Investigating Polypharmacology Through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3

Using a combination of state-of-the-art free energy computational approaches together with in vitro IC50 assays, we evaluated the polypharmacological potential of a scaffold currently in clinical trials for inhibition of human neutrophil elastase (HNE), targeting cardiopulmonary disease, for efficacious inhibition of Proteinase 3 (PR3), a related neutrophil serine proteinase. Based on benchmarking of a series of ligands with known inhibitory activity against HNE using multisite λ-dynamics (MSλD) and multiple force field models, we demonstrated the best agreement between measured IC50 values and computed binding free energies using a hybrid force field of CHARMM c36m for the protein and ligand parameters from OPLS LigParGen that utilizes a CM1A-LBCC charge model. Using this computational model, the ligands were assessed as potential inhibitors of PR3 by anchoring the computed relative binding affinities to a single measured IC50. This led to suggested potential additional inhibitors for PR3 from those tested and characterized to be good binders to HNE. We synthesized and assayed a number of these compounds to further test our predicted binding affinities and discovered that both prediction and experiment demonstrated that the compounds bound less well to PR3, we observed a range of IC50s from 7.7-190 nM in PR3 to 0.5-1.3 nM for the same inhibitors for HNE. However, the affinities we observe suggest that the scaffold can serve as a suitable starting point for the establishment of polypharmacologically targeting both enzymes and enhancing the potential for treatments addressing diseases like chronic obstructive pulmonary disease.