Structural optimization and de novo design of dengue virus entry inhibitory peptides.
Structural optimization and de novo design of dengue virus entry inhibitory peptides.
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DOI：
10.1371/journal.pntd.0000721
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发表时间：
2010-06-22
影响因子：
3.8
通讯作者：
Michael SF
中科院分区：
文献类型：
--
作者：
Costin JM;Jenwitheesuk E;Lok SM;Hunsperger E;Conrads KA;Fontaine KA;Rees CR;Rossmann MG;Isern S;Samudrala R;Michael SF
病毒融合包膜蛋白是开发病毒进入抑制剂的重要靶点。我们报告了一种用于登革热2型病毒（DENV-2）包膜（E）蛋白的肽抑制剂的计算设计方法，该方法使用来自蛋白质的预进入二聚体形式的高分辨率结构数据。通过使用预测策略以及结合“伪能量”的计算优化，我们能够设计出显示出低微摩尔病毒进入抑制活性的多个肽序列。两种最具活性的肽DN 57 opt和10AN 1被设计为分别置换结构域II铰链中的区域和第一个结构域I/结构域II β折叠连接，并且在病灶形成单位测定中分别显示出8 μ M和7 μM的50%抑制浓度。抗病毒肽被证明干扰病毒：细胞结合，直接与E蛋白相互作用，并分别使用生物层干涉法和冷冻电子显微镜观察病毒表面。这些肽可用于表征膜融合过程中的中间状态，DENV受体分子的研究，以及作为药物发现的先导化合物。病毒表面蛋白在感染过程的初始事件期间介导与靶细胞的相互作用。因此，抑制这些蛋白质是开发抗病毒药物的主要目标。然而，有大量不同的病毒，每种病毒都有自己独特的表面蛋白，除了少数例外，目前还不清楚如何构建新的分子来抑制它们。在这里，我们将计算结合优化策略应用于登革热病毒血清2型包膜蛋白的原子分辨率结构，以生成应与该蛋白强烈相互作用的肽序列。我们选择登革热病毒作为目标，因为它是最重要的蚊子传播病毒性疾病的病原体。在设计和测试的少量候选物中，我们鉴定了两种不同的高度抑制性肽。为了验证我们的结果，我们表明这些肽阻断病毒：细胞结合，干扰病毒进入过程中的一个步骤，改变登革病毒颗粒的表面结构，并且它们直接与登革病毒包膜蛋白相互作用。我们希望我们的方法可以普遍适用于其他病毒表面蛋白的高分辨率结构是可用的。
Viral fusogenic envelope proteins are important targets for the development of inhibitors of viral entry. We report an approach for the computational design of peptide inhibitors of the dengue 2 virus (DENV-2) envelope (E) protein using high-resolution structural data from a pre-entry dimeric form of the protein. By using predictive strategies together with computational optimization of binding “pseudoenergies”, we were able to design multiple peptide sequences that showed low micromolar viral entry inhibitory activity. The two most active peptides, DN57opt and 1OAN1, were designed to displace regions in the domain II hinge, and the first domain I/domain II beta sheet connection, respectively, and show fifty percent inhibitory concentrations of 8 and 7 µM respectively in a focus forming unit assay. The antiviral peptides were shown to interfere with virus:cell binding, interact directly with the E proteins and also cause changes to the viral surface using biolayer interferometry and cryo-electron microscopy, respectively. These peptides may be useful for characterization of intermediate states in the membrane fusion process, investigation of DENV receptor molecules, and as lead compounds for drug discovery. Virus surface proteins mediate interactions with target cells during the initial events in the process of infection. Inhibiting these proteins is therefore a major target for the development of antiviral drugs. However, there are a very large number of different viruses, each with their own distinct surface proteins and, with just a few exceptions, it is not clear how to build novel molecules to inhibit them. Here we applied a computational binding optimization strategy to an atomic resolution structure of dengue virus serotype 2 envelope protein to generate peptide sequences that should interact strongly with this protein. We picked dengue virus as a target because it is the causative agent for the most important mosquito transmitted viral disease. Out of a small number of candidates designed and tested, we identified two different highly inhibitory peptides. To verify our results, we showed that these peptides block virus:cell binding, interfere with a step during viral entry, alter the surface structure of dengue viral particles, and that they interact directly with dengue virus envelope protein. We expect that our approach may be generally applicable to other viral surface proteins where a high resolution structure is available.
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