Michihiro Araki1, Robert Sidney Cox1, Hiroki Makiguchi1, Teppei Ogawa1, Takeshi Taniguchi1, Kohei Miyaoku1, Masahiko Nakatsui1, Kiyotaka Y Hara1, Akihiko Kondo1. 1. Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.
Abstract
MOTIVATION: Construction of synthetic metabolic pathways promises sustainable production of diverse chemicals and materials. To design synthetic metabolic pathways of high value, computational methods are needed to expand present knowledge by mining comprehensive chemical and enzymatic information databases. Several computational methods have been already reported for the metabolic pathway design, but until now computation complexity has limited the diversity of chemical and enzymatic data used. RESULTS: We introduce a computational platform, M-path, to explore synthetic metabolic pathways including putative enzymatic reactions and compounds. M-path is an iterative random algorithm, which makes efficient use of chemical and enzymatic databases to find potential synthetic metabolic pathways. M-path can readily control the search space and perform well compared with exhaustively enumerating possible pathways. A web-based pathway viewer is also developed to check extensive metabolic pathways with evaluation scores on the basis of chemical similarities. We further produce extensive synthetic metabolic pathways for a comprehensive set of alpha amino acids. The scalable nature of M-path enables us to calculate potential metabolic pathways for any given chemicals.
MOTIVATION: Construction of synthetic metabolic pathways promises sustainable production of diverse chemicals and materials. To design synthetic metabolic pathways of high value, computational methods are needed to expand present knowledge by mining comprehensive chemical and enzymatic information databases. Several computational methods have been already reported for the metabolic pathway design, but until now computation complexity has limited the diversity of chemical and enzymatic data used. RESULTS: We introduce a computational platform, M-path, to explore synthetic metabolic pathways including putative enzymatic reactions and compounds. M-path is an iterative random algorithm, which makes efficient use of chemical and enzymatic databases to find potential synthetic metabolic pathways. M-path can readily control the search space and perform well compared with exhaustively enumerating possible pathways. A web-based pathway viewer is also developed to check extensive metabolic pathways with evaluation scores on the basis of chemical similarities. We further produce extensive synthetic metabolic pathways for a comprehensive set of alpha amino acids. The scalable nature of M-path enables us to calculate potential metabolic pathways for any given chemicals.
Authors: Tobias Goris; Álvaro Pérez-Valero; Igor Martínez; Dong Yi; Luis Fernández-Calleja; David San León; Uwe T Bornscheuer; Patricia Magadán-Corpas; Felipe Lombó; Juan Nogales Journal: Microb Biotechnol Date: 2020-10-13 Impact factor: 5.813