S3: Inhibitor-enzyme interactions

The devil is in the details – A comprehensive analysis of inhibitor-enzyme interactions by using a combined in silico/in vitro approach
Mirko Buchholz, PhD, Fraunhofer Institute for Cell Therapy and Immunology

Mirko Buchholz, PhD


Fraunhofer Institute for Cell Therapy and Immunology, Department of Drug Design and Target Validation, Germany


Mirko Buchholz, Birgit Koch, Michael Wermann, Ulrich Heiser, Stephan Schilling and Hans-Ulrich Demuth


Glutaminyl Cyclases are responsible for the formation of pyroglutamyl residues at the N-terminus of peptides out of glutamines and glutamates. Recently N-truncated forms of pyroglutamylated Aβ-peptides came into the focus of Alzheimer’s Disease (AD) research.

The reason is their enforced amyloidogenicity, likely contributing to progression of the disorder.

Inhibitors of QC are currently in clinical investigations as new therapeutic approach for AD patients. For the drug development process the binding mode of inhibitors in the active site of the target enzyme are useful tools for understanding the necessarily molecular interactions.

Hereby we characterized the binding mode of the inhibitor PBD150, an early tool compound in the drug discovery program, by applying a combined approach of in silico analysis and site directed mutagenesis.

The co-crystallized compound reveals different poses in QC’s of several origins. These poses were characterized via a semi- empirical approach based on a linear-scaling divide-and-conquer methodology, and further analyzed using the SE-COMBINE approach.

Following this approach, site directed mutagenesis was performed to replace key amino acids of the active site. The results indicate strong evidence for different binding modes of PBD150 in the crystal structures compared with that in solution.