Mining Predicted Essential Genes of Brugia malayi for Nematode Drug Targets

Abstract

We report results from the first genome-wide application of a rational drug target selection methodology to a metazoan pathogen genome, the completed draft sequence of Brugia malayi, a parasitic nematode responsible for human lymphatic filariasis. More than 1.5 billion people worldwide are at risk of contracting lymphatic filariasis and onchocerciasis, a related filarial disease. Drug treatments for filariasis have not changed significantly in over 20 years, and with the risk of resistance rising, there is an urgent need for the development of new anti-filarial drug therapies. The recent publication of the draft genomic sequence for B. malayi enables a genome-wide search for new drug targets. However, there is no functional genomics data in B. malayi to guide the selection of potential drug targets. To circumvent this problem, we have utilized the free-living model nematode Caenorhabditis elegans as a surrogate for B. malayi. Sequence comparisons between the two genomes allow us to map C. elegans orthologs to B. malayi genes. Using these orthology mappings and by incorporating the extensive genomic and functional genomic data, including genome-wide RNAi screens, that already exist for C. elegans, we identify potentially essential genes in B. malayi. Further incorporation of human host genome sequence data and a custom algorithm for prioritization enables us to collect and rank nearly 600 drug target candidates. Previously identified potential drug targets cluster near the top of our prioritized list, lending credibility to our methodology. Over-represented Gene Ontology terms, predicted InterPro domains, and RNAi phenotypes of C. elegans orthologs associated with the potential target pool are identified. By virtue of the selection procedure, the potential B. malayi drug targets highlight components of key processes in nematode biology such as central metabolism, molting and regulation of gene expression.

Functional and Phylogenetic Characterization of Proteins Detected in Various Nematode Intestinal Compartments*

“…This suggests that orthologs of PFN-2 could serve as a novel target for disrupting intestinal membrane integrity in parasitic nematodes while not affecting the mammalian host. Likewise, GS_11702 is orthologous to the C. elegans glycolytic and gluconeogenic protein "cofactor-independent phosphoglycerate mutase" (iPGM; F57B10.3a), which has been previously identified as being conserved across nematodes but distinct from mammalian PGM (95,96). Although iPGM was previously considered an excellent potential drug target for the control of parasitic nematodes, studies have recently shown that it has limited druggability because of difficulty in accessing the active site (97).…”

An improved method for the large scale preparation of α,α′-trehalose-6-phosphate

“…[1][2][3][4][5] Because a,a 0 -trehalose synthesis is restricted to plants and in particular to lower organisms, including parasitic nematodes, opportunistic fungi and pathogenic bacteria, T6PP has been identified as an attractive platform for the development of small molecule inhibitors to serve as antihelminthics, antifungals and antibacterials. 2,6,7 To this end, large quantities of homogenous T6P are required to support high-throughput inhibitor screening, evaluation and SAR analyses. However, commercial T6P is costly, and its contamination with inorganic phosphate interferes with the T6PP activity assay.…”

RNA Interference in Infectious Tropical Diseases

“…Since RNAi machinery is well characterized in C. elegans, this experimental system can provide a potent tool for unveiling gene functions in other nematodes via comparative genomics [101]. The feasibility of this approach has been recently demonstrated in B. malayi [102]. Using sequence analyses and comparisons including gene functional studies with RNAi knockdowns in C. elegans, 589 B. malayi genes were identified as being critical to the survival of the filarial worm, representing potential targets for antifilarial drug discovery.…”