Malaria and schistosomiasis are tropical parasitic diseases, which affect more than 800 million people worldwide, especially in developing countries. Multidrug-resistance of malarial strains toward broadly used antimalarial drug treatment (e.g. chloroquine, quinine) has spread all over the world in the last five decades. Despite the humanitarian emergency, pharmaceutical industries are not investing in the research and production of new therapies for diseases of poverty.In order to develop new potential ethical drugs against these parasites, a library of polysubstituted 3-benzyl-2-methylnaphthoquine derivatives functionalized at the benzylic core were previously synthetized in the host laboratory. Despite the strong antimalarial activity of an identified lead compound, the infected mice were not totally cured, suggesting that the naphthoquinones are rapidly metabolized under biological conditions.A platform of synthetic methodologies has been established in order to produce, via straightforward routes, new polysubstituted benzylmenadione derivatives functionalized at the aromatic ring of the naphthoquinone core, and to improve their pharmacokinetic properties by (i) increasing their half-life, solubility, bioavailability, (ii) modifying their redox potentials, and (iii) studying their active metabolites. The synthetic methodologies exemplified with 50 described compounds provide the structure–activity relationships as the basis for the development of new cheminformatics tools to be used in redox medicinal chemistry .