The Contribution of COBRA to the Design of Synthetic Pathways

Genome-scale metabolic reconstructions (GEMs) capture the known metabolic capabilities of organisms and their analysis has provided many insights into complex biochemical networks. However, significant knowledge gaps still exist in the reconstructed metabolic networks and it is crucial to discover missing functions in metabolism. In addition, finding novel hypothetical pathways opens up new opportunities for metabolic engineering applications for the sustainable production of fuels and chemicals.

BNICE.ch is an established computational framework for design, evaluation, ranking and visualization of the promising de novo pathways for several applications ranging from metabolic gap-filling to metabolic engineering and drug design. BNICE.ch has several components that are integrated in a computational framework, namely: a database of generalized enzymatic reaction rules, integrated biological and chemical databases, metabolic network generation and pathway enumeration algorithms, and several cheminformatics and bioinformatics tools for the pathway feasibility studies.

In BNICE.ch we start by reconstructing a comprehensive metabolic network of compounds and reactions, we further enumerate de novo pathways of interest, and we next perform the feasibility analysis to determine the fitness and performance of individual pathways and pruning the proposed pathways to a set of most biologically feasible ones.

Methods for the constraint-based reconstruction and analysis (COBRA) allow us to incorporate the synthetic pathways one at a time into the metabolic network of a given organism and perform several analyses such as Flux Balance Analysis (FBA), yield calculations and gap filling to assess the network feasibility of the de novo pathways. These analyses allow us to identify the functionality of the proposed synthetic pathways and to examine their feasibility for implementation purposes.

We illustrate the application of COBRA in the design and evaluation of synthetic pathways through different examples of retrobiosynthesis studies.