Technical Highlight - May 2013
Short description: Screens with substrates and inhibitors, followed by molecular modeling, reveal details of an enzyme's ligand binding specificity.
Bacterial pathogens that plague the human population are becoming increasingly resistant to broad-spectrum antibiotics. In order to develop new antibiotics, a clear understanding of the mode of action of potential bacterial targets is necessary, including knowledge of the contacts between enzymes and their substrates, to design drugs that thwart those interactions and stop the pathogen in its tracks. Mucha and colleagues (PSI MCSG) have now performed such an analysis for the alanine aminopeptidase of Neisseria meningitides (NmAPN) —a pathogen that can cause meningitis, a disease still prevalent in the developing world.
First, the authors determined the substrate specificity of NmAPN. As this enzyme catalyzes the removal of N-terminal amino acids from substrate proteins, a library of fluorogenic substrates was used to measure hydrolysis rates. The analysis revealed that the enzyme prefers substrates with bulky, hydrophobic side chains: L-homoarginine, L-arginine and L-alanine were the top three substrates. Substrate preferences were notably different than those of human APN, a dissimilarity that could be important in the design of drug inhibitors specific to the bacterial enzyme.
Next, a set of six inhibitors was tested; these were organophosphorus compounds derived from arginine and homophenylalanine, which yielded inhibition constants ranging from 0.05μM to 2.5μM. The researchers then modeled the NmAPN–inhibitor complexes, based on known structures of native NmAPN and Plasmodium falciparum APN in complex with an inhibitor. This analysis pinpointed the specific interactions responsible for tighter binding and thus greater inhibitory activity of the best inhibitor for NmAPN. This integrated work should aid in the treatment of meningitis through the design of inhibitors of NmAPN with high affinity and specificity.
E. Węglarz-Tomczak et al. An integrated approach to the ligand binding specificity of Neisseria meningitidis M1 alanine aminopeptidase by fluorogenic substrate profiling, inhibitory studies and molecular modeling.
Biochimie. 95, 419-428 (2013). doi:10.1016/j.biochi.2012.10.018