Update and elucidation of Plasmodium kinomes: Prioritization of kinases as potential drug targets for malaria

Abstract

Malaria is a tropical disease caused by Plasmodium spp. and transmitted by the bite of infected Anopheles mosquitoes. Protein kinases (PKs) play key roles in the life cycle of the etiological agent of malaria, turning these proteins attractive targets for antimalarial drug discovery campaigns. As part of an effort to understand parasite signaling functions, we report the results of a bioinformatics pipeline analysis of PKs of eight Plasmodium species. To date, no P. malariae and P. ovale kinome assemble has been conducted. We classified, curated and annotated predicted kinases to update P. falciparum, P. vivax, P. yoelii, P. berghei, P. chabaudi, and P. knowlesi kinomes published to date, as well as report for the first time the kinomes of P. malariae and P. ovale. Overall, from 76 to 97 PKs were identified among all Plasmodium spp. kinomes. Most of the kinases were assigned to seven of nine major kinase groups: AGC, CAMK, CMGC, CK1, STE, TKL, OTHER; and the Plasmodium-specific group FIKK. About 30% of kinases have been deeply classified into group, family and subfamily levels and only about 10% remained unclassified. Furthermore, updating and comparing the kinomes of P. vivax and P. falciparum allowed for the prioritization and selection of kinases as potential drug targets that could be explored for discovering new drugs against malaria. This integrated approach resulted in the selection of 37 protein kinases as potential targets and the identification of investigational compounds with moderate in vitro activity against asexual P. falciparum (3D7 and Dd2 strains) stages that could serve as starting points for the search of potent antimalarial leads in the future.

Keywords: Drug discovery; Kinome; Malaria; Plasmodium; Protein kinase; Target prioritization.

Graphical abstract

Fig. 1

Chemogenomics and bioinformatics pipeline used to update Plasmodium falciparum, P. vivax, P. yoelii, P. berghei, P. chabaudi, and P. knowlesi kinomes, elucidate the kinomes of P. malariae and P. ovale, to prioritize kinases as drug targets, and select drugs for testing. First, we searched for kinase motifs in proteomes of each Plasmodium species using Kinannote software. Then, the draft kinome was refined comparing the kinase classifications with ortholog kinases of close related organisms using both OrthoMCL and HMMer. Then, the refined kinomes were used to build phyolgenetic trees of each kinase group, comparing those kinases among species. We further conducted target prioritization approaches to select and experimentally test some approved drugs and investigational compounds related to those targets.

Fig. 2

Distribution of protein kinases of each Plasmodium specie into eight kinase groups.

Fig. 3

Target prioritization approach. A protein–protein interaction network of P. vivax kinome proteins was constructed using the web server STRING and a sub-network was extracted using CytONCA, a Cytoscape plugin that calculates graph centrality measures. According to this criterion, the most important nodes were output into that graph, leading to the target selection.

Fig. 4

In vitro antimalarial activity of selected compounds against P. falciparum. (A) Inhibition curves in vitro against chloroquine-sensitive (3D7) (B) and multidrug-resistant (Dd2) P. falciparum strains. Data are derived from three independent experiments. CQ = Chloroquine.