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.