TY - JOUR

T1 - Is Simultaneous Binding to DNA and Gyrase Important for the Antibacterial Activity of Cystobactamids?

AU - Solga, Danny

AU - Wieske, Lianne H.E.

AU - Wilcox, Scott

AU - Zeilinger, Carsten

AU - Jansen-Olliges, Linda

AU - Cirnski, Katarina

AU - Herrmann, Jennifer

AU - Müller, Rolf

AU - Erdelyi, Mate

AU - Kirschning, Andreas

N1 - Funding Information: This work was supported by the German Center for Infection Research (DZIF) and the Bundesministerium für Bildung und Forschung (BMBF; project OpCyBac 16GW0220). We thank Armando Navarro‐Vazquez (Universidade Federal de Pernambuco, Brazil) for helpful discussions and a generous donation of PAN gel for alignment. We also thank Viktoria George and Alexandra Amann for technical assistance with cell‐based activity screening. This study made use of the NMR Uppsala infrastructure, which is funded by the Department of Chemistry – BMC and the Disciplinary Domain of Medicine and Pharmacy. The computations were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at Tetralith, partially funded by the Swedish Research Council through grant agreement no. 2018‐05973, under project numbers 2021/5‐359 and 2021/22‐350. We are grateful to the Swedish Research Council for financial support (2020‐03431). M. E. and A. K. thank the Wenner‐Gren Foundation for financial support (GFOh2022‐0018). Open Access funding enabled and organized by Projekt DEAL.

PY - 2024/4/5

Y1 - 2024/4/5

N2 - 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.

AB - 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.

KW - antibiotics

KW - cystobactamids

KW - DNA-binding

KW - NMR-studies

KW - oligoamides

UR - http://www.scopus.com/inward/record.url?scp=85185140456&partnerID=8YFLogxK

U2 - 10.1002/chem.202303796

DO - 10.1002/chem.202303796

M3 - Article

AN - SCOPUS:85185140456

VL - 30

JO - Chemistry - a European journal

JF - Chemistry - a European journal

SN - 0947-6539

IS - 19

M1 - e202303796

ER -