PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Articles
Microbiome: Expanding the Gut Gene Catalog
November 2014
Complex Search
September 2014
Repairing a Rift
September 2014
iTRAQing the Ubiquitinome
July 2014
Immunity: Clustering Immunoglobulins
June 2014
Mining Protein Dynamics
May 2014
Design and Discovery: Identifying New Enzymes and Metabolic Pathways
January 2014
Epigenetics: Tracing Histone Demethylase Inhibitors
December 2013
Cancer Networks: Predicting Catalytic Residues from 3D Protein Structures
November 2013
Protein-Nucleic Acid Interaction: Inhibition Through Allostery
July 2013
Infectious Diseases: Targeting Meningitis
May 2013
Protein Interaction Networks: Reading Between the Lines
April 2013
Design and Discovery: A Cocktail for Proteins Without ID
February 2013
Targeting Enzyme Function with Structural Genomics
July 2012
More in one
June 2012
Disordered Proteins
February 2012
RNA Chaperone NMB1681
July 2011
Capsid assembly in motion
April 2011
One at a time
April 2011
A growing family
February 2011
Predicting functions within a superfamily
January 2011
Isoxanthopterin Deaminase
November 2010
Scaling up mutational scanning
November 2010
Alpha/Beta Barrels
October 2010
Mre11 Nuclease
May 2010
Assigning protein function: GeMMA
April 2010
Face off
October 2009

Technology Topics Annotation/Function

Infectious Diseases: Targeting Meningitis

SBKB [doi:10.1038/sbkb.2012.140]
Technical Highlight - May 2013
Short description: Screens with substrates and inhibitors, followed by molecular modeling, reveal details of an enzyme's ligand binding specificity.

Model of NmAPN with its most potent inhibitor, with interactions indicated in green. Figure courtesy of Artur Mucha.

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.

Irene Kaganman


  1. 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

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health