Structural studies of target recognition by large natural product antibiotics

说明(申请人提供)：本提案侧重于抗菌天然产品的结构和功能特征。这些药物如何折叠以及它们如何识别其靶标的精确分子细节将从药物和药物：靶标复合体的高分辨率X射线晶体结构中获得。我们将研究三类化合物。第一类包括万古霉素和相关的糖肽类抗生素。结构实验将检验有关配基识别的构象变化和高阶结构组件在万古霉素识别肽聚糖中的作用的假说。还将确定第三组(替考拉宁类)抗生素的结构，包括新推出的治疗剂Dalbavancin，以便对第一组(类万古霉素)和第三组抗生素进行比较，并说明两组之间的配体识别和寡聚行为有何不同。根据已有的结构数据设计了新的糖肽化合物，并将进行合成和表征。待研究的第二类杀菌天然产物是识别细菌细胞上含有聚戊烯基焦磷酸配体的分子，如肽聚糖生物合成中的Lipid II中间体。结晶学研究将被用来揭示这些不同药物的分子识别决定因素，以努力建立它们的作用机制，并为未来相关治疗剂的设计提供信息。正在研究的特定分子包括雷莫拉宁、耐酸和杆菌肽。第三类抗生素包括能穿透细菌膜的环状十肽。虽然它们是有效的抗菌剂，但它们也可以溶血；因此，将使用结晶学来研究一系列具有不同杀菌和溶血活性的化合物的结构。对这些进行比较，将确定控制预期抗菌活性和有害副作用的结构决定因素，从而有助于改进试剂的开发。 与公共卫生相关：耐药细菌病原体的流行使目前的抗生素无效，并使开发抗击感染的新药变得至关重要。该项目将提供有关天然抗菌化合物的基本信息。这些信息将有助于将这些天然化合物合理开发为下一代治疗剂。

DESCRIPTION (provided by applicant): This proposal focuses on the structural and functional characterization of antimicrobial natural products. The precise molecular details of how these agents fold and how they recognize their targets will be derived from high resolution X-ray crystal structures of drugs and drug:target complexes. Three classes of compounds will be studied. The first class includes vancomycin and related glycopeptide antibiotics. Structural experiments will test hypotheses about the conformational changes accompanying ligand recognition and the role of higher order structural assemblies in peptidoglycan recognition by vancomycin. Structures will also be determined for Group III (teicoplanin-like) antibiotics, including the newly introduced therapeutic agent dalbavancin, allowing for a comparison of Group I (vancomycin-like) and Group III antibiotics, and illuminating how ligand recognition and oligomerization behavior differ between the two groups. Novel glycopeptide compounds have been designed based upon existing structural data, and will be synthesized and characterized. The second class of bacteriocidal natural products to be studied are molecules that recognize polyprenyl pyrophosphate-containing ligands on bacterial cells, such as the Lipid II intermediate in peptidoglycan biosynthesis. Crystallographic studies will be used to reveal the determinants of molecular recognition for these different agents, in an effort to establish their mechanisms of action and informing the future design of related therapeutic agents. The specific molecules under study include ramoplanin, enduracidin, and bacitracin. The third class of antibiotics comprises cyclic decapeptides that permeabilize bacterial membranes. While these are effective antimicrobials, they can also be hemolytic; therefore crystallography will be used to study the structures of an array of compounds with differing bacteriocidal and hemolytic activities. Comparison of these will identify the structural determinants that control the desired antibacterial activity and the unwanted side effects, and thus aid in the development of improved agents. Relevance to public health: The prevalence of resistant bacterial pathogens is rendering current antibiotics ineffective, and making it essential that new drugs be developed to fight infection. This project will provide essential information about naturally occurring antimicrobial compounds. This information will facilitate the rational development of these natural compounds into next generation therapeutic agents.