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As with the other known pathogenic free-living amoebas (<jats:italic>Naegleria fowleri<\/jats:italic> and <jats:italic>Acanthamoeba<\/jats:italic> species), drug discovery efforts to combat <jats:italic>Balamuthia<\/jats:italic> infections of the central nervous system are sparse; few targets have been validated or characterized at the molecular level, and little is known about\u00a0the biochemical pathways necessary for parasite survival. Current treatments of encephalitis due to <jats:italic>B. mandrillaris<\/jats:italic> lack efficacy, leading to case fatality rates above 90%. Using our recently published methodology to discover potential drugs against pathogenic amoebas, we screened a collection of 85 compounds with known antiparasitic activity and identified 59 compounds that impacted the growth of <jats:italic>Balamuthia<\/jats:italic> trophozoites at concentrations below 220\u00a0\u00b5M. Since there is no fully annotated genome or proteome of <jats:italic>B. mandrillaris<\/jats:italic>, we sequenced and assembled its transcriptome from a high-throughput RNA-sequencing (RNA-Seq)\u00a0experiment and located the coding sequences of the genes potentially targeted by the growth inhibitors from our compound screens. We determined the sequence of 17 of these target genes and obtained expression clones for 15 that we validated by direct sequencing. These will be used in the future in combination with the identified hits in structure guided drug discovery campaigns to develop new approaches for the treatment of <jats:italic>Balamuthia<\/jats:italic> infections.<\/jats:p>","DOI":"10.1038\/s41598-021-99903-8","type":"journal-article","created":{"date-parts":[[2021,11,4]],"date-time":"2021-11-04T11:37:43Z","timestamp":1636025863000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design"],"prefix":"10.1038","volume":"11","author":[{"given":"Isabelle Q.","family":"Phan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher A.","family":"Rice","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin","family":"Craig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rooksana E.","family":"Noorai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacquelyn R.","family":"McDonald","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandhya","family":"Subramanian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Logan","family":"Tillery","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynn K.","family":"Barrett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vijay","family":"Shankar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James C.","family":"Morris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wesley C.","family":"Van Voorhis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dennis E.","family":"Kyle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter J.","family":"Myler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,11,4]]},"reference":[{"key":"99903_CR1","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1111\/j.1550-7408.1993.tb04943.x","volume":"40","author":"GS Visvesvara","year":"1993","unstructured":"Visvesvara, G. 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