Defining the Product Chemical Space of Monoterpenoid Synthases

Terpenoid synthases create diverse carbon skeletons by catalyzing complex carbocation rearrangements, making them particularly challenging for enzyme function prediction. To begin to address this challenge, we have developed a computational approach for the systematic enumeration of terpenoid carbocations. Application of this approach allows us to systematically define a nearly complete chemical space for the potential carbon skeletons of products from monoterpenoid synthases. Specifically, 18758 carbocations were generated, which we cluster into 74 cyclic skeletons. Five of the 74 skeletons are found in known natural products; some of the others are plausible for new functions, either in nature or engineered. This work systematizes the description of function for this class of enzymes, and provides a basis for predicting functions of uncharacterized enzymes. To our knowledge, this is the first computational study to explore the complete product chemical space of this important class of enzymes.Author Summary: Terpenoids, as one of the largest classes of natural products, provide complex carbocycle structures for many drugs (e.g. taxol) and prodrugs. The diverse carbocycle structures arise from complex carbocation rearrangements catalyzed by terpenoid synthases. Many putative terpene synthase enzymes identified in genome sequencing efforts remain functionally uncharacterized, and some of these will undoubtedly have novel products, potentially including previously undiscovered carbocycles. In this work, we present a computational approach that systematically enumerates all plausible carbocations of monoterpenoid synthases in order to define and organize the potentially large product chemical space of this important class of enzymes.