AbstractCystobactamids are aromatic oligoamides that exert their natural antibacterial properties by inhibition of bacterial gyrases. Such aromatic oligoamides were proposed to inhibit α‐helix‐mediated protein‐protein interactions and may serve for specific recognition of DNA. Based on this suggestion, we designed new derivatives that have duplicated cystobactamid triarene units as model systems to decipher the specific binding mode of cystobactamids to double stranded DNA. Solution NMR analyses revealed that natural cystobactamids as well as their elongated analogues show an overall bent shape at their central aliphatic unit, with an average CX‐CY‐CZ angle of ~110 degrees. Our finding is corroborated by the target‐bound structure of close analogues, as established by cryo‐EM very recently. Cystobactamid CN‐861‐2 binds directly to the bacterial gyrase with an affinity of 9 μM, and also exhibits DNA‐binding properties with specificity for AT‐rich DNA. Elongation/dimerization of the triarene subunit of native cystobactamids is demonstrated to lead to an increase in DNA binding affinity. This implies that cystobactamids’ gyrase inhibitory activity necessitates not just interaction with the gyrase itself, but also with DNA via their triarene unit.
摘要胱杆菌酰胺是一种芳香族低聚酰胺,通过抑制细菌的回旋酶而发挥其天然抗菌特性。有人认为这种芳香族低聚酰胺可抑制α-螺旋介导的蛋白质与蛋白质之间的相互作用,并可用于 DNA 的特异性识别。基于这一观点,我们设计了具有重复的胱杆菌酰胺三芳基单元的新衍生物作为模型系统,以破译胱杆菌酰胺与双链 DNA 的特异性结合模式。溶液核磁共振分析表明,天然胱内酰胺及其拉长的类似物在其中央脂肪族单元处显示出整体弯曲的形状,平均 CX-CY-CZ 角约为 110 度。最近通过低温电子显微镜(cryo-EM)确定的近似类似物的靶结合结构也证实了我们的发现。胱杆菌酰胺 CN-861-2 可直接与细菌回旋酶结合,亲和力为 9 μM,还具有 DNA 结合特性,对富含 AT 的 DNA 有特异性。事实证明,原生胱内酰胺的三烯亚基伸长/二聚化会导致 DNA 结合亲和力的增加。这意味着胱巴坦类药物的回旋酶抑制活性不仅需要与回旋酶本身相互作用,还需要通过其三芳邻单元与 DNA 相互作用。