Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design.
Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design.
复制标题
DOI：
10.1016/j.crstbi.2023.100095
复制
发表时间：
2023
影响因子：
2.8
通讯作者：
Ji, Xinhua
中科院分区：
文献类型：
--
作者：
Shaw, Gary X;Fan, Lixin;Cherry, Scott;Shi, Genbin;Tropea, Joseph E;Ji, Xinhua
二氢新蝶呤醛缩酶（DHNA）是微生物叶酸生物合成的必需酶。在哺乳动物中没有对应物，DHNA是抗微生物剂的有吸引力的靶标。幽门螺杆菌感染发生在超过50%的世界人口的胃中，但用于感染的一线治疗正面临快速增加的耐药性。新的抗生素是迫切需要的，对潜在目标的结构信息是至关重要的。我们已经确定了幽门螺杆菌DHNA（HpDHNA）与蝶呤分子（HpDHNA：蝶呤）的复合物的晶体结构，分辨率为1.49- 10 nm。HpDHNA：蝶呤复合物在晶体中形成四聚体。四聚体也观察到在溶液中的动态光散射和小角X-射线散射证实。迄今为止，除了一个报道的DHNA结构是八聚体复合物。作为唯一的例外，无配体的结核分枝杆菌DHNA（apo-MtDHNA）在晶体中形成四聚体，但其活性位点仅部分形成。相比之下，四聚体HpDHNA：蝶呤复合物具有良好形成的活性位点。每个活性位点容纳一个蝶呤分子，但活性位点的出口被两个氨基酸残基阻断，表现出5.2 μ m的接触距离。相比之下，金黄色葡萄球菌DHNA（SaDHNA）中的相应接触距离是无配体酶、底物复合物、产物复合物和抑制剂复合物的两倍大小，范围为9.8至10.5 μ m。这种大的接触距离表明SaDHNA的活性位点是敞开的。我们认为这种同工酶特异性接触距离（ISCD）是DHNA活性位点的一个特征。HpDHNA和SaDHNA结构的比较分析表明，基于片段的策略，用于开发同工酶特异性抑制剂。幽门螺杆菌DHNA与蝶呤复合物在1.49 nm处的晶体结构幽门螺杆菌DHNA在晶体中以四聚体形式存在，具有良好的活性位点。四聚体幽门螺杆菌DHNA组装体也存在于溶液中。结构比较揭示了DHNA活性位点的同工酶特异性特征。幽门螺杆菌DHNA结构提示同工酶特异性抑制剂设计的策略。
Dihydroneopterin aldolase (DHNA) is essential for folate biosynthesis in microorganisms. Without a counterpart in mammals, DHNA is an attractive target for antimicrobial agents. Helicobacter pylori infection occurs in human stomach of over 50% of the world population, but first-line therapies for the infection are facing rapidly increasing resistance. Novel antibiotics are urgently needed, toward which structural information on potential targets is critical. We have determined the crystal structure of H. pylori DHNA (HpDHNA) in complex with a pterin molecule (HpDHNA:Pterin) at 1.49-Å resolution. The HpDHNA:Pterin complex forms a tetramer in crystal. The tetramer is also observed in solution by dynamic light scattering and confirmed by small-angle X-ray scattering. To date, all but one reported DHNA structures are octameric complexes. As the only exception, ligand-free Mycobacterium tuberculosis DHNA (apo-MtDHNA) forms a tetramer in crystal, but its active sites are only partially formed. In contrast, the tetrameric HpDHNA:Pterin complex has well-formed active sites. Each active site accommodates one pterin molecule, but the exit of active site is blocked by two amino acid residues exhibiting a contact distance of 5.2 Å. In contrast, the corresponding contact distance in Staphylococcus aureus DHNA (SaDHNA) is twice the size, ranging from 9.8 to 10.5 Å, for ligand-free enzyme, the substrate complex, the product complex, and an inhibitor complex. This large contact distance indicates that the active site of SaDHNA is wide open. We propose that this isozyme-specific contact distance (ISCD) is a characteristic feature of DHNA active site. Comparative analysis of HpDHNA and SaDHNA structures suggests a fragment-based strategy for the development of isozyme-specific inhibitors. Crystal structure of Helicobacter pylori DHNA in complex with pterin at 1.49 Å. H. pylori DHNA exists as a tetramer in crystal with well-formed active sites. The tetrameric H. pylori DHNA assembly also exits in solution. Structural comparison reveals an isozyme-specific feature of DHNA active sites. H. pylori DHNA structure suggests a strategy for isozyme-specific inhibitor design.