Targeting the Plasmodium falciparum proteome and organelles for potential antimalarial drug candidates

Abstract

There is an unmet need to unearth alternative treatment options for malaria, wherein this quest is more pressing in recent times due to high morbidity and mortality data arising mostly from the endemic countries coupled with partial diversion of attention from the disease in view of the SARS-Cov-2 pandemic. Available therapeutic options for malaria have been severely threatened with the emergence of resistance to almost all the antimalarial drugs by the Plasmodium falciparum parasite in humans, which is a worrying situation. Artemisinin combination therapies (ACT) that have so far been the mainstay of malaria have encountered resistance by malaria parasite in South East Asia, which is regarded as a notorious ground zero for the emergence of resistance to antimalarial drugs. This review analyzes a few key druggable targets for the parasite and the potential of specific inhibitors to mitigate the emerging antimalarial drug resistance problem by providing a concise assessment of the essential proteins of the malaria parasite that could serve as targets. Moreover, this work provides a summary of the advances made in malaria parasite biology and the potential to leverage these findings for antimalarial drug production.

Keywords: Apical membrane antigen; Dipeptidyl aminopeptidases; Glucose transporters; Malaria; Plasmepsins; Plasmodium rhomboids; Proteases; Schizogony; Subtilisin-like proteins.

Figure 1

Life Cycle of P. falciparum indicating stage specific expression of essential parasite proteins. The malaria parasite expresses crucial stage specific proteins which facilitates its survival in the human host. Typical among these are Falcipain-1 (FP1), Falcipain-2 (FP2), Plasmepsin (PM) II and IV among others. The roles of these proteins are indicated in (Table 1) (Figure 1 created using Biorender.com).

Figure 2

Protein network of the interaction partners for falcipain 2a. This protein network shows the closest proteins that associate with it and may imply a functional relationship with interacting partners such as Plasmepsins (PM) I, III and IV, falcipain 2b. This was generated using string-db.org. Legend: Q8I6U4: Falcipain 2a-cysteine protease and haemoglobinase, Q8I6V3: Plasmepsin II, Q8I6U5: Falcipain 2b-cysteine protease and haemoglobinase, Q7KQM4: Plasmepsin-I, Q8IM15: Plasmepsin III, Q81570: Independent K + K + translocation inorganic pyrophosphatase of type V, Q8IJ74: Haloacid dehalogenase-like hydrolase, Q8I2M3: Uncharacterized protein, Q8IKC8: Exported protein 2, Q8IM16: Plasmepsin IV, Q9U0J2: Chaperone protein DnaJ.

Figure 3

Protein network interaction diagram for SUB2. Subtilisin-like protein 2 and its closest interacting partners. This network is suggestive and predictive of the close association of Subtilisin-like protease 2 with putative photosensitised INA-labeled protein 1, putative RNA binding protein, putative Kelc motif containing protein, putative coronin, Myosin motor domain containing myosin pfm-b domain and belongs to the TRAFAC class myosin-kinesin ATPase superfamily, trophozoite stage antigen, erythrocyte binding antigen -181, Zinc finger C-x8-C-x5-C-x3-H type, putative serine/threonine protein kinase, putative reticulocyte binding protein 3 and erythrocyte binding antigen -140. Network created using cytoscape 3.8.1. Legend: SUB2 = Subtilisin-like protease 2, PFB0475c = Conserved Uncharacterized protein, PPPDE = PPPDE Peptidase, PhIL1 = Photosensitized INA-Labeled Protein 1, Putative, RNAbp = RNA binding protein, putative, KmP = Kelc motif containing protein, putative, Coronin = coronin, Myosin pfm-b = Myosin motor domain-containing protein, an unconventional myosin pfm-b; , belonging to the TRAFAC class myosin-kinesin ATPase superfamily, Tsa = Trophozoite stage antigen, eba-181 = erythrocyte binding antigen -181, ZF C-x8. = Zinc finger C-x8-C-x5-C-x3-H type, putative, S/TPK = Serine/threonine protein kinase, putative, Rh3 = Reticulocyte-binding protein 3, eba-140 = erythrocyte binding antigen -140.

Figure 4

Protein network interaction diagram for Rhomboid protease (ROM7). ROM7 possesses serine-type endopeptidase activity, which activates its serine nucleophile by a proton and performs hydrolysis of internal, alpha-peptide bonds in a polypeptide chain (Neafsey et al., 2013). This protein has shown putative interactions with ROM8 and ROM9. The Plasmodium rhomboid proteases are involved in most enzymatic events during the invasive stages of the malaria lifecycle. The invasion of Plasmodium depends on the parasite transmembrane adhesins and these adhesins have to be processed by cleavage to be activated by PfROMs such as PfROM1, PfROM4 PfROM7, etc (Baker et al., 2006). Interaction network created using cytoscape 3.8.1. Legend: ROM = Rhomboid protease, MAL8P1.45 = Uncharacterized protein.

Figure 5

Protein network interaction diagram for tRNA binding protein (tRNAbp). The tRNAbp interacts closely with Histone acetyltransferase, DNA replication licensing factor MCM5 belongs to the MCM family, methyl transferase, nucleolar peribosomal GTPase, Rhodanese-like protein, homologue of ubiquitin-related modifier, ubiquitin binding protein, and ubiquitin activating enzyme E1. Interaction network created using cytoscape 3.8.1. Legend: TSC = Tubulin-specific chaperone, putative, MAP1 = Microtubule-associated protein 1, putative, UBLP = Ubiquitin-like protein, UB_N8H = homologue of the nedd8 protein, putative, UBRMH = homologue of the ubiquitin-related modifier, pfSUMO = small ubiquitin-related modifier, putative, UB_AE = Ubiquitin activating enzyme, NLP4 = Nuclear pore associated protein 4, putative, UBAEe1 = Ubiquitin activating enzyme E1, putative UBAEeAos1 = Ubiquitin activating enzyme (E1), subunit Aos1, PfAOP = 1 cy peroxidoxin, UBAbp = UBA/THIF type NAD/FAD binding protein, putative, tRNAbp = cytoplasmic tRNA 2- thiolation protein 1, HAT = Histone acetyltransferase, putative, MCM5 = DNA replication licensing factor MCM5, putative, MT = methyl transferase, putative, DMBP = DPH-type MB domain-containing protein, NPG = Nucleolar Peribosomal GTPase, putative, RLP = Rhodanese like protein, putative, pfSUMO.

Figure 6

A Schematic showing the mechanism of action of plasmepsins I and II in the destruction of erythrocytes of P. falciparum. This illustrates the role of Plasmepsin I and II in the destruction of spectrin and actin. A) Amplified plasma membrane with imbedded spectrin, B) expanded spectrin network with a glycophorin anchor, and C) vertically flipped plasma membrane with the spectrin complex network and other anchored moieties making a suitable surface for the actions of plasmepsins. D) Plasmepsin I & II act on the spectrin complex leading to cleavage.

Figure 7

Illustration of “spectrinase activity” of plasmepsin II (PDB ID: 1SME) and falcipain of the malarial parasite on the human Erythroid Spectrin molecule (PDB ID:1S35). The spectrin linker region was extracted using PyMol (Schrödinger, Inc.), where it was prepared as a ligand and docked onto the active site of Plasmepsin II chain B using PyRx software. Relative free binding energies of the interaction between Plasmepsin II and spectrin indicated a positive interaction between the two molecules indicative of the role of plasmepsin II in spectrin cleavages into short peptides.