Structural and Mechanistic Insights into Atypical Bacterial Topoisomerase Inhibitors

Area of Science:

• Microbiology
• Medicinal Chemistry
• Structural Biology

Background:

• Novel bacterial topoisomerase inhibitors (NBTIs) represent a promising new class of antibacterials.
• These inhibitors target essential bacterial enzymes like DNA gyrase and topoisomerase IV, crucial for combating pathogens such as MRSA.
• A subset of amide NBTIs is known to induce both single- and double-strand DNA breaks, differentiating them from most NBTIs.

Purpose of the Study:

• To elucidate the structural basis of an unusual binding mode for two amide NBTIs (148 and 185).
• To synthesize and characterize novel isosteric triazole NBTIs.
• To investigate the differential DNA cleavage mechanisms induced by these new compounds.

Main Methods:

• X-ray crystallography was used to determine the structures of amide NBTIs 148 and 185.
• Synthesis of two isosteric triazole NBTIs (342 and 276) was performed.
• Docking and molecular dynamics simulations were employed to analyze DNA cleavage mechanisms.

Main Results:

• The X-ray crystal structures revealed an unusual binding mode for NBTIs 148 and 185, engaging both GyrA D83 and R122.
• Triazole NBTI 342 induced only single-strand DNA breaks, while triazole NBTI 276 induced both single- and double-strand DNA breaks.
• Computational simulations provided insights into the structural factors underlying the distinct DNA cleavage activities.

Conclusions:

• The study reveals a unique binding interaction of amide NBTIs with bacterial topoisomerases.
• The development of isosteric triazole NBTIs with varying DNA cleavage profiles expands the NBTI class.
• Understanding these structural and mechanistic differences is key for designing next-generation antibacterials.