Computational Elucidation of the Mechanism by which a Pericyclase Controls Periselectivity in the Biosynthesis of Natural Product (−)-PF-1018

The fungal enzyme PfB catalyzes the conversion of pre-(−)-PF-1018,
a linear polyene with an anionic tetramate group, into (−)-PF-1018
via a mechanism with four sequential pericyclic reactions. DFT calculations
indicate that the final stereospecific Diels–Alder reaction
is intrinsically less favorable than 6π electrocyclic pathways,
yet only the product of the Diels–Alder reaction is observed
in the enzymatic process. The structures of PfB-ligand were obtained
using a combination of AlphaFold 3 and microsecond molecular dynamics
simulations. Selectivity arises from the relatively rigid hydrophobic
pocket and flexible polar pocket in PfB. The hydrocarbon chain of
the Diels–Alder transition state fits well in the hydrophobic
pocket, positioning the tetramate group to maximize H-bonding and
promote catalysis. Competing 6π electrocyclic reaction transition
states can occupy the hydrophobic pocket but result in tetramate group
orientations that prevent optimal H-bonding interactions.