Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery

Abstract

Identification of novel targets for the development of more effective antimalarial drugs and vaccines is a primary goal of the Plasmodium genome project. However, deciding which gene products are ideal drug/vaccine targets remains a difficult task. Currently, a systematic disruption of every single gene in Plasmodium is technically challenging. Hence, we have developed a computational approach to prioritize potential targets. A pathway/genome database (PGDB) integrates pathway information with information about the complete genome of an organism. We have constructed PlasmoCyc, a PGDB for Plasmodium falciparum 3D7, using its annotated genomic sequence. In addition to the annotations provided in the genome database, we add 956 additional annotations to proteins annotated as "hypothetical" using the GeneQuiz annotation system. We apply a novel computational algorithm to PlasmoCyc to identify 216 "chokepoint enzymes." All three clinically validated drug targets are chokepoint enzymes. A total of 87.5% of proposed drug targets with biological evidence in the literature are chokepoint reactions. Therefore, identifying chokepoint enzymes represents one systematic way to identify potential metabolic drug targets.

Figure 1

Both of these reactions are catalyzed by the same protein, MAL6P1.121. Therefore, MAL6P1.121 is associated with two distinct Enzymatic-Reaction frames, each linking the protein to one specific reaction. In this manner, inhibitors can be specified for a particular enzyme/reaction pair instead of for a reaction (which may be catalyzed by numerous enzymes with different inhibitor sensitivities) or for a protein (which may have multiple active sites).

Figure 2

Overview of the metabolic map for P. falciparum. Each node represents a metabolite, with the type of metabolite indicated by the shape of the node as indicated by the legend. The lines connecting the metabolites represent reactions. Bold lines correspond to reactions with an identified enzyme; gray lines correspond to reactions without an identified enzyme.

Figure 3

The description of the polypeptide from gene PF11_0338, annotated as aquaglyceroporin. The unification links contain links to an article abstract in PubMed, and protein annotations in GeneQuiz and PlasmoDB.

Figure 4

The thick arrows represent reactions that are catalyzed by enzymes, whereas the thin arrows represent reactions that are present, but with no evidence of the corresponding enzymes. When determining chokepoint reactions, we only consider the catalyzed reaction. (1) A chokepoint, because it produces a unique product; (2) a chokepoint, because it consumes a unique substrate; (3) a chokepoint, because it consumes a unique substrate and produces a unique product.

Figure 5

Pathway evidence report for folic acid biosynthesis pathway. The pathway glyph shows reactions with enzyme present in the genome and unique to the pathway (green), reactions with enzyme present but nonunique (present in other pathways—orange), reactions with enzyme absent and unique to the pathway (black), reactions with enzyme absent and present in other pathways (blue), and spontaneous reactions (pink). In this example, of the total of 15 reactions that make up the pathway, 10 have enzyme present, and only two of these participate in other pathways. The other pathways are listed at right.