Determination of the Bridging Ligand in the Active Site of Tyrosinase

Abstract

Tyrosinase is a type-3 copper enzyme that is widely distributed in plants, fungi, insects, and mammals. Developing high potent inhibitors against tyrosinase is of great interest in diverse fields including tobacco curing, food processing, bio-insecticides development, cosmetic development, and human healthcare-related research. In the crystal structure of Agaricus bisporus mushroom tyrosinase, there is an oxygen atom bridging the two copper ions in the active site. It is unclear whether the identity of this bridging oxygen is a water molecule or a hydroxide anion. In the present study, we theoretically determine the identity of this critical bridging oxygen by performing first-principles hybrid quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area (QM/MM-PBSA) calculations along with a thermodynamic cycle that aim to improve the accuracy. Our results show that the binding with water molecule is energy favored and the QM/MM-optimized structure is very close to the crystal structure, whereas the binding with hydroxide anions causes the increase of energy and significant structural changes of the active site, indicating that the identity of the bridging oxygen must be a water molecule rather than a hydroxide anion. The different binding behavior between water and hydroxide anions may explain why molecules with a carboxyl group or too many negative charges have lower inhibitory activity. In light of this, the design of high potent active inhibitors against tyrosinase should satisfy both the affinity to the copper ions and the charge neutrality of the entire molecule.

Evaluating the Performance of a Non-Bonded Cu2+ Model Including Jahn−Teller Effect into the Binding of Tyrosinase Inhibitors

“…In the simulations of TYRBm with the CuDum model, His208 residue prefers to interact with the axial dummy atom of Cu 2+ A, while the His204 and the His231 residues interact with the equatorial dummy atoms. For Cu 2+ B, the His60 residue prefers to interact with the axial dummy atom, while His42 and His69 residues interact with equatorial dummy atoms, which agrees with findings from the experiment [62][63][64][65] and other quantum-mechanics-based calculations [66][67][68] (Figure 7). Materials).…”

“…In the simulations of TYRBm with the CuDum model, His208 residue prefers to interact with the axial dummy atom of Cu 2+ A, while the His204 and the His231 residues interact with the equatorial dummy atoms. For Cu 2+ B, the His60 residue prefers to interact with the axial dummy atom, while His42 and His69 residues interact with equatorial dummy atoms, which agrees with findings from the experiment [62][63][64][65] and other quantum-mechanics-based calculations [66][67][68] (Figure 7). Throughout the MD simulations, the coordination geometry remains a distorted octahedral for the CuDum model with the His residues, and the bond distances are quite close to those in the crystal structure (PDB ID: 5138) [45] (Table 3).…”

On the Metal Cofactor in the Tyrosinase Family

“…All tyrosinases, including bacterial tyrosinases and plant polyphenol oxidases, contain a pair of copper ions at the flexible active site [ 44 ]. These enzymes belong to the type-3 copper-protein class, and they are currently being studied intensively [ 5 , 6 , 9 , 45 , 46 ]. These sites comprise six histidine residues that coordinate the two copper ions CuA and CuB.…”

Kinetic Characterization of Tyrosinase-catalyzed Oxidation of Four Polyphenols

“…All molecular docking simulations were carried out using AutoDock Vina [33] . The tyrosinase structure was taken from our previous study [34] which was constructed from crystal structure 2Y9W [35] and optimized by quantum mechanics/ molecular mechanics (QM/MM) calculations. The four polyphenols, i.e., chlorogenic acid, neochlorogenic acid, cryptochlorogenic acid, and caffeic acid, were built up by using OpenBabel program [36] .…”