Iterative Structure-Based Optimization of Short Peptides Targeting the Bacterial Sliding Clamp

Area of Science:

• Microbiology
• Structural Biology
• Medicinal Chemistry

Background:

• The bacterial DNA sliding clamp (SC) is a crucial replication processivity factor and a potential target for novel antibiotics.
• Developing effective inhibitors of the bacterial SC is essential for combating antibiotic resistance.

Purpose of the Study:

• To conduct a structure-activity relationship (SAR) study of novel peptides targeting the *Escherichia coli* SC binding pocket.
• To identify modifications that enhance peptide affinity and inhibitory activity against the bacterial SC.

Main Methods:

• Systematic chemical modifications of peptide sequences, including N-alkylation, N-terminal extension, and C-terminal residue introduction (hydrophobic and constrained).
• Affinity measurements using dissociation constants (Kd) to quantify peptide-SC interactions.
• X-ray crystallography to determine the structural basis of peptide-SC binding at the atomic level.

Main Results:

• Single peptide modifications led to increased affinity for the *E. coli* SC.
• Combined modifications resulted in substantially improved peptide affinity, with Kd values ranging from 30-80 nM.
• X-ray structures revealed novel interactions (stacking, hydrogen bonds, hydrophobic contacts) at the peptide-protein interface, explaining enhanced binding.
• The most potent peptide inhibitors effectively blocked SC-dependent DNA synthesis.

Conclusions:

• Peptide modifications can significantly enhance binding affinity to the bacterial DNA sliding clamp.
• Structural insights provide a basis for rational drug design of SC-targeting antibiotics.
• These findings offer a promising strategy for developing new antibacterial agents against *E. coli*.