小柯机器人

瑞士巴塞尔大学Sebastian Hiller等研究人员合作揭示抗生素darobactin的作用机制。2021年4月14日，《自然》杂志在线发表了这项成果。

通过结合冷冻电镜、X射线晶体学、天然质谱、体内实验和分子动力学模拟，研究人员在原子水平上解析了darobactin的作用方式。两次环化使darobactin肽以刚性β链构象进行预组织。这样就可以模拟天然底物的识别信号，并具有与BamA的横向门结合的出色能力。

结合后，darobactin将取代侧门的脂质分子，从而将膜环境用作延伸的结合袋。因为darobactin和BamA之间的相互作用主要是由骨架接触介导的，所以它能够强力地抵抗潜在的抗性突变。这些结果将侧门确定为BamA中的功能性热点，并可以合理设计靶向这种细菌“阿喀琉斯之踵”的抗生素。

据了解，目前需要通过新方式靶向革兰氏阴性菌的抗生素来解决抗菌素耐药性危机。革兰氏阴性细菌受到额外的外膜的保护，使细胞表面的蛋白质吸引药物靶标。天然化合物darobactin靶向细菌插入酶BamA6（必不可少的BAM复合物的中心单元），它有助于外膜蛋白的折叠和插入。BamA缺乏典型的催化中心，而且尚不清楚darobactin这样的小分子如何抑制其功能。

附：英文原文

Title: The antibiotic darobactin mimics a β-strand to inhibit outer membrane insertase

Author: Hundeep Kaur, Roman P. Jakob, Jan K. Marzinek, Robert Green, Yu Imai, Jani Reddy Bolla, Elia Agustoni, Carol V. Robinson, Peter J. Bond, Kim Lewis, Timm Maier, Sebastian Hiller

Issue&Volume: 2021-04-14

Abstract: Antibiotics that target Gram-negative bacteria in new ways are needed to resolve the antimicrobial resistance crisis1,2,3. Gram-negative bacteria are protected by an additional outer membrane, rendering proteins on the cell surface attractive drug targets4,5. The natural compound darobactin targets the bacterial insertase BamA6—the central unit of the essential BAM complex, which facilitates the folding and insertion of outer membrane proteins7,8,9,10,11,12,13. BamA lacks a typical catalytic centre, and it is not obvious how a small molecule such as darobactin might inhibit its function. Here we resolve the mode of action of darobactin at the atomic level using a combination of cryo-electron microscopy, X-ray crystallography, native mass spectrometry, in vivo experiments and molecular dynamics simulations. Two cyclizations pre-organize the darobactin peptide in a rigid β-strand conformation. This creates a mimic of the recognition signal of native substrates with a superior ability to bind to the lateral gate of BamA. Upon binding, darobactin replaces a lipid molecule from the lateral gate to use the membrane environment as an extended binding pocket. Because the interaction between darobactin and BamA is largely mediated by backbone contacts, it is particularly robust against potential resistance mutations. Our results identify the lateral gate as a functional hotspot in BamA and will allow the rational design of antibiotics that target this bacterial Achilles heel.

DOI: 10.1038/s41586-021-03455-w

Source: https://www.nature.com/articles/s41586-021-03455-w

Nature：《自然》，创刊于1869年。隶属于施普林格·自然出版集团，最新IF：69.504
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