Protein; novel; novel strategies; novel therapeutic intervention; protein complex; receptor downregulation; recruit; relapse prevention; response; small molecule; src Homology Region 2 Domain; src-Family Kinases; therapeutic target; virtual

Summary. Existing antiretroviral drugs do not clear HIV-1 latent reservoirs, underscoring the urgent need for new therapeutic strategies. The HIV-1 Nef accessory factor is an attractive target for drug development because of its critical roles in the HIV-1 life cycle and immune system escape. Our group has discovered novel small molecules that bind directly to Nef and block many of its functions, including enhancement of viral infectivity and replication in donor PBMCs. Importantly, our Nef inhibitors rescue cell-surface MHC-I expression in latently infected, patient-derived CD4+ T-cells, enabling recognition and killing by autologous CTLs. Thus, Nef inhibitors represent an innovative approach to antiretroviral therapy that may provide a path to eradication of viral reservoirs. Our most promising class of inhibitors (hydroxypyrazoles) bind tightly to their Nef protein target in vitro and are active against multiple Nef functions in cell-based systems without cytotoxicity. Experiments proposed here will leverage these compounds as chemical probes to shed new light on Nef functions while unraveling their mechanism of action with the following Specific Aims: Aim 1. Map the binding site for hydroxy- pyrazole Nef inhibitors by X-ray crystallography. Preliminary and published data strongly suggest that hydroxy- pyrazole Nef inhibitors, which disrupt multiple Nef functions, may perturb the structure of functional Nef-effector complexes. X-ray crystallography of inhibitors with Nef alone and in complexes with host cell effector proteins will be used to test this idea and identify inhibitor binding sites. Aim 2. Identification of Nef residues essential for inhibitor action through in vitro selection. Using PCR-based saturation mutagenesis, we have replaced every codon in the Nef core region with each of the 64 nucleotide triplets in the context of HIV-1. CD4 T cells will be infected with the Nef mutant viral ‘library’ in the presence or absence of Nef inhibitors, and viral supernatants analyzed by deep sequencing to identify mutations enriched by inhibitor treatment. This method has the potential to identify Nef regions that allosterically influence inhibitor action in addition to residues directly involved in ligand binding. Aim 3. Explore the mechanisms by which Nef inhibitors suppress HIV-1 infectivity. Hydroxypyrazole Nef inhibitors reduce HIV-1 infectivity in TZM-bl reporter cells to the same extent as Nef-deleted viruses. This Aim will explore the whether Nef inhibitors restore virion incorporation of SERINC proteins and Ezrin, two host cell restriction factors linked to Nef. We will also pursue Nef inhibitor effects on overall HIV-1 protein composition by whole-virus proteomics, which has the potential to identify host cell factors that are uniquely incorporated (or excluded) by Nef inhibition. Aim 4. Investigate the mechanism of Nef inhibitor action on MHC-I downregulation. This Aim will explore the effect of Nef inhibitors on crystal structures of Nef in complexes with the MHC-I cyto- plasmic tail and the AP-1 µ1 subunit, interactions essential for immune escape. Inhibitor effects on Nef interac- tions with MHC-I and AP-1 will also be explored in cells using bimolecular fluorescence complementation (BiFC). These studies will clarify the mechanisms by which Nef inhibitors restore CTL responses to HIV infection.

总结。现有的抗逆转录病毒药物并没有清除HIV-1潜伏的宿主，这突显出迫切需要 新的治疗策略。HIV-1 Nef辅助因子是药物开发的一个有吸引力的目标，因为 它在艾滋病毒-1生命周期和免疫系统逃逸中的关键作用。我们小组发现了新奇的小 直接与Nef结合并阻断其许多功能的分子，包括增强病毒感染性和 供者外周血单核细胞的复制。重要的是，我们的Nef抑制剂潜伏地拯救细胞表面MHC-I的表达 受感染的患者来源的CD4+T细胞，能够通过自体CTL识别和杀伤。因此，Nef 抑制剂代表了一种抗逆转录病毒治疗的创新方法，可能提供一条根除 病毒库。我们最有希望的一类抑制剂(羟基吡唑)与其Nef蛋白靶标紧密结合 在体外，并且在基于细胞的系统中对多种Nef功能具有活性，而没有细胞毒性。实验 将利用这些化合物作为化学探针来揭示Nef的功能，同时 目的1.绘制羟基的结合部位图。 用X-射线结晶学方法研究了吡唑类Nef抑制剂。初步和已发表的数据强烈表明，羟基- 吡唑类Nef抑制剂可干扰多种Nef功能，可能扰乱功能性Nef效应器的结构 复合体。Nef单独及与宿主细胞效应蛋白复配的抑制剂的X射线结晶学研究 将被用来测试这一想法并确定抑制剂结合位点。目标2.鉴定Nef残留物 通过体外筛选发挥抑制作用。使用基于聚合酶链式反应的饱和突变，我们已经取代了每一个 Nef核心区的密码子与HIV-1背景下的每个核苷酸三联体。CD4T细胞将是 在存在或不存在Nef抑制剂和病毒上清液的情况下感染Nef突变病毒‘文库’ 通过深度测序分析，以确定通过抑制剂处理而丰富的突变。这种方法有可能 除了与配基直接相关的残基外，确定影响抑制剂作用的变构的Nef区域 有约束力的。目的3.探讨Nef抑制剂抑制HIV-1感染性的机制。羟基吡拉唑 Nef抑制剂可降低TZM-bl报告细胞中HIV-1的传染性，其程度与Nef缺失病毒的程度相同。这 目的探讨Nef抑制剂是否能恢复SERINC蛋白和Ezrin两种宿主的病毒粒子掺入 与Nef相关的细胞限制因子。我们还将研究Nef抑制剂对整体HIV-1蛋白质组成的影响 通过全病毒蛋白质组学，它有可能识别唯一结合的宿主细胞因子(或 被Nef抑制。目的4.探讨Nef抑制剂对MHC-I下调的作用机制。 本研究旨在探讨Nef抑制剂对MHC-I细胞与Nef形成的复合物中Nef晶体结构的影响。 胞浆尾巴和AP-1µ1亚基，相互作用是免疫逃逸所必需的。抑制剂对Nef相互作用的影响 还将使用双分子荧光互补(BIFC)在细胞中探索带有MHC-I和AP-1的TIONS。 这些研究将阐明Nef抑制剂恢复对HIV感染的CTL反应的机制。

项目成果

Inhibitors of HIV-1 Nef-Mediated Activation of the Myeloid Src-Family Kinase Hck Block HIV-1 Replication in Macrophages and Disrupt MHC-I Downregulation.

• DOI: 10.1021/acsinfecdis.1c00288
• 发表时间: 2022-01-14
• 期刊: ACS INFECTIOUS DISEASES
• 影响因子: 5.3
• 作者: Emert-Sedlak, Lori A.;Moukha-Chafiq, Omar;Shi, Haibin;Du, Shoucheng;Alvarado, John J.;Pathak, Vibha;Tanner, Samuel G.;Hunter, Robert N.;Nebane, Miranda;Chen, Li;Ilina, Tatiana, V;Ishima, Rieko;Zhang, Sixue;Kuzmichev, Yury, V;Wonderlich, Elizabeth R.;Schader, Susan M.;Augelli-Szafran, Corinne E.;Ptak, Roger G.;Smithgall, Thomas E.
• 通讯作者: Smithgall, Thomas E.

Antiretroviral Drug Discovery Targeting the HIV-1 Nef Virulence Factor.

靶向HIV-1 NEF毒力因子的抗逆转录病毒药物发现。

• DOI: 10.3390/v14092025
• 发表时间: 2022-09-13
• 期刊: Viruses
• 作者: Emert-Sedlak LA;Shi H;Tice CM;Chen L;Alvarado JJ;Shu ST;Du S;Thomas CE;Wrobel JE;Reitz AB;Smithgall TE
• 通讯作者: Smithgall TE

Visualization of Host Cell Kinase Activation by Viral Proteins Using GFP Fluorescence Complementation and Immunofluorescence Microscopy.

使用 GFP 荧光互补和免疫荧光显微镜观察病毒蛋白对宿主细胞激酶的激活。

• DOI: 10.21769/bioprotoc.4068
• 发表时间: 2021
• 期刊: Bio-protocol
• 影响因子: 0.8
• 作者: Shu,SherryT;Li,WingFai;Smithgall,ThomasE
• 通讯作者: Smithgall,ThomasE

Tight-Binding Hydroxypyrazole HIV-1 Nef Inhibitors Suppress Viral Replication in Donor Mononuclear Cells and Reverse Nef-Mediated MHC-I Downregulation.

• DOI: 10.1021/acsinfecdis.9b00382
• 发表时间: 2020-02-14
• 期刊: ACS infectious diseases
• 影响因子: 5.3
• 作者: Shi H;Tice CM;Emert-Sedlak L;Chen L;Li WF;Carlsen M;Wrobel JE;Reitz AB;Smithgall TE
• 通讯作者: Smithgall TE