Plasmodium Kinases as Potential Drug Targets for Malaria: Challenges and Opportunities

Abstract

Protein and phosphoinositide kinases have been successfully exploited as drug targets in various disease areas, principally in oncology. In malaria, several protein kinases are under investigation as potential drug targets, and an inhibitor of Plasmodium phosphatidylinositol 4-kinase type III beta (PI4KIIIβ) is currently in phase 2 clinical studies. In this Perspective, we review the potential of kinases as drug targets for the treatment of malaria. Kinases are known to be readily druggable, and many are essential for parasite survival. A key challenge in the design of Plasmodium kinase inhibitors is obtaining selectivity over the corresponding human orthologue(s) and other human kinases due to the highly conserved nature of the shared ATP binding site. Notwithstanding this, there are some notable differences between the Plasmodium and human kinome that may be exploitable. There is also the potential for designed polypharmacology, where several Plasmodium kinases are inhibited by the same drug. Prior to starting the drug discovery process, it is important to carefully assess potential kinase targets to ensure that the inhibition of the desired kinase will kill the parasites in the required life-cycle stages with a sufficiently fast rate of kill. Here, we highlight key target attributes and experimental approaches to consider and summarize the progress that has been made targeting Plasmodium PI4KIIIβ, cGMP-dependent protein kinase, and cyclin-dependent-like kinase 3.

Keywords: Plasmodium; drug discovery; lipid kinase; malaria; protein kinase; target validation.

Figure 1

Overview of the P. falciparum(17) and human kinomes. Eukaryotic protein kinase (ePK) groups include AGC (named after protein kinase A, G, and C families, containing cyclic nucleotide and calcium/phospholipid-dependent kinases), CAMK (calmodulin/calcium-dependent kinase), CK1 (casein or cell kinase 1), CMGC (named after CDK, MAPK, GSK3, and CLK families), STE (homologues of yeast STE7, STE11, and STE20 genes, including kinases in MAPK pathways but not MAPKs), TK (tyrosine kinase), TKL (tyrosine kinase-like serine/threonine kinase), RGC (receptor guanylate cyclase), and other (other protein kinases including the NEK (never in mitosis A (NIMA)-related kinase) family). The apicomplexan specific ePK-related kinase family FIKK (Phe (F)–Ile (I)–Lys (K)–Lys (K)) consists of 19 members, of which 18 are specific to P. falciparum and closely related species. Atypical protein kinases (aPKs) include PIKKs (phosphatidylinositol 3-kinase-related kinases, all three of which are classified as PIKs in the section below) and RIO (right open reading frame) families in Plasmodium.

Figure 2

Overview of human and Plasmodium phosphoinositide kinases (PIKs) and their putative substates. (A) Human PIKs and substrates clustered into 3 groups based on structure similarity. (B) Plasmodium PIKs/PIK-related proteins and substrates. Proteins are labeled using PlasmoDB (https://plasmodb.org/) gene indentifiers for the P. falciparum 3D7 strain. Putative PIKs that have not yet been studied are enclosed by dotted lines (PF3D7_0419900, PF3D7_0311300, PF3D7_1129600, PF3D7_1412400). Proteins are colored to match the human PIK(s) that they most closely resemble on the basis of sequence similarity according to Hassett and Roepe, and their proposed substrates are indicated.^, Genetic essentiality is indicated according to available data in the PhenoPlasm database (http://phenoplasm.org/) on the basis of gene disruption studies performed in P. falciparum 3D7 (piggyBac insertion mutagenesis) and in P. berghei ANKA (PlasmoGem/RMgmDB): tick (checkmark), essential; cross (X), nonessential; question mark (?), conflicting data between studies.

Figure 3

Key conserved features of the kinase domain and ATP binding site. (A) Overview of the PvPKG kinase domain and (B) enlarged view of the ATP binding site. Key features are indicated as follows: N-terminal lobe in pale green; C-terminal lobe in gray; hinge region in red; P-loop in blue; AxK motif within β3 in purple; catalytic αC-helix in cyan; activation segment with the DFG motif, phosphorylation site (Thr688), and APE motif in yellow; catalytic loop with the YRD motif in magenta; ATP analogue (phosphoaminophosphonic acid–adenylate ester) bound within the ATP binding site in bright green (PDB ID: 5DZC). (C) Two-dimensional schematic of ATP binding site showing “donor–acceptor–donor” interactions with the hinge residues observed for ATP and typical small molecule ATP-competitive inhibitors.

Figure 4

Integration of phenotypic- and target-based malaria drug discovery approaches. DEL, DNA-encoded libraries; TCP, target product profile; MoR, mechanism of resistance; MoA, mechanism of action; cKD, conditional knockdown.

Figure 5

Examples of Plasmodium kinase inhibitors. (A) PI4K inhibitors, (B) PKG inhibitors, and (C) CLK3 inhibitor.