Characterization of JT-4-173, a Potent Antiviral that Inhibits HIV-1 by a Novel Mechanism of Action

摘要 截至2021年，超过3800万人感染了人类免疫缺陷病毒1型（HIV-1）。目前， 艾滋病病毒无法治愈，这些人必须终生接受口服药物治疗。高活性 抗逆转录病毒疗法（HAART）是一种标准的治疗方案， 毒品高效抗逆转录病毒疗法在控制病毒载量、减少传播和预防 为获得性免疫缺陷综合症（艾滋病）患者提供治疗。然而，长期以来- HAART的长期有效性由于耐药性而受到威胁。因此，开发小说 需要具有不同作用机制（MOA）的抗逆转录病毒药物来改进治疗选择。所有 HIV-1逆转录酶（RT）是HIV-1感染中最常见的靶向酶之一。 病毒RT的主要作用是将单链病毒RNA基因组转化为双链DNA （dsDNA）用于宿主基因组整合。非核苷类逆转录酶抑制剂（NNRTI）是FDA批准的 抗逆转录病毒药物通常包括在HAART中。它通过与RT结合，以阻止病毒dsDNA的形成。 不同的疏水口袋（NNIBP）在附近，但不重叠的酶的聚合酶活性位点。JT- 4-173（JT）是一种新的有效的HIV-1特异性抑制剂，以前在Sarafianos实验室中发现。最近的结构 我们实验室的研究表明，JT与NNIBP结合，但它不抑制正常的聚合。我们的初步 数据显示，JT对早期或晚期RT产品没有显著影响，但整合的数量 前病毒显著减少。在目前已知的任何NNRTI中均未观察到该行为。我 假设JT抑制链置换合成所需的聚合活性， 在后期逆转录步骤中完成dsDNA的形成。在这份提案中，我的目标是 确定JT对早期、中期和晚期逆转录产物的影响，沿着1-和2- 长末端重复序列（LTR）环和整合的前病毒（Aim 1.1），逆转录病毒的确切终止位点， 使用测序技术通过JT转录（目的1.2），以及JT对HIV-1 RT链的影响 使用引物延伸生物化学测定进行置换合成（目的1.3）。以测定分子 JT机制，我将使用低温电子显微镜（cryo-EM）来解决HIV-1 RT/JT结构， 与链置换位点相关的dsDNA底物复合（目的2.1），然后鉴定并突变 RT上的关键相互作用残基，以确认其对使用引物延伸的链置换合成的影响 含量测定（目的2.2）。这些研究将揭示JT对HIV-1逆转录的确切影响，并阐明JT对HIV-1逆转录的影响。 一种新型NNRTI的独特MOA。我将充分利用我们实验室在RT生物学方面的背景， 合作者在结构，测序和生物化学研究方面的专业知识，以完成这些建议 实验和提高我的训练。这些计划中的研究不仅将为制定一项 新的抗逆转录病毒药物，但也将提高我们对HIV-1 RT生物学的理解。

ABSTRACT As of 2021, over 38 million individuals are living with human immunodeficiency virus type 1 (HIV-1). Currently, there is no cure for HIV, and these individuals are subjected to life-long, oral drug therapy. Highly active antiretroviral therapy (HAART) is the standard treatment regimen comprising a cocktail of several antiretroviral drugs. HAART has made remarkable strides in controlling viral loads, reducing transmission, and preventing the onset of acquired immunodeficiency syndrome (AIDS) for patients with access to treatment. However, the long- term effectiveness of HAART remains threatened due to drug resistance. Therefore, developing novel antiretroviral drugs with different mechanisms of action (MOA) is required to improve therapeutic options. Of all approved antiretrovirals, the HIV-1 reverse transcriptase (RT) is one of the most frequently targeted enzymes in the virus. The primary role of RT is to convert the single-strand viral RNA genome into double-strand DNA (dsDNA) for host-genome integration. Non-nucleoside RT inhibitors (NNRTI) are one of the FDA-approved classes of antiretroviral often included in HAART. It stops the formation of the viral dsDNA by binding to RT at a distinct hydrophobic pocket (NNIBP) in proximity but not overlapping the enzyme’s polymerase active site. JT- 4-173 (JT) is a novel potent HIV-1 specific inhibitor previously identified in the Sarafianos lab. A recent structural study in our lab revealed that JT binds to the NNIBP, yet it does not inhibit normal polymerization. Our preliminary data showed that JT has no significant impact on early nor late-stage RT products, but the number of integrated proviruses significantly reduced. This behavior was not observed in any of the currently known NNRTIs. I hypothesize that JT inhibits the polymerization activity required for strand displacement synthesis, an essential step in late-stage reverse transcription for the complete formation of the dsDNA. In the proposal, I aim to determine the impact of JT on early-, intermediate- and late-reverse transcription products along with 1- and 2- long terminal repeat (LTR) circles and integrated provirus (Aim 1.1), the exact stopping site(s) of reverse transcription by JT using sequencing techniques (Aim 1.2), and the impact of JT on HIV-1 RT in strand displacement synthesis using a primer-extension biochemical assay (Aim 1.3). To determine the molecular mechanism of JT, I will use cryogenic electron microscopy (cryo-EM) to solve the HIV-1 RT/JT structures in complex with dsDNA substrates relevant to sites of strand displacement (Aim 2.1), then identify and mutate the key interactive residues on RT to confirm its effect on strand displacement synthesis using the primer-extension assay (Aim 2.2). These studies will reveal JT’s exact impact on HIV-1 reverse transcription and elucidate the unique MOA of a novel NNRTI. I will take full advantage of our lab’s background in RT biology and our collaborators’ specialties in structural, sequencing, and biochemical studies to complete these proposed experiments and advance my training. These planned studies will not only lay the foundation for developing a novel antiretroviral but will also improve our understanding of HIV-1 RT biology.