Study of the docking of competitive inhibitors at a model of tyrosinase active site: Insights from joint broken-symmetry/spin-flip DFT computations and ELF topological analysis

• Published in: Interdisciplinary sciences : computational life sciences Vol. 2; no. 1; pp. 3 - 11
• Main Authors: de la Lande, A., Maddaluno, J., Parisel, O., Darden, T. A., Piquemal, J. -P.
• Format: Journal Article
• Language: English
• Published: Springer International Association of Scientists in the Interdisciplinary Areas 01.03.2010; Springer Nature B.V
• Subjects: Binding, Competitive; Biomedical and Life Sciences; Catalytic Domain; Chemistry, Pharmaceutical - methods; Computational Biology - methods; Computational Biology/Bioinformatics; Computational Science and Engineering; Computer Appl. in Life Sciences; Computer Simulation; Copper - chemistry; Drug Design; Health Sciences; Imidazoles - chemistry; Life Sciences; Mathematical and Computational Physics; Medicine; Models, Chemical; Models, Molecular; Models, Theoretical; Molecular Conformation; Monophenol Monooxygenase - chemistry; Protein Binding; Software; Statistics for Life Sciences; Theoretical; Theoretical and Computational Chemistry; copper; oxygenase; tyrosinase; Spin-Flip TD-DFT; Density Functional Theory; competitive inhibition; Tyrosinase
• ISSN: 1913-2751; 1867-1462
• DOI: 10.1007/s12539-010-0096-8

Following our previous study (Piquemal et al. , 2003), we present here a DFT study of the inhibition of the Tyrosinase enzyme. Broken-symmetry DFT computations are supplemented with Spin-Flip TD-DFT calculations, which, for the first time, are applied to such a dicopper enzyme. The chosen biomimetic model encompasses a dioxygen molecule, two Cu(II) cations, and six imidazole rings. The docking energy of a natural substrate, namely phenolate, together with those of several inhibitor and non-inhibitor compounds, are reported and show the ability of the model to rank the most potent inhibitors in agreement with experimental data. With respect to broken-symmetry calculations, the Spin-Flip TD-DFT approach reinforces the possibility for theory to point out potent inhibitors: the need for the deprotonation of the substrates, natural or inhibitors, is now clearly established. Moreover, Electron Localization Function (ELF) topological analysis computations are used to deeply track the particular electronic distribution of the Cu-O-Cu three-center bonds involved in the enzymatic Cu 2 O 2 metallic core (Piquemal and Pilmé, 2006). It is shown that such bonds exhibit very resilient out-of-plane density expansions that play a key role in docking interactions: their 3D-orientation could be the topological electronic signature of oxygen activation within such systems.