Designing novel biochemical pathways to commodity chemicals using ReactPRED and RetroPath2.0

Commodity chemicals are high-demand chemicals, used by chemical industries to synthesise cocountless chemical products of daily use. For many of these chemicals, the main production process uses petroleum-based feedstocks. Concerns over these limited resources and their associated environmental problems, as well as mounting global pressure to reduce CO2 emissions have motivated efforts to find biochemical pathways capable of producing these chemicals. Advances in metabolic engineering have led to the development of technologies capable of designing novel biochemical pathways to commodity chemicals. Computational software tools, ReactPRED and RetroPath2.0 were utilised to design 49 novel pathways to produce benzene, phenol, and 1,2-propanediol -- all industrially important chemicals with limited biochemical knowledge. A pragmatic methodology for pathway curation was developed to analyse thousands and millions of pathways that were generated using the software. This method utilises publicly accessible biological databases, including MetaNetX, PubChem, and MetaCyc to analyse the generated outputs and assign EC numbers to the predicted reactions. The workflow described here for pathway generation and curation can be used to develop novel biochemical pathways to commodity chemicals from numerous starting compounds.