This invention relates to biology and medicine and, in particular, can be used in medicine to make a pharmaceutical composition for targeted delivery of biologically active substances into mitochondria, driven by proton electro-chemical potential in the mitochondria. This invention also relates to the method to affect an organism by the targeted delivery of biologically active compounds to mitochondria. The invention can be useful in treatment of diseases or disorders associated with not normal functioning of mitochondria, in particular diseases associated with increased production of free radicals and reactive oxygen species.