New Chemotypes for the Inhibition of (p)ppGpp Synthesis in the Quest for New Antimicrobial Compounds

Area of Science:

• Microbiology
• Medicinal Chemistry
• Drug Discovery

Background:

• Antimicrobial resistance (AMR) is a significant global health and economic threat.
• The dwindling antibiotic discovery pipeline necessitates novel therapeutic strategies.
• Bacterial persistence, a bet-hedging mechanism, offers a target for developing antibiotics with reduced resistance development.

Purpose of the Study:

• To identify novel molecular entities targeting the (p)ppGpp signaling pathway, a key regulator of bacterial persistence.
• To explore a structure-based approach for inhibiting the RelA/SpoT Homolog (RSH) enzyme superfamily.
• To develop new antibiotics that exert low selective pressure, thereby combating AMR.

Main Methods:

• Virtual screening of fragment libraries against the (p)ppGpp synthetase domain of the RSH enzyme Rel.
• Selection of promising chemotypes based on virtual screening results.
• Experimental validation of fragment interactions with Rel using thermal shift assay and STD-NMR.

Main Results:

• Identification of three main chemotypes with inhibitory potential against the Rel enzyme.
• Demonstration of selective interaction of most tested fragments with the (p)ppGpp synthetase domain.
• Selection of the aminobenzoic acid scaffold as a promising hit for further lead development.

Conclusions:

• Targeting the (p)ppGpp signaling pathway presents a viable strategy to combat bacterial persistence and reduce AMR.
• Structure-based drug design enabled the identification of novel chemotypes, including aminobenzoic acid, for antibiotic development.
• Further optimization of identified hits holds potential for developing new antibiotics with low selective pressure.