MurC, D, E, and F are ATP-dependent ligases involved in the stepwise assembly of the tetrapeptide stem of forming peptidoglycan. As highly conserved targets found exclusively in bacterial cells, they are of significant interest for antibacterial drug discovery. In this study, we employed a computer-aided molecular design approach to identify potential inhibitors of MurF. A biochemical inhibition assay was conducted, screening twenty-four flavonoids and related compounds against MurC-F, resulting in the identification of quercitrin, myricetin, and (–)-epicatechin as MurF inhibitors with IC₅₀ values of 143 µM, 139 µM, and 92 µM, respectively. Notably, (–)-epicatechin demonstrated mixed type inhibition with ATP and uncompetitive inhibition with d-Ala-d-Ala dipeptide and UM3DAP substrates. Furthermore, in silico analysis using Sitemap and subsequent docking analysis using Glide revealed two plausible binding sites for (–)-epicatechin. The study also investigated the crucial structural features required for activity, with a particular focus on the substitution pattern and hydroxyl group positions, which were found to be important for the activity. The study highlights the significance of computational approaches in targeting essential enzymes involved in bacterial peptidoglycan synthesis.

Graphical abstract

中文翻译：

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Mur 连接酶 F 作为类黄酮槲皮素、杨梅素和 (–)-表儿茶素的新靶标

MurC、D、E 和 F 是 ATP 依赖性连接酶，参与形成肽聚糖的四肽茎的逐步组装。作为仅在细菌细胞中发现的高度保守的靶标，它们对于抗菌药物的发现具有重要意义。在这项研究中，我们采用计算机辅助分子设计方法来识别 MurF 的潜在抑制剂。进行了生化抑制测定，针对 MurC-F 筛选了 24 种类黄酮和相关化合物，结果鉴定出槲皮苷、杨梅素和 (–)-表儿茶素为 MurF 抑制剂，IC ₅₀值为 143 µM、139 µM 和分别为 92 µM。值得注意的是，(–)-表儿茶素表现出与 ATP 的混合型抑制以及与d -Ala- d -Ala 二肽和 UM3DAP 底物的非竞争性抑制。此外，使用 Sitemap的计算机分析和随后使用 Glide 的对接分析揭示了 (–)-表儿茶素的两个可能的结合位点。该研究还研究了活性所需的关键结构特征，特别关注取代模式和羟基位置，发现这对活性很重要。该研究强调了计算方法在针对细菌肽聚糖合成所涉及的必需酶方面的重要性。

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