Bacterial cell walls contain peptidoglycan (PG), a scaffold that provides proper rigidity to resist lysis from internal osmotic pressure and a barrier to protect cells against external stressors. It consists of repeating sugar units with a linkage to a stem peptide that becomes cross-linked by cell wall transpeptidases (TP). While synthetic PG fragments containing l-lysine in the third position on the stem peptide are easier to access, those with meso-diaminopimelic acid (m-DAP) pose a severe synthetic challenge. Herein, we describe a solid phase synthetic scheme based on widely available building blocks to assemble meso-cystine (m-CYT), which mimics key structural features of m-DAP. To demonstrate proper mimicry of m-DAP, cell wall probes were synthesized with m-CYT in place of m-DAP and evaluated for their metabolic processing in live bacterial cells. We found that m-CYT-based cell wall probes were properly processed by TPs in various bacterial species that endogenously contain m-DAP in their PG. Additionally, we have used hybrid quantum mechanical/molecular mechanical (QM/MM) and molecular dynamics (MD) simulations to explore the influence of m-DAP analogs on the PG cross-linking. The results showed that the cross-linking mechanism of transpeptidases occurred through a concerted process. We anticipate that this strategy, which is based on the use of inexpensive and commercially available building blocks, can be widely adopted to provide greater accessibility of PG mimics for m-DAP containing organisms.

中文翻译：

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m-DAP 生物电子等排体的简便合成和代谢掺入活细菌的细胞壁

细菌细胞壁含有肽聚糖 (PG)，它是一种支架，可提供适当的刚度以抵抗内部渗透压的裂解，并且是保护细胞免受外部压力的屏障。它由重复的糖单元组成，并与干肽相连，干肽被细胞壁转肽酶 (TP) 交联。虽然在茎肽的第三个位置含有l -赖氨酸的合成 PG 片段更容易获得，但那些含有内消旋二氨基庚二酸 ( m -DAP) 的合成 PG 片段构成了严重的合成挑战。在此，我们描述了基于广泛使用的构建块的固相合成方案来组装内消旋-cystine（米-CYT），其模仿键的结构特征米-DAP。为了证明m- DAP 的正确模拟，用m- CYT 代替m- DAP合成了细胞壁探针，并评估了它们在活细菌细胞中的代谢过程。我们发现基于m -CYT 的细胞壁探针在其 PG中内源性含有m- DAP 的各种细菌物种中被 TP 正确处理。此外，我们还使用了混合量子力学/分子力学 (QM/MM) 和分子动力学 (MD) 模拟来探索m- PG 交联上的 DAP 类似物。结果表明，转肽酶的交联机制是通过协同过程发生的。我们预计，这种基于使用廉价和市售构建块的策略可以被广泛采用，为含m- DAP 的生物体提供更大的 PG 模拟物。