Considering the widespread occurrence of antibiotic resistance, the need for new therapeutic strategies is inevitable. Bacterial proteases are a broad set of enzymes that play a vital role in cell survival, stress response, and pathogenicity. This in silico study was aimed to focus on the crucial role of Lon protease in the regulation of toxin-antitoxin systems in E. coli and to design inhibitory peptides against the action of this protease. With the help of relevant servers and softwares, the communication network, the evolutionary history, and the interaction of Lon with the corresponding antitoxins were examined, following which the inhibitory peptides were designed against these interactions. The results showed that Lon protease plays a central role in the control of these systems and is a conserved protein, especially among the Enterobacteriaceae family. The docking results of the designed peptides with the Lon protease were significant. This study showed that Lon protease may have the characteristics of a new therapeutic target.
