基于片段药物设计发现B族β-内酰胺酶抑制剂

Bacterial resistance to β-lactam antibiotics is alarmingly severe. One mechanism of resistance is that bacteria produce β-lactamases. Especially class B β-lactamases, which are metalloproteases, catalyze the hydrolysis of almost all β-lactams, even including carbapenems. There are no class B β-lactamase inhibitors in clinic. The most promising way of finding class B β-lactamase inhibitors is to investigate scaffolds which induce-fit the active pocket and interact with zinc ion(s) in the active pocket in the meantime. Our project is to find class B β-lactamase inhibitors based on fragment-based drug discovery. We first run virtual screen with several libraries by NDM-1 and pick out fragments and fragment-like compounds based on docking total scores of compounds. Then we use a new SPR method to screen this integrated fragment library. SPR hits will be ranked according to affinities and their inhibitory activities of NDM-1 and so on. Higher priority molecules will be soaked to get the co-crystal structures with NDM-1. Then we will carry on structure-based lead design and synthesis to get class B β-lactamase inhibitors with novel scaffold and well-defined mechanism.

β-内酰胺类抗生素耐药形势严峻，机制之一是耐药菌产生β-内酰胺酶。其中B族β-内酰胺酶是金属酶，能水解几乎所有的β-内酰胺类抗生素，甚至包括碳青霉烯类抗生素。临床上没有B族β-内酰胺酶抑制剂。有望找到B族β-内酰胺酶抑制剂的方向是发现与活性位点契合并与金属离子相互作用的结构。本课题利用基于片段药物发现策略寻找B族β-内酰胺酶抑制剂。首先将NDM-1与多个化合物库进行虚拟对接，根据对接打分等挑选片段和类片段分子，构建金属结合基团丰富的片段和类片段库。其次使用首次发现的SPR方法对该实体库进行筛选，筛得片段用NDM-1酶活抑制实验等进行初步的评价验证，以对SPR筛得片段进行优先级排序。优先级较高的片段分子与NDM-1培养共晶结构并进行解析。然后开展基于结构的先导物设计和合成，获得结构骨架新颖、作用机制明确、可以恢复β-内酰胺抗生素敏感性的B族β-内酰胺酶抑制剂。

本课题采用B族β-内酰胺酶NDM-1对多个化合物库进行虚拟筛选后，从虚拟命中分子中进行挑选，组成了金属结合片段丰富的片段库。通过SPR对该片段库的筛选，获得了多种与NDM-1结合的片段分子，均为未见文献报导的潜在NDM-1抑制剂新化学骨架。其中，片段分子A1被NMR监测到其在溶液中可以结合NDM-1活性口袋中2号金属离子Zn2。基于A1的结构改造获得了在产NDM-1菌株中具有B族β-内酰胺酶NDM-1抑制活性的分子。A1及其他本课题发现的具有对产NDM-1菌株具有改善β-内酰胺类抗生素MIC的分子均是未见报道的全新化学骨架，对发现新的NDM-1抑制剂药物提供了重要基础。