N1-Benzofused Modification of Fluoroquinolones Reduces Activity Against Gram-Negative Bacteria

Area of Science:

• Medicinal Chemistry
• Antibiotic Resistance
• Molecular Pharmacology

Background:

• Fluoroquinolones are a clinically important antibiotic class with established structure-activity relationships (SAR).
• The impact of electron-rich benzofused substituents at the N1 position of fluoroquinolones is largely unexplored.
• N1 substituents interact with the topoisomerase-DNA binding complex, potentially influencing hydrophobic interactions with DNA.

Purpose of the Study:

• To investigate the effect of electron-rich benzofused N1 substituents on fluoroquinolone activity against Gram-negative bacteria.
• To evaluate the influence of N1 substituent hydrophobicity on bacterial outer membrane penetration and target inhibition.
• To expand the understanding of fluoroquinolone SAR.

Main Methods:

• Molecular modeling was used to predict binding affinities of N1-modified fluoroquinolones to DNA gyrase targets.
• Seven N1-modified fluoroquinolones were synthesized and tested for minimum inhibitory concentration (MIC) against Gram-negative pathogens.
• Outer membrane penetration and efflux pump activity were assessed using polymyxin B nonapeptide and phenylalanine-arginine β-naphthylamide, respectively.
• Cell-free assays determined the target inhibitory activity of a representative compound.

Main Results:

• A correlation between N1 substituent hydrophobicity and antibacterial activity was observed, with activity decreasing as hydrophobicity increased.
• Highly hydrophobic compounds exhibited poor solubility, leading to inactivity.
• Compounds with intermediate hydrophobicity showed reduced outer membrane penetration and diminished topoisomerase target inhibition, contrary to modeling predictions.

Conclusions:

• Large hydrophobic substituents at the N1 position of fluoroquinolones have limited utility for enhancing antibacterial activity against Gram-negative pathogens.
• Hydrophobicity is a critical factor influencing solubility, membrane permeability, and target engagement of N1-modified fluoroquinolones.
• This research contributes novel insights into fluoroquinolone SAR, particularly concerning N1 modifications.