Antibiotics of the ADEP and empedopeptin class - Molecular modes of action and studies on bacterial resistance

ADEP(一类新的酰基多肽的首字母缩写)和恩培多肽是具有良好抗菌活性的天然产物或其衍生物。在项目开始时，他们的行动机制没有得到很好的探索。在之前的资助期间，我们确定了恩培多肽的靶点，并阐明了ADEP如何失调靶点功能。结果表明，恩培多肽与几种脂类结合的肽聚糖前体结合，并在体外阻止不同的晚期肽聚糖合成酶的活性。我们申请进一步的资金，以验证恩佩多肽识别的肽聚糖前体的特定区域。ADEP作用于一个前所未有的靶标--细菌CLP-蛋白酶。自项目启动以来，我们进行了各种生化实验来研究靶抑制的分子性质，并解决了ADEP-ClpP的共晶结构。ADEP阻断了调节伙伴分子在ClpP上的重要结合位点，并触发了通往蛋白水解室的门控进入孔的打开，导致柔性或新生细菌蛋白的过早降解。我们还发现，一个首选的靶点是细胞分裂蛋白FtsZ。我们申请进一步的资金，以探索FtsZ这种特殊敏感性的分子原因，并通过蛋白质组学寻找更多ADEP激活的ClpP的首选降解靶点。此外，我们计划通过分析从靶水平到感染过程的典型病原菌属来研究细菌对ADEP自发耐药的分子本质。

ADEPs (an acronym for a novel class of acyldepsipeptides) and empedopeptin are natural products or derivatives thereof with promising antibacterial activity. At project start, their mechanisms of action had been poorly explored. During the previous funding period we determined the target of empedopeptin and elucidated how ADEPs dysregulate target function. It turned out that empedopeptin binds to several lipid-bound peptidoglycan precursors and prevents the activity of distinct late-stage peptidoglycan synthesis enzymes in vitro. We apply for further funding to verify the specific region of the peptidoglycan precursors recognised by empedopeptin. ADEPs act on an unprecedented target, the bacterial Clp-protease. Since project start, we performed various biochemical experiments to study the molecular nature of target inhibition and the ADEP-ClpP co-crystal structure was solved. ADEP blocks important binding sites at ClpP for regulatory partner molecules and triggers opening of the gated entry pores to the proteolytic chamber resulting in untimely degradation of flexible or nascent bacterial proteins. We also found that a preferred target is the cell division protein FtsZ. We apply for further funding to explore the molecular reason for this particular sensitivity of FtsZ and to search for further preferred degradation targets of ADEP-activated ClpP by proteomics. In addition, we plan to investigate the molecular nature of spontaneous bacterial resistance against ADEPs by analysing exemplary pathogen genera from the target level to the infection process.