Lon is a homo-oligomeric ATP-dependent serine protease which functions in the degradation of damaged and certain regulatory proteins. The importance of Lon activity in bacterial pathogenicity has led to its emergence as a target in the development of novel antibiotics. As no potent inhibitors of Lon activity have been reported to date, we sought to identify an inhibitor which could serve as a lead compound in the development of a potent Lon-specific inhibitor. To determine whether a nucleotide-or peptide-based inhibitor would be more effective, we evaluated the steady-state kinetic parameters associated with both ATP and peptide hydrolysis by human and Salmonella enterica serovar Typhimurium Lon. Although the ATP hydrolysis activities of both homologs are kinetically indistinguishable, they display marked differences in peptide substrate specificity. This suggests that a peptide-based inhibitor could be developed which would target bacterial Lon, thereby decreasing side-effects due to cross-reactivity with human Lon. Using Salmonella enterica serovar Typhimurium Lon as a model, we evaluated the IC 50 values of a series of commercially available peptide-based inhibitors. Those inhibitors which behave as transition state analogs were the most useful in inhibiting Lon activity. The peptidyl boronate, MG262, was the most potent inhibitor tested (IC 50 = 122 Ā± 9 nM) and required binding, but not hydrolysis of ATP to initiate inhibition. We hope to use MG262 as a lead compound in the development of future Lon specific inhibitors.The number of pathogenic, antibiotic resistant bacteria increases each year, however the development of new antibiotics to treat them lags behind (1). Recent studies aimed at identifying proteins necessary for virulence have implicated the importance of Lon protease (2,3). Pathogenic Salmonella enterica are responsible for causing a range of human diseases from mild gastroenteritis (serovar Typhimurium and serovar Enteritidis) to typhoid fever (serovar Typhi). It has been demonstrated that Salmonella enteria serovar Typhimurium (S. Typhimurium) Lon protease activity is required for systemic infection in mice, a common study model for S. Typhi infection in humans (3). In fact, Lon-deficient S. Typhimurium, when administered as an oral vaccine to mice, conferred subsequent protection against infection by virulent S. Typhimurium (4). Taken together, these studies highlight Lon as an important target in the development of novel therapeutic agents.Lon, also known as the protease La, is a homo-oligomeric ATP-dependent serine protease, which functions in the degradation of damaged and certain short-lived regulatory proteins (5)(6)(7)(8)(9)(10)(11)(12)(13)(14). Homologs exist ubiquitously in nature, however they localize to the cytosol in prokaryotes and to the mitochondrial matrix in eukaryotes (8,15,16 (11,(18)(19)(20)(21)(22)(23).Lon protease is a member of the AAA + superfamily (ATPases Associated with different cellular Activities) along with other ATP-dependent proteases such as ClpXP, H...