Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways

The emergence of antimicrobial resistance has led to an increase in research directed toward the engineering of novel polyketicles. To date, less than 10 000 polyketide structures have been discovered experimentally; however, the theoretical analysis of polyketicle biosynthesis performed suggests that over a billion possible structures can be synthesized. Polyketicle synthesis, which involves the formation of a linear chain and its subsequent cyclization, is catalyzed by an enzyme complex called polyketicle synthase (PKS). There are a number of variables in the linear chain synthesis controlled by the PKS: the number, identity, stereochemistry and sequence of the monomer units used in the elongation steps, and the degree of reduction that occurs after each of the condensation reactions. The theoretical analysis performed demonstrates that changes in these variables lead to the formation of different polyketicle linear chains and, consequently, a high diversity of polyketicle structures. The complexity in the number of possible structures led to the implementation of this system in BNICE, a computational framework that generates all possible biochemical pathways using a given set of enzyme reaction rules. This formulation allowed the analysis of the evolution of diversity in the synthesis mechanism and the construction of the pathway architecture of polyketicle biosynthesis. It is expected that, after future implementation of the cyclization reactions, this framework can be used to identify all possible polyketicles and their corresponding synthesis pathways. Consequently, this formulation would prove useful in guiding experimental approaches to engineer novel polyketides, a number of which will likely have medicinal properties.