Abstract：
The novel coronavirus SARS-CoV-2 is the causative agent of the COVID-19 outbreak that is affecting the entire planet. As the pandemic is still spreading worldwide, with multiple mutations of the virus, it is of interest and of help to employ computational methods for identifying potential inhibitors of the enzymes responsible for viral replication. Attractive antiviral nucleotide analogue RNA-dependent RNA polymerase (RdRp) chain terminator inhibitors are investigated with this purpose. This study, based on molecular dynamics (MD) simulations, addresses the important aspects of the incorporation of an endogenously synthesized nucleoside triphosphate, ddhCTP, in comparison with the natural nucleobase cytidine triphosphate (CTP) in RdRp. The ddhCTP species is the product of the viperin antiviral protein as part of the innate immune response. The absence of the ribose 3\'-OH in ddhCTP could have important implications in its inhibitory mechanism of RdRp. We built an in silico model of the RNA strand embedded in RdRp using experimental methods, starting from the cryo-electron microscopy structure and exploiting the information obtained by spectrometry on the RNA sequence. We determined that the model was stable during the MD simulation time. The obtained results provide deeper insights into the incorporation of nucleoside triphosphates, whose molecular mechanism by the RdRp active site still remains elusive.
摘要：
新型冠状病毒SARS-CoV-2是影响整个地球的COVID-19爆发的病原体。由于疫情仍在全球蔓延，随着病毒的多个突变，采用计算方法来鉴定负责病毒复制的酶的潜在抑制剂是有意义的，也是有帮助的。为此研究了有吸引力的抗病毒核苷酸类似物RNA依赖性RNA聚合酶（RdRp）链终止剂抑制剂。这项研究,基于分子动力学(MD)模拟，解决了内源性合成的核苷三磷酸的掺入的重要方面，ddhCTP,与RdRp中的天然核碱基胞苷三磷酸（CTP）相比。ddhCTP物种是作为先天免疫应答的一部分的viperin抗病毒蛋白的产物。ddhCTP中不存在核糖3'-OH可能对其RdRp的抑制机制具有重要意义。我们使用实验方法建立了嵌入RdRp中的RNA链的计算机模型，从低温电子显微镜结构开始，并利用通过光谱法对RNA序列获得的信息。我们确定模型在MD模拟时间内是稳定的。获得的结果为核苷三磷酸的掺入提供了更深入的见解，其通过RdRp活性位点的分子机制仍然难以捉摸。
