Dual enzymatic inhibitory mechanism of WM382 on plasmepsin IX and X: Atomistic perspectives from dynamic analysis

Abstract

The unprecedented occurrence of malaria and the increase rate of parasite resistance to current therapeutics have over the past decade elicited researchers’ interest in probing novel drug targets and unabatedly searching for competitive inhibitors. Plasmepsin (PM) family of aspartic proteases has recently been at the forefront in this pursuit to augment malaria treatment. In malaria infections engineered by P. falciparum, PMIX and PMX are highlighted as mediators of egress, invasion and spread of the infection in humans. Despite these proteases' druggability, there is currently no authorized inhibitor. WM382, a small molecule inhibitor, has been demonstrated to have dual inhibitory properties against both proteases, which is promising. However, the structural dynamics associated with the dual inhibition mechanism remain unclear. As such, we employed integrative computer-assisted atomistic techniques to provide thorough structural dynamic insights. The binding WM382 confers structural stability on both proteases through a mesh of hydrogen and hydrophobic interactions with binding site residues. The overall binding energies of PMIX and PMX were estimated to be −27.27 kcal/mol and −23.95 kcal/mol respectively, however, the trademark aspartic acid residues in the binding pocket of these proteases contributed minimally to this effect. WM382 increased structural flexibility creating excessively loose conformation that distorts the characteristic “twist motion” of the members of the plasmepsin family. These assimilated conformations further affect the biological role of both proteases. Energy decomposition analysis proved that Phe77/Phe75 contributed significantly to the overall binding of WM382 within the binding pockets of both PMIX and PMX eliciting strong intermolecular interactions, thus favouring binding affinity. The stable orientations of WM382 within the respective hydrophobic pockets allowed favorable interactions with binding site residues which accounted for its high binding free energy.