PDF(Pubmed)
Abstract：
The peptidoglycan biosynthesis pathway plays a vital role in bacterial cells, and facilitates peptidoglycan layer formation, a fundamental structural component of the bacterial cell wall. The enzymes in this pathway are candidates for antibiotic development, as most do not have mammalian homologues. The UDP-N-acetylglucosamine (UNAG) enolpyruvyl transferase enzyme (MurA) in the peptidoglycan pathway cytoplasmic step is responsible for the phosphoenolpyruvate (PEP)-UNAG catalytic reaction, forming UNAG enolpyruvate and inorganic phosphate. Reportedly, UDP-N-acetylmuramic acid (UNAM) binds tightly to MurA forming a dormant UNAM-PEP-MurA complex and acting as a MurA feedback inhibitor. MurA inhibitors are complex, owing to competitive binding interactions with PEP, UNAM, and UNAG at the MurA active site. We used computational methods to explore UNAM and UNAG binding. UNAM showed stronger hydrogen-bond interactions with the Arg120 and Arg91 residues, which help to stabilize the closed conformation of MurA, than UNAG. Binding free energy calculations using end-point computational methods showed that UNAM has a higher binding affinity than UNAG, when PEP is attached to Cys115. The unbinding process, simulated using τ-random acceleration molecular dynamics, showed that UNAM has a longer relative residence time than UNAG, which is related to several complex dissociation pathways, each with multiple intermediate metastable states. This prevents the loop from opening and exposing the Arg120 residue to accommodate UNAG and potential new ligands. Moreover, we demonstrate the importance of Cys115-linked PEP in closed-state loop stabilization. We provide a basis for evaluating novel UNAM analogues as potential MurA inhibitors. PUBLIC SIGNIFICANCE: MurA is a critical enzyme involved in bacterial cell wall biosynthesis and is involved in antibiotic resistance development. UNAM can remain in the target protein\'s active site for an extended time compared to its natural substrate, UNAG. The prolonged interaction of this highly stable complex known as the \'dormant complex\' comprises UNAM-PEP-MurA and offers insights into antibiotic development, providing potential options against drug-resistant bacteria and advancing our understanding of microbial biology.
摘要：
肽聚糖生物合成途径在细菌细胞中起着至关重要的作用,并促进肽聚糖层的形成，细菌细胞壁的基本结构成分。该途径中的酶是抗生素开发的候选酶，因为大多数没有哺乳动物同源物。肽聚糖途径细胞质步骤中的UDP-N-乙酰葡糖胺（UNAG）烯醇丙酮酸转移酶（MurA）负责磷酸烯醇丙酮酸（PEP）-UNAG催化反应，形成UNAG烯醇丙酮酸和无机磷酸盐。据报道,UDP-N-乙酰胞壁酸（UNAM）与MurA紧密结合，形成休眠的UNAM-PEP-MurA复合物，并充当MurA反馈抑制剂。MurA抑制剂很复杂,由于与PEP的竞争性结合相互作用，UNAM,和UNAG在MurA活动场所。我们使用计算方法来探索UNAM和UNAG结合。UNAM与Arg120和Arg91残基表现出更强的氢键相互作用，这有助于稳定MurA的封闭构象，比UNAG。使用终点计算方法的结合自由能计算表明，UNAM具有比UNAG更高的结合亲和力，当PEP连接到Cys115时。解除绑定的过程，用τ-随机加速分子动力学模拟，表明UNAM的相对停留时间比UNAG长，这与几种复杂的解离途径有关，每个都有多个中间亚稳态。这防止环打开和暴露Arg120残基以容纳UNAG和潜在的新配体。此外，我们证明了Cys115连接的PEP在闭环稳定中的重要性.我们为评估新型UNAM类似物作为潜在的MurA抑制剂提供了基础。公众意义：MurA是参与细菌细胞壁生物合成的关键酶，并参与抗生素抗性的发展。与天然底物相比，UNAM可以在靶蛋白的活性位点上保留一段延长的时间，UNAG.这种被称为“休眠复合物”的高度稳定复合物的长期相互作用包括UNAM-PEP-MurA，并提供了对抗生素开发的见解，提供针对耐药细菌的潜在选择，并提高我们对微生物生物学的理解。
