Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China.
College of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China.
Comput Biol Chem. 2022 Aug;99:107715. doi: 10.1016/j.compbiolchem.2022.107715. Epub 2022 Jun 20.
Bovine viral diarrhea virus (BVDV) is an enveloped virus with an RNA genome, causing serious economic losses to the areas dominated by livestock industry. Currently, although several compounds with biological activities of inhibiting virus replication have been reported, amino acid mutations (especially F224S mutation) frequently occurring in the RNA-dependent RNA polymerase (RdRp) have greatly reduce their value of further research. In this study, we introduced an effective and rapid in silico strategy to explore the differences in the binding modes of VP32947 between the wild/mutant-type RdRp at the molecular level, and further explained the main reasons for the variations in the inhibitory activities of VP32947 against the two types of enzymes. Firstly, the binding site of VP32947 in the finger domain was determined based on the previously reported experimental data, and the initial conformation of VP32947 in the wild RdRp was constructed using molecular docking. Then, the mutant research system was obtained directly by artificial mutation strategy. Afterwards, the built research systems were subjected to microsecond-timescale molecular dynamic simulation, and the conformational and energic profile analyses were performed according to the simulation trajectories. It was found that after 1 μs simulation, VP32947 in the mutant system was transferred to the left side of Loop α, and its interactions with the residues in the loop region were weakened. However, VP32947 in the wild system remained at the right side of Loop α, and could have a good fit with the sub-pocket formed by F224, I261, P262, N264, S532, which was conducive to maintaining its stable binding conformation in the wild RdRp. The illustration of the difference in the binding mechanisms of VP32947 in the wild/mutant RdRp would provide a theoretical basis for the rational design of innovative inhibitors based on the enzyme.
牛病毒性腹泻病毒（BVDV）是一种具有 RNA 基因组的包膜病毒，给以畜牧业为主的地区造成严重的经济损失。目前，虽然已有报道称几种具有抑制病毒复制的生物活性的化合物，但 RNA 依赖性 RNA 聚合酶（RdRp）中经常发生的氨基酸突变（尤其是 F224S 突变）极大地降低了它们进一步研究的价值。在这项研究中，我们介绍了一种有效的快速计算策略，从分子水平上探索野生型/突变型 RdRp 中 VP32947 结合模式的差异，并进一步解释了 VP32947 对两种酶抑制活性变化的主要原因。首先，根据先前报道的实验数据确定了 VP32947 在手指域中的结合位点，并使用分子对接构建了野生型 RdRp 中 VP32947 的初始构象。然后，通过人工突变策略直接获得突变研究系统。之后，对构建的研究系统进行微秒时间尺度的分子动力学模拟，并根据模拟轨迹进行构象和能量分布分析。结果发现，经过 1μs 模拟后，突变系统中的 VP32947 转移到 Loop α 的左侧，其与环区残基的相互作用减弱。然而，野生型系统中的 VP32947 仍保留在 Loop α 的右侧，并且可以与由 F224、I261、P262、N264、S532 形成的亚口袋很好地吻合，这有助于在野生型 RdRp 中保持其稳定的结合构象。阐明 VP32947 在野生型/突变型 RdRp 中结合机制的差异，可为基于酶的创新抑制剂的合理设计提供理论依据。
