novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection

Area of Science:

• Synthetic biology
• Metabolic engineering
• Biochemical engineering

Background:

• Computational pathway design is crucial for developing novel biochemical production routes and biodegradation strategies.
• Effective pathway design requires a deep understanding of biochemistry, enzyme kinetics, and thermodynamic principles.
• Existing methods often lack integration, hindering the design of efficient and feasible metabolic pathways.

Purpose of the Study:

• To introduce novoStoic2.0, an integrated computational platform for designing and optimizing biochemical pathways.
• To provide a unified web-based interface for pathway design, thermodynamic assessment, and enzyme selection.
• To facilitate the development of sustainable biotechnological solutions through streamlined pathway engineering.

Main Methods:

• novoStoic2.0 integrates tools for estimating stoichiometry, designing de novo synthesis pathways, and assessing thermodynamic feasibility.
• The platform incorporates an enzyme selection module for re-engineering novel reaction steps.
• A web-based interface within the AlphaSynthesis platform (http://novostoic.platform.moleculemaker.org/) provides access to these tools.

Main Results:

• novoStoic2.0 enables the design of thermodynamically viable metabolic pathways.
• The platform facilitates the selection of appropriate enzymes for pathway construction and optimization.
• Demonstrated utility in identifying novel, shorter hydroxytyrosol synthesis pathways with reduced cofactor requirements.

Conclusions:

• novoStoic2.0 significantly streamlines the process of computational pathway design.
• The platform supports the development of innovative and sustainable biotechnological applications.
• By integrating key design steps, novoStoic2.0 accelerates the engineering of novel bioproduction routes.