Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
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DOI：
10.1007/s10969-011-9102-6
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发表时间：
2011-07
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影响因子：
--
通讯作者：
Stewart, Lance J
中科院分区：
文献类型：
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作者：
Begley, Darren W;Hartley, Robert C;Davies, Douglas R;Edwards, Thomas E;Leonard, Jess T;Abendroth, Jan;Burris, Courtney A;Bhandari, Janhavi;Myler, Peter J;Staker, Bart L;Stewart, Lance J
作为西雅图传染病结构基因组学中心的一部分，我们寻求用配体结合的结构数据来增强结构基因组学，这些数据可以作为基于结构的药物设计的蓝图。我们已经将基于片段的筛选方法应用于我们的结构基因组学管道，以从病原生物体中产生高优先级药物靶标的多个配体结合结构。在这项研究中，我们报告的片段筛选方法和结构测定结果的2C-甲基-D-β-2，4-环二磷酸（MECP）合酶从类鼻疽伯克霍尔德氏菌，革兰氏阴性菌引起类鼻疽。通过核磁共振光谱法以及晶体浸泡，然后通过X射线衍射进行筛选，鉴定了几种在关键代谢途径中结合这种酶的小分子。通过筛选获得的一系列复杂结构揭示了不同的结合口袋和一系列与靶点形成复合物的小分子。用这些化合物进行的额外浸泡进一步证明了片段的子集仅在以特定组合存在时结合蛋白质。这个合奏的片段结合的复合物阐明了几个特点的MECP合酶，包括一个以前未知的结合表面外部的催化活性位点。这些配体结合的结构现在可以指导药物化学家和结构生物学家合理设计这种酶的新型抑制剂。
As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.