Abstract <p>The paper presents the results of studying the intermolecular interactions of enzymes of the <i>Danio rerio</i> antioxidant system (superoxide dismutase 1, glutathione peroxidase 8, and catalase) and Cds and ZnS nanoparticles. The virtual molecular structures of target enzymes and metal sulfide nanoparticles were modeled and optimized. For all proteins except glutathione peroxidase 8, the topology of amino acid residues potentially involved in binding to nanotubes was precisely localized. The number of amino acid residues involved in the formation of the molecular cavity ranged from 13 to 30. According to the results of the study, it was found that the formation of nanoparticle-enzyme complexes with average binding energy values from –3.43 to –8.24 kcal/mol is possible. All nanoparticles were characterized by the formation of electrostatic bonds in the ligand-binding sites of proteins, which in general should lead to the same scenario in the form of inhibition of protein function. The presented approach is promising for studying the eco- and cytotoxicity of such pollutants as nanoparticles of cadmium and zinc sulfides.</p>