Quantum Mechanics/Molecular Mechanics Insights into the Enantioselectivity of the O-Acetylation of (R,S)-Propranolol Catalyzed by Candida antarctica Lipase B

Abstract

Classical molecular dynamics (MD) simulations and combined quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the origin of the enantioselectivity of the Candida antarctica lipase B (CalB) catalyzed O-acetylation of (R,S)-propranolol. The reaction is a two-step process. The initial step is the formation of a reactive acyl enzyme (AcCalB) via a tetrahedral intermediate (TI-1). The stereoselectivity originates from the second step, when AcCalB reacts with the racemic substrate via a second tetrahedral intermediate (TI-2). Reaction barriers for the conversion of (R)- and (S)-propranolol to O-acetylpropranolol were computed for several distinct conformations of TI-2. In QM/MM geometry optimizations and reaction path calculations the QM region was described by density functional theory (B3LYP/TZVP) and the MM region by the CHARMM force field. The QM/MM calculations show that the formation of TI-2 is the rate-determining step. The energy barrier for transformation of (R)-propranolol to O-acetylpropranolol is 4.5 kcal/mol lower than that of the reaction of (S)-propranolol. Enzyme–substrate interactions were identified that play an important role in the enantioselectivity of the reaction. Our QM/MM calculations reproduce and rationalize the experimentally observed enantioselectivity in favor of (R)-propranolol. Furthermore, in contrast to what is commonly suggested for lipase-catalyzed reactions, our results indicate that the tetrahedral intermediate is not a good approximation of the corresponding transition states

Molecular dynamics study of taxadiene synthase catalysis

“…The simulation system consisted of 23,641 atoms (TXS: 6133; cation: 53; PPi: 9; Mg 2+ : 3; Na + : 10; water: 17,433). The chosen MD setup is analogous to that of previous studies reported in the literature …”

“…Three MD simulations with different initial velocity distributions (referred to as MD1, MD2, and MD3) were performed for each complex to enhance sampling . All MD simulations were done with the CHARMM software package (version 35b2) .…”

“…In the present study, we aim at gaining a more detailed understanding of TXS catalysis, by addressing the dynamic behavior of the complexes TXS·C to TXS·F . Starting from the structures obtained by Schrepfer et al, we carry out multiple 1 ns MD simulations in explicit water using different initial velocity distributions . Through an extensive sampling of the system, these MD simulations allow us to assess the hypothesis of carbocation tumbling and to explore the probabilities for accessing different reaction pathways leading to the formation of taxadiene and reaction side products.…”

“…Through an extensive sampling of the system, these MD simulations allow us to assess the hypothesis of carbocation tumbling and to explore the probabilities for accessing different reaction pathways leading to the formation of taxadiene and reaction side products. Enzyme reactions are known to involve multiple configurations of enzyme‐substrate complexes and an extensive sampling of the configurational space is required to fully understand the origin of the catalytic properties (activity, specificity, and selectivity) of enzymes . Thus, our MD simulations aim at providing new insights into the molecular basis of TXS promiscuity and of the preference for taxadiene formation.…”

“…Thus, our MD simulations aim at providing new insights into the molecular basis of TXS promiscuity and of the preference for taxadiene formation. In addition, they may serve as starting point for subsequent quantum mechanics/molecular mechanics (QM/MM) studies on the mechanism of TXS catalysis …”