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.