Woodward and Hoffmann introduced the concept of pericyclic reactions in “The Conservation of Orbital Symmetry” and defined them as “reactions in which all first-order changes in bonding relationships take place in concert on a closed curve.” Since this seminal publication, pericyclic reactions like the Diels–Alder reaction, the sigmatropic Claisen rearrangement, or the Alder-ene reaction have been applied to countless syntheses. Such reactions are often referred to as classics in synthesis or as “powerful” synthetic transformations. Herein, pericyclases are defined as those enzymes that catalyze pericyclic reactions. Many researchers have proposed that such enzymes must exist based on primary and secondary metabolite structure, but these cryptic enzymes have remained elusive until now. In Chapters One through Six, I describe enzymes that cannibalize canonical enzyme folds to catalyze classic organic reactions; this fact makes uncovering these enzymes require retro-biosynthetic logic. Using modern genomics, sequence data, retro-biosynthetic and chemical logic, I was able to uncover multiple examples of enzymes that catalyze pericyclic reactions and name these enzymes the pericyclases. This transdisciplinary work led to discoveries of Diels–Alder reactions in varicidin, ilicicolin, leporin, and eupenifeldin biosynthesis, and Alder-ene reactions in pyridoxatin biosynthesis. Such discoveries laid the groundwork for this new enzyme superfamily named the pericyclases. Lastly, these are not isolated examples: genome mining revealed related enzymes to be spread all across the fungi kingdom and indicates nature’s utility of pericyclic reactions in all walks of life.
Chapter One is a review article on characterized examples of pericyclic reactions in nature. First, this chapter outlines the class of pericyclic reactions and their utility in synthesis. Then goes on to highlight known examples of enzyme catalyzed pericyclic reactions in natural systems. This chapter closes by showcasing which pericyclic reactions are yet to be discovered in natural systems.
Chapter Two describes the biosynthesis of the varicidins. Computational studies proposed a unique “carboxylative deactivation” strategy where a six-electron oxidation of a terminal methyl group to a carboxylic acid slows the non-enzymatic Diels–Alder reaction by > 104-fold. This rate reduction allows for the enzyme PvhB to control the cycloaddition step and catalyze the more challenging exo Diels–Alder to form the key cis-fused decalin moiety of the varicidins.
Chapter Three describes the biosynthesis of the ilicicolins. Computational studies determined that the key enzymatic Diels–Alder step is an ambimodal reaction in which both epi-8 ilicicolin H and ilicicolin I form from a single transition state. The enzyme IccD that catalyzes the Diels–Alder reaction accelerates it by 105-fold and selectively forms epi-8 ilicicolin H in greater than 99%. This report is the first example of an ambimodal Diels–Alder/Diels–Alder reaction catalyzed by an enzyme. Furthermore, at the time of publication this is the greatest rate acceleration of a pericyclic reaction in a natural system.
Chapter Four describes the biosynthesis of neosetophomone B and eupenifeldin natural products. Calculations verified that this intermolecular Diels–Alder reaction is a concerted process and rationalized how stereoselectivity is achieved. This report is the first example of an enzymatic intermolecular Diels–Alder reaction.
Chapter Five describes how LepI catalyzes a stereoselective dehydration and three pericyclic reactions: a Diels–Alder reaction, a hetero-Diels–Alder reaction, and a retro-Claisen rearrangement. Molecular dynamics simulations revealed how the stereoselective dehydration is achieved. Docking of transition state structures aided in rationalizing endo/exo selectivity and observed periselectivity. In total, our studies of LepI provide mechanistic insight into enzymatic dehydration-triggered Diels–Alder and hetero-Diels–Alder reactions, as well as hydrogen bonding and electrostatic catalysis of the retro-Claisen rearrangement.
Chapter Six describes the first enzymatic example of the Alder-ene reaction in biology. Computational studies played a crucial role in proposing that the pyridoxatin system would be a good choice to discover an enzymatic Alder-ene reaction. Furthermore, molecular dynamics simulations and ‘theozyme’ calculations rationalized how catalysis is achieved. These simple quantum mechanical models predicted single point mutations that allowed for the pericyclic reaction type to switch from Alder-ene to hetero-Diels–Alder and vice versa.
Chapter Seven is a theoretical investigation on early examples of the [6+4] cycloaddition reaction. Related cycloaddition reactions have recently discovered in spinosyn, heronamide, and streptoseomycin biosynthesis. This study proposes a general postulate that all endo higher-order cycloadditions are ambimodal and lead to multiple products from a single transition state.
