Mitochondrial optic neuropathies (MON) represent an important cause of chronic visual impairment, affecting at least 1 in 10,000 individuals in the United Kingdom. Despite the efforts of recent years, the treatment options remain limited, with only a few drug candidates and therapeutic approaches, either approved or in development. Recently, Idebenone has been investigated as drug therapy in the treatment of Leber's hereditary optic neuropathy (LHON), a rare genetic MON, although evidence for the efficacy of Idebenone is limited in the literature. Cytoplasmic NAD(P)H:quinone oxidoreductase 1 (NQO1) and mitochondrial complex III were recently identified as the major enzymes involved in Idebenone activity. Based on this mode of action, computer-aided techniques were employed to identify potential Idebenone-related small molecules which are capable of interacting selectively with both enzymes. A series of quinone compounds were selected and evaluated in in vitro assays, and one of them was found to rescue the effects of LHON in cell models at a low M concentration. Based on these observations, 50 derivatives were rationally designed and synthesised in order to enhance activity, and investigate the structure-activity relationship (SAR) and mode of action of this quinone family. Of these, 7 compounds showed improved activity compared to the original hit in the nM range, and these were further evaluated in a range of biological assays. The culmination of this study was the identification a novel naphthoquinone compound 2-((4-fluoro-3-(trifluoromethyl)phenyl)amino)-3-(methylthio)naphthalene-1,3,-dione (92) which demonstrated significantly greater potency in the ex-vivo assays, in addition to lower cytotoxicity, compared to Idebenone. Although further studies are needed to further elucidate the mechanism of action, this new compound has potential for being taken forward into pre-clinical development.