With antimicrobial resistance (AMR) reaching alarming levels, new anti‐infectives with unpreceded mechanisms of action are urgently needed. The 2‐C‐methylerythritol‐D‐erythritol‐4‐phosphate (MEP) pathway represents an attractive source of drug targets due to its essential role in numerous pathogenic Gram‐negative bacteria and Mycobacterium tuberculosis (Mt), whilst being absent in human cells. Here, we solved the first crystal structure of Pseudomonas aeruginosa (Pa) IspD, the third enzyme in the MEP pathway and present the discovery of a fragment‐based compound class identified through crystallographic screening of PaIspD. The initial fragment occupies the CTP binding cavity within the active site. Confirmation of fragment–protein interactions was achieved through 1H saturation–transfer difference nuclear magnetic resonance (1H‐STD‐NMR). Building upon these findings and insights from the co‐crystal structures, we identified two growth vectors for fragment growing. We synthesized derivatives addressing both growth vectors, which showed improved affinities for PaIspD. Our new fragment class targets PaIspD, displays promising affinity and favorable growth vectors for further optimization.

中文翻译：

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通过靶向铜绿假单胞菌 IspD 的 CTP 结合位点的 X 射线晶体学筛选发现片段


随着抗菌素耐药性 （AMR） 达到令人担忧的水平，迫切需要具有前所未有的作用机制的新型抗感染药。2-C-甲基赤藓糖醇-D-赤藓糖醇-4-磷酸 （MEP） 途径代表了一个有吸引力的药物靶标来源，因为它在许多致病性革兰氏阴性菌和结核分枝杆菌 （Mt） 中起着重要作用，而在人体细胞中却不存在。在这里，我们解决了铜绿假单胞菌 （Pa） IspD 的第一个晶体结构，MEP 通路中的第三个酶，并提出了通过 PaIspD 的晶体学筛选鉴定的基于片段的化合物类别的发现。初始片段占据活性位点内的 CTP 结合腔。通过 1H 饱和-转移差核磁共振 （1H-STD-NMR） 确认片段-蛋白质相互作用。基于这些发现和共晶体结构的见解，我们确定了片段生长的两个生长载体。我们合成了针对两种生长载体的衍生物，显示出对 PaIspD 的亲和力提高。我们的新片段类靶向 PaIspD，显示出有希望的亲和力和有利的生长载体，以便进一步优化。