Vithani Neha, Ward Michael D, Zimmerman Maxwell I, Novak Borna, Borowsky Jonathan H, Singh Sukrit, Bowman Gregory R
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States.
Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States.
bioRxiv. 2020 Dec 10:2020.12.10.420109. doi: 10.1101/2020.12.10.420109.
Coronaviruses have caused multiple epidemics in the past two decades, in addition to the current COVID-19 pandemic that is severely damaging global health and the economy. Coronaviruses employ between twenty and thirty proteins to carry out their viral replication cycle including infection, immune evasion, and replication. Among these, nonstructural protein 16 (Nsp16), a 2'-O-methyltransferase, plays an essential role in immune evasion. Nsp16 achieves this by mimicking its human homolog, CMTr1, which methylates mRNA to enhance translation efficiency and distinguish self from other. Unlike human CMTr1, Nsp16 requires a binding partner, Nsp10, to activate its enzymatic activity. The requirement of this binding partner presents two questions that we investigate in this manuscript. First, how does Nsp10 activate Nsp16? While experimentally-derived structures of the active Nsp16/Nsp10 complex exist, structures of inactive, monomeric Nsp16 have yet to be solved. Therefore, it is unclear how Nsp10 activates Nsp16. Using over one millisecond of molecular dynamics simulations of both Nsp16 and its complex with Nsp10, we investigate how the presence of Nsp10 shifts Nsp16's conformational ensemble in order to activate it. Second, guided by this activation mechanism and Markov state models (MSMs), we investigate if Nsp16 adopts inactive structures with cryptic pockets that, if targeted with a small molecule, could inhibit Nsp16 by stabilizing its inactive state. After identifying such a pocket in SARS-CoV-2 Nsp16, we show that this cryptic pocket also opens in SARS-CoV-1 and MERS, but not in human CMTr1. Therefore, it may be possible to develop pan-coronavirus antivirals that target this cryptic pocket.
Coronaviruses are a major threat to human health. These viruses employ molecular machines, called proteins, to infect host cells and replicate. Characterizing the structure and dynamics of these proteins could provide a basis for designing small molecule antivirals. In this work, we use computer simulations to understand the moving parts of an essential SARS-CoV-2 protein, understand how a binding partner turns it on and off, and identify a novel pocket that antivirals could target to shut this protein off. The pocket is also present in other coronaviruses but not in the related human protein, so it could be a valuable target for pan-coronavirus antivirals.
在过去二十年中，冠状病毒已引发多次疫情，此外还有当前严重损害全球健康和经济的新冠疫情。冠状病毒利用二十到三十种蛋白质来完成其病毒复制周期，包括感染、免疫逃逸和复制。其中，非结构蛋白16（Nsp16）作为一种2'-O-甲基转移酶，在免疫逃逸中起着至关重要的作用。Nsp16通过模仿其人类同源物CMTr1来实现这一点，CMTr1会使mRNA甲基化以提高翻译效率并区分自身与其他物质。与人类CMTr1不同，Nsp16需要一个结合伴侣Nsp10来激活其酶活性。这种结合伴侣的需求提出了两个我们在本论文中研究的问题。第一，Nsp10如何激活Nsp16？虽然存在活性Nsp16/Nsp10复合物的实验性结构，但无活性的单体Nsp16的结构尚未得到解析。因此，尚不清楚Nsp10如何激活Nsp16。我们通过对Nsp16及其与Nsp10的复合物进行超过一毫秒的分子动力学模拟，研究Nsp10的存在如何改变Nsp16的构象集合以激活它。第二，在这种激活机制和马尔可夫状态模型（MSM）的指导下，我们研究Nsp16是否会采用具有隐秘口袋的无活性结构，如果用小分子靶向这些口袋，是否可以通过稳定其无活性状态来抑制Nsp16。在确定了新冠病毒Nsp16中的这样一个口袋后，我们表明这个隐秘口袋在非典冠状病毒-1和中东呼吸综合征冠状病毒中也会打开，但在人类CMTr1中不会。因此，有可能开发针对这个隐秘口袋的泛冠状病毒抗病毒药物。
冠状病毒是对人类健康的重大威胁。这些病毒利用被称为蛋白质的分子机器来感染宿主细胞并进行复制。表征这些蛋白质的结构和动力学可为设计小分子抗病毒药物提供基础。在这项工作中，我们使用计算机模拟来了解新冠病毒一种必需蛋白质的运动部件，理解一个结合伴侣如何开启和关闭它，并确定一个抗病毒药物可以靶向以关闭这种蛋白质的新口袋。这个口袋也存在于其他冠状病毒中，但不存在于相关的人类蛋白质中，因此它可能是泛冠状病毒抗病毒药物的一个有价值的靶点。
