Transcriptome of Balamuthia mandrillaris trophozoites for structure-based drug design

Balamuthia mandrillaris, a pathogenic free-living amoeba (FLA), causes cutaneous skin lesions as well as the brain-eating disease: Balamuthia amoebic encephalitis (BAE). These diseases, and other diseases caused by pathogenic FLA, Naegleria fowleri or Acanthamoeba species, are minimally studied not only from a drug discovery or development approach but also from the molecular characterization of drug target validation or biochemical pathways necessary for parasite daily survival. Combinational chemotherapies for CNS disease caused by B. mandrillaris are distant and require vast improvement. Current therapeutics are limited to a small number of inhibitors that were previously discovered last century through in vitro testing or identified and routinely used from the small pool of surviving cases.Using our recently published methodology to identify potentially useful therapeutics, we screened a collection of 85 compounds that have previously been reported to have anti-parasitic activity. We identified 59 compounds with less than 220 micro-molar activity. Since there is no fully annotated genome or proteome, we used RNA-Seq to determine the coding sequence of the specific genes potentially targeted by the compounds in B. mandrillaris trophozoites. We characterized the sequence of 17 of these genes and obtained expression clones for 15 potential targets that we validated by direct sequencing.