Background: The ability of Pseudouridimycin (PUM) to occupy the nucleotide addition site of bacterial RNA Polymerase (RNAP) underlies its inhibitory potency, as previously reported. PUM has gained high research interest as a broad-spectrum nucleoside analog that has demonstrated exciting potentials in treating drug-resistant bacterial infections.

Objective: Herein, we identified, for the first time, a novel complementary mechanism by which PUM elicits its inhibitory effects on bacterial RNAP.

Materials and Methods: The dynamic binding behavior of PUM to bacterial RNAP was studied using various dynamic analysis approaches.

Results: Findings revealed that in addition to occupying the nucleotide addition site, PUM also interrupts the unimpeded entry and exit of DNA by reducing the mechanistic extension of the RNAP cleft and perturbing the primary conformations of the switch regions. Moreover, PUM binding reduced the distances between key residues in the β and β’ subunits that extend to accommodate the DNA.

Conclusion: This study’s findings present structural insights that would contribute to the structurebased design of potent and selective PUM inhibitors.

背景：如先前报道，假尿嘧啶 (PUM) 占据细菌 RNA 聚合酶 (RNAP) 核苷酸添加位点的能力是其抑制效力的基础。作为一种广谱核苷类似物，PUM 获得了很高的研究兴趣，在治疗耐药细菌感染方面表现出令人兴奋的潜力。

目的：在此，我们首次发现了 PUM 对细菌 RNAP 产生抑制作用的新型互补机制。

材料和方法：使用各种动态分析方法研究了 PUM 与细菌 RNAP 的动态结合行为。

结果：研究结果表明，除了占据核苷酸添加位点外，PUM 还通过减少 RNAP 裂隙的机械延伸和扰乱开关区域的主要构象来中断 DNA 的畅通无阻的进入和退出。此外，PUM 结合减少了延伸以容纳 DNA 的 β 和 β' 亚基中关键残基之间的距离。

结论：本研究的发现提供了结构见解，有助于有效和选择性 PUM 抑制剂的基于结构的设计。