Mechanism of the Stereoselective Catalysis of Diels–Alderase PyrE3 Involved in Pyrroindomycin Biosynthesis

Abstract

The biosynthesis of pyrroindomycins A and B features a complexity-building [4 + 2] cycloaddition cascade, which generates the spirotetramate core under the catalytic effects of monofunctional Diels–Alderases PyrE3 and PyrI4. We recently showed that the main functions of PyrI4 include acid catalysis and induced-fit/conformational selection. We now present quantum mechanical and molecular dynamics studies implicating a different mode of action by PyrE3, which prearranges an anionic polyene substrate into a high-energy reactive conformation at which an inverse-electron-demand Diels–Alder reaction can occur with a low barrier. Stereoselection is realized by strong binding interactions at the endo stereochemical relationship and a local steric constraint on the endo-1,3-diene unit. These findings, illustrating distinct mechanisms for PyrE3 and PyrI4, highlight how nature has evolved multiple ways to catalyze Diels–Alder reactions.

Biosynthesis of Sordarin Revealing a Diels–Alderase for the Formation of the Norbornene Skeleton

“…Thus, we reasoned that once the substrate 19 entered the active site, the carboxylic and aldehyde group would be anchored by salt bridges and hydrogen bonds. In addition, the hydrophobic interaction between SdnG and 19 would position the 1,3‐diene and dienophile groups of the substrate in the pocket, thereby allowing for the formation of the norbornene skeleton through IMDA [32, 33] …”

“…In addition, the hydrophobic interaction between SdnG and 19 would position the 1,3-diene and dienophile groups of the substrate in the pocket, thereby allowing for the formation of the norbornene skeleton through IMDA. [32,33]…”

A Bacterial Cytochrome P450 Enzyme Catalyzes Multistep Oxidation Reactions in Pyrroindomycin Biosynthesis

“…[ 3, 4 ] Consequently, two dedicated cyclases catalyze the formation of two cyclohexene rings in tandem. PyrE3, a flavin‐ dependent endo ‐selective cyclase catalyzing trans ‐decalin formation, generates the partially cyclized intermediate 2 ; [ 5–8 ] and PyrI4, an exo ‐selective spiro‐conjugate synthase, continues to complete the pentacyclic framework to produce the intermediate 3 . [ 5–7, 9, 10 ] The only difference between intermediate 3 and the aglycone of PYRs ( i.e ., 4 ) is that 3 has a methyl group instead of a carboxylic acid at C20 (Figure 1B).…”

Hetero-Diels-Alder Reaction Coupled with Semipinacol Rearrangement for the Biosynthesis of Structurally Diversified Notoamides

“…Crystallographic data have been deposited at the Cambridge Crystallographic Data Centre (CCDC) as CCDC 2034890 (1), 2034888 (2), 2034894 (3), 2034891 (5), 2034886 (6), 2034887 (10), and 2034889 (11) can be obtained free of charge from the CCDC via https://www.ccdc.cam.ac.uk/data_request/cif. The experimental procedures, characterization of the new compounds, and computational studies in this study are provided in Supplementary Information and Supplementary Data.…”

“…4,5 Therefore, clarifying the role of each enzyme during the cyclization event and characterizing the nature of the transition state(s) represent considerable challenges. 5,6,7,8,9,10,11 Fungal prenylated indole alkaloids with unique bicyclo[2.2.2]diazaoctane rings, such as brevianamides, paraherquamides, notoamides, stephacidins, avrainvillamides, versicolamides, taichunamides, and amoenamides, constitute a class of natural products with complex structures that exhibit a diverse spectrum of biological activities, including insecticidal, cytotoxic, anthelmintic, and antibacterial properties (Fig. 1a, S1).…”