Computational Study Into the Oxidative Ring-Closure Mechanism During the Biosynthesis of Deoxypodophyllotoxin.

The nonheme iron dioxygenase deoxypodophyllotoxin synthase performs an oxidative ring-closure reaction as part of natural product synthesis in plants. How the enzyme enables the oxidative ring-closure reaction of (-)-yatein and avoids substrate hydroxylation remains unknown. To gain insight into the reaction mechanism and understand the details of the pathways leading to products and by-products we performed a comprehensive computational study. The work shows that substrate is bound tightly into the substrate binding pocket with the C7'-H bond closest to the iron(IV)-oxo species. The reaction proceeds through a radical mechanism starting with hydrogen atom abstraction from the C7'-H position followed by ring-closure and a final hydrogen transfer to form iron(II)-water and deoxypodophyllotoxin. Alternative mechanisms including substrate hydroxylation and an electron transfer pathway were explored but found to be higher in energy. The mechanism is guided by electrostatic perturbations of charged residues in the second-coordination sphere that prevent alternative pathways.

Can the isonitrile biosynthesis enzyme ScoE assist with the biosynthesis of isonitrile groups in drug molecules? A computational study.

Many drug molecules contain isonitrile substituents; however, synthesizing these compounds remains challenging in organic chemistry. The isonitrile synthesizing enzyme ScoE utilizes a substrate with the γ-Gly substituent, and using two molecules of dioxygen and α-ketoglutarate converts it to an isonitrile group through an oxidative decarboxylation reaction. To explore its substrate scope and whether this process could be used for the biosynthesis of isonitrile-containing drug molecules, we performed a predictive computational study. We started with the recent crystal structure coordinates of ScoE, removed the substrate and inserted two potential precursor molecules of the drug molecules axisonitrile-1 and xanthocillin into the structure, whereby both molecules have their isonitrile groups replaced by γ-Gly. Both substrates fit into the substrate binding pocket of the enzyme well and position them in the correct orientation for catalysis on the iron center. Based on a molecular dynamics simulation, we created a quantum chemical cluster model of the enzyme active site with γ-Gly-substituted axisonitrile-1 and studied the oxidative decarboxylation reaction to form axisonitrile-1 products. The calculations give similar barriers to wildtype substrate for either the initial C-H or N-H hydrogen atom abstraction, which leads to a radical intermediate and form desaturated reactants. We then took the desaturated substrate and created another iron(IV)-oxo model complex to study the subsequent hydrogen atom abstraction and decarboxylation and found this to be feasible as well although we predict to see by-products for hydroxylation in the second cycle. Nevertheless, we believe that the ScoE enzyme can be utilized for the biosynthesis of isonitrile substituents in substrates with γ-Gly components as an environmentally benign alternative to organic chemistry approaches for the synthesis of isonitrile groups. We hope that experimental studies will be able to confirm our hypothesis.