Complementation of Saccharomyces cerevisiae pik1ts by a phosphatidylinositol 4-kinase from Plasmodium falciparum

Torin 2 Derivative, NCATS-SM3710, Has Potent Multistage Antimalarial Activity through Inhibition of P. falciparum Phosphatidylinositol 4-Kinase (Pf PI4KIIIβ)

Drug resistance is a constant threat to malaria control efforts making it important to maintain a good pipeline of new drug candidates. Of particular need are compounds that also block transmission by targeting sexual stage parasites. Mature sexual stages are relatively resistant to all currently used antimalarials except the 8-aminoquinolines that are not commonly used due to potential side effects. Here, we synthesized a new Torin 2 derivative, NCATS-SM3710 with increased aqueous solubility and specificity for Plasmodium and demonstrate potent in vivo activity against all P. berghei life cycle stages. NCATS-SM3710 also has low nanomolar EC₅₀s against in vitro cultured asexual P. falciparum parasites (0.38 ± 0.04 nM) and late stage gametocytes (5.77 ± 1 nM). Two independent NCATS-SM3710/Torin 2 resistant P. falciparum parasite lines produced by growth in sublethal Torin 2 concentrations both had genetic changes in PF3D7_0509800, annotated as a phosphatidylinositol 4 kinase (Pf PI4KIIIβ). One line had a point mutation in the putative active site (V1357G), and the other line had a duplication of a locus containing Pf PI4KIIIβ. Both lines were also resistant to other Pf PI4K inhibitors. In addition NCATS-SM3710 inhibited purified Pf PI4KIIIβ with an IC₅₀ of 2.0 ± 0.30 nM. Together the results demonstrate that Pf PI4KIIIβ is the target of Torin 2 and NCATS-SM3710 and provide new options for potent multistage drug development.

Heterologous Expression, Purification, and Functional Analysis of the Plasmodium falciparum Phosphatidylinositol 4-Kinase IIIβ

Recently, we heterologously expressed, purified, and analyzed the function of the sole Plasmodium falciparum phosphatidylinositol 3-kinase (PI3K), found that the enzyme is a "class III" or "Vps34" PI3K, and found that it is irreversibly inhibited by Fe²⁺-mediated covalent, nonspecific interactions with the leading antimalarial drug, dihydroartemisinin [Hassett, M. R., et al. (2017) Biochemistry 56, 4335-4345]. One of several P. falciparum phosphatidylinositol 4-kinases [putative IIIβ isoform (PfPI4KIIIβ)] has generated similar interest as a druggable target; however, no validation of the mechanism of action for putative PfPI4K inhibitors has yet been possible due to the lack of purified PfPI4KIIIβ. We therefore codon optimized the pfpi4kIIIβ gene, successfully expressed the protein in yeast, and purified an N-lobe catalytic domain PfPI4KIIIβ protein. Using an enzyme-linked immunosorbent assay strategy previously perfected for analysis of PfPI3K (PfVps34), we measured the apparent initial rate, K_m,app(ATP), and other enzyme characteristics and found full activity for the construct and that PfPI4KIIIβ activity is most consistent with the class IIIβ designation. Because several novel antimalarial drug candidates with different chemical scaffolds have been proposed to target PfPI4KIIIβ, we titrated enzyme inhibition for these candidates versus purified PfPI4KIIIβ and PfVps34. We also analyzed the activity versus purified PfPI4KIIIβ mutants previously expressed in P. falciparum selected for resistance to these drugs. Interestingly, we found that a putative PfPI4KIIIβ inhibitor currently in advanced trials (MMV390048; MMV '0048) is a potent inhibitor of both PfVps34 and PfPI4KIIIβ. These data are helpful for further preclinical optimization of an exciting new class of P. falciparum PI kinase inhibitor ("PfPIKi") antimalarial drugs.

PIK-ing New Malaria Chemotherapy

Phosphatidylinositol (PI) kinases (PIKs) regulate cell proliferation, survival, membrane trafficking, and other processes. PIK classes are distinguished by substrate preference and their distinct phosphorylated PI products. Recently two Plasmodium falciparum PIKs (PfPIKs) have been recognized as attractive new drug targets. Here we briefly summarize PIK biochemistry and recent progress with PfPIKs.

Phosphoinositides and their functions in apicomplexan parasites

Phosphoinositides are the phosphorylated derivatives of the structural membrane phospholipid phosphatidylinositol. Single or combined phosphorylation at the 3, 4 and 5 positions of the inositol ring gives rise to the seven different species of phosphoinositides. All are quantitatively minor components of cellular membranes but have been shown to have important functions in multiple cellular processes. Here we describe our current knowledge of phosphoinositide metabolism and functions in apicomplexan parasites, mainly focusing on Toxoplasma gondii and Plasmodium spp. Even though our understanding is still rudimentary, phosphoinositides have already shown their importance in parasite biology and revealed some very particular and parasite-specific functions. Not surprisingly, there is a strong potential for phosphoinositide synthesis to be exploited for future anti-parasitic drug development.

UDP-galactose and acetyl-CoA transporters as Plasmodium multidrug resistance genes

A molecular understanding of drug resistance mechanisms enables surveillance of the effectiveness of new antimicrobial therapies during development and deployment in the field. We used conventional drug resistance selection as well as a regime of limiting dilution at early stages of drug treatment to probe two antimalarial imidazolopiperazines, KAF156 and GNF179. The latter approach permits the isolation of low-fitness mutants that might otherwise be out-competed during selection. Whole-genome sequencing of 24 independently derived resistant Plasmodium falciparum clones revealed four parasites with mutations in the known cyclic amine resistance locus (pfcarl) and a further 20 with mutations in two previously unreported P. falciparum drug resistance genes, an acetyl-CoA transporter (pfact) and a UDP-galactose transporter (pfugt). Mutations were validated both in vitro by CRISPR editing in P. falciparum and in vivo by evolution of resistant Plasmodium berghei mutants. Both PfACT and PfUGT were localized to the endoplasmic reticulum by fluorescence microscopy. As mutations in pfact and pfugt conveyed resistance against additional unrelated chemical scaffolds, these genes are probably involved in broad mechanisms of antimalarial drug resistance.

Targeting Plasmodium PI(4)K to eliminate malaria

Achieving the goal of malaria elimination will depend on targeting Plasmodium pathways essential across all life stages. Here we identify a lipid kinase, phosphatidylinositol-4-OH kinase (PI(4)K), as the target of imidazopyrazines, a new antimalarial compound class that inhibits the intracellular development of multiple Plasmodium species at each stage of infection in the vertebrate host. Imidazopyrazines demonstrate potent preventive, therapeutic, and transmission-blocking activity in rodent malaria models, are active against blood-stage field isolates of the major human pathogens P. falciparum and P. vivax, and inhibit liver-stage hypnozoites in the simian parasite P. cynomolgi. We show that imidazopyrazines exert their effect through inhibitory interaction with the ATP-binding pocket of PI(4)K, altering the intracellular distribution of phosphatidylinositol-4-phosphate. Collectively, our data define PI(4)K as a key Plasmodium vulnerability, opening up new avenues of target-based discovery to identify drugs with an ideal activity profile for the prevention, treatment and elimination of malaria.

Phosphoinositides: tiny lipids with giant impact on cell regulation

Phosphoinositides (PIs) make up only a small fraction of cellular phospholipids, yet they control almost all aspects of a cell's life and death. These lipids gained tremendous research interest as plasma membrane signaling molecules when discovered in the 1970s and 1980s. Research in the last 15 years has added a wide range of biological processes regulated by PIs, turning these lipids into one of the most universal signaling entities in eukaryotic cells. PIs control organelle biology by regulating vesicular trafficking, but they also modulate lipid distribution and metabolism via their close relationship with lipid transfer proteins. PIs regulate ion channels, pumps, and transporters and control both endocytic and exocytic processes. The nuclear phosphoinositides have grown from being an epiphenomenon to a research area of its own. As expected from such pleiotropic regulators, derangements of phosphoinositide metabolism are responsible for a number of human diseases ranging from rare genetic disorders to the most common ones such as cancer, obesity, and diabetes. Moreover, it is increasingly evident that a number of infectious agents hijack the PI regulatory systems of host cells for their intracellular movements, replication, and assembly. As a result, PI converting enzymes began to be noticed by pharmaceutical companies as potential therapeutic targets. This review is an attempt to give an overview of this enormous research field focusing on major developments in diverse areas of basic science linked to cellular physiology and disease.

Target identification and validation of novel antimalarials

It has been recognized that new antimalarials with a novel mode of action are critical to combat the continued emergence and dissemination of drug-resistant parasites that threaten the efficacy of current malaria treatments. Thus, recent high-throughput screening campaigns have been initiated using asexual intraerythrocytic stage cell-based assays of Plasmodium falciparum. These have led to the unprecedented identification of over 10,000 new antimalarial compounds. Inherently, novel compounds identified by cell-based assays will have poorly defined modes of action. While some of these compounds may have recognizable targets, the majority of cell-based hits are comprised of unique chemical scaffolds usually lacking cross-resistance with known drugs. It is likely that these novel antimalarial scaffolds will reveal new targets. A challenge for the community will be to assign these small molecules to their targets. In this article, we review methodologies to assist in the determination of a compound's mode of action.

Glycerophospholipid acquisition in Plasmodium - a puzzling assembly of biosynthetic pathways

Throughout the Plasmodium life cycle, malaria parasites repeatedly undergo rapid cellular growth and prolific divisions, necessitating intense membrane neogenesis and, in particular, the acquisition of high amounts of phospholipids. At the intraerythrocytic stage, glycerophospholipids are the main parasite membrane constituents, which mostly originate from the Plasmodium-encoded enzymatic machinery. Several proteins and entire pathways have been characterized and their features reported, thereby generating a global view of glycerophospholipid synthesis across Plasmodium spp. The malaria parasite displays a panoply of pathways that are seldom found together in a single organism. The major glycerophospholipids are synthesized via ancestral prokaryotic CDP-diacylglycerol-dependent pathways and eukaryotic-type de novo pathways. The parasite exhibits additional reactions that bridge some of these routes and are otherwise restricted to some organisms, such as plants, while base-exchange mechanisms are largely unexplored in Plasmodium. Marked differences between Plasmodium spp. have also been reported in phosphatidylcholine and phosphatidylethanolamine synthesis. Little is currently known about glycerophospholipid acquisition at non-erythrocytic stages, but recent data reveal that intrahepatocytic parasites, oocysts and sporozoites import various host lipids, and that de novo fatty acid synthesis is only crucial at the late liver stage. More studies on the different Plasmodium developmental stages are needed, to further assemble the different pieces of this glycerophospholipid synthesis puzzle, which contains highly promising therapeutic targets.