Targeted therapies attacking specific genetic alterations in tumor cells have been an effective strategy in the treatment of many cancers and underlie the concept of “precision medicine.” Successes in various cancers have resulted almost exclusively from targeting activated oncogenes, but this approach has not been proven effective in patients with glioblastoma. We have taken a radically different approach to molecular therapy by targeting genomic deletions, which heretofore have not been considered to be therapeutically actionable. In a chemical biology drug screen of gliomas with passenger deletions in the glycolytic gene Enolase 1 (ENO1), we found that the most cytotoxic agents were those that inhibited mitochondrial oxidative phosphorylation (OxPhos), including a new drug developed at MD Anderson Cancer Center by the Institute of Applied Cancer Science (IACS), which inhibits OxPhos by binding mitochondrial complex I with nM affinity. Exquisite sensitivity to OxPhos inhibition derives from impaired glycolysis, as ENO1-deleted cells are unable to compensatory upregulate glycolysis in the face of inhibition of OxPhos, and succumb to bioenergetic failure. In addition to ENO1-deletions, we find that passenger deletion of other metabolic genes, including 6-phosphogluconate dehydrogenase (PGD), also exhibit selective sensitivity to OxPhos inhibition by the same underlying biochemical mechanism. The IACS compound was found to penetrate the blood brain-barrier and to eradicate PGD and ENO1-deleted intracranial xenografts. The lead OxPhos inhibitor, IACS-10759, is currently in phase 1 clinical trial for leukemia, and our data provide a strong rationale for advancing this agent to clinical trials in glioblastoma patients.