In this paper we present our approaches and results concerning application of molecular modelling techniques in the design of new chemotherapeutic agents for the control of eukariotic systems, comprising compounds for the treatment of systemic fungal infections and tumor deseases. In the case of anti-tumor agents we focused our attention on molecular properties of natural and synthetic anthraquinones. In the area of antifungal compounds we adopted two approaches. In one of them we examine

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... lar nature of undesirable properties of polyene macrolide antifungal antibiotic — amphotericin B using molecular modelling techniques. Another approach was aimed at the development of selective inactivator of glucosamine synthase, a novel target for antifungal compounds. In this problem we have used computational chemistry methods to identify structural features responsible for the selective inactivation of the target enzyme.