PhD defence N.V. (Nika) Sokolova

Exploring nature’s toolbox: discovery, characterisation and application of biosynthetic enzymes for pharmaceutical synthesis

Traditional methods for producing chemicals and pharmaceuticals often rely on toxic solvents and require extreme temperatures or pressures. With the recent regulations limiting the use of toxic chemicals such as dimethylformamide in the European Union, biocatalysis – the use of enzymes or whole cells to carry out chemical reactions – is getting traction as a more sustainable alternative.

Enzymes are typically known for their high specificity, but many can also act on non-native substrates. This flexibility, known as substrate promiscuity, is commonly observed in enzymes involved in natural product biosynthesis and helps explain the high structural diversity of compounds like flavonoids or coumarins. Importantly, this promiscuity can be exploited to develop new synthetic routes for making valuable industrial and pharmaceutical compounds.

This thesis focused on the discovery of new promiscuous biocatalysts through genome mining, functional and structural enzyme characterisation, and biocatalytic cascade development. These newly identified enzymes were tested for their ability to produce pharmaceutical precursors, bioactive compounds, and entirely new molecules not previously accessible through biocatalysis.

As a result, this work uncovered over 30 previously uncharacterized enzymes from lesser-known organisms, identified more than 500 unique enzyme-substrate combinations suitable for machine learning, and determined three new enzyme crystal structures. It also provided important insights into the likely natural roles of these enzymes.