A dual target of Plasmepsin IX and X: Unveiling the atomistic superiority of a core chemical scaffold in malaria therapy

Abstract

Plasmepsin IX and X, members of the prominent aspartic family of proteases whose function were hitherto unknown have only recently been established as key mediators of erythrocyte invasion and egress of the virulent malarial parasite. Inhibitor 49c, a potent antimalarial peptidomimetic inhibitor initially developed to target Plasmepsin II has lately been proven to exhibit potent inhibitory activity against Plasmepsin IX and X. However, the molecular and structural dynamics supporting its inhibitory activity remain inconclusive. Hindering the motion of the flap and hinge region of an aspartic protease remains essential for disabling the catalytic activity of the enzyme. Integrating molecular dynamic simulations coupled with other advanced biocomputational tools, we reveal the enhanced structural mechanistic competence of 49c in complex with Plasmepsin IX and X relative to Pepstatin. Pepstatin, a known aspartic protease inhibitor which actively hinders the opening and closing of the flap tip and flexible loop and consequently limits access to the catalytic aspartic residues, however, its administration has been related to elevated levels of toxicity. Thermodynamic calculations reveal a higher relative binding free energy associated with Plasmepsin IX and X in complex with 49c as opposed to Pepstatin. A relatively compact and structurally rigid 49c bound complexes sequel into the restriction of the flap and hinge residues by restraining cohesive movement, consequently hindering their “twisting motion” from transpiring. Findings unveil an atomistic perspective into the structural superiority of 49c in complex with Plasmepsin IX and X.

Adapt or Die: Targeting Unique Transmission-Stage Biology for Malaria Elimination

“…Egress is mediated by the osmiophilic body proteins Pf g377, Pf MDV-1 and gamete egress and sporozoite survival (GEST) protein ( De Koning-Ward et al., 2008 ; Bargieri et al., 2016 ), as well as the egress vesicle proteins, perforin-like protein (PPLP2) that mediates the formation of pores in the erythrocyte membrane ( Sologub et al., 2011 ) ( Figure 4 ). Cysteine and serine proteases (falcipain-1, plasmepsin IX, plasmalepsin X, SERA-6, SERA-7, and PfSUB3), MTRAP and PfDPAP2 are involved in PVM and erythrocyte membrane rupture, and aspartic proteases in gamete round-up ( Munsamy et al., 2018 ). Egress is followed by exflagellation, mediated by the male-specific axoneme assembly (flagellum formation) proteins (e.g., the armadillo repeat protein PF16, Kinesin 8B, SAS-6 ( Straschil et al., 2010 ; Depoix et al., 2020 ); MAP2 and CDC20 ( Kumar et al., 2021 ); cytoskeletal proteins α-tubulin II and actin II ( Elena et al., 2011 ) and Pf MR5 ( Eksi et al., 2006 ).…”

Plasmepsin Inhibitors in Antimalarial Drug Discovery: Medicinal Chemistry and Target Validation (2000 to Present)

“…Through conditional excision of PM IX, Pino and co-workers also recently corroborated the role of this protease in invasion and further reported on the multistage antiplasmodium activity of the aspartic protease inhibitor hydroxyethylamine-based scaffold compound, 6 (Figure ), which inhibited the pre-exocytosis processing of several secreted rhoptry and microneme proteins by targeting the corresponding maturases PMs IX and X, respectively . Using molecular dynamic simulations, Munsamy and colleagues recently explored the structural mechanistic competence of compound 6 in complex with PMs IX and X and showed the restrictive effect of the binding of this inhibitor to the flap and hinge residues which consequently hinders requisite twisting motion …”

Protein-Protein Interactions in Malaria: Emerging Arena for Future Chemotherapeutics

“…A hydroxyl-ethyl-amine (HEA) scaffoldbased compound, 49c, was shown to potently inhibit both the proteases in vitro and in vivo at nanomolar concentrations and reiterated the role of these two proteases in egress and invasion [29]. MD simulations indicated that the flap tip and hinge regions present in both the plasmepsins were very well stabilized by the rigid structure of compound 49c, leading to higher-binding free energy as compared to control plasmepsin inhibitor pepstatin [30].…”