Cell2Chem: mining explored and unexplored biosynthetic chemical spaces

Area of Science:

• Biochemistry
• Bioinformatics
• Synthetic Biology

Background:

• Living cell strains are crucial for synthesizing native compounds and exploring chemical spaces.
• Understanding biosynthesis pathways is key to unlocking the potential of these cell strains.

Purpose of the Study:

• To present Cell2Chem, a web server designed to accelerate the search for compounds within organisms.
• To facilitate the investigation of biosynthesis in both explored and unexplored chemical spaces.

Main Methods:

• Utilized co-occurrence networks and natural language processing to link organisms with biosynthesized compounds.
• Integrated in silico prediction methods for reaction pathways and enzyme functions.
• Developed a platform comprising 40,370 species and 125,212 compounds.

Main Results:

• Cell2Chem systematically links living organisms to their biosynthesized compounds and production processes.
• The platform predicts potential biosynthetic pathways and catalytic protein functions.
• Expanded the scope of unexplored biosynthetic chemical spaces.

Conclusions:

• Cell2Chem enhances the efficiency of synthetic biology research.
• The tool aids in improving biosynthesis research by providing systematic data linking organisms and compounds.