Exploring the pH- and Ligand-Dependent Flap Dynamics of Malarial Plasmepsin II

Abstract

Malaria remains a global health threatover 400,000 deaths occurred in 2019. Plasmepsins are promising targets of antimalarial therapeutics; however, no inhibitors have reached the clinic. To fuel the progress, a detailed understanding of the pH-and ligand-dependent conformational dynamics of plasmepsins is needed. Here we present the continuous constant pH molecular dynamics study of the prototypical plasmepsin II and its complexed form with a substrate analogue. The simulations revealed that the catalytic dyads D34 and D214 are highly coupled in the apo protein and that the pepstatin binding enhances the difference in proton affinity, making D34 the general base and D214 the general acid. The simulations showed that the flap adopts an open state regardless of pH; however, upon pepstatin binding the flap can close or open depending on the protonation state of D214. These and other data are discussed and compared with the off-targets human cathepsin D and renin. This study lays the groundwork for a systematic investigation of pH-and ligand-modulated dynamics of the entire family of plasmepsins to help design more potent and selective inhibitors.

Exploring Aspartic Protease Inhibitor Binding to Design Selective Antimalarials

“…17−20 There have been numerous, mostly computational, studies focused on the characterization of the flap loop dynamics of aspartic proteases. 18,19,21−32 It is commonly acknowledged 21 that the flap loop of aspartic proteases occupies a semi-open conformation in the apo state. However, a hinge-like motion of the flap loop is also capable of exposing a hydrophobic pocket (see Figure 1B) under the flap loop, producing the so-called open-flap conformation.…”

“…Recent studies have shown that the plm inhibitor selectivity over human aspartic proteases can be achieved by targeting the flap loop region of plms. Flap loop is a single long β-hairpin structure that lies perpendicularly over the aspartic dyad (see Figure A) and is believed to be involved in substrate recognition. − There have been numerous, mostly computational, studies focused on the characterization of the flap loop dynamics of aspartic proteases. ,,− It is commonly acknowledged that the flap loop of aspartic proteases occupies a semi-open conformation in the apo state. However, a hinge-like motion of the flap loop is also capable of exposing a hydrophobic pocket (see Figure B) under the flap loop, producing the so-called open-flap conformation. − Inhibitors that bind partly under the flap loop (also known as open-flap inhibitors) have improved selectivity over human aspartic proteases, and the increased selectivity is attributed to differences in the enzyme flexibility: plms easily reach open-flap conformations where an additional hydrophobic pocket is formed, whereas cathepsins either do not have or do not easily reach an open-flap conformation.…”

Exploring aspartic protease inhibitor binding to design selective antimalarials

“…Flap loop is a single long β-hairpin structure that lies perpendicularly over the aspartic dyad (see Figure 1.A), and is believed to be involved in the substrate recognition [17][18][19][20] . There have been numerous, mostly computational, studies focused on the characterisation of aspartic protease flap loop dynamics [18,19,[21][22][23][24][25][26][27][28][29][30][31][32] . It is commonly acknowledged [25] , that the flap-loop of aspartic proteases occupies a semi-open conformation in apo state.…”

“…There have been numerous, mostly computational, studies focused on the characterisation of aspartic protease flap loop dynamics [18,19,[21][22][23][24][25][26][27][28][29][30][31][32] . It is commonly acknowledged [25] , that the flap-loop of aspartic proteases occupies a semi-open conformation in apo state. However, the hinge like motion of the flap loop is also capable of exposing a hydrophobic pocket (see Figure 1.B) under the flap loop producing so called open-flap conformation [33][34][35][36][37] .…”

Pharmacokinetic Predictions and Molecular Dynamic Analysis of Terpenoid and Flavonoid Compounds From Miana Leaves (Plectranthus Scutellarioides (L.) R. Br.) as an Antimalarial Candidates on Plasmepsin Ii Receptor

“…The binding slot on plasmepsin II contains Asp34 and Asp 214, catalytic dyads. The plasmepsin II inhibitors are characterized by a hydroxyl group that displaces the catalytic water molecule at the active site, forming hydrogen bonds with catalytic Asp34 and Asp214 [10][11][12].…”