Predicting the number of biochemical transformations needed to synthesize a compound

Abstract

Exploiting the natural metabolic abilities of microorganisms for the production of bioactive compounds has been a research problem of great interest. The economical and environmental costs associated with petrochemical-derived industries have promoted the emergence of biochemical processes from renewable carbon sources. However, optimally rewiring microbial metabolism in a competitive and sustainable manner is still a challenge. Recently, some retrobiosynthesis tools for the design of de novo biosynthetic pathways have been proposed. These tools generate a large number of intermediate compounds that are beyond experimental feasibility. Thus, effective methods to reduce the number of compounds by selecting the most promising ones are still needed. Here, we propose the use of classification and regression deep learning models, such as fully-connected neural networks and 1D convolutional neural networks, to predict the number of biochemical transformations needed to produce a compound. The data to train and evaluate the models was generated using a set of 13055 reaction rules and 673 compounds from Escherichia coli metabolism as starting compounds. The data was generated up to 5 steps resulting in a dataset of over 2.6 million compounds. This approach can be effectively used in biochemical applications, including retrobiosyntesis, to prioritize compounds that can be produced using fewer biochemical transformations.