Is Simultaneous Binding to DNA and Gyrase Important for the Antibacterial Activity of Cystobactamids?

• Published in: Chemistry : a European journal 2024-04, Vol.30 (19), p.e202303796-n/a
• Main Authors: Solga, Danny, Wieske, Lianne H. E., Wilcox, Scott, Zeilinger, Carsten, Jansen‐Olliges, Linda, Cirnski, Katarina, Herrmann, Jennifer, Müller, Rolf, Erdelyi, Mate, Kirschning, Andreas
• Format: Article
• Language: English
• Subjects: Affinity; Antibacterial activity; antibiotics; Binding; cystobactamids; Deoxyribonucleic acid; Dimerization; DNA; DNA-binding; NMR; NMR-studies; Nuclear magnetic resonance; oligoamides; Protein interaction; Proteins
• ISSN: 0947-6539; 1521-3765; 1521-3765
• DOI: 10.1002/chem.202303796

Cystobactamids 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. How do they bind ? New cystobactamid derivatives with duplicated triarene unit served to elucidate their bent shape conformation (CX‐CY‐CZ angle of ~110 degrees) by NMR analysis. Elongation of the triarene unit of cystobactamids lead to increased DNA binding affinity implying that they exert their inhibitory activity by interaction with the gyrase itself as well as with DNA via their triarene unit.