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

Abstract

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 byproducts 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 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.

Unraveling the Mechanism of the Oxidative C–C Bond Coupling Reaction Catalyzed by Deoxypodophyllotoxin Synthase

“…Our calculation showed that the hydrogen abstraction from the target C7′–H bond generates Fe III –OH and the substrate C7′-centered radical with a barrier of 15.5 kcal/mol. This barrier matches the one (14.0 kcal/mol) obtained from the cluster model calculations by de Visser et al…”

“…As such, the C–C bond cyclization is preferred over the hydroxylation. The calculated barrier exceeds the value of 12.5 kcal/mol reported in a QM-cluster model study . The comparison of structures showed that the substrate radical generated after hydrogen abstraction in the QM-cluster study lies 6.4 kcal/mol higher than that in our study (Figure S11).…”

“…Our calculation showed that the hydrogen abstraction from the target C7′−H bond generates Fe III −OH and the substrate C7′-centered radical with a barrier of 15.5 kcal/mol. This barrier matches the one (14.0 kcal/mol) obtained from the cluster model calculations by de Visser et al 19 It can be seen from Figure 4 that the substrate approaches the iron center from above, leading to a large Fe−O−H angle of 147.3°in TS3. In this transition state, the C−H bond elongates to 1.25 Å, while the nascent O−H bond has a distance of 1.31 Å.…”

“…The calculated barrier exceeds the value of 12.5 kcal/mol reported in a QM-cluster model study. 19 The comparison of structures showed that the substrate radical generated after hydrogen abstraction in the QM-cluster study lies 6.4 kcal/mol higher than that in our study (Figure S11). Nevertheless, the calculated barrier for the rate-determining ring closure is consistent with the value obtained from our QM-only calculation using the smallest model, which includes only the substrate radical (19.7 kcal/mol in Figure S1).…”

“…This barrier is much higher than the value obtained from the previous cluster model study (12.5 kcal/mol). 19 It is questionable how the rotation of Here, the reaction mechanism of DPS-catalyzed conversion of native substrate 1 to 2 was explored by means of quantum mechanics/molecular mechanics (QM/MM) methods, incorporating the surrounding enzyme into the calculations. Various possible pathways were investigated.…”