Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening
Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening
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DOI：
10.1021/jm000017s
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发表时间：
2000-07-13
影响因子：
7.3
通讯作者：
Meunier-Keller, N
中科院分区：
文献类型：
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作者：
Boehm, HJ;Boehringer, M;Meunier-Keller, N
在寻找细菌 DNA 旋转酶的新型抑制剂时，随机筛选没有提供合适的先导结构。因此，必须开发一种替代方法。依靠目标 ATP 结合位点的详细 3D 结构信息，我们的方法结合了关键技术 (1) 潜在低分子量抑制剂的计算机筛选，(2) 有偏差的高通量 DNA 旋转酶筛选，(3) 通过生物物理方法验证筛选命中，以及 (4) 3D 引导优化过程。当进行计算机筛选时，包含 350 000 种化合物的初始数据集可以减少到 3000 个分子。在 DNA 旋转酶测定中测试这 3000 种选定的化合物，得到了 150 个命中结果，分为 14 个类别。七类可被验证为真正的新型 DNA 旋转酶抑制剂，它们通过与位于 B 亚基上的 ATP 结合位点结合而发挥作用：酚类、2-氨基三嗪、4-氨基嘧啶、2-氨基嘧啶、吡咯并嘧啶、吲唑和 2-羟甲基吲哚。 3D 引导优化提供了高效的 DNA 旋转酶抑制剂，例如 3,4-二取代吲唑 23 的 DNA 旋转酶抑制剂的效力是新生霉素的 10 倍 (3)。
Random screening provided no suitable lead structures in a search for novel inhibitors of the bacterial enzyme DNA gyrase. Therefore, an alternative approach had to be developed. Relying on the detailed 3D structural information of the targeted ATP binding site, our approach combines as key techniques (1) an in silico screening for potential low molecular weight inhibitors, (2) a biased high throughput DNA gyrase screen, (3) validation of the screening hits by biophysical methods, and (4) a 3D guided optimization process. When the in silico screening was performed, the initial data set containing 350 000 compounds could be reduced to 3000 molecules. Testing these 3000 selected compounds in the DNA gyrase assay provided 150 hits clustered in 14 classes. Seven classes could be validated as true, novel DNA gyrase inhibitors that act by binding to the ATP binding site located on subunit B: phenols, 2-amino-triazines, 4-amino-pyrimidines, 2-amino-pyrimidines, pyrrolopyrimidines, indazoles, and 2-hydroxymethyl-indoles. The 3D guided optimization provided highly potent DNA gyrase inhibitors, e.g., the 3,4-disubstituted indazole 23 being a 10 times more potent DNA gyrase inhibitor than novobiocin (3).