Despite the success of genomics in identifying new essential bacterial genes, there is a lack of sustainable leads in antibacterial drug discovery to address increasing multidrug resistance. Type IIA topoisomerases cleave and religate DNA to regulate DNA topology and are a major class of antibacterial and anticancer drug targets, yet there is no well developed structural basis for understanding drug action. Here we report the 2.1âÃ
crystal structure of a potent, new class, broad-spectrum antibacterial agent in complex with Staphylococcus aureus DNA gyrase and DNA, showing a new mode of inhibition that circumvents fluoroquinolone resistance in this clinically important drug target. The inhibitor âbridgesâ the DNA and a transient non-catalytic pocket on the two-fold axis at the GyrA dimer interface, and is close to the active sites and fluoroquinolone binding sites. In the inhibitor complex the active site seems poised to cleave the DNA, with a single metal ion observed between the TOPRIM (topoisomerase/primase) domain and the scissile phosphate. This work provides new insights into the mechanism of topoisomerase action and a platform for structure-based drug design of a new class of antibacterial agents against a clinically proven, but conformationally flexible, enzyme class. Enzymes that move along a DNA strand, such as DNA and RNA polymerases, tend to cause the build-up of supercoiling ahead of their motion. Unchecked, this would cause the DNA to become overwound, like a twisted rubber band. Topoisomerases relieve this stress by first cleaving and then re-ligating the DNA. Topoisomerase inhibitors are used as antibacterial and anticancer drugs â for example, antibacterials of the quinolone family have been in clinical use since 1962, but are now compromised by the emergence of multidrug-resistant bacteria. The crystal structure of a type II topoisomerase from Staphylococcus aureus, DNA gyrase, has now been determined in a complex with DNA and with the broad-spectrum antibiotic GSK299423. This is an example of a new class of antibiotics that interact with the same targets as fluoroquinolones, but are structurally and mechanistically distinct from them. The structure reveals a mechanism that circumvents fluoroquinolone resistance and opens up strategies of exploiting alternative inhibition mechanisms for clinically validated targets. Enzymes that move along DNA, such as DNA and RNA polymerases, cause the DNA ahead of them to become supercoiled. This would lead to the DNA becoming overwound, were the stress not relieved by topoisomerases. Topoisomerase inhibitors have been used as antibacterial and anticancer drugs, but the structural basis for their activity has been unclear. Here, the crystal structures are presented of a topoisomerase on DNA, either alone or in the presence of a new type of antibiotic.
尽管
基因组学在鉴定新的重要细菌
基因方面取得了成功,但在抗菌药物发现方面却缺乏可持续的线索,以应对日益增长的多药耐药性。IIA 型拓扑异构酶可裂解和重构 DNA 以调节 DNA 拓扑结构,是一类主要的抗菌和抗癌药物靶点,但目前还没有完善的结构基础来了解药物的作用。在这里,我们报告了一种强效、新型、广谱抗菌剂与
金黄色葡萄球菌DNA回旋酶和DNA复合物的2.1μm晶体结构,显示了一种新的抑制模式,可规避这一临床上重要的药物靶点对
氟喹诺酮类药物的耐药性。该
抑制剂 "桥接 "DNA和GyrA二聚体界面二折轴上的瞬时非催化口袋,并靠近活性位点和
氟喹诺酮结合位点。在
抑制剂复合物中,活性位点似乎准备裂解 DNA,在 TOPRIM(拓扑异构酶/primase)结构域和 scissile
磷酸盐之间观察到一个
金属离子。这项研究为拓扑异构酶的作用机理提供了新的见解,也为针对临床上已被证实但构象灵活的一类酶设计新的抗菌药物提供了一个基于结构的平台。沿着DNA链运动的酶,如DNA和RNA聚合酶,往往会在其运动前形成超卷曲。如果不加以控制,这将导致 DNA 过度缠绕,就像一根扭曲的橡皮筋。拓扑异构酶通过先切割然后重新连接 DNA 来缓解这种压力。拓扑异构酶
抑制剂被用作抗菌药和抗癌药,例如,喹诺
酮类抗菌药自 1962 年以来一直在临床上使用,但现在由于出现了耐多药细菌而受到影响。现在已经确定了
金黄色葡萄球菌II型拓扑异构酶(DNA回旋酶)与DNA和广谱抗生素GSK299423复合物的晶体结构。这是一类新型抗生素的实例,它们与
氟喹诺酮类药物具有相同的作用靶点,但在结构和机理上却与
氟喹诺酮类药物截然不同。该结构揭示了一种规避
氟喹诺酮类药物耐药性的机制,并开辟了针对临床验证靶点利用替代抑制机制的策略。沿着 DNA 运动的酶,如 DNA 和 RNA 聚合酶,会使其前方的 DNA 超卷曲。如果拓扑异构酶不缓解这种压力,就会导致 DNA 过度缠绕。拓扑异构酶
抑制剂已被用作抗菌和抗癌药物,但其活性的结构基础尚不清楚。本文展示了 DNA 上拓扑异构酶的晶体结构,无论是单独存在还是在一种新型抗生素存在的情况下。