Exploring Aspartic Protease Inhibitor Binding to Design Selective Antimalarials

Abstract

Selectivity is a major issue in the development of drugs targeting pathogen aspartic proteases. Here, we explore the selectivity-determining factors by studying specifically designed malaria aspartic protease (plasmepsin) open-flap inhibitors. Metadynamics simulations are used to uncover the complex binding/unbinding pathways of these inhibitors and describe the critical transition states in atomistic resolution. The simulation results are compared with experimentally determined enzymatic activities. Our findings demonstrate that plasmepsin inhibitor selectivity can be achieved by targeting the flap loop with hydrophobic substituents that enable ligand binding under the flap loop, as such a behavior is not observed for several other aspartic proteases. The ability to estimate the selectivity of compounds before they are synthesized is of considerable importance in drug design; therefore, we expect that our approach will be useful in selective inhibitor designs against not only aspartic proteases but also other enzyme classes.

AlphaFold-SFA: accelerated sampling ofcryptic pocketopening,protein-ligandbinding andallosteryby AlphaFold, slow feature analysis and metadynamics

“…Moreover, SFA-funnel metadynamics captures opening of the flap as well as flipping of Trp41, two key conformational events require for ligand binding ( Figure 5 ). Previously Bobrovs and co-workers 40 highlighted the necessity of using dynamical information associated with flap opening via ‘path’ as orthogonal CVs to capture accelerated ligand binding when compared with traditional funnel metadynamics. SFA trained on AlphaFold seeded MD simulations captures flipping of Tyr77, key residue governing flap opening in plasmepsin II.…”

Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors

“…The intermolecular distance CV can be combined with CVs that describe protein flexibility. 22,45 However, since the computational cost to reconstruct the free energy surface (FES) grows exponentially with the number of CVs used, it is undesirable.…”

“…This CV alone, however, is unsuitable for systems where the protein binding site is highly flexible, as it has no control over the protein binding site flexibility and might result in situations where the protein conformational space of interest is poorly explored. The intermolecular distance CV can be combined with CVs that describe protein flexibility. , However, since the computational cost to reconstruct the free energy surface (FES) grows exponentially with the number of CVs used, it is undesirable.…”

“…Alternatives to perturbation-based methods are collective variable-based free energy calculation methods, like metadynamics, which permit ABFE calculation along a physical binding trajectory. ,− Metadynamics allows us to sample target conformations relevant to the binding process and explore transition states along the binding pathway. Besides, it is usually advantageous to understand the inhibitor binding at an atomic scale (key protein–inhibitor and protein–protein interactions, ligand flexibility, solvation effects, etc.…”

“…Besides, it is usually advantageous to understand the inhibitor binding at an atomic scale (key protein–inhibitor and protein–protein interactions, ligand flexibility, solvation effects, etc. ), as information on inhibitor binding/unbinding pathway, potential transition states can provide the basis for targeted lead compound development to design compounds with higher activity and specificity. ,, The ability of metadynamics to sample the complete binding pathway, including target flexibility upon ligand binding and unbinding, makes it an excellent choice for ligand binding studies. In contrast, alchemical methods rely on sampling only the end states of the binding process and, thus, do not provide a mechanistic insight into how the inhibitor binds/unbinds.…”