Influence of water and enzyme SpnF on the dynamics and energetics of the ambimodal [6+4]/[4+2] cycloaddition

Abstract

SpnF is the first monofunctional Diels-Alder/[6+4]-ase that catalyzes a reaction leading to both Diels-Alder and [6+4] adducts through a single transition state. The environment-perturbed transition-state sampling method has been developed to calculate free energies, kinetic isotope effects, and quasi-classical reaction trajectories of enzyme-catalyzed reactions and the uncatalyzed reaction in water. Energetics calculated in this way reproduce the experiment and show that the normal Diels-Alder transition state is stabilized by H bonds with water molecules, while the ambimodal transition state is favored in the enzyme SpnF by both intramolecular hydrogen bonding and hydrophobic binding. Molecular dynamics simulations show that trajectories passing through the ambimodal transition state bifurcate to the [6+4] adduct and the Diels-Alder adduct with a ratio of 1:1 in the gas phase, 1:1.6 in water, and 1:11 in the enzyme. This example shows how an enzyme acts on a vibrational time scale to steer post-transition state trajectories toward the Diels-Alder adduct.

Biocatalytic Strategies towards [4+2] Cycloadditions

“…The [4+2] mechanism suggested by Yang et al . is remarkably different in the proposed nature of catalysis (Scheme B).…”

“… A) SpnF in spinosyn A biosynthesis apparently favours a [4+2] over a [6+4] cycloaddition. B) Computational studies by Chen et al., Zheng and Thiel and Yang et al . suggest slightly different catalytic contributions of SpnF.…”

“…] over a[ 6 + +4] cycloaddition. B) Computational studies by Chen et al, [61] Zheng and Thiel [62] and Yang et al [63] suggest slightly different catalytic contributions of SpnF.C)LepIsteers the reaction towards leporin Cpreferentially via ahetero-Diels-Alder pathway.…”

“…There have been extensive computational investigations into the SpnF‐catalysed reaction utilising multiple approaches (Scheme B) . These simulations are based on the SpnF crystal structure and computational docking and show multiple mechanisms in the gas‐phase leading to the [4+2] product 23 .…”

“…[60,64] There have been extensive computational investigations into the SpnF-catalysed reaction utilisingm ultiple approaches (Scheme 4B). [61][62][63][65][66][67][68] These simulations are based on the SpnF crystal structurea nd computational docking [64] and show multiple mechanisms in the gas-phase leading to the [4+ +2] product 23.A longside the direct route via ac oncerted [4+ +2] transition state, Patel et al [67] proposed an alternative route via [6+ +4] intermediate 24 whichundergoes aCope rearrangement to revealt he [4+ +2] product 23.F urthermore, they propose that the initial transition state is ambimodal and able to lead to either [4+ +2] or [6+ +4] adducts.…”