Li Yongfang, Yuan Shiling
Key Lab of Colloid and Interface Chemistry, Shandong University, Jinan 250100, Shandong, PR China.
J Chem Inf Model. 2025 Jun 23;65(12):6102-6113. doi: 10.1021/acs.jcim.5c00152. Epub 2025 Jun 6.
As a promising drug target, RNA-dependent RNA polymerase (RdRp) has attracted much attention recently due to its notable conserved active site, especially in the context of COVID-19 spreading. To inhibit the function of RdRp, a nucleotide analogue is a common choice for acting as a chain terminator or RNA corruptor. Although some nucleotide analogues have shown the ability to terminate the extension of a nascent strand of SARS-CoV-2, most of them are likely to be excised due to the proofreading of SARS-CoV-2 nsp14/nsp10. A previous experimental study found that introducing sulfur modification into analogues' phosphate moieties (α-thiotriphosphate; "thio" modification) can break the bottleneck. For instance, Sofosbuvir with α-thiotriphosphate modification successfully escaped the excision of nsp14/10. However, it is unknown how the α-thiotriphosphate affects the structural stability of nucleotide analogues with different ribose modifications at the active site of SARS-CoV-2 RdRp. Thus, in this study, we performed extensive molecular dynamics simulations on four nucleotide analogues with α-thiotriphosphate to elucidate what kind of ribose modification combined with "thio" modification would benefit the analogue's structural stability at the active site. We found that the "thio" modification led to the torsion of phosphate moieties, profoundly affecting the overall conformation of analogues and surrounding residues, determining the Watson-Crick base pairing and catalytic efficiency. Interestingly, chemical modification on the ribose, especially the 1' and 3'-ribose positions, increases the structural stability of analogues through hydrogen bond interactions. Our results revealed nucleotide analogues' structural and dynamical features with "thio" modification at the active site, which may contribute to future drug design or repurposing aimed at the SARS-CoV-2 RdRp.
作为一种有前景的药物靶点，RNA依赖性RNA聚合酶（RdRp）因其显著保守的活性位点，近来备受关注，尤其是在新冠病毒传播的背景下。为抑制RdRp的功能，核苷酸类似物是作为链终止剂或RNA破坏剂的常见选择。尽管一些核苷酸类似物已显示出能够终止新冠病毒新生链的延伸，但由于新冠病毒nsp14/nsp10的校对功能，它们中的大多数可能会被切除。先前的一项实验研究发现，在类似物的磷酸基团中引入硫修饰（α-硫代三磷酸；“硫代”修饰）可以突破这一瓶颈。例如，具有α-硫代三磷酸修饰的索磷布韦成功逃脱了nsp14/10的切除。然而，尚不清楚α-硫代三磷酸如何影响新冠病毒RdRp活性位点处具有不同核糖修饰的核苷酸类似物的结构稳定性。因此，在本研究中，我们对四种具有α-硫代三磷酸的核苷酸类似物进行了广泛的分子动力学模拟，以阐明哪种核糖修饰与“硫代”修饰相结合将有利于类似物在活性位点的结构稳定性。我们发现，“硫代”修饰导致磷酸基团扭转，深刻影响类似物及其周围残基的整体构象，决定了沃森-克里克碱基配对和催化效率。有趣的是，核糖上的化学修饰，尤其是1'和3'-核糖位置上的修饰，通过氢键相互作用增加了类似物的结构稳定性。我们的结果揭示了活性位点处具有“硫代”修饰的核苷酸类似物的结构和动力学特征，这可能有助于未来针对新冠病毒RdRp的药物设计或药物重新利用。
