Elucidation of Monoterpenoid Indole Alkaloid biosynthetic pathways, leveraging AlphaFold in conjunction with the Molecular Operating Environment

Abstract

Monoterpenoid indole alkaloids (MIAs) are among the most structurally and functionally diverse classes of plant natural products, with many possessing important clinical applications. Understanding the enzymatic mechanisms underlying their biosynthesis is essential for elucidating their chemical diversity and for future pathway engineering. Challenges in obtaining crystallographic enzyme structures have long prevented further comprehension of many of these enzymatic mechanisms, leading to the advent of computational modeling using AlphaFold and homology-based methods.

This thesis investigates a series of cytochrome P450 monooxygenases, methyltransferases, and acyltransferases modeled to examine their active site architecture and substrate binding modes. Comparative structural analyses revealed divergent catalytic pocket features that dictate substrate orientation and regioselectivity.

These findings provide critical insights into the structural enzymology of MIA biosynthesis, highlighting the molecular basis of reaction specificity and expanding our understanding of how plants generate chemical complexity.