Structure‐Based Drug Design for Developing Small Molecule Inhibitors of RelA

Abstract Antimicrobial resistance poses a significant challenge to global public health leading to decreased efficacy of antibiotics. Overuse or misuse of antibiotics fosters bacterial tolerance, allowing microorganisms to survive harsh environments like nutrient deprivation. One such mechanism is the formation of biofilms through persister cells. Escherichia coli ( E.coli ) is known for causing chronic infections and forming biofilms that contribute to antibiotic treatment failure. The signal molecule (p)ppGpp plays a crucial role in E.coli ’s stringent response that contributes to the biofilm formation. One (p)ppGpp synthetase RelA is of particular importance due to its role in regulating (p)ppGpp level within the bacteria. In this study, we investigated the inhibitory potential of over half a million small molecules available in online databases. We selected top compounds based on their high predicted binding affinities, as assessed by AutoDock Vina. Afterward, we generated twelve additional structures by modifying the initial hit compounds based on their protein‐ligand interactions. These modified structures demonstrated significantly higher binding scores and improved predicted solubility properties positioning them as promising candidates for the next generation of RelA inhibitors. Molecular dynamics simulation has also been performed to evaluate the stability of the three highest‐scoring modified structures.